4JA
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP2 | P | sing | 1.61Å | 1.48Å | |
| C6 | C5 | sing | 1.53Å | 1.52Å | |
| P | O5' | sing | 1.61Å | 1.61Å | |
| P | OP1 | doub | 1.48Å | 1.48Å | |
| O5' | C5' | sing | 1.43Å | 1.42Å | |
| C5 | O5 | sing | 1.43Å | 1.47Å | |
| C5 | C4 | sing | 1.53Å | 1.53Å | |
| O5 | C1 | sing | 1.43Å | 1.47Å | |
| C5' | C3' | sing | 1.53Å | 1.54Å | |
| C3' | C2' | sing | 1.53Å | 1.54Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C2' | O1 | sing | 1.43Å | 1.42Å | |
| O4 | C4 | sing | 1.43Å | 1.44Å | |
| C4 | C3 | sing | 1.53Å | 1.53Å | |
| C1 | O1 | sing | 1.43Å | 1.46Å | |
| C1 | C2 | sing | 1.53Å | 1.54Å | |
| C3 | C2 | sing | 1.53Å | 1.53Å | |
| C3 | O3 | sing | 1.43Å | 1.44Å | |
| C2 | O2 | sing | 1.43Å | 1.45Å | |
| O2 | HO2 | sing | 0.97Å | 0.95Å | |
| O3 | HO3 | sing | 0.97Å | 0.95Å | |
| O4 | HO4 | sing | 0.97Å | 0.95Å | |
| C1 | H1 | sing | 1.09Å | 1.10Å | |
| C2 | H2 | sing | 1.09Å | 1.10Å | |
| C3 | H3 | sing | 1.09Å | 1.10Å | |
| C4 | H4 | sing | 1.09Å | 1.10Å | |
| C5 | H5 | sing | 1.09Å | 1.10Å | |
| C6 | H61 | sing | 1.09Å | 1.10Å | |
| C6 | H62 | sing | 1.09Å | 1.10Å | |
| C6 | H63 | sing | 1.09Å | 1.10Å | |
| OP2 | HOP2 | sing | 0.97Å | 0.95Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| C2' | H2'' | sing | 1.09Å | 1.10Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| P | OP3 | sing | 1.61Å | 9.49Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP2 | P | O5' | 108.9° | 109.5° |
| OP2 | P | OP1 | 119.8° | 109.5° |
| P | OP2 | HOP2 | 109.5° | 113.9° |
| OP2 | P | OP3 | 107.8° | 109.5° |
| C6 | C5 | O5 | 105.1° | 109.5° |
| C6 | C5 | C4 | 115.7° | 109.5° |
| C6 | C5 | H5 | 109.3° | 109.5° |
| C5 | C6 | H61 | 109.5° | 109.4° |
| C5 | C6 | H62 | 109.5° | 109.5° |
| C5 | C6 | H63 | 109.5° | 109.4° |
| O5' | P | OP1 | 109.2° | 109.4° |
| P | O5' | C5' | 120.1° | 123.0° |
| O5' | P | OP3 | 87.3° | 109.4° |
| OP1 | P | OP3 | 118.7° | 109.5° |
| O5' | C5' | C3' | 112.8° | 109.5° |
| O5' | C5' | H5'' | 108.6° | 109.5° |
| O5' | C5' | H5' | 108.6° | 109.5° |
| O5 | C5 | C4 | 107.5° | 109.4° |
| C5 | O5 | C1 | 117.2° | 114.1° |
| O5 | C5 | H5 | 110.0° | 109.5° |
| C5 | C4 | O4 | 109.8° | 109.5° |
| C5 | C4 | C3 | 108.6° | 109.2° |
| C5 | C4 | H4 | 109.9° | 109.6° |
| C4 | C5 | H5 | 109.1° | 109.5° |
| O5 | C1 | O1 | 110.2° | 109.4° |
| O5 | C1 | C2 | 108.6° | 109.4° |
| O5 | C1 | H1 | 110.2° | 109.5° |
| C5' | C3' | C2' | 108.5° | 109.5° |
| C5' | C3' | O3' | 110.5° | 109.5° |
| C3' | C5' | H5'' | 108.6° | 109.5° |
| C3' | C5' | H5' | 108.7° | 109.5° |
| C5' | C3' | H3' | 107.9° | 109.5° |
| C2' | C3' | O3' | 112.5° | 109.5° |
| C3' | C2' | O1 | 112.9° | 109.5° |
| C2' | C3' | H3' | 107.9° | 109.5° |
| C3' | C2' | H2'' | 108.6° | 109.5° |
| C3' | C2' | H2' | 108.6° | 109.4° |
| O3' | C3' | H3' | 109.4° | 109.4° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| C2' | O1 | C1 | 112.7° | 114.0° |
| O1 | C2' | H2'' | 108.6° | 109.5° |
| O1 | C2' | H2' | 108.6° | 109.5° |
| O4 | C4 | C3 | 107.4° | 109.5° |
| C4 | O4 | HO4 | 109.5° | 114.0° |
| O4 | C4 | H4 | 111.2° | 109.5° |
| C4 | C3 | C2 | 111.1° | 109.0° |
| C4 | C3 | O3 | 109.0° | 109.5° |
| C4 | C3 | H3 | 108.9° | 109.6° |
| C3 | C4 | H4 | 109.9° | 109.5° |
| O1 | C1 | C2 | 108.3° | 109.5° |
| O1 | C1 | H1 | 110.3° | 109.5° |
| C1 | C2 | C3 | 110.2° | 109.2° |
| C1 | C2 | O2 | 109.7° | 109.5° |
| C2 | C1 | H1 | 109.2° | 109.5° |
| C1 | C2 | H2 | 109.1° | 109.5° |
| C2 | C3 | O3 | 108.9° | 109.6° |
| C3 | C2 | O2 | 108.2° | 109.5° |
| C3 | C2 | H2 | 109.2° | 109.5° |
| C2 | C3 | H3 | 108.9° | 109.6° |
| C3 | O3 | HO3 | 109.5° | 114.0° |
| O3 | C3 | H3 | 110.1° | 109.5° |
| C2 | O2 | HO2 | 109.5° | 114.0° |
| O2 | C2 | H2 | 110.4° | 109.5° |
| H61 | C6 | H62 | 109.5° | 109.5° |
| H61 | C6 | H63 | 109.5° | 109.5° |
| H62 | C6 | H63 | 109.4° | 109.5° |
| H5'' | C5' | H5' | 109.5° | 109.4° |
| H2'' | C2' | H2' | 109.5° | 109.5° |
| P | OP3 | HOP3 | 90.0° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP2 | P | O5' | OP1 | 132.5° | 120.0° |
| OP2 | P | O5' | OP3 | 107.9° | 120.0° |
| OP2 | P | OP1 | OP3 | 135.7° | 120.0° |
| OP2 | P | O5' | C5' | 169.4° | 175.0° |
| OP2 | P | OP3 | HOP3 | 90.0° | 59.9° |
| C6 | C5 | O5 | C4 | 123.8° | 120.0° |
| C6 | C5 | O5 | H5 | 117.5° | 120.0° |
| C6 | C5 | C4 | H5 | 123.7° | 120.0° |
| C6 | C5 | O5 | C1 | 175.9° | 178.9° |
| C6 | C5 | C4 | O4 | 67.7° | 62.5° |
| C6 | C5 | C4 | C3 | 175.1° | 177.6° |
| C6 | C5 | C4 | H4 | 54.9° | 57.6° |
| C5 | C6 | H61 | H62 | 120.0° | 120.0° |
| C5 | C6 | H61 | H63 | 120.0° | 119.9° |
| C5 | C6 | H62 | H63 | 120.0° | 120.0° |
| O5' | P | OP1 | OP3 | 97.7° | 120.0° |
| P | O5' | C5' | C3' | 175.7° | 180.0° |
| O5' | P | OP2 | HOP2 | 126.7° | 180.0° |
| P | O5' | C5' | H5'' | 55.1° | 60.0° |
| P | O5' | C5' | H5' | 63.8° | 60.0° |
| O5' | P | OP3 | HOP3 | 90.0° | 60.0° |
| OP1 | P | O5' | C5' | 58.1° | 55.0° |
| OP1 | P | OP2 | HOP2 | 0.0° | 60.0° |
| OP1 | P | OP3 | HOP3 | 90.0° | 180.0° |
| O5' | C5' | C3' | H5'' | 120.5° | 120.0° |
| O5' | C5' | C3' | H5' | 120.5° | 120.0° |
| O5' | C5' | C3' | C2' | 150.1° | 175.0° |
| O5' | C5' | C3' | O3' | 86.1° | 65.0° |
| O5' | C5' | H5'' | H5' | 118.4° | 120.0° |
| O5' | C5' | C3' | H3' | 33.4° | 55.0° |
| C5' | O5' | P | OP3 | 61.5° | 65.0° |
| O5 | C5 | C4 | H5 | 119.3° | 120.0° |
| O5 | C5 | C4 | O4 | 175.2° | 177.5° |
| O5 | C5 | C4 | C3 | 58.1° | 57.6° |
| C5 | O5 | C1 | O1 | 175.6° | 178.9° |
| C5 | O5 | C1 | C2 | 57.1° | 61.1° |
| C5 | O5 | C1 | H1 | 62.5° | 58.9° |
| O5 | C5 | C4 | H4 | 62.1° | 62.3° |
| O5 | C5 | C6 | H61 | 180.0° | 60.0° |
| O5 | C5 | C6 | H62 | 60.0° | 180.0° |
| O5 | C5 | C6 | H63 | 60.0° | 60.0° |
| C4 | C5 | O5 | C1 | 60.3° | 61.1° |
| C5 | C4 | O4 | C3 | 117.9° | 119.7° |
| C5 | C4 | O4 | H4 | 121.8° | 120.2° |
| C5 | C4 | C3 | H4 | 120.2° | 120.0° |
| C5 | C4 | C3 | C2 | 59.5° | 57.0° |
| C5 | C4 | C3 | O3 | 179.5° | 176.9° |
| C5 | C4 | O4 | HO4 | 180.0° | 60.3° |
| C5 | C4 | C3 | H3 | 60.3° | 62.9° |
| C4 | C5 | C6 | H61 | 61.7° | 179.9° |
| C4 | C5 | C6 | H62 | 58.4° | 60.1° |
| C4 | C5 | C6 | H63 | 178.3° | 60.0° |
| O5 | C1 | O1 | C2' | 60.4° | 65.0° |
| O5 | C1 | O1 | C2 | 118.6° | 119.9° |
| O5 | C1 | O1 | H1 | 121.9° | 120.0° |
| O5 | C1 | C2 | H1 | 120.2° | 120.0° |
| O5 | C1 | C2 | C3 | 52.2° | 57.6° |
| O5 | C1 | C2 | O2 | 171.2° | 177.5° |
| O5 | C1 | C2 | H2 | 67.8° | 62.4° |
| C1 | O5 | C5 | H5 | 58.4° | 58.9° |
| C5' | C3' | C2' | O3' | 122.6° | 120.0° |
| C5' | C3' | C2' | H3' | 116.7° | 120.1° |
| C5' | C3' | O3' | H3' | 118.7° | 120.0° |
| C5' | C3' | C2' | O1 | 48.9° | 175.0° |
| C3' | C5' | H5'' | H5' | 118.5° | 120.0° |
| C5' | C3' | C2' | H2'' | 71.6° | 65.0° |
| C5' | C3' | C2' | H2' | 169.4° | 55.0° |
| C5' | C3' | O3' | HO3' | 180.0° | 60.0° |
| C2' | C3' | O3' | H3' | 119.9° | 120.0° |
| C3' | C2' | O1 | H2'' | 120.5° | 120.0° |
| C3' | C2' | O1 | H2' | 120.5° | 120.0° |
| C3' | C2' | O1 | C1 | 149.1° | 180.0° |
| C2' | C3' | C5' | H5'' | 89.4° | 65.0° |
| C2' | C3' | C5' | H5' | 29.6° | 55.0° |
| C3' | C2' | H2'' | H2' | 118.4° | 120.0° |
| C2' | C3' | O3' | HO3' | 58.5° | 60.0° |
| O3' | C3' | C2' | O1 | 73.7° | 65.0° |
| O3' | C3' | C5' | H5'' | 34.4° | 55.0° |
| O3' | C3' | C5' | H5' | 153.4° | 175.0° |
| O3' | C3' | C2' | H2'' | 165.8° | 55.0° |
| O3' | C3' | C2' | H2' | 46.8° | 175.0° |
| C2' | O1 | C1 | C2 | 179.0° | 175.1° |
| C2' | O1 | C1 | H1 | 61.5° | 55.0° |
| O1 | C2' | C3' | H3' | 165.6° | 55.0° |
| O1 | C2' | H2'' | H2' | 118.4° | 120.0° |
| O4 | C4 | C3 | H4 | 121.1° | 120.1° |
| O4 | C4 | C3 | C2 | 178.2° | 176.8° |
| O4 | C4 | C3 | O3 | 61.8° | 63.2° |
| O4 | C4 | C3 | H3 | 58.3° | 57.0° |
| O4 | C4 | C5 | H5 | 55.9° | 57.5° |
| C4 | C3 | C2 | C1 | 56.6° | 57.0° |
| C4 | C3 | C2 | O3 | 120.0° | 119.9° |
| C4 | C3 | C2 | H3 | 119.9° | 119.9° |
| C4 | C3 | O3 | H3 | 119.4° | 120.2° |
| C4 | C3 | C2 | O2 | 176.6° | 176.9° |
| C4 | C3 | O3 | HO3 | 180.0° | 179.5° |
| C3 | C4 | O4 | HO4 | 62.1° | 180.0° |
| C4 | C3 | C2 | H2 | 63.3° | 63.0° |
| C3 | C4 | C5 | H5 | 61.2° | 62.4° |
| O1 | C1 | C2 | H1 | 120.2° | 120.1° |
| O1 | C1 | C2 | C3 | 171.9° | 177.6° |
| O1 | C1 | C2 | O2 | 69.1° | 62.5° |
| O1 | C1 | C2 | H2 | 51.9° | 57.6° |
| C1 | O1 | C2' | H2'' | 28.6° | 60.0° |
| C1 | O1 | C2' | H2' | 90.4° | 60.0° |
| C1 | C2 | C3 | O2 | 119.9° | 119.9° |
| C1 | C2 | C3 | H2 | 119.9° | 120.0° |
| C1 | C2 | C3 | O3 | 176.7° | 176.9° |
| C1 | C2 | O2 | H2 | 120.3° | 120.1° |
| C1 | C2 | O2 | HO2 | 180.0° | 60.0° |
| C1 | C2 | C3 | H3 | 63.2° | 63.0° |
| C2 | C3 | O3 | H3 | 119.3° | 120.2° |
| C3 | C2 | O2 | H2 | 119.4° | 120.1° |
| C3 | C2 | O2 | HO2 | 59.8° | 179.8° |
| C2 | C3 | O3 | HO3 | 58.7° | 59.9° |
| C3 | C2 | C1 | H1 | 68.0° | 62.4° |
| C2 | C3 | C4 | H4 | 60.7° | 63.0° |
| O3 | C3 | C2 | O2 | 63.4° | 63.2° |
| O3 | C3 | C2 | H2 | 56.8° | 56.9° |
| O3 | C3 | C4 | H4 | 59.3° | 56.9° |
| O2 | C2 | C1 | H1 | 51.0° | 57.5° |
| O2 | C2 | C3 | H3 | 56.7° | 57.0° |
| HO2 | O2 | C2 | H2 | 59.7° | 60.1° |
| HO3 | O3 | C3 | H3 | 60.6° | 60.3° |
| HO4 | O4 | C4 | H4 | 58.2° | 59.9° |
| H1 | C1 | C2 | H2 | 172.1° | 177.7° |
| H2 | C2 | C3 | H3 | 176.9° | 177.1° |
| H3 | C3 | C4 | H4 | 179.5° | 177.1° |
| H4 | C4 | C5 | H5 | 178.6° | 177.7° |
| H5 | C5 | C6 | H61 | 61.9° | 60.0° |
| H5 | C5 | C6 | H62 | 178.0° | 59.9° |
| H5 | C5 | C6 | H63 | 58.1° | 180.0° |
| H61 | C6 | H62 | H63 | 120.0° | 120.1° |
| HOP2 | OP2 | P | OP3 | 140.0° | 60.0° |
| H5'' | C5' | C3' | H3' | 153.9° | 175.0° |
| H5' | C5' | C3' | H3' | 87.1° | 65.0° |
| H3' | C3' | C2' | H2'' | 45.1° | 175.0° |
| H3' | C3' | C2' | H2' | 73.9° | 65.0° |
| H3' | C3' | O3' | HO3' | 61.3° | 180.0° |
