PDB Chemical Component GDP

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 GDP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PB O1B 1.469 1.480
PB O2B 1.495 1.610
PB O3B 1.554 1.610
PB O3A 1.719 1.610
O2B HOB2 0.950 0.968
O3B HOB3 0.950 0.967
O3A PA 1.664 1.610
PA O1A 1.499 1.480
PA O2A 1.467 1.610
PA O5' 1.600 1.610
O2A HOA2 0.950 0.967
O5' C5' 1.425 1.429
C5' C4' 1.526 1.530
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.089
C4' O4' 1.459 1.437
C4' C3' 1.547 1.541
C4' H4' 1.100 1.091
O4' C1' 1.407 1.444
C3' O3' 1.445 1.429
C3' C2' 1.542 1.548
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.968
C2' O2' 1.422 1.429
C2' C1' 1.516 1.550
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.968
C1' N9 1.502 1.465
C1' H1' 1.100 1.090
N9 C8 1.366 1.364
N9 C4 1.387 1.369
C8 N7 1.299 1.301
C8 H8 1.080 1.080
N7 C5 1.389 1.356
C5 C6 1.417 1.414
C5 C4 1.382 1.400
C6 O6 1.244 1.219
C6 N1 1.402 1.352
N1 C2 1.369 1.363
N1 HN1 1.000 0.969
C2 N2 1.330 1.372
C2 N3 1.339 1.314
N2 HN21 1.000 0.970
N2 HN22 1.000 0.970
N3 C4 1.340 1.339

Bond Angles for GDP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1B PB O2B 118.0 109.5
O1B PB O3B 116.3 109.5
O1B PB O3A 107.4 109.5
O2B PB O3B 96.3 109.5
O2B PB O3A 101.0 109.5
PB O2B HOB2 109.5 114.0
O3B PB O3A 116.9 109.4
PB O3B HOB3 109.5 114.0
PB O3A PA 123.0 134.0
O3A PA O1A 98.6 109.5
O3A PA O2A 127.0 109.5
O3A PA O5' 91.0 109.5
O1A PA O2A 121.8 109.5
O1A PA O5' 103.7 109.4
O2A PA O5' 108.8 109.5
PA O2A HOA2 109.5 114.0
PA O5' C5' 124.8 123.0
O5' C5' C4' 107.0 109.5
O5' C5' H5' 110.1 109.4
O5' C5' H5'' 110.1 109.5
C4' C5' H5' 110.1 109.4
C4' C5' H5'' 110.1 109.5
C5' C4' O4' 111.2 109.9
C5' C4' C3' 111.0 109.9
C5' C4' H4' 112.1 109.8
H5' C5' H5'' 109.5 109.5
O4' C4' C3' 96.8 107.3
O4' C4' H4' 113.1 109.9
C4' O4' C1' 111.1 107.0
C3' C4' H4' 111.8 110.0
C4' C3' O3' 104.2 110.5
C4' C3' C2' 100.8 104.2
C4' C3' H3' 113.8 110.5
O4' C1' C2' 106.7 103.5
O4' C1' N9 105.2 110.6
O4' C1' H1' 112.4 110.6
O3' C3' C2' 107.1 110.5
O3' C3' H3' 115.6 110.4
C3' O3' HO3' 109.5 114.0
C2' C3' H3' 113.9 110.6
C3' C2' O2' 112.4 110.9
C3' C2' C1' 99.6 102.1
C3' C2' H2' 111.2 110.9
O2' C2' C1' 108.3 110.9
O2' C2' H2' 113.1 110.8
C2' O2' HO2' 109.5 114.0
C1' C2' H2' 111.6 110.9
C2' C1' N9 110.8 110.6
C2' C1' H1' 110.7 110.6
N9 C1' H1' 110.9 110.7
C1' N9 C8 132.1 126.3
C1' N9 C4 121.3 126.2
C8 N9 C4 106.6 107.5
N9 C8 N7 113.1 109.8
N9 C8 H8 123.4 125.1
N9 C4 C5 104.9 106.1
N9 C4 N3 124.2 134.2
N7 C8 H8 123.4 125.1
C8 N7 C5 105.0 109.4
N7 C5 C6 131.9 134.2
N7 C5 C4 110.4 107.2
C6 C5 C4 117.8 118.6
C5 C6 O6 128.0 120.8
C5 C6 N1 111.5 118.3
C5 C4 N3 130.8 119.6
O6 C6 N1 120.5 120.9
C6 N1 C2 125.5 120.3
C6 N1 HN1 117.3 119.8
C2 N1 HN1 117.3 119.9
N1 C2 N2 115.9 119.0
N1 C2 N3 123.8 121.9
N2 C2 N3 120.3 119.1
C2 N2 HN21 120.0 120.0
C2 N2 HN22 120.0 120.0
C2 N3 C4 110.6 121.2
HN21 N2 HN22 120.0 120.0

Torsion Angles for GDP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2B PB O1B O3B 246.4 240.0
O2B PB O1B O3A 113.2 120.0
O1B PB O2B HOB2 360.0 60.0
O3B PB O1B O3A 226.8 240.0
O1B PB O3B HOB3 360.0 180.0
O1B PB O3A PA 311.5 320.1
O1B PB O2B O3B 124.3 120.0
O1B PB O2B O3A 243.3 240.0
O3B PB O2B O3A 119.1 120.0
O2B PB O3B HOB3 125.5 300.1
O2B PB O3A PA 187.3 200.0
O1B PB O3B O2B 234.5 240.0
O1B PB O3B O3A 128.7 120.0
O2B PB O3B O3A 254.2 240.0
O3B PB O2B HOB2 235.7 300.0
O3B PB O3A PA 84.3 80.0
O1B PB O3A O2B 124.2 120.0
O1B PB O3A O3B 227.2 240.0
O2B PB O3A O3B 103.0 120.0
O3A PB O2B HOB2 116.6 180.0
O3A PB O3B HOB3 231.3 60.1
PB O3A PA O1A 210.4 320.0
PB O3A PA O2A 351.7 79.9
PB O3A PA O5' 106.3 200.0
HOB2 O2B PB O3B 235.7 300.0
HOB2 O2B PB O3A 116.6 180.0
HOB3 O3B PB O3A 231.3 60.1
O1A PA O3A O2A 218.7 240.0
O1A PA O3A O5' 104.0 120.0
O2A PA O3A O5' 245.4 240.0
O3A PA O2A HOA2 226.6 60.0
O3A PA O5' C5' 281.6 175.0
O3A PA O1A O2A 144.0 120.0
O3A PA O1A O5' 266.8 240.0
O2A PA O1A O5' 122.8 120.0
O1A PA O2A HOA2 360.0 180.0
O1A PA O5' C5' 182.5 55.1
O3A PA O2A O1A 226.7 240.0
O3A PA O2A O5' 106.3 120.0
O1A PA O2A O5' 239.6 240.0
O2A PA O5' C5' 51.5 295.1
O3A PA O5' O1A 99.1 120.0
O3A PA O5' O2A 230.1 240.0
O1A PA O5' O2A 131.0 120.0
O5' PA O2A HOA2 120.4 299.9
PA O5' C5' C4' 211.8 180.0
PA O5' C5' H5' 331.4 299.9
PA O5' C5' H5'' 92.2 60.0
HOA2 O2A PA O5' 120.4 299.9
C4' C5' O5' H5' 240.4 240.1
C4' C5' O5' H5'' 119.6 120.1
O5' C5' C4' O4' 311.3 66.4
O5' C5' C4' C3' 57.8 184.2
O5' C5' C4' H4' 183.5 305.4
H5' C5' O5' H5'' 239.3 240.0
O5' C5' C4' H5' 119.6 119.9
O5' C5' C4' H5'' 240.4 239.9
H5' C5' C4' H5'' 120.8 120.0
O4' C4' C5' C3' 253.5 242.2
O4' C4' C5' H4' 127.8 121.0
C5' C4' O4' C1' 152.1 146.0
C3' C4' C5' H4' 234.3 238.9
C5' C4' C3' O3' 85.1 119.8
C5' C4' C3' C2' 196.0 238.5
C5' C4' C3' H3' 318.3 357.3
O5' C5' H5' C4' 242.3 240.0
O5' C5' H5' H5'' 121.1 120.0
C4' C5' H5' H5'' 238.9 240.0
H5' C5' C4' O4' 191.6 306.5
H5' C5' C4' C3' 298.1 64.3
H5' C5' C4' H4' 63.9 185.4
O5' C5' H5'' C4' 117.7 120.1
O5' C5' H5'' H5' 238.9 240.0
C4' C5' H5'' H5' 121.2 119.9
H5'' C5' C4' O4' 70.8 186.5
H5'' C5' C4' C3' 177.3 304.3
H5'' C5' C4' H4' 303.1 65.4
O4' C4' C5' H5' 191.6 306.5
O4' C4' C5' H5'' 70.8 186.5
C5' C4' O4' C3' 115.6 119.5
C5' C4' O4' H4' 232.8 239.0
C3' C4' O4' H4' 117.2 119.5
O4' C4' C3' O3' 200.9 239.3
O4' C4' C3' C2' 311.8 358.0
O4' C4' C3' H3' 74.1 116.8
C4' O4' C1' C2' 350.3 319.9
C4' O4' C1' N9 232.6 201.5
C4' O4' C1' H1' 111.8 78.4
C3' C4' C5' H5' 298.1 64.3
C3' C4' C5' H5'' 177.3 304.3
C5' C4' C3' O4' 244.2 240.5
C5' C4' C3' H4' 125.9 121.0
O4' C4' C3' H4' 241.7 240.5
C3' C4' O4' C1' 36.4 26.5
O3' C3' C4' C2' 249.1 241.3
O3' C3' C4' H3' 126.8 122.5
C4' C3' O3' HO3' 180.0 180.0
C2' C3' C4' H3' 237.7 241.2
C4' C3' C2' O2' 289.1 220.9
C4' C3' C2' C1' 43.5 339.1
C4' C3' C2' H2' 161.2 97.3
H4' C4' C5' H5' 63.9 185.4
H4' C4' C5' H5'' 303.1 65.4
C5' C4' H4' O4' 126.7 121.1
C5' C4' H4' C3' 234.7 238.9
O4' C4' H4' C3' 108.0 117.8
H4' C4' O4' C1' 279.2 267.0
H4' C4' C3' O3' 319.1 358.8
H4' C4' C3' C2' 70.0 117.5
H4' C4' C3' H3' 192.3 236.3
C1' O4' C4' C3' 36.4 26.5
C1' O4' C4' H4' 279.2 267.0
C3' C2' C1' O4' 338.1 37.0
O2' C2' C1' O4' 95.6 155.2
O4' C1' C2' H2' 220.6 278.8
C2' C1' O4' N9 117.7 118.5
C2' C1' O4' H1' 238.5 241.5
N9 C1' O4' H1' 120.8 123.1
O4' C1' N9 C8 10.7 23.5
O4' C1' N9 C4 190.8 203.2
O3' C3' C4' H4' 319.1 358.8
C4' C3' O3' C2' 106.2 114.8
C4' C3' O3' H3' 234.3 237.5
C2' C3' O3' H3' 128.2 122.7
O3' C3' C2' O2' 37.7 339.6
O3' C3' C2' C1' 152.1 97.8
O3' C3' C2' H2' 269.8 216.0
C2' C3' C4' H4' 70.0 117.5
C4' C3' C2' O3' 251.4 241.3
C4' C3' C2' H3' 122.2 118.7
O4' C1' C2' C3' 338.1 37.0
O3' C3' C2' H3' 230.8 237.4
C2' C3' O3' HO3' 73.8 65.2
O2' C2' C3' C1' 245.6 241.8
O2' C2' C3' H2' 127.9 123.6
C3' C2' O2' HO2' 180.0 298.5
C1' C2' C3' H2' 242.3 241.7
C3' C2' C1' N9 92.1 155.5
C3' C2' C1' H1' 215.5 278.6
H3' C3' C4' H4' 192.3 236.3
C4' C3' H3' O3' 120.6 122.5
C4' C3' H3' C2' 245.3 245.2
O3' C3' H3' C2' 124.7 122.7
H3' C3' O3' HO3' 305.6 302.5
H3' C3' C2' O2' 166.9 102.2
H3' C3' C2' C1' 281.3 220.4
H3' C3' C2' H2' 39.0 338.6
HO3' O3' C3' C2' 73.8 65.2
HO3' O3' C3' H3' 305.6 302.5
O4' C1' C2' O2' 95.6 155.2
O2' C2' C3' H3' 166.9 102.2
C3' C2' O2' C1' 108.9 112.7
C3' C2' O2' H2' 233.1 236.4
C1' C2' O2' H2' 124.1 123.7
O2' C2' C1' N9 209.6 273.7
O2' C2' C1' H1' 333.0 36.8
O4' C1' C2' N9 246.0 241.6
O4' C1' C2' H1' 122.6 118.5
C1' C2' C3' H3' 281.3 220.4
C3' C2' C1' O2' 242.5 241.8
C3' C2' C1' H2' 117.5 118.2
O2' C2' C1' H2' 234.9 236.4
C1' C2' O2' HO2' 71.1 185.8
N9 C1' C2' H1' 236.6 236.9
C2' C1' N9 C8 255.8 269.5
C2' C1' N9 C4 75.9 89.2
H2' C2' C3' H3' 39.0 338.6
C3' C2' H2' O2' 127.5 123.6
C3' C2' H2' C1' 249.8 247.2
O2' C2' H2' C1' 122.3 123.6
H2' C2' O2' HO2' 306.9 62.2
H2' C2' C1' N9 334.6 37.2
H2' C2' C1' H1' 98.0 160.3
HO2' O2' C2' C1' 71.1 185.8
HO2' O2' C2' H2' 306.9 62.2
O4' C1' N9 C2' 114.9 114.0
O4' C1' N9 H1' 238.2 237.0
N9 C1' C2' H2' 334.6 37.2
C2' C1' N9 H1' 123.3 123.0
C8 N9 C1' C4 180.0 180.3
C1' N9 C8 N7 180.1 180.0
C1' N9 C8 H8 0.0 360.0
C1' N9 C4 C5 179.9 179.9
C1' N9 C4 N3 359.9 0.7
O4' C1' H1' C2' 240.8 246.0
O4' C1' H1' N9 117.5 123.0
H1' C1' C2' H2' 98.0 160.3
C2' C1' H1' N9 236.6 237.0
H1' C1' N9 C8 132.5 146.5
H1' C1' N9 C4 312.6 326.2
C8 N9 C1' H1' 132.5 146.5
C1' N9 C8 C4 180.0 179.7
C8 N9 C4 C5 359.9 359.6
C8 N9 C4 N3 180.0 180.5
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 0.0 360.0
C4 N9 C1' H1' 312.6 326.2
C1' N9 C4 C8 180.0 180.3
C4 N9 C8 N7 0.0 0.3
C4 N9 C8 H8 180.0 180.2
N7 C5 C4 N9 0.1 0.4
C6 C5 C4 N9 179.9 180.2
C5 C4 N9 N3 180.0 179.1
C2 N3 C4 N9 180.0 179.6
N7 C8 N9 C4 0.0 0.3
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 180.2 180.0
C8 N7 C5 C4 359.9 359.8
H8 C8 N9 C4 180.0 180.2
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.0 180.0
N9 C4 C5 N7 0.1 0.4
C5 N7 C8 H8 180.0 180.0
C6 C5 N7 C4 180.2 180.3
N7 C5 C6 O6 359.9 360.0
N7 C5 C6 N1 179.9 180.0
N7 C5 C4 N3 180.0 179.7
N9 C4 C5 C6 179.9 180.2
N7 C5 C6 C4 179.8 179.7
C6 C5 C4 N3 359.8 359.4
O6 C6 C5 N1 180.0 180.0
C5 C6 N1 C2 359.9 0.0
C5 C6 N1 HN1 179.9 180.0
N9 C4 C5 N3 180.0 180.7
N7 C5 C4 C6 180.2 180.2
C4 C5 C6 O6 180.1 180.3
C4 C5 C6 N1 0.1 0.3
C2 N3 C4 C5 0.1 0.6
O6 C6 C5 C4 180.1 180.3
C5 C6 O6 N1 180.0 180.0
O6 C6 N1 C2 180.0 180.0
O6 C6 N1 HN1 360.0 360.0
N1 C6 C5 C4 0.1 0.3
C5 C6 N1 O6 180.0 180.0
C2 N1 C6 HN1 180.0 180.0
C6 N1 C2 N2 180.1 180.0
C6 N1 C2 N3 0.0 360.0
C6 N1 C2 HN1 180.0 180.0
N2 C2 N1 N3 180.1 180.1
N1 C2 N2 HN21 179.9 360.0
N1 C2 N2 HN22 360.0 180.0
N1 C2 N3 C4 360.0 359.7
C6 N1 HN1 C2 180.0 180.0
HN1 N1 C2 N2 0.1 0.1
HN1 N1 C2 N3 180.0 180.0
N2 C2 N1 HN1 0.1 0.1
N1 C2 N2 N3 179.9 179.9
N2 C2 N3 C4 179.9 179.7
HN21 N2 C2 HN22 180.0 180.0
N9 C4 N3 C2 180.0 179.6
C5 C4 N3 C2 0.1 0.6
N3 C2 N1 HN1 180.0 180.0
N1 C2 N3 N2 180.1 180.1
N3 C2 N2 HN21 360.0 180.0
N3 C2 N2 HN22 180.0 0.1
HN21 N2 C2 N3 360.0 180.0
C2 N2 HN21 HN22 180.0 180.0
HN22 N2 C2 N3 180.0 0.1
C2 N2 HN22 HN21 180.0 180.0
N9 C4 N3 C5 180.0 179.0