MDK
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | O1P | doub | 1.48Å | 1.48Å | |
| P | O2P | sing | 1.61Å | 1.51Å | |
| P | O5' | sing | 1.61Å | 1.52Å | |
| N1 | C2 | sing | 1.35Å | 1.38Å | |
| N1 | C6 | sing | 1.36Å | 1.37Å | |
| N1 | C1' | sing | 1.46Å | 1.46Å | |
| C2 | O2 | doub | 1.22Å | 1.26Å | |
| C2 | C3 | sing | 1.40Å | 1.42Å | |
| C3 | C4 | doub | 1.39Å | 1.42Å | |
| C3 | C21 | sing | 1.51Å | 1.49Å | |
| C4 | N4 | sing | 1.38Å | 1.40Å | |
| C4 | C5 | sing | 1.41Å | 1.40Å | |
| N4 | HN4 | sing | 0.97Å | 1.00Å | |
| N4 | HN4A | sing | 0.97Å | 1.00Å | |
| C5 | C6 | doub | 1.35Å | 1.40Å | |
| C5 | H5 | sing | 1.08Å | 1.08Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C1' | C2' | sing | 1.54Å | 1.55Å | |
| C1' | O4' | sing | 1.44Å | 1.44Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C2' | C3' | sing | 1.55Å | 1.53Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C2' | H2'A | sing | 1.09Å | 1.10Å | |
| C21 | H21 | sing | 1.09Å | 1.10Å | |
| C21 | H21A | sing | 1.09Å | 1.10Å | |
| C21 | H21B | sing | 1.09Å | 1.10Å | |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | C4' | sing | 1.55Å | 1.54Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C4' | O4' | sing | 1.44Å | 1.44Å | |
| C4' | C5' | sing | 1.53Å | 1.55Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| C5' | O5' | sing | 1.43Å | 1.34Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'A | sing | 1.09Å | 1.10Å | |
| O7 | P | sing | 1.61Å | 1.51Å | |
| O2P | H16 | sing | 0.97Å | 0.95Å | |
| O7 | H17 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O1P | P | O2P | 109.7° | 109.5° |
| O1P | P | O5' | 111.6° | 109.5° |
| O1P | P | O7 | 109.9° | 109.5° |
| O2P | P | O5' | 108.3° | 109.5° |
| O2P | P | O7 | 108.8° | 109.5° |
| P | O2P | H16 | 109.5° | 114.0° |
| P | O5' | C5' | 128.9° | 123.0° |
| O5' | P | O7 | 108.4° | 109.4° |
| C2 | N1 | C6 | 119.3° | 121.2° |
| C2 | N1 | C1' | 120.3° | 119.4° |
| N1 | C2 | O2 | 119.8° | 119.9° |
| N1 | C2 | C3 | 121.6° | 120.2° |
| C6 | N1 | C1' | 120.3° | 119.4° |
| N1 | C6 | C5 | 121.6° | 120.9° |
| N1 | C6 | H6 | 119.2° | 119.6° |
| N1 | C1' | C2' | 112.0° | 109.9° |
| N1 | C1' | O4' | 116.0° | 109.9° |
| N1 | C1' | H1' | 102.2° | 109.9° |
| O2 | C2 | C3 | 118.6° | 120.0° |
| C2 | C3 | C4 | 118.1° | 119.1° |
| C2 | C3 | C21 | 122.5° | 120.4° |
| C4 | C3 | C21 | 119.5° | 120.5° |
| C3 | C4 | N4 | 121.8° | 120.6° |
| C3 | C4 | C5 | 119.8° | 118.9° |
| C3 | C21 | H21 | 109.5° | 109.5° |
| C3 | C21 | H21A | 109.5° | 109.5° |
| C3 | C21 | H21B | 109.4° | 109.5° |
| N4 | C4 | C5 | 118.3° | 120.5° |
| C4 | N4 | HN4 | 109.5° | 120.0° |
| C4 | N4 | HN4A | 109.4° | 120.1° |
| C4 | C5 | C6 | 119.5° | 119.8° |
| C4 | C5 | H5 | 120.2° | 120.1° |
| HN4 | N4 | HN4A | 109.5° | 120.0° |
| C6 | C5 | H5 | 120.3° | 120.1° |
| C5 | C6 | H6 | 119.2° | 119.6° |
| C2' | C1' | O4' | 106.8° | 107.3° |
| C2' | C1' | H1' | 112.1° | 109.9° |
| C1' | C2' | C3' | 103.6° | 104.2° |
| C1' | C2' | H2' | 111.5° | 110.5° |
| C1' | C2' | H2'A | 111.5° | 110.5° |
| O4' | C1' | H1' | 107.8° | 110.0° |
| C1' | O4' | C4' | 110.1° | 107.0° |
| C3' | C2' | H2' | 111.5° | 110.5° |
| C3' | C2' | H2'A | 111.5° | 110.5° |
| C2' | C3' | O3' | 110.9° | 110.9° |
| C2' | C3' | C4' | 102.1° | 102.1° |
| C2' | C3' | H3' | 113.5° | 110.9° |
| H2' | C2' | H2'A | 107.4° | 110.5° |
| H21 | C21 | H21A | 109.4° | 109.5° |
| H21 | C21 | H21B | 109.5° | 109.5° |
| H21A | C21 | H21B | 109.5° | 109.4° |
| O3' | C3' | C4' | 110.2° | 110.9° |
| O3' | C3' | H3' | 105.9° | 110.8° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| C4' | C3' | H3' | 114.2° | 110.9° |
| C3' | C4' | O4' | 105.8° | 103.5° |
| C3' | C4' | C5' | 114.6° | 110.6° |
| C3' | C4' | H4' | 108.9° | 110.6° |
| O4' | C4' | C5' | 110.3° | 110.7° |
| O4' | C4' | H4' | 113.3° | 110.6° |
| C5' | C4' | H4' | 104.2° | 110.7° |
| C4' | C5' | O5' | 108.7° | 109.5° |
| C4' | C5' | H5' | 109.7° | 109.5° |
| C4' | C5' | H5'A | 109.7° | 109.4° |
| O5' | C5' | H5' | 109.7° | 109.5° |
| O5' | C5' | H5'A | 109.7° | 109.5° |
| H5' | C5' | H5'A | 109.2° | 109.5° |
| P | O7 | H17 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1P | P | O2P | O5' | 122.1° | 120.0° |
| O1P | P | O2P | O7 | 120.3° | 120.0° |
| O1P | P | O5' | O7 | 121.2° | 120.0° |
| O1P | P | O5' | C5' | 15.3° | 54.9° |
| O1P | P | O2P | H16 | 0.0° | 60.0° |
| O1P | P | O7 | H17 | 0.0° | 180.0° |
| O2P | P | O5' | O7 | 117.9° | 120.0° |
| O2P | P | O5' | C5' | 136.3° | 175.0° |
| O2P | P | O7 | H17 | 120.2° | 60.0° |
| P | O5' | C5' | C4' | 167.3° | 180.0° |
| P | O5' | C5' | H5' | 72.7° | 60.1° |
| P | O5' | C5' | H5'A | 47.3° | 60.0° |
| O5' | P | O2P | H16 | 122.1° | 179.9° |
| O5' | P | O7 | H17 | 122.2° | 60.0° |
| C2 | N1 | C6 | C1' | 178.9° | 179.7° |
| N1 | C2 | O2 | C3 | 180.0° | 179.9° |
| N1 | C2 | C3 | C4 | 0.1° | 0.0° |
| N1 | C2 | C3 | C21 | 179.9° | 180.0° |
| C2 | N1 | C6 | C5 | 2.4° | 0.1° |
| C2 | N1 | C6 | H6 | 177.6° | 180.0° |
| C2 | N1 | C1' | C2' | 68.7° | 115.0° |
| C2 | N1 | C1' | O4' | 168.4° | 127.1° |
| C2 | N1 | C1' | H1' | 51.5° | 6.0° |
| C6 | N1 | C2 | O2 | 177.9° | 180.0° |
| C6 | N1 | C2 | C3 | 2.1° | 0.1° |
| N1 | C6 | C5 | C4 | 0.8° | 0.1° |
| N1 | C6 | C5 | H6 | 180.0° | 180.0° |
| N1 | C6 | C5 | H5 | 179.2° | 180.0° |
| C6 | N1 | C1' | C2' | 110.2° | 65.3° |
| C6 | N1 | C1' | O4' | 12.7° | 52.5° |
| C6 | N1 | C1' | H1' | 129.6° | 173.7° |
| C1' | N1 | C2 | O2 | 3.2° | 0.3° |
| C1' | N1 | C2 | C3 | 176.8° | 179.7° |
| C1' | N1 | C6 | C5 | 176.5° | 179.7° |
| C1' | N1 | C6 | H6 | 3.5° | 0.3° |
| N1 | C1' | C2' | O4' | 127.9° | 119.5° |
| N1 | C1' | C2' | H1' | 114.2° | 121.0° |
| N1 | C1' | O4' | H1' | 113.7° | 121.1° |
| N1 | C1' | C2' | C3' | 146.8° | 121.4° |
| N1 | C1' | C2' | H2' | 93.2° | 119.9° |
| N1 | C1' | C2' | H2'A | 26.8° | 2.8° |
| N1 | C1' | O4' | C4' | 123.2° | 145.9° |
| O2 | C2 | C3 | C4 | 179.8° | 180.0° |
| O2 | C2 | C3 | C21 | 0.1° | 0.1° |
| C2 | C3 | C4 | C21 | 179.7° | 180.0° |
| C2 | C3 | C4 | N4 | 178.6° | 180.0° |
| C2 | C3 | C4 | C5 | 1.5° | 0.0° |
| C2 | C3 | C21 | H21 | 180.0° | 90.0° |
| C2 | C3 | C21 | H21A | 60.0° | 150.0° |
| C2 | C3 | C21 | H21B | 60.0° | 30.1° |
| C3 | C4 | N4 | C5 | 179.9° | 180.0° |
| C3 | C4 | N4 | HN4 | 180.0° | 0.0° |
| C3 | C4 | N4 | HN4A | 60.0° | 180.0° |
| C3 | C4 | C5 | C6 | 1.2° | 0.0° |
| C3 | C4 | C5 | H5 | 178.8° | 180.0° |
| C4 | C3 | C21 | H21 | 0.3° | 90.0° |
| C4 | C3 | C21 | H21A | 120.3° | 30.0° |
| C4 | C3 | C21 | H21B | 119.7° | 150.0° |
| C21 | C3 | C4 | N4 | 1.7° | 0.0° |
| C21 | C3 | C4 | C5 | 178.2° | 180.0° |
| C3 | C21 | H21 | H21A | 120.0° | 120.0° |
| C3 | C21 | H21 | H21B | 120.0° | 120.1° |
| C3 | C21 | H21A | H21B | 120.0° | 120.0° |
| C4 | N4 | HN4 | HN4A | 120.0° | 180.0° |
| N4 | C4 | C5 | C6 | 178.9° | 180.0° |
| N4 | C4 | C5 | H5 | 1.1° | 0.0° |
| C5 | C4 | N4 | HN4 | 0.1° | 180.0° |
| C5 | C4 | N4 | HN4A | 120.1° | 0.0° |
| C4 | C5 | C6 | H5 | 180.0° | 179.9° |
| C4 | C5 | C6 | H6 | 179.2° | 180.0° |
| H5 | C5 | C6 | H6 | 0.8° | 0.0° |
| C2' | C1' | O4' | H1' | 120.7° | 119.5° |
| C1' | C2' | C3' | H2' | 120.0° | 118.7° |
| C1' | C2' | C3' | H2'A | 120.0° | 118.7° |
| C1' | C2' | H2' | H2'A | 122.4° | 122.6° |
| C1' | C2' | C3' | O3' | 86.4° | 139.1° |
| C1' | C2' | C3' | C4' | 31.1° | 20.9° |
| C1' | C2' | C3' | H3' | 154.5° | 97.3° |
| C2' | C1' | O4' | C4' | 2.4° | 26.5° |
| O4' | C1' | C2' | C3' | 18.8° | 2.0° |
| O4' | C1' | C2' | H2' | 138.8° | 120.7° |
| O4' | C1' | C2' | H2'A | 101.2° | 116.7° |
| C1' | O4' | C4' | C3' | 22.7° | 40.0° |
| C1' | O4' | C4' | C5' | 101.7° | 158.5° |
| C1' | O4' | C4' | H4' | 141.9° | 78.4° |
| H1' | C1' | C2' | C3' | 99.0° | 117.5° |
| H1' | C1' | C2' | H2' | 20.9° | 1.1° |
| H1' | C1' | C2' | H2'A | 141.0° | 123.8° |
| H1' | C1' | O4' | C4' | 123.1° | 93.0° |
| C3' | C2' | H2' | H2'A | 122.4° | 122.6° |
| C2' | C3' | O3' | C4' | 112.4° | 112.7° |
| C2' | C3' | O3' | H3' | 123.6° | 123.7° |
| C2' | C3' | C4' | H3' | 123.0° | 118.2° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.5° |
| C2' | C3' | C4' | O4' | 33.5° | 37.0° |
| C2' | C3' | C4' | C5' | 88.2° | 155.5° |
| C2' | C3' | C4' | H4' | 155.6° | 81.5° |
| H2' | C2' | C3' | O3' | 33.6° | 20.4° |
| H2' | C2' | C3' | C4' | 151.1° | 97.8° |
| H2' | C2' | C3' | H3' | 85.5° | 144.0° |
| H2'A | C2' | C3' | O3' | 153.6° | 102.3° |
| H2'A | C2' | C3' | C4' | 88.9° | 139.6° |
| H2'A | C2' | C3' | H3' | 34.5° | 21.4° |
| H21 | C21 | H21A | H21B | 120.0° | 120.0° |
| O3' | C3' | C4' | H3' | 119.1° | 123.6° |
| O3' | C3' | C4' | O4' | 84.4° | 155.2° |
| O3' | C3' | C4' | C5' | 153.9° | 86.3° |
| O3' | C3' | C4' | H4' | 37.6° | 36.7° |
| C4' | C3' | O3' | HO3' | 67.6° | 174.2° |
| C3' | C4' | O4' | C5' | 124.4° | 118.5° |
| C3' | C4' | O4' | H4' | 119.2° | 118.5° |
| C3' | C4' | C5' | H4' | 118.9° | 122.9° |
| C3' | C4' | C5' | O5' | 177.2° | 175.0° |
| C3' | C4' | C5' | H5' | 57.2° | 55.0° |
| C3' | C4' | C5' | H5'A | 62.8° | 65.0° |
| H3' | C3' | O3' | HO3' | 56.4° | 62.1° |
| H3' | C3' | C4' | O4' | 156.5° | 81.2° |
| H3' | C3' | C4' | C5' | 34.8° | 37.3° |
| H3' | C3' | C4' | H4' | 81.4° | 160.3° |
| O4' | C4' | C5' | H4' | 121.9° | 123.0° |
| O4' | C4' | C5' | O5' | 63.6° | 70.9° |
| O4' | C4' | C5' | H5' | 176.4° | 169.1° |
| O4' | C4' | C5' | H5'A | 56.4° | 49.1° |
| C4' | C5' | O5' | H5' | 120.0° | 120.0° |
| C4' | C5' | O5' | H5'A | 120.0° | 120.0° |
| C4' | C5' | H5' | H5'A | 120.3° | 119.9° |
| H4' | C4' | C5' | O5' | 58.4° | 52.1° |
| H4' | C4' | C5' | H5' | 61.6° | 67.9° |
| H4' | C4' | C5' | H5'A | 178.3° | 172.1° |
| O5' | C5' | H5' | H5'A | 120.3° | 120.1° |
| C5' | O5' | P | O7 | 105.9° | 65.0° |
| O7 | P | O2P | H16 | 120.2° | 60.0° |
