PDB Chemical Component DDN

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for DDN

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P 1.522 1.480
P OP1 1.501 1.610
P OP2 1.518 1.610
P O5' 1.632 1.610
OP1 H1P 0.950 0.967
OP2 H2P 0.950 0.967
O5' C5' 1.442 1.428
C5' C4' 1.519 1.530
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.090
C4' O4' 1.427 1.446
C4' C3' 1.539 1.545
C4' H4' 1.115 1.091
O4' C1' 1.434 1.445
C3' O3' 1.398 1.430
C3' C2' 1.478 1.545
C3' H3' 1.115 1.091
O3' H1 0.950 0.967
C2' C1' 1.499 1.545
C2' H2' 1.115 1.090
C2' H2'' 1.115 1.089
C1' N1 1.636 1.465
C1' H1' 1.115 1.090
N1 C2 1.411 1.340
N1 C6 1.379 1.386
C2 O2 1.231 1.216
C2 N3 1.398 1.349
N3 C4 1.574 1.472
N3 HN3 1.020 0.970
C4 O4 1.435 1.428
C4 C5 1.552 1.515
C4 H4 1.115 1.091
O4 HO4 0.950 0.967
C5 C6 1.367 1.321
C5 H5 1.103 1.079
C6 H6 1.103 1.080

Bond Angles for DDN

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP3 P OP1 112.6 109.5
OP3 P OP2 111.5 109.4
OP3 P O5' 107.2 109.5
OP1 P OP2 114.4 109.5
OP1 P O5' 105.0 109.5
P OP1 H1P 112.7 106.8
OP2 P O5' 105.5 109.4
P OP2 H2P 111.5 106.8
P O5' C5' 121.0 106.8
O5' C5' C4' 109.2 109.5
O5' C5' H5' 112.3 109.5
O5' C5' H5'' 112.3 109.5
C4' C5' H5' 112.3 109.4
C4' C5' H5'' 112.3 109.4
C5' C4' O4' 111.6 110.4
C5' C4' C3' 114.7 110.7
C5' C4' H4' 103.3 110.3
H5' C5' H5'' 98.1 109.5
O4' C4' C3' 106.4 104.7
O4' C4' H4' 112.1 110.4
C4' O4' C1' 102.4 105.4
C3' C4' H4' 108.8 110.2
C4' C3' O3' 110.5 110.5
C4' C3' C2' 107.2 104.2
C4' C3' H3' 110.4 110.5
O4' C1' C2' 116.3 104.8
O4' C1' N1 97.8 110.5
O4' C1' H1' 149.1 110.4
O3' C3' C2' 109.8 110.5
O3' C3' H3' 107.8 110.4
C3' O3' H1 110.5 106.8
C2' C3' H3' 111.1 110.5
C3' C2' C1' 99.1 104.0
C3' C2' H2' 116.2 110.5
C3' C2' H2'' 116.2 110.5
C1' C2' H2' 116.2 110.5
C1' C2' H2'' 116.2 110.5
C2' C1' N1 143.2 110.4
C2' C1' H1' 60.3 110.4
H2' C2' H2'' 94.2 110.6
N1 C1' H1' 97.4 110.4
C1' N1 C2 118.0 118.3
C1' N1 C6 106.5 118.3
C2 N1 C6 124.4 123.4
N1 C2 O2 123.9 119.1
N1 C2 N3 114.4 121.8
N1 C6 C5 120.7 121.3
N1 C6 H6 120.1 119.4
O2 C2 N3 121.3 119.2
C2 N3 C4 123.4 118.3
C2 N3 HN3 112.0 120.8
C4 N3 HN3 124.6 120.9
N3 C4 O4 113.0 107.9
N3 C4 C5 111.0 117.2
N3 C4 H4 105.1 107.9
O4 C4 C5 106.7 107.9
O4 C4 H4 109.5 107.8
C4 O4 HO4 113.1 106.8
C5 C4 H4 111.6 107.9
C4 C5 C6 120.7 118.1
C4 C5 H5 126.0 120.9
C6 C5 H5 113.3 121.0
C5 C6 H6 119.2 119.4

Torsion Angles for DDN

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2 229.9 120.0
OP1 P OP3 O5' 115.0 239.9
OP3 P OP1 H1P 180.0 300.0
OP2 P OP3 O5' 245.1 120.0
OP3 P OP2 H2P 180.0 179.9
OP3 P O5' C5' 169.8 55.0
OP3 P OP1 OP2 128.6 240.1
OP3 P OP1 O5' 243.7 120.1
OP2 P OP1 O5' 115.1 240.0
OP1 P OP2 H2P 309.2 60.0
OP1 P O5' C5' 49.8 175.0
OP3 P OP2 OP1 230.8 120.0
OP3 P OP2 O5' 116.0 240.0
OP1 P OP2 O5' 245.2 120.0
OP2 P OP1 H1P 51.4 60.0
OP2 P O5' C5' 288.6 295.0
OP3 P O5' OP1 120.0 240.0
OP3 P O5' OP2 241.1 120.0
OP1 P O5' OP2 121.1 240.0
O5' P OP1 H1P 296.2 180.0
O5' P OP2 H2P 64.1 299.9
P O5' C5' C4' 156.0 180.0
P O5' C5' H5' 30.7 60.1
P O5' C5' H5'' 281.3 300.0
H1P OP1 P OP2 51.4 60.0
H1P OP1 P O5' 296.2 180.0
H2P OP2 P O5' 64.1 299.9
C4' C5' O5' H5' 125.3 120.0
C4' C5' O5' H5'' 234.7 240.0
O5' C5' C4' O4' 158.7 66.4
O5' C5' C4' C3' 279.8 181.9
O5' C5' C4' H4' 38.1 304.2
H5' C5' O5' H5'' 109.5 120.1
O5' C5' C4' H5' 234.7 240.0
O5' C5' C4' H5'' 125.3 120.0
H5' C5' C4' H5'' 250.5 240.1
O4' C4' C5' C3' 238.9 244.6
O4' C4' C5' H4' 120.6 122.3
C5' C4' O4' C1' 99.7 159.5
C3' C4' C5' H4' 241.7 237.7
C5' C4' C3' O3' 147.1 98.5
C5' C4' C3' C2' 266.8 217.3
C5' C4' C3' H3' 28.0 336.0
O5' C5' H5' C4' 123.5 120.0
O5' C5' H5' H5'' 241.8 239.9
C4' C5' H5' H5'' 118.2 119.9
H5' C5' C4' O4' 284.0 186.5
H5' C5' C4' C3' 45.1 301.9
H5' C5' C4' H4' 163.3 64.2
O5' C5' H5'' C4' 236.5 240.0
O5' C5' H5'' H5' 118.2 120.1
C4' C5' H5'' H5' 241.7 240.1
H5'' C5' C4' O4' 33.4 306.4
H5'' C5' C4' C3' 154.5 61.9
H5'' C5' C4' H4' 272.8 184.2
O4' C4' C5' H5' 284.0 186.5
O4' C4' C5' H5'' 33.4 306.4
C5' C4' O4' C3' 125.8 119.2
C5' C4' O4' H4' 244.7 237.8
C3' C4' O4' H4' 118.9 118.6
O4' C4' C3' O3' 271.1 217.5
O4' C4' C3' C2' 30.7 336.2
O4' C4' C3' H3' 151.9 94.9
C4' O4' C1' C2' 14.6 319.6
C4' O4' C1' N1 208.9 200.7
C4' O4' C1' H1' 90.1 78.4
C3' C4' C5' H5' 45.1 301.9
C3' C4' C5' H5'' 154.5 61.9
C5' C4' C3' O4' 236.1 241.1
C5' C4' C3' H4' 115.1 122.4
O4' C4' C3' H4' 239.0 241.3
C3' C4' O4' C1' 333.9 40.3
O3' C3' C4' C2' 240.3 241.3
O3' C3' C4' H3' 119.2 122.5
C4' C3' O3' H1 180.0 178.2
C2' C3' C4' H3' 238.8 241.3
C4' C3' C2' C1' 340.2 359.9
C4' C3' C2' H2' 214.9 118.5
C4' C3' C2' H2'' 105.5 241.3
H4' C4' C5' H5' 163.3 64.2
H4' C4' C5' H5'' 272.8 184.2
C5' C4' H4' O4' 120.3 122.3
C5' C4' H4' C3' 237.7 237.4
O4' C4' H4' C3' 117.4 115.2
H4' C4' O4' C1' 215.0 281.7
H4' C4' C3' O3' 32.0 336.2
H4' C4' C3' C2' 151.7 94.9
H4' C4' C3' H3' 272.9 213.6
C1' O4' C4' C3' 333.9 40.3
C1' O4' C4' H4' 215.0 281.7
C3' C2' C1' O4' 3.9 24.0
O4' C1' C2' H2' 129.2 265.4
O4' C1' C2' H2'' 238.6 142.6
C2' C1' O4' N1 165.7 118.9
C2' C1' O4' H1' 284.5 241.2
N1 C1' O4' H1' 118.8 122.3
O4' C1' N1 C2 236.2 50.1
O4' C1' N1 C6 90.7 230.4
O3' C3' C4' H4' 32.0 336.2
C4' C3' O3' C2' 118.1 114.9
C4' C3' O3' H3' 239.3 237.4
C2' C3' O3' H3' 121.2 122.6
O3' C3' C2' C1' 100.4 118.7
O3' C3' C2' H2' 335.1 237.3
O3' C3' C2' H2'' 225.6 0.0
C2' C3' C4' H4' 151.7 94.9
C4' C3' C2' O3' 239.9 241.3
C4' C3' C2' H3' 120.7 118.7
O4' C1' C2' C3' 3.9 24.0
O3' C3' C2' H3' 240.8 237.4
C2' C3' O3' H1 61.9 63.3
C1' C2' C3' H2' 125.3 241.4
C1' C2' C3' H2'' 234.8 118.6
C3' C2' C1' N1 159.8 142.9
C3' C2' C1' H1' 218.8 265.2
H2' C2' C3' H2'' 109.5 237.3
H3' C3' C4' H4' 272.9 213.6
C4' C3' H3' O3' 120.8 122.6
C4' C3' H3' C2' 241.2 245.2
O3' C3' H3' C2' 120.3 122.6
H3' C3' O3' H1 300.8 300.7
H3' C3' C2' C1' 219.5 241.2
H3' C3' C2' H2' 94.2 359.8
H3' C3' C2' H2'' 344.8 122.6
H1 O3' C3' C2' 61.9 63.3
H1 O3' C3' H3' 300.8 300.7
O4' C1' C2' N1 204.1 241.1
O4' C1' C2' H1' 145.1 118.8
C1' C2' C3' H3' 219.5 241.2
C3' C2' C1' H2' 234.7 118.6
C3' C2' C1' H2'' 125.3 241.4
H2' C2' C1' H2'' 250.5 122.7
N1 C1' C2' H1' 301.0 237.7
C2' C1' N1 C2 78.0 294.7
C2' C1' N1 C6 292.4 115.0
H2' C2' C3' H3' 94.2 359.8
C3' C2' H2' C1' 116.0 245.4
C3' C2' H2' H2'' 238.0 122.7
C1' C2' H2' H2'' 122.0 237.3
H2' C2' C1' N1 285.1 24.3
H2' C2' C1' H1' 344.1 146.6
H2'' C2' C3' H3' 344.8 122.6
C3' C2' H2'' C1' 244.0 114.6
C3' C2' H2'' H2' 122.0 237.3
C1' C2' H2'' H2' 238.0 122.7
H2'' C2' C1' N1 34.5 261.6
H2'' C2' C1' H1' 93.6 23.8
O4' C1' N1 C2' 158.3 115.4
O4' C1' N1 H1' 207.0 237.7
N1 C1' C2' H2' 285.1 24.3
N1 C1' C2' H2'' 34.5 261.6
C2' C1' N1 H1' 48.7 122.2
C2 N1 C1' C6 145.6 179.7
C1' N1 C2 O2 5.7 0.3
C1' N1 C2 N3 193.2 179.7
C1' N1 C6 C5 168.0 180.0
C1' N1 C6 H6 348.0 359.9
O4' C1' H1' C2' 267.7 244.7
O4' C1' H1' N1 118.9 122.4
H1' C1' C2' H2' 344.1 146.6
H1' C1' C2' H2'' 93.6 23.8
C2' C1' H1' N1 211.2 237.8
H1' C1' N1 C2 29.2 172.5
H1' C1' N1 C6 243.7 352.8
C2 N1 C1' H1' 29.2 172.5
C1' N1 C2 C6 221.1 180.3
C2 N1 C6 C5 25.2 0.4
C2 N1 C6 H6 205.2 180.3
O2 C2 N1 N3 172.5 180.5
N1 C2 N3 C4 19.0 0.6
N1 C2 N3 HN3 199.0 180.3
C6 N1 C1' H1' 243.7 352.8
C1' N1 C6 C2 142.8 179.7
C6 N1 C2 O2 144.7 179.9
C6 N1 C2 N3 332.1 359.4
C4 C5 C6 N1 348.1 359.9
N1 C6 C5 H5 168.1 180.0
C5 C6 N1 H6 180.0 180.1
O2 C2 N1 C6 144.7 179.9
N1 C2 O2 N3 188.0 179.5
O2 C2 N3 C4 206.3 180.0
O2 C2 N3 HN3 26.3 359.7
N3 C2 N1 C6 332.1 359.4
N1 C2 N3 O2 172.7 180.5
C4 N3 C2 HN3 180.0 180.3
C2 N3 C4 O4 111.6 121.7
C2 N3 C4 C5 351.8 359.7
C2 N3 C4 H4 231.0 237.8
C2 N3 C4 HN3 180.0 179.7
O4 C4 N3 C5 119.8 122.0
O4 C4 N3 H4 240.7 243.8
N3 C4 O4 HO4 180.0 52.5
C5 C4 N3 H4 120.8 121.9
N3 C4 C5 C6 3.9 0.1
N3 C4 C5 H5 183.9 180.0
C2 N3 HN3 C4 180.0 180.3
HN3 N3 C4 O4 291.6 301.9
HN3 N3 C4 C5 171.8 180.0
HN3 N3 C4 H4 51.0 58.1
O4 C4 N3 HN3 291.6 301.9
N3 C4 O4 C5 237.8 232.5
N3 C4 O4 H4 116.8 116.2
C5 C4 O4 H4 239.0 243.8
O4 C4 C5 C6 240.4 238.1
O4 C4 C5 H5 60.3 58.1
N1 C6 C5 C4 348.1 359.9
C5 C4 N3 HN3 171.8 180.0
N3 C4 C5 O4 123.5 122.0
N3 C4 C5 H4 243.1 238.1
O4 C4 C5 H4 119.6 116.2
C5 C4 O4 HO4 302.3 180.0
C6 C5 C4 H5 180.0 180.1
C4 C5 C6 H6 168.1 180.0
H4 C4 N3 HN3 51.0 58.1
N3 C4 H4 O4 238.3 243.7
N3 C4 H4 C5 120.4 127.5
O4 C4 H4 C5 242.1 243.7
H4 C4 O4 HO4 63.2 296.2
H4 C4 C5 C6 120.8 121.9
H4 C4 C5 H5 300.8 301.9
HO4 O4 C4 C5 302.3 180.0
HO4 O4 C4 H4 63.2 296.2
N1 C6 C5 H6 180.0 179.9
C6 C5 C4 H4 120.8 121.9
C4 C5 C6 H5 180.0 179.9
H5 C5 C4 H4 300.8 301.9
C4 C5 H5 C6 180.0 180.1
H5 C5 C6 H6 348.1 0.1
N1 C6 H6 C5 180.0 180.1
H6 C6 C5 H5 348.1 0.1