ZDU
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | OP1 | doub | 1.50Å | 1.45Å | |
| P | OP2 | sing | 1.62Å | 1.47Å | |
| P | O5' | sing | 1.62Å | 1.59Å | |
| P | OP3 | sing | 1.62Å | 47.43Å | |
| OP2 | HOP2 | sing | 0.98Å | 0.95Å | |
| O5' | C5' | sing | 1.42Å | 1.41Å | |
| N1 | C6 | sing | 1.39Å | 1.38Å | |
| N1 | C2 | sing | 1.41Å | 1.38Å | |
| N1 | C1' | sing | 1.43Å | 1.48Å | |
| C6 | C5 | doub | 1.34Å | 1.34Å | |
| C6 | H6 | sing | 1.09Å | 1.10Å | |
| C2 | O2 | doub | 1.23Å | 1.22Å | |
| C2 | N3 | sing | 1.40Å | 1.39Å | |
| N3 | C4 | sing | 1.39Å | 1.41Å | |
| N3 | HN3 | sing | 1.02Å | 1.02Å | |
| C4 | O4 | doub | 1.23Å | 1.25Å | |
| C4 | C5 | sing | 1.49Å | 1.46Å | |
| C5 | C5A | sing | 1.49Å | 1.51Å | |
| C5A | C5B | sing | 1.53Å | 1.55Å | |
| C5A | H5A1 | sing | 1.09Å | 1.11Å | |
| C5A | H5A2 | sing | 1.09Å | 1.12Å | |
| C5B | C5G | sing | 1.53Å | 1.51Å | |
| C5B | H5B1 | sing | 1.10Å | 1.12Å | |
| C5B | H5B2 | sing | 1.10Å | 1.12Å | |
| C5G | N5D | sing | 1.44Å | 1.50Å | |
| C5G | H5G1 | sing | 1.09Å | 1.11Å | |
| C5G | H5G2 | sing | 1.09Å | 1.12Å | |
| N5D | H5D1 | sing | 1.01Å | 1.02Å | |
| N5D | H5D2 | sing | 1.01Å | 1.02Å | |
| C2' | C1' | sing | 1.52Å | 1.53Å | |
| C2' | C3' | sing | 1.51Å | 1.53Å | |
| C2' | H2' | sing | 1.10Å | 1.12Å | |
| C2' | H2'' | sing | 1.09Å | 1.12Å | |
| C5' | C4' | sing | 1.52Å | 1.51Å | |
| C5' | H5' | sing | 1.09Å | 1.11Å | |
| C5' | H5'' | sing | 1.09Å | 1.11Å | |
| C4' | O4' | sing | 1.44Å | 1.43Å | |
| C4' | C3' | sing | 1.52Å | 1.52Å | |
| C4' | H4' | sing | 1.09Å | 1.11Å | |
| O4' | C1' | sing | 1.43Å | 1.41Å | |
| C1' | H1' | sing | 1.10Å | 1.11Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C3' | H3' | sing | 1.09Å | 1.12Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| OP3 | HOP3 | sing | 0.98Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | OP2 | 121.0° | 115.3° |
| OP1 | P | O5' | 108.5° | 115.0° |
| OP1 | P | OP3 | 37.0° | 115.0° |
| OP2 | P | O5' | 108.1° | 103.7° |
| OP2 | P | OP3 | 118.9° | 103.3° |
| P | OP2 | HOP2 | 120.9° | 118.9° |
| O5' | P | OP3 | 75.3° | 102.9° |
| P | O5' | C5' | 119.7° | 118.5° |
| P | OP3 | HOP3 | 37.0° | 118.9° |
| O5' | C5' | C4' | 109.9° | 108.9° |
| O5' | C5' | H5' | 112.0° | 109.0° |
| O5' | C5' | H5'' | 112.0° | 108.9° |
| C6 | N1 | C2 | 121.2° | 120.4° |
| C6 | N1 | C1' | 119.8° | 118.4° |
| N1 | C6 | C5 | 124.8° | 124.5° |
| N1 | C6 | H6 | 119.2° | 114.9° |
| C2 | N1 | C1' | 118.9° | 121.2° |
| N1 | C2 | O2 | 122.6° | 123.8° |
| N1 | C2 | N3 | 114.5° | 115.1° |
| N1 | C1' | C2' | 119.6° | 112.8° |
| N1 | C1' | O4' | 106.9° | 109.3° |
| N1 | C1' | H1' | 102.8° | 107.8° |
| C5 | C6 | H6 | 116.0° | 120.7° |
| C6 | C5 | C4 | 117.8° | 118.3° |
| C6 | C5 | C5A | 121.6° | 123.6° |
| O2 | C2 | N3 | 122.9° | 121.1° |
| C2 | N3 | C4 | 127.0° | 127.0° |
| C2 | N3 | HN3 | 115.5° | 116.4° |
| C4 | N3 | HN3 | 117.5° | 116.6° |
| N3 | C4 | O4 | 120.2° | 123.6° |
| N3 | C4 | C5 | 114.6° | 114.8° |
| O4 | C4 | C5 | 125.2° | 121.6° |
| C4 | C5 | C5A | 120.6° | 118.1° |
| C5 | C5A | C5B | 112.9° | 110.9° |
| C5 | C5A | H5A1 | 111.0° | 107.2° |
| C5 | C5A | H5A2 | 111.0° | 108.8° |
| C5B | C5A | H5A1 | 110.9° | 109.5° |
| C5B | C5A | H5A2 | 110.9° | 111.8° |
| C5A | C5B | C5G | 109.9° | 113.9° |
| C5A | C5B | H5B1 | 112.0° | 109.5° |
| C5A | C5B | H5B2 | 112.1° | 108.4° |
| H5A1 | C5A | H5A2 | 99.4° | 108.4° |
| C5G | C5B | H5B1 | 112.0° | 108.6° |
| C5G | C5B | H5B2 | 112.1° | 109.2° |
| C5B | C5G | N5D | 112.7° | 112.6° |
| C5B | C5G | H5G1 | 111.1° | 111.6° |
| C5B | C5G | H5G2 | 111.0° | 109.8° |
| H5B1 | C5B | H5B2 | 98.3° | 107.0° |
| N5D | C5G | H5G1 | 111.0° | 107.8° |
| N5D | C5G | H5G2 | 111.0° | 106.9° |
| C5G | N5D | H5D1 | 112.7° | 119.2° |
| C5G | N5D | H5D2 | 111.1° | 119.2° |
| H5G1 | C5G | H5G2 | 99.3° | 108.0° |
| H5D1 | N5D | H5D2 | 111.1° | 120.2° |
| C1' | C2' | C3' | 101.7° | 102.5° |
| C1' | C2' | H2' | 115.2° | 110.6° |
| C1' | C2' | H2'' | 115.2° | 111.7° |
| C2' | C1' | O4' | 103.9° | 107.4° |
| C2' | C1' | H1' | 105.9° | 111.5° |
| C3' | C2' | H2' | 115.2° | 109.7° |
| C3' | C2' | H2'' | 115.2° | 114.1° |
| C2' | C3' | C4' | 105.5° | 103.1° |
| C2' | C3' | O3' | 111.9° | 109.7° |
| C2' | C3' | H3' | 109.6° | 113.2° |
| H2' | C2' | H2'' | 95.2° | 108.3° |
| C4' | C5' | H5' | 112.1° | 110.3° |
| C4' | C5' | H5'' | 112.0° | 110.3° |
| C5' | C4' | O4' | 110.7° | 107.9° |
| C5' | C4' | C3' | 113.4° | 112.9° |
| C5' | C4' | H4' | 104.8° | 109.5° |
| H5' | C5' | H5'' | 98.4° | 109.3° |
| O4' | C4' | C3' | 105.5° | 106.2° |
| O4' | C4' | H4' | 112.7° | 107.9° |
| C4' | O4' | C1' | 107.9° | 109.3° |
| C3' | C4' | H4' | 110.0° | 112.2° |
| C4' | C3' | O3' | 106.6° | 109.9° |
| C4' | C3' | H3' | 114.7° | 113.5° |
| O4' | C1' | H1' | 118.8° | 108.0° |
| O3' | C3' | H3' | 108.5° | 107.4° |
| C3' | O3' | HO3' | 111.9° | 107.3° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | OP2 | O5' | 125.8° | 126.6° |
| OP1 | P | OP2 | OP3 | 42.9° | 126.3° |
| OP1 | P | O5' | OP3 | 16.7° | 125.8° |
| OP1 | P | OP2 | HOP2 | 180.0° | 48.8° |
| OP1 | P | O5' | C5' | 167.1° | 179.9° |
| OP1 | P | OP3 | HOP3 | 180.0° | 48.0° |
| OP2 | P | O5' | OP3 | 116.1° | 107.4° |
| OP2 | P | O5' | C5' | 60.1° | 53.2° |
| OP2 | P | OP3 | HOP3 | 75.9° | 78.5° |
| O5' | P | OP2 | HOP2 | 54.2° | 175.4° |
| P | O5' | C5' | C4' | 168.5° | 180.0° |
| P | O5' | C5' | H5' | 66.2° | 59.6° |
| P | O5' | C5' | H5'' | 43.3° | 59.6° |
| O5' | P | OP3 | HOP3 | 26.9° | 173.8° |
| OP3 | P | OP2 | HOP2 | 137.1° | 77.5° |
| OP3 | P | O5' | C5' | 176.2° | 54.2° |
| O5' | C5' | C4' | H5' | 125.2° | 119.6° |
| O5' | C5' | C4' | H5'' | 125.2° | 119.5° |
| O5' | C5' | H5' | H5'' | 118.0° | 119.0° |
| O5' | C5' | C4' | O4' | 66.7° | 62.4° |
| O5' | C5' | C4' | C3' | 51.7° | 179.5° |
| O5' | C5' | C4' | H4' | 171.6° | 54.7° |
| C6 | N1 | C2 | C1' | 176.8° | 180.0° |
| N1 | C6 | C5 | H6 | 180.0° | 180.0° |
| C6 | N1 | C2 | O2 | 177.1° | 180.0° |
| C6 | N1 | C2 | N3 | 2.6° | 0.0° |
| N1 | C6 | C5 | C4 | 1.0° | 0.0° |
| N1 | C6 | C5 | C5A | 179.5° | 180.0° |
| C6 | N1 | C1' | C2' | 63.7° | 86.5° |
| C6 | N1 | C1' | O4' | 53.7° | 32.9° |
| C6 | N1 | C1' | H1' | 179.5° | 150.0° |
| C2 | N1 | C6 | C5 | 2.9° | 0.0° |
| C2 | N1 | C6 | H6 | 177.0° | 180.0° |
| N1 | C2 | O2 | N3 | 179.7° | 180.0° |
| N1 | C2 | N3 | C4 | 0.8° | 0.0° |
| N1 | C2 | N3 | HN3 | 179.3° | 180.0° |
| C2 | N1 | C1' | C2' | 119.4° | 93.5° |
| C2 | N1 | C1' | O4' | 123.1° | 147.2° |
| C2 | N1 | C1' | H1' | 2.6° | 30.0° |
| C1' | N1 | C6 | C5 | 173.9° | 180.0° |
| C1' | N1 | C6 | H6 | 6.2° | 0.0° |
| C1' | N1 | C2 | O2 | 6.1° | 0.0° |
| C1' | N1 | C2 | N3 | 174.2° | 180.0° |
| N1 | C1' | C2' | O4' | 119.0° | 120.5° |
| N1 | C1' | C2' | H1' | 115.2° | 121.4° |
| N1 | C1' | C2' | C3' | 154.9° | 147.4° |
| N1 | C1' | C2' | H2' | 79.8° | 30.6° |
| N1 | C1' | C2' | H2'' | 29.6° | 90.1° |
| N1 | C1' | O4' | C4' | 167.5° | 131.7° |
| N1 | C1' | O4' | H1' | 115.5° | 117.0° |
| C6 | C5 | C4 | N3 | 0.8° | 0.1° |
| C6 | C5 | C4 | O4 | 179.1° | 179.9° |
| C6 | C5 | C4 | C5A | 179.4° | 180.0° |
| C6 | C5 | C5A | C5B | 107.1° | 90.0° |
| C6 | C5 | C5A | H5A1 | 127.6° | 150.4° |
| C6 | C5 | C5A | H5A2 | 18.1° | 33.4° |
| H6 | C6 | C5 | C4 | 178.9° | 180.0° |
| H6 | C6 | C5 | C5A | 0.5° | 0.0° |
| O2 | C2 | N3 | C4 | 178.9° | 179.9° |
| O2 | C2 | N3 | HN3 | 1.0° | 0.0° |
| C2 | N3 | C4 | HN3 | 179.9° | 179.9° |
| C2 | N3 | C4 | O4 | 179.0° | 179.9° |
| C2 | N3 | C4 | C5 | 0.9° | 0.1° |
| N3 | C4 | O4 | C5 | 179.9° | 180.0° |
| N3 | C4 | C5 | C5A | 178.6° | 180.0° |
| HN3 | N3 | C4 | O4 | 1.1° | 0.0° |
| HN3 | N3 | C4 | C5 | 179.0° | 180.0° |
| O4 | C4 | C5 | C5A | 1.5° | 0.0° |
| C4 | C5 | C5A | C5B | 72.3° | 90.0° |
| C4 | C5 | C5A | H5A1 | 53.0° | 29.5° |
| C4 | C5 | C5A | H5A2 | 162.5° | 146.6° |
| C5 | C5A | C5B | H5A1 | 125.3° | 118.1° |
| C5 | C5A | C5B | H5A2 | 125.3° | 121.6° |
| C5 | C5A | H5A1 | H5A2 | 116.8° | 117.3° |
| C5 | C5A | C5B | C5G | 171.1° | 178.2° |
| C5 | C5A | C5B | H5B1 | 63.7° | 60.0° |
| C5 | C5A | C5B | H5B2 | 45.8° | 56.5° |
| C5B | C5A | H5A1 | H5A2 | 116.8° | 122.3° |
| C5A | C5B | C5G | H5B1 | 125.3° | 122.3° |
| C5A | C5B | C5G | H5B2 | 125.3° | 121.4° |
| C5A | C5B | H5B1 | H5B2 | 118.0° | 117.4° |
| C5A | C5B | C5G | N5D | 170.7° | 178.7° |
| C5A | C5B | C5G | H5G1 | 64.1° | 60.0° |
| C5A | C5B | C5G | H5G2 | 45.5° | 59.7° |
| H5A1 | C5A | C5B | C5G | 45.8° | 60.1° |
| H5A1 | C5A | C5B | H5B1 | 171.0° | 178.1° |
| H5A1 | C5A | C5B | H5B2 | 79.5° | 61.7° |
| H5A2 | C5A | C5B | C5G | 63.6° | 60.1° |
| H5A2 | C5A | C5B | H5B1 | 61.6° | 61.6° |
| H5A2 | C5A | C5B | H5B2 | 171.0° | 178.1° |
| C5G | C5B | H5B1 | H5B2 | 117.9° | 117.7° |
| C5B | C5G | N5D | H5G1 | 125.3° | 123.5° |
| C5B | C5G | N5D | H5G2 | 125.3° | 120.7° |
| C5B | C5G | H5G1 | H5G2 | 117.0° | 120.8° |
| C5B | C5G | N5D | H5D1 | 179.9° | 129.5° |
| C5B | C5G | N5D | H5D2 | 54.7° | 63.9° |
| H5B1 | C5B | C5G | N5D | 45.4° | 56.4° |
| H5B1 | C5B | C5G | H5G1 | 170.7° | 177.7° |
| H5B1 | C5B | C5G | H5G2 | 79.8° | 62.6° |
| H5B2 | C5B | C5G | N5D | 64.0° | 60.0° |
| H5B2 | C5B | C5G | H5G1 | 61.2° | 61.4° |
| H5B2 | C5B | C5G | H5G2 | 170.8° | 178.9° |
| N5D | C5G | H5G1 | H5G2 | 116.9° | 115.1° |
| C5G | N5D | H5D1 | H5D2 | 125.4° | 166.4° |
| H5G1 | C5G | N5D | H5D1 | 54.8° | 107.1° |
| H5G1 | C5G | N5D | H5D2 | 70.6° | 59.5° |
| H5G2 | C5G | N5D | H5D1 | 54.7° | 8.8° |
| H5G2 | C5G | N5D | H5D2 | 180.0° | 175.4° |
| C1' | C2' | C3' | H2' | 125.3° | 117.5° |
| C1' | C2' | C3' | H2'' | 125.3° | 120.8° |
| C1' | C2' | H2' | H2'' | 121.0° | 122.7° |
| C2' | C1' | O4' | C4' | 40.2° | 9.0° |
| C1' | C2' | C3' | C4' | 19.5° | 33.4° |
| C2' | C1' | O4' | H1' | 117.2° | 120.3° |
| C1' | C2' | C3' | O3' | 96.1° | 83.6° |
| C1' | C2' | C3' | H3' | 143.4° | 156.4° |
| C3' | C2' | H2' | H2'' | 121.0° | 125.1° |
| C2' | C3' | C4' | C5' | 124.3° | 88.8° |
| C2' | C3' | C4' | O4' | 3.1° | 29.2° |
| C2' | C3' | C4' | O3' | 119.1° | 116.9° |
| C2' | C3' | C4' | H3' | 120.7° | 122.8° |
| C2' | C3' | C4' | H4' | 118.7° | 146.9° |
| C3' | C2' | C1' | O4' | 35.9° | 26.9° |
| C3' | C2' | C1' | H1' | 90.0° | 91.2° |
| C2' | C3' | O3' | H3' | 121.1° | 123.4° |
| C2' | C3' | O3' | HO3' | 179.9° | 119.3° |
| H2' | C2' | C3' | C4' | 144.8° | 84.1° |
| H2' | C2' | C1' | O4' | 161.2° | 90.0° |
| H2' | C2' | C1' | H1' | 35.4° | 151.9° |
| H2' | C2' | C3' | O3' | 29.2° | 158.9° |
| H2' | C2' | C3' | H3' | 91.3° | 38.9° |
| H2'' | C2' | C3' | C4' | 105.8° | 154.3° |
| H2'' | C2' | C1' | O4' | 89.4° | 149.4° |
| H2'' | C2' | C1' | H1' | 144.7° | 31.3° |
| H2'' | C2' | C3' | O3' | 138.6° | 37.2° |
| H2'' | C2' | C3' | H3' | 18.1° | 82.7° |
| C4' | C5' | H5' | H5'' | 118.0° | 121.5° |
| C5' | C4' | O4' | C3' | 123.0° | 121.4° |
| C5' | C4' | O4' | H4' | 117.0° | 118.2° |
| C5' | C4' | C3' | H4' | 116.9° | 124.3° |
| C5' | C4' | O4' | C1' | 150.1° | 108.6° |
| C5' | C4' | C3' | O3' | 116.5° | 154.2° |
| C5' | C4' | C3' | H3' | 3.6° | 34.0° |
| H5' | C5' | C4' | O4' | 168.1° | 57.1° |
| H5' | C5' | C4' | C3' | 73.5° | 60.0° |
| H5' | C5' | C4' | H4' | 46.4° | 174.3° |
| H5'' | C5' | C4' | O4' | 58.6° | 178.1° |
| H5'' | C5' | C4' | C3' | 176.9° | 61.0° |
| H5'' | C5' | C4' | H4' | 63.2° | 64.8° |
| O4' | C4' | C3' | H4' | 121.8° | 117.6° |
| C4' | O4' | C1' | H1' | 77.0° | 111.3° |
| O4' | C4' | C3' | O3' | 122.2° | 87.7° |
| O4' | C4' | C3' | H3' | 117.6° | 152.1° |
| C3' | C4' | O4' | C1' | 27.1° | 12.7° |
| C4' | C3' | O3' | H3' | 124.0° | 123.9° |
| C4' | C3' | O3' | HO3' | 65.2° | 128.0° |
| H4' | C4' | O4' | C1' | 92.9° | 133.2° |
| H4' | C4' | C3' | O3' | 0.4° | 29.9° |
| H4' | C4' | C3' | H3' | 120.6° | 90.3° |
| H3' | C3' | O3' | HO3' | 58.8° | 4.1° |
