PDB Chemical Component OMG

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 OMG

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.491 1.479
P OP2 1.484 1.610
P OP3 1.609 1.609
P O5' 1.597 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.967
O5' C5' 1.423 1.428
C5' C4' 1.507 1.530
C5' H5' 1.116 1.089
C5' H5'' 1.114 1.090
C4' O4' 1.444 1.437
C4' C3' 1.521 1.540
C4' H4' 1.115 1.090
O4' C1' 1.410 1.443
C3' O3' 1.434 1.428
C3' C2' 1.530 1.547
C3' H3' 1.115 1.091
O3' HO3' 0.951 0.967
C2' O2' 1.449 1.429
C2' C1' 1.528 1.549
C2' H2' 1.116 1.091
O2' CM2 1.449 1.429
CM2 HM21 1.116 1.090
CM2 HM22 1.114 1.091
CM2 HM23 1.115 1.090
C1' N9 1.456 1.465
C1' H1' 1.115 1.089
N9 C8 1.377 1.364
N9 C4 1.376 1.369
C8 N7 1.306 1.301
C8 H8 1.102 1.080
N7 C5 1.390 1.355
C5 C6 1.429 1.415
C5 C4 1.387 1.399
C6 O6 1.252 1.220
C6 N1 1.400 1.351
N1 C2 1.386 1.362
N1 HN1 1.020 0.970
C2 N2 1.348 1.373
C2 N3 1.329 1.314
N2 HN21 1.020 0.970
N2 HN22 1.020 0.970
N3 C4 1.358 1.337

Bond Angles for OMG

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.4 109.5
OP1 P OP3 106.3 109.5
OP1 P O5' 109.4 109.5
OP2 P OP3 109.1 109.4
OP2 P O5' 108.3 109.5
P OP2 HOP2 119.4 106.8
OP3 P O5' 103.3 109.5
P OP3 HOP3 106.3 106.9
P O5' C5' 121.4 106.8
O5' C5' C4' 109.9 109.5
O5' C5' H5' 112.0 109.5
O5' C5' H5'' 112.1 109.4
C4' C5' H5' 112.0 109.5
C4' C5' H5'' 112.0 109.4
C5' C4' O4' 107.3 110.0
C5' C4' C3' 115.1 109.9
C5' C4' H4' 105.6 109.9
H5' C5' H5'' 98.4 109.5
O4' C4' C3' 103.9 107.3
O4' C4' H4' 116.5 109.9
C4' O4' C1' 109.5 107.0
C3' C4' H4' 108.9 109.8
C4' C3' O3' 112.0 110.7
C4' C3' C2' 103.0 104.2
C4' C3' H3' 113.1 110.5
O4' C1' C2' 108.4 103.5
O4' C1' N9 108.1 110.6
O4' C1' H1' 113.1 110.6
O3' C3' C2' 112.1 110.5
O3' C3' H3' 104.1 110.4
C3' O3' HO3' 112.0 106.8
C2' C3' H3' 112.9 110.5
C3' C2' O2' 115.4 110.9
C3' C2' C1' 102.6 102.1
C3' C2' H2' 110.4 110.9
O2' C2' C1' 109.9 110.9
O2' C2' H2' 103.1 110.8
C2' O2' CM2 119.4 106.8
C1' C2' H2' 115.8 110.9
C2' C1' N9 114.8 110.8
C2' C1' H1' 106.1 110.6
O2' CM2 HM21 119.4 109.5
O2' CM2 HM22 108.7 109.5
O2' CM2 HM23 108.6 109.5
HM21 CM2 HM22 108.7 109.4
HM21 CM2 HM23 108.5 109.5
HM22 CM2 HM23 101.4 109.5
N9 C1' H1' 106.4 110.5
C1' N9 C8 127.0 126.2
C1' N9 C4 126.6 126.2
C8 N9 C4 106.4 107.5
N9 C8 N7 113.4 109.8
N9 C8 H8 125.6 125.1
N9 C4 C5 105.2 106.0
N9 C4 N3 125.9 134.3
N7 C8 H8 121.0 125.1
C8 N7 C5 104.2 109.3
N7 C5 C6 130.3 134.1
N7 C5 C4 110.8 107.3
C6 C5 C4 118.9 118.6
C5 C6 O6 128.7 120.9
C5 C6 N1 111.3 118.4
C5 C4 N3 128.9 119.7
O6 C6 N1 120.0 120.8
C6 N1 C2 125.3 120.3
C6 N1 HN1 117.9 119.9
C2 N1 HN1 116.8 119.8
N1 C2 N2 116.3 119.0
N1 C2 N3 123.8 121.9
N2 C2 N3 119.8 119.0
C2 N2 HN21 116.4 120.0
C2 N2 HN22 109.8 120.0
C2 N3 C4 111.9 121.2
HN21 N2 HN22 109.6 120.0

Torsion Angles for OMG

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 236.3 119.9
OP2 P OP1 O5' 125.4 240.0
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 249.1 120.1
OP1 P OP3 HOP3 180.0 180.0
OP1 P O5' C5' 80.3 60.0
OP1 P OP2 OP3 122.4 240.0
OP1 P OP2 O5' 234.1 120.0
OP3 P OP2 O5' 111.7 240.0
OP2 P OP3 HOP3 309.9 60.1
OP2 P O5' C5' 308.7 180.0
OP1 P OP3 OP2 230.1 120.0
OP1 P OP3 O5' 115.1 239.9
OP2 P OP3 O5' 245.0 119.9
OP3 P OP2 HOP2 57.6 60.0
OP3 P O5' C5' 193.2 299.9
OP1 P O5' OP2 131.6 240.0
OP1 P O5' OP3 247.1 120.1
OP2 P O5' OP3 115.6 240.1
O5' P OP2 HOP2 305.9 180.0
O5' P OP3 HOP3 64.9 300.1
P O5' C5' C4' 108.2 180.1
P O5' C5' H5' 233.5 60.0
P O5' C5' H5'' 343.0 300.0
HOP2 OP2 P OP3 57.6 60.0
HOP2 OP2 P O5' 305.9 180.0
HOP3 OP3 P O5' 64.9 300.1
C4' C5' O5' H5' 234.8 120.0
C4' C5' O5' H5'' 125.3 240.1
O5' C5' C4' O4' 292.5 62.1
O5' C5' C4' C3' 47.6 180.0
O5' C5' C4' H4' 167.7 301.0
H5' C5' O5' H5'' 250.5 120.0
O5' C5' C4' H5' 125.2 240.0
O5' C5' C4' H5'' 234.7 119.9
H5' C5' C4' H5'' 109.5 240.0
O4' C4' C5' C3' 244.9 242.1
O4' C4' C5' H4' 124.9 121.1
C5' C4' O4' C1' 150.8 146.0
C3' C4' C5' H4' 239.9 239.0
C5' C4' C3' O3' 86.7 119.6
C5' C4' C3' C2' 207.3 238.4
C5' C4' C3' H3' 329.5 357.0
O5' C5' H5' C4' 236.0 120.0
O5' C5' H5' H5'' 118.0 240.0
C4' C5' H5' H5'' 242.0 120.0
H5' C5' C4' O4' 167.3 182.1
H5' C5' C4' C3' 282.4 300.0
H5' C5' C4' H4' 42.4 61.0
O5' C5' H5'' C4' 124.1 240.0
O5' C5' H5'' H5' 242.0 120.0
C4' C5' H5'' H5' 118.0 240.0
H5'' C5' C4' O4' 57.8 302.1
H5'' C5' C4' C3' 172.9 60.1
H5'' C5' C4' H4' 292.9 181.0
O4' C4' C5' H5' 167.3 182.1
O4' C4' C5' H5'' 57.8 302.1
C5' C4' O4' C3' 122.3 119.5
C5' C4' O4' H4' 242.0 238.9
C3' C4' O4' H4' 119.7 119.4
O4' C4' C3' O3' 203.7 239.2
O4' C4' C3' C2' 324.4 358.0
O4' C4' C3' H3' 86.6 116.6
C4' O4' C1' C2' 350.5 320.0
C4' O4' C1' N9 225.5 201.3
C4' O4' C1' H1' 107.9 78.5
C3' C4' C5' H5' 282.4 300.0
C3' C4' C5' H5'' 172.9 60.1
C5' C4' C3' O4' 243.0 240.4
C5' C4' C3' H4' 118.2 121.0
O4' C4' C3' H4' 235.3 240.6
C3' C4' O4' C1' 28.5 26.5
O3' C3' C4' C2' 239.4 241.2
O3' C3' C4' H3' 117.2 122.6
C4' C3' O3' HO3' 180.0 294.9
C2' C3' C4' H3' 237.8 241.4
C4' C3' C2' O2' 269.9 220.9
C4' C3' C2' C1' 29.4 339.1
C4' C3' C2' H2' 153.4 97.3
H4' C4' C5' H5' 42.4 61.0
H4' C4' C5' H5'' 292.9 181.0
C5' C4' H4' O4' 118.9 121.2
C5' C4' H4' C3' 235.9 239.0
O4' C4' H4' C3' 117.0 117.8
H4' C4' O4' C1' 268.8 267.1
H4' C4' C3' O3' 328.5 358.6
H4' C4' C3' C2' 89.1 117.4
H4' C4' C3' H3' 211.3 236.0
C1' O4' C4' C3' 28.5 26.5
C1' O4' C4' H4' 268.8 267.1
C3' C2' C1' O4' 346.7 37.0
O2' C2' C1' O4' 110.0 155.2
O4' C1' C2' H2' 226.4 278.8
C2' C1' O4' N9 125.1 118.7
C2' C1' O4' H1' 242.6 241.5
N9 C1' O4' H1' 117.6 122.8
O4' C1' N9 C8 353.2 28.4
O4' C1' N9 C4 174.9 208.3
O3' C3' C4' H4' 328.5 358.6
C4' C3' O3' C2' 115.2 114.9
C4' C3' O3' H3' 237.5 237.4
C2' C3' O3' H3' 122.4 122.5
O3' C3' C2' O2' 30.4 339.8
O3' C3' C2' C1' 149.9 98.0
O3' C3' C2' H2' 274.0 216.2
C2' C3' C4' H4' 89.1 117.4
C4' C3' C2' O3' 239.5 241.1
C4' C3' C2' H3' 122.3 118.6
O4' C1' C2' C3' 346.7 37.0
O3' C3' C2' H3' 242.8 237.5
C2' C3' O3' HO3' 64.9 180.0
O2' C2' C3' C1' 240.5 241.8
O2' C2' C3' H2' 116.4 123.6
C3' C2' O2' CM2 192.5 265.7
C1' C2' C3' H2' 236.0 241.8
C3' C2' C1' N9 107.7 155.6
C3' C2' C1' H1' 225.0 278.5
H3' C3' C4' H4' 211.3 236.0
C4' C3' H3' O3' 121.7 122.7
C4' C3' H3' C2' 243.6 245.3
O3' C3' H3' C2' 121.8 122.5
H3' C3' O3' HO3' 302.5 57.5
H3' C3' C2' O2' 147.6 102.3
H3' C3' C2' C1' 267.1 220.5
H3' C3' C2' H2' 31.2 338.7
HO3' O3' C3' C2' 64.9 180.0
HO3' O3' C3' H3' 302.5 57.5
O4' C1' C2' O2' 110.0 155.2
O2' C2' C3' H3' 147.6 102.3
C3' C2' O2' C1' 115.4 112.7
C3' C2' O2' H2' 239.5 236.3
C1' C2' O2' H2' 124.1 123.6
O2' C2' C1' N9 231.0 273.8
O2' C2' C1' H1' 348.2 36.7
C2' O2' CM2 HM21 179.9 180.0
C2' O2' CM2 HM22 305.3 299.9
C2' O2' CM2 HM23 54.8 60.0
O4' C1' C2' N9 239.0 241.4
O4' C1' C2' H1' 121.8 118.5
C1' C2' C3' H3' 267.1 220.5
C3' C2' C1' O2' 236.7 241.8
C3' C2' C1' H2' 120.3 118.2
O2' C2' C1' H2' 243.6 236.4
C1' C2' O2' CM2 77.1 152.9
N9 C1' C2' H1' 242.8 237.1
C2' C1' N9 C8 232.0 274.3
C2' C1' N9 C4 53.7 94.1
H2' C2' C3' H3' 31.2 338.7
C3' C2' H2' O2' 123.8 123.6
C3' C2' H2' C1' 243.9 247.3
O2' C2' H2' C1' 120.1 123.6
H2' C2' O2' CM2 313.0 29.3
H2' C2' C1' N9 347.4 37.4
H2' C2' C1' H1' 104.6 160.3
CM2 O2' C2' C1' 77.1 152.9
CM2 O2' C2' H2' 313.0 29.3
HM21 CM2 O2' HM22 234.6 240.1
HM21 CM2 O2' HM23 125.1 120.1
HM22 CM2 O2' HM23 250.5 240.0
O2' CM2 HM21 HM22 125.4 120.0
O2' CM2 HM21 HM23 234.8 239.9
HM22 CM2 HM21 HM23 109.5 120.0
O2' CM2 HM22 HM21 228.6 240.0
O2' CM2 HM22 HM23 114.3 120.0
HM21 CM2 HM22 HM23 245.8 240.0
O2' CM2 HM23 HM21 131.3 120.0
O2' CM2 HM23 HM22 245.7 240.0
HM21 CM2 HM23 HM22 114.4 120.0
O4' C1' N9 C2' 121.2 114.2
O4' C1' N9 H1' 238.2 237.1
N9 C1' C2' H2' 347.4 37.4
C2' C1' N9 H1' 117.1 122.9
C8 N9 C1' C4 178.3 180.1
C1' N9 C8 N7 182.6 180.0
C1' N9 C8 H8 2.6 0.2
C1' N9 C4 C5 177.3 179.8
C1' N9 C4 N3 358.6 0.6
O4' C1' H1' C2' 241.3 245.9
O4' C1' H1' N9 118.6 122.9
H1' C1' C2' H2' 104.6 160.3
C2' C1' H1' N9 237.3 237.0
H1' C1' N9 C8 114.9 151.3
H1' C1' N9 C4 296.7 331.2
C8 N9 C1' H1' 114.9 151.3
C1' N9 C8 C4 181.4 179.9
C8 N9 C4 C5 358.8 359.7
C8 N9 C4 N3 180.1 180.5
N7 C8 N9 H8 180.0 179.8
N9 C8 N7 C5 359.5 0.1
C4 N9 C1' H1' 296.7 331.2
C1' N9 C4 C8 178.6 180.1
C4 N9 C8 N7 1.1 0.1
C4 N9 C8 H8 181.2 180.3
N7 C5 C4 N9 1.0 0.4
C6 C5 C4 N9 181.7 180.1
C5 C4 N9 N3 178.7 179.2
C2 N3 C4 N9 178.3 179.6
N7 C8 N9 C4 1.1 0.1
N9 C8 N7 H8 180.0 180.2
C8 N7 C5 C6 178.9 180.0
C8 N7 C5 C4 359.7 359.7
H8 C8 N9 C4 181.2 180.3
N9 C8 H8 N7 180.0 179.8
H8 C8 N7 C5 179.5 179.9
N9 C4 C5 N7 1.0 0.4
C5 N7 C8 H8 179.5 179.9
C6 C5 N7 C4 179.2 180.3
N7 C5 C6 O6 0.6 359.9
N7 C5 C6 N1 180.6 179.9
N7 C5 C4 N3 179.6 179.7
N9 C4 C5 C6 181.7 180.1
N7 C5 C6 C4 180.8 179.7
C6 C5 C4 N3 0.3 359.4
O6 C6 C5 N1 180.0 180.0
C5 C6 N1 C2 359.9 0.0
C5 C6 N1 HN1 180.0 179.9
N9 C4 C5 N3 181.4 180.7
N7 C5 C4 C6 179.3 180.3
C4 C5 C6 O6 179.8 180.3
C4 C5 C6 N1 359.8 0.3
C2 N3 C4 C5 360.0 0.6
O6 C6 C5 C4 179.8 180.3
C5 C6 O6 N1 180.0 180.0
O6 C6 N1 C2 179.9 180.0
O6 C6 N1 HN1 360.0 359.9
N1 C6 C5 C4 359.8 0.3
C5 C6 N1 O6 180.0 180.0
C2 N1 C6 HN1 179.9 180.1
C6 N1 C2 N2 180.5 179.9
C6 N1 C2 N3 0.4 360.0
C6 N1 C2 HN1 180.1 179.9
N2 C2 N1 N3 180.1 180.0
N1 C2 N2 HN21 179.9 180.0
N1 C2 N2 HN22 54.7 360.0
N1 C2 N3 C4 359.7 359.8
C6 N1 HN1 C2 179.9 180.1
HN1 N1 C2 N2 0.4 0.0
HN1 N1 C2 N3 180.3 180.0
N2 C2 N1 HN1 0.4 0.0
N1 C2 N2 N3 179.9 180.0
N2 C2 N3 C4 179.6 179.8
HN21 N2 C2 HN22 125.2 180.0
N9 C4 N3 C2 178.3 179.6
C5 C4 N3 C2 360.0 0.6
N3 C2 N1 HN1 180.3 180.0
N1 C2 N3 N2 180.1 180.0
N3 C2 N2 HN21 0.0 360.0
N3 C2 N2 HN22 234.8 180.0
HN21 N2 C2 N3 0.0 360.0
C2 N2 HN21 HN22 234.7 180.0
HN22 N2 C2 N3 234.8 180.0
C2 N2 HN22 HN21 129.0 180.0
N9 C4 N3 C5 178.4 179.1