PDB Chemical Component 5GP

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 5GP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.466 1.480
P O2P 1.516 1.610
P O3P 1.568 1.609
P O5' 1.638 1.610
O2P HOP2 0.950 0.967
O3P HOP3 0.950 0.967
O5' C5' 1.475 1.429
C5' C4' 1.548 1.530
C5' H5'1 1.101 1.090
C5' H5'2 1.100 1.090
C4' O4' 1.497 1.444
C4' C3' 1.526 1.545
C4' H4' 1.100 1.090
O4' C1' 1.467 1.444
C3' O3' 1.420 1.428
C3' C2' 1.533 1.547
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C2' O2' 1.444 1.429
C2' C1' 1.520 1.545
C2' H2' 1.099 1.090
O2' HO2' 0.950 0.967
C1' N9 1.497 1.465
C1' H1' 1.100 1.090
N9 C8 1.378 1.364
N9 C4 1.379 1.369
C8 N7 1.317 1.301
C8 H8 1.081 1.081
N7 C5 1.409 1.355
C5 C6 1.434 1.415
C5 C4 1.390 1.399
C6 O6 1.226 1.219
C6 N1 1.430 1.351
N1 C2 1.393 1.363
N1 HN1 1.000 0.970
C2 N2 1.349 1.372
C2 N3 1.347 1.315
N2 HN21 1.000 0.970
N2 HN22 1.000 0.970
N3 C4 1.377 1.337

Bond Angles for 5GP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 112.3 109.5
O1P P O3P 110.5 109.5
O1P P O5' 113.0 109.4
O2P P O3P 111.0 109.5
O2P P O5' 106.2 109.5
P O2P HOP2 109.5 106.7
O3P P O5' 103.6 109.5
P O3P HOP3 109.5 106.8
P O5' C5' 121.6 106.8
O5' C5' C4' 114.5 109.5
O5' C5' H5'1 107.9 109.5
O5' C5' H5'2 106.7 109.5
C4' C5' H5'1 107.8 109.5
C4' C5' H5'2 106.7 109.4
C5' C4' O4' 106.3 110.4
C5' C4' C3' 119.7 110.5
C5' C4' H4' 102.9 110.3
H5'1 C5' H5'2 113.5 109.5
O4' C4' C3' 102.8 104.8
O4' C4' H4' 119.8 110.4
C4' O4' C1' 109.0 105.3
C3' C4' H4' 106.4 110.4
C4' C3' O3' 113.9 110.5
C4' C3' C2' 104.7 104.1
C4' C3' H3' 110.3 110.5
O4' C1' C2' 107.9 104.9
O4' C1' N9 111.3 110.4
O4' C1' H1' 113.7 110.4
O3' C3' C2' 111.0 110.6
O3' C3' H3' 103.9 110.5
C3' O3' HO3' 109.5 106.9
C2' C3' H3' 113.3 110.6
C3' C2' O2' 112.2 110.5
C3' C2' C1' 102.6 104.0
C3' C2' H2' 113.4 110.5
O2' C2' C1' 112.7 110.8
O2' C2' H2' 103.4 110.5
C2' O2' HO2' 109.5 106.8
C1' C2' H2' 112.9 110.5
C2' C1' N9 119.5 110.4
C2' C1' H1' 104.1 110.4
N9 C1' H1' 100.1 110.3
C1' N9 C8 129.6 126.3
C1' N9 C4 124.8 126.3
C8 N9 C4 105.4 107.5
N9 C8 N7 115.5 109.8
N9 C8 H8 122.2 125.1
N9 C4 C5 105.7 106.1
N9 C4 N3 126.2 134.2
N7 C8 H8 122.3 125.1
C8 N7 C5 102.0 109.3
N7 C5 C6 128.6 134.1
N7 C5 C4 111.4 107.3
C6 C5 C4 120.0 118.6
C5 C6 O6 128.2 120.8
C5 C6 N1 111.5 118.3
C5 C4 N3 128.1 119.7
O6 C6 N1 120.3 120.8
C6 N1 C2 124.0 120.3
C6 N1 HN1 118.0 119.8
C2 N1 HN1 118.0 119.8
N1 C2 N2 114.0 119.0
N1 C2 N3 124.7 121.9
N2 C2 N3 121.3 119.1
C2 N2 HN21 108.6 120.0
C2 N2 HN22 125.7 120.0
C2 N3 C4 111.8 121.1
HN21 N2 HN22 125.7 120.0

Torsion Angles for 5GP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O3P 235.6 120.0
O2P P O1P O5' 120.1 240.0
O1P P O2P HOP2 103.4 180.0
O3P P O1P O5' 244.5 120.0
O1P P O3P HOP3 56.3 60.0
O1P P O5' C5' 188.0 305.0
O1P P O2P O3P 124.1 240.0
O1P P O2P O5' 236.1 120.0
O3P P O2P O5' 111.9 240.0
O2P P O3P HOP3 181.5 300.0
O2P P O5' C5' 64.5 65.0
O1P P O3P O2P 234.8 120.0
O1P P O3P O5' 121.2 240.0
O2P P O3P O5' 246.4 120.0
O3P P O2P HOP2 339.3 300.0
O3P P O5' C5' 307.6 185.0
O1P P O5' O2P 123.5 240.0
O1P P O5' O3P 240.5 120.0
O2P P O5' O3P 117.0 240.0
O5' P O2P HOP2 227.3 60.0
O5' P O3P HOP3 295.1 180.0
P O5' C5' C4' 180.1 180.0
P O5' C5' H5'1 300.1 60.0
P O5' C5' H5'2 62.4 300.0
HOP2 O2P P O3P 339.3 300.0
HOP2 O2P P O5' 227.3 60.0
HOP3 O3P P O5' 295.1 180.0
C4' C5' O5' H5'1 240.0 120.0
C4' C5' O5' H5'2 117.8 240.0
O5' C5' C4' O4' 135.6 66.4
O5' C5' C4' C3' 251.3 181.9
O5' C5' C4' H4' 8.9 304.2
H5'1 C5' O5' H5'2 237.8 120.0
O5' C5' C4' H5'1 120.0 240.0
O5' C5' C4' H5'2 242.2 120.0
H5'1 C5' C4' H5'2 122.2 240.0
O4' C4' C5' C3' 244.3 244.5
O4' C4' C5' H4' 126.7 122.2
C5' C4' O4' C1' 149.2 159.5
C3' C4' C5' H4' 242.4 237.7
C5' C4' C3' O3' 86.1 98.3
C5' C4' C3' C2' 207.5 217.1
C5' C4' C3' H3' 329.7 335.8
O5' C5' H5'1 C4' 235.9 120.0
O5' C5' H5'1 H5'2 118.0 240.0
C4' C5' H5'1 H5'2 242.1 120.0
H5'1 C5' C4' O4' 15.6 186.4
H5'1 C5' C4' C3' 131.3 301.9
H5'1 C5' C4' H4' 248.9 64.2
O5' C5' H5'2 C4' 122.8 240.0
O5' C5' H5'2 H5'1 241.4 120.0
C4' C5' H5'2 H5'1 118.6 240.0
H5'2 C5' C4' O4' 253.4 306.5
H5'2 C5' C4' C3' 9.1 61.9
H5'2 C5' C4' H4' 126.7 184.3
O4' C4' C5' H5'1 15.6 186.4
O4' C4' C5' H5'2 253.4 306.5
C5' C4' O4' C3' 126.6 119.0
C5' C4' O4' H4' 244.2 237.8
C3' C4' O4' H4' 117.6 118.9
O4' C4' C3' O3' 203.6 217.2
O4' C4' C3' C2' 325.0 336.0
O4' C4' C3' H3' 87.2 94.7
C4' O4' C1' C2' 358.7 319.5
C4' O4' C1' N9 225.7 200.6
C4' O4' C1' H1' 113.6 78.5
C3' C4' C5' H5'1 131.3 301.9
C3' C4' C5' H5'2 9.1 61.9
C5' C4' C3' O4' 242.5 241.1
C5' C4' C3' H4' 115.8 122.3
O4' C4' C3' H4' 233.3 241.2
C3' C4' O4' C1' 22.6 40.5
O3' C3' C4' C2' 238.6 241.3
O3' C3' C4' H3' 116.4 122.6
C4' C3' O3' HO3' 71.1 180.0
C2' C3' C4' H3' 237.8 241.3
C4' C3' C2' O2' 272.9 241.2
C4' C3' C2' C1' 34.1 0.1
C4' C3' C2' H2' 156.2 118.6
H4' C4' C5' H5'1 248.9 64.2
H4' C4' C5' H5'2 126.7 184.3
C5' C4' H4' O4' 117.5 122.2
C5' C4' H4' C3' 233.3 237.6
O4' C4' H4' C3' 115.8 115.4
H4' C4' O4' C1' 265.0 281.6
H4' C4' C3' O3' 330.3 336.1
H4' C4' C3' C2' 91.7 94.8
H4' C4' C3' H3' 213.9 213.5
C1' O4' C4' C3' 22.6 40.5
C1' O4' C4' H4' 265.0 281.6
C3' C2' C1' O4' 339.7 23.9
O2' C2' C1' O4' 100.6 142.6
O4' C1' C2' H2' 217.3 265.3
C2' C1' O4' N9 132.9 118.9
C2' C1' O4' H1' 245.1 241.1
N9 C1' O4' H1' 112.1 122.2
O4' C1' N9 C8 242.1 22.1
O4' C1' N9 C4 56.2 202.0
O3' C3' C4' H4' 330.3 336.1
C4' C3' O3' C2' 117.8 114.7
C4' C3' O3' H3' 239.9 237.4
C2' C3' O3' H3' 122.1 122.7
O3' C3' C2' O2' 36.2 359.9
O3' C3' C2' C1' 157.4 118.8
O3' C3' C2' H2' 279.5 237.3
C2' C3' C4' H4' 91.7 94.8
C4' C3' C2' O3' 236.7 241.3
C4' C3' C2' H3' 120.2 118.6
O4' C1' C2' C3' 339.7 23.9
O3' C3' C2' H3' 243.5 237.3
C2' C3' O3' HO3' 313.3 65.3
O2' C2' C3' C1' 238.7 241.1
O2' C2' C3' H2' 116.7 122.6
C3' C2' O2' HO2' 119.8 298.6
C1' C2' C3' H2' 237.9 241.5
C3' C2' C1' N9 108.1 142.8
C3' C2' C1' H1' 218.6 265.0
H3' C3' C4' H4' 213.9 213.5
C4' C3' H3' O3' 122.5 122.6
C4' C3' H3' C2' 243.1 245.3
O3' C3' H3' C2' 120.6 122.7
H3' C3' O3' HO3' 191.2 302.6
H3' C3' C2' O2' 152.6 122.6
H3' C3' C2' C1' 273.9 241.5
H3' C3' C2' H2' 35.9 360.0
HO3' O3' C3' C2' 313.3 65.3
HO3' O3' C3' H3' 191.2 302.6
O4' C1' C2' O2' 100.6 142.6
O2' C2' C3' H3' 152.6 122.6
C3' C2' O2' C1' 115.3 114.7
C3' C2' O2' H2' 237.5 237.4
C1' C2' O2' H2' 122.2 122.7
O2' C2' C1' N9 229.0 261.5
O2' C2' C1' H1' 339.5 23.7
O4' C1' C2' N9 231.6 241.1
O4' C1' C2' H1' 121.1 118.9
C1' C2' C3' H3' 273.9 241.5
C3' C2' C1' O2' 239.1 241.3
C3' C2' C1' H2' 122.4 118.6
O2' C2' C1' H2' 243.3 237.3
C1' C2' O2' HO2' 4.5 183.9
N9 C1' C2' H1' 249.5 237.8
C2' C1' N9 C8 115.3 266.6
C2' C1' N9 C4 289.3 86.5
H2' C2' C3' H3' 35.9 360.0
C3' C2' H2' O2' 121.8 122.6
C3' C2' H2' C1' 243.9 245.5
O2' C2' H2' C1' 122.1 122.9
H2' C2' O2' HO2' 242.3 61.2
H2' C2' C1' N9 345.7 24.2
H2' C2' C1' H1' 96.2 146.4
HO2' O2' C2' C1' 4.5 183.9
HO2' O2' C2' H2' 242.3 61.2
O4' C1' N9 C2' 126.8 115.5
O4' C1' N9 H1' 239.5 237.8
N9 C1' C2' H2' 345.7 24.2
C2' C1' N9 H1' 112.7 122.3
C8 N9 C1' C4 186.0 180.1
C1' N9 C8 N7 174.8 180.0
C1' N9 C8 H8 354.8 360.0
C1' N9 C4 C5 184.9 180.0
C1' N9 C4 N3 4.7 0.0
O4' C1' H1' C2' 242.9 244.5
O4' C1' H1' N9 118.8 122.2
H1' C1' C2' H2' 96.2 146.4
C2' C1' H1' N9 235.9 237.7
H1' C1' N9 C8 2.6 144.3
H1' C1' N9 C4 176.7 324.2
C8 N9 C1' H1' 2.6 144.3
C1' N9 C8 C4 174.9 180.0
C8 N9 C4 C5 0.1 360.0
C8 N9 C4 N3 180.0 180.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 0.1 0.0
C4 N9 C1' H1' 176.7 324.2
C1' N9 C4 C8 184.8 180.0
C4 N9 C8 N7 359.9 0.0
C4 N9 C8 H8 179.9 180.0
N7 C5 C4 N9 359.9 0.0
C6 C5 C4 N9 179.9 180.0
C5 C4 N9 N3 180.2 180.0
C2 N3 C4 N9 180.1 180.0
N7 C8 N9 C4 359.9 0.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 180.1 180.0
C8 N7 C5 C4 0.0 360.0
H8 C8 N9 C4 179.9 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.1 180.0
N9 C4 C5 N7 359.9 0.0
C5 N7 C8 H8 180.1 180.0
C6 C5 N7 C4 180.1 180.1
N7 C5 C6 O6 359.9 359.9
N7 C5 C6 N1 180.0 179.7
N7 C5 C4 N3 180.1 180.0
N9 C4 C5 C6 179.9 180.0
N7 C5 C6 C4 179.9 179.9
C6 C5 C4 N3 0.0 360.0
O6 C6 C5 N1 179.9 180.2
C5 C6 N1 C2 359.9 0.5
C5 C6 N1 HN1 179.9 179.9
N9 C4 C5 N3 179.8 180.0
N7 C5 C4 C6 180.1 180.1
C4 C5 C6 O6 180.0 180.0
C4 C5 C6 N1 0.1 359.8
C2 N3 C4 C5 359.9 360.0
O6 C6 C5 C4 180.0 180.0
C5 C6 O6 N1 180.1 179.8
O6 C6 N1 C2 180.0 180.3
O6 C6 N1 HN1 360.0 359.7
N1 C6 C5 C4 0.1 359.8
C5 C6 N1 O6 179.9 180.2
C2 N1 C6 HN1 180.0 180.6
C6 N1 C2 N2 179.9 179.7
C6 N1 C2 N3 0.0 359.4
C6 N1 C2 HN1 180.0 179.4
N2 C2 N1 N3 179.9 180.3
N1 C2 N2 HN21 180.0 179.7
N1 C2 N2 HN22 360.0 359.4
N1 C2 N3 C4 0.1 0.3
C6 N1 HN1 C2 180.0 180.6
HN1 N1 C2 N2 359.9 0.3
HN1 N1 C2 N3 180.0 180.0
N2 C2 N1 HN1 359.9 0.3
N1 C2 N2 N3 180.1 179.7
N2 C2 N3 C4 180.2 180.0
HN21 N2 C2 HN22 180.0 180.3
N9 C4 N3 C2 180.1 180.0
C5 C4 N3 C2 359.9 360.0
N3 C2 N1 HN1 180.0 180.0
N1 C2 N3 N2 179.9 180.3
N3 C2 N2 HN21 359.9 0.0
N3 C2 N2 HN22 179.9 179.7
HN21 N2 C2 N3 359.9 0.0
C2 N2 HN21 HN22 180.0 179.7
HN22 N2 C2 N3 179.9 179.7
C2 N2 HN22 HN21 180.0 180.3
N9 C4 N3 C5 180.2 180.0