D4D
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| PA | O1A | doub | 1.48Å | 1.48Å | |
| PA | O2A | sing | 1.61Å | 1.49Å | |
| PA | O3A | sing | 1.61Å | 1.60Å | |
| PA | O5' | sing | 1.61Å | 1.59Å | |
| O2A | H2AO | sing | 0.97Å | 0.95Å | |
| O3A | PB | sing | 1.61Å | 1.60Å | |
| PB | O1B | sing | 1.61Å | 1.49Å | |
| PB | O2B | doub | 1.48Å | 1.49Å | |
| PB | O3B | sing | 1.61Å | 1.49Å | |
| O1B | H1BO | sing | 0.97Å | 0.95Å | |
| O3B | H3BO | sing | 0.97Å | 0.95Å | |
| O5' | C5' | sing | 1.43Å | 1.43Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| C5' | H5'1 | sing | 1.09Å | 1.11Å | |
| C5' | H5'2 | sing | 1.09Å | 1.12Å | |
| C4' | O4' | sing | 1.44Å | 1.45Å | |
| C4' | C3' | sing | 1.51Å | 1.51Å | |
| C4' | H4'C | sing | 1.09Å | 1.11Å | |
| O4' | C1' | sing | 1.44Å | 1.41Å | |
| C3' | C2' | doub | 1.31Å | 1.34Å | |
| C3' | H3'C | sing | 1.08Å | 1.10Å | |
| C2' | C1' | sing | 1.51Å | 1.51Å | |
| C2' | H2'C | sing | 1.08Å | 1.10Å | |
| C1' | N1 | sing | 1.46Å | 1.47Å | |
| C1' | H1'C | sing | 1.09Å | 1.11Å | |
| N1 | C2 | sing | 1.35Å | 1.38Å | Aromatic |
| N1 | C6 | sing | 1.37Å | 1.38Å | Aromatic |
| C2 | O2 | doub | 1.22Å | 1.22Å | |
| C2 | N3 | sing | 1.35Å | 1.37Å | Aromatic |
| N3 | C4 | sing | 1.35Å | 1.38Å | Aromatic |
| N3 | HN3 | sing | 0.97Å | 1.02Å | |
| C4 | O4 | doub | 1.22Å | 1.23Å | |
| C4 | C5 | sing | 1.42Å | 1.45Å | Aromatic |
| C5 | C5M | sing | 1.51Å | 1.50Å | |
| C5 | C6 | doub | 1.35Å | 1.34Å | Aromatic |
| C5M | H5M1 | sing | 1.09Å | 1.11Å | |
| C5M | H5M2 | sing | 1.09Å | 1.12Å | |
| C5M | H5M3 | sing | 1.09Å | 1.11Å | |
| C6 | H66 | sing | 1.08Å | 1.10Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O1A | PA | O2A | 119.6° | 109.5° |
| O1A | PA | O3A | 108.5° | 109.5° |
| O1A | PA | O5' | 107.6° | 109.4° |
| O2A | PA | O3A | 109.2° | 109.5° |
| O2A | PA | O5' | 108.6° | 109.5° |
| PA | O2A | H2AO | 119.7° | 106.8° |
| O3A | PA | O5' | 101.9° | 109.5° |
| PA | O3A | PB | 132.5° | 106.8° |
| PA | O5' | C5' | 120.8° | 106.8° |
| O3A | PB | O1B | 105.1° | 109.5° |
| O3A | PB | O2B | 105.0° | 109.5° |
| O3A | PB | O3B | 103.5° | 109.5° |
| O1B | PB | O2B | 118.0° | 109.5° |
| O1B | PB | O3B | 105.3° | 109.5° |
| PB | O1B | H1BO | 105.0° | 106.8° |
| O2B | PB | O3B | 118.2° | 109.4° |
| PB | O3B | H3BO | 103.4° | 106.8° |
| O5' | C5' | C4' | 110.2° | 109.5° |
| O5' | C5' | H5'1 | 111.9° | 109.5° |
| O5' | C5' | H5'2 | 111.9° | 109.5° |
| C4' | C5' | H5'1 | 111.9° | 109.5° |
| C4' | C5' | H5'2 | 111.9° | 109.4° |
| C5' | C4' | O4' | 109.1° | 110.2° |
| C5' | C4' | C3' | 115.6° | 110.3° |
| C5' | C4' | H4'C | 104.2° | 110.2° |
| H5'1 | C5' | H5'2 | 98.5° | 109.5° |
| O4' | C4' | C3' | 104.8° | 105.7° |
| O4' | C4' | H4'C | 115.1° | 110.2° |
| C4' | O4' | C1' | 109.0° | 103.7° |
| C3' | C4' | H4'C | 108.5° | 110.2° |
| C4' | C3' | C2' | 108.9° | 108.4° |
| C4' | C3' | H3'C | 130.3° | 125.8° |
| O4' | C1' | C2' | 105.7° | 105.8° |
| O4' | C1' | N1 | 108.0° | 110.2° |
| O4' | C1' | H1'C | 113.7° | 110.2° |
| C2' | C3' | H3'C | 120.8° | 125.8° |
| C3' | C2' | C1' | 109.1° | 108.3° |
| C3' | C2' | H2'C | 120.7° | 125.8° |
| C1' | C2' | H2'C | 130.2° | 125.9° |
| C2' | C1' | N1 | 112.0° | 110.2° |
| C2' | C1' | H1'C | 109.9° | 110.2° |
| N1 | C1' | H1'C | 107.6° | 110.1° |
| C1' | N1 | C2 | 118.7° | 119.7° |
| C1' | N1 | C6 | 120.0° | 119.7° |
| C2 | N1 | C6 | 121.3° | 120.6° |
| N1 | C2 | O2 | 123.3° | 119.6° |
| N1 | C2 | N3 | 114.5° | 120.9° |
| N1 | C6 | C5 | 123.8° | 119.7° |
| N1 | C6 | H66 | 119.7° | 120.2° |
| O2 | C2 | N3 | 122.2° | 119.5° |
| C2 | N3 | C4 | 127.2° | 120.3° |
| C2 | N3 | HN3 | 116.1° | 119.8° |
| C4 | N3 | HN3 | 116.7° | 119.9° |
| N3 | C4 | O4 | 119.8° | 120.3° |
| N3 | C4 | C5 | 115.3° | 119.4° |
| O4 | C4 | C5 | 124.9° | 120.3° |
| C4 | C5 | C5M | 119.2° | 120.5° |
| C4 | C5 | C6 | 118.0° | 119.1° |
| C5M | C5 | C6 | 122.8° | 120.4° |
| C5 | C5M | H5M1 | 119.2° | 109.5° |
| C5 | C5M | H5M2 | 108.8° | 109.5° |
| C5 | C5M | H5M3 | 108.8° | 109.5° |
| C5 | C6 | H66 | 116.5° | 120.1° |
| H5M1 | C5M | H5M2 | 108.7° | 109.5° |
| H5M1 | C5M | H5M3 | 108.7° | 109.5° |
| H5M2 | C5M | H5M3 | 101.2° | 109.4° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1A | PA | O2A | O3A | 125.8° | 120.0° |
| O1A | PA | O2A | O5' | 123.9° | 120.0° |
| O1A | PA | O3A | O5' | 113.3° | 120.0° |
| O1A | PA | O2A | H2AO | 180.0° | 180.0° |
| O1A | PA | O3A | PB | 38.2° | 40.0° |
| O1A | PA | O5' | C5' | 36.7° | 55.0° |
| O2A | PA | O3A | O5' | 114.7° | 120.0° |
| O2A | PA | O3A | PB | 93.8° | 80.0° |
| O2A | PA | O5' | C5' | 167.5° | 65.0° |
| O3A | PA | O2A | H2AO | 54.2° | 60.0° |
| PA | O3A | PB | O1B | 28.8° | 80.0° |
| PA | O3A | PB | O2B | 96.3° | 40.0° |
| PA | O3A | PB | O3B | 139.0° | 160.0° |
| O3A | PA | O5' | C5' | 77.3° | 175.0° |
| O5' | PA | O2A | H2AO | 56.1° | 60.0° |
| O5' | PA | O3A | PB | 151.5° | 160.0° |
| PA | O5' | C5' | C4' | 135.7° | 180.0° |
| PA | O5' | C5' | H5'1 | 10.4° | 60.0° |
| PA | O5' | C5' | H5'2 | 99.0° | 60.0° |
| O3A | PB | O1B | O2B | 116.6° | 120.0° |
| O3A | PB | O1B | O3B | 108.9° | 120.1° |
| O3A | PB | O2B | O3B | 114.7° | 120.0° |
| O3A | PB | O1B | H1BO | 179.9° | 60.0° |
| O3A | PB | O3B | H3BO | 180.0° | 180.0° |
| O1B | PB | O2B | O3B | 128.7° | 120.0° |
| O1B | PB | O3B | H3BO | 70.0° | 60.0° |
| O2B | PB | O1B | H1BO | 63.4° | 180.0° |
| O2B | PB | O3B | H3BO | 64.4° | 60.0° |
| O3B | PB | O1B | H1BO | 71.2° | 60.1° |
| O5' | C5' | C4' | H5'1 | 125.2° | 120.0° |
| O5' | C5' | C4' | H5'2 | 125.2° | 120.0° |
| O5' | C5' | H5'1 | H5'2 | 117.8° | 120.0° |
| O5' | C5' | C4' | O4' | 63.5° | 66.4° |
| O5' | C5' | C4' | C3' | 54.2° | 177.2° |
| O5' | C5' | C4' | H4'C | 173.1° | 55.4° |
| C4' | C5' | H5'1 | H5'2 | 117.9° | 119.9° |
| C5' | C4' | O4' | C3' | 124.3° | 119.2° |
| C5' | C4' | O4' | H4'C | 116.6° | 121.8° |
| C5' | C4' | C3' | H4'C | 116.5° | 121.8° |
| C5' | C4' | O4' | C1' | 139.8° | 146.4° |
| C5' | C4' | C3' | C2' | 129.5° | 136.6° |
| C5' | C4' | C3' | H3'C | 50.4° | 43.5° |
| H5'1 | C5' | C4' | O4' | 171.2° | 173.5° |
| H5'1 | C5' | C4' | C3' | 71.1° | 57.2° |
| H5'1 | C5' | C4' | H4'C | 47.9° | 64.7° |
| H5'2 | C5' | C4' | O4' | 61.7° | 53.5° |
| H5'2 | C5' | C4' | C3' | 179.4° | 62.8° |
| H5'2 | C5' | C4' | H4'C | 61.7° | 175.4° |
| O4' | C4' | C3' | H4'C | 123.4° | 119.0° |
| O4' | C4' | C3' | C2' | 9.5° | 17.4° |
| O4' | C4' | C3' | H3'C | 170.5° | 162.7° |
| C4' | O4' | C1' | C2' | 15.3° | 27.2° |
| C4' | O4' | C1' | N1 | 135.4° | 146.3° |
| C4' | O4' | C1' | H1'C | 105.3° | 92.0° |
| C3' | C4' | O4' | C1' | 15.4° | 27.2° |
| C4' | C3' | C2' | H3'C | 180.0° | 179.9° |
| C4' | C3' | C2' | C1' | 0.3° | 0.1° |
| C4' | C3' | C2' | H2'C | 179.7° | 179.9° |
| H4'C | C4' | O4' | C1' | 103.6° | 91.8° |
| H4'C | C4' | C3' | C2' | 113.9° | 101.6° |
| H4'C | C4' | C3' | H3'C | 66.1° | 78.3° |
| O4' | C1' | C2' | C3' | 9.3° | 17.2° |
| O4' | C1' | C2' | N1 | 117.4° | 119.1° |
| O4' | C1' | C2' | H1'C | 123.1° | 119.1° |
| O4' | C1' | C2' | H2'C | 170.7° | 162.6° |
| O4' | C1' | N1 | H1'C | 123.2° | 121.7° |
| O4' | C1' | N1 | C2 | 133.8° | 52.6° |
| O4' | C1' | N1 | C6 | 46.7° | 127.5° |
| C3' | C2' | C1' | H2'C | 180.0° | 179.8° |
| C3' | C2' | C1' | N1 | 126.7° | 136.3° |
| C3' | C2' | C1' | H1'C | 113.8° | 101.9° |
| H3'C | C3' | C2' | C1' | 179.7° | 180.0° |
| H3'C | C3' | C2' | H2'C | 0.3° | 0.1° |
| C2' | C1' | N1 | H1'C | 120.8° | 121.8° |
| C2' | C1' | N1 | C2 | 110.2° | 63.9° |
| C2' | C1' | N1 | C6 | 69.3° | 116.1° |
| H2'C | C2' | C1' | N1 | 53.3° | 43.5° |
| H2'C | C2' | C1' | H1'C | 66.2° | 78.3° |
| C1' | N1 | C2 | C6 | 179.5° | 180.0° |
| C1' | N1 | C2 | O2 | 1.0° | 0.0° |
| C1' | N1 | C2 | N3 | 179.0° | 180.0° |
| C1' | N1 | C6 | C5 | 179.0° | 180.0° |
| C1' | N1 | C6 | H66 | 1.0° | 0.0° |
| H1'C | C1' | N1 | C2 | 10.6° | 174.3° |
| H1'C | C1' | N1 | C6 | 169.9° | 5.7° |
| N1 | C2 | O2 | N3 | 180.0° | 180.0° |
| N1 | C2 | N3 | C4 | 0.1° | 0.2° |
| N1 | C2 | N3 | HN3 | 179.9° | 180.0° |
| C2 | N1 | C6 | C5 | 0.5° | 0.0° |
| C2 | N1 | C6 | H66 | 179.5° | 180.0° |
| C6 | N1 | C2 | O2 | 179.5° | 180.0° |
| C6 | N1 | C2 | N3 | 0.4° | 0.0° |
| N1 | C6 | C5 | C4 | 0.0° | 0.2° |
| N1 | C6 | C5 | C5M | 179.9° | 180.0° |
| N1 | C6 | C5 | H66 | 180.0° | 180.0° |
| O2 | C2 | N3 | C4 | 179.9° | 179.8° |
| O2 | C2 | N3 | HN3 | 0.1° | 0.0° |
| C2 | N3 | C4 | HN3 | 180.0° | 179.7° |
| C2 | N3 | C4 | O4 | 179.2° | 180.0° |
| C2 | N3 | C4 | C5 | 0.6° | 0.5° |
| N3 | C4 | O4 | C5 | 179.8° | 179.5° |
| N3 | C4 | C5 | C5M | 179.6° | 179.8° |
| N3 | C4 | C5 | C6 | 0.5° | 0.5° |
| HN3 | N3 | C4 | O4 | 0.8° | 0.2° |
| HN3 | N3 | C4 | C5 | 179.4° | 179.8° |
| O4 | C4 | C5 | C5M | 0.6° | 0.2° |
| O4 | C4 | C5 | C6 | 179.3° | 180.0° |
| C4 | C5 | C5M | C6 | 179.9° | 179.7° |
| C4 | C5 | C5M | H5M1 | 180.0° | 90.3° |
| C4 | C5 | C5M | H5M2 | 54.7° | 29.8° |
| C4 | C5 | C5M | H5M3 | 54.7° | 149.7° |
| C4 | C5 | C6 | H66 | 180.0° | 179.7° |
| C5 | C5M | H5M1 | H5M2 | 125.3° | 120.0° |
| C5 | C5M | H5M1 | H5M3 | 125.3° | 120.0° |
| C5 | C5M | H5M2 | H5M3 | 114.4° | 120.0° |
| C5M | C5 | C6 | H66 | 0.1° | 0.0° |
| C6 | C5 | C5M | H5M1 | 0.1° | 90.0° |
| C6 | C5 | C5M | H5M2 | 125.2° | 150.0° |
| C6 | C5 | C5M | H5M3 | 125.4° | 30.0° |
| H5M1 | C5M | H5M2 | H5M3 | 114.4° | 120.0° |
