PDB Chemical Component GNE

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 GNE

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.476 1.617
P OP2 1.471 1.501
P OP3   1.617
P O5' 1.607 1.619
OP1 HO1 0.951 0.981
OP3 HO3   0.981
O5' C5' 1.426 1.417
C5' C4' 1.531 1.523
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.091
C4' O4' 1.439 1.443
C4' C3' 1.531 1.525
C4' H4' 1.115 1.095
O4' C1' 1.435 1.439
C3' O3' 1.429 1.425
C3' C2' 1.525 1.512
C3' H3' 1.115 1.093
O3' HA 0.950 0.969
C2' C1' 1.526 1.522
C2' H2' 1.115 1.097
C2' H2'' 1.115 1.094
C1' N9 1.479 1.459
C1' H1' 1.115 1.095
N9 C8 1.331 1.373
N9 C4 1.331 1.364
C8 N7 1.332 1.319
C8 H8 1.103 1.082
N7 C5 1.327 1.365
C5 C6 1.392 1.445
C5 C4 1.387 1.381
C6 O6 1.234 1.223
C6 N1 1.393 1.398
N1 C2 1.405 1.433
N1 C11 1.340 1.385
C2 N2 1.336 1.381
C2 N3 1.340 1.301
N2 CM2 1.466 1.374
N2 H2 1.020 1.010
CM2 C11 1.523 1.344
CM2 HM2 1.103 1.077
N3 C4 1.344 1.356
C11 H11 1.104 1.077

Bond Angles for GNE

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 118.9 115.3
OP1 P OP3   103.3
OP1 P O5' 108.2 103.7
P OP1 HO1 118.9 118.9
OP2 P OP3   115.0
OP2 P O5' 109.8 115.0
OP3 P O5'   102.9
P OP3 HO3   118.9
P O5' C5' 122.1 118.5
O5' C5' C4' 113.4 108.7
O5' C5' H5' 110.7 109.2
O5' C5' H5'' 110.7 109.2
C4' C5' H5' 110.8 110.1
C4' C5' H5'' 110.8 110.1
C5' C4' O4' 113.5 108.0
C5' C4' C3' 115.1 112.7
C5' C4' H4' 107.6 109.4
H5' C5' H5'' 99.6 109.6
O4' C4' C3' 105.1 106.8
O4' C4' H4' 107.6 107.7
C4' O4' C1' 103.9 108.7
C3' C4' H4' 107.6 112.0
C4' C3' O3' 109.1 109.6
C4' C3' C2' 102.4 103.2
C4' C3' H3' 112.7 114.0
O4' C1' C2' 100.8 106.7
O4' C1' N9 115.1 110.0
O4' C1' H1' 108.7 108.1
O3' C3' C2' 106.5 108.4
O3' C3' H3' 112.8 107.8
C3' O3' HA 109.1 106.5
C2' C3' H3' 112.7 113.7
C3' C2' C1' 94.0 101.6
C3' C2' H2' 118.3 110.0
C3' C2' H2'' 118.3 114.2
C1' C2' H2' 118.3 110.5
C1' C2' H2'' 118.3 111.7
C2' C1' N9 114.5 114.3
C2' C1' H1' 108.7 111.7
H2' C2' H2'' 91.9 108.7
N9 C1' H1' 108.7 105.9
C1' N9 C8 125.9 125.9
C1' N9 C4 125.4 127.1
C8 N9 C4 108.7 107.0
N9 C8 N7 109.2 112.4
N9 C8 H8 125.4 122.1
N9 C4 C5 106.3 104.7
N9 C4 N3 132.9 125.8
N7 C8 H8 125.4 125.5
C8 N7 C5 107.8 104.0
N7 C5 C6 133.1 128.0
N7 C5 C4 108.1 111.9
C6 C5 C4 118.9 120.1
C5 C6 O6 119.5 123.5
C5 C6 N1 119.3 109.3
C5 C4 N3 120.8 129.6
O6 C6 N1 121.1 127.1
C6 N1 C2 119.5 125.5
C6 N1 C11 130.5 126.8
C2 N1 C11 110.0 107.8
N1 C2 N2 110.5 105.1
N1 C2 N3 119.3 124.1
N1 C11 CM2 107.7 108.4
N1 C11 H11 126.1 122.2
N2 C2 N3 130.2 130.7
C2 N2 CM2 109.3 109.4
C2 N2 H2 125.3 127.7
C2 N3 C4 122.1 111.4
CM2 N2 H2 125.3 122.9
N2 CM2 C11 102.4 109.3
N2 CM2 HM2 128.8 120.8
C11 CM2 HM2 128.8 129.9
CM2 C11 H11 126.1 129.4

Torsion Angles for GNE

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3   126.3
OP2 P OP1 O5' 126.1 233.4
OP3 P OP1 O5'   107.1
OP1 P OP3 HO3   78.5
OP1 P O5' C5' 143.9 53.2
OP1 P OP2 OP3   239.9
OP1 P OP2 O5' 234.7 120.6
OP2 P OP1 HO1 180.0 48.8
OP3 P OP2 O5'   240.7
OP2 P OP3 HO3   312.0
OP2 P O5' C5' 12.6 180.0
OP1 P OP3 OP2   126.5
OP1 P OP3 O5'   252.3
OP3 P OP1 HO1   282.5
OP2 P OP3 O5'   125.8
OP3 P O5' C5'   305.8
OP1 P O5' OP2 131.3 233.2
OP1 P O5' OP3   107.4
O5' P OP1 HO1 53.9 175.4
OP2 P O5' OP3   234.2
O5' P OP3 HO3   186.1
P O5' C5' C4' 154.2 180.0
P O5' C5' H5' 29.0 300.1
P O5' C5' H5'' 279.5 59.9
HO1 OP1 P OP2 180.0 48.8
HO1 OP1 P OP3   282.5
HO1 OP1 P O5' 53.9 175.4
HO3 OP3 P O5'   186.1
C4' C5' O5' H5' 125.3 239.9
C4' C5' O5' H5'' 234.7 120.1
O5' C5' C4' O4' 290.7 61.8
O5' C5' C4' C3' 51.9 179.5
O5' C5' C4' H4' 171.8 304.8
H5' C5' O5' H5'' 109.5 240.2
O5' C5' C4' H5' 234.8 119.6
O5' C5' C4' H5'' 125.2 240.5
H5' C5' C4' H5'' 250.5 120.9
O4' C4' C5' C3' 238.8 242.3
O4' C4' C5' H4' 118.9 117.0
C5' C4' O4' C1' 144.6 116.0
C3' C4' C5' H4' 240.1 234.7
C5' C4' C3' O3' 140.2 152.1
C5' C4' C3' C2' 252.8 267.4
C5' C4' C3' H3' 14.2 31.2
O5' C5' H5' C4' 126.7 240.8
O5' C5' H5' H5'' 243.4 119.6
C4' C5' H5' H5'' 116.7 238.8
H5' C5' C4' O4' 56.0 302.2
H5' C5' C4' C3' 177.2 60.0
H5' C5' C4' H4' 297.1 185.3
O5' C5' H5'' C4' 233.3 119.2
O5' C5' H5'' H5' 116.6 240.4
C4' C5' H5'' H5' 243.3 121.2
H5'' C5' C4' O4' 165.5 181.3
H5'' C5' C4' C3' 286.7 299.1
H5'' C5' C4' H4' 46.6 64.3
O4' C4' C5' H5' 56.0 302.2
O4' C4' C5' H5'' 165.5 181.3
C5' C4' O4' C3' 126.7 121.5
C5' C4' O4' H4' 241.1 242.0
C3' C4' O4' H4' 114.4 120.5
O4' C4' C3' O3' 265.9 270.6
O4' C4' C3' C2' 18.4 25.9
O4' C4' C3' H3' 139.8 149.7
C4' O4' C1' C2' 312.0 342.7
C4' O4' C1' N9 188.2 218.2
C4' O4' C1' H1' 66.1 103.1
C3' C4' C5' H5' 177.2 60.0
C3' C4' C5' H5'' 286.7 299.1
C5' C4' C3' O4' 234.3 241.5
C5' C4' C3' H4' 119.9 123.8
O4' C4' C3' H4' 245.6 242.3
C3' C4' O4' C1' 17.9 354.5
O3' C3' C4' C2' 247.5 244.7
O3' C3' C4' H3' 126.1 120.9
C4' C3' O3' HA 180.0 43.1
C2' C3' C4' H3' 238.6 236.3
C4' C3' C2' C1' 315.8 325.2
C4' C3' C2' H2' 190.5 82.2
C4' C3' C2' H2'' 81.1 204.8
H4' C4' C5' H5' 297.1 185.3
H4' C4' C5' H5'' 46.6 64.3
C5' C4' H4' O4' 122.7 117.2
C5' C4' H4' C3' 235.4 234.3
O4' C4' H4' C3' 112.8 117.2
H4' C4' O4' C1' 263.5 234.0
H4' C4' C3' O3' 20.4 28.3
H4' C4' C3' C2' 132.9 143.6
H4' C4' C3' H3' 254.3 267.4
C1' O4' C4' C3' 17.9 354.5
C1' O4' C4' H4' 263.5 234.0
C3' C2' C1' O4' 56.8 32.7
O4' C1' C2' H2' 182.1 276.0
O4' C1' C2' H2'' 291.6 154.9
C2' C1' O4' N9 123.8 124.5
C2' C1' O4' H1' 245.9 239.7
N9 C1' O4' H1' 122.1 115.2
O4' C1' N9 C8 78.2 33.5
O4' C1' N9 C4 257.7 213.4
O3' C3' C4' H4' 20.4 28.3
C4' C3' O3' C2' 109.8 111.9
C4' C3' O3' H3' 233.9 235.4
C2' C3' O3' H3' 124.1 123.5
O3' C3' C2' C1' 70.2 81.3
O3' C3' C2' H2' 305.0 198.4
O3' C3' C2' H2'' 195.5 320.9
C2' C3' C4' H4' 132.9 143.6
C4' C3' C2' O3' 245.6 243.8
C4' C3' C2' H3' 121.4 123.9
O4' C1' C2' C3' 56.8 32.7
O3' C3' C2' H3' 235.9 240.1
C2' C3' O3' HA 70.2 291.2
C1' C2' C3' H2' 125.3 243.0
C1' C2' C3' H2'' 234.7 120.4
C3' C2' C1' N9 181.0 154.5
C3' C2' C1' H1' 302.7 274.8
H2' C2' C3' H2'' 109.5 237.5
H3' C3' C4' H4' 254.3 267.4
C4' C3' H3' O3' 124.1 121.9
C4' C3' H3' C2' 244.7 242.1
O3' C3' H3' C2' 120.6 120.2
H3' C3' O3' HA 306.1 167.7
H3' C3' C2' C1' 194.4 201.2
H3' C3' C2' H2' 69.1 318.3
H3' C3' C2' H2'' 319.7 80.8
HA O3' C3' C2' 70.2 291.2
HA O3' C3' H3' 306.1 167.7
O4' C1' C2' N9 235.8 238.2
O4' C1' C2' H1' 114.1 117.9
C1' C2' C3' H3' 194.4 201.2
C3' C2' C1' H2' 234.7 116.7
C3' C2' C1' H2'' 125.2 237.8
H2' C2' C1' H2'' 250.5 121.1
N9 C1' C2' H1' 238.3 239.7
C2' C1' N9 C8 322.0 273.4
C2' C1' N9 C4 141.5 93.4
H2' C2' C3' H3' 69.1 318.3
C3' C2' H2' C1' 112.3 248.6
C3' C2' H2' H2'' 236.2 125.7
C1' C2' H2' H2'' 123.9 237.1
H2' C2' C1' N9 306.3 37.8
H2' C2' C1' H1' 68.0 158.1
H2'' C2' C3' H3' 319.7 80.8
C3' C2' H2'' C1' 247.7 114.6
C3' C2' H2'' H2' 123.9 236.7
C1' C2' H2'' H2' 236.1 122.1
H2'' C2' C1' N9 55.8 276.7
H2'' C2' C1' H1' 177.5 37.0
O4' C1' N9 C2' 116.2 120.0
O4' C1' N9 H1' 237.9 243.5
N9 C1' C2' H2' 306.3 37.8
N9 C1' C2' H2'' 55.8 276.7
C2' C1' N9 H1' 121.7 123.5
C8 N9 C1' C4 180.5 180.1
C1' N9 C8 N7 179.9 180.0
C1' N9 C8 H8 359.9 359.9
C1' N9 C4 C5 179.9 180.0
C1' N9 C4 N3 0.3 360.0
O4' C1' H1' C2' 251.2 242.9
O4' C1' H1' N9 126.0 117.8
H1' C1' C2' H2' 68.0 158.1
H1' C1' C2' H2'' 177.5 37.0
C2' C1' H1' N9 234.8 234.9
H1' C1' N9 C8 200.3 150.0
H1' C1' N9 C4 19.8 329.9
C8 N9 C1' H1' 200.3 150.0
C1' N9 C8 C4 179.6 179.9
C8 N9 C4 C5 359.5 360.0
C8 N9 C4 N3 179.9 179.9
N7 C8 N9 H8 180.0 180.1
N9 C8 N7 C5 0.0 360.0
C4 N9 C1' H1' 19.8 329.9
C1' N9 C4 C8 180.4 180.1
C4 N9 C8 N7 0.3 0.0
C4 N9 C8 H8 180.3 179.9
N7 C5 C4 N9 0.5 360.0
C6 C5 C4 N9 180.5 179.9
C5 C4 N9 N3 179.6 180.1
C2 N3 C4 N9 179.6 180.1
N7 C8 N9 C4 0.3 0.0
N9 C8 N7 H8 180.0 179.9
C8 N7 C5 C6 179.7 180.1
C8 N7 C5 C4 359.7 0.0
H8 C8 N9 C4 180.3 179.9
N9 C8 H8 N7 180.0 180.1
H8 C8 N7 C5 180.1 180.1
N9 C4 C5 N7 0.5 360.0
C5 N7 C8 H8 180.1 180.1
C6 C5 N7 C4 180.0 180.1
N7 C5 C6 O6 358.2 0.0
N7 C5 C6 N1 179.8 180.0
N7 C5 C4 N3 180.2 180.1
N9 C4 C5 C6 180.5 179.9
N7 C5 C6 C4 180.0 179.9
C6 C5 C4 N3 0.1 360.0
O6 C6 C5 N1 178.4 180.1
C5 C6 N1 C2 360.0 360.0
C5 C6 N1 C11 181.1 180.1
N9 C4 C5 N3 180.3 179.9
N7 C5 C4 C6 180.0 180.1
C4 C5 C6 O6 178.2 180.1
C4 C5 C6 N1 359.8 0.0
C2 N3 C4 C5 0.1 0.0
O6 C6 C5 C4 178.2 180.1
C5 C6 O6 N1 181.6 179.9
O6 C6 N1 C2 181.6 179.9
O6 C6 N1 C11 2.7 360.0
N1 C6 C5 C4 359.8 0.0
C5 C6 N1 O6 178.4 180.1
C2 N1 C6 C11 178.9 179.9
C6 N1 C2 N2 181.3 180.0
C6 N1 C2 N3 0.2 0.1
C6 N1 C11 CM2 179.9 180.0
C6 N1 C11 H11 359.9 359.9
C6 N1 C2 C11 180.9 180.1
C2 N1 C11 CM2 0.9 0.1
C2 N1 C11 H11 180.9 180.0
N2 C2 N1 N3 181.1 180.0
N1 C2 N2 CM2 358.3 0.1
N1 C2 N2 H2 178.4 179.6
N1 C2 N3 C4 359.8 360.0
C6 N1 C11 C2 179.0 179.9
C11 N1 C2 N2 0.5 359.9
C11 N1 C2 N3 179.4 179.9
N2 CM2 C11 N1 358.3 360.0
N1 C11 CM2 HM2 178.3 180.0
CM2 C11 N1 H11 180.0 180.1
N2 C2 N1 C11 0.5 359.9
N1 C2 N2 N3 178.7 180.0
N2 C2 N3 C4 178.4 180.0
CM2 N2 C2 H2 180.0 180.4
C2 N2 CM2 C11 2.1 360.0
C2 N2 CM2 HM2 182.0 180.0
N9 C4 N3 C2 179.6 180.1
C5 C4 N3 C2 0.1 0.0
N3 C2 N1 C11 179.4 179.9
N1 C2 N3 N2 181.4 180.0
N3 C2 N2 CM2 179.6 180.0
N3 C2 N2 H2 359.6 359.6
N1 C11 CM2 N2 358.3 360.0
CM2 N2 C2 N3 179.6 180.0
C2 N2 CM2 H2 180.0 179.6
C11 CM2 N2 HM2 180.0 180.0
N2 CM2 C11 H11 178.3 180.0
H2 N2 C2 N3 359.6 359.6
C2 N2 H2 CM2 180.0 180.5
H2 N2 CM2 C11 182.0 180.4
H2 N2 CM2 HM2 2.0 0.4
N1 C11 CM2 H11 180.0 179.9
C11 CM2 N2 H2 182.0 180.4
N2 CM2 C11 HM2 180.0 180.0
HM2 CM2 N2 H2 2.0 0.4
N2 CM2 HM2 C11 180.0 180.0
HM2 CM2 C11 H11 358.3 0.1
N9 C4 N3 C5 179.6 180.1
N1 C11 H11 CM2 180.0 180.1
H11 C11 CM2 HM2 358.3 0.1