PDB Chemical Component GMS

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 GMS

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.492 1.481
P SE 2.131 2.269
P O5' 1.598 1.610
P OP2   1.610
SE HS 1.500 1.560
O5' C5' 1.454 1.429
N9 C4 1.359 1.368
N9 C8 1.357 1.364
N9 C1' 1.450 1.465
C4 N3 1.346 1.338
C4 C5 1.368 1.399
N3 C2 1.297 1.314
C2 N2 1.314 1.373
C2 N1 1.385 1.363
N2 H21 1.000 0.970
N2 H22 1.000 0.970
N1 C6 1.377 1.352
N1 H1 1.000 0.970
C6 O6 1.249 1.219
C6 C5 1.418 1.414
C5 N7 1.396 1.355
N7 C8 1.285 1.301
C8 H8 1.080 1.080
C2' C1' 1.479 1.545
C2' C3' 1.515 1.545
C2' H2' 1.100 1.090
C2' H2'' 1.100 1.090
C5' C4' 1.532 1.530
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.090
C4' O4' 1.404 1.445
C4' C3' 1.487 1.545
C4' H4' 1.100 1.090
O4' C1' 1.485 1.444
C1' H1' 1.100 1.090
C3' O3' 1.456 1.429
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
OP2 HOP2   0.967

Bond Angles for GMS

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P SE 114.0 109.5
OP1 P O5' 104.8 109.4
OP1 P OP2   109.4
SE P O5' 112.4 109.5
SE P OP2   109.5
P SE HS 109.5 101.0
O5' P OP2   109.5
P O5' C5' 122.6 123.0
P OP2 HOP2   114.0
O5' C5' C4' 108.3 109.5
O5' C5' H5' 109.9 109.5
O5' C5' H5'' 110.1 109.5
C4 N9 C8 106.8 107.5
C4 N9 C1' 128.1 126.3
N9 C4 N3 127.6 134.2
N9 C4 C5 104.1 106.1
C8 N9 C1' 125.0 126.2
N9 C8 N7 114.9 109.8
N9 C8 H8 122.6 125.1
N9 C1' C2' 118.2 110.4
N9 C1' O4' 105.4 110.4
N9 C1' H1' 105.1 110.3
N3 C4 C5 128.3 119.7
C4 N3 C2 113.2 121.1
C4 C5 C6 118.6 118.6
C4 C5 N7 112.3 107.2
N3 C2 N2 120.4 119.0
N3 C2 N1 123.0 122.0
N2 C2 N1 116.6 119.0
C2 N2 H21 111.4 120.0
C2 N2 H22 124.3 120.0
C2 N1 C6 125.3 120.3
C2 N1 H1 117.4 119.9
H21 N2 H22 124.3 120.0
C6 N1 H1 117.3 119.8
N1 C6 O6 120.4 120.8
N1 C6 C5 111.6 118.4
O6 C6 C5 127.9 120.8
C6 C5 N7 129.1 134.1
C5 N7 C8 102.0 109.3
N7 C8 H8 122.5 125.1
C1' C2' C3' 106.6 104.1
C1' C2' H2' 110.4 110.5
C1' C2' H2'' 111.1 110.5
C2' C1' O4' 104.7 104.8
C2' C1' H1' 105.8 110.4
C3' C2' H2' 110.4 110.5
C3' C2' H2'' 111.1 110.6
C2' C3' C4' 104.0 104.1
C2' C3' O3' 112.1 110.5
C2' C3' H3' 111.8 110.5
H2' C2' H2'' 107.3 110.5
C4' C5' H5' 109.9 109.4
C4' C5' H5'' 110.1 109.4
C5' C4' O4' 109.0 110.4
C5' C4' C3' 112.9 110.4
C5' C4' H4' 106.4 110.3
H5' C5' H5'' 108.5 109.5
O4' C4' C3' 106.0 104.8
O4' C4' H4' 113.2 110.4
C4' O4' C1' 110.9 105.3
C3' C4' H4' 109.4 110.4
C4' C3' O3' 110.8 110.5
C4' C3' H3' 113.0 110.5
O4' C1' H1' 118.5 110.4
O3' C3' H3' 105.2 110.6
C3' O3' HO3' 109.5 114.0

Torsion Angles for GMS

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
SE P OP1 O5' 236.7 120.0
SE P OP1 OP2   240.0
OP1 P SE HS 147.0 180.0
O5' P OP1 OP2   119.9
OP1 P O5' C5' 174.7 45.1
OP1 P OP2 HOP2   300.0
OP1 P SE O5' 119.1 240.0
OP1 P SE OP2   120.0
O5' P SE OP2   239.9
SE P O5' C5' 299.0 285.1
SE P OP2 HOP2   60.0
OP1 P O5' SE 235.7 120.0
OP1 P O5' OP2   240.1
SE P O5' OP2   120.1
O5' P SE HS 27.9 300.0
O5' P OP2 HOP2   180.1
P O5' C5' C4' 188.6 179.9
P O5' C5' H5' 308.6 299.9
P O5' C5' H5'' 68.2 59.9
OP1 P OP2 SE   240.0
OP1 P OP2 O5'   119.9
SE P OP2 O5'   239.9
OP2 P SE HS   60.0
OP2 P O5' C5'   165.0
HS SE P O5' 27.9 300.0
HS SE P OP2   60.0
C5' O5' P OP2   165.0
C4' C5' O5' H5' 240.0 240.1
C4' C5' O5' H5'' 120.5 120.0
O5' C5' C4' O4' 59.7 66.4
O5' C5' C4' C3' 177.2 181.8
O5' C5' C4' H4' 297.2 304.2
H5' C5' O5' H5'' 240.5 239.9
C8 N9 C4 C1' 179.3 180.2
C4 N9 C8 N7 0.4 0.1
C4 N9 C8 H8 180.5 180.0
C4 N9 C1' C2' 310.7 85.0
C4 N9 C1' O4' 67.1 200.4
C4 N9 C1' H1' 193.1 322.7
N3 C4 N9 C5 180.5 180.1
N9 C4 N3 C2 180.1 180.0
N9 C4 C5 C6 180.5 180.0
N9 C4 C5 N7 360.0 360.0
C4 N9 C8 C1' 180.6 179.8
C8 N9 C4 N3 180.3 180.0
C8 N9 C4 C5 359.8 360.0
C8 N9 C1' C2' 131.5 264.8
C8 N9 C1' O4' 247.9 20.2
C8 N9 C1' H1' 13.8 142.5
C5 N7 C8 N9 359.6 359.9
N7 C8 N9 H8 180.0 180.1
C4 N9 C1' C8 179.2 180.2
C1' N9 C4 N3 0.9 359.9
C1' N9 C4 C5 180.4 179.8
C1' N9 C8 N7 179.8 180.2
C1' N9 C8 H8 359.8 0.1
N9 C1' C2' C3' 104.7 142.8
N9 C1' C2' H2' 224.6 261.5
N9 C1' C2' H2'' 343.5 24.1
C2' C1' N9 O4' 243.6 244.6
C2' C1' N9 H1' 117.6 122.3
C4' O4' C1' N9 228.9 200.6
O4' C1' N9 H1' 234.1 237.7
N3 C4 N9 C8 180.3 180.0
N3 C4 N9 C1' 0.9 359.9
N9 C4 N3 C5 179.4 179.9
N3 C4 C5 C6 0.0 360.0
N3 C4 C5 N7 179.5 179.9
C4 N3 C2 N2 179.7 180.0
C4 N3 C2 N1 358.8 359.9
C5 C4 N9 C8 359.8 360.0
C5 C4 N9 C1' 180.4 179.8
N9 C4 C5 N3 180.5 180.1
C5 C4 N3 C2 0.7 0.0
N1 C6 C5 C4 359.8 0.1
O6 C6 C5 C4 180.2 180.0
C6 C5 C4 N7 180.5 180.0
C4 C5 N7 C8 0.3 0.1
C2 N3 C4 C5 0.7 0.0
N2 C2 N3 N1 180.9 180.1
N3 C2 N2 H21 180.0 360.0
N3 C2 N2 H22 360.0 180.0
N3 C2 N1 C6 1.1 0.1
N3 C2 N1 H1 181.1 180.0
N3 C2 N2 N1 179.2 179.9
N2 C2 N1 C6 180.2 180.0
N2 C2 N1 H1 0.2 359.9
H21 N2 C2 H22 180.0 180.0
N3 C2 N1 N2 180.8 180.1
N1 C2 N2 H21 0.8 180.1
N1 C2 N2 H22 180.8 0.1
C6 N1 C2 H1 180.0 180.1
C2 N1 C6 O6 179.3 180.0
C2 N1 C6 C5 359.8 359.9
H21 N2 C2 N1 0.8 180.1
C2 N2 H21 H22 180.0 180.0
H22 N2 C2 N1 180.8 0.1
C2 N2 H22 H21 180.0 180.0
C4 C5 C6 N1 359.8 0.1
C2 N1 C6 H1 180.0 179.9
O6 C6 N1 C5 179.6 180.1
N1 C6 C5 N7 180.4 180.1
C2 N1 H1 C6 180.0 180.1
H1 N1 C6 O6 359.3 0.1
H1 N1 C6 C5 179.7 180.0
C4 C5 C6 O6 180.2 180.0
O6 C6 N1 H1 359.3 0.1
N1 C6 O6 C5 180.5 179.9
O6 C6 C5 N7 0.9 0.0
C4 C5 C6 N7 179.4 180.0
C5 C6 N1 H1 179.7 180.0
N1 C6 C5 O6 179.5 180.1
C6 C5 N7 C8 179.6 180.0
N9 C8 N7 C5 359.6 359.9
C4 C5 N7 C6 180.6 180.0
C5 N7 C8 H8 179.6 180.0
N7 C8 N9 C1' 179.8 180.2
N9 C8 N7 H8 180.0 179.9
H8 C8 N9 C1' 359.8 0.1
N9 C8 H8 N7 180.0 180.1
N9 C1' C2' O4' 116.8 118.8
N9 C1' C2' H1' 242.7 237.7
C3' C2' C1' H2' 240.0 241.4
C3' C2' C1' H2'' 121.1 118.7
C1' C2' C3' C4' 24.8 360.0
C1' C2' C3' O3' 144.6 118.7
C1' C2' C3' H3' 262.5 241.3
H2' C2' C1' H2'' 241.1 237.3
C4' O4' C1' C2' 354.2 319.5
O4' C1' C2' H1' 125.9 118.9
C1' C2' C3' H2' 120.0 118.6
C1' C2' C3' H2'' 238.9 241.3
C3' C2' C1' O4' 347.8 24.0
C3' C2' C1' H1' 221.9 265.1
H2' C2' C3' H2'' 118.9 122.7
C5' C4' C3' C2' 212.5 217.2
O4' C4' C3' C2' 331.8 336.1
C2' C3' C4' H4' 94.2 94.9
C4' C3' C2' O3' 240.2 241.3
C4' C3' C2' H3' 122.3 118.6
O3' C3' C2' H3' 242.2 237.3
C2' C3' O3' HO3' 56.0 61.4
C1' C2' H2' C3' 242.4 245.4
C1' C2' H2' H2'' 121.2 122.6
H2' C2' C1' O4' 107.8 142.6
H2' C2' C1' H1' 341.9 23.7
C3' C2' H2' H2'' 238.8 237.3
H2' C2' C3' C4' 264.8 241.3
H2' C2' C3' O3' 24.6 0.0
H2' C2' C3' H3' 142.5 122.7
C1' C2' H2'' C3' 118.5 114.7
C1' C2' H2'' H2' 239.2 237.4
H2'' C2' C1' O4' 226.7 265.3
H2'' C2' C1' H1' 100.8 146.4
C3' C2' H2'' H2' 120.8 122.7
H2'' C2' C3' C4' 145.9 118.6
H2'' C2' C3' O3' 265.7 237.3
H2'' C2' C3' H3' 23.6 360.0
O5' C5' C4' H5' 120.0 120.0
O5' C5' C4' H5'' 239.5 240.0
C2' C3' C4' C5' 212.5 217.2
H5' C5' C4' H5'' 119.5 120.0
O4' C4' C5' C3' 242.5 244.6
O4' C4' C5' H4' 122.5 122.2
C5' C4' O4' C1' 143.5 159.3
C3' C4' C5' H4' 240.0 237.6
C5' C4' C3' O3' 91.8 98.5
C5' C4' C3' H3' 334.0 335.8
O5' C5' H5' C4' 240.9 240.0
O5' C5' H5' H5'' 120.5 120.1
C4' C5' H5' H5'' 239.6 240.1
H5' C5' C4' O4' 299.7 306.4
H5' C5' C4' C3' 57.2 61.8
H5' C5' C4' H4' 177.2 184.2
O5' C5' H5'' C4' 119.4 120.0
O5' C5' H5'' H5' 239.7 239.9
C4' C5' H5'' H5' 120.3 119.9
H5'' C5' C4' O4' 180.2 186.5
H5'' C5' C4' C3' 297.7 301.8
H5'' C5' C4' H4' 57.7 64.2
N9 C1' O4' C4' 228.9 200.6
C2' C1' O4' C4' 354.2 319.5
C2' C3' C4' O4' 331.8 336.1
O4' C4' C5' H5' 299.7 306.4
O4' C4' C5' H5'' 180.2 186.5
C5' C4' O4' C3' 121.8 118.9
C5' C4' O4' H4' 241.8 237.8
C3' C4' O4' H4' 120.0 118.9
O4' C4' C3' O3' 211.1 217.4
O4' C4' C3' H3' 93.3 94.7
C4' O4' C1' H1' 111.7 78.4
C4' C3' C2' H2' 264.8 241.3
C4' C3' C2' H2'' 145.9 118.6
C2' C3' C4' O3' 120.7 118.7
C2' C3' C4' H3' 238.5 241.4
C3' C4' C5' H5' 57.2 61.8
C3' C4' C5' H5'' 297.7 301.8
C5' C4' C3' O4' 240.7 241.1
C5' C4' C3' H4' 118.3 122.3
O4' C4' C3' H4' 237.6 241.2
C3' C4' O4' C1' 21.7 40.5
O3' C3' C4' H3' 117.8 122.7
C4' C3' O3' HO3' 171.8 176.1
H4' C4' C5' H5' 177.2 184.2
H4' C4' C5' H5'' 57.7 64.2
C5' C4' H4' O4' 119.8 122.3
C5' C4' H4' C3' 237.7 237.7
O4' C4' H4' C3' 118.0 115.4
H4' C4' O4' C1' 261.7 281.6
H4' C4' C3' O3' 333.5 336.2
H4' C4' C3' H3' 215.7 213.5
N9 C1' O4' C2' 234.7 241.1
N9 C1' O4' H1' 117.2 122.3
O4' C1' C2' C3' 347.8 24.0
O4' C1' C2' H2' 107.8 142.6
O4' C1' C2' H2'' 226.7 265.3
C2' C1' O4' H1' 242.5 241.1
C1' O4' C4' C3' 21.7 40.5
C1' O4' C4' H4' 261.7 281.6
N9 C1' H1' C2' 125.7 122.3
N9 C1' H1' O4' 242.6 237.7
H1' C1' C2' C3' 221.9 265.1
H1' C1' C2' H2' 341.9 23.7
H1' C1' C2' H2'' 100.8 146.4
C2' C1' H1' O4' 116.9 115.4
O3' C3' C2' H2' 24.6 0.0
O3' C3' C2' H2'' 265.7 237.3
C2' C3' O3' C4' 244.2 245.3
C2' C3' O3' H3' 121.7 122.6
O3' C3' C4' H4' 333.5 336.2
C4' C3' O3' H3' 237.5 237.3
H3' C3' C2' H2' 142.5 122.7
H3' C3' C2' H2'' 23.6 360.0
C2' C3' H3' C4' 117.0 114.6
C2' C3' H3' O3' 238.1 237.3
H3' C3' C4' H4' 215.7 213.5
C4' C3' H3' O3' 121.1 122.7
H3' C3' O3' HO3' 294.3 298.8
HO3' O3' C3' H3' 294.3 298.8