PDB Chemical Component ZDU

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 ZDU

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.451 1.501
P OP2 1.471 1.618
P O5' 1.591 1.619
P OP3   1.616
OP2 HOP2 0.949 0.981
O5' C5' 1.406 1.418
N1 C6 1.381 1.389
N1 C2 1.383 1.411
N1 C1' 1.483 1.434
C6 C5 1.341 1.339
C6 H6 1.103 1.086
C2 O2 1.225 1.232
C2 N3 1.389 1.399
N3 C4 1.413 1.387
N3 HN3 1.020 1.016
C4 O4 1.252 1.228
C4 C5 1.459 1.487
C5 C5A 1.509 1.495
C5A C5B 1.546 1.526
C5A H5A1 1.115 1.095
C5A H5A2 1.115 1.093
C5B C5G 1.507 1.528
C5B H5B1 1.116 1.098
C5B H5B2 1.115 1.097
C5G N5D 1.503 1.437
C5G H5G1 1.114 1.094
C5G H5G2 1.115 1.095
N5D H5D1 1.020 1.008
N5D H5D2 1.020 1.008
C2' C1' 1.526 1.520
C2' C3' 1.532 1.511
C2' H2' 1.115 1.097
C2' H2'' 1.116 1.095
C5' C4' 1.507 1.523
C5' H5' 1.114 1.092
C5' H5'' 1.114 1.093
C4' O4' 1.433 1.441
C4' C3' 1.520 1.522
C4' H4' 1.114 1.094
O4' C1' 1.413 1.434
C1' H1' 1.114 1.095
C3' O3' 1.423 1.426
C3' H3' 1.115 1.094
O3' HO3' 0.949 0.973
OP3 HOP3   0.981

Bond Angles for ZDU

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 121.0 115.3
OP1 P O5' 108.5 115.0
OP1 P OP3   115.0
OP2 P O5' 108.1 103.7
OP2 P OP3   103.3
P OP2 HOP2 120.9 118.9
O5' P OP3   102.9
P O5' C5' 119.7 118.5
P OP3 HOP3   118.9
O5' C5' C4' 109.9 108.9
O5' C5' H5' 112.0 109.0
O5' C5' H5'' 112.0 108.9
C6 N1 C2 121.2 120.4
C6 N1 C1' 119.8 118.4
N1 C6 C5 124.8 124.5
N1 C6 H6 119.2 114.9
C2 N1 C1' 118.9 121.2
N1 C2 O2 122.6 123.8
N1 C2 N3 114.5 115.1
N1 C1' C2' 119.6 112.8
N1 C1' O4' 106.9 109.3
N1 C1' H1' 102.8 107.8
C5 C6 H6 116.0 120.7
C6 C5 C4 117.8 118.3
C6 C5 C5A 121.6 123.6
O2 C2 N3 122.9 121.1
C2 N3 C4 127.0 127.0
C2 N3 HN3 115.5 116.4
C4 N3 HN3 117.5 116.6
N3 C4 O4 120.2 123.6
N3 C4 C5 114.6 114.8
O4 C4 C5 125.2 121.6
C4 C5 C5A 120.6 118.1
C5 C5A C5B 112.9 110.9
C5 C5A H5A1 111.0 107.2
C5 C5A H5A2 111.0 108.8
C5B C5A H5A1 110.9 109.5
C5B C5A H5A2 110.9 111.8
C5A C5B C5G 109.9 113.9
C5A C5B H5B1 112.0 109.5
C5A C5B H5B2 112.1 108.4
H5A1 C5A H5A2 99.4 108.4
C5G C5B H5B1 112.0 108.6
C5G C5B H5B2 112.1 109.2
C5B C5G N5D 112.7 112.6
C5B C5G H5G1 111.1 111.6
C5B C5G H5G2 111.0 109.8
H5B1 C5B H5B2 98.3 107.0
N5D C5G H5G1 111.0 107.8
N5D C5G H5G2 111.0 106.9
C5G N5D H5D1 112.7 119.2
C5G N5D H5D2 111.1 119.2
H5G1 C5G H5G2 99.3 108.0
H5D1 N5D H5D2 111.1 120.2
C1' C2' C3' 101.7 102.5
C1' C2' H2' 115.2 110.6
C1' C2' H2'' 115.2 111.7
C2' C1' O4' 103.9 107.4
C2' C1' H1' 105.9 111.5
C3' C2' H2' 115.2 109.7
C3' C2' H2'' 115.2 114.1
C2' C3' C4' 105.5 103.1
C2' C3' O3' 111.9 109.7
C2' C3' H3' 109.6 113.2
H2' C2' H2'' 95.2 108.3
C4' C5' H5' 112.1 110.3
C4' C5' H5'' 112.0 110.3
C5' C4' O4' 110.7 107.9
C5' C4' C3' 113.4 112.9
C5' C4' H4' 104.8 109.5
H5' C5' H5'' 98.4 109.3
O4' C4' C3' 105.5 106.2
O4' C4' H4' 112.7 107.9
C4' O4' C1' 107.9 109.3
C3' C4' H4' 110.0 112.2
C4' C3' O3' 106.6 109.9
C4' C3' H3' 114.7 113.5
O4' C1' H1' 118.8 108.0
O3' C3' H3' 108.5 107.4
C3' O3' HO3' 111.9 107.3

Torsion Angles for ZDU

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 125.6 120.6
OP2 P OP1 OP3   239.9
OP1 P OP2 HOP2 180.0 48.8
O5' P OP1 OP3   119.3
OP1 P O5' C5' 192.9 179.9
OP1 P OP3 HOP3   312.0
OP1 P OP2 O5' 234.2 233.4
OP1 P OP2 OP3   126.3
O5' P OP2 OP3   252.9
OP2 P O5' C5' 60.1 53.2
OP2 P OP3 HOP3   78.5
OP1 P O5' OP2 132.8 126.8
OP1 P O5' OP3   234.2
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 305.8 175.4
O5' P OP3 HOP3   186.2
P O5' C5' C4' 168.5 180.0
P O5' C5' H5' 293.8 300.4
P O5' C5' H5'' 43.3 59.6
OP1 P OP3 OP2   233.5
OP1 P OP3 O5'   125.8
OP2 P OP3 O5'   252.3
OP3 P OP2 HOP2   282.5
OP3 P O5' C5'   305.8
HOP2 OP2 P O5' 305.8 175.4
HOP2 OP2 P OP3   282.5
C5' O5' P OP3   305.8
C4' C5' O5' H5' 234.7 239.6
C4' C5' O5' H5'' 125.2 120.4
O5' C5' C4' O4' 293.3 62.4
O5' C5' C4' C3' 51.7 179.5
O5' C5' C4' H4' 171.6 305.3
H5' C5' O5' H5'' 250.5 240.8
C2 N1 C6 C1' 176.8 180.0
C6 N1 C2 O2 177.1 180.0
C6 N1 C2 N3 357.4 360.0
C6 N1 C1' C2' 296.3 273.5
C6 N1 C1' O4' 53.7 32.9
C6 N1 C1' H1' 179.5 150.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 359.0 0.0
N1 C6 C5 C5A 179.5 180.0
C6 N1 C2 C1' 183.2 180.0
C2 N1 C6 C5 2.9 0.0
C2 N1 C6 H6 183.0 180.0
C2 N1 C1' C2' 119.4 93.5
C2 N1 C1' O4' 236.9 212.8
C2 N1 C1' H1' 2.6 330.0
O2 C2 N1 N3 179.7 180.0
N1 C2 N3 C4 0.8 360.0
N1 C2 N3 HN3 180.7 180.0
C6 N1 C1' C2 176.9 180.0
C1' N1 C6 C5 186.1 180.0
C1' N1 C6 H6 6.2 360.0
C1' N1 C2 O2 353.9 0.0
C1' N1 C2 N3 174.2 180.0
N1 C1' C2' C3' 154.9 147.4
N1 C1' C2' H2' 280.2 30.6
N1 C1' C2' H2'' 29.6 269.9
C2' C1' N1 O4' 242.6 240.6
C2' C1' N1 H1' 116.8 123.5
C4' O4' C1' N1 192.5 228.3
O4' C1' N1 H1' 234.2 242.9
C5 C6 N1 C2 2.9 0.0
C5 C6 N1 C1' 186.1 180.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 359.2 359.9
O4 C4 C5 C6 179.1 179.9
C4 C5 C6 C5A 179.4 180.0
C6 C5 C5A C5B 107.1 90.0
C6 C5 C5A H5A1 232.4 209.6
C6 C5 C5A H5A2 341.9 326.6
H6 C6 N1 C2 183.0 180.0
H6 C6 N1 C1' 6.2 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 178.9 180.0
H6 C6 C5 C5A 359.5 360.0
O2 C2 N1 C1' 353.9 0.0
N1 C2 O2 N3 180.3 180.0
O2 C2 N3 C4 181.1 179.9
O2 C2 N3 HN3 1.0 0.0
N3 C2 N1 C1' 174.2 180.0
N1 C2 N3 O2 179.7 180.0
C4 N3 C2 HN3 180.1 179.9
C2 N3 C4 O4 181.0 180.1
C2 N3 C4 C5 0.9 0.1
C6 C5 C4 N3 359.2 359.9
C2 N3 C4 HN3 179.9 180.1
O4 C4 N3 C5 180.1 180.0
N3 C4 C5 C5A 178.6 180.0
C2 N3 HN3 C4 180.1 179.9
HN3 N3 C4 O4 1.1 0.0
HN3 N3 C4 C5 181.0 180.0
C6 C5 C4 O4 179.1 179.9
O4 C4 N3 HN3 1.1 0.0
N3 C4 O4 C5 179.9 180.0
O4 C4 C5 C5A 358.5 360.0
C4 C5 C6 H6 178.9 180.0
C6 C5 C4 C5A 180.6 180.0
C5 C4 N3 HN3 181.0 180.0
N3 C4 C5 O4 180.1 180.0
C4 C5 C5A C5B 287.7 270.0
C4 C5 C5A H5A1 53.0 29.5
C4 C5 C5A H5A2 162.5 146.6
C5A C5 C6 H6 359.5 360.0
C6 C5 C5A C4 179.4 180.0
C5B C5A C5 H5A1 234.7 240.5
C5B C5A C5 H5A2 125.3 123.4
C5 C5A C5B C5G 171.1 178.2
C5 C5A C5B H5B1 296.3 300.0
C5 C5A C5B H5B2 45.8 56.5
H5A1 C5A C5 H5A2 250.5 243.0
C5 C5A C5B H5A1 125.3 118.1
C5 C5A C5B H5A2 234.7 238.4
H5A1 C5A C5B H5A2 109.4 120.2
C5G C5B C5A H5B1 234.7 238.2
C5G C5B C5A H5B2 125.3 121.8
C5A C5B C5G N5D 170.7 178.7
C5A C5B C5G H5G1 295.9 300.0
C5A C5B C5G H5G2 45.5 59.7
H5B1 C5B C5A H5B2 250.6 243.5
C5 C5A H5A1 C5B 233.6 239.6
C5 C5A H5A1 H5A2 116.8 117.3
C5B C5A H5A1 H5A2 243.2 237.7
H5A1 C5A C5B C5G 45.8 60.1
H5A1 C5A C5B H5B1 171.0 181.9
H5A1 C5A C5B H5B2 280.5 298.3
C5 C5A H5A2 C5B 126.4 122.9
C5 C5A H5A2 H5A1 243.1 243.7
C5B C5A H5A2 H5A1 116.8 120.9
H5A2 C5A C5B C5G 296.4 299.9
H5A2 C5A C5B H5B1 61.6 61.6
H5A2 C5A C5B H5B2 171.0 178.1
C5G C5B C5A H5A1 45.8 60.1
C5G C5B C5A H5A2 296.4 299.9
C5A C5B C5G H5B1 125.3 122.3
C5A C5B C5G H5B2 234.7 238.6
H5B1 C5B C5G H5B2 109.4 116.4
N5D C5G C5B H5G1 234.8 238.7
N5D C5G C5B H5G2 125.2 119.0
C5B C5G N5D H5D1 180.1 230.5
C5B C5G N5D H5D2 54.7 63.9
H5G1 C5G C5B H5G2 250.4 240.3
H5B1 C5B C5A H5A1 171.0 181.9
H5B1 C5B C5A H5A2 61.6 61.6
C5A C5B H5B1 C5G 235.9 235.1
C5A C5B H5B1 H5B2 118.0 117.4
C5G C5B H5B1 H5B2 242.1 242.3
H5B1 C5B C5G N5D 45.4 56.4
H5B1 C5B C5G H5G1 170.7 177.7
H5B1 C5B C5G H5G2 280.2 297.4
H5B2 C5B C5A H5A1 280.5 298.3
H5B2 C5B C5A H5A2 171.0 178.1
C5A C5B H5B2 C5G 124.1 124.6
C5A C5B H5B2 H5B1 242.1 242.0
C5G C5B H5B2 H5B1 117.9 117.3
H5B2 C5B C5G N5D 296.0 300.0
H5B2 C5B C5G H5G1 61.2 61.4
H5B2 C5B C5G H5G2 170.8 181.1
N5D C5G C5B H5B1 45.4 56.4
N5D C5G C5B H5B2 296.0 300.0
C5B C5G N5D H5G1 125.3 123.5
C5B C5G N5D H5G2 234.7 239.3
H5G1 C5G N5D H5G2 109.5 115.9
H5D1 N5D C5G H5D2 125.3 166.6
H5G1 C5G C5B H5B1 170.7 177.7
H5G1 C5G C5B H5B2 61.2 61.4
C5B C5G H5G1 N5D 233.8 235.9
C5B C5G H5G1 H5G2 117.0 120.8
N5D C5G H5G1 H5G2 243.1 244.9
H5G1 C5G N5D H5D1 54.8 107.1
H5G1 C5G N5D H5D2 289.4 300.5
H5G2 C5G C5B H5B1 280.2 297.4
H5G2 C5G C5B H5B2 170.8 181.1
C5B C5G H5G2 N5D 126.2 122.4
C5B C5G H5G2 H5G1 243.0 238.2
N5D C5G H5G2 H5G1 116.9 115.7
H5G2 C5G N5D H5D1 305.3 351.2
H5G2 C5G N5D H5D2 180.0 184.6
H5D1 N5D C5G H5G1 54.8 107.1
H5D1 N5D C5G H5G2 305.3 351.2
C5G N5D H5D1 H5D2 234.6 193.6
H5D2 N5D C5G H5G1 289.4 300.5
H5D2 N5D C5G H5G2 180.0 184.6
C5G N5D H5D2 H5D1 126.3 166.4
N1 C1' C2' O4' 119.0 120.5
N1 C1' C2' H1' 244.8 238.6
C3' C2' C1' H2' 234.7 116.9
C3' C2' C1' H2'' 125.3 237.5
C1' C2' C3' C4' 340.5 326.6
C1' C2' C3' O3' 96.1 83.6
C1' C2' C3' H3' 216.6 203.6
H2' C2' C1' H2'' 250.6 120.7
C4' O4' C1' C2' 319.8 351.0
O4' C1' C2' H1' 125.8 118.1
C1' C2' C3' H2' 125.3 242.5
C1' C2' C3' H2'' 234.7 120.8
C3' C2' C1' O4' 35.9 26.9
C3' C2' C1' H1' 270.0 268.8
H2' C2' C3' H2'' 109.4 238.3
C5' C4' C3' C2' 235.7 271.2
O4' C4' C3' C2' 356.9 29.2
C2' C3' C4' H4' 118.7 146.9
C4' C3' C2' O3' 244.4 242.9
C4' C3' C2' H3' 123.9 123.0
O3' C3' C2' H3' 239.5 240.1
C2' C3' O3' HO3' 179.9 119.3
C1' C2' H2' C3' 242.0 112.3
C1' C2' H2' H2'' 121.0 237.3
H2' C2' C1' O4' 161.2 270.0
H2' C2' C1' H1' 35.4 151.9
C3' C2' H2' H2'' 239.0 125.1
H2' C2' C3' C4' 215.2 84.1
H2' C2' C3' O3' 330.8 201.1
H2' C2' C3' H3' 91.3 321.1
C1' C2' H2'' C3' 117.9 244.4
C1' C2' H2'' H2' 239.0 122.0
H2'' C2' C1' O4' 270.6 149.4
H2'' C2' C1' H1' 144.7 31.3
C3' C2' H2'' H2' 121.1 237.5
H2'' C2' C3' C4' 105.8 205.7
H2'' C2' C3' O3' 221.4 322.8
H2'' C2' C3' H3' 341.9 82.7
O5' C5' C4' H5' 125.2 119.6
O5' C5' C4' H5'' 234.8 240.5
C2' C3' C4' C5' 235.7 271.2
H5' C5' C4' H5'' 109.5 120.9
O4' C4' C5' C3' 241.7 242.9
O4' C4' C5' H4' 121.7 117.1
C5' C4' O4' C1' 150.1 108.6
C3' C4' C5' H4' 240.1 234.2
C5' C4' C3' O3' 116.5 154.2
C5' C4' C3' H3' 356.4 34.0
O5' C5' H5' C4' 236.0 240.5
O5' C5' H5' H5'' 118.0 119.0
C4' C5' H5' H5'' 242.0 238.5
H5' C5' C4' O4' 168.1 302.9
H5' C5' C4' C3' 286.5 60.0
H5' C5' C4' H4' 46.4 185.7
O5' C5' H5'' C4' 124.0 119.4
O5' C5' H5'' H5' 242.1 241.0
C4' C5' H5'' H5' 118.0 121.5
H5'' C5' C4' O4' 58.6 181.9
H5'' C5' C4' C3' 176.9 299.0
H5'' C5' C4' H4' 296.8 64.8
N1 C1' O4' C4' 192.5 228.3
C2' C1' O4' C4' 319.8 351.0
C2' C3' C4' O4' 356.9 29.2
O4' C4' C5' H5' 168.1 302.9
O4' C4' C5' H5'' 58.6 181.9
C5' C4' O4' C3' 123.0 121.4
C5' C4' O4' H4' 243.0 241.8
C3' C4' O4' H4' 120.0 120.5
O4' C4' C3' O3' 237.8 272.3
O4' C4' C3' H3' 117.6 152.1
C4' O4' C1' H1' 77.0 111.3
C4' C3' C2' H2' 215.2 84.1
C4' C3' C2' H2'' 105.8 205.7
C2' C3' C4' O3' 119.1 116.9
C2' C3' C4' H3' 239.3 237.2
C3' C4' C5' H5' 286.5 60.0
C3' C4' C5' H5'' 176.9 299.0
C5' C4' C3' O4' 238.7 241.9
C5' C4' C3' H4' 116.9 124.3
O4' C4' C3' H4' 238.2 242.4
C3' C4' O4' C1' 27.1 347.3
O3' C3' C4' H3' 120.2 120.2
C4' C3' O3' HO3' 294.8 232.0
H4' C4' C5' H5' 46.4 185.7
H4' C4' C5' H5'' 296.8 64.8
C5' C4' H4' O4' 120.4 117.1
C5' C4' H4' C3' 237.8 233.8
O4' C4' H4' C3' 117.4 116.7
H4' C4' O4' C1' 267.1 226.8
H4' C4' C3' O3' 359.6 29.9
H4' C4' C3' H3' 239.4 269.7
N1 C1' O4' C2' 232.7 237.3
N1 C1' O4' H1' 115.5 117.0
O4' C1' C2' C3' 35.9 26.9
O4' C1' C2' H2' 161.2 270.0
O4' C1' C2' H2'' 270.6 149.4
C2' C1' O4' H1' 242.8 239.7
C1' O4' C4' C3' 27.1 347.3
C1' O4' C4' H4' 267.1 226.8
N1 C1' H1' C2' 126.2 124.3
N1 C1' H1' O4' 242.3 242.0
H1' C1' C2' C3' 270.0 268.8
H1' C1' C2' H2' 35.4 151.9
H1' C1' C2' H2'' 144.7 31.3
C2' C1' H1' O4' 116.1 117.7
O3' C3' C2' H2' 330.8 201.1
O3' C3' C2' H2'' 221.4 322.8
C2' C3' O3' C4' 245.2 247.3
C2' C3' O3' H3' 121.1 123.4
O3' C3' C4' H4' 359.6 29.9
C4' C3' O3' H3' 236.0 236.1
H3' C3' C2' H2' 91.3 321.1
H3' C3' C2' H2'' 341.9 82.7
C2' C3' H3' C4' 118.4 117.1
C2' C3' H3' O3' 237.5 238.7
H3' C3' C4' H4' 239.4 269.7
C4' C3' H3' O3' 119.1 121.7
H3' C3' O3' HO3' 58.8 355.9
HO3' O3' C3' H3' 58.8 355.9