HDV
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O3G | PG | doub | 1.48Å | 1.49Å | |
| O2B | PB | doub | 1.48Å | 1.48Å | |
| O1G | PG | sing | 1.61Å | 1.49Å | |
| O1B | PB | sing | 1.61Å | 1.45Å | |
| PG | O3B | sing | 1.61Å | 1.63Å | |
| PG | O2G | sing | 1.61Å | 1.44Å | |
| PB | O3B | sing | 1.61Å | 1.57Å | |
| PB | O3A | sing | 1.61Å | 1.57Å | |
| O3A | PA | sing | 1.61Å | 1.62Å | |
| O2A | PA | doub | 1.48Å | 1.43Å | |
| PA | O5' | sing | 1.61Å | 1.63Å | |
| PA | O1A | sing | 1.61Å | 1.46Å | |
| O5' | C5' | sing | 1.43Å | 1.41Å | |
| F2' | C2' | sing | 1.40Å | 1.44Å | |
| C3' | O3' | sing | 1.43Å | 1.45Å | |
| C3' | C2' | sing | 1.55Å | 1.50Å | |
| C3' | C4' | sing | 1.55Å | 1.51Å | |
| C5' | C4' | sing | 1.53Å | 1.54Å | |
| C2' | C1' | sing | 1.54Å | 1.49Å | |
| C4' | O4' | sing | 1.44Å | 1.47Å | |
| O4' | C1' | sing | 1.44Å | 1.47Å | |
| C8 | N9 | sing | 1.36Å | 1.38Å | Aromatic |
| C8 | N7 | doub | 1.30Å | 1.36Å | Aromatic |
| C1' | N9 | sing | 1.46Å | 1.45Å | |
| N9 | C4 | sing | 1.37Å | 1.34Å | Aromatic |
| N7 | C5 | sing | 1.35Å | 1.43Å | Aromatic |
| C4 | C5 | doub | 1.40Å | 1.42Å | Aromatic |
| C4 | N3 | sing | 1.33Å | 1.31Å | Aromatic |
| C5 | C6 | sing | 1.41Å | 1.40Å | Aromatic |
| N3 | C2 | doub | 1.32Å | 1.36Å | Aromatic |
| C6 | N6 | sing | 1.38Å | 1.41Å | |
| C6 | N1 | doub | 1.33Å | 1.28Å | Aromatic |
| C2 | N1 | sing | 1.32Å | 1.32Å | Aromatic |
| C2 | CL2 | sing | 1.51Å | 1.50Å | |
| O1A | H1 | sing | 0.97Å | 0.95Å | |
| O1B | H2 | sing | 0.97Å | 0.95Å | |
| O2G | H3 | sing | 0.97Å | 0.95Å | |
| O1G | H4 | sing | 0.97Å | 0.95Å | |
| C5' | H5 | sing | 1.09Å | 1.10Å | |
| C5' | H6 | sing | 1.09Å | 1.10Å | |
| C4' | H7 | sing | 1.09Å | 1.10Å | |
| C3' | H8 | sing | 1.09Å | 1.10Å | |
| O3' | H9 | sing | 0.97Å | 0.95Å | |
| C2' | H10 | sing | 1.09Å | 1.10Å | |
| C1' | H11 | sing | 1.09Å | 1.10Å | |
| C8 | H12 | sing | 1.08Å | 1.08Å | |
| CL2 | H13 | sing | 1.09Å | 1.10Å | |
| CL2 | H14 | sing | 1.09Å | 1.10Å | |
| CL2 | H15 | sing | 1.09Å | 1.10Å | |
| N6 | H16 | sing | 0.97Å | 1.00Å | |
| N6 | H17 | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O3G | PG | O1G | 115.9° | 109.5° |
| O3G | PG | O3B | 110.9° | 109.4° |
| O3G | PG | O2G | 108.9° | 109.5° |
| O2B | PB | O1B | 116.4° | 109.5° |
| O2B | PB | O3B | 114.3° | 109.5° |
| O2B | PB | O3A | 98.6° | 109.5° |
| O1G | PG | O3B | 100.6° | 109.5° |
| O1G | PG | O2G | 112.2° | 109.5° |
| PG | O1G | H4 | 109.5° | 114.0° |
| O1B | PB | O3B | 108.7° | 109.5° |
| O1B | PB | O3A | 113.3° | 109.5° |
| PB | O1B | H2 | 109.5° | 114.0° |
| O3B | PG | O2G | 107.8° | 109.4° |
| PG | O3B | PB | 129.9° | 134.0° |
| PG | O2G | H3 | 109.5° | 114.0° |
| O3B | PB | O3A | 104.7° | 109.4° |
| PB | O3A | PA | 128.8° | 134.0° |
| O3A | PA | O2A | 114.7° | 109.5° |
| O3A | PA | O5' | 96.1° | 109.5° |
| O3A | PA | O1A | 106.1° | 109.5° |
| O2A | PA | O5' | 105.4° | 109.5° |
| O2A | PA | O1A | 117.9° | 109.5° |
| O5' | PA | O1A | 114.8° | 109.4° |
| PA | O5' | C5' | 116.3° | 123.0° |
| PA | O1A | H1 | 109.5° | 114.0° |
| O5' | C5' | C4' | 107.3° | 109.5° |
| O5' | C5' | H5 | 110.0° | 109.4° |
| O5' | C5' | H6 | 110.0° | 109.6° |
| F2' | C2' | C3' | 111.4° | 110.5° |
| F2' | C2' | C1' | 109.1° | 110.5° |
| F2' | C2' | H10 | 110.9° | 110.5° |
| O3' | C3' | C2' | 109.4° | 110.9° |
| O3' | C3' | C4' | 107.8° | 110.9° |
| O3' | C3' | H8 | 111.0° | 110.8° |
| C3' | O3' | H9 | 109.5° | 114.0° |
| C2' | C3' | C4' | 108.2° | 102.1° |
| C3' | C2' | C1' | 104.9° | 104.2° |
| C2' | C3' | H8 | 110.3° | 111.0° |
| C3' | C2' | H10 | 110.1° | 110.5° |
| C3' | C4' | C5' | 118.4° | 110.6° |
| C3' | C4' | O4' | 101.8° | 103.5° |
| C3' | C4' | H7 | 110.4° | 110.8° |
| C4' | C3' | H8 | 110.1° | 110.9° |
| C5' | C4' | O4' | 104.7° | 110.6° |
| C4' | C5' | H5 | 110.0° | 109.4° |
| C4' | C5' | H6 | 110.0° | 109.5° |
| C5' | C4' | H7 | 110.0° | 110.5° |
| C2' | C1' | O4' | 102.9° | 107.3° |
| C2' | C1' | N9 | 121.0° | 109.9° |
| C1' | C2' | H10 | 110.2° | 110.5° |
| C2' | C1' | H11 | 110.2° | 109.9° |
| C4' | O4' | C1' | 113.6° | 106.9° |
| O4' | C4' | H7 | 111.0° | 110.6° |
| O4' | C1' | N9 | 100.4° | 109.9° |
| O4' | C1' | H11 | 110.5° | 110.0° |
| N9 | C8 | N7 | 111.2° | 110.0° |
| C8 | N9 | C1' | 129.0° | 126.3° |
| C8 | N9 | C4 | 109.8° | 107.4° |
| N9 | C8 | H12 | 124.4° | 125.0° |
| C8 | N7 | C5 | 104.0° | 109.4° |
| N7 | C8 | H12 | 124.4° | 125.1° |
| C1' | N9 | C4 | 121.1° | 126.3° |
| N9 | C1' | H11 | 110.8° | 109.8° |
| N9 | C4 | C5 | 105.9° | 106.0° |
| N9 | C4 | N3 | 134.5° | 134.9° |
| N7 | C5 | C4 | 109.0° | 107.2° |
| N7 | C5 | C6 | 129.4° | 134.7° |
| C5 | C4 | N3 | 119.5° | 119.1° |
| C4 | C5 | C6 | 121.6° | 118.2° |
| C4 | N3 | C2 | 113.4° | 120.6° |
| C5 | C6 | N6 | 121.0° | 120.8° |
| C5 | C6 | N1 | 116.8° | 118.5° |
| N3 | C2 | N1 | 129.7° | 122.5° |
| N3 | C2 | CL2 | 117.3° | 118.8° |
| N6 | C6 | N1 | 122.1° | 120.7° |
| C6 | N6 | H16 | 109.5° | 120.0° |
| C6 | N6 | H17 | 109.5° | 120.0° |
| C6 | N1 | C2 | 118.9° | 121.2° |
| N1 | C2 | CL2 | 113.0° | 118.8° |
| C2 | CL2 | H13 | 109.5° | 109.5° |
| C2 | CL2 | H14 | 109.5° | 109.5° |
| C2 | CL2 | H15 | 109.5° | 109.4° |
| H5 | C5' | H6 | 109.5° | 109.5° |
| H13 | CL2 | H14 | 109.4° | 109.5° |
| H13 | CL2 | H15 | 109.5° | 109.5° |
| H14 | CL2 | H15 | 109.5° | 109.4° |
| H16 | N6 | H17 | 109.5° | 119.9° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O3G | PG | O1G | O3B | 119.6° | 120.0° |
| O3G | PG | O1G | O2G | 126.0° | 120.0° |
| O3G | PG | O3B | O2G | 119.1° | 120.0° |
| O3G | PG | O3B | PB | 24.0° | 40.0° |
| O3G | PG | O2G | H3 | 0.0° | 180.0° |
| O3G | PG | O1G | H4 | 0.0° | 60.1° |
| O2B | PB | O1B | O3B | 130.8° | 120.1° |
| O2B | PB | O1B | O3A | 113.3° | 120.0° |
| O2B | PB | O3B | PG | 1.9° | 45.0° |
| O2B | PB | O3B | O3A | 106.7° | 120.0° |
| O2B | PB | O3A | PA | 162.2° | 40.0° |
| O2B | PB | O1B | H2 | 0.0° | 180.0° |
| O1G | PG | O3B | O2G | 117.7° | 120.0° |
| O1G | PG | O3B | PB | 147.2° | 160.0° |
| O1G | PG | O2G | H3 | 129.7° | 60.0° |
| O1B | PB | O3B | PG | 130.0° | 75.0° |
| O1B | PB | O3B | O3A | 121.3° | 120.0° |
| O1B | PB | O3A | PA | 38.5° | 80.0° |
| PG | O3B | PB | O3A | 108.7° | 165.0° |
| O3B | PG | O2G | H3 | 120.4° | 60.0° |
| O3B | PG | O1G | H4 | 119.7° | 180.0° |
| O2G | PG | O3B | PB | 95.2° | 80.0° |
| O2G | PG | O1G | H4 | 126.0° | 60.0° |
| O3B | PB | O3A | PA | 79.8° | 160.0° |
| O3B | PB | O1B | H2 | 130.8° | 59.9° |
| PB | O3A | PA | O2A | 8.9° | 45.0° |
| PB | O3A | PA | O5' | 119.0° | 165.0° |
| PB | O3A | PA | O1A | 123.0° | 75.0° |
| O3A | PB | O1B | H2 | 113.3° | 60.0° |
| O3A | PA | O2A | O5' | 104.4° | 120.0° |
| O3A | PA | O2A | O1A | 126.0° | 120.0° |
| O3A | PA | O5' | O1A | 110.9° | 120.0° |
| O3A | PA | O5' | C5' | 76.1° | 175.0° |
| O3A | PA | O1A | H1 | 130.1° | 60.0° |
| O2A | PA | O5' | O1A | 131.4° | 120.0° |
| O2A | PA | O5' | C5' | 166.2° | 54.9° |
| O2A | PA | O1A | H1 | 0.0° | 180.0° |
| PA | O5' | C5' | C4' | 150.8° | 180.0° |
| O5' | PA | O1A | H1 | 125.1° | 60.0° |
| PA | O5' | C5' | H5 | 89.5° | 60.1° |
| PA | O5' | C5' | H6 | 31.1° | 59.9° |
| O1A | PA | O5' | C5' | 34.8° | 65.1° |
| O5' | C5' | C4' | C3' | 48.4° | 179.5° |
| O5' | C5' | C4' | H5 | 119.7° | 119.9° |
| O5' | C5' | C4' | H6 | 119.6° | 120.1° |
| O5' | C5' | C4' | O4' | 64.1° | 66.4° |
| O5' | C5' | H5 | H6 | 121.0° | 120.1° |
| O5' | C5' | C4' | H7 | 176.5° | 56.4° |
| F2' | C2' | C3' | O3' | 153.3° | 102.2° |
| F2' | C2' | C3' | C1' | 117.9° | 118.7° |
| F2' | C2' | C3' | H10 | 123.6° | 122.7° |
| F2' | C2' | C3' | C4' | 89.6° | 139.6° |
| F2' | C2' | C1' | H10 | 122.0° | 122.6° |
| F2' | C2' | C1' | O4' | 91.1° | 116.7° |
| F2' | C2' | C1' | N9 | 19.6° | 2.8° |
| F2' | C2' | C3' | H8 | 30.9° | 21.3° |
| F2' | C2' | C1' | H11 | 151.1° | 123.8° |
| O3' | C3' | C2' | C4' | 117.2° | 118.2° |
| O3' | C3' | C2' | H8 | 122.3° | 123.5° |
| O3' | C3' | C4' | H8 | 121.2° | 123.5° |
| O3' | C3' | C4' | C5' | 143.3° | 86.3° |
| O3' | C3' | C2' | C1' | 88.9° | 139.1° |
| O3' | C3' | C4' | O4' | 102.6° | 155.2° |
| O3' | C3' | C4' | H7 | 15.3° | 36.6° |
| O3' | C3' | C2' | H10 | 29.7° | 20.4° |
| C2' | C3' | C4' | H8 | 120.6° | 118.3° |
| C2' | C3' | C4' | C5' | 98.5° | 155.5° |
| C3' | C2' | C1' | H10 | 118.5° | 118.7° |
| C2' | C3' | C4' | O4' | 15.6° | 37.0° |
| C3' | C2' | C1' | O4' | 28.4° | 2.0° |
| C3' | C2' | C1' | N9 | 139.1° | 121.5° |
| C2' | C3' | C4' | H7 | 133.5° | 81.6° |
| C2' | C3' | O3' | H9 | 180.0° | 61.5° |
| C3' | C2' | C1' | H11 | 89.5° | 117.5° |
| C3' | C4' | C5' | O4' | 112.5° | 114.1° |
| C3' | C4' | C5' | H7 | 128.1° | 123.1° |
| C4' | C3' | C2' | C1' | 28.3° | 20.9° |
| C3' | C4' | O4' | H7 | 117.4° | 118.8° |
| C3' | C4' | O4' | C1' | 3.0° | 40.0° |
| C3' | C4' | C5' | H5 | 71.3° | 60.6° |
| C3' | C4' | C5' | H6 | 168.0° | 59.4° |
| C4' | C3' | O3' | H9 | 62.6° | 174.2° |
| C4' | C3' | C2' | H10 | 146.9° | 97.8° |
| C5' | C4' | O4' | H7 | 118.7° | 122.7° |
| C5' | C4' | O4' | C1' | 126.8° | 158.6° |
| C4' | C5' | H5 | H6 | 121.0° | 120.0° |
| C5' | C4' | C3' | H8 | 22.1° | 37.3° |
| C2' | C1' | O4' | C4' | 20.0° | 26.5° |
| C2' | C1' | O4' | N9 | 125.4° | 119.4° |
| C2' | C1' | O4' | H11 | 117.6° | 119.5° |
| C2' | C1' | N9 | C8 | 36.5° | 95.4° |
| C2' | C1' | N9 | H11 | 131.2° | 121.0° |
| C2' | C1' | N9 | C4 | 146.5° | 85.0° |
| C1' | C2' | C3' | H8 | 148.8° | 97.4° |
| C4' | O4' | C1' | N9 | 145.4° | 145.9° |
| O4' | C4' | C5' | H5 | 176.2° | 53.5° |
| O4' | C4' | C5' | H6 | 55.5° | 173.5° |
| O4' | C4' | C3' | H8 | 136.2° | 81.2° |
| C4' | O4' | C1' | H11 | 97.6° | 93.0° |
| O4' | C1' | N9 | C8 | 75.5° | 22.5° |
| O4' | C1' | N9 | H11 | 116.8° | 121.2° |
| O4' | C1' | N9 | C4 | 101.5° | 157.1° |
| C1' | O4' | C4' | H7 | 114.5° | 78.7° |
| O4' | C1' | C2' | H10 | 146.9° | 120.7° |
| N9 | C8 | N7 | H12 | 180.0° | 179.8° |
| C8 | N9 | C1' | C4 | 177.0° | 179.6° |
| N9 | C8 | N7 | C5 | 1.6° | 0.5° |
| C8 | N9 | C4 | C5 | 0.3° | 0.3° |
| C8 | N9 | C4 | N3 | 179.3° | 179.8° |
| C8 | N9 | C1' | H11 | 167.6° | 143.7° |
| N7 | C8 | N9 | C1' | 178.5° | 179.9° |
| N7 | C8 | N9 | C4 | 1.3° | 0.5° |
| C8 | N7 | C5 | C4 | 1.5° | 0.3° |
| C8 | N7 | C5 | C6 | 177.4° | 179.7° |
| C1' | N9 | C4 | C5 | 177.8° | 180.0° |
| C1' | N9 | C4 | N3 | 1.8° | 0.1° |
| N9 | C1' | C2' | H10 | 102.4° | 119.8° |
| C1' | N9 | C8 | H12 | 1.5° | 0.1° |
| N9 | C4 | C5 | N7 | 0.8° | 0.0° |
| N9 | C4 | C5 | N3 | 179.6° | 179.9° |
| N9 | C4 | C5 | C6 | 178.2° | 180.0° |
| N9 | C4 | N3 | C2 | 179.4° | 179.9° |
| C4 | N9 | C1' | H11 | 15.4° | 35.9° |
| C4 | N9 | C8 | H12 | 178.7° | 179.7° |
| N7 | C5 | C4 | C6 | 179.0° | 180.0° |
| N7 | C5 | C4 | N3 | 179.6° | 180.0° |
| N7 | C5 | C6 | N6 | 0.9° | 0.0° |
| N7 | C5 | C6 | N1 | 179.1° | 180.0° |
| C5 | N7 | C8 | H12 | 178.3° | 179.8° |
| C5 | C4 | N3 | C2 | 0.1° | 0.0° |
| C4 | C5 | C6 | N6 | 179.7° | 180.0° |
| C4 | C5 | C6 | N1 | 2.1° | 0.0° |
| N3 | C4 | C5 | C6 | 1.4° | 0.0° |
| C4 | N3 | C2 | N1 | 0.6° | 0.0° |
| C4 | N3 | C2 | CL2 | 178.6° | 180.0° |
| C5 | C6 | N6 | N1 | 178.1° | 180.0° |
| C5 | C6 | N1 | C2 | 1.5° | 0.0° |
| C5 | C6 | N6 | H16 | 178.1° | 0.0° |
| C5 | C6 | N6 | H17 | 61.9° | 180.0° |
| N3 | C2 | N1 | C6 | 0.2° | 0.0° |
| N3 | C2 | N1 | CL2 | 178.1° | 180.0° |
| N3 | C2 | CL2 | H13 | 0.0° | 90.0° |
| N3 | C2 | CL2 | H14 | 120.0° | 150.0° |
| N3 | C2 | CL2 | H15 | 120.0° | 30.0° |
| N6 | C6 | N1 | C2 | 179.7° | 180.0° |
| C6 | N6 | H16 | H17 | 120.0° | 180.0° |
| C6 | N1 | C2 | CL2 | 177.9° | 180.0° |
| N1 | C6 | N6 | H16 | 0.0° | 180.0° |
| N1 | C6 | N6 | H17 | 120.0° | 0.1° |
| N1 | C2 | CL2 | H13 | 178.4° | 89.9° |
| N1 | C2 | CL2 | H14 | 58.4° | 30.1° |
| N1 | C2 | CL2 | H15 | 61.6° | 150.0° |
| C2 | CL2 | H13 | H14 | 120.0° | 120.0° |
| C2 | CL2 | H13 | H15 | 120.0° | 120.0° |
| C2 | CL2 | H14 | H15 | 120.0° | 119.9° |
| H5 | C5' | C4' | H7 | 56.9° | 176.3° |
| H6 | C5' | C4' | H7 | 63.8° | 63.7° |
| H7 | C4' | C3' | H8 | 105.9° | 160.2° |
| H8 | C3' | O3' | H9 | 58.1° | 62.2° |
| H8 | C3' | C2' | H10 | 92.6° | 144.0° |
| H10 | C2' | C1' | H11 | 29.0° | 1.1° |
| H13 | CL2 | H14 | H15 | 120.0° | 120.1° |
