GDP
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| PB | O1B | doub | 1.48Å | 1.47Å | |
| PB | O2B | sing | 1.61Å | 1.49Å | |
| PB | O3B | sing | 1.61Å | 1.55Å | |
| PB | O3A | sing | 1.61Å | 1.72Å | |
| O2B | HOB2 | sing | 0.97Å | 0.95Å | |
| O3B | HOB3 | sing | 0.97Å | 0.95Å | |
| O3A | PA | sing | 1.61Å | 1.66Å | |
| PA | O1A | doub | 1.48Å | 1.50Å | |
| PA | O2A | sing | 1.61Å | 1.47Å | |
| PA | O5' | sing | 1.61Å | 1.60Å | |
| O2A | HOA2 | sing | 0.97Å | 0.95Å | |
| O5' | C5' | sing | 1.43Å | 1.43Å | |
| C5' | C4' | sing | 1.53Å | 1.53Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.46Å | |
| C4' | C3' | sing | 1.54Å | 1.55Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.44Å | 1.41Å | |
| C3' | O3' | sing | 1.43Å | 1.44Å | |
| C3' | C2' | sing | 1.55Å | 1.54Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C2' | O2' | sing | 1.43Å | 1.42Å | |
| C2' | C1' | sing | 1.55Å | 1.52Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| O2' | HO2' | sing | 0.97Å | 0.95Å | |
| C1' | N9 | sing | 1.47Å | 1.50Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| N9 | C8 | sing | 1.36Å | 1.37Å | Aromatic |
| N9 | C4 | sing | 1.37Å | 1.39Å | Aromatic |
| C8 | N7 | doub | 1.30Å | 1.30Å | Aromatic |
| C8 | H8 | sing | 1.08Å | 1.08Å | |
| N7 | C5 | sing | 1.36Å | 1.39Å | Aromatic |
| C5 | C6 | sing | 1.41Å | 1.42Å | |
| C5 | C4 | doub | 1.40Å | 1.38Å | Aromatic |
| C6 | O6 | doub | 1.22Å | 1.24Å | |
| C6 | N1 | sing | 1.35Å | 1.40Å | |
| N1 | C2 | sing | 1.36Å | 1.37Å | |
| N1 | HN1 | sing | 0.97Å | 1.00Å | |
| C2 | N2 | sing | 1.37Å | 1.33Å | |
| C2 | N3 | doub | 1.31Å | 1.34Å | |
| N2 | HN21 | sing | 0.97Å | 1.00Å | |
| N2 | HN22 | sing | 0.97Å | 1.00Å | |
| N3 | C4 | sing | 1.34Å | 1.34Å |
Angles
| First atom | Second atom | Third atom | 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° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1B | PB | O2B | O3B | 124.3° | 120.0° |
| O1B | PB | O2B | O3A | 116.7° | 120.0° |
| O1B | PB | O3B | O3A | 128.7° | 120.0° |
| O1B | PB | O2B | HOB2 | 0.0° | 60.0° |
| O1B | PB | O3B | HOB3 | 0.0° | 180.0° |
| O1B | PB | O3A | PA | 48.5° | 39.9° |
| O2B | PB | O3B | O3A | 105.8° | 120.0° |
| O2B | PB | O3B | HOB3 | 125.5° | 59.9° |
| O2B | PB | O3A | PA | 172.7° | 160.0° |
| O3B | PB | O2B | HOB2 | 124.3° | 60.0° |
| O3B | PB | O3A | PA | 84.3° | 80.0° |
| O3A | PB | O2B | HOB2 | 116.6° | 180.0° |
| O3A | PB | O3B | HOB3 | 128.7° | 60.1° |
| PB | O3A | PA | O1A | 149.6° | 40.0° |
| PB | O3A | PA | O2A | 8.3° | 79.9° |
| PB | O3A | PA | O5' | 106.3° | 160.0° |
| O3A | PA | O1A | O2A | 144.0° | 120.0° |
| O3A | PA | O1A | O5' | 93.2° | 120.0° |
| O3A | PA | O2A | O5' | 106.3° | 120.0° |
| O3A | PA | O2A | HOA2 | 133.4° | 60.0° |
| O3A | PA | O5' | C5' | 78.4° | 175.0° |
| O1A | PA | O2A | O5' | 120.4° | 120.0° |
| O1A | PA | O2A | HOA2 | 0.0° | 180.0° |
| O1A | PA | O5' | C5' | 177.5° | 55.1° |
| O2A | PA | O5' | C5' | 51.5° | 64.9° |
| O5' | PA | O2A | HOA2 | 120.4° | 60.1° |
| PA | O5' | C5' | C4' | 148.2° | 180.0° |
| PA | O5' | C5' | H5' | 28.6° | 60.1° |
| PA | O5' | C5' | H5'' | 92.2° | 60.0° |
| O5' | C5' | C4' | H5' | 119.6° | 119.9° |
| O5' | C5' | C4' | H5'' | 119.6° | 120.1° |
| O5' | C5' | H5' | H5'' | 121.1° | 120.0° |
| O5' | C5' | C4' | O4' | 48.7° | 66.4° |
| O5' | C5' | C4' | C3' | 57.8° | 175.8° |
| O5' | C5' | C4' | H4' | 176.5° | 54.6° |
| C4' | C5' | H5' | H5'' | 121.1° | 120.0° |
| C5' | C4' | O4' | C3' | 115.6° | 119.5° |
| C5' | C4' | O4' | H4' | 127.2° | 121.0° |
| C5' | C4' | C3' | H4' | 125.9° | 121.0° |
| C5' | C4' | O4' | C1' | 152.1° | 146.0° |
| C5' | C4' | C3' | O3' | 85.1° | 119.8° |
| C5' | C4' | C3' | C2' | 164.0° | 121.5° |
| C5' | C4' | C3' | H3' | 41.7° | 2.7° |
| H5' | C5' | C4' | O4' | 168.4° | 53.5° |
| H5' | C5' | C4' | C3' | 61.9° | 64.3° |
| H5' | C5' | C4' | H4' | 63.9° | 174.6° |
| H5'' | C5' | C4' | O4' | 70.8° | 173.5° |
| H5'' | C5' | C4' | C3' | 177.3° | 55.7° |
| H5'' | C5' | C4' | H4' | 56.9° | 65.4° |
| O4' | C4' | C3' | H4' | 118.3° | 119.5° |
| O4' | C4' | C3' | O3' | 159.1° | 120.7° |
| O4' | C4' | C3' | C2' | 48.2° | 2.0° |
| O4' | C4' | C3' | H3' | 74.1° | 116.8° |
| C4' | O4' | C1' | C2' | 9.7° | 40.1° |
| C4' | O4' | C1' | N9 | 127.4° | 158.5° |
| C4' | O4' | C1' | H1' | 111.8° | 78.4° |
| C3' | C4' | O4' | C1' | 36.4° | 26.5° |
| C4' | C3' | O3' | C2' | 106.2° | 114.8° |
| C4' | C3' | O3' | H3' | 125.7° | 122.5° |
| C4' | C3' | C2' | H3' | 122.2° | 118.7° |
| C4' | C3' | O3' | HO3' | 180.0° | 180.0° |
| C4' | C3' | C2' | O2' | 70.9° | 139.1° |
| C4' | C3' | C2' | C1' | 43.5° | 20.9° |
| C4' | C3' | C2' | H2' | 161.2° | 97.3° |
| H4' | C4' | O4' | C1' | 80.8° | 93.0° |
| H4' | C4' | C3' | O3' | 40.9° | 1.2° |
| H4' | C4' | C3' | C2' | 70.0° | 117.5° |
| H4' | C4' | C3' | H3' | 167.7° | 123.7° |
| O4' | C1' | C2' | C3' | 21.9° | 37.0° |
| O4' | C1' | C2' | O2' | 95.6° | 155.2° |
| O4' | C1' | C2' | N9 | 114.0° | 118.4° |
| O4' | C1' | C2' | H1' | 122.6° | 118.5° |
| O4' | C1' | C2' | H2' | 139.4° | 81.2° |
| O4' | C1' | N9 | H1' | 121.8° | 123.0° |
| O4' | C1' | N9 | C8 | 10.7° | 23.5° |
| O4' | C1' | N9 | C4 | 169.2° | 156.8° |
| O3' | C3' | C2' | H3' | 129.2° | 122.6° |
| O3' | C3' | C2' | O2' | 37.7° | 20.4° |
| O3' | C3' | C2' | C1' | 152.1° | 97.8° |
| O3' | C3' | C2' | H2' | 90.2° | 144.0° |
| C2' | C3' | O3' | HO3' | 73.8° | 65.2° |
| C3' | C2' | O2' | C1' | 108.9° | 112.7° |
| C3' | C2' | O2' | H2' | 126.9° | 123.6° |
| C3' | C2' | C1' | H2' | 117.5° | 118.2° |
| C3' | C2' | O2' | HO2' | 180.0° | 61.5° |
| C3' | C2' | C1' | N9 | 92.1° | 155.5° |
| C3' | C2' | C1' | H1' | 144.5° | 81.4° |
| H3' | C3' | O3' | HO3' | 54.4° | 57.5° |
| H3' | C3' | C2' | O2' | 166.9° | 102.2° |
| H3' | C3' | C2' | C1' | 78.7° | 139.6° |
| H3' | C3' | C2' | H2' | 39.0° | 21.4° |
| O2' | C2' | C1' | H2' | 125.1° | 123.6° |
| O2' | C2' | C1' | N9 | 150.4° | 86.3° |
| O2' | C2' | C1' | H1' | 27.0° | 36.8° |
| C1' | C2' | O2' | HO2' | 71.1° | 174.2° |
| C2' | C1' | N9 | H1' | 123.3° | 123.0° |
| C2' | C1' | N9 | C8 | 104.2° | 90.5° |
| C2' | C1' | N9 | C4 | 75.9° | 89.2° |
| H2' | C2' | O2' | HO2' | 53.1° | 62.2° |
| H2' | C2' | C1' | N9 | 25.4° | 37.2° |
| H2' | C2' | C1' | H1' | 98.0° | 160.3° |
| C1' | N9 | C8 | C4 | 180.0° | 179.7° |
| C1' | N9 | C8 | N7 | 179.9° | 180.0° |
| C1' | N9 | C8 | H8 | 0.0° | 0.0° |
| C1' | N9 | C4 | C5 | 179.9° | 179.9° |
| C1' | N9 | C4 | N3 | 0.1° | 0.7° |
| H1' | C1' | N9 | C8 | 132.5° | 146.5° |
| H1' | C1' | N9 | C4 | 47.4° | 33.8° |
| N9 | C8 | N7 | H8 | 180.0° | 180.0° |
| N9 | C8 | N7 | C5 | 0.0° | 0.0° |
| C8 | N9 | C4 | C5 | 0.1° | 0.4° |
| C8 | N9 | C4 | N3 | 180.0° | 179.5° |
| C4 | N9 | C8 | N7 | 0.0° | 0.3° |
| C4 | N9 | C8 | H8 | 180.0° | 179.8° |
| N9 | C4 | C5 | N7 | 0.1° | 0.4° |
| N9 | C4 | C5 | C6 | 179.9° | 179.8° |
| N9 | C4 | C5 | N3 | 180.0° | 179.3° |
| N9 | C4 | N3 | C2 | 180.0° | 179.6° |
| C8 | N7 | C5 | C6 | 179.8° | 180.0° |
| C8 | N7 | C5 | C4 | 0.1° | 0.2° |
| H8 | C8 | N7 | C5 | 180.0° | 180.0° |
| N7 | C5 | C6 | C4 | 179.8° | 179.7° |
| N7 | C5 | C6 | O6 | 0.1° | 0.0° |
| N7 | C5 | C6 | N1 | 179.9° | 180.0° |
| N7 | C5 | C4 | N3 | 180.0° | 179.7° |
| C5 | C6 | O6 | N1 | 180.0° | 180.0° |
| C5 | C6 | N1 | C2 | 0.1° | 0.0° |
| C5 | C6 | N1 | HN1 | 179.9° | 180.0° |
| C6 | C5 | C4 | N3 | 0.2° | 0.6° |
| C4 | C5 | C6 | O6 | 179.9° | 179.7° |
| C4 | C5 | C6 | N1 | 0.1° | 0.3° |
| C5 | C4 | N3 | C2 | 0.1° | 0.6° |
| O6 | C6 | N1 | C2 | 180.0° | 180.0° |
| O6 | C6 | N1 | HN1 | 0.0° | 0.0° |
| C6 | N1 | C2 | HN1 | 180.0° | 180.0° |
| C6 | N1 | C2 | N2 | 179.9° | 180.0° |
| C6 | N1 | C2 | N3 | 0.0° | 0.0° |
| N1 | C2 | N2 | N3 | 179.9° | 179.9° |
| N1 | C2 | N2 | HN21 | 179.9° | 0.0° |
| N1 | C2 | N2 | HN22 | 0.0° | 180.0° |
| N1 | C2 | N3 | C4 | 0.0° | 0.3° |
| HN1 | N1 | C2 | N2 | 0.1° | 0.1° |
| HN1 | N1 | C2 | N3 | 180.0° | 180.0° |
| C2 | N2 | HN21 | HN22 | 180.0° | 180.0° |
| N2 | C2 | N3 | C4 | 179.9° | 179.7° |
| N3 | C2 | N2 | HN21 | 0.0° | 180.0° |
| N3 | C2 | N2 | HN22 | 180.0° | 0.1° |
