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dna_final.ff
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[ macros ]
base_pairs "DA5|DA|DA3|DC5|DC|DC3|DT5|DT|DT3|DG5|DG|DG3"
[ citations ]
parmbsc1
polyply
[ moleculetype ]
DA5 3
[ atoms ]
1 HO 1 DA5 H5T 1 0.44220
2 OH 1 DA5 O5' 2 -0.63180
3 CI 1 DA5 C5' 3 -0.00690
4 H1 1 DA5 H5'1 4 0.07540
5 H1 1 DA5 H5'2 5 0.07540
6 CT 1 DA5 C4' 6 0.16290
7 H1 1 DA5 H4' 7 0.11760
8 OS 1 DA5 O4' 8 -0.36910
9 CT 1 DA5 C1' 9 0.04310
10 H2 1 DA5 H1' 10 0.18380
11 N* 1 DA5 N9 11 -0.02680
12 C1 1 DA5 C8 12 0.16070
13 H5 1 DA5 H8 13 0.18770
14 NB 1 DA5 N7 14 -0.61750
15 CB 1 DA5 C5 15 0.07250
16 CA 1 DA5 C6 16 0.68970
17 N2 1 DA5 N6 17 -0.91230
18 H 1 DA5 H61 18 0.41670
19 H 1 DA5 H62 19 0.41670
20 NC 1 DA5 N1 20 -0.76240
21 CQ 1 DA5 C2 21 0.57160
22 H5 1 DA5 H2 22 0.05980
23 NC 1 DA5 N3 23 -0.74170
24 CB 1 DA5 C4 24 0.38000
25 CE 1 DA5 C3' 25 0.07130
26 H1 1 DA5 H3' 26 0.09850
27 CT 1 DA5 C2' 27 -0.08540
28 HC 1 DA5 H2'1 28 0.07180
29 HC 1 DA5 H2'2 29 0.07180
30 OS 1 DA5 O3' 30 -0.52320
[ 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' 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 ]
H5'1 C5' O5' H5T 9
H5'2 C5' O5' H5T 9
C4' C5' O5' H5T 9
H4' C4' C5' O5' 9
O4' C4' C5' O5' 9
C3' C4' C5' O5' 9
C1' O4' C4' C5' 9
H3' C3' C4' C5' 9
C2' C3' C4' C5' 9
O3' C3' C4' C5' 9
H4' C4' C5' H5'1 9
O4' C4' C5' H5'1 9
C3' C4' C5' H5'1 9
H4' C4' C5' H5'2 9
O4' C4' C5' H5'2 9
C3' C4' C5' H5'2 9
H1' C1' O4' C4' 9
N9 C1' O4' C4' 9
H2'1 C2' C3' C4' 9
H2'2 C2' C3' C4' 9
C1' O4' C4' H4' 9
H3' C3' C4' H4' 9
C2' C3' C4' H4' 9
O3' C3' C4' H4' 9
H3' C3' C4' O4' 9
O3' C3' C4' O4' 9
C8 N9 C1' O4' 9
C4 N9 C1' O4' 9
H2'1 C2' C1' O4' 9
H2'2 C2' C1' O4' 9
H8 C8 N9 C1' 9
N7 C8 N9 C1' 9
C5 C4 N9 C1' 9
N3 C4 N9 C1' 9
H3' C3' C2' C1' 9
O3' C3' C2' C1' 9
C8 N9 C1' H1' 9
C4 N9 C1' H1' 9
C3' C2' C1' H1' 9
H2'1 C2' C1' H1' 9
H2'2 C2' C1' H1' 9
C3' C2' C1' N9 9
H2'1 C2' C1' N9 9
H2'2 C2' C1' N9 9
C6 C5 C4 N9 9
C2 N3 C4 N9 9
C2' C1' N9 C8 9
N3 C4 N9 C8 9
C6 C5 N7 C8 9
C4 N9 C8 H8 9
C5 N7 C8 H8 9
N6 C6 C5 N7 9
N1 C6 C5 N7 9
N3 C4 C5 N7 9
H61 N6 C6 C5 9
H62 N6 C6 C5 9
C2 N1 C6 C5 9
C6 C5 C4 N3 9
H2 C2 N1 C6 9
C4 C5 C6 N6 9
C2 N1 C6 N6 9
N1 C6 N6 H61 9
N1 C6 N6 H62 9
C4 C5 C6 N1 9
C4 N3 C2 H2 9
N3 C2 N1 C6 9
C2' C1' N9 C4 9
H2'1 C2' C3' H3' 9
H2'2 C2' C3' H3' 9
O3' C3' C2' H2'1 9
O3' C3' C2' H2'2 9
;
C1' O4' C4' C3' 9
C2' C3' C4' O4' 9
C2' C1' O4' C4' 9
C3' C2' C1' O4' 9
;
N7 C8 N9 C4 9
C5 C4 N9 C8 9
C5 N7 C8 N9 9
C4 C5 N7 C8 9
N9 C4 C5 N7 9
;
C4 N3 C2 N1 9
C5 C4 N3 C2 9
C1' C2' C3' C4' 9
[ pairs ]
H5'1 H5T 1
H5'2 H5T 1
C4' H5T 1
H4' O5' 1
O4' O5' 1
C3' O5' 1
C1' C5' 1
H3' C5' 1
C2' C5' 1
O3' C5' 1
H4' H5'1 1
O4' H5'1 1
C3' H5'1 1
H4' H5'2 1
O4' H5'2 1
C3' H5'2 1
H1' C4' 1
N9 C4' 1
H2'1 C4' 1
H2'2 C4' 1
C1' H4' 1
H3' H4' 1
C2' H4' 1
O3' H4' 1
H3' O4' 1
O3' O4' 1
C8 O4' 1
C4 O4' 1
H2'1 O4' 1
H2'2 O4' 1
H8 C1' 1
N7 C1' 1
C5 C1' 1
N3 C1' 1
H3' C1' 1
O3' C1' 1
C8 H1' 1
C4 H1' 1
C3' H1' 1
H2'1 H1' 1
H2'2 H1' 1
C3' N9 1
H2'1 N9 1
H2'2 N9 1
C6 N9 1
C2 N9 1
C2' C8 1
N3 C8 1
C6 C8 1
C4 H8 1
C5 H8 1
N6 N7 1
N1 N7 1
N3 N7 1
H61 C5 1
H62 C5 1
C2 C5 1
N3 C6 1
H2 C6 1
C4 N6 1
C2 N6 1
N1 H61 1
N1 H62 1
C4 N1 1
C4 H2 1
C2' C4 1
H2'1 H3' 1
H2'2 H3' 1
O3' H2'1 1
O3' H2'2 1
[ angles ]
C5' O5' H5T 1
H5'1 C5' O5' 1
H5'2 C5' O5' 1
C4' C5' O5' 1
H4' C4' C5' 1
O4' C4' C5' 1
C3' C4' C5' 1
H5'2 C5' H5'1 1
C4' C5' H5'1 1
C4' C5' H5'2 1
C1' O4' C4' 1
H3' C3' C4' 1
C2' C3' C4' 1
O3' C3' C4' 1
O4' C4' H4' 1
C3' C4' H4' 1
C3' C4' O4' 1
H1' C1' O4' 1
N9 C1' O4' 1
C2' C1' O4' 1
C8 N9 C1' 1
C4 N9 C1' 1
C3' C2' C1' 1
H2'1 C2' C1' 1
H2'2 C2' C1' 1
N9 C1' H1' 1
C2' C1' H1' 1
C2' C1' N9 1
H8 C8 N9 1
N7 C8 N9 1
C5 C4 N9 1
N3 C4 N9 1
C4 N9 C8 1
C5 N7 C8 1
N7 C8 H8 1
C6 C5 N7 1
C4 C5 N7 1
N6 C6 C5 1
N1 C6 C5 1
N3 C4 C5 1
C4 C5 C6 1
H61 N6 C6 1
H62 N6 C6 1
C2 N1 C6 1
N1 C6 N6 1
H62 N6 H61 1
H2 C2 N1 1
N3 C2 N1 1
C4 N3 C2 1
N3 C2 H2 1
H2'1 C2' C3' 1
H2'2 C2' C3' 1
C2' C3' H3' 1
O3' C3' H3' 1
O3' C3' C2' 1
H2'2 C2' H2'1 1
[ moleculetype ]
DA 3
[ atoms ]
[ moleculetype ]
DA 3
[ atoms ]
;id type resnr residu atom cgnr charge
1 P 1 DA P 1 1.16590
2 O2 1 DA O1P 2 -0.77610
3 O2 1 DA O2P 3 -0.77610
4 OS 1 DA O5' 4 -0.49540
5 CI 1 DA C5' 5 -0.00690
6 H1 1 DA H5'1 6 0.07540
7 H1 1 DA H5'2 7 0.07540
8 CT 1 DA C4' 8 0.16290
9 H1 1 DA H4' 9 0.11760
10 OS 1 DA O4' 10 -0.36910
11 CT 1 DA C1' 11 0.04310
12 H2 1 DA H1' 12 0.18380
13 N* 1 DA N9 13 -0.02680
14 C1 1 DA C8 14 0.16070
15 H5 1 DA H8 15 0.18770
16 NB 1 DA N7 16 -0.61750
17 CB 1 DA C5 17 0.07250
18 CA 1 DA C6 18 0.68970
19 N2 1 DA N6 19 -0.91230
20 H 1 DA H61 20 0.41670
21 H 1 DA H62 21 0.41670
22 NC 1 DA N1 22 -0.76240
23 CQ 1 DA C2 23 0.57160
24 H5 1 DA H2 24 0.05980
25 NC 1 DA N3 25 -0.74170
26 CB 1 DA C4 26 0.38000
27 CE 1 DA C3' 27 0.07130
28 H1 1 DA H3' 28 0.09850
29 CT 1 DA C2' 29 -0.08540
30 HC 1 DA H2'1 30 0.07180
31 HC 1 DA H2'2 31 0.07180
32 OS 1 DA O3' 32 -0.52320
[ 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' 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 ]
H5'1 C5' O5' P 9
H5'2 C5' O5' P 9
C4' C5' O5' P 9
C5' O5' P O1P 9
C5' O5' P O2P 9
H4' C4' C5' O5' 9
O4' C4' C5' O5' 9
C3' C4' C5' O5' 9
C1' O4' C4' C5' 9
H3' C3' C4' C5' 9
C2' C3' C4' C5' 9
O3' C3' C4' C5' 9
H4' C4' C5' H5'1 9
O4' C4' C5' H5'1 9
C3' C4' C5' H5'1 9
H4' C4' C5' H5'2 9
O4' C4' C5' H5'2 9
C3' C4' C5' H5'2 9
H1' C1' O4' C4' 9
N9 C1' O4' C4' 9
H2'1 C2' C3' C4' 9
H2'2 C2' C3' C4' 9
C1' O4' C4' H4' 9
H3' C3' C4' H4' 9
C2' C3' C4' H4' 9
O3' C3' C4' H4' 9
H3' C3' C4' O4' 9
O3' C3' C4' O4' 9
C8 N9 C1' O4' 9
C4 N9 C1' O4' 9
H2'1 C2' C1' O4' 9
H2'2 C2' C1' O4' 9
H8 C8 N9 C1' 9
N7 C8 N9 C1' 9
C5 C4 N9 C1' 9
N3 C4 N9 C1' 9
H3' C3' C2' C1' 9
O3' C3' C2' C1' 9
C8 N9 C1' H1' 9
C4 N9 C1' H1' 9
C3' C2' C1' H1' 9
H2'1 C2' C1' H1' 9
H2'2 C2' C1' H1' 9
C3' C2' C1' N9 9
H2'1 C2' C1' N9 9
H2'2 C2' C1' N9 9
C6 C5 C4 N9 9
C2 N3 C4 N9 9
C2' C1' N9 C8 9
N3 C4 N9 C8 9
C6 C5 N7 C8 9
C4 N9 C8 H8 9
C5 N7 C8 H8 9
N6 C6 C5 N7 9
N1 C6 C5 N7 9
N3 C4 C5 N7 9
H61 N6 C6 C5 9
H62 N6 C6 C5 9
C2 N1 C6 C5 9
C6 C5 C4 N3 9
H2 C2 N1 C6 9
C4 C5 C6 N6 9
C2 N1 C6 N6 9
N1 C6 N6 H61 9
N1 C6 N6 H62 9
C4 C5 C6 N1 9
C4 N3 C2 H2 9
N3 C2 N1 C6 9
C2' C1' N9 C4 9
H2'1 C2' C3' H3' 9
H2'2 C2' C3' H3' 9
O3' C3' C2' H2'1 9
O3' C3' C2' H2'2 9
;
C1' O4' C4' C3' 9
C2' C3' C4' O4' 9
C2' C1' O4' C4' 9
C3' C2' C1' O4' 9
;
N7 C8 N9 C4 9
C5 C4 N9 C8 9
C5 N7 C8 N9 9
C4 C5 N7 C8 9
N9 C4 C5 N7 9
;
C4 N3 C2 N1 9
C5 C4 N3 C2 9
C1' C2' C3' C4' 9
[ pairs ]
H5'1 P 1
H5'2 P 1
C4' P 1
C5' O1P 1
C5' O2P 1
H4' O5' 1
O4' O5' 1
C3' O5' 1
C1' C5' 1
H3' C5' 1
C2' C5' 1
O3' C5' 1
H4' H5'1 1
O4' H5'1 1
C3' H5'1 1
H4' H5'2 1
O4' H5'2 1
C3' H5'2 1
H1' C4' 1
N9 C4' 1
H2'1 C4' 1
H2'2 C4' 1
C1' H4' 1
H3' H4' 1
C2' H4' 1
O3' H4' 1
H3' O4' 1
O3' O4' 1
C8 O4' 1
C4 O4' 1
H2'1 O4' 1
H2'2 O4' 1
H8 C1' 1
N7 C1' 1
C5 C1' 1
N3 C1' 1
H3' C1' 1
O3' C1' 1
C8 H1' 1
C4 H1' 1
C3' H1' 1
H2'1 H1' 1
H2'2 H1' 1
C3' N9 1
H2'1 N9 1
H2'2 N9 1
C6 N9 1
C2 N9 1
C2' C8 1
N3 C8 1
C6 C8 1
C4 H8 1
C5 H8 1
N6 N7 1
N1 N7 1
N3 N7 1
H61 C5 1
H62 C5 1
C2 C5 1
N3 C6 1
H2 C6 1
C4 N6 1
C2 N6 1
N1 H61 1
N1 H62 1
C4 N1 1
C4 H2 1
C2' C4 1
H2'1 H3' 1
H2'2 H3' 1
O3' H2'1 1
O3' H2'2 1
[ angles ]
C5' O5' P 1
O2P P O1P 1
O5' P O1P 1
O5' P O2P 1
H5'1 C5' O5' 1
H5'2 C5' O5' 1
C4' C5' O5' 1
H4' C4' C5' 1
O4' C4' C5' 1
C3' C4' C5' 1
H5'2 C5' H5'1 1
C4' C5' H5'1 1
C4' C5' H5'2 1
C1' O4' C4' 1
H3' C3' C4' 1
C2' C3' C4' 1
O3' C3' C4' 1
O4' C4' H4' 1
C3' C4' H4' 1
C3' C4' O4' 1
H1' C1' O4' 1
N9 C1' O4' 1
C2' C1' O4' 1
C8 N9 C1' 1
C4 N9 C1' 1
C3' C2' C1' 1
H2'1 C2' C1' 1
H2'2 C2' C1' 1
N9 C1' H1' 1
C2' C1' H1' 1
C2' C1' N9 1
H8 C8 N9 1
N7 C8 N9 1
C5 C4 N9 1
N3 C4 N9 1
C4 N9 C8 1
C5 N7 C8 1
N7 C8 H8 1
C6 C5 N7 1
C4 C5 N7 1
N6 C6 C5 1
N1 C6 C5 1
N3 C4 C5 1
C4 C5 C6 1
H61 N6 C6 1
H62 N6 C6 1
C2 N1 C6 1
N1 C6 N6 1
H62 N6 H61 1
H2 C2 N1 1
N3 C2 N1 1
C4 N3 C2 1
N3 C2 H2 1
H2'1 C2' C3' 1
H2'2 C2' C3' 1
C2' C3' H3' 1
O3' C3' H3' 1
O3' C3' C2' 1
H2'2 C2' H2'1 1
[ moleculetype ]
DA3 3
[ atoms ]
1 P 1 DA3 P 1 1.16590
2 O2 1 DA3 O1P 2 -0.77610
3 O2 1 DA3 O2P 3 -0.77610
4 OS 1 DA3 O5' 4 -0.49540
5 CI 1 DA3 C5' 5 -0.00690
6 H1 1 DA3 H5'1 6 0.07540
7 H1 1 DA3 H5'2 7 0.07540
8 CT 1 DA3 C4' 8 0.16290
9 H1 1 DA3 H4' 9 0.11760
10 OS 1 DA3 O4' 10 -0.36910
11 CT 1 DA3 C1' 11 0.04310
12 H2 1 DA3 H1' 12 0.18380
13 N* 1 DA3 N9 13 -0.02680
14 C1 1 DA3 C8 14 0.16070
15 H5 1 DA3 H8 15 0.18770
16 NB 1 DA3 N7 16 -0.61750
17 CB 1 DA3 C5 17 0.07250
18 CA 1 DA3 C6 18 0.68970
19 N2 1 DA3 N6 19 -0.91230
20 H 1 DA3 H61 20 0.41670
21 H 1 DA3 H62 21 0.41670
22 NC 1 DA3 N1 22 -0.76240
23 CQ 1 DA3 C2 23 0.57160
24 H5 1 DA3 H2 24 0.05980
25 NC 1 DA3 N3 25 -0.74170
26 CB 1 DA3 C4 26 0.38000
27 CE 1 DA3 C3' 27 0.07130
28 H1 1 DA3 H3' 28 0.09850
29 CT 1 DA3 C2' 29 -0.08540
30 HC 1 DA3 H2'1 30 0.07180
31 HC 1 DA3 H2'2 31 0.07180
32 OH 1 DA3 O3' 32 -0.65490
33 HO 1 DA3 H3T 33 0.43960
[ 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' 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 ]
H5'1 C5' O5' P 9
H5'2 C5' O5' P 9
C4' C5' O5' P 9
C5' O5' P O1P 9
C5' O5' P O2P 9
H4' C4' C5' O5' 9
O4' C4' C5' O5' 9
C3' C4' C5' O5' 9
C1' O4' C4' C5' 9
H3' C3' C4' C5' 9
C2' C3' C4' C5' 9
O3' C3' C4' C5' 9
H4' C4' C5' H5'1 9
O4' C4' C5' H5'1 9
C3' C4' C5' H5'1 9
H4' C4' C5' H5'2 9
O4' C4' C5' H5'2 9
C3' C4' C5' H5'2 9
H1' C1' O4' C4' 9
N9 C1' O4' C4' 9
H2'1 C2' C3' C4' 9
H2'2 C2' C3' C4' 9
H3T O3' C3' C4' 9
C1' O4' C4' H4' 9
H3' C3' C4' H4' 9
C2' C3' C4' H4' 9
O3' C3' C4' H4' 9
H3' C3' C4' O4' 9
O3' C3' C4' O4' 9
C8 N9 C1' O4' 9
C4 N9 C1' O4' 9
H2'1 C2' C1' O4' 9
H2'2 C2' C1' O4' 9
H8 C8 N9 C1' 9
N7 C8 N9 C1' 9
C5 C4 N9 C1' 9
N3 C4 N9 C1' 9
H3' C3' C2' C1' 9
O3' C3' C2' C1' 9
C8 N9 C1' H1' 9
C4 N9 C1' H1' 9
C3' C2' C1' H1' 9
H2'1 C2' C1' H1' 9
H2'2 C2' C1' H1' 9
C3' C2' C1' N9 9
H2'1 C2' C1' N9 9
H2'2 C2' C1' N9 9
C6 C5 C4 N9 9
C2 N3 C4 N9 9
C2' C1' N9 C8 9
N3 C4 N9 C8 9
C6 C5 N7 C8 9
C4 N9 C8 H8 9
C5 N7 C8 H8 9
N6 C6 C5 N7 9
N1 C6 C5 N7 9
N3 C4 C5 N7 9
H61 N6 C6 C5 9
H62 N6 C6 C5 9
C2 N1 C6 C5 9
C6 C5 C4 N3 9
H2 C2 N1 C6 9
C4 C5 C6 N6 9
C2 N1 C6 N6 9
N1 C6 N6 H61 9
N1 C6 N6 H62 9
C4 C5 C6 N1 9
C4 N3 C2 H2 9
N3 C2 N1 C6 9
C2' C1' N9 C4 9
H2'1 C2' C3' H3' 9
H2'2 C2' C3' H3' 9
H3T O3' C3' H3' 9
H3T O3' C3' C2' 9
O3' C3' C2' H2'1 9
O3' C3' C2' H2'2 9
;
C1' O4' C4' C3' 9
C2' C3' C4' O4' 9
C2' C1' O4' C4' 9
C3' C2' C1' O4' 9
;
N7 C8 N9 C4 9
C5 C4 N9 C8 9
C5 N7 C8 N9 9
C4 C5 N7 C8 9
N9 C4 C5 N7 9
;
C4 N3 C2 N1 9
C5 C4 N3 C2 9
C1' C2' C3' C4' 9
[ pairs ]
H5'1 P 1
H5'2 P 1
C4' P 1
C5' O1P 1
C5' O2P 1
H4' O5' 1
O4' O5' 1
C3' O5' 1
C1' C5' 1
H3' C5' 1
C2' C5' 1
O3' C5' 1
H4' H5'1 1
O4' H5'1 1
C3' H5'1 1
H4' H5'2 1
O4' H5'2 1
C3' H5'2 1
H1' C4' 1
N9 C4' 1
H2'1 C4' 1
H2'2 C4' 1
H3T C4' 1
C1' H4' 1
H3' H4' 1
C2' H4' 1
O3' H4' 1
H3' O4' 1
O3' O4' 1
C8 O4' 1
C4 O4' 1
H2'1 O4' 1
H2'2 O4' 1
H8 C1' 1
N7 C1' 1
C5 C1' 1
N3 C1' 1
H3' C1' 1
O3' C1' 1
C8 H1' 1
C4 H1' 1
C3' H1' 1
H2'1 H1' 1
H2'2 H1' 1
C3' N9 1
H2'1 N9 1
H2'2 N9 1
C6 N9 1
C2 N9 1
C2' C8 1
N3 C8 1
C6 C8 1
C4 H8 1
C5 H8 1
N6 N7 1
N1 N7 1
N3 N7 1
H61 C5 1
H62 C5 1
C2 C5 1
N3 C6 1
H2 C6 1
C4 N6 1
C2 N6 1
N1 H61 1
N1 H62 1
C4 N1 1
C4 H2 1
C2' C4 1
H2'1 H3' 1
H2'2 H3' 1
H3T H3' 1
H3T C2' 1
O3' H2'1 1
O3' H2'2 1
[ angles ]
C5' O5' P 1
O2P P O1P 1
O5' P O1P 1
O5' P O2P 1
H5'1 C5' O5' 1
H5'2 C5' O5' 1
C4' C5' O5' 1
H4' C4' C5' 1
O4' C4' C5' 1
C3' C4' C5' 1
H5'2 C5' H5'1 1
C4' C5' H5'1 1
C4' C5' H5'2 1
C1' O4' C4' 1
H3' C3' C4' 1
C2' C3' C4' 1
O3' C3' C4' 1
O4' C4' H4' 1
C3' C4' H4' 1
C3' C4' O4' 1
H1' C1' O4' 1
N9 C1' O4' 1
C2' C1' O4' 1
C8 N9 C1' 1
C4 N9 C1' 1
C3' C2' C1' 1
H2'1 C2' C1' 1
H2'2 C2' C1' 1
N9 C1' H1' 1
C2' C1' H1' 1
C2' C1' N9 1
H8 C8 N9 1
N7 C8 N9 1
C5 C4 N9 1
N3 C4 N9 1
C4 N9 C8 1
C5 N7 C8 1
N7 C8 H8 1
C6 C5 N7 1
C4 C5 N7 1
N6 C6 C5 1
N1 C6 C5 1
N3 C4 C5 1
C4 C5 C6 1
H61 N6 C6 1
H62 N6 C6 1
C2 N1 C6 1
N1 C6 N6 1
H62 N6 H61 1
H2 C2 N1 1
N3 C2 N1 1
C4 N3 C2 1
N3 C2 H2 1
H2'1 C2' C3' 1
H2'2 C2' C3' 1
H3T O3' C3' 1
C2' C3' H3' 1
O3' C3' H3' 1
O3' C3' C2' 1
H2'2 C2' H2'1 1
[ moleculetype ]
DT5 3
[ atoms ]
1 HO 1 DT5 H5T 1 0.44220
2 OH 1 DT5 O5' 2 -0.63180
3 CI 1 DT5 C5' 3 -0.00690
4 H1 1 DT5 H5'1 4 0.07540
5 H1 1 DT5 H5'2 5 0.07540
6 CT 1 DT5 C4' 6 0.16290
7 H1 1 DT5 H4' 7 0.11760
8 OS 1 DT5 O4' 8 -0.36910
9 CT 1 DT5 C1' 9 0.06800
10 H2 1 DT5 H1' 10 0.18040
11 N* 1 DT5 N1 11 -0.02390
12 C2 1 DT5 C6 12 -0.22090
13 H4 1 DT5 H6 13 0.26070
14 C2 1 DT5 C5 14 0.00250
15 CT 1 DT5 C7 15 -0.22690
16 HC 1 DT5 H71 16 0.07700
17 HC 1 DT5 H72 17 0.07700
18 HC 1 DT5 H73 18 0.07700
19 C 1 DT5 C4 19 0.51940
20 O 1 DT5 O4 20 -0.55630
21 NA 1 DT5 N3 21 -0.43400
22 H 1 DT5 H3 22 0.34200
23 C 1 DT5 C2 23 0.56770
24 O 1 DT5 O2 24 -0.58810
25 CE 1 DT5 C3' 25 0.07130
26 H1 1 DT5 H3' 26 0.09850
27 CT 1 DT5 C2' 27 -0.08540
28 HC 1 DT5 H2'1 28 0.07180
29 HC 1 DT5 H2'2 29 0.07180
30 OS 1 DT5 O3' 30 -0.52320
[ impropers ]
C1' C2' N1 O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DTC1'", "ifdef":"eq_polyply"}
C3' O3' C4' C2' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DTC3'", "ifdef":"eq_polyply"}
C4' C5' C3' O4' 2 3.5264390e+01 3.3484625e+03 {"group": "chiral-center DTO4'", "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 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