D5M
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O5' | C5' | sing | 1.42Å | 1.43Å | |
| O5' | P | sing | 1.62Å | 80.37Å | |
| C5' | C4' | sing | 1.52Å | 1.51Å | |
| C5' | H5'1 | sing | 1.09Å | 1.10Å | |
| C5' | H5'2 | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.45Å | |
| C4' | C3' | sing | 1.52Å | 1.53Å | |
| C4' | H4' | sing | 1.10Å | 1.10Å | |
| O4' | C1' | sing | 1.44Å | 1.43Å | |
| C3' | O3' | sing | 1.43Å | 1.44Å | |
| C3' | C2' | sing | 1.51Å | 1.52Å | |
| C3' | H1 | sing | 1.09Å | 1.10Å | |
| O3' | H3' | sing | 0.97Å | 0.95Å | |
| C2' | C1' | sing | 1.52Å | 1.53Å | |
| C2' | H2'1 | sing | 1.10Å | 1.10Å | |
| C2' | H2'2 | sing | 1.09Å | 1.10Å | |
| C1' | N9 | sing | 1.46Å | 1.47Å | |
| C1' | H1' | sing | 1.10Å | 1.10Å | |
| N9 | C8 | sing | 1.37Å | 1.38Å | Aromatic |
| N9 | C4 | sing | 1.37Å | 1.38Å | Aromatic |
| C8 | N7 | doub | 1.32Å | 1.31Å | Aromatic |
| C8 | H8 | sing | 1.08Å | 1.08Å | |
| N7 | C5 | sing | 1.37Å | 1.39Å | Aromatic |
| C5 | C6 | sing | 1.39Å | 1.41Å | Aromatic |
| C5 | C4 | doub | 1.39Å | 1.39Å | Aromatic |
| C6 | N6 | sing | 1.41Å | 1.34Å | |
| C6 | N1 | doub | 1.35Å | 1.36Å | Aromatic |
| N6 | HN61 | sing | 1.00Å | 1.00Å | |
| N6 | HN62 | sing | 1.00Å | 1.00Å | |
| N1 | C2 | sing | 1.36Å | 1.35Å | Aromatic |
| C2 | N3 | doub | 1.35Å | 1.34Å | Aromatic |
| C2 | H2 | sing | 1.08Å | 1.08Å | |
| N3 | C4 | sing | 1.34Å | 1.35Å | Aromatic |
| P | O1P | doub | 1.50Å | 0.00Å | |
| P | O3P | sing | 1.62Å | 0.00Å | |
| P | O2P | sing | 1.62Å | 0.00Å | |
| O3P | H3P | sing | 0.98Å | 0.00Å | |
| O2P | H2P | sing | 0.98Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C5' | O5' | P | 43.0° | 118.5° |
| O5' | C5' | C4' | 111.4° | 108.7° |
| O5' | C5' | H5'1 | 108.8° | 109.2° |
| O5' | C5' | H5'2 | 108.4° | 109.2° |
| O5' | P | O1P | 90.0° | 115.0° |
| O5' | P | O3P | 90.0° | 103.7° |
| O5' | P | O2P | 90.0° | 102.9° |
| C4' | C5' | H5'1 | 108.8° | 110.1° |
| C4' | C5' | H5'2 | 108.4° | 110.1° |
| C5' | C4' | O4' | 109.0° | 108.0° |
| C5' | C4' | C3' | 114.9° | 112.7° |
| C5' | C4' | H4' | 105.0° | 109.4° |
| H5'1 | C5' | H5'2 | 111.0° | 109.6° |
| O4' | C4' | C3' | 105.7° | 106.8° |
| O4' | C4' | H4' | 114.3° | 107.7° |
| C4' | O4' | C1' | 109.9° | 108.7° |
| C3' | C4' | H4' | 108.3° | 112.0° |
| C4' | C3' | O3' | 110.2° | 109.6° |
| C4' | C3' | C2' | 102.6° | 103.2° |
| C4' | C3' | H1 | 112.7° | 114.0° |
| O4' | C1' | C2' | 106.0° | 106.7° |
| O4' | C1' | N9 | 107.9° | 110.0° |
| O4' | C1' | H1' | 115.1° | 108.1° |
| O3' | C3' | C2' | 107.3° | 108.4° |
| O3' | C3' | H1 | 108.4° | 107.8° |
| C3' | O3' | H3' | 109.5° | 106.6° |
| C2' | C3' | H1 | 115.4° | 113.7° |
| C3' | C2' | C1' | 101.7° | 101.6° |
| C3' | C2' | H2'1 | 112.2° | 110.0° |
| C3' | C2' | H2'2 | 113.8° | 114.2° |
| C1' | C2' | H2'1 | 112.2° | 110.5° |
| C1' | C2' | H2'2 | 113.8° | 111.7° |
| C2' | C1' | N9 | 115.8° | 114.3° |
| C2' | C1' | H1' | 107.1° | 111.7° |
| H2'1 | C2' | H2'2 | 103.6° | 108.7° |
| N9 | C1' | H1' | 105.2° | 105.9° |
| C1' | N9 | C8 | 128.5° | 126.2° |
| C1' | N9 | C4 | 125.8° | 126.9° |
| C8 | N9 | C4 | 105.7° | 106.9° |
| N9 | C8 | N7 | 113.8° | 112.3° |
| N9 | C8 | H8 | 123.1° | 122.2° |
| N9 | C4 | C5 | 105.9° | 105.3° |
| N9 | C4 | N3 | 127.3° | 127.5° |
| N7 | C8 | H8 | 123.1° | 125.6° |
| C8 | N7 | C5 | 103.9° | 104.9° |
| N7 | C5 | C6 | 132.3° | 132.4° |
| N7 | C5 | C4 | 110.7° | 110.7° |
| C6 | C5 | C4 | 117.0° | 116.9° |
| C5 | C6 | N6 | 123.6° | 120.7° |
| C5 | C6 | N1 | 117.6° | 119.1° |
| C5 | C4 | N3 | 126.8° | 127.2° |
| N6 | C6 | N1 | 118.8° | 120.2° |
| C6 | N6 | HN61 | 109.5° | 119.5° |
| C6 | N6 | HN62 | 109.5° | 119.4° |
| C6 | N1 | C2 | 118.7° | 117.5° |
| HN61 | N6 | HN62 | 109.5° | 120.8° |
| N1 | C2 | N3 | 129.3° | 128.8° |
| N1 | C2 | H2 | 115.4° | 115.5° |
| N3 | C2 | H2 | 115.3° | 115.7° |
| C2 | N3 | C4 | 110.6° | 110.5° |
| O1P | P | O3P | 90.0° | 115.3° |
| O1P | P | O2P | 90.0° | 115.0° |
| O3P | P | O2P | 90.0° | 103.3° |
| P | O3P | H3P | 90.0° | 118.9° |
| P | O2P | H2P | 90.0° | 118.9° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O5' | C5' | C4' | H5'1 | 120.0° | 119.6° |
| O5' | C5' | C4' | H5'2 | 119.2° | 119.5° |
| O5' | C5' | H5'1 | H5'2 | 119.2° | 119.6° |
| O5' | C5' | C4' | O4' | 57.8° | 61.8° |
| O5' | C5' | C4' | C3' | 176.2° | 179.5° |
| O5' | C5' | C4' | H4' | 65.0° | 55.2° |
| C5' | O5' | P | O1P | 90.0° | 180.0° |
| C5' | O5' | P | O3P | 90.0° | 53.2° |
| C5' | O5' | P | O2P | 90.0° | 54.2° |
| P | O5' | C5' | C4' | 28.7° | 180.0° |
| P | O5' | C5' | H5'1 | 91.3° | 59.9° |
| P | O5' | C5' | H5'2 | 147.9° | 59.9° |
| O5' | P | O1P | O3P | 90.0° | 120.6° |
| O5' | P | O1P | O2P | 90.0° | 119.3° |
| O5' | P | O3P | O2P | 90.0° | 107.1° |
| O5' | P | O3P | H3P | 90.0° | 175.4° |
| O5' | P | O2P | H2P | 90.0° | 173.9° |
| C4' | C5' | H5'1 | H5'2 | 119.2° | 121.2° |
| C5' | C4' | O4' | C3' | 123.9° | 121.5° |
| C5' | C4' | O4' | H4' | 117.1° | 118.0° |
| C5' | C4' | C3' | H4' | 117.0° | 123.8° |
| C5' | C4' | O4' | C1' | 116.5° | 116.0° |
| C5' | C4' | C3' | O3' | 153.8° | 152.1° |
| C5' | C4' | C3' | C2' | 92.1° | 92.6° |
| C5' | C4' | C3' | H1 | 32.6° | 31.2° |
| H5'1 | C5' | C4' | O4' | 62.2° | 57.8° |
| H5'1 | C5' | C4' | C3' | 56.1° | 60.0° |
| H5'1 | C5' | C4' | H4' | 175.0° | 174.7° |
| H5'2 | C5' | C4' | O4' | 177.0° | 178.7° |
| H5'2 | C5' | C4' | C3' | 64.7° | 60.9° |
| H5'2 | C5' | C4' | H4' | 54.2° | 64.3° |
| O4' | C4' | C3' | H4' | 122.9° | 117.7° |
| O4' | C4' | C3' | O3' | 86.0° | 89.4° |
| O4' | C4' | C3' | C2' | 28.0° | 25.9° |
| O4' | C4' | C3' | H1 | 152.7° | 149.7° |
| C4' | O4' | C1' | C2' | 16.4° | 17.3° |
| C4' | O4' | C1' | N9 | 141.1° | 141.8° |
| C4' | O4' | C1' | H1' | 101.8° | 103.1° |
| C3' | C4' | O4' | C1' | 7.4° | 5.5° |
| C4' | C3' | O3' | C2' | 111.0° | 111.9° |
| C4' | C3' | O3' | H1 | 123.8° | 124.6° |
| C4' | C3' | C2' | H1 | 123.0° | 123.9° |
| C4' | C3' | O3' | H3' | 159.3° | 46.6° |
| C4' | C3' | C2' | C1' | 36.7° | 34.8° |
| C4' | C3' | C2' | H2'1 | 83.3° | 82.2° |
| C4' | C3' | C2' | H2'2 | 159.5° | 155.2° |
| H4' | C4' | O4' | C1' | 126.4° | 126.0° |
| H4' | C4' | C3' | O3' | 36.8° | 28.3° |
| H4' | C4' | C3' | C2' | 150.9° | 143.6° |
| H4' | C4' | C3' | H1 | 84.4° | 92.6° |
| O4' | C1' | C2' | C3' | 33.4° | 32.7° |
| O4' | C1' | C2' | N9 | 119.7° | 121.8° |
| O4' | C1' | C2' | H1' | 123.4° | 117.9° |
| O4' | C1' | C2' | H2'1 | 86.7° | 84.0° |
| O4' | C1' | C2' | H2'2 | 156.1° | 154.9° |
| O4' | C1' | N9 | H1' | 123.4° | 116.5° |
| O4' | C1' | N9 | C8 | 85.9° | 33.5° |
| O4' | C1' | N9 | C4 | 92.6° | 146.5° |
| O3' | C3' | C2' | H1 | 120.9° | 119.9° |
| O3' | C3' | C2' | C1' | 79.4° | 81.3° |
| O3' | C3' | C2' | H2'1 | 160.6° | 161.6° |
| O3' | C3' | C2' | H2'2 | 43.3° | 39.1° |
| C2' | C3' | O3' | H3' | 48.3° | 65.3° |
| C3' | C2' | C1' | H2'1 | 120.0° | 116.7° |
| C3' | C2' | C1' | H2'2 | 122.8° | 122.2° |
| C3' | C2' | H2'1 | H2'2 | 123.2° | 125.7° |
| C3' | C2' | C1' | N9 | 153.0° | 154.5° |
| C3' | C2' | C1' | H1' | 90.1° | 85.2° |
| H1 | C3' | O3' | H3' | 76.9° | 171.2° |
| H1 | C3' | C2' | C1' | 159.6° | 158.8° |
| H1 | C3' | C2' | H2'1 | 39.6° | 41.7° |
| H1 | C3' | C2' | H2'2 | 77.6° | 80.8° |
| C1' | C2' | H2'1 | H2'2 | 123.1° | 122.9° |
| C2' | C1' | N9 | H1' | 118.0° | 123.5° |
| C2' | C1' | N9 | C8 | 32.7° | 86.6° |
| C2' | C1' | N9 | C4 | 148.8° | 93.5° |
| H2'1 | C2' | C1' | N9 | 33.0° | 37.8° |
| H2'1 | C2' | C1' | H1' | 149.9° | 158.1° |
| H2'2 | C2' | C1' | N9 | 84.2° | 83.3° |
| H2'2 | C2' | C1' | H1' | 32.7° | 37.0° |
| C1' | N9 | C8 | C4 | 178.7° | 179.9° |
| C1' | N9 | C8 | N7 | 177.5° | 180.0° |
| C1' | N9 | C8 | H8 | 2.5° | 0.0° |
| C1' | N9 | C4 | C5 | 177.4° | 180.0° |
| C1' | N9 | C4 | N3 | 1.8° | 0.1° |
| H1' | C1' | N9 | C8 | 150.7° | 150.0° |
| H1' | C1' | N9 | C4 | 30.8° | 29.9° |
| N9 | C8 | N7 | H8 | 180.0° | 180.0° |
| N9 | C8 | N7 | C5 | 0.5° | 0.0° |
| C8 | N9 | C4 | C5 | 1.4° | 0.0° |
| C8 | N9 | C4 | N3 | 179.4° | 180.0° |
| C4 | N9 | C8 | N7 | 1.2° | 0.0° |
| C4 | N9 | C8 | H8 | 178.8° | 180.0° |
| N9 | C4 | C5 | N7 | 1.2° | 0.0° |
| N9 | C4 | C5 | C6 | 178.5° | 180.0° |
| N9 | C4 | C5 | N3 | 179.2° | 179.9° |
| N9 | C4 | N3 | C2 | 178.9° | 180.0° |
| C8 | N7 | C5 | C6 | 179.2° | 180.0° |
| C8 | N7 | C5 | C4 | 0.4° | 0.0° |
| H8 | C8 | N7 | C5 | 179.5° | 180.0° |
| N7 | C5 | C6 | C4 | 179.6° | 180.0° |
| N7 | C5 | C6 | N6 | 0.8° | 0.0° |
| N7 | C5 | C6 | N1 | 179.6° | 180.0° |
| N7 | C5 | C4 | N3 | 179.6° | 180.0° |
| C5 | C6 | N6 | N1 | 179.6° | 180.0° |
| C5 | C6 | N6 | HN61 | 62.6° | 85.4° |
| C5 | C6 | N6 | HN62 | 177.4° | 88.4° |
| C5 | C6 | N1 | C2 | 0.4° | 0.0° |
| C6 | C5 | C4 | N3 | 0.7° | 0.1° |
| C4 | C5 | C6 | N6 | 178.9° | 180.0° |
| C4 | C5 | C6 | N1 | 0.8° | 0.1° |
| C5 | C4 | N3 | C2 | 0.1° | 0.1° |
| C6 | N6 | HN61 | HN62 | 120.0° | 173.7° |
| N6 | C6 | N1 | C2 | 179.3° | 180.0° |
| N1 | C6 | N6 | HN61 | 117.8° | 94.6° |
| N1 | C6 | N6 | HN62 | 2.3° | 91.6° |
| C6 | N1 | C2 | N3 | 0.2° | 0.0° |
| C6 | N1 | C2 | H2 | 179.8° | 180.0° |
| N1 | C2 | N3 | H2 | 180.0° | 180.0° |
| N1 | C2 | N3 | C4 | 0.3° | 0.0° |
| H2 | C2 | N3 | C4 | 179.7° | 180.0° |
| O1P | P | O3P | O2P | 90.0° | 126.3° |
| O1P | P | O3P | H3P | 90.0° | 48.8° |
| O1P | P | O2P | H2P | 90.0° | 48.0° |
| O3P | P | O2P | H2P | 90.0° | 78.5° |
| O2P | P | O3P | H3P | 90.0° | 77.5° |
