From bb24844d906445646decce2f52f49c49b959367f Mon Sep 17 00:00:00 2001 From: "f.grunewald" Date: Wed, 8 Feb 2023 14:06:01 +0100 Subject: [PATCH 1/7] prelim RNA test --- polyply/data/ol21/rna.ff | 4860 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 4860 insertions(+) create mode 100644 polyply/data/ol21/rna.ff diff --git a/polyply/data/ol21/rna.ff b/polyply/data/ol21/rna.ff new file mode 100644 index 000000000..84305da54 --- /dev/null +++ b/polyply/data/ol21/rna.ff @@ -0,0 +1,4860 @@ +[ macros ] +rna_bases "RA5|RA|RA3|RC5|RC|RC3|RU5|RU|RU3|RG5|RG|RG3" + +[ moleculetype ] +RA5 3 +[ atoms ] +1 HO 1 RA5 H5T 1 0.4295 +2 OH 1 RA5 O5' 2 -0.6223 +3 CI 1 RA5 C5' 3 0.0558 +4 H1 1 RA5 H5'1 4 0.0679 +5 H1 1 RA5 H5'2 5 0.0679 +6 CT 1 RA5 C4' 6 0.1065 +7 H1 1 RA5 H4' 7 0.1174 +8 OS 1 RA5 O4' 8 -0.3548 +9 CT 1 RA5 C1' 9 0.0394 +10 H2 1 RA5 H1' 10 0.2007 +11 N* 1 RA5 N9 11 -0.0251 +12 C5 1 RA5 C8 12 0.2006 +13 H5 1 RA5 H8 13 0.1553 +14 NB 1 RA5 N7 14 -0.6073 +15 CB 1 RA5 C5 15 0.0515 +16 CA 1 RA5 C6 16 0.7009 +17 N2 1 RA5 N6 17 -0.9019 +18 H 1 RA5 H61 18 0.4115 +19 H 1 RA5 H62 19 0.4115 +20 NC 1 RA5 N1 20 -0.7615 +21 CQ 1 RA5 C2 21 0.5875 +22 H5 1 RA5 H2 22 0.0473 +23 NC 1 RA5 N3 23 -0.6997 +24 CB 1 RA5 C4 24 0.3053 +25 CT 1 RA5 C3' 25 0.2022 +26 H1 1 RA5 H3' 26 0.0615 +27 CT 1 RA5 C2' 27 0.067 +28 H1 1 RA5 H2'1 28 0.0972 +29 OH 1 RA5 O2' 29 -0.6139 +30 HO 1 RA5 HO'2 30 0.4186 +31 OS 1 RA5 O3' 31 -0.5246 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RA 3 +[ atoms ] +1 P 1 RA P 1 1.1662 +2 O2 1 RA O1P 2 -0.776 +3 O2 1 RA O2P 3 -0.776 +4 OS 1 RA O5' 4 -0.4989 +5 CI 1 RA C5' 5 0.0558 +6 H1 1 RA H5'1 6 0.0679 +7 H1 1 RA H5'2 7 0.0679 +8 CT 1 RA C4' 8 0.1065 +9 H1 1 RA H4' 9 0.1174 +10 OS 1 RA O4' 10 -0.3548 +11 CT 1 RA C1' 11 0.0394 +12 H2 1 RA H1' 12 0.2007 +13 N* 1 RA N9 13 -0.0251 +14 C5 1 RA C8 14 0.2006 +15 H5 1 RA H8 15 0.1553 +16 NB 1 RA N7 16 -0.6073 +17 CB 1 RA C5 17 0.0515 +18 CA 1 RA C6 18 0.7009 +19 N2 1 RA N6 19 -0.9019 +20 H 1 RA H61 20 0.4115 +21 H 1 RA H62 21 0.4115 +22 NC 1 RA N1 22 -0.7615 +23 CQ 1 RA C2 23 0.5875 +24 H5 1 RA H2 24 0.0473 +25 NC 1 RA N3 25 -0.6997 +26 CB 1 RA C4 26 0.3053 +27 CT 1 RA C3' 27 0.2022 +28 H1 1 RA H3' 28 0.0615 +29 CT 1 RA C2' 29 0.067 +30 H1 1 RA H2'1 30 0.0972 +31 OH 1 RA O2' 31 -0.6139 +32 HO 1 RA HO'2 32 0.4186 +33 OS 1 RA O3' 33 -0.5246 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RA3 3 +[ atoms ] +1 P 1 RA3 P 1 1.1662 +2 O2 1 RA3 O1P 2 -0.776 +3 O2 1 RA3 O2P 3 -0.776 +4 OS 1 RA3 O5' 4 -0.4989 +5 CI 1 RA3 C5' 5 0.0558 +6 H1 1 RA3 H5'1 6 0.0679 +7 H1 1 RA3 H5'2 7 0.0679 +8 CT 1 RA3 C4' 8 0.1065 +9 H1 1 RA3 H4' 9 0.1174 +10 OS 1 RA3 O4' 10 -0.3548 +11 CT 1 RA3 C1' 11 0.0394 +12 H2 1 RA3 H1' 12 0.2007 +13 N* 1 RA3 N9 13 -0.0251 +14 C5 1 RA3 C8 14 0.2006 +15 H5 1 RA3 H8 15 0.1553 +16 NB 1 RA3 N7 16 -0.6073 +17 CB 1 RA3 C5 17 0.0515 +18 CA 1 RA3 C6 18 0.7009 +19 N2 1 RA3 N6 19 -0.9019 +20 H 1 RA3 H61 20 0.4115 +21 H 1 RA3 H62 21 0.4115 +22 NC 1 RA3 N1 22 -0.7615 +23 CQ 1 RA3 C2 23 0.5875 +24 H5 1 RA3 H2 24 0.0473 +25 NC 1 RA3 N3 25 -0.6997 +26 CB 1 RA3 C4 26 0.3053 +27 CT 1 RA3 C3' 27 0.2022 +28 H1 1 RA3 H3' 28 0.0615 +29 CT 1 RA3 C2' 29 0.067 +30 H1 1 RA3 H2'1 30 0.0972 +31 OH 1 RA3 O2' 31 -0.6139 +32 HO 1 RA3 HO'2 32 0.4186 +33 OH 1 RA3 O3' 33 -0.6541 +34 HO 1 RA3 H3T 34 0.4376 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RAN 3 +[ atoms ] +1 HO 1 RAN H5T 1 0.4295 +2 OH 1 RAN O5' 2 -0.6223 +3 CI 1 RAN C5' 3 0.0558 +4 H1 1 RAN H5'1 4 0.0679 +5 H1 1 RAN H5'2 5 0.0679 +6 CT 1 RAN C4' 6 0.1065 +7 H1 1 RAN H4' 7 0.1174 +8 OS 1 RAN O4' 8 -0.3548 +9 CT 1 RAN C1' 9 0.0394 +10 H2 1 RAN H1' 10 0.2007 +11 N* 1 RAN N9 11 -0.0251 +12 C5 1 RAN C8 12 0.2006 +13 H5 1 RAN H8 13 0.1553 +14 NB 1 RAN N7 14 -0.6073 +15 CB 1 RAN C5 15 0.0515 +16 CA 1 RAN C6 16 0.7009 +17 N2 1 RAN N6 17 -0.9019 +18 H 1 RAN H61 18 0.4115 +19 H 1 RAN H62 19 0.4115 +20 NC 1 RAN N1 20 -0.7615 +21 CQ 1 RAN C2 21 0.5875 +22 H5 1 RAN H2 22 0.0473 +23 NC 1 RAN N3 23 -0.6997 +24 CB 1 RAN C4 24 0.3053 +25 CT 1 RAN C3' 25 0.2022 +26 H1 1 RAN H3' 26 0.0615 +27 CT 1 RAN C2' 27 0.067 +28 H1 1 RAN H2'1 28 0.0972 +29 OH 1 RAN O2' 29 -0.6139 +30 HO 1 RAN HO'2 30 0.4186 +31 OH 1 RAN O3' 31 -0.6541 +32 HO 1 RAN H3T 32 0.4376 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RU5 3 +[ atoms ] +1 HO 1 RU5 H5T 1 0.4295 +2 OH 1 RU5 O5' 2 -0.6223 +3 CI 1 RU5 C5' 3 0.0558 +4 H1 1 RU5 H5'1 4 0.0679 +5 H1 1 RU5 H5'2 5 0.0679 +6 CT 1 RU5 C4' 6 0.1065 +7 H1 1 RU5 H4' 7 0.1174 +8 OS 1 RU5 O4' 8 -0.3548 +9 CT 1 RU5 C1' 9 0.0674 +10 H2 1 RU5 H1' 10 0.1824 +11 N* 1 RU5 N1 11 0.0418 +12 CS 1 RU5 C6 12 -0.1126 +13 H4 1 RU5 H6 13 0.2188 +14 CS 1 RU5 C5 14 -0.3635 +15 HA 1 RU5 H5 15 0.1811 +16 C 1 RU5 C4 16 0.5952 +17 O 1 RU5 O4 17 -0.5761 +18 NA 1 RU5 N3 18 -0.3549 +19 H 1 RU5 H3 19 0.3154 +20 C 1 RU5 C2 20 0.4687 +21 O 1 RU5 O2 21 -0.5477 +22 CT 1 RU5 C3' 22 0.2022 +23 H1 1 RU5 H3' 23 0.0615 +24 CT 1 RU5 C2' 24 0.067 +25 H1 1 RU5 H2'1 25 0.0972 +26 OH 1 RU5 O2' 26 -0.6139 +27 HO 1 RU5 HO'2 27 0.4186 +28 OS 1 RU5 O3' 28 -0.5246 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C6 C4 C5 H5 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +H5 O4 1 {} +H5 N3 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RU 3 +[ atoms ] +1 P 1 RU P 1 1.1662 +2 O2 1 RU O1P 2 -0.776 +3 O2 1 RU O2P 3 -0.776 +4 OS 1 RU O5' 4 -0.4989 +5 CI 1 RU C5' 5 0.0558 +6 H1 1 RU H5'1 6 0.0679 +7 H1 1 RU H5'2 7 0.0679 +8 CT 1 RU C4' 8 0.1065 +9 H1 1 RU H4' 9 0.1174 +10 OS 1 RU O4' 10 -0.3548 +11 CT 1 RU C1' 11 0.0674 +12 H2 1 RU H1' 12 0.1824 +13 N* 1 RU N1 13 0.0418 +14 CS 1 RU C6 14 -0.1126 +15 H4 1 RU H6 15 0.2188 +16 CS 1 RU C5 16 -0.3635 +17 HA 1 RU H5 17 0.1811 +18 C 1 RU C4 18 0.5952 +19 O 1 RU O4 19 -0.5761 +20 NA 1 RU N3 20 -0.3549 +21 H 1 RU H3 21 0.3154 +22 C 1 RU C2 22 0.4687 +23 O 1 RU O2 23 -0.5477 +24 CT 1 RU C3' 24 0.2022 +25 H1 1 RU H3' 25 0.0615 +26 CT 1 RU C2' 26 0.067 +27 H1 1 RU H2'1 27 0.0972 +28 OH 1 RU O2' 28 -0.6139 +29 HO 1 RU HO'2 29 0.4186 +30 OS 1 RU O3' 30 -0.5246 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C6 C4 C5 H5 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +H5 O4 1 {} +H5 N3 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RU3 3 +[ atoms ] +1 P 1 RU3 P 1 1.1662 +2 O2 1 RU3 O1P 2 -0.776 +3 O2 1 RU3 O2P 3 -0.776 +4 OS 1 RU3 O5' 4 -0.4989 +5 CI 1 RU3 C5' 5 0.0558 +6 H1 1 RU3 H5'1 6 0.0679 +7 H1 1 RU3 H5'2 7 0.0679 +8 CT 1 RU3 C4' 8 0.1065 +9 H1 1 RU3 H4' 9 0.1174 +10 OS 1 RU3 O4' 10 -0.3548 +11 CT 1 RU3 C1' 11 0.0674 +12 H2 1 RU3 H1' 12 0.1824 +13 N* 1 RU3 N1 13 0.0418 +14 CS 1 RU3 C6 14 -0.1126 +15 H4 1 RU3 H6 15 0.2188 +16 CS 1 RU3 C5 16 -0.3635 +17 HA 1 RU3 H5 17 0.1811 +18 C 1 RU3 C4 18 0.5952 +19 O 1 RU3 O4 19 -0.5761 +20 NA 1 RU3 N3 20 -0.3549 +21 H 1 RU3 H3 21 0.3154 +22 C 1 RU3 C2 22 0.4687 +23 O 1 RU3 O2 23 -0.5477 +24 CT 1 RU3 C3' 24 0.2022 +25 H1 1 RU3 H3' 25 0.0615 +26 CT 1 RU3 C2' 26 0.067 +27 H1 1 RU3 H2'1 27 0.0972 +28 OH 1 RU3 O2' 28 -0.6139 +29 HO 1 RU3 HO'2 29 0.4186 +30 OH 1 RU3 O3' 30 -0.6541 +31 HO 1 RU3 H3T 31 0.4376 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C6 C4 C5 H5 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +H5 O4 1 {} +H5 N3 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RUN 3 +[ atoms ] +1 HO 1 RUN H5T 1 0.4295 +2 OH 1 RUN O5' 2 -0.6223 +3 CI 1 RUN C5' 3 0.0558 +4 H1 1 RUN H5'1 4 0.0679 +5 H1 1 RUN H5'2 5 0.0679 +6 CT 1 RUN C4' 6 0.1065 +7 H1 1 RUN H4' 7 0.1174 +8 OS 1 RUN O4' 8 -0.3548 +9 CT 1 RUN C1' 9 0.0674 +10 H2 1 RUN H1' 10 0.1824 +11 N* 1 RUN N1 11 0.0418 +12 CS 1 RUN C6 12 -0.1126 +13 H4 1 RUN H6 13 0.2188 +14 CS 1 RUN C5 14 -0.3635 +15 HA 1 RUN H5 15 0.1811 +16 C 1 RUN C4 16 0.5952 +17 O 1 RUN O4 17 -0.5761 +18 NA 1 RUN N3 18 -0.3549 +19 H 1 RUN H3 19 0.3154 +20 C 1 RUN C2 20 0.4687 +21 O 1 RUN O2 21 -0.5477 +22 CT 1 RUN C3' 22 0.2022 +23 H1 1 RUN H3' 23 0.0615 +24 CT 1 RUN C2' 24 0.067 +25 H1 1 RUN H2'1 25 0.0972 +26 OH 1 RUN O2' 26 -0.6139 +27 HO 1 RUN HO'2 27 0.4186 +28 OH 1 RUN O3' 28 -0.6541 +29 HO 1 RUN H3T 29 0.4376 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C6 C4 C5 H5 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +H5 O4 1 {} +H5 N3 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RG5 3 +[ atoms ] +1 HO 1 RG5 H5T 1 0.4295 +2 OH 1 RG5 O5' 2 -0.6223 +3 CI 1 RG5 C5' 3 0.0558 +4 H1 1 RG5 H5'1 4 0.0679 +5 H1 1 RG5 H5'2 5 0.0679 +6 CT 1 RG5 C4' 6 0.1065 +7 H1 1 RG5 H4' 7 0.1174 +8 OS 1 RG5 O4' 8 -0.3548 +9 CT 1 RG5 C1' 9 0.0191 +10 H2 1 RG5 H1' 10 0.2006 +11 N* 1 RG5 N9 11 0.0492 +12 CP 1 RG5 C8 12 0.1374 +13 H5 1 RG5 H8 13 0.164 +14 NB 1 RG5 N7 14 -0.5709 +15 CB 1 RG5 C5 15 0.1744 +16 C 1 RG5 C6 16 0.477 +17 O 1 RG5 O6 17 -0.5597 +18 NA 1 RG5 N1 18 -0.4787 +19 H 1 RG5 H1 19 0.3424 +20 CA 1 RG5 C2 20 0.7657 +21 N2 1 RG5 N2 21 -0.9672 +22 H 1 RG5 H21 22 0.4364 +23 H 1 RG5 H22 23 0.4364 +24 NC 1 RG5 N3 24 -0.6323 +25 CB 1 RG5 C4 25 0.1222 +26 CT 1 RG5 C3' 26 0.2022 +27 H1 1 RG5 H3' 27 0.0615 +28 CT 1 RG5 C2' 28 0.067 +29 H1 1 RG5 H2'1 29 0.0972 +30 OH 1 RG5 O2' 30 -0.6139 +31 HO 1 RG5 HO'2 31 0.4186 +32 OS 1 RG5 O3' 32 -0.5246 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RG 3 +[ atoms ] +1 P 1 RG P 1 1.1662 +2 O2 1 RG O1P 2 -0.776 +3 O2 1 RG O2P 3 -0.776 +4 OS 1 RG O5' 4 -0.4989 +5 CI 1 RG C5' 5 0.0558 +6 H1 1 RG H5'1 6 0.0679 +7 H1 1 RG H5'2 7 0.0679 +8 CT 1 RG C4' 8 0.1065 +9 H1 1 RG H4' 9 0.1174 +10 OS 1 RG O4' 10 -0.3548 +11 CT 1 RG C1' 11 0.0191 +12 H2 1 RG H1' 12 0.2006 +13 N* 1 RG N9 13 0.0492 +14 CP 1 RG C8 14 0.1374 +15 H5 1 RG H8 15 0.164 +16 NB 1 RG N7 16 -0.5709 +17 CB 1 RG C5 17 0.1744 +18 C 1 RG C6 18 0.477 +19 O 1 RG O6 19 -0.5597 +20 NA 1 RG N1 20 -0.4787 +21 H 1 RG H1 21 0.3424 +22 CA 1 RG C2 22 0.7657 +23 N2 1 RG N2 23 -0.9672 +24 H 1 RG H21 24 0.4364 +25 H 1 RG H22 25 0.4364 +26 NC 1 RG N3 26 -0.6323 +27 CB 1 RG C4 27 0.1222 +28 CT 1 RG C3' 28 0.2022 +29 H1 1 RG H3' 29 0.0615 +30 CT 1 RG C2' 30 0.067 +31 H1 1 RG H2'1 31 0.0972 +32 OH 1 RG O2' 32 -0.6139 +33 HO 1 RG HO'2 33 0.4186 +34 OS 1 RG O3' 34 -0.5246 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RG3 3 +[ atoms ] +1 P 1 RG3 P 1 1.1662 +2 O2 1 RG3 O1P 2 -0.776 +3 O2 1 RG3 O2P 3 -0.776 +4 OS 1 RG3 O5' 4 -0.4989 +5 CI 1 RG3 C5' 5 0.0558 +6 H1 1 RG3 H5'1 6 0.0679 +7 H1 1 RG3 H5'2 7 0.0679 +8 CT 1 RG3 C4' 8 0.1065 +9 H1 1 RG3 H4' 9 0.1174 +10 OS 1 RG3 O4' 10 -0.3548 +11 CT 1 RG3 C1' 11 0.0191 +12 H2 1 RG3 H1' 12 0.2006 +13 N* 1 RG3 N9 13 0.0492 +14 CP 1 RG3 C8 14 0.1374 +15 H5 1 RG3 H8 15 0.164 +16 NB 1 RG3 N7 16 -0.5709 +17 CB 1 RG3 C5 17 0.1744 +18 C 1 RG3 C6 18 0.477 +19 O 1 RG3 O6 19 -0.5597 +20 NA 1 RG3 N1 20 -0.4787 +21 H 1 RG3 H1 21 0.3424 +22 CA 1 RG3 C2 22 0.7657 +23 N2 1 RG3 N2 23 -0.9672 +24 H 1 RG3 H21 24 0.4364 +25 H 1 RG3 H22 25 0.4364 +26 NC 1 RG3 N3 26 -0.6323 +27 CB 1 RG3 C4 27 0.1222 +28 CT 1 RG3 C3' 28 0.2022 +29 H1 1 RG3 H3' 29 0.0615 +30 CT 1 RG3 C2' 30 0.067 +31 H1 1 RG3 H2'1 31 0.0972 +32 OH 1 RG3 O2' 32 -0.6139 +33 HO 1 RG3 HO'2 33 0.4186 +34 OH 1 RG3 O3' 34 -0.6541 +35 HO 1 RG3 H3T 35 0.4376 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RGN 3 +[ atoms ] +1 HO 1 RGN H5T 1 0.4295 +2 OH 1 RGN O5' 2 -0.6223 +3 CI 1 RGN C5' 3 0.0558 +4 H1 1 RGN H5'1 4 0.0679 +5 H1 1 RGN H5'2 5 0.0679 +6 CT 1 RGN C4' 6 0.1065 +7 H1 1 RGN H4' 7 0.1174 +8 OS 1 RGN O4' 8 -0.3548 +9 CT 1 RGN C1' 9 0.0191 +10 H2 1 RGN H1' 10 0.2006 +11 N* 1 RGN N9 11 0.0492 +12 CP 1 RGN C8 12 0.1374 +13 H5 1 RGN H8 13 0.164 +14 NB 1 RGN N7 14 -0.5709 +15 CB 1 RGN C5 15 0.1744 +16 C 1 RGN C6 16 0.477 +17 O 1 RGN O6 17 -0.5597 +18 NA 1 RGN N1 18 -0.4787 +19 H 1 RGN H1 19 0.3424 +20 CA 1 RGN C2 20 0.7657 +21 N2 1 RGN N2 21 -0.9672 +22 H 1 RGN H21 22 0.4364 +23 H 1 RGN H22 23 0.4364 +24 NC 1 RGN N3 24 -0.6323 +25 CB 1 RGN C4 25 0.1222 +26 CT 1 RGN C3' 26 0.2022 +27 H1 1 RGN H3' 27 0.0615 +28 CT 1 RGN C2' 28 0.067 +29 H1 1 RGN H2'1 29 0.0972 +30 OH 1 RGN O2' 30 -0.6139 +31 HO 1 RGN HO'2 31 0.4186 +32 OH 1 RGN O3' 32 -0.6541 +33 HO 1 RGN H3T 33 0.4376 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' O2' 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 O2' 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RC5 3 +[ atoms ] +1 HO 1 RC5 H5T 1 0.4295 +2 OH 1 RC5 O5' 2 -0.6223 +3 CI 1 RC5 C5' 3 0.0558 +4 H1 1 RC5 H5'1 4 0.0679 +5 H1 1 RC5 H5'2 5 0.0679 +6 CT 1 RC5 C4' 6 0.1065 +7 H1 1 RC5 H4' 7 0.1174 +8 OS 1 RC5 O4' 8 -0.3548 +9 CT 1 RC5 C1' 9 0.0066 +10 H2 1 RC5 H1' 10 0.2029 +11 N* 1 RC5 N1 11 -0.0484 +12 C4 1 RC5 C6 12 0.0053 +13 H4 1 RC5 H6 13 0.1958 +14 C4 1 RC5 C5 14 -0.5215 +15 HA 1 RC5 H5 15 0.1928 +16 CA 1 RC5 C4 16 0.8185 +17 N2 1 RC5 N4 17 -0.953 +18 H 1 RC5 H41 18 0.4234 +19 H 1 RC5 H42 19 0.4234 +20 NC 1 RC5 N3 20 -0.7584 +21 C 1 RC5 C2 21 0.7538 +22 O 1 RC5 O2 22 -0.6252 +23 CT 1 RC5 C3' 23 0.2022 +24 H1 1 RC5 H3' 24 0.0615 +25 CT 1 RC5 C2' 25 0.067 +26 H1 1 RC5 H2'1 26 0.0972 +27 OH 1 RC5 O2' 27 -0.6139 +28 HO 1 RC5 HO'2 28 0.4186 +29 OS 1 RC5 O3' 29 -0.5246 +[ impropers ] +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} + +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RC 3 +[ atoms ] +1 P 1 RC P 1 1.1662 +2 O2 1 RC O1P 2 -0.776 +3 O2 1 RC O2P 3 -0.776 +4 OS 1 RC O5' 4 -0.4989 +5 CI 1 RC C5' 5 0.0558 +6 H1 1 RC H5'1 6 0.0679 +7 H1 1 RC H5'2 7 0.0679 +8 CT 1 RC C4' 8 0.1065 +9 H1 1 RC H4' 9 0.1174 +10 OS 1 RC O4' 10 -0.3548 +11 CT 1 RC C1' 11 0.0066 +12 H2 1 RC H1' 12 0.2029 +13 N* 1 RC N1 13 -0.0484 +14 C4 1 RC C6 14 0.0053 +15 H4 1 RC H6 15 0.1958 +16 C4 1 RC C5 16 -0.5215 +17 HA 1 RC H5 17 0.1928 +18 CA 1 RC C4 18 0.8185 +19 N2 1 RC N4 19 -0.953 +20 H 1 RC H41 20 0.4234 +21 H 1 RC H42 21 0.4234 +22 NC 1 RC N3 22 -0.7584 +23 C 1 RC C2 23 0.7538 +24 O 1 RC O2 24 -0.6252 +25 CT 1 RC C3' 25 0.2022 +26 H1 1 RC H3' 26 0.0615 +27 CT 1 RC C2' 27 0.067 +28 H1 1 RC H2'1 28 0.0972 +29 OH 1 RC O2' 29 -0.6139 +30 HO 1 RC HO'2 30 0.4186 +31 OS 1 RC O3' 31 -0.5246 +[ impropers ] +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} + +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RC3 3 +[ atoms ] +1 P 1 RC3 P 1 1.1662 +2 O2 1 RC3 O1P 2 -0.776 +3 O2 1 RC3 O2P 3 -0.776 +4 OS 1 RC3 O5' 4 -0.4989 +5 CI 1 RC3 C5' 5 0.0558 +6 H1 1 RC3 H5'1 6 0.0679 +7 H1 1 RC3 H5'2 7 0.0679 +8 CT 1 RC3 C4' 8 0.1065 +9 H1 1 RC3 H4' 9 0.1174 +10 OS 1 RC3 O4' 10 -0.3548 +11 CT 1 RC3 C1' 11 0.0066 +12 H2 1 RC3 H1' 12 0.2029 +13 N* 1 RC3 N1 13 -0.0484 +14 C4 1 RC3 C6 14 0.0053 +15 H4 1 RC3 H6 15 0.1958 +16 C4 1 RC3 C5 16 -0.5215 +17 HA 1 RC3 H5 17 0.1928 +18 CA 1 RC3 C4 18 0.8185 +19 N2 1 RC3 N4 19 -0.953 +20 H 1 RC3 H41 20 0.4234 +21 H 1 RC3 H42 21 0.4234 +22 NC 1 RC3 N3 22 -0.7584 +23 C 1 RC3 C2 23 0.7538 +24 O 1 RC3 O2 24 -0.6252 +25 CT 1 RC3 C3' 25 0.2022 +26 H1 1 RC3 H3' 26 0.0615 +27 CT 1 RC3 C2' 27 0.067 +28 H1 1 RC3 H2'1 28 0.0972 +29 OH 1 RC3 O2' 29 -0.6139 +30 HO 1 RC3 HO'2 30 0.4186 +31 OH 1 RC3 O3' 31 -0.6541 +32 HO 1 RC3 H3T 32 0.4376 +[ impropers ] +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} + +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} +[ moleculetype ] +RCN 3 +[ atoms ] +1 HO 1 RCN H5T 1 0.4295 +2 OH 1 RCN O5' 2 -0.6223 +3 CI 1 RCN C5' 3 0.0558 +4 H1 1 RCN H5'1 4 0.0679 +5 H1 1 RCN H5'2 5 0.0679 +6 CT 1 RCN C4' 6 0.1065 +7 H1 1 RCN H4' 7 0.1174 +8 OS 1 RCN O4' 8 -0.3548 +9 CT 1 RCN C1' 9 0.0066 +10 H2 1 RCN H1' 10 0.2029 +11 N* 1 RCN N1 11 -0.0484 +12 C4 1 RCN C6 12 0.0053 +13 H4 1 RCN H6 13 0.1958 +14 C4 1 RCN C5 14 -0.5215 +15 HA 1 RCN H5 15 0.1928 +16 CA 1 RCN C4 16 0.8185 +17 N2 1 RCN N4 17 -0.953 +18 H 1 RCN H41 18 0.4234 +19 H 1 RCN H42 19 0.4234 +20 NC 1 RCN N3 20 -0.7584 +21 C 1 RCN C2 21 0.7538 +22 O 1 RCN O2 22 -0.6252 +23 CT 1 RCN C3' 23 0.2022 +24 H1 1 RCN H3' 24 0.0615 +25 CT 1 RCN C2' 25 0.067 +26 H1 1 RCN H2'1 26 0.0972 +27 OH 1 RCN O2' 27 -0.6139 +28 HO 1 RCN HO'2 28 0.4186 +29 OH 1 RCN O3' 29 -0.6541 +30 HO 1 RCN H3T 30 0.4376 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' O2' 1 {} +O2' HO'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' O2' 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' O2' 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' O2' 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +O2' C2' C3' C4' 9 {} +O2' C2' C3' H3' 9 {} +O2' C2' C3' O3' 9 {} +C1' C2' O2' HO'2 9 {} +C3' C2' O2' HO'2 9 {} +H2'1 C2' O2' HO'2 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' O2' 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' O2' 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +C2' O2' HO'2 1 {} +H2'1 C2' O2' 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' O2' 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' O2' 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +C1' HO'2 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' O2' 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 O2' 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +C3' HO'2 1 {} +H3' H2'1 1 {} +H3' O2' 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'1 HO'2 1 {} +O2' O3' 1 {} + +[ link ] +resname $rna_bases +[ bonds ] +-O3' P 1 +[ angles ] +P -O3' -C3' 1 +O1P P -O3' 1 +O2P P -O3' 1 +O5' P -O3' 1 +[ dihedrals ] +P -O3' -C3' -C4' 9 {"group": "link"} +O1P P -O3' -C3' 9 {"group": "link"} +O2P P -O3' -C3' 9 {"group": "link"} +O5' P -O3' -C3' 9 {"group": "link"} +P -O3' -C3' -C2' 9 {"group": "link"} +C5' O5' P -O3' 9 {"group": "link"} +P -O3' -C3' -H3' 9 {"group": "link"} +[ pairs ] +P -C4' 1 +O1P -C3' 1 +O2P -C3' 1 +O5' -C3' 1 +P -C2' 1 +C5' -O3' 1 +P -H3' 1 From fe7c113d3222cfc6e3c69e32f58bcb087bf98f4b Mon Sep 17 00:00:00 2001 From: "f.grunewald" Date: Wed, 8 Feb 2023 14:38:48 +0100 Subject: [PATCH 2/7] RNA fix chirality --- polyply/data/ol21/rna.ff | 75 +++++++++++++++++++++++++++++++++------- 1 file changed, 63 insertions(+), 12 deletions(-) diff --git a/polyply/data/ol21/rna.ff b/polyply/data/ol21/rna.ff index 84305da54..c900756f8 100644 --- a/polyply/data/ol21/rna.ff +++ b/polyply/data/ol21/rna.ff @@ -43,6 +43,11 @@ C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -346,6 +351,9 @@ C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] P O1P 1 {} P O2P 1 {} @@ -659,6 +667,9 @@ C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] P O1P 1 {} @@ -936,6 +947,7 @@ C2' H3T 1 {} H2'1 O3' 1 {} H2'1 HO'2 1 {} O2' O3' 1 {} + [ moleculetype ] RAN 3 [ atoms ] @@ -1270,13 +1282,17 @@ RU5 3 27 HO 1 RU5 HO'2 27 0.4186 28 OS 1 RU5 O3' 28 -0.5246 [ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} + +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] H5T O5' 1 {} @@ -1551,14 +1567,18 @@ RU 3 29 HO 1 RU HO'2 29 0.4186 30 OS 1 RU O3' 30 -0.5246 [ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] P O1P 1 {} P O2P 1 {} @@ -1842,13 +1862,18 @@ RU3 3 30 OH 1 RU3 O3' 30 -0.6541 31 HO 1 RU3 H3T 31 0.4376 [ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] P O1P 1 {} P O2P 1 {} @@ -2427,6 +2452,11 @@ C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -2744,6 +2774,10 @@ C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'" C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] P O1P 1 {} P O2P 1 {} @@ -3071,6 +3105,10 @@ C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'" C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] P O1P 1 {} P O2P 1 {} @@ -3715,6 +3753,10 @@ C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'" C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -3998,6 +4040,11 @@ C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] P O1P 1 {} P O2P 1 {} @@ -4292,6 +4339,10 @@ C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'" C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] P O1P 1 {} P O2P 1 {} From d831214a161248b596311b2d60b921d4e6e89ddb Mon Sep 17 00:00:00 2001 From: "f.grunewald" Date: Wed, 8 Feb 2023 14:40:40 +0100 Subject: [PATCH 3/7] tests for RNA --- .../library_tests/ol21/RNA/polyply/RNA.itp | 1974 +++++++++++++++++ .../library_tests/ol21/RNA/polyply/command | 1 + polyply/tests/test_lib_files.py | 1 + 3 files changed, 1976 insertions(+) create mode 100644 polyply/tests/test_data/library_tests/ol21/RNA/polyply/RNA.itp create mode 100644 polyply/tests/test_data/library_tests/ol21/RNA/polyply/command diff --git a/polyply/tests/test_data/library_tests/ol21/RNA/polyply/RNA.itp b/polyply/tests/test_data/library_tests/ol21/RNA/polyply/RNA.itp new file mode 100644 index 000000000..e0367b677 --- /dev/null +++ b/polyply/tests/test_data/library_tests/ol21/RNA/polyply/RNA.itp @@ -0,0 +1,1974 @@ + +[ moleculetype ] +; Name nrexcl +RNA 3 + +[ atoms ] +; nr type resnr residue atom cgnr charge mass typeB chargeB massB +; residue 1 RA5 rtp RA5 q -0.3 + 1 HO 1 RA5 H5T 1 0.4295 1.008 + 2 OH 1 RA5 O5' 2 -0.6223 16 + 3 CI 1 RA5 C5' 3 0.0558 12.01 + 4 H1 1 RA5 H5'1 4 0.0679 1.008 + 5 H1 1 RA5 H5'2 5 0.0679 1.008 + 6 CT 1 RA5 C4' 6 0.1065 12.01 + 7 H1 1 RA5 H4' 7 0.1174 1.008 + 8 OS 1 RA5 O4' 8 -0.3548 16 + 9 CT 1 RA5 C1' 9 0.0394 12.01 + 10 H2 1 RA5 H1' 10 0.2007 1.008 + 11 N* 1 RA5 N9 11 -0.0251 14.01 + 12 C5 1 RA5 C8 12 0.2006 12.01 + 13 H5 1 RA5 H8 13 0.1553 1.008 + 14 NB 1 RA5 N7 14 -0.6073 14.01 + 15 CB 1 RA5 C5 15 0.0515 12.01 + 16 CA 1 RA5 C6 16 0.7009 12.01 + 17 N2 1 RA5 N6 17 -0.9019 14.01 + 18 H 1 RA5 H61 18 0.4115 1.008 + 19 H 1 RA5 H62 19 0.4115 1.008 + 20 NC 1 RA5 N1 20 -0.7615 14.01 + 21 CQ 1 RA5 C2 21 0.5875 12.01 + 22 H5 1 RA5 H2 22 0.0473 1.008 + 23 NC 1 RA5 N3 23 -0.6997 14.01 + 24 CB 1 RA5 C4 24 0.3053 12.01 + 25 CT 1 RA5 C3' 25 0.2022 12.01 + 26 H1 1 RA5 H3' 26 0.0615 1.008 + 27 CT 1 RA5 C2' 27 0.067 12.01 + 28 H1 1 RA5 H2'1 28 0.0972 1.008 + 29 OH 1 RA5 O2' 29 -0.6139 16 + 30 HO 1 RA5 HO'2 30 0.4186 1.008 + 31 OS 1 RA5 O3' 31 -0.5246 16 ; qtot -0.3081 +; residue 2 RA rtp RA q -1.0 + 32 P 2 RA P 32 1.1662 30.97 + 33 O2 2 RA O1P 33 -0.776 16 + 34 O2 2 RA O2P 34 -0.776 16 + 35 OS 2 RA O5' 35 -0.4989 16 + 36 CI 2 RA C5' 36 0.0558 12.01 + 37 H1 2 RA H5'1 37 0.0679 1.008 + 38 H1 2 RA H5'2 38 0.0679 1.008 + 39 CT 2 RA C4' 39 0.1065 12.01 + 40 H1 2 RA H4' 40 0.1174 1.008 + 41 OS 2 RA O4' 41 -0.3548 16 + 42 CT 2 RA C1' 42 0.0394 12.01 + 43 H2 2 RA H1' 43 0.2007 1.008 + 44 N* 2 RA N9 44 -0.0251 14.01 + 45 C5 2 RA C8 45 0.2006 12.01 + 46 H5 2 RA H8 46 0.1553 1.008 + 47 NB 2 RA N7 47 -0.6073 14.01 + 48 CB 2 RA C5 48 0.0515 12.01 + 49 CA 2 RA C6 49 0.7009 12.01 + 50 N2 2 RA N6 50 -0.9019 14.01 + 51 H 2 RA H61 51 0.4115 1.008 + 52 H 2 RA H62 52 0.4115 1.008 + 53 NC 2 RA N1 53 -0.7615 14.01 + 54 CQ 2 RA C2 54 0.5875 12.01 + 55 H5 2 RA H2 55 0.0473 1.008 + 56 NC 2 RA N3 56 -0.6997 14.01 + 57 CB 2 RA C4 57 0.3053 12.01 + 58 CT 2 RA C3' 58 0.2022 12.01 + 59 H1 2 RA H3' 59 0.0615 1.008 + 60 CT 2 RA C2' 60 0.067 12.01 + 61 H1 2 RA H2'1 61 0.0972 1.008 + 62 OH 2 RA O2' 62 -0.6139 16 + 63 HO 2 RA HO'2 63 0.4186 1.008 + 64 OS 2 RA O3' 64 -0.5246 16 ; qtot -1.308 +; residue 3 RA rtp RA q -1.0 + 65 P 3 RA P 65 1.1662 30.97 + 66 O2 3 RA O1P 66 -0.776 16 + 67 O2 3 RA O2P 67 -0.776 16 + 68 OS 3 RA O5' 68 -0.4989 16 + 69 CI 3 RA C5' 69 0.0558 12.01 + 70 H1 3 RA H5'1 70 0.0679 1.008 + 71 H1 3 RA H5'2 71 0.0679 1.008 + 72 CT 3 RA C4' 72 0.1065 12.01 + 73 H1 3 RA H4' 73 0.1174 1.008 + 74 OS 3 RA O4' 74 -0.3548 16 + 75 CT 3 RA C1' 75 0.0394 12.01 + 76 H2 3 RA H1' 76 0.2007 1.008 + 77 N* 3 RA N9 77 -0.0251 14.01 + 78 C5 3 RA C8 78 0.2006 12.01 + 79 H5 3 RA H8 79 0.1553 1.008 + 80 NB 3 RA N7 80 -0.6073 14.01 + 81 CB 3 RA C5 81 0.0515 12.01 + 82 CA 3 RA C6 82 0.7009 12.01 + 83 N2 3 RA N6 83 -0.9019 14.01 + 84 H 3 RA H61 84 0.4115 1.008 + 85 H 3 RA H62 85 0.4115 1.008 + 86 NC 3 RA N1 86 -0.7615 14.01 + 87 CQ 3 RA C2 87 0.5875 12.01 + 88 H5 3 RA H2 88 0.0473 1.008 + 89 NC 3 RA N3 89 -0.6997 14.01 + 90 CB 3 RA C4 90 0.3053 12.01 + 91 CT 3 RA C3' 91 0.2022 12.01 + 92 H1 3 RA H3' 92 0.0615 1.008 + 93 CT 3 RA C2' 93 0.067 12.01 + 94 H1 3 RA H2'1 94 0.0972 1.008 + 95 OH 3 RA O2' 95 -0.6139 16 + 96 HO 3 RA HO'2 96 0.4186 1.008 + 97 OS 3 RA O3' 97 -0.5246 16 ; qtot -2.308 +; residue 4 RA rtp RA q -1.0 + 98 P 4 RA P 98 1.1662 30.97 + 99 O2 4 RA O1P 99 -0.776 16 + 100 O2 4 RA O2P 100 -0.776 16 + 101 OS 4 RA O5' 101 -0.4989 16 + 102 CI 4 RA C5' 102 0.0558 12.01 + 103 H1 4 RA H5'1 103 0.0679 1.008 + 104 H1 4 RA H5'2 104 0.0679 1.008 + 105 CT 4 RA C4' 105 0.1065 12.01 + 106 H1 4 RA H4' 106 0.1174 1.008 + 107 OS 4 RA O4' 107 -0.3548 16 + 108 CT 4 RA C1' 108 0.0394 12.01 + 109 H2 4 RA H1' 109 0.2007 1.008 + 110 N* 4 RA N9 110 -0.0251 14.01 + 111 C5 4 RA C8 111 0.2006 12.01 + 112 H5 4 RA H8 112 0.1553 1.008 + 113 NB 4 RA N7 113 -0.6073 14.01 + 114 CB 4 RA C5 114 0.0515 12.01 + 115 CA 4 RA C6 115 0.7009 12.01 + 116 N2 4 RA N6 116 -0.9019 14.01 + 117 H 4 RA H61 117 0.4115 1.008 + 118 H 4 RA H62 118 0.4115 1.008 + 119 NC 4 RA N1 119 -0.7615 14.01 + 120 CQ 4 RA C2 120 0.5875 12.01 + 121 H5 4 RA H2 121 0.0473 1.008 + 122 NC 4 RA N3 122 -0.6997 14.01 + 123 CB 4 RA C4 123 0.3053 12.01 + 124 CT 4 RA C3' 124 0.2022 12.01 + 125 H1 4 RA H3' 125 0.0615 1.008 + 126 CT 4 RA C2' 126 0.067 12.01 + 127 H1 4 RA H2'1 127 0.0972 1.008 + 128 OH 4 RA O2' 128 -0.6139 16 + 129 HO 4 RA HO'2 129 0.4186 1.008 + 130 OS 4 RA O3' 130 -0.5246 16 ; qtot -3.308 +; residue 5 RA rtp RA q -1.0 + 131 P 5 RA P 131 1.1662 30.97 + 132 O2 5 RA O1P 132 -0.776 16 + 133 O2 5 RA O2P 133 -0.776 16 + 134 OS 5 RA O5' 134 -0.4989 16 + 135 CI 5 RA C5' 135 0.0558 12.01 + 136 H1 5 RA H5'1 136 0.0679 1.008 + 137 H1 5 RA H5'2 137 0.0679 1.008 + 138 CT 5 RA C4' 138 0.1065 12.01 + 139 H1 5 RA H4' 139 0.1174 1.008 + 140 OS 5 RA O4' 140 -0.3548 16 + 141 CT 5 RA C1' 141 0.0394 12.01 + 142 H2 5 RA H1' 142 0.2007 1.008 + 143 N* 5 RA N9 143 -0.0251 14.01 + 144 C5 5 RA C8 144 0.2006 12.01 + 145 H5 5 RA H8 145 0.1553 1.008 + 146 NB 5 RA N7 146 -0.6073 14.01 + 147 CB 5 RA C5 147 0.0515 12.01 + 148 CA 5 RA C6 148 0.7009 12.01 + 149 N2 5 RA N6 149 -0.9019 14.01 + 150 H 5 RA H61 150 0.4115 1.008 + 151 H 5 RA H62 151 0.4115 1.008 + 152 NC 5 RA N1 152 -0.7615 14.01 + 153 CQ 5 RA C2 153 0.5875 12.01 + 154 H5 5 RA H2 154 0.0473 1.008 + 155 NC 5 RA N3 155 -0.6997 14.01 + 156 CB 5 RA C4 156 0.3053 12.01 + 157 CT 5 RA C3' 157 0.2022 12.01 + 158 H1 5 RA H3' 158 0.0615 1.008 + 159 CT 5 RA C2' 159 0.067 12.01 + 160 H1 5 RA H2'1 160 0.0972 1.008 + 161 OH 5 RA O2' 161 -0.6139 16 + 162 HO 5 RA HO'2 162 0.4186 1.008 + 163 OS 5 RA O3' 163 -0.5246 16 ; qtot -4.308 +; residue 6 RA3 rtp RA3 q -0.7 + 164 P 6 RA3 P 164 1.1662 30.97 + 165 O2 6 RA3 O1P 165 -0.776 16 + 166 O2 6 RA3 O2P 166 -0.776 16 + 167 OS 6 RA3 O5' 167 -0.4989 16 + 168 CI 6 RA3 C5' 168 0.0558 12.01 + 169 H1 6 RA3 H5'1 169 0.0679 1.008 + 170 H1 6 RA3 H5'2 170 0.0679 1.008 + 171 CT 6 RA3 C4' 171 0.1065 12.01 + 172 H1 6 RA3 H4' 172 0.1174 1.008 + 173 OS 6 RA3 O4' 173 -0.3548 16 + 174 CT 6 RA3 C1' 174 0.0394 12.01 + 175 H2 6 RA3 H1' 175 0.2007 1.008 + 176 N* 6 RA3 N9 176 -0.0251 14.01 + 177 C5 6 RA3 C8 177 0.2006 12.01 + 178 H5 6 RA3 H8 178 0.1553 1.008 + 179 NB 6 RA3 N7 179 -0.6073 14.01 + 180 CB 6 RA3 C5 180 0.0515 12.01 + 181 CA 6 RA3 C6 181 0.7009 12.01 + 182 N2 6 RA3 N6 182 -0.9019 14.01 + 183 H 6 RA3 H61 183 0.4115 1.008 + 184 H 6 RA3 H62 184 0.4115 1.008 + 185 NC 6 RA3 N1 185 -0.7615 14.01 + 186 CQ 6 RA3 C2 186 0.5875 12.01 + 187 H5 6 RA3 H2 187 0.0473 1.008 + 188 NC 6 RA3 N3 188 -0.6997 14.01 + 189 CB 6 RA3 C4 189 0.3053 12.01 + 190 CT 6 RA3 C3' 190 0.2022 12.01 + 191 H1 6 RA3 H3' 191 0.0615 1.008 + 192 CT 6 RA3 C2' 192 0.067 12.01 + 193 H1 6 RA3 H2'1 193 0.0972 1.008 + 194 OH 6 RA3 O2' 194 -0.6139 16 + 195 HO 6 RA3 HO'2 195 0.4186 1.008 + 196 OH 6 RA3 O3' 196 -0.6541 16 + 197 HO 6 RA3 H3T 197 0.4376 1.008 ; qtot 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1 + 171 176 1 + 171 193 1 + 171 194 1 + 171 197 1 + 172 174 1 + 172 191 1 + 172 192 1 + 172 196 1 + 173 177 1 + 173 189 1 + 173 191 1 + 173 193 1 + 173 194 1 + 173 196 1 + 174 178 1 + 174 179 1 + 174 180 1 + 174 188 1 + 174 191 1 + 174 195 1 + 174 196 1 + 175 177 1 + 175 189 1 + 175 190 1 + 175 193 1 + 175 194 1 + 176 181 1 + 176 186 1 + 176 190 1 + 176 193 1 + 176 194 1 + 177 181 1 + 177 188 1 + 177 192 1 + 178 180 1 + 178 189 1 + 179 182 1 + 179 185 1 + 179 188 1 + 180 183 1 + 180 184 1 + 180 186 1 + 181 187 1 + 181 188 1 + 182 186 1 + 182 189 1 + 183 185 1 + 184 185 1 + 185 189 1 + 187 189 1 + 189 192 1 + 190 195 1 + 191 193 1 + 191 194 1 + 191 197 1 + 192 197 1 + 193 195 1 + 193 196 1 + 194 196 1 + +[ angles ] +; ai aj ak funct c0 c1 c2 c3 + 1 2 3 1 + 2 3 4 1 + 2 3 5 1 + 2 3 6 1 + 4 3 5 1 + 4 3 6 1 + 5 3 6 1 + 3 6 7 1 + 3 6 8 1 + 3 6 25 1 + 7 6 8 1 + 7 6 25 1 + 8 6 25 1 + 6 8 9 1 + 8 9 10 1 + 8 9 11 1 + 8 9 27 1 + 10 9 11 1 + 10 9 27 1 + 11 9 27 1 + 9 11 12 1 + 9 11 24 1 + 12 11 24 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3.5264390e+01 3.3484625e+03 +108 126 110 107 2 3.5264390e+01 3.3484625e+03 +141 159 143 140 2 3.5264390e+01 3.3484625e+03 +174 192 176 173 2 3.5264390e+01 3.3484625e+03 +#endif + +#ifdef eq_polyply +; chiral-center C2' + 27 25 9 28 2 -3.5264390e+01 3.3484625e+03 + 27 25 9 29 2 3.5264390e+01 3.3484625e+03 + 60 58 42 61 2 -3.5264390e+01 3.3484625e+03 + 60 58 42 62 2 3.5264390e+01 3.3484625e+03 + 93 91 75 94 2 -3.5264390e+01 3.3484625e+03 + 93 91 75 95 2 3.5264390e+01 3.3484625e+03 +126 124 108 127 2 -3.5264390e+01 3.3484625e+03 +126 124 108 128 2 3.5264390e+01 3.3484625e+03 +159 157 141 160 2 -3.5264390e+01 3.3484625e+03 +159 157 141 161 2 3.5264390e+01 3.3484625e+03 +192 190 174 193 2 -3.5264390e+01 3.3484625e+03 +192 190 174 194 2 3.5264390e+01 3.3484625e+03 +#endif + +#ifdef eq_polyply +; chiral-center C3' + 25 31 6 27 2 3.5264390e+01 3.3484625e+03 + 58 64 39 60 2 3.5264390e+01 3.3484625e+03 + 91 97 72 93 2 3.5264390e+01 3.3484625e+03 +124 130 105 126 2 3.5264390e+01 3.3484625e+03 +157 163 138 159 2 3.5264390e+01 3.3484625e+03 +190 196 171 192 2 3.5264390e+01 3.3484625e+03 +#endif + +#ifdef eq_polyply +; chiral-center HC1' + 9 27 11 10 2 -3.5264390e+01 3.3484625e+03 + 42 60 44 43 2 -3.5264390e+01 3.3484625e+03 + 75 93 77 76 2 -3.5264390e+01 3.3484625e+03 +108 126 110 109 2 -3.5264390e+01 3.3484625e+03 +141 159 143 142 2 -3.5264390e+01 3.3484625e+03 +174 192 176 175 2 -3.5264390e+01 3.3484625e+03 +#endif + +#ifdef eq_polyply +; chiral-center HC3' + 25 31 6 26 2 -3.5264390e+01 3.3484625e+03 + 58 64 39 59 2 -3.5264390e+01 3.3484625e+03 + 91 97 72 92 2 -3.5264390e+01 3.3484625e+03 +124 130 105 125 2 -3.5264390e+01 3.3484625e+03 +157 163 138 158 2 -3.5264390e+01 3.3484625e+03 +190 196 171 191 2 -3.5264390e+01 3.3484625e+03 +#endif + +#ifdef eq_polyply +; chiral-center HO4' + 6 3 25 7 2 -3.5264390e+01 3.3484625e+03 + 39 36 58 40 2 -3.5264390e+01 3.3484625e+03 + 72 69 91 73 2 -3.5264390e+01 3.3484625e+03 +105 102 124 106 2 -3.5264390e+01 3.3484625e+03 +138 135 157 139 2 -3.5264390e+01 3.3484625e+03 +171 168 190 172 2 -3.5264390e+01 3.3484625e+03 +#endif + +#ifdef eq_polyply +; chiral-center O4' + 6 3 25 8 2 3.5264390e+01 3.3484625e+03 + 39 36 58 41 2 3.5264390e+01 3.3484625e+03 + 72 69 91 74 2 3.5264390e+01 3.3484625e+03 +105 102 124 107 2 3.5264390e+01 3.3484625e+03 +138 135 157 140 2 3.5264390e+01 3.3484625e+03 +171 168 190 173 2 3.5264390e+01 3.3484625e+03 +#endif + diff --git a/polyply/tests/test_data/library_tests/ol21/RNA/polyply/command b/polyply/tests/test_data/library_tests/ol21/RNA/polyply/command new file mode 100644 index 000000000..41d4e714d --- /dev/null +++ b/polyply/tests/test_data/library_tests/ol21/RNA/polyply/command @@ -0,0 +1 @@ +polyply gen_params -lib ol21 -seq RA5:1 RA:4 RA3:1 -name RNA -o RNA.itp diff --git a/polyply/tests/test_lib_files.py b/polyply/tests/test_lib_files.py index 79afccc51..c27bea2fa 100644 --- a/polyply/tests/test_lib_files.py +++ b/polyply/tests/test_lib_files.py @@ -170,6 +170,7 @@ def _interaction_equal(interaction1, interaction2, inter_type): return False @pytest.mark.parametrize("library, polymer", [ + ['ol21', 'RNA'], ['2016H66', 'PP'], ['2016H66', 'C12E4'], ['2016H66', 'PE'], From dc69304377796fac391eb57ba313e2552eb52317 Mon Sep 17 00:00:00 2001 From: "f.grunewald" Date: Wed, 16 Aug 2023 15:10:49 +0200 Subject: [PATCH 4/7] add OL21 DNA --- polyply/data/ol21/citations.bib | 42 + polyply/data/ol21/dna.ff | 5254 +++++++++++++++++++++++++++++++ polyply/data/ol21/rna.ff | 4 + 3 files changed, 5300 insertions(+) create mode 100644 polyply/data/ol21/citations.bib create mode 100644 polyply/data/ol21/dna.ff diff --git a/polyply/data/ol21/citations.bib b/polyply/data/ol21/citations.bib new file mode 100644 index 000000000..d449040e7 --- /dev/null +++ b/polyply/data/ol21/citations.bib @@ -0,0 +1,42 @@ +@article{ol21_DNA_a, + title={Refinement of the sugar--phosphate backbone torsion beta for AMBER force fields improves the description of Z-and B-DNA}, + author={Zgarbov{\'a}, Marie and Sponer, Jiri and Otyepka, Michal and Cheatham III, Thomas E and Galindo-Murillo, Rodrigo and Jurecka, Petr}, + journal={Journal of chemical theory and computation}, + volume={11}, + number={12}, + pages={5723--5736}, + year={2015}, + publisher={ACS Publications} +} + +@article{ol21_DNA_b, + title={Z-DNA as a touchstone for additive empirical force fields and a refinement of the alpha/gamma DNA torsions for AMBER}, + author={Zgarbov{\'a}, Marie and Sponer, Jiri and Jurecka, Petr}, + journal={Journal of Chemical Theory and Computation}, + volume={17}, + number={10}, + pages={6292--6301}, + year={2021}, + publisher={ACS Publications} +} + +@article{ol21_RNA, + title={Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles}, + author={Zgarbov{\'a}, Marie and Otyepka, Michal and Šponer, Jiří and Mládek, Arnošt and Banáš, Pavel and Cheatham III, Thomas E and Jurecka, Petr}, + journal={Journal of chemical theory and computation}, + volume={7}, + number={9}, + pages={2886--2902}, + year={2011}, + publisher={ACS Publications} +} + +@article{polyply, + title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials}, + author={Grunewald, Fabian and Alessandri, Riccardo and Kroon, Peter C and Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J}, + journal={Nature Communications}, + doi={10.1038/s41467-021-27627-4}, + year={2022}, + volume={13}, + pages={68} +} diff --git a/polyply/data/ol21/dna.ff b/polyply/data/ol21/dna.ff new file mode 100644 index 000000000..d7a90ed20 --- /dev/null +++ b/polyply/data/ol21/dna.ff @@ -0,0 +1,5254 @@ +[ macros ] +base_pairs "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3" + +[ citations ] +ol21_DNA_a +ol21_DNA_b +polyply + +[ moleculetype ] +DA5 3 +[ atoms ] +1 HO 1 DA5 H5T 1 0.4422 +2 OH 1 DA5 O5' 2 -0.6318 +3 CJ 1 DA5 C5' 3 -0.0069 +4 H1 1 DA5 H5'1 4 0.0754 +5 H1 1 DA5 H5'2 5 0.0754 +6 CT 1 DA5 C4' 6 0.1629 +7 H1 1 DA5 H4' 7 0.1176 +8 OS 1 DA5 O4' 8 -0.3691 +9 CT 1 DA5 C1' 9 0.0431 +10 H2 1 DA5 H1' 10 0.1838 +11 N* 1 DA5 N9 11 -0.0268 +12 C2 1 DA5 C8 12 0.1607 +13 H5 1 DA5 H8 13 0.1877 +14 NB 1 DA5 N7 14 -0.6175 +15 CB 1 DA5 C5 15 0.0725 +16 CA 1 DA5 C6 16 0.6897 +17 N2 1 DA5 N6 17 -0.9123 +18 H 1 DA5 H61 18 0.4167 +19 H 1 DA5 H62 19 0.4167 +20 NC 1 DA5 N1 20 -0.7624 +21 CQ 1 DA5 C2 21 0.5716 +22 H5 1 DA5 H2 22 0.0598 +23 NC 1 DA5 N3 23 -0.7417 +24 CB 1 DA5 C4 24 0.38 +25 C7 1 DA5 C3' 25 0.0713 +26 H1 1 DA5 H3' 26 0.0985 +27 CT 1 DA5 C2' 27 -0.0854 +28 HC 1 DA5 H2'1 28 0.0718 +29 HC 1 DA5 H2'2 29 0.0718 +30 OS 1 DA5 O3' 30 -0.5232 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 N6 +C6 N1 +N6 H61 +N6 H62 +N1 C2 +C2 H2 +C2 N3 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DA 3 +[ atoms ] +1 P 1 DA P 1 1.1659 +2 O2 1 DA O1P 2 -0.7761 +3 O2 1 DA O2P 3 -0.7761 +4 OS 1 DA O5' 4 -0.4954 +5 CJ 1 DA C5' 5 -0.0069 +6 H1 1 DA H5'1 6 0.0754 +7 H1 1 DA H5'2 7 0.0754 +8 CT 1 DA C4' 8 0.1629 +9 H1 1 DA H4' 9 0.1176 +10 OS 1 DA O4' 10 -0.3691 +11 CT 1 DA C1' 11 0.0431 +12 H2 1 DA H1' 12 0.1838 +13 N* 1 DA N9 13 -0.0268 +14 C2 1 DA C8 14 0.1607 +15 H5 1 DA H8 15 0.1877 +16 NB 1 DA N7 16 -0.6175 +17 CB 1 DA C5 17 0.0725 +18 CA 1 DA C6 18 0.6897 +19 N2 1 DA N6 19 -0.9123 +20 H 1 DA H61 20 0.4167 +21 H 1 DA H62 21 0.4167 +22 NC 1 DA N1 22 -0.7624 +23 CQ 1 DA C2 23 0.5716 +24 H5 1 DA H2 24 0.0598 +25 NC 1 DA N3 25 -0.7417 +26 CB 1 DA C4 26 0.38 +27 C7 1 DA C3' 27 0.0713 +28 H1 1 DA H3' 28 0.0985 +29 CT 1 DA C2' 29 -0.0854 +30 HC 1 DA H2'1 30 0.0718 +31 HC 1 DA H2'2 31 0.0718 +32 OS 1 DA O3' 32 -0.5232 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 N6 +C6 N1 +N6 H61 +N6 H62 +N1 C2 +C2 H2 +C2 N3 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DA3 3 +[ atoms ] +1 P 1 DA3 P 1 1.1659 +2 O2 1 DA3 O1P 2 -0.7761 +3 O2 1 DA3 O2P 3 -0.7761 +4 OS 1 DA3 O5' 4 -0.4954 +5 CJ 1 DA3 C5' 5 -0.0069 +6 H1 1 DA3 H5'1 6 0.0754 +7 H1 1 DA3 H5'2 7 0.0754 +8 CT 1 DA3 C4' 8 0.1629 +9 H1 1 DA3 H4' 9 0.1176 +10 OS 1 DA3 O4' 10 -0.3691 +11 CT 1 DA3 C1' 11 0.0431 +12 H2 1 DA3 H1' 12 0.1838 +13 N* 1 DA3 N9 13 -0.0268 +14 C2 1 DA3 C8 14 0.1607 +15 H5 1 DA3 H8 15 0.1877 +16 NB 1 DA3 N7 16 -0.6175 +17 CB 1 DA3 C5 17 0.0725 +18 CA 1 DA3 C6 18 0.6897 +19 N2 1 DA3 N6 19 -0.9123 +20 H 1 DA3 H61 20 0.4167 +21 H 1 DA3 H62 21 0.4167 +22 NC 1 DA3 N1 22 -0.7624 +23 CQ 1 DA3 C2 23 0.5716 +24 H5 1 DA3 H2 24 0.0598 +25 NC 1 DA3 N3 25 -0.7417 +26 CB 1 DA3 C4 26 0.38 +27 C7 1 DA3 C3' 27 0.0713 +28 H1 1 DA3 H3' 28 0.0985 +29 CT 1 DA3 C2' 29 -0.0854 +30 HC 1 DA3 H2'1 30 0.0718 +31 HC 1 DA3 H2'2 31 0.0718 +32 OH 1 DA3 O3' 32 -0.6549 +33 HO 1 DA3 H3T 33 0.4396 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 N6 +C6 N1 +N6 H61 +N6 H62 +N1 C2 +C2 H2 +C2 N3 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DAN 3 +[ atoms ] +1 HO 1 DAN H5T 1 0.4422 +2 OH 1 DAN O5' 2 -0.6318 +3 CJ 1 DAN C5' 3 -0.0069 +4 H1 1 DAN H5'1 4 0.0754 +5 H1 1 DAN H5'2 5 0.0754 +6 CT 1 DAN C4' 6 0.1629 +7 H1 1 DAN H4' 7 0.1176 +8 OS 1 DAN O4' 8 -0.3691 +9 CT 1 DAN C1' 9 0.0431 +10 H2 1 DAN H1' 10 0.1838 +11 N* 1 DAN N9 11 -0.0268 +12 C2 1 DAN C8 12 0.1607 +13 H5 1 DAN H8 13 0.1877 +14 NB 1 DAN N7 14 -0.6175 +15 CB 1 DAN C5 15 0.0725 +16 CA 1 DAN C6 16 0.6897 +17 N2 1 DAN N6 17 -0.9123 +18 H 1 DAN H61 18 0.4167 +19 H 1 DAN H62 19 0.4167 +20 NC 1 DAN N1 20 -0.7624 +21 CQ 1 DAN C2 21 0.5716 +22 H5 1 DAN H2 22 0.0598 +23 NC 1 DAN N3 23 -0.7417 +24 CB 1 DAN C4 24 0.38 +25 C7 1 DAN C3' 25 0.0713 +26 H1 1 DAN H3' 26 0.0985 +27 CT 1 DAN C2' 27 -0.0854 +28 HC 1 DAN H2'1 28 0.0718 +29 HC 1 DAN H2'2 29 0.0718 +30 OH 1 DAN O3' 30 -0.6549 +31 HO 1 DAN H3T 31 0.4396 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 N6 1 {} +C6 N1 1 {} +N6 H61 1 {} +N6 H62 1 {} +N1 C2 1 {} +C2 H2 1 {} +C2 N3 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C6 H61 N6 H62 4 {} +N9 N7 C8 H8 4 {} +N1 N3 C2 H2 4 {} +C5 N6 C6 N1 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +H2 C2 N1 C6 9 {} +N3 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +H2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 N6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 N6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 C2 9 {} +N6 C6 N1 C2 9 {} +C5 C6 N6 H61 9 {} +C5 C6 N6 H62 9 {} +N1 C6 N6 H61 9 {} +N1 C6 N6 H62 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 N6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N6 H61 1 {} +C6 N6 H62 1 {} +C6 N1 C2 1 {} +N6 C6 N1 1 {} +H61 N6 H62 1 {} +N1 C2 H2 1 {} +N1 C2 N3 1 {} +C2 N3 C4 1 {} +H2 C2 N3 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 N6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H61 1 {} +C5 H62 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 H2 1 {} +N6 C4 1 {} +N6 C2 1 {} +H61 N1 1 {} +H62 N1 1 {} +N1 C4 1 {} +H2 C4 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 N6 +C6 N1 +N6 H61 +N6 H62 +N1 C2 +C2 H2 +C2 N3 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DT5 3 +[ atoms ] +1 HO 1 DT5 H5T 1 0.4422 +2 OH 1 DT5 O5' 2 -0.6318 +3 CJ 1 DT5 C5' 3 -0.0069 +4 H1 1 DT5 H5'1 4 0.0754 +5 H1 1 DT5 H5'2 5 0.0754 +6 CT 1 DT5 C4' 6 0.1629 +7 H1 1 DT5 H4' 7 0.1176 +8 OS 1 DT5 O4' 8 -0.3691 +9 CT 1 DT5 C1' 9 0.068 +10 H2 1 DT5 H1' 10 0.1804 +11 N* 1 DT5 N1 11 -0.0239 +12 CM 1 DT5 C6 12 -0.2209 +13 H4 1 DT5 H6 13 0.2607 +14 CM 1 DT5 C5 14 0.0025 +15 CT 1 DT5 C7 15 -0.2269 +16 HC 1 DT5 H71 16 0.077 +17 HC 1 DT5 H72 17 0.077 +18 HC 1 DT5 H73 18 0.077 +19 C 1 DT5 C4 19 0.5194 +20 O 1 DT5 O4 20 -0.5563 +21 NA 1 DT5 N3 21 -0.434 +22 H 1 DT5 H3 22 0.342 +23 C 1 DT5 C2 23 0.5677 +24 O 1 DT5 O2 24 -0.5881 +25 C7 1 DT5 C3' 25 0.0713 +26 H1 1 DT5 H3' 26 0.0985 +27 CT 1 DT5 C2' 27 -0.0854 +28 HC 1 DT5 H2'1 28 0.0718 +29 HC 1 DT5 H2'2 29 0.0718 +30 OS 1 DT5 O3' 30 -0.5232 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 C7 1 {} +C5 C4 1 {} +C7 H71 1 {} +C7 H72 1 {} +C7 H73 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C4 C6 C5 C7 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 C7 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 C7 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +C7 C5 C6 N1 9 {} +C7 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +C6 C5 C7 H71 9 {} +C6 C5 C7 H72 9 {} +C6 C5 C7 H73 9 {} +C4 C5 C7 H71 9 {} +C4 C5 C7 H72 9 {} +C4 C5 C7 H73 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 C7 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C7 H71 1 {} +C5 C7 H72 1 {} +C5 C7 H73 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +C7 C5 C4 1 {} +H71 C7 H72 1 {} +H71 C7 H73 1 {} +H72 C7 H73 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 C7 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 H71 1 {} +C6 H72 1 {} +C6 H73 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 C7 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +C7 O4 1 {} +C7 N3 1 {} +H71 C4 1 {} +H72 C4 1 {} +H73 C4 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 C7 +C5 C4 +C7 H71 +C7 H72 +C7 H73 +C4 O4 +C4 N3 +N3 H3 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DT 3 +[ atoms ] +1 P 1 DT P 1 1.1659 +2 O2 1 DT O1P 2 -0.7761 +3 O2 1 DT O2P 3 -0.7761 +4 OS 1 DT O5' 4 -0.4954 +5 CJ 1 DT C5' 5 -0.0069 +6 H1 1 DT H5'1 6 0.0754 +7 H1 1 DT H5'2 7 0.0754 +8 CT 1 DT C4' 8 0.1629 +9 H1 1 DT H4' 9 0.1176 +10 OS 1 DT O4' 10 -0.3691 +11 CT 1 DT C1' 11 0.068 +12 H2 1 DT H1' 12 0.1804 +13 N* 1 DT N1 13 -0.0239 +14 CM 1 DT C6 14 -0.2209 +15 H4 1 DT H6 15 0.2607 +16 CM 1 DT C5 16 0.0025 +17 CT 1 DT C7 17 -0.2269 +18 HC 1 DT H71 18 0.077 +19 HC 1 DT H72 19 0.077 +20 HC 1 DT H73 20 0.077 +21 C 1 DT C4 21 0.5194 +22 O 1 DT O4 22 -0.5563 +23 NA 1 DT N3 23 -0.434 +24 H 1 DT H3 24 0.342 +25 C 1 DT C2 25 0.5677 +26 O 1 DT O2 26 -0.5881 +27 C7 1 DT C3' 27 0.0713 +28 H1 1 DT H3' 28 0.0985 +29 CT 1 DT C2' 29 -0.0854 +30 HC 1 DT H2'1 30 0.0718 +31 HC 1 DT H2'2 31 0.0718 +32 OS 1 DT O3' 32 -0.5232 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 C7 1 {} +C5 C4 1 {} +C7 H71 1 {} +C7 H72 1 {} +C7 H73 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C4 C6 C5 C7 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 C7 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 C7 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +C7 C5 C6 N1 9 {} +C7 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +C6 C5 C7 H71 9 {} +C6 C5 C7 H72 9 {} +C6 C5 C7 H73 9 {} +C4 C5 C7 H71 9 {} +C4 C5 C7 H72 9 {} +C4 C5 C7 H73 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 C7 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C7 H71 1 {} +C5 C7 H72 1 {} +C5 C7 H73 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +C7 C5 C4 1 {} +H71 C7 H72 1 {} +H71 C7 H73 1 {} +H72 C7 H73 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 C7 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 H71 1 {} +C6 H72 1 {} +C6 H73 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 C7 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +C7 O4 1 {} +C7 N3 1 {} +H71 C4 1 {} +H72 C4 1 {} +H73 C4 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 C7 +C5 C4 +C7 H71 +C7 H72 +C7 H73 +C4 O4 +C4 N3 +N3 H3 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DT3 3 +[ atoms ] +1 P 1 DT3 P 1 1.1659 +2 O2 1 DT3 O1P 2 -0.7761 +3 O2 1 DT3 O2P 3 -0.7761 +4 OS 1 DT3 O5' 4 -0.4954 +5 CJ 1 DT3 C5' 5 -0.0069 +6 H1 1 DT3 H5'1 6 0.0754 +7 H1 1 DT3 H5'2 7 0.0754 +8 CT 1 DT3 C4' 8 0.1629 +9 H1 1 DT3 H4' 9 0.1176 +10 OS 1 DT3 O4' 10 -0.3691 +11 CT 1 DT3 C1' 11 0.068 +12 H2 1 DT3 H1' 12 0.1804 +13 N* 1 DT3 N1 13 -0.0239 +14 CM 1 DT3 C6 14 -0.2209 +15 H4 1 DT3 H6 15 0.2607 +16 CM 1 DT3 C5 16 0.0025 +17 CT 1 DT3 C7 17 -0.2269 +18 HC 1 DT3 H71 18 0.077 +19 HC 1 DT3 H72 19 0.077 +20 HC 1 DT3 H73 20 0.077 +21 C 1 DT3 C4 21 0.5194 +22 O 1 DT3 O4 22 -0.5563 +23 NA 1 DT3 N3 23 -0.434 +24 H 1 DT3 H3 24 0.342 +25 C 1 DT3 C2 25 0.5677 +26 O 1 DT3 O2 26 -0.5881 +27 C7 1 DT3 C3' 27 0.0713 +28 H1 1 DT3 H3' 28 0.0985 +29 CT 1 DT3 C2' 29 -0.0854 +30 HC 1 DT3 H2'1 30 0.0718 +31 HC 1 DT3 H2'2 31 0.0718 +32 OH 1 DT3 O3' 32 -0.6549 +33 HO 1 DT3 H3T 33 0.4396 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 C7 1 {} +C5 C4 1 {} +C7 H71 1 {} +C7 H72 1 {} +C7 H73 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C4 C6 C5 C7 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 C7 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 C7 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +C7 C5 C6 N1 9 {} +C7 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +C6 C5 C7 H71 9 {} +C6 C5 C7 H72 9 {} +C6 C5 C7 H73 9 {} +C4 C5 C7 H71 9 {} +C4 C5 C7 H72 9 {} +C4 C5 C7 H73 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 C7 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C7 H71 1 {} +C5 C7 H72 1 {} +C5 C7 H73 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +C7 C5 C4 1 {} +H71 C7 H72 1 {} +H71 C7 H73 1 {} +H72 C7 H73 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 C7 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 H71 1 {} +C6 H72 1 {} +C6 H73 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 C7 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +C7 O4 1 {} +C7 N3 1 {} +H71 C4 1 {} +H72 C4 1 {} +H73 C4 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 C7 +C5 C4 +C7 H71 +C7 H72 +C7 H73 +C4 O4 +C4 N3 +N3 H3 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DTN 3 +[ atoms ] +1 HO 1 DTN H5T 1 0.4422 +2 OH 1 DTN O5' 2 -0.6318 +3 CJ 1 DTN C5' 3 -0.0069 +4 H1 1 DTN H5'1 4 0.0754 +5 H1 1 DTN H5'2 5 0.0754 +6 CT 1 DTN C4' 6 0.1629 +7 H1 1 DTN H4' 7 0.1176 +8 OS 1 DTN O4' 8 -0.3691 +9 CT 1 DTN C1' 9 0.068 +10 H2 1 DTN H1' 10 0.1804 +11 N* 1 DTN N1 11 -0.0239 +12 CM 1 DTN C6 12 -0.2209 +13 H4 1 DTN H6 13 0.2607 +14 CM 1 DTN C5 14 0.0025 +15 CT 1 DTN C7 15 -0.2269 +16 HC 1 DTN H71 16 0.077 +17 HC 1 DTN H72 17 0.077 +18 HC 1 DTN H73 18 0.077 +19 C 1 DTN C4 19 0.5194 +20 O 1 DTN O4 20 -0.5563 +21 NA 1 DTN N3 21 -0.434 +22 H 1 DTN H3 22 0.342 +23 C 1 DTN C2 23 0.5677 +24 O 1 DTN O2 24 -0.5881 +25 C7 1 DTN C3' 25 0.0713 +26 H1 1 DTN H3' 26 0.0985 +27 CT 1 DTN C2' 27 -0.0854 +28 HC 1 DTN H2'1 28 0.0718 +29 HC 1 DTN H2'2 29 0.0718 +30 OH 1 DTN O3' 30 -0.6549 +31 HO 1 DTN H3T 31 0.4396 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 C7 1 {} +C5 C4 1 {} +C7 H71 1 {} +C7 H72 1 {} +C7 H73 1 {} +C4 O4 1 {} +C4 N3 1 {} +N3 H3 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +C4 C6 C5 C7 4 {} +N1 N3 C2 O2 4 {} +C5 N3 C4 O4 4 {} +C4 C2 N3 H3 4 {} +N1 C5 C6 H6 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +N1 C2 N3 H3 9 {} +O2 C2 N3 C4 9 {} +O2 C2 N3 H3 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +O4 C4 C5 C6 9 {} +O4 C4 C5 C7 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 C7 9 {} +C5 C4 N3 H3 9 {} +C5 C4 N3 C2 9 {} +O4 C4 N3 H3 9 {} +O4 C4 N3 C2 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +C7 C5 C6 N1 9 {} +C7 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +C6 C5 C7 H71 9 {} +C6 C5 C7 H72 9 {} +C6 C5 C7 H73 9 {} +C4 C5 C7 H71 9 {} +C4 C5 C7 H72 9 {} +C4 C5 C7 H73 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 C7 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C7 H71 1 {} +C5 C7 H72 1 {} +C5 C7 H73 1 {} +C5 C4 O4 1 {} +C5 C4 N3 1 {} +C7 C5 C4 1 {} +H71 C7 H72 1 {} +H71 C7 H73 1 {} +H72 C7 H73 1 {} +C4 N3 H3 1 {} +C4 N3 C2 1 {} +O4 C4 N3 1 {} +N3 C2 O2 1 {} +H3 N3 C2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 C7 1 {} +N1 C4 1 {} +N1 H3 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 H71 1 {} +C6 H72 1 {} +C6 H73 1 {} +C6 O4 1 {} +H6 C2 1 {} +H6 C7 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H3 1 {} +C7 O4 1 {} +C7 N3 1 {} +H71 C4 1 {} +H72 C4 1 {} +H73 C4 1 {} +C4 O2 1 {} +O4 H3 1 {} +O4 C2 1 {} +H3 O2 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 C7 +C5 C4 +C7 H71 +C7 H72 +C7 H73 +C4 O4 +C4 N3 +N3 H3 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DG5 3 +[ atoms ] +1 HO 1 DG5 H5T 1 0.4422 +2 OH 1 DG5 O5' 2 -0.6318 +3 CJ 1 DG5 C5' 3 -0.0069 +4 H1 1 DG5 H5'1 4 0.0754 +5 H1 1 DG5 H5'2 5 0.0754 +6 CT 1 DG5 C4' 6 0.1629 +7 H1 1 DG5 H4' 7 0.1176 +8 OS 1 DG5 O4' 8 -0.3691 +9 CT 1 DG5 C1' 9 0.0358 +10 H2 1 DG5 H1' 10 0.1746 +11 N* 1 DG5 N9 11 0.0577 +12 CK 1 DG5 C8 12 0.0736 +13 H5 1 DG5 H8 13 0.1997 +14 NB 1 DG5 N7 14 -0.5725 +15 CB 1 DG5 C5 15 0.1991 +16 C 1 DG5 C6 16 0.4918 +17 O 1 DG5 O6 17 -0.5699 +18 NA 1 DG5 N1 18 -0.5053 +19 H 1 DG5 H1 19 0.352 +20 CA 1 DG5 C2 20 0.7432 +21 N2 1 DG5 N2 21 -0.923 +22 H 1 DG5 H21 22 0.4235 +23 H 1 DG5 H22 23 0.4235 +24 NC 1 DG5 N3 24 -0.6636 +25 CB 1 DG5 C4 25 0.1814 +26 C7 1 DG5 C3' 26 0.0713 +27 H1 1 DG5 H3' 27 0.0985 +28 CT 1 DG5 C2' 28 -0.0854 +29 HC 1 DG5 H2'1 29 0.0718 +30 HC 1 DG5 H2'2 30 0.0718 +31 OS 1 DG5 O3' 31 -0.5232 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 O6 +C6 N1 +N1 H1 +N1 C2 +C2 N2 +C2 N3 +N2 H21 +N2 H22 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DG 3 +[ atoms ] +1 P 1 DG P 1 1.1659 +2 O2 1 DG O1P 2 -0.7761 +3 O2 1 DG O2P 3 -0.7761 +4 OS 1 DG O5' 4 -0.4954 +5 CJ 1 DG C5' 5 -0.0069 +6 H1 1 DG H5'1 6 0.0754 +7 H1 1 DG H5'2 7 0.0754 +8 CT 1 DG C4' 8 0.1629 +9 H1 1 DG H4' 9 0.1176 +10 OS 1 DG O4' 10 -0.3691 +11 CT 1 DG C1' 11 0.0358 +12 H2 1 DG H1' 12 0.1746 +13 N* 1 DG N9 13 0.0577 +14 CK 1 DG C8 14 0.0736 +15 H5 1 DG H8 15 0.1997 +16 NB 1 DG N7 16 -0.5725 +17 CB 1 DG C5 17 0.1991 +18 C 1 DG C6 18 0.4918 +19 O 1 DG O6 19 -0.5699 +20 NA 1 DG N1 20 -0.5053 +21 H 1 DG H1 21 0.352 +22 CA 1 DG C2 22 0.7432 +23 N2 1 DG N2 23 -0.923 +24 H 1 DG H21 24 0.4235 +25 H 1 DG H22 25 0.4235 +26 NC 1 DG N3 26 -0.6636 +27 CB 1 DG C4 27 0.1814 +28 C7 1 DG C3' 28 0.0713 +29 H1 1 DG H3' 29 0.0985 +30 CT 1 DG C2' 30 -0.0854 +31 HC 1 DG H2'1 31 0.0718 +32 HC 1 DG H2'2 32 0.0718 +33 OS 1 DG O3' 33 -0.5232 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 O6 +C6 N1 +N1 H1 +N1 C2 +C2 N2 +C2 N3 +N2 H21 +N2 H22 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DG3 3 +[ atoms ] +1 P 1 DG3 P 1 1.1659 +2 O2 1 DG3 O1P 2 -0.7761 +3 O2 1 DG3 O2P 3 -0.7761 +4 OS 1 DG3 O5' 4 -0.4954 +5 CJ 1 DG3 C5' 5 -0.0069 +6 H1 1 DG3 H5'1 6 0.0754 +7 H1 1 DG3 H5'2 7 0.0754 +8 CT 1 DG3 C4' 8 0.1629 +9 H1 1 DG3 H4' 9 0.1176 +10 OS 1 DG3 O4' 10 -0.3691 +11 CT 1 DG3 C1' 11 0.0358 +12 H2 1 DG3 H1' 12 0.1746 +13 N* 1 DG3 N9 13 0.0577 +14 CK 1 DG3 C8 14 0.0736 +15 H5 1 DG3 H8 15 0.1997 +16 NB 1 DG3 N7 16 -0.5725 +17 CB 1 DG3 C5 17 0.1991 +18 C 1 DG3 C6 18 0.4918 +19 O 1 DG3 O6 19 -0.5699 +20 NA 1 DG3 N1 20 -0.5053 +21 H 1 DG3 H1 21 0.352 +22 CA 1 DG3 C2 22 0.7432 +23 N2 1 DG3 N2 23 -0.923 +24 H 1 DG3 H21 24 0.4235 +25 H 1 DG3 H22 25 0.4235 +26 NC 1 DG3 N3 26 -0.6636 +27 CB 1 DG3 C4 27 0.1814 +28 C7 1 DG3 C3' 28 0.0713 +29 H1 1 DG3 H3' 29 0.0985 +30 CT 1 DG3 C2' 30 -0.0854 +31 HC 1 DG3 H2'1 31 0.0718 +32 HC 1 DG3 H2'2 32 0.0718 +33 OH 1 DG3 O3' 33 -0.6549 +34 HO 1 DG3 H3T 34 0.4396 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 O6 +C6 N1 +N1 H1 +N1 C2 +C2 N2 +C2 N3 +N2 H21 +N2 H22 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DGN 3 +[ atoms ] +1 HO 1 DGN H5T 1 0.4422 +2 OH 1 DGN O5' 2 -0.6318 +3 CJ 1 DGN C5' 3 -0.0069 +4 H1 1 DGN H5'1 4 0.0754 +5 H1 1 DGN H5'2 5 0.0754 +6 CT 1 DGN C4' 6 0.1629 +7 H1 1 DGN H4' 7 0.1176 +8 OS 1 DGN O4' 8 -0.3691 +9 CT 1 DGN C1' 9 0.0358 +10 H2 1 DGN H1' 10 0.1746 +11 N* 1 DGN N9 11 0.0577 +12 CK 1 DGN C8 12 0.0736 +13 H5 1 DGN H8 13 0.1997 +14 NB 1 DGN N7 14 -0.5725 +15 CB 1 DGN C5 15 0.1991 +16 C 1 DGN C6 16 0.4918 +17 O 1 DGN O6 17 -0.5699 +18 NA 1 DGN N1 18 -0.5053 +19 H 1 DGN H1 19 0.352 +20 CA 1 DGN C2 20 0.7432 +21 N2 1 DGN N2 21 -0.923 +22 H 1 DGN H21 22 0.4235 +23 H 1 DGN H22 23 0.4235 +24 NC 1 DGN N3 24 -0.6636 +25 CB 1 DGN C4 25 0.1814 +26 C7 1 DGN C3' 26 0.0713 +27 H1 1 DGN H3' 27 0.0985 +28 CT 1 DGN C2' 28 -0.0854 +29 HC 1 DGN H2'1 29 0.0718 +30 HC 1 DGN H2'2 30 0.0718 +31 OH 1 DGN O3' 31 -0.6549 +32 HO 1 DGN H3T 32 0.4396 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N9 1 {} +C1' C2' 1 {} +N9 C8 1 {} +N9 C4 1 {} +C8 H8 1 {} +C8 N7 1 {} +N7 C5 1 {} +C5 C6 1 {} +C5 C4 1 {} +C6 O6 1 {} +C6 N1 1 {} +N1 H1 1 {} +N1 C2 1 {} +C2 N2 1 {} +C2 N3 1 {} +N2 H21 1 {} +N2 H22 1 {} +N3 C4 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C4 C8 N9 C1' 4 {} +C5 N1 C6 O6 4 {} +C6 C2 N1 H1 4 {} +C2 H21 N2 H22 4 {} +N9 N7 C8 H8 4 {} +N2 N1 C2 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N9 C1' C2' C3' 9 {} +N9 C1' C2' H2'1 9 {} +N9 C1' C2' H2'2 9 {} +O4' C1' N9 C8 9 {} +O4' C1' N9 C4 9 {} +H1' C1' N9 C8 9 {} +H1' C1' N9 C4 9 {} +C2' C1' N9 C8 9 {} +C2' C1' N9 C4 9 {} +H1' C1' O4' C4' 9 {} +N9 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N2 C2 N1 C6 9 {} +N2 C2 N1 H1 9 {} +N3 C2 N1 C6 9 {} +N3 C2 N1 H1 9 {} +N1 C2 N2 H21 9 {} +N1 C2 N2 H22 9 {} +N3 C2 N2 H21 9 {} +N3 C2 N2 H22 9 {} +N1 C2 N3 C4 9 {} +N2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N9 C4 C5 N7 9 {} +N9 C4 C5 C6 9 {} +N3 C4 C5 N7 9 {} +N3 C4 C5 C6 9 {} +N9 C4 N3 C2 9 {} +C5 C4 N3 C2 9 {} +C5 C4 N9 C1' 9 {} +C5 C4 N9 C8 9 {} +N3 C4 N9 C1' 9 {} +N3 C4 N9 C8 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +N7 C5 C6 O6 9 {} +N7 C5 C6 N1 9 {} +C4 C5 C6 O6 9 {} +C4 C5 C6 N1 9 {} +C6 C5 N7 C8 9 {} +C4 C5 N7 C8 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +C5 C6 N1 H1 9 {} +C5 C6 N1 C2 9 {} +O6 C6 N1 H1 9 {} +O6 C6 N1 C2 9 {} +N9 C8 N7 C5 9 {} +H8 C8 N7 C5 9 {} +H8 C8 N9 C1' 9 {} +H8 C8 N9 C4 9 {} +N7 C8 N9 C1' 9 {} +N7 C8 N9 C4 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N9 1 {} +O4' C1' C2' 1 {} +C1' N9 C8 1 {} +C1' N9 C4 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N9 1 {} +H1' C1' C2' 1 {} +N9 C1' C2' 1 {} +N9 C8 H8 1 {} +N9 C8 N7 1 {} +N9 C4 C5 1 {} +N9 C4 N3 1 {} +C8 N9 C4 1 {} +C8 N7 C5 1 {} +H8 C8 N7 1 {} +N7 C5 C6 1 {} +N7 C5 C4 1 {} +C5 C6 O6 1 {} +C5 C6 N1 1 {} +C5 C4 N3 1 {} +C6 C5 C4 1 {} +C6 N1 H1 1 {} +C6 N1 C2 1 {} +O6 C6 N1 1 {} +N1 C2 N2 1 {} +N1 C2 N3 1 {} +H1 N1 C2 1 {} +C2 N2 H21 1 {} +C2 N2 H22 1 {} +C2 N3 C4 1 {} +N2 C2 N3 1 {} +H21 N2 H22 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N9 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C8 1 {} +O4' C4 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H8 1 {} +C1' N7 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C8 1 {} +H1' C4 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N9 C3' 1 {} +N9 H2'1 1 {} +N9 H2'2 1 {} +N9 C6 1 {} +N9 C2 1 {} +C8 C2' 1 {} +C8 N3 1 {} +C8 C6 1 {} +H8 C4 1 {} +H8 C5 1 {} +N7 O6 1 {} +N7 N1 1 {} +N7 N3 1 {} +C5 H1 1 {} +C5 C2 1 {} +C6 N3 1 {} +C6 N2 1 {} +O6 C4 1 {} +O6 H1 1 {} +O6 C2 1 {} +N1 C4 1 {} +N1 H21 1 {} +N1 H22 1 {} +H1 N2 1 {} +H1 N3 1 {} +N2 C4 1 {} +H21 N3 1 {} +H22 N3 1 {} +C4 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N9 +C1' C2' +N9 C8 +N9 C4 +C8 H8 +C8 N7 +N7 C5 +C5 C6 +C5 C4 +C6 O6 +C6 N1 +N1 H1 +N1 C2 +C2 N2 +C2 N3 +N2 H21 +N2 H22 +N3 C4 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DC5 3 +[ atoms ] +1 HO 1 DC5 H5T 1 0.4422 +2 OH 1 DC5 O5' 2 -0.6318 +3 CJ 1 DC5 C5' 3 -0.0069 +4 H1 1 DC5 H5'1 4 0.0754 +5 H1 1 DC5 H5'2 5 0.0754 +6 CT 1 DC5 C4' 6 0.1629 +7 H1 1 DC5 H4' 7 0.1176 +8 OS 1 DC5 O4' 8 -0.3691 +9 CT 1 DC5 C1' 9 -0.0116 +10 H2 1 DC5 H1' 10 0.1963 +11 N* 1 DC5 N1 11 -0.0339 +12 C1 1 DC5 C6 12 -0.0183 +13 H4 1 DC5 H6 13 0.2293 +14 C1 1 DC5 C5 14 -0.5222 +15 HA 1 DC5 H5 15 0.1863 +16 CA 1 DC5 C4 16 0.8439 +17 N2 1 DC5 N4 17 -0.9773 +18 H 1 DC5 H41 18 0.4314 +19 H 1 DC5 H42 19 0.4314 +20 NC 1 DC5 N3 20 -0.7748 +21 C 1 DC5 C2 21 0.7959 +22 O 1 DC5 O2 22 -0.6548 +23 C7 1 DC5 C3' 23 0.0713 +24 H1 1 DC5 H3' 24 0.0985 +25 CT 1 DC5 C2' 25 -0.0854 +26 HC 1 DC5 H2'1 26 0.0718 +27 HC 1 DC5 H2'2 27 0.0718 +28 OS 1 DC5 O3' 28 -0.5232 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C1' N1 C6 C2 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 H5 +C5 C4 +C4 N4 +C4 N3 +N4 H41 +N4 H42 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DC 3 +[ atoms ] +1 P 1 DC P 1 1.1659 +2 O2 1 DC O1P 2 -0.7761 +3 O2 1 DC O2P 3 -0.7761 +4 OS 1 DC O5' 4 -0.4954 +5 CJ 1 DC C5' 5 -0.0069 +6 H1 1 DC H5'1 6 0.0754 +7 H1 1 DC H5'2 7 0.0754 +8 CT 1 DC C4' 8 0.1629 +9 H1 1 DC H4' 9 0.1176 +10 OS 1 DC O4' 10 -0.3691 +11 CT 1 DC C1' 11 -0.0116 +12 H2 1 DC H1' 12 0.1963 +13 N* 1 DC N1 13 -0.0339 +14 C1 1 DC C6 14 -0.0183 +15 H4 1 DC H6 15 0.2293 +16 C1 1 DC C5 16 -0.5222 +17 HA 1 DC H5 17 0.1863 +18 CA 1 DC C4 18 0.8439 +19 N2 1 DC N4 19 -0.9773 +20 H 1 DC H41 20 0.4314 +21 H 1 DC H42 21 0.4314 +22 NC 1 DC N3 22 -0.7748 +23 C 1 DC C2 23 0.7959 +24 O 1 DC O2 24 -0.6548 +25 C7 1 DC C3' 25 0.0713 +26 H1 1 DC H3' 26 0.0985 +27 CT 1 DC C2' 27 -0.0854 +28 HC 1 DC H2'1 28 0.0718 +29 HC 1 DC H2'2 29 0.0718 +30 OS 1 DC O3' 30 -0.5232 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 H5 +C5 C4 +C4 N4 +C4 N3 +N4 H41 +N4 H42 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +[ moleculetype ] +DC3 3 +[ atoms ] +1 P 1 DC3 P 1 1.1659 +2 O2 1 DC3 O1P 2 -0.7761 +3 O2 1 DC3 O2P 3 -0.7761 +4 OS 1 DC3 O5' 4 -0.4954 +5 CJ 1 DC3 C5' 5 -0.0069 +6 H1 1 DC3 H5'1 6 0.0754 +7 H1 1 DC3 H5'2 7 0.0754 +8 CT 1 DC3 C4' 8 0.1629 +9 H1 1 DC3 H4' 9 0.1176 +10 OS 1 DC3 O4' 10 -0.3691 +11 CT 1 DC3 C1' 11 -0.0116 +12 H2 1 DC3 H1' 12 0.1963 +13 N* 1 DC3 N1 13 -0.0339 +14 C1 1 DC3 C6 14 -0.0183 +15 H4 1 DC3 H6 15 0.2293 +16 C1 1 DC3 C5 16 -0.5222 +17 HA 1 DC3 H5 17 0.1863 +18 CA 1 DC3 C4 18 0.8439 +19 N2 1 DC3 N4 19 -0.9773 +20 H 1 DC3 H41 20 0.4314 +21 H 1 DC3 H42 21 0.4314 +22 NC 1 DC3 N3 22 -0.7748 +23 C 1 DC3 C2 23 0.7959 +24 O 1 DC3 O2 24 -0.6548 +25 C7 1 DC3 C3' 25 0.0713 +26 H1 1 DC3 H3' 26 0.0985 +27 CT 1 DC3 C2' 27 -0.0854 +28 HC 1 DC3 H2'1 28 0.0718 +29 HC 1 DC3 H2'2 29 0.0718 +30 OH 1 DC3 O3' 30 -0.6549 +31 HO 1 DC3 H3T 31 0.4396 +[ bonds ] +P O1P 1 {} +P O2P 1 {} +P O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +C5 N4 C4 N3 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' P 9 {} +H5'2 C5' O5' P 9 {} +C4' C5' O5' P 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +C5' O5' P O1P 9 {} +C5' O5' P O2P 9 {} +[ angles ] +P O5' C5' 1 {} +O1P P O2P 1 {} +O1P P O5' 1 {} +O2P P O5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +P H5'1 1 {} +P H5'2 1 {} +P C4' 1 {} +O1P C5' 1 {} +O2P C5' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +P O1P +P O2P +P O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 H5 +C5 C4 +C4 N4 +C4 N3 +N4 H41 +N4 H42 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T +[ moleculetype ] +DCN 3 +[ atoms ] +1 HO 1 DCN H5T 1 0.4422 +2 OH 1 DCN O5' 2 -0.6318 +3 CJ 1 DCN C5' 3 -0.0069 +4 H1 1 DCN H5'1 4 0.0754 +5 H1 1 DCN H5'2 5 0.0754 +6 CT 1 DCN C4' 6 0.1629 +7 H1 1 DCN H4' 7 0.1176 +8 OS 1 DCN O4' 8 -0.3691 +9 CT 1 DCN C1' 9 -0.0116 +10 H2 1 DCN H1' 10 0.1963 +11 N* 1 DCN N1 11 -0.0339 +12 C1 1 DCN C6 12 -0.0183 +13 H4 1 DCN H6 13 0.2293 +14 C1 1 DCN C5 14 -0.5222 +15 HA 1 DCN H5 15 0.1863 +16 CA 1 DCN C4 16 0.8439 +17 N2 1 DCN N4 17 -0.9773 +18 H 1 DCN H41 18 0.4314 +19 H 1 DCN H42 19 0.4314 +20 NC 1 DCN N3 20 -0.7748 +21 C 1 DCN C2 21 0.7959 +22 O 1 DCN O2 22 -0.6548 +23 C7 1 DCN C3' 23 0.0713 +24 H1 1 DCN H3' 24 0.0985 +25 CT 1 DCN C2' 25 -0.0854 +26 HC 1 DCN H2'1 26 0.0718 +27 HC 1 DCN H2'2 27 0.0718 +28 OH 1 DCN O3' 28 -0.6549 +29 HO 1 DCN H3T 29 0.4396 +[ bonds ] +H5T O5' 1 {} +O5' C5' 1 {} +C5' H5'1 1 {} +C5' H5'2 1 {} +C5' C4' 1 {} +C4' H4' 1 {} +C4' O4' 1 {} +C4' C3' 1 {} +O4' C1' 1 {} +C1' H1' 1 {} +C1' N1 1 {} +C1' C2' 1 {} +N1 C6 1 {} +N1 C2 1 {} +C6 H6 1 {} +C6 C5 1 {} +C5 H5 1 {} +C5 C4 1 {} +C4 N4 1 {} +C4 N3 1 {} +N4 H41 1 {} +N4 H42 1 {} +N3 C2 1 {} +C2 O2 1 {} +C3' H3' 1 {} +C3' C2' 1 {} +C3' O3' 1 {} +C2' H2'1 1 {} +C2' H2'2 1 {} +O3' H3T 1 {} +[ impropers ] +C2 C6 N1 C1' 4 {} +N1 N3 C2 O2 4 {} +C4 H41 N4 H42 4 {} +N1 C5 C6 H6 4 {} +C6 C4 C5 H5 4 {} +N3 C4 N4 C5 4 {} +[ dihedrals ] +O4' C1' C2' C3' 9 {} +O4' C1' C2' H2'1 9 {} +O4' C1' C2' H2'2 9 {} +H1' C1' C2' C3' 9 {} +H1' C1' C2' H2'1 9 {} +H1' C1' C2' H2'2 9 {} +N1 C1' C2' C3' 9 {} +N1 C1' C2' H2'1 9 {} +N1 C1' C2' H2'2 9 {} +O4' C1' N1 C6 9 {} +O4' C1' N1 C2 9 {} +H1' C1' N1 C6 9 {} +H1' C1' N1 C2 9 {} +C2' C1' N1 C6 9 {} +C2' C1' N1 C2 9 {} +H1' C1' O4' C4' 9 {} +N1 C1' O4' C4' 9 {} +C2' C1' O4' C4' 9 {} +N3 C2 N1 C1' 9 {} +N3 C2 N1 C6 9 {} +O2 C2 N1 C1' 9 {} +O2 C2 N1 C6 9 {} +N1 C2 N3 C4 9 {} +O2 C2 N3 C4 9 {} +C1' C2' C3' C4' 9 {} +C1' C2' C3' H3' 9 {} +C1' C2' C3' O3' 9 {} +H2'1 C2' C3' C4' 9 {} +H2'1 C2' C3' H3' 9 {} +H2'1 C2' C3' O3' 9 {} +H2'2 C2' C3' C4' 9 {} +H2'2 C2' C3' H3' 9 {} +H2'2 C2' C3' O3' 9 {} +H3' C3' C4' C5' 9 {} +H3' C3' C4' H4' 9 {} +H3' C3' C4' O4' 9 {} +C2' C3' C4' C5' 9 {} +C2' C3' C4' H4' 9 {} +C2' C3' C4' O4' 9 {} +O3' C3' C4' C5' 9 {} +O3' C3' C4' H4' 9 {} +O3' C3' C4' O4' 9 {} +C4' C3' O3' H3T 9 {} +H3' C3' O3' H3T 9 {} +C2' C3' O3' H3T 9 {} +N4 C4 C5 C6 9 {} +N4 C4 C5 H5 9 {} +N3 C4 C5 C6 9 {} +N3 C4 C5 H5 9 {} +C5 C4 N3 C2 9 {} +N4 C4 N3 C2 9 {} +C5 C4 N4 H41 9 {} +C5 C4 N4 H42 9 {} +N3 C4 N4 H41 9 {} +N3 C4 N4 H42 9 {} +H4' C4' C5' O5' 9 {} +H4' C4' C5' H5'1 9 {} +H4' C4' C5' H5'2 9 {} +O4' C4' C5' O5' 9 {} +O4' C4' C5' H5'1 9 {} +O4' C4' C5' H5'2 9 {} +C3' C4' C5' O5' 9 {} +C3' C4' C5' H5'1 9 {} +C3' C4' C5' H5'2 9 {} +C5' C4' O4' C1' 9 {} +H4' C4' O4' C1' 9 {} +C3' C4' O4' C1' 9 {} +H5 C5 C6 N1 9 {} +H5 C5 C6 H6 9 {} +C4 C5 C6 N1 9 {} +C4 C5 C6 H6 9 {} +H5'1 C5' O5' H5T 9 {} +H5'2 C5' O5' H5T 9 {} +C4' C5' O5' H5T 9 {} +H6 C6 N1 C1' 9 {} +H6 C6 N1 C2 9 {} +C5 C6 N1 C1' 9 {} +C5 C6 N1 C2 9 {} +[ angles ] +H5T O5' C5' 1 {} +O5' C5' H5'1 1 {} +O5' C5' H5'2 1 {} +O5' C5' C4' 1 {} +C5' C4' H4' 1 {} +C5' C4' O4' 1 {} +C5' C4' C3' 1 {} +H5'1 C5' H5'2 1 {} +H5'1 C5' C4' 1 {} +H5'2 C5' C4' 1 {} +C4' O4' C1' 1 {} +C4' C3' H3' 1 {} +C4' C3' C2' 1 {} +C4' C3' O3' 1 {} +H4' C4' O4' 1 {} +H4' C4' C3' 1 {} +O4' C4' C3' 1 {} +O4' C1' H1' 1 {} +O4' C1' N1 1 {} +O4' C1' C2' 1 {} +C1' N1 C6 1 {} +C1' N1 C2 1 {} +C1' C2' C3' 1 {} +C1' C2' H2'1 1 {} +C1' C2' H2'2 1 {} +H1' C1' N1 1 {} +H1' C1' C2' 1 {} +N1 C1' C2' 1 {} +N1 C6 H6 1 {} +N1 C6 C5 1 {} +N1 C2 N3 1 {} +N1 C2 O2 1 {} +C6 N1 C2 1 {} +C6 C5 H5 1 {} +C6 C5 C4 1 {} +H6 C6 C5 1 {} +C5 C4 N4 1 {} +C5 C4 N3 1 {} +H5 C5 C4 1 {} +C4 N4 H41 1 {} +C4 N4 H42 1 {} +C4 N3 C2 1 {} +N4 C4 N3 1 {} +H41 N4 H42 1 {} +N3 C2 O2 1 {} +C3' C2' H2'1 1 {} +C3' C2' H2'2 1 {} +C3' O3' H3T 1 {} +H3' C3' C2' 1 {} +H3' C3' O3' 1 {} +C2' C3' O3' 1 {} +H2'1 C2' H2'2 1 {} +[ pairs ] +H5T H5'1 1 {} +H5T H5'2 1 {} +H5T C4' 1 {} +O5' H4' 1 {} +O5' O4' 1 {} +O5' C3' 1 {} +C5' C1' 1 {} +C5' H3' 1 {} +C5' C2' 1 {} +C5' O3' 1 {} +H5'1 H4' 1 {} +H5'1 O4' 1 {} +H5'1 C3' 1 {} +H5'2 H4' 1 {} +H5'2 O4' 1 {} +H5'2 C3' 1 {} +C4' H1' 1 {} +C4' N1 1 {} +C4' H2'1 1 {} +C4' H2'2 1 {} +C4' H3T 1 {} +H4' C1' 1 {} +H4' H3' 1 {} +H4' C2' 1 {} +H4' O3' 1 {} +O4' H3' 1 {} +O4' O3' 1 {} +O4' C6 1 {} +O4' C2 1 {} +O4' H2'1 1 {} +O4' H2'2 1 {} +C1' H6 1 {} +C1' C5 1 {} +C1' N3 1 {} +C1' O2 1 {} +C1' H3' 1 {} +C1' O3' 1 {} +H1' C6 1 {} +H1' C2 1 {} +H1' C3' 1 {} +H1' H2'1 1 {} +H1' H2'2 1 {} +N1 C3' 1 {} +N1 H2'1 1 {} +N1 H2'2 1 {} +N1 H5 1 {} +N1 C4 1 {} +C6 C2' 1 {} +C6 N3 1 {} +C6 O2 1 {} +C6 N4 1 {} +H6 C2 1 {} +H6 H5 1 {} +H6 C4 1 {} +C5 C2 1 {} +C5 H41 1 {} +C5 H42 1 {} +H5 N4 1 {} +H5 N3 1 {} +C4 O2 1 {} +N4 C2 1 {} +H41 N3 1 {} +H42 N3 1 {} +C2 C2' 1 {} +H3' H2'1 1 {} +H3' H2'2 1 {} +H3' H3T 1 {} +C2' H3T 1 {} +H2'1 O3' 1 {} +H2'2 O3' 1 {} +[ edges ] +H5T O5' +O5' C5' +C5' H5'1 +C5' H5'2 +C5' C4' +C4' H4' +C4' O4' +C4' C3' +O4' C1' +C1' H1' +C1' N1 +C1' C2' +N1 C6 +N1 C2 +C6 H6 +C6 C5 +C5 H5 +C5 C4 +C4 N4 +C4 N3 +N4 H41 +N4 H42 +N3 C2 +C2 O2 +C3' H3' +C3' C2' +C3' O3' +C2' H2'1 +C2' H2'2 +O3' H3T + +[ link ] +resname $base_pairs +[ bonds ] +-O3' P 1 +[ angles ] +P -O3' -C3' 1 +O1P P -O3' 1 +O2P P -O3' 1 +O5' P -O3' 1 +[ dihedrals ] +P -O3' -C3' -C4' 9 {"group": "link"} +O1P P -O3' -C3' 9 {"group": "link"} +O2P P -O3' -C3' 9 {"group": "link"} +O5' P -O3' -C3' 9 {"group": "link"} +P -O3' -C3' -C2' 9 {"group": "link"} +C5' O5' P -O3' 9 {"group": "link"} +P -O3' -C3' -H3' 9 {"group": "link"} +[ pairs ] +P -C4' 1 +O1P -C3' 1 +O2P -C3' 1 +O5' -C3' 1 +P -C2' 1 +C5' -O3' 1 +P -H3' 1 diff --git a/polyply/data/ol21/rna.ff b/polyply/data/ol21/rna.ff index c900756f8..fb940ff20 100644 --- a/polyply/data/ol21/rna.ff +++ b/polyply/data/ol21/rna.ff @@ -1,6 +1,10 @@ [ macros ] rna_bases "RA5|RA|RA3|RC5|RC|RC3|RU5|RU|RU3|RG5|RG|RG3" +[ citations ] +ol21_RNA +polyply + [ moleculetype ] RA5 3 [ atoms ] From ee799918f142cc71e5ae8a9b125bcd2e1b8f5712 Mon Sep 17 00:00:00 2001 From: "f.grunewald" Date: Wed, 16 Aug 2023 15:23:00 +0200 Subject: [PATCH 5/7] add extra dihedrals for polyply coord generation --- polyply/data/ol21/citations.bib | 6 +++--- polyply/data/ol21/dna.ff | 13 +++++++++++++ 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/polyply/data/ol21/citations.bib b/polyply/data/ol21/citations.bib index d449040e7..88f46e5f0 100644 --- a/polyply/data/ol21/citations.bib +++ b/polyply/data/ol21/citations.bib @@ -1,6 +1,6 @@ @article{ol21_DNA_a, title={Refinement of the sugar--phosphate backbone torsion beta for AMBER force fields improves the description of Z-and B-DNA}, - author={Zgarbov{\'a}, Marie and Sponer, Jiri and Otyepka, Michal and Cheatham III, Thomas E and Galindo-Murillo, Rodrigo and Jurecka, Petr}, + author={Zgarbova, Marie and Sponer, Jiri and Otyepka, Michal and Cheatham III, Thomas E and Galindo-Murillo, Rodrigo and Jurecka, Petr}, journal={Journal of chemical theory and computation}, volume={11}, number={12}, @@ -11,7 +11,7 @@ @article{ol21_DNA_a @article{ol21_DNA_b, title={Z-DNA as a touchstone for additive empirical force fields and a refinement of the alpha/gamma DNA torsions for AMBER}, - author={Zgarbov{\'a}, Marie and Sponer, Jiri and Jurecka, Petr}, + author={Zgarbova, Marie and Sponer, Jiri and Jurecka, Petr}, journal={Journal of Chemical Theory and Computation}, volume={17}, number={10}, @@ -22,7 +22,7 @@ @article{ol21_DNA_b @article{ol21_RNA, title={Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles}, - author={Zgarbov{\'a}, Marie and Otyepka, Michal and Šponer, Jiří and Mládek, Arnošt and Banáš, Pavel and Cheatham III, Thomas E and Jurecka, Petr}, + author={Zgarbova, Marie and Otyepka, Michal and Sponer, Jiri and Mladek, Arnost and Banas, Pavel and Cheatham III, Thomas E and Jurecka, Petr}, journal={Journal of chemical theory and computation}, volume={7}, number={9}, diff --git a/polyply/data/ol21/dna.ff b/polyply/data/ol21/dna.ff index d7a90ed20..2454aa976 100644 --- a/polyply/data/ol21/dna.ff +++ b/polyply/data/ol21/dna.ff @@ -1,5 +1,6 @@ [ macros ] base_pairs "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3" +all_nts "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3|DAN|DTN|DGN|DCN" [ citations ] ol21_DNA_a @@ -78,6 +79,7 @@ C6 H61 N6 H62 4 {} N9 N7 C8 H8 4 {} N1 N3 C2 H2 4 {} C5 N6 C6 N1 4 {} + [ dihedrals ] O4' C1' C2' C3' 9 {} O4' C1' C2' H2'1 9 {} @@ -5252,3 +5254,14 @@ O5' -C3' 1 P -C2' 1 C5' -O3' 1 P -H3' 1 + +[ link ] +resname $all_nts +[ impropers ] +; dihedrals for chirality building +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} From 98c27f4a807d573ca5384f6696aeb55cc0b50f8a Mon Sep 17 00:00:00 2001 From: lgruenewald <126408421+lgruenewald@users.noreply.github.com> Date: Wed, 5 Jun 2024 18:49:45 +0200 Subject: [PATCH 6/7] Fixed impropers for chirality --- polyply/data/ol21/dna.ff | 16 +++++++++++- polyply/data/ol21/rna.ff | 54 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+), 1 deletion(-) diff --git a/polyply/data/ol21/dna.ff b/polyply/data/ol21/dna.ff index 2454aa976..93f0c1ef3 100644 --- a/polyply/data/ol21/dna.ff +++ b/polyply/data/ol21/dna.ff @@ -1,6 +1,8 @@ [ macros ] base_pairs "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3" all_nts "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3|DAN|DTN|DGN|DCN" +all_purine_nts "DA5|DA|DA3|DG5|DG|DG3|DGN|DAN" +all_pyrimidine_nts "DC5|DC|DC3|DT5|DT|DT3|DTN|DCN" [ citations ] ol21_DNA_a @@ -5256,7 +5258,7 @@ C5' -O3' 1 P -H3' 1 [ link ] -resname $all_nts +resname $all_purine_nts [ impropers ] ; dihedrals for chirality building C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} @@ -5265,3 +5267,15 @@ C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +[ link ] +resname $all_pyrimidine_nts +[ impropers ] +; dihedrals for chirality building +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + diff --git a/polyply/data/ol21/rna.ff b/polyply/data/ol21/rna.ff index fb940ff20..0c384ce73 100644 --- a/polyply/data/ol21/rna.ff +++ b/polyply/data/ol21/rna.ff @@ -1,5 +1,8 @@ [ macros ] rna_bases "RA5|RA|RA3|RC5|RC|RC3|RU5|RU|RU3|RG5|RG|RG3" +all_purine_nts "RA5|RA|RA3|RG5|RG|RG3|RGN|RAN" +all_pyrimidine_nts "RC5|RC|RC3|RT5|RT|RT3|RTN|RCN" + [ citations ] ol21_RNA @@ -987,6 +990,19 @@ RAN 3 30 HO 1 RAN HO'2 30 0.4186 31 OH 1 RAN O3' 31 -0.6541 32 HO 1 RAN H3T 32 0.4376 + +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -2166,6 +2182,20 @@ RUN 3 27 HO 1 RUN HO'2 27 0.4186 28 OH 1 RUN O3' 28 -0.6541 29 HO 1 RUN H3T 29 0.4376 + +[ impropers ] +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} + + +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -3437,6 +3467,18 @@ RGN 3 31 HO 1 RGN HO'2 31 0.4186 32 OH 1 RGN O3' 32 -0.6541 33 HO 1 RGN H3T 33 0.4376 +[ impropers ] +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} + +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -4638,6 +4680,18 @@ RCN 3 28 HO 1 RCN HO'2 28 0.4186 29 OH 1 RCN O3' 29 -0.6541 30 HO 1 RCN H3T 30 0.4376 +[ impropers ] +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} + +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} + +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] H5T O5' 1 {} O5' C5' 1 {} From 7ac02e0e22d5475e814615edde1c9749fa6b23c6 Mon Sep 17 00:00:00 2001 From: lgruenewald <126408421+lgruenewald@users.noreply.github.com> Date: Thu, 6 Jun 2024 10:45:18 +0200 Subject: [PATCH 7/7] Improper as Links RNA --- polyply/data/ol21/rna.ff | 235 +++++---------------------------------- 1 file changed, 30 insertions(+), 205 deletions(-) diff --git a/polyply/data/ol21/rna.ff b/polyply/data/ol21/rna.ff index 0c384ce73..ee4cae80d 100644 --- a/polyply/data/ol21/rna.ff +++ b/polyply/data/ol21/rna.ff @@ -1,7 +1,7 @@ [ macros ] rna_bases "RA5|RA|RA3|RC5|RC|RC3|RU5|RU|RU3|RG5|RG|RG3" all_purine_nts "RA5|RA|RA3|RG5|RG|RG3|RGN|RAN" -all_pyrimidine_nts "RC5|RC|RC3|RT5|RT|RT3|RTN|RCN" +all_pyrimidine_nts "RC5|RC|RC3|RU5|RU|RU3|RUN|RCN" [ citations ] @@ -42,19 +42,6 @@ RA5 3 29 OH 1 RA5 O2' 29 -0.6139 30 HO 1 RA5 HO'2 30 0.4186 31 OS 1 RA5 O3' 31 -0.5246 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -350,17 +337,6 @@ RA 3 31 OH 1 RA O2' 31 -0.6139 32 HO 1 RA HO'2 32 0.4186 33 OS 1 RA O3' 33 -0.5246 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] P O1P 1 {} P O2P 1 {} @@ -666,18 +642,6 @@ RA3 3 32 HO 1 RA3 HO'2 32 0.4186 33 OH 1 RA3 O3' 33 -0.6541 34 HO 1 RA3 H3T 34 0.4376 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -990,19 +954,6 @@ RAN 3 30 HO 1 RAN HO'2 30 0.4186 31 OH 1 RAN O3' 31 -0.6541 32 HO 1 RAN H3T 32 0.4376 - -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -1301,19 +1252,6 @@ RU5 3 26 OH 1 RU5 O2' 26 -0.6139 27 HO 1 RU5 HO'2 27 0.4186 28 OS 1 RU5 O3' 28 -0.5246 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -1586,19 +1524,6 @@ RU 3 28 OH 1 RU O2' 28 -0.6139 29 HO 1 RU HO'2 29 0.4186 30 OS 1 RU O3' 30 -0.5246 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -1881,19 +1806,6 @@ RU3 3 29 HO 1 RU3 HO'2 29 0.4186 30 OH 1 RU3 O3' 30 -0.6541 31 HO 1 RU3 H3T 31 0.4376 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -2182,20 +2094,6 @@ RUN 3 27 HO 1 RUN HO'2 27 0.4186 28 OH 1 RUN O3' 28 -0.6541 29 HO 1 RUN H3T 29 0.4376 - -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -2478,19 +2376,6 @@ RG5 3 30 OH 1 RG5 O2' 30 -0.6139 31 HO 1 RG5 HO'2 31 0.4186 32 OS 1 RG5 O3' 32 -0.5246 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -2799,19 +2684,6 @@ RG 3 32 OH 1 RG O2' 32 -0.6139 33 HO 1 RG HO'2 33 0.4186 34 OS 1 RG O3' 34 -0.5246 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -3130,19 +3002,6 @@ RG3 3 33 HO 1 RG3 HO'2 33 0.4186 34 OH 1 RG3 O3' 34 -0.6541 35 HO 1 RG3 H3T 35 0.4376 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -3467,18 +3326,6 @@ RGN 3 31 HO 1 RGN HO'2 31 0.4186 32 OH 1 RGN O3' 32 -0.6541 33 HO 1 RGN H3T 33 0.4376 -[ impropers ] -C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DGO4'", "ifdef":"eq_polyply"} - -C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -3790,19 +3637,6 @@ RC5 3 27 OH 1 RC5 O2' 27 -0.6139 28 HO 1 RC5 HO'2 28 0.4186 29 OS 1 RC5 O3' 29 -0.5246 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -4078,19 +3912,6 @@ RC 3 29 OH 1 RC O2' 29 -0.6139 30 HO 1 RC HO'2 30 0.4186 31 OS 1 RC O3' 31 -0.5246 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -4376,19 +4197,6 @@ RC3 3 30 HO 1 RC3 HO'2 30 0.4186 31 OH 1 RC3 O3' 31 -0.6541 32 HO 1 RC3 H3T 32 0.4376 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} - [ bonds ] P O1P 1 {} P O2P 1 {} @@ -4680,18 +4488,6 @@ RCN 3 28 HO 1 RCN HO'2 28 0.4186 29 OH 1 RCN O3' 29 -0.6541 30 HO 1 RCN H3T 30 0.4376 -[ impropers ] -C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} -C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} -C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} - -C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} -C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} -C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} - -; RNA specific -C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} -C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} [ bonds ] H5T O5' 1 {} O5' C5' 1 {} @@ -4967,3 +4763,32 @@ O5' -C3' 1 P -C2' 1 C5' -O3' 1 P -H3' 1 + +[ link ] +resname $all_purine_nts +[ impropers ] +; dihedrals for chirality building +C1' C2' N9 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center O4'", "ifdef":"eq_polyply"} +C1' C2' N9 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} + +[ link ] +resname $all_pyrimidine_nts +[ impropers ] +; dihedrals for chirality building +C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC1'", "ifdef":"eq_polyply"} +C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCC3'", "ifdef":"eq_polyply"} +C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DCO4'", "ifdef":"eq_polyply"} +C1' C2' N1 H1' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC1'", "ifdef":"eq_polyply"} +C3' O3' C4' H3' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HC3'", "ifdef":"eq_polyply"} +C4' C5' C3' H4' 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center HO4'", "ifdef":"eq_polyply"} +; RNA specific +C2' C3' C1' H2'1 2 -3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +C2' C3' C1' O2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center C2'", "ifdef":"eq_polyply"} +