3PD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O5' | C5' | sing | 1.42Å | 1.43Å | |
| O5' | H5' | sing | 0.97Å | 0.95Å | |
| C5' | C4' | sing | 1.52Å | 1.52Å | |
| C5' | H5'1 | sing | 1.09Å | 1.10Å | |
| C5' | H5'2 | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.46Å | |
| C4' | C3' | sing | 1.52Å | 1.54Å | |
| C4' | H4' | sing | 1.10Å | 1.10Å | |
| O4' | C1' | sing | 1.44Å | 1.41Å | |
| C1' | C2' | sing | 1.52Å | 1.54Å | |
| C1' | N9 | sing | 1.46Å | 1.52Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C2' | C3' | sing | 1.51Å | 1.56Å | |
| C2' | H2'1 | sing | 1.09Å | 1.10Å | |
| C2' | H2'2 | sing | 1.10Å | 1.10Å | |
| C3' | O3' | sing | 1.41Å | 1.45Å | |
| C3' | H3' | sing | 1.10Å | 1.10Å | |
| O3' | P | sing | 1.61Å | 1.60Å | |
| N9 | C4 | sing | 1.37Å | 1.40Å | Aromatic |
| N9 | C8 | sing | 1.37Å | 1.39Å | Aromatic |
| C4 | N3 | sing | 1.35Å | 1.40Å | Aromatic |
| C4 | C5 | doub | 1.37Å | 1.41Å | Aromatic |
| N3 | C2 | doub | 1.32Å | 1.37Å | Aromatic |
| C2 | N2 | sing | 1.37Å | 1.34Å | |
| C2 | N1 | sing | 1.41Å | 1.41Å | Aromatic |
| N2 | HN21 | sing | 0.99Å | 1.00Å | |
| N2 | HN22 | sing | 0.99Å | 1.00Å | |
| N1 | C6 | sing | 1.40Å | 1.44Å | Aromatic |
| N1 | HN1 | sing | 1.02Å | 1.00Å | |
| C6 | O6 | doub | 1.22Å | 1.23Å | |
| C6 | C5 | sing | 1.44Å | 1.44Å | Aromatic |
| C5 | N7 | sing | 1.36Å | 1.39Å | Aromatic |
| N7 | C8 | doub | 1.32Å | 1.31Å | Aromatic |
| C8 | H8 | sing | 1.08Å | 1.08Å | |
| P | O1P | sing | 1.62Å | 1.47Å | |
| P | O2P | sing | 1.62Å | 1.48Å | |
| P | O1 | doub | 1.50Å | 20.75Å | |
| O1P | H1P | sing | 0.98Å | 0.95Å | |
| O2P | H2P | sing | 0.98Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C5' | O5' | H5' | 109.5° | 107.1° |
| O5' | C5' | C4' | 111.2° | 108.7° |
| O5' | C5' | H5'1 | 108.5° | 109.2° |
| O5' | C5' | H5'2 | 108.9° | 109.2° |
| C4' | C5' | H5'1 | 108.5° | 110.1° |
| C4' | C5' | H5'2 | 108.9° | 110.1° |
| C5' | C4' | O4' | 112.2° | 109.7° |
| C5' | C4' | C3' | 115.7° | 113.6° |
| C5' | C4' | H4' | 101.8° | 108.6° |
| H5'1 | C5' | H5'2 | 110.8° | 109.6° |
| O4' | C4' | C3' | 105.2° | 105.5° |
| O4' | C4' | H4' | 112.9° | 108.2° |
| C4' | O4' | C1' | 111.0° | 108.1° |
| C3' | C4' | H4' | 109.2° | 111.1° |
| C4' | C3' | C2' | 103.0° | 101.8° |
| C4' | C3' | O3' | 106.9° | 112.4° |
| C4' | C3' | H3' | 116.5° | 111.5° |
| O4' | C1' | C2' | 108.5° | 107.7° |
| O4' | C1' | N9 | 108.7° | 109.4° |
| O4' | C1' | H1' | 113.1° | 109.1° |
| C2' | C1' | N9 | 115.9° | 113.8° |
| C2' | C1' | H1' | 105.5° | 111.7° |
| C1' | C2' | C3' | 103.1° | 103.2° |
| C1' | C2' | H2'1 | 113.0° | 114.1° |
| C1' | C2' | H2'2 | 111.6° | 110.0° |
| N9 | C1' | H1' | 105.2° | 105.1° |
| C1' | N9 | C4 | 129.3° | 127.3° |
| C1' | N9 | C8 | 126.5° | 126.1° |
| C3' | C2' | H2'1 | 113.0° | 112.8° |
| C3' | C2' | H2'2 | 111.6° | 109.9° |
| C2' | C3' | O3' | 113.2° | 111.3° |
| C2' | C3' | H3' | 110.5° | 110.2° |
| H2'1 | C2' | H2'2 | 104.7° | 106.8° |
| O3' | C3' | H3' | 106.9° | 109.4° |
| C3' | O3' | P | 125.0° | 118.2° |
| O3' | P | O1P | 108.4° | 103.8° |
| O3' | P | O2P | 109.8° | 102.6° |
| O3' | P | O1 | 48.6° | 115.1° |
| C4 | N9 | C8 | 104.2° | 106.6° |
| N9 | C4 | N3 | 126.3° | 126.0° |
| N9 | C4 | C5 | 105.8° | 104.9° |
| N9 | C8 | N7 | 115.4° | 112.5° |
| N9 | C8 | H8 | 122.3° | 122.0° |
| N3 | C4 | C5 | 127.9° | 129.1° |
| C4 | N3 | C2 | 113.5° | 113.0° |
| C4 | C5 | C6 | 118.6° | 119.3° |
| C4 | C5 | N7 | 110.9° | 112.1° |
| N3 | C2 | N2 | 121.5° | 122.0° |
| N3 | C2 | N1 | 122.1° | 122.7° |
| N2 | C2 | N1 | 116.5° | 115.3° |
| C2 | N2 | HN21 | 124.9° | 118.3° |
| C2 | N2 | HN22 | 110.3° | 118.3° |
| C2 | N1 | C6 | 125.2° | 125.3° |
| C2 | N1 | HN1 | 117.4° | 117.4° |
| HN21 | N2 | HN22 | 124.8° | 123.4° |
| C6 | N1 | HN1 | 117.4° | 117.4° |
| N1 | C6 | O6 | 119.2° | 125.4° |
| N1 | C6 | C5 | 112.7° | 110.7° |
| O6 | C6 | C5 | 128.1° | 123.8° |
| C6 | C5 | N7 | 130.5° | 128.6° |
| C5 | N7 | C8 | 103.8° | 103.9° |
| N7 | C8 | H8 | 122.3° | 125.5° |
| O1P | P | O2P | 116.7° | 103.3° |
| O1P | P | O1 | 134.6° | 115.2° |
| P | O1P | H1P | 109.5° | 118.9° |
| O2P | P | O1 | 108.4° | 115.0° |
| P | O2P | H2P | 109.5° | 118.9° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O5' | C5' | C4' | H5'1 | 119.3° | 119.6° |
| O5' | C5' | C4' | H5'2 | 120.0° | 119.5° |
| O5' | C5' | H5'1 | H5'2 | 119.5° | 119.5° |
| O5' | C5' | C4' | O4' | 63.8° | 61.8° |
| O5' | C5' | C4' | C3' | 57.0° | 179.5° |
| O5' | C5' | C4' | H4' | 175.2° | 56.3° |
| H5' | O5' | C5' | C4' | 111.4° | 165.7° |
| H5' | O5' | C5' | H5'1 | 129.3° | 45.6° |
| H5' | O5' | C5' | H5'2 | 8.6° | 74.2° |
| C4' | C5' | H5'1 | H5'2 | 119.6° | 121.2° |
| C5' | C4' | O4' | C3' | 126.7° | 122.8° |
| C5' | C4' | O4' | H4' | 114.3° | 118.3° |
| C5' | C4' | C3' | H4' | 114.0° | 122.8° |
| C5' | C4' | O4' | C1' | 146.6° | 148.9° |
| C5' | C4' | C3' | C2' | 154.0° | 157.2° |
| C5' | C4' | C3' | O3' | 86.5° | 83.6° |
| C5' | C4' | C3' | H3' | 32.9° | 39.7° |
| H5'1 | C5' | C4' | O4' | 55.5° | 57.8° |
| H5'1 | C5' | C4' | C3' | 176.3° | 60.0° |
| H5'1 | C5' | C4' | H4' | 65.5° | 175.9° |
| H5'2 | C5' | C4' | O4' | 176.2° | 178.7° |
| H5'2 | C5' | C4' | C3' | 63.0° | 60.9° |
| H5'2 | C5' | C4' | H4' | 55.2° | 63.3° |
| O4' | C4' | C3' | H4' | 121.5° | 117.0° |
| C4' | O4' | C1' | C2' | 1.4° | 4.6° |
| C4' | O4' | C1' | N9 | 128.3° | 128.8° |
| C4' | O4' | C1' | H1' | 115.2° | 116.8° |
| O4' | C4' | C3' | C2' | 29.5° | 37.0° |
| O4' | C4' | C3' | O3' | 149.0° | 156.2° |
| O4' | C4' | C3' | H3' | 91.7° | 80.5° |
| C3' | C4' | O4' | C1' | 19.9° | 26.2° |
| C4' | C3' | C2' | C1' | 28.0° | 33.0° |
| C4' | C3' | C2' | O3' | 115.1° | 119.9° |
| C4' | C3' | C2' | H3' | 125.1° | 118.4° |
| C4' | C3' | C2' | H2'1 | 150.3° | 156.6° |
| C4' | C3' | C2' | H2'2 | 92.0° | 84.3° |
| C4' | C3' | O3' | H3' | 125.4° | 124.5° |
| C4' | C3' | O3' | P | 164.1° | 173.4° |
| H4' | C4' | O4' | C1' | 99.1° | 92.8° |
| H4' | C4' | C3' | C2' | 92.0° | 80.0° |
| H4' | C4' | C3' | O3' | 27.5° | 39.2° |
| H4' | C4' | C3' | H3' | 146.9° | 162.5° |
| O4' | C1' | C2' | N9 | 122.6° | 121.4° |
| O4' | C1' | C2' | H1' | 121.4° | 119.8° |
| O4' | C1' | N9 | H1' | 121.4° | 117.1° |
| O4' | C1' | C2' | C3' | 17.3° | 18.6° |
| O4' | C1' | C2' | H2'1 | 139.6° | 141.4° |
| O4' | C1' | C2' | H2'2 | 102.7° | 98.6° |
| O4' | C1' | N9 | C4 | 63.8° | 147.1° |
| O4' | C1' | N9 | C8 | 116.4° | 33.0° |
| C2' | C1' | N9 | H1' | 116.1° | 122.5° |
| C1' | C2' | C3' | H2'1 | 122.3° | 123.7° |
| C1' | C2' | C3' | H2'2 | 120.0° | 117.3° |
| C1' | C2' | H2'1 | H2'2 | 121.7° | 121.8° |
| C1' | C2' | C3' | O3' | 143.1° | 152.9° |
| C1' | C2' | C3' | H3' | 97.1° | 85.5° |
| C2' | C1' | N9 | C4 | 58.6° | 92.5° |
| C2' | C1' | N9 | C8 | 121.2° | 87.5° |
| N9 | C1' | C2' | C3' | 105.3° | 102.8° |
| N9 | C1' | C2' | H2'1 | 17.0° | 20.0° |
| N9 | C1' | C2' | H2'2 | 134.7° | 140.0° |
| C1' | N9 | C4 | C8 | 179.8° | 180.0° |
| C1' | N9 | C4 | N3 | 0.1° | 0.0° |
| C1' | N9 | C4 | C5 | 179.8° | 180.0° |
| C1' | N9 | C8 | N7 | 179.8° | 180.0° |
| C1' | N9 | C8 | H8 | 0.2° | 0.1° |
| H1' | C1' | C2' | C3' | 138.7° | 138.4° |
| H1' | C1' | C2' | H2'1 | 99.0° | 98.8° |
| H1' | C1' | C2' | H2'2 | 18.7° | 21.2° |
| H1' | C1' | N9 | C4 | 174.7° | 30.0° |
| H1' | C1' | N9 | C8 | 5.1° | 150.0° |
| C3' | C2' | H2'1 | H2'2 | 121.7° | 120.9° |
| C2' | C3' | O3' | H3' | 121.9° | 122.1° |
| C2' | C3' | O3' | P | 51.4° | 60.0° |
| H2'1 | C2' | C3' | O3' | 94.6° | 83.4° |
| H2'1 | C2' | C3' | H3' | 25.2° | 38.2° |
| H2'2 | C2' | C3' | O3' | 23.1° | 35.7° |
| H2'2 | C2' | C3' | H3' | 142.9° | 157.3° |
| C3' | O3' | P | O1P | 99.2° | 173.1° |
| C3' | O3' | P | O2P | 29.4° | 65.7° |
| C3' | O3' | P | O1 | 126.9° | 60.0° |
| H3' | C3' | O3' | P | 70.5° | 62.1° |
| O3' | P | O1P | O2P | 124.6° | 106.9° |
| O3' | P | O1P | O1 | 49.5° | 126.8° |
| O3' | P | O2P | O1 | 51.7° | 125.8° |
| O3' | P | O1P | H1P | 46.4° | 175.7° |
| O3' | P | O2P | H2P | 179.9° | 173.8° |
| N9 | C4 | N3 | C5 | 179.9° | 180.0° |
| N9 | C4 | N3 | C2 | 179.7° | 180.0° |
| N9 | C4 | C5 | C6 | 179.8° | 180.0° |
| N9 | C4 | C5 | N7 | 0.0° | 0.0° |
| C4 | N9 | C8 | N7 | 0.0° | 0.0° |
| C4 | N9 | C8 | H8 | 179.9° | 180.0° |
| C8 | N9 | C4 | N3 | 179.9° | 180.0° |
| C8 | N9 | C4 | C5 | 0.0° | 0.0° |
| N9 | C8 | N7 | C5 | 0.0° | 0.0° |
| N9 | C8 | N7 | H8 | 180.0° | 179.9° |
| C4 | N3 | C2 | N2 | 179.6° | 180.0° |
| C4 | N3 | C2 | N1 | 0.1° | 0.0° |
| N3 | C4 | C5 | C6 | 0.1° | 0.0° |
| N3 | C4 | C5 | N7 | 179.9° | 180.0° |
| C5 | C4 | N3 | C2 | 0.2° | 0.0° |
| C4 | C5 | C6 | N1 | 0.1° | 0.0° |
| C4 | C5 | C6 | O6 | 179.9° | 180.0° |
| C4 | C5 | C6 | N7 | 179.8° | 180.0° |
| C4 | C5 | N7 | C8 | 0.0° | 0.0° |
| N3 | C2 | N2 | N1 | 179.8° | 180.0° |
| N3 | C2 | N2 | HN21 | 0.0° | 137.4° |
| N3 | C2 | N2 | HN22 | 180.0° | 42.6° |
| N3 | C2 | N1 | C6 | 0.1° | 0.0° |
| N3 | C2 | N1 | HN1 | 179.9° | 180.0° |
| C2 | N2 | HN21 | HN22 | 180.0° | 180.0° |
| N2 | C2 | N1 | C6 | 179.8° | 180.0° |
| N2 | C2 | N1 | HN1 | 0.2° | 0.1° |
| N1 | C2 | N2 | HN21 | 179.7° | 42.6° |
| N1 | C2 | N2 | HN22 | 0.2° | 137.4° |
| C2 | N1 | C6 | HN1 | 180.0° | 180.0° |
| C2 | N1 | C6 | O6 | 180.0° | 180.0° |
| C2 | N1 | C6 | C5 | 0.2° | 0.0° |
| N1 | C6 | O6 | C5 | 179.8° | 180.0° |
| N1 | C6 | C5 | N7 | 179.7° | 180.0° |
| HN1 | N1 | C6 | O6 | 0.0° | 0.0° |
| HN1 | N1 | C6 | C5 | 179.8° | 180.0° |
| O6 | C6 | C5 | N7 | 0.1° | 0.0° |
| C6 | C5 | N7 | C8 | 179.8° | 180.0° |
| C5 | N7 | C8 | H8 | 179.9° | 179.9° |
| O1P | P | O2P | O1 | 175.5° | 126.4° |
| O1P | P | O2P | H2P | 56.0° | 78.5° |
| O2P | P | O1P | H1P | 78.2° | 77.4° |
| O1 | P | O1P | H1P | 95.9° | 48.8° |
| O1 | P | O2P | H2P | 128.5° | 48.0° |
