PDB Chemical Component GOM

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 GOM

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N CA 1.458 1.468
N HN2 1.020 1.009
N HN3 1.020 1.009
N H 1.020 1.009
C CA 1.536 1.530
C OP3 1.425 1.429
C HC1 1.115 1.090
C HC2 1.115 1.090
CA CB 1.530 1.530
CA HA 1.115 1.090
CB CG 1.517 1.530
CB HB1 1.115 1.090
CB HB2 1.115 1.090
CG CD 1.512 1.507
CG HG1 1.115 1.090
CG HG2 1.115 1.090
CD OE1 1.253 1.219
CD OE2 1.244 1.220
P OP1 1.487 1.544
P OP2 1.494 1.545
P OP3 1.596 1.610
P O5' 1.594 1.610
O5' C5' 1.424 1.429
C5' C4' 1.524 1.529
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.091
C4' O4' 1.458 1.445
C4' C3' 1.533 1.544
C4' H4' 1.115 1.090
O4' C1' 1.415 1.444
C1' N9 1.465 1.464
C1' C2' 1.529 1.545
C1' H1' 1.115 1.091
N9 C4 1.374 1.372
N9 C8 1.375 1.363
C4 N3 1.347 1.329
C4 C5 1.382 1.406
N3 C2 1.330 1.316
C2 N1 1.340 1.321
C2 H2 1.103 1.080
N1 C6 1.354 1.330
C6 N6 1.331 1.383
C6 C5 1.405 1.405
N6 HN61 1.020 0.970
N6 HN62 1.020 0.970
C5 N7 1.388 1.355
N7 C8 1.314 1.302
C8 H8 1.103 1.080
C2' O2' 1.412 1.429
C2' C3' 1.527 1.547
C2' H2' 1.115 1.090
O2' HO2' 0.950 0.967
C3' O3' 1.429 1.429
C3' H3' 1.115 1.090
O3' HO3' 0.950 0.967

Bond Angles for GOM

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
CA N HN2 111.6 109.5
CA N HN3 111.1 109.5
CA N H 111.6 109.5
N CA C 111.1 109.5
N CA CB 109.5 109.5
N CA HA 108.4 109.5
HN2 N HN3 111.6 109.5
HN2 N H 98.8 109.4
HN3 N H 111.6 109.4
CA C OP3 110.3 109.5
CA C HC1 111.9 109.4
CA C HC2 111.9 109.5
C CA CB 109.9 109.5
C CA HA 108.1 109.4
OP3 C HC1 111.9 109.4
OP3 C HC2 111.9 109.5
C OP3 P 121.1 106.8
HC1 C HC2 98.5 109.5
CB CA HA 109.8 109.4
CA CB CG 114.4 109.4
CA CB HB1 110.4 109.5
CA CB HB2 110.4 109.5
CG CB HB1 110.4 109.5
CG CB HB2 110.4 109.5
CB CG CD 112.5 109.4
CB CG HG1 111.1 109.5
CB CG HG2 111.1 109.5
HB1 CB HB2 99.9 109.5
CD CG HG1 111.1 109.5
CD CG HG2 111.1 109.5
CG CD OE1 119.3 120.0
CG CD OE2 117.3 120.0
HG1 CG HG2 99.2 109.5
OE1 CD OE2 123.4 120.0
OP1 P OP2 119.4 109.5
OP1 P OP3 107.0 109.5
OP1 P O5' 109.6 109.4
OP2 P OP3 108.7 109.4
OP2 P O5' 106.7 109.4
OP3 P O5' 104.5 109.5
P O5' C5' 121.7 106.8
O5' C5' C4' 110.5 109.5
O5' C5' H5' 111.8 109.5
O5' C5' H5'' 111.8 109.4
C4' C5' H5' 111.8 109.5
C4' C5' H5'' 111.8 109.5
C5' C4' O4' 109.4 110.4
C5' C4' C3' 111.8 110.5
C5' C4' H4' 106.8 110.3
H5' C5' H5'' 98.6 109.5
O4' C4' C3' 105.6 104.8
O4' C4' H4' 112.9 110.4
C4' O4' C1' 110.1 105.3
C3' C4' H4' 110.5 110.4
C4' C3' C2' 106.7 104.1
C4' C3' O3' 117.5 110.5
C4' C3' H3' 109.7 110.5
O4' C1' N9 111.2 110.4
O4' C1' C2' 110.2 104.9
O4' C1' H1' 111.8 110.4
N9 C1' C2' 118.7 110.4
N9 C1' H1' 101.6 110.3
C1' N9 C4 123.3 126.3
C1' N9 C8 130.9 126.3
C2' C1' H1' 102.8 110.4
C1' C2' O2' 108.4 110.8
C1' C2' C3' 101.6 104.0
C1' C2' H2' 115.7 110.4
C4 N9 C8 105.8 107.4
N9 C4 N3 127.0 134.9
N9 C4 C5 105.9 106.0
N9 C8 N7 113.7 110.0
N9 C8 H8 125.2 125.0
N3 C4 C5 127.0 119.1
C4 N3 C2 110.6 120.6
C4 C5 C6 116.8 118.1
C4 C5 N7 110.7 107.1
N3 C2 N1 129.1 122.5
N3 C2 H2 115.0 118.8
N1 C2 H2 115.8 118.7
C2 N1 C6 118.6 121.2
N1 C6 N6 118.4 120.8
N1 C6 C5 117.8 118.5
N6 C6 C5 123.8 120.8
C6 N6 HN61 109.0 120.0
C6 N6 HN62 118.4 120.0
C6 C5 N7 132.5 134.7
HN61 N6 HN62 109.0 119.9
C5 N7 C8 103.9 109.4
N7 C8 H8 121.2 125.0
O2' C2' C3' 111.3 110.5
O2' C2' H2' 106.8 110.5
C2' O2' HO2' 108.4 106.7
C3' C2' H2' 113.0 110.5
C2' C3' O3' 118.3 110.5
C2' C3' H3' 108.7 110.5
O3' C3' H3' 94.9 110.5
C3' O3' HO3' 117.6 106.8

Torsion Angles for GOM

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
HN2 N CA HN3 234.7 239.9
HN2 N CA H 109.5 120.0
HN3 N CA H 234.8 240.0
N CA C OP3 32.2 64.9
N CA C HC1 266.9 305.0
N CA C HC2 157.4 185.0
C CA N CB 121.6 120.0
C CA N HA 241.3 240.0
CB CA N HA 119.8 120.0
N CA CB CG 178.4 295.0
N CA CB HB1 53.2 55.0
N CA CB HB2 303.7 175.0
CA N HN2 HN3 125.0 120.0
CA N HN2 H 242.5 240.0
HN2 N CA C 54.7 300.0
HN2 N CA CB 293.2 180.0
HN2 N CA HA 173.4 60.0
HN3 N HN2 H 117.5 120.0
CA N HN3 HN2 234.7 240.0
CA N HN3 H 125.2 120.0
HN3 N CA C 180.0 60.0
HN3 N CA CB 58.5 300.0
HN3 N CA HA 298.7 180.0
HN2 N HN3 H 250.5 240.0
CA N H HN2 117.5 120.0
CA N H HN3 235.0 240.0
H N CA C 305.3 180.0
H N CA CB 183.7 60.0
H N CA HA 63.9 300.0
HN2 N H HN3 117.5 120.0
C CA N HN2 54.7 300.0
C CA N HN3 180.0 60.0
C CA N H 305.3 180.0
N CA C CB 238.7 240.0
N CA C HA 118.9 120.0
OP3 C CA HC1 125.3 119.9
OP3 C CA HC2 234.8 239.9
CA C OP3 P 180.6 180.0
HC1 C CA HC2 109.5 120.0
CB CA C HA 240.2 240.1
C CA CB CG 56.1 175.0
C CA CB HB1 290.9 295.0
C CA CB HB2 181.4 55.0
CA C OP3 HC1 234.7 240.1
CA C OP3 HC2 125.2 120.1
OP3 C CA CB 153.5 185.0
OP3 C CA HA 273.3 304.9
HC1 C OP3 HC2 250.5 240.0
OP1 P OP3 C 122.2 305.1
OP2 P OP3 C 252.4 65.1
C OP3 P O5' 6.0 185.0
CA C HC1 OP3 124.4 119.9
CA C HC1 HC2 242.2 239.9
HC1 C CA CB 28.3 65.1
HC1 C CA HA 148.0 185.0
OP3 C HC1 HC2 117.8 120.0
HC1 C OP3 P 305.9 299.9
CA C HC2 OP3 235.6 240.0
CA C HC2 HC1 117.8 120.0
HC2 C CA CB 278.8 305.0
HC2 C CA HA 38.5 65.0
OP3 C HC2 HC1 242.2 240.1
HC2 C OP3 P 55.4 59.9
CB CA N HN2 293.2 180.0
CB CA N HN3 58.5 300.0
CB CA N H 183.7 60.0
N CA CB C 122.3 120.0
N CA CB HA 241.1 239.9
CB CA C OP3 153.5 185.0
CB CA C HC1 28.3 65.1
CB CA C HC2 278.8 305.0
C CA CB HA 118.7 119.9
CG CB CA HB1 125.3 240.0
CG CB CA HB2 234.7 120.0
CA CB CG CD 176.8 180.0
CA CB CG HG1 51.5 300.0
CA CB CG HG2 302.0 60.0
HB1 CB CA HB2 109.5 240.0
HA CA N HN2 173.4 60.0
HA CA N HN3 298.7 180.0
HA CA N H 63.9 300.0
N CA HA C 239.4 240.0
N CA HA CB 119.6 120.0
HA CA C OP3 273.3 304.9
HA CA C HC1 148.0 185.0
HA CA C HC2 38.5 65.0
C CA HA CB 240.2 240.1
HA CA CB CG 297.4 55.0
HA CA CB HB1 172.1 175.1
HA CA CB HB2 62.7 295.0
CG CB CA HA 297.4 55.0
CA CB CG HB1 234.7 120.0
CA CB CG HB2 125.3 240.0
HB1 CB CG HB2 250.5 120.0
CD CG CB HG1 125.2 240.0
CD CG CB HG2 234.7 120.0
CB CG CD OE1 281.7 0.0
CB CG CD OE2 101.2 179.9
HG1 CG CB HG2 109.5 240.0
HB1 CB CA HA 172.1 175.1
CA CB HB1 CG 127.5 240.0
CA CB HB1 HB2 243.7 120.0
CG CB HB1 HB2 116.2 240.0
HB1 CB CG CD 302.0 60.0
HB1 CB CG HG1 176.8 180.0
HB1 CB CG HG2 67.3 300.0
HB2 CB CA HA 62.7 295.0
CA CB HB2 CG 232.5 120.0
CA CB HB2 HB1 116.2 240.0
CG CB HB2 HB1 243.8 120.0
HB2 CB CG CD 51.5 300.0
HB2 CB CG HG1 286.2 60.0
HB2 CB CG HG2 176.8 180.0
CD CG CB HB1 302.0 60.0
CD CG CB HB2 51.5 300.0
CB CG CD HG1 234.8 120.0
CB CG CD HG2 125.3 240.0
HG1 CG CD HG2 250.5 120.0
OE1 CD CG OE2 180.5 180.1
HG1 CG CB HB1 176.8 180.0
HG1 CG CB HB2 286.2 60.0
CB CG HG1 CD 126.0 240.0
CB CG HG1 HG2 243.0 120.0
CD CG HG1 HG2 117.0 240.0
HG1 CG CD OE1 46.9 240.0
HG1 CG CD OE2 226.4 59.9
HG2 CG CB HB1 67.3 300.0
HG2 CG CB HB2 176.8 180.0
CB CG HG2 CD 234.0 120.0
CB CG HG2 HG1 117.0 240.0
CD CG HG2 HG1 243.0 120.0
HG2 CG CD OE1 156.4 120.0
HG2 CG CD OE2 335.9 299.9
OE1 CD CG HG1 46.9 240.0
OE1 CD CG HG2 156.4 120.0
CG CD OE1 OE2 179.4 179.9
OE2 CD CG HG1 226.4 59.9
OE2 CD CG HG2 335.9 299.9
CG CD OE2 OE1 180.6 180.1
C OP3 P OP1 122.2 305.1
OP2 P OP1 OP3 236.2 240.0
OP2 P OP1 O5' 123.4 120.0
OP3 P OP1 O5' 247.2 240.0
OP1 P O5' C5' 336.5 55.0
C OP3 P OP2 252.4 65.1
OP1 P OP2 OP3 123.0 120.1
OP1 P OP2 O5' 235.2 240.0
OP3 P OP2 O5' 112.2 120.0
OP2 P O5' C5' 205.9 295.0
P OP3 C HC1 305.9 299.9
P OP3 C HC2 55.4 59.9
OP1 P OP3 OP2 229.9 240.0
OP1 P OP3 O5' 116.2 120.0
OP2 P OP3 O5' 246.4 240.0
OP3 P O5' C5' 90.9 175.1
OP1 P O5' OP2 130.6 120.0
OP1 P O5' OP3 245.6 239.9
OP2 P O5' OP3 115.0 120.0
P O5' C5' C4' 188.4 180.0
P O5' C5' H5' 63.1 59.9
P O5' C5' H5'' 313.7 300.0
C4' C5' O5' H5' 125.3 120.1
C4' C5' O5' H5'' 234.7 240.0
O5' C5' C4' O4' 290.6 66.4
O5' C5' C4' C3' 47.2 181.9
O5' C5' C4' H4' 168.2 304.2
H5' C5' O5' H5'' 109.5 120.0
O5' C5' C4' H5' 234.8 239.9
O5' C5' C4' H5'' 125.2 119.9
H5' C5' C4' H5'' 250.5 240.0
O4' C4' C5' C3' 243.4 244.5
O4' C4' C5' H4' 122.4 122.2
C5' C4' O4' C1' 113.1 159.4
C3' C4' C5' H4' 239.0 237.7
C5' C4' C3' C2' 261.1 217.1
C5' C4' C3' O3' 125.5 98.4
C5' C4' C3' H3' 18.7 335.8
O5' C5' H5' C4' 124.5 120.1
O5' C5' H5' H5'' 242.3 240.1
C4' C5' H5' H5'' 117.8 120.0
H5' C5' C4' O4' 55.8 186.5
H5' C5' C4' C3' 172.5 301.9
H5' C5' C4' H4' 293.4 64.3
O5' C5' H5'' C4' 235.5 240.0
O5' C5' H5'' H5' 117.7 120.0
C4' C5' H5'' H5' 242.2 240.0
H5'' C5' C4' O4' 165.4 306.5
H5'' C5' C4' C3' 282.0 61.9
H5'' C5' C4' H4' 42.9 184.2
O4' C4' C5' H5' 55.8 186.5
O4' C4' C5' H5'' 165.4 306.5
C5' C4' O4' C3' 120.5 119.0
C5' C4' O4' H4' 241.3 237.8
C3' C4' O4' H4' 120.8 118.8
O4' C4' C3' C2' 20.0 336.0
O4' C4' C3' O3' 244.4 217.3
O4' C4' C3' H3' 137.6 94.7
C4' O4' C1' N9 218.2 200.7
C4' O4' C1' C2' 351.8 319.6
C4' O4' C1' H1' 105.4 78.5
C3' C4' C5' H5' 172.5 301.9
C3' C4' C5' H5'' 282.0 61.9
C5' C4' C3' O4' 241.1 241.1
C5' C4' C3' H4' 118.8 122.3
O4' C4' C3' H4' 237.6 241.2
C3' C4' O4' C1' 352.6 40.5
C1' C2' C3' C4' 336.3 0.1
O2' C2' C3' C4' 221.1 241.2
C4' C3' C2' H2' 101.0 118.6
C2' C3' C4' O3' 135.6 118.7
C2' C3' C4' H3' 242.4 241.3
O3' C3' C4' H3' 106.8 122.6
C4' C3' O3' HO3' 180.0 180.0
H4' C4' C5' H5' 293.4 64.3
H4' C4' C5' H5'' 42.9 184.2
C5' C4' H4' O4' 120.2 122.2
C5' C4' H4' C3' 238.2 237.6
O4' C4' H4' C3' 118.0 115.4
H4' C4' O4' C1' 231.8 281.6
H4' C4' C3' C2' 142.4 94.8
H4' C4' C3' O3' 6.7 336.1
H4' C4' C3' H3' 259.9 213.5
C1' O4' C4' C3' 352.6 40.5
C1' O4' C4' H4' 231.8 281.6
N9 C1' O4' C2' 226.3 241.1
N9 C1' O4' H1' 112.8 122.2
O4' C1' N9 C4 252.7 202.1
O4' C1' N9 C8 75.2 22.1
C2' C1' O4' H1' 246.4 241.1
O4' C1' C2' O2' 137.3 142.6
O4' C1' C2' C3' 19.9 23.8
O4' C1' C2' H2' 257.1 265.3
O4' C1' N9 C2' 129.3 115.5
O4' C1' N9 H1' 241.0 237.8
C2' C1' N9 H1' 111.7 122.2
N9 C1' C2' O2' 267.0 261.5
N9 C1' C2' C3' 149.7 142.8
N9 C1' C2' H2' 26.9 24.2
C4 N9 C1' C8 177.6 180.0
C1' N9 C4 N3 2.8 360.0
C1' N9 C4 C5 183.6 180.3
C1' N9 C8 N7 176.2 180.0
C1' N9 C8 H8 356.2 359.9
C4' C3' C2' C1' 336.3 0.1
O4' C1' C2' N9 230.3 241.1
O4' C1' C2' H1' 119.2 118.9
N9 C1' C2' H1' 249.0 237.8
C2' C1' N9 C4 123.4 86.5
C2' C1' N9 C8 305.9 266.6
O2' C2' C1' C3' 117.4 118.7
O2' C2' C1' H2' 240.2 237.3
C1' C2' O2' HO2' 180.0 183.8
C3' C2' C1' H2' 122.8 118.6
C1' C2' C3' O3' 111.5 118.8
C1' C2' C3' H3' 218.1 241.4
O4' C1' H1' N9 118.6 122.2
O4' C1' H1' C2' 241.9 244.5
N9 C1' H1' C2' 123.3 122.3
H1' C1' N9 C4 11.8 324.3
H1' C1' N9 C8 194.2 144.3
H1' C1' C2' O2' 18.1 23.7
H1' C1' C2' C3' 260.7 265.0
H1' C1' C2' H2' 137.9 146.4
C4 N9 C1' C2' 123.4 86.5
C4 N9 C1' H1' 11.8 324.3
C1' N9 C4 C8 181.9 180.0
C4 N9 C8 N7 358.4 0.0
C4 N9 C8 H8 178.3 179.9
N3 C4 N9 C5 179.1 179.7
N9 C4 N3 C2 181.4 180.0
N9 C4 C5 C6 178.5 180.4
N9 C4 C5 N7 358.7 359.6
C8 N9 C1' C2' 305.9 266.6
C8 N9 C1' H1' 194.2 144.3
C1' N9 C8 C4 177.9 180.0
C8 N9 C4 N3 180.9 180.0
C8 N9 C4 C5 1.7 0.2
C5 N7 C8 N9 0.8 359.7
N7 C8 N9 H8 180.0 180.1
N3 C4 N9 C8 180.9 180.0
N9 C4 N3 C5 181.0 180.3
N3 C4 C5 C6 359.3 0.6
N3 C4 C5 N7 179.5 179.8
C4 N3 C2 N1 0.1 0.1
C4 N3 C2 H2 180.1 180.0
C5 C4 N9 C8 1.7 0.2
N9 C4 C5 N3 179.1 179.8
C5 C4 N3 C2 0.4 359.6
N1 C6 C5 C4 0.5 359.4
N6 C6 C5 C4 180.9 179.7
C6 C5 C4 N7 179.8 180.8
C4 C5 N7 C8 0.3 0.5
C2 N3 C4 C5 0.4 359.6
N1 C2 N3 H2 180.0 180.0
N3 C2 N1 C6 359.8 359.9
N3 C2 N1 H2 180.0 180.0
C2 N1 C6 N6 179.5 180.0
C2 N1 C6 C5 359.9 0.3
N3 C2 H2 N1 180.0 180.0
H2 C2 N1 C6 179.8 180.0
C4 C5 C6 N1 0.5 359.4
C6 N1 C2 H2 179.8 180.0
N6 C6 N1 C5 179.6 179.7
N1 C6 N6 HN61 54.7 0.0
N1 C6 N6 HN62 180.0 179.7
N1 C6 C5 N7 180.3 180.5
C4 C5 C6 N6 180.9 179.7
N1 C6 N6 C5 180.4 180.3
N6 C6 C5 N7 0.6 0.8
HN61 N6 C6 HN62 234.7 180.3
C4 C5 C6 N7 180.2 178.9
N1 C6 C5 N6 179.6 179.7
C5 C6 N6 HN61 234.4 179.7
C5 C6 N6 HN62 359.6 359.4
C6 C5 N7 C8 180.6 179.5
HN61 N6 C6 C5 234.4 179.7
C6 N6 HN61 HN62 130.6 179.7
HN62 N6 C6 C5 359.6 359.4
C6 N6 HN62 HN61 234.7 180.3
N9 C8 N7 C5 0.8 359.7
C4 C5 N7 C6 179.8 181.0
C5 N7 C8 H8 180.8 179.8
N9 C8 N7 H8 180.0 179.9
N9 C8 H8 N7 180.0 180.1
C4' C3' C2' O2' 221.1 241.2
O2' C2' C1' H1' 18.1 23.7
C1' C2' O2' C3' 249.0 245.3
C1' C2' O2' H2' 125.3 122.6
C3' C2' O2' H2' 236.3 237.3
O2' C2' C3' O3' 356.3 359.9
O2' C2' C3' H3' 102.9 122.5
C2' C3' C4' H4' 142.4 94.8
C4' C3' C2' O3' 224.8 241.3
C4' C3' C2' H3' 118.3 118.7
C3' C2' C1' H1' 260.7 265.0
C1' C2' C3' O2' 115.2 118.9
C1' C2' C3' H2' 235.3 241.5
O2' C2' C3' H2' 120.1 122.7
C3' C2' O2' HO2' 290.9 298.5
O3' C3' C2' H3' 253.5 237.4
C2' C3' O3' HO3' 49.5 65.3
H2' C2' C1' H1' 137.9 146.4
C1' C2' H2' O2' 239.3 237.2
C1' C2' H2' C3' 116.6 114.5
O2' C2' H2' C3' 237.3 237.3
H2' C2' O2' HO2' 54.7 61.2
H2' C2' C3' O3' 236.2 237.3
H2' C2' C3' H3' 342.7 359.9
HO2' O2' C2' C3' 290.9 298.5
HO2' O2' C2' H2' 54.7 61.2
O3' C3' C4' H4' 6.7 336.1
C4' C3' O3' C2' 130.5 114.7
C4' C3' O3' H3' 244.7 237.3
O3' C3' C2' H2' 236.2 237.3
C2' C3' O3' H3' 114.3 122.6
H3' C3' C4' H4' 259.9 213.5
C4' C3' H3' C2' 243.7 245.3
C4' C3' H3' O3' 121.6 122.7
H3' C3' C2' H2' 342.7 359.9
C2' C3' H3' O3' 237.9 237.4
H3' C3' O3' HO3' 295.2 302.7
HO3' O3' C3' H3' 295.2 302.7