SJO
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O1P | P | sing | 1.61Å | 1.48Å | |
| O2P | P | sing | 1.61Å | 1.48Å | |
| P | O5' | sing | 1.61Å | 1.62Å | |
| O5' | C5' | sing | 1.43Å | 1.43Å | |
| C5' | C4' | sing | 1.53Å | 1.54Å | |
| O4' | C4' | sing | 1.45Å | 1.43Å | |
| O4' | C1' | sing | 1.44Å | 1.44Å | |
| C4' | C3' | sing | 1.54Å | 1.53Å | |
| N2 | C2 | sing | 1.37Å | 1.33Å | |
| N1 | C2 | sing | 1.36Å | 1.37Å | |
| N1 | C6 | sing | 1.35Å | 1.39Å | |
| O6 | C6 | doub | 1.22Å | 1.23Å | |
| C2 | N3 | doub | 1.31Å | 1.33Å | |
| C6 | C5 | sing | 1.41Å | 1.42Å | |
| N3 | C4 | sing | 1.34Å | 1.35Å | |
| C5 | C4 | doub | 1.40Å | 1.37Å | Aromatic |
| C5 | N7 | sing | 1.36Å | 1.40Å | Aromatic |
| C4 | N9 | sing | 1.37Å | 1.37Å | Aromatic |
| N7 | C8 | doub | 1.30Å | 1.31Å | Aromatic |
| N9 | C8 | sing | 1.37Å | 1.37Å | Aromatic |
| N9 | C1' | sing | 1.47Å | 1.47Å | |
| C8 | C8A | sing | 1.51Å | 1.53Å | |
| C1' | C2' | sing | 1.54Å | 1.52Å | |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | C2' | sing | 1.55Å | 1.52Å | |
| C2' | O2' | sing | 1.43Å | 1.43Å | |
| O2' | C2A | sing | 1.43Å | 1.43Å | |
| O1P | H2 | sing | 0.97Å | 0.95Å | |
| O2P | H3 | sing | 0.97Å | 0.95Å | |
| C2A | H31 | sing | 1.09Å | 1.10Å | |
| C2A | H32 | sing | 1.09Å | 1.10Å | |
| C2A | H33 | sing | 1.09Å | 1.10Å | |
| C2' | H2'' | sing | 1.09Å | 1.10Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| N2 | H21 | sing | 0.97Å | 1.00Å | |
| N2 | H22 | sing | 0.97Å | 1.00Å | |
| N1 | H1 | sing | 0.97Å | 1.00Å | |
| C8A | H81 | sing | 1.09Å | 1.10Å | |
| C8A | H82 | sing | 1.09Å | 1.10Å | |
| C8A | H83 | sing | 1.09Å | 1.10Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | H4 | sing | 0.97Å | 0.95Å | |
| P | O1 | doub | 1.48Å | 1.61Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O1P | P | O2P | 119.9° | 109.5° |
| O1P | P | O5' | 108.2° | 109.5° |
| P | O1P | H2 | 109.5° | 114.0° |
| O1P | P | O1 | 108.2° | 109.5° |
| O2P | P | O5' | 108.2° | 109.5° |
| P | O2P | H3 | 109.5° | 114.0° |
| O2P | P | O1 | 108.2° | 109.5° |
| P | O5' | C5' | 121.0° | 123.0° |
| O5' | P | O1 | 102.9° | 109.4° |
| O5' | C5' | C4' | 111.6° | 109.5° |
| O5' | C5' | H5' | 108.9° | 109.4° |
| O5' | C5' | H5'' | 109.0° | 109.5° |
| C5' | C4' | O4' | 109.4° | 110.4° |
| C5' | C4' | C3' | 109.6° | 110.4° |
| C4' | C5' | H5' | 108.9° | 109.5° |
| C4' | C5' | H5'' | 108.9° | 109.5° |
| C5' | C4' | H4' | 109.4° | 110.4° |
| C4' | O4' | C1' | 111.3° | 105.3° |
| O4' | C4' | C3' | 107.9° | 104.7° |
| O4' | C4' | H4' | 111.0° | 110.4° |
| O4' | C1' | N9 | 110.6° | 110.4° |
| O4' | C1' | C2' | 107.8° | 104.8° |
| O4' | C1' | H1' | 110.0° | 110.3° |
| C4' | C3' | O3' | 109.4° | 110.5° |
| C4' | C3' | C2' | 105.8° | 104.1° |
| C3' | C4' | H4' | 109.6° | 110.4° |
| C4' | C3' | H3' | 110.0° | 110.5° |
| N2 | C2 | N1 | 116.1° | 119.0° |
| N2 | C2 | N3 | 120.1° | 119.1° |
| C2 | N2 | H21 | 120.0° | 119.9° |
| C2 | N2 | H22 | 120.0° | 120.0° |
| C2 | N1 | C6 | 125.1° | 120.3° |
| N1 | C2 | N3 | 123.8° | 121.9° |
| C2 | N1 | H1 | 117.5° | 119.8° |
| N1 | C6 | O6 | 120.4° | 120.8° |
| N1 | C6 | C5 | 111.5° | 118.4° |
| C6 | N1 | H1 | 117.5° | 119.9° |
| O6 | C6 | C5 | 128.0° | 120.9° |
| C2 | N3 | C4 | 112.0° | 121.1° |
| C6 | C5 | C4 | 119.3° | 118.6° |
| C6 | C5 | N7 | 130.3° | 134.1° |
| N3 | C4 | C5 | 128.2° | 119.7° |
| N3 | C4 | N9 | 125.5° | 134.2° |
| C4 | C5 | N7 | 110.4° | 107.3° |
| C5 | C4 | N9 | 106.4° | 106.1° |
| C5 | N7 | C8 | 103.7° | 109.4° |
| C4 | N9 | C8 | 105.6° | 107.5° |
| C4 | N9 | C1' | 124.8° | 126.3° |
| N7 | C8 | N9 | 114.0° | 109.8° |
| N7 | C8 | C8A | 122.4° | 125.1° |
| C8 | N9 | C1' | 129.6° | 126.2° |
| N9 | C8 | C8A | 123.6° | 125.1° |
| N9 | C1' | C2' | 109.9° | 110.4° |
| N9 | C1' | H1' | 109.6° | 110.4° |
| C8 | C8A | H81 | 109.5° | 109.5° |
| C8 | C8A | H82 | 109.5° | 109.5° |
| C8 | C8A | H83 | 109.5° | 109.4° |
| C1' | C2' | C3' | 106.1° | 104.2° |
| C1' | C2' | O2' | 109.6° | 110.5° |
| C1' | C2' | H2'' | 110.0° | 110.5° |
| C2' | C1' | H1' | 108.9° | 110.4° |
| O3' | C3' | C2' | 109.5° | 110.5° |
| O3' | C3' | H3' | 111.6° | 110.4° |
| C3' | O3' | H4 | 109.5° | 114.0° |
| C3' | C2' | O2' | 109.5° | 110.5° |
| C3' | C2' | H2'' | 110.1° | 110.5° |
| C2' | C3' | H3' | 110.3° | 110.6° |
| C2' | O2' | C2A | 111.7° | 114.0° |
| O2' | C2' | H2'' | 111.3° | 110.4° |
| O2' | C2A | H31 | 109.5° | 109.4° |
| O2' | C2A | H32 | 109.5° | 109.5° |
| O2' | C2A | H33 | 109.4° | 109.5° |
| H31 | C2A | H32 | 109.5° | 109.4° |
| H31 | C2A | H33 | 109.5° | 109.5° |
| H32 | C2A | H33 | 109.5° | 109.5° |
| H5' | C5' | H5'' | 109.4° | 109.5° |
| H21 | N2 | H22 | 120.0° | 120.0° |
| H81 | C8A | H82 | 109.4° | 109.5° |
| H81 | C8A | H83 | 109.4° | 109.4° |
| H82 | C8A | H83 | 109.5° | 109.4° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1P | P | O2P | O5' | 124.5° | 120.0° |
| O1P | P | O2P | O1 | 124.6° | 120.0° |
| O1P | P | O5' | O1 | 114.3° | 120.0° |
| O1P | P | O5' | C5' | 137.6° | 65.0° |
| O1P | P | O2P | H3 | 124.6° | 60.0° |
| O2P | P | O5' | O1 | 114.4° | 120.0° |
| O2P | P | O5' | C5' | 6.4° | 175.0° |
| O2P | P | O1P | H2 | 124.6° | 60.0° |
| P | O5' | C5' | C4' | 125.6° | 180.0° |
| O5' | P | O1P | H2 | 110.9° | 60.0° |
| O5' | P | O2P | H3 | 110.9° | 180.0° |
| P | O5' | C5' | H5' | 114.0° | 60.0° |
| P | O5' | C5' | H5'' | 5.3° | 60.0° |
| O5' | C5' | C4' | H5' | 120.3° | 120.0° |
| O5' | C5' | C4' | H5'' | 120.4° | 120.0° |
| O5' | C5' | C4' | O4' | 10.2° | 69.7° |
| O5' | C5' | C4' | C3' | 128.2° | 175.0° |
| O5' | C5' | H5' | H5'' | 119.1° | 120.0° |
| O5' | C5' | C4' | H4' | 111.6° | 52.7° |
| C5' | O5' | P | O1 | 108.0° | 55.0° |
| C5' | C4' | O4' | C3' | 119.1° | 118.8° |
| C5' | C4' | O4' | H4' | 120.8° | 122.3° |
| C5' | C4' | O4' | C1' | 119.6° | 159.3° |
| C5' | C4' | C3' | H4' | 120.1° | 122.3° |
| C5' | C4' | C3' | O3' | 116.3° | 98.5° |
| C5' | C4' | C3' | C2' | 125.7° | 142.8° |
| C4' | C5' | H5' | H5'' | 119.0° | 120.0° |
| C5' | C4' | C3' | H3' | 6.6° | 24.0° |
| O4' | C4' | C3' | H4' | 120.9° | 118.9° |
| C4' | O4' | C1' | N9 | 114.2° | 159.2° |
| C4' | O4' | C1' | C2' | 6.0° | 40.4° |
| O4' | C4' | C3' | O3' | 124.7° | 142.6° |
| O4' | C4' | C3' | C2' | 6.8° | 23.9° |
| O4' | C4' | C5' | H5' | 110.2° | 50.3° |
| O4' | C4' | C5' | H5'' | 130.5° | 170.3° |
| C4' | O4' | C1' | H1' | 124.5° | 78.5° |
| O4' | C4' | C3' | H3' | 112.4° | 94.8° |
| C1' | O4' | C4' | C3' | 0.5° | 40.4° |
| O4' | C1' | N9 | C4 | 66.1° | 136.2° |
| O4' | C1' | N9 | C8 | 114.9° | 43.5° |
| O4' | C1' | N9 | C2' | 118.9° | 115.4° |
| O4' | C1' | N9 | H1' | 121.5° | 122.3° |
| O4' | C1' | C2' | H1' | 119.3° | 118.8° |
| O4' | C1' | C2' | C3' | 10.0° | 23.9° |
| O4' | C1' | C2' | O2' | 108.1° | 142.6° |
| O4' | C1' | C2' | H2'' | 129.2° | 94.8° |
| C1' | O4' | C4' | H4' | 119.5° | 78.4° |
| C4' | C3' | C2' | C1' | 10.1° | 0.1° |
| C4' | C3' | O3' | C2' | 115.6° | 114.7° |
| C4' | C3' | O3' | H3' | 122.0° | 122.6° |
| C4' | C3' | C2' | H3' | 119.0° | 118.7° |
| C4' | C3' | C2' | O2' | 108.1° | 118.6° |
| C4' | C3' | C2' | H2'' | 129.1° | 118.8° |
| C3' | C4' | C5' | H5' | 7.9° | 65.0° |
| C3' | C4' | C5' | H5'' | 111.4° | 55.0° |
| C4' | C3' | O3' | H4 | 180.0° | 61.4° |
| N2 | C2 | N1 | N3 | 180.0° | 179.9° |
| N2 | C2 | N1 | C6 | 180.0° | 180.0° |
| N2 | C2 | N3 | C4 | 180.0° | 180.0° |
| C2 | N2 | H21 | H22 | 180.0° | 179.9° |
| N2 | C2 | N1 | H1 | 0.0° | 0.1° |
| C2 | N1 | C6 | H1 | 180.0° | 179.9° |
| C2 | N1 | C6 | O6 | 179.9° | 180.0° |
| C2 | N1 | C6 | C5 | 0.0° | 0.0° |
| N1 | C2 | N3 | C4 | 0.0° | 0.1° |
| N1 | C2 | N2 | H21 | 180.0° | 180.0° |
| N1 | C2 | N2 | H22 | 0.0° | 0.1° |
| N1 | C6 | O6 | C5 | 180.0° | 179.9° |
| C6 | N1 | C2 | N3 | 0.0° | 0.1° |
| N1 | C6 | C5 | C4 | 0.0° | 0.0° |
| N1 | C6 | C5 | N7 | 179.9° | 179.9° |
| O6 | C6 | C5 | C4 | 180.0° | 179.9° |
| O6 | C6 | C5 | N7 | 0.1° | 0.0° |
| O6 | C6 | N1 | H1 | 0.0° | 0.1° |
| C2 | N3 | C4 | C5 | 0.0° | 0.0° |
| C2 | N3 | C4 | N9 | 179.9° | 180.0° |
| N3 | C2 | N2 | H21 | 0.0° | 0.1° |
| N3 | C2 | N2 | H22 | 180.0° | 180.0° |
| N3 | C2 | N1 | H1 | 180.0° | 180.0° |
| C6 | C5 | C4 | N3 | 0.0° | 0.0° |
| C6 | C5 | C4 | N7 | 179.9° | 180.0° |
| C6 | C5 | C4 | N9 | 179.9° | 180.0° |
| C6 | C5 | N7 | C8 | 179.9° | 179.9° |
| C5 | C6 | N1 | H1 | 180.0° | 180.0° |
| N3 | C4 | C5 | N9 | 179.9° | 179.9° |
| N3 | C4 | C5 | N7 | 179.9° | 180.0° |
| N3 | C4 | N9 | C8 | 179.9° | 179.9° |
| N3 | C4 | N9 | C1' | 0.9° | 0.2° |
| C4 | C5 | N7 | C8 | 0.0° | 0.0° |
| C5 | C4 | N9 | C8 | 0.0° | 0.0° |
| C5 | C4 | N9 | C1' | 179.2° | 179.8° |
| N7 | C5 | C4 | N9 | 0.0° | 0.0° |
| C5 | N7 | C8 | N9 | 0.0° | 0.0° |
| C5 | N7 | C8 | C8A | 179.8° | 179.8° |
| C4 | N9 | C8 | N7 | 0.0° | 0.0° |
| C4 | N9 | C8 | C1' | 179.1° | 179.8° |
| C4 | N9 | C8 | C8A | 179.8° | 179.8° |
| C4 | N9 | C1' | C2' | 52.8° | 108.4° |
| C4 | N9 | C1' | H1' | 172.4° | 13.9° |
| N7 | C8 | N9 | C8A | 179.8° | 179.8° |
| N7 | C8 | N9 | C1' | 179.1° | 179.8° |
| N7 | C8 | C8A | H81 | 0.0° | 90.3° |
| N7 | C8 | C8A | H82 | 120.0° | 29.8° |
| N7 | C8 | C8A | H83 | 120.0° | 149.7° |
| C8 | N9 | C1' | C2' | 126.1° | 71.9° |
| C8 | N9 | C1' | H1' | 6.5° | 165.8° |
| N9 | C8 | C8A | H81 | 179.8° | 89.9° |
| N9 | C8 | C8A | H82 | 59.8° | 150.0° |
| N9 | C8 | C8A | H83 | 60.2° | 30.0° |
| C1' | N9 | C8 | C8A | 0.7° | 0.0° |
| N9 | C1' | C2' | H1' | 120.1° | 122.4° |
| N9 | C1' | C2' | C3' | 110.6° | 142.8° |
| N9 | C1' | C2' | O2' | 131.2° | 98.5° |
| N9 | C1' | C2' | H2'' | 8.5° | 24.0° |
| C8 | C8A | H81 | H82 | 120.0° | 120.1° |
| C8 | C8A | H81 | H83 | 120.0° | 120.0° |
| C8 | C8A | H82 | H83 | 120.0° | 120.0° |
| C1' | C2' | C3' | O3' | 128.0° | 118.7° |
| C1' | C2' | C3' | O2' | 118.2° | 118.7° |
| C1' | C2' | C3' | H2'' | 119.1° | 118.7° |
| C1' | C2' | O2' | H2'' | 122.0° | 122.6° |
| C1' | C2' | O2' | C2A | 160.2° | 151.9° |
| C1' | C2' | C3' | H3' | 108.9° | 118.6° |
| O3' | C3' | C2' | H3' | 123.2° | 122.6° |
| O3' | C3' | C2' | O2' | 9.7° | 0.0° |
| O3' | C3' | C2' | H2'' | 113.0° | 122.5° |
| O3' | C3' | C4' | H4' | 3.8° | 23.7° |
| C3' | C2' | O2' | H2'' | 122.0° | 122.6° |
| C3' | C2' | O2' | C2A | 83.7° | 93.3° |
| C2' | C3' | C4' | H4' | 114.2° | 94.9° |
| C3' | C2' | C1' | H1' | 129.3° | 94.9° |
| C2' | C3' | O3' | H4 | 64.4° | 176.1° |
| C2' | O2' | C2A | H31 | 180.0° | 180.0° |
| C2' | O2' | C2A | H32 | 60.0° | 60.1° |
| C2' | O2' | C2A | H33 | 60.0° | 60.0° |
| O2' | C2' | C1' | H1' | 11.2° | 23.8° |
| O2' | C2' | C3' | H3' | 132.9° | 122.6° |
| O2' | C2A | H31 | H32 | 120.0° | 120.0° |
| O2' | C2A | H31 | H33 | 120.0° | 120.0° |
| O2' | C2A | H32 | H33 | 120.0° | 120.1° |
| C2A | O2' | C2' | H2'' | 38.3° | 29.3° |
| H2 | O1P | P | O1 | 0.0° | 180.0° |
| H3 | O2P | P | O1 | 0.0° | 60.0° |
| H31 | C2A | H32 | H33 | 120.0° | 120.0° |
| H2'' | C2' | C1' | H1' | 111.6° | 146.4° |
| H2'' | C2' | C3' | H3' | 10.2° | 0.1° |
| H5' | C5' | C4' | H4' | 128.1° | 172.7° |
| H5'' | C5' | C4' | H4' | 8.7° | 67.3° |
| H4' | C4' | C3' | H3' | 126.7° | 146.3° |
| H81 | C8A | H82 | H83 | 119.9° | 119.9° |
| H3' | C3' | O3' | H4 | 58.0° | 61.2° |
