MDU
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | O1P | sing | 1.61Å | 1.51Å | |
| P | O2P | doub | 1.48Å | 1.48Å | |
| P | O5' | sing | 1.61Å | 1.52Å | |
| N1 | C2 | sing | 1.35Å | 1.38Å | |
| N1 | C6 | sing | 1.37Å | 1.37Å | |
| N1 | C1' | sing | 1.46Å | 1.46Å | |
| C2 | O2 | doub | 1.22Å | 1.26Å | |
| C2 | N3 | sing | 1.35Å | 1.38Å | |
| N3 | C4 | sing | 1.35Å | 1.38Å | |
| N3 | C21 | sing | 1.46Å | 1.46Å | |
| C4 | O4 | doub | 1.22Å | 1.26Å | |
| C4 | C5 | sing | 1.42Å | 1.41Å | |
| C5 | C6 | doub | 1.35Å | 1.41Å | |
| C5 | C5M | sing | 1.51Å | 1.49Å | |
| 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 | |
| O1P | H14 | sing | 0.97Å | 0.95Å | |
| C2' | C3' | sing | 1.55Å | 1.53Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C2' | H2'A | sing | 1.09Å | 1.10Å | |
| C21 | O22 | sing | 1.43Å | 1.43Å | |
| C21 | H21 | 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 | |
| C5M | H5M | sing | 1.09Å | 1.10Å | |
| C5M | H5MA | sing | 1.09Å | 1.10Å | |
| C5M | H5MB | sing | 1.09Å | 1.10Å | |
| O9 | P | sing | 1.61Å | 1.51Å | |
| O9 | H15 | sing | 0.97Å | 0.95Å | |
| C21 | H16 | sing | 1.09Å | 1.10Å | |
| O22 | H17 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O1P | P | O2P | 109.3° | 109.4° |
| O1P | P | O5' | 108.3° | 109.4° |
| P | O1P | H14 | 109.5° | 113.9° |
| O1P | P | O9 | 109.0° | 109.5° |
| O2P | P | O5' | 109.2° | 109.5° |
| O2P | P | O9 | 109.6° | 109.5° |
| P | O5' | C5' | 130.5° | 123.0° |
| O5' | P | O9 | 111.4° | 109.5° |
| C2 | N1 | C6 | 118.5° | 120.6° |
| C2 | N1 | C1' | 121.0° | 119.6° |
| N1 | C2 | O2 | 118.4° | 119.6° |
| N1 | C2 | N3 | 122.0° | 120.9° |
| C6 | N1 | C1' | 120.5° | 119.7° |
| N1 | C6 | C5 | 122.5° | 119.7° |
| N1 | C6 | H6 | 118.8° | 120.2° |
| N1 | C1' | C2' | 111.1° | 109.9° |
| N1 | C1' | O4' | 115.7° | 109.9° |
| N1 | C1' | H1' | 103.3° | 109.9° |
| O2 | C2 | N3 | 119.6° | 119.5° |
| C2 | N3 | C4 | 119.1° | 120.3° |
| C2 | N3 | C21 | 121.6° | 119.9° |
| C4 | N3 | C21 | 119.2° | 119.9° |
| N3 | C4 | O4 | 120.6° | 120.3° |
| N3 | C4 | C5 | 121.2° | 119.3° |
| N3 | C21 | O22 | 111.6° | 109.5° |
| N3 | C21 | H21 | 108.8° | 109.4° |
| N3 | C21 | H16 | 108.8° | 109.5° |
| O4 | C4 | C5 | 118.2° | 120.4° |
| C4 | C5 | C6 | 116.7° | 119.2° |
| C4 | C5 | C5M | 124.3° | 120.4° |
| C6 | C5 | C5M | 119.1° | 120.4° |
| C5 | C6 | H6 | 118.8° | 120.1° |
| C5 | C5M | H5M | 109.5° | 109.5° |
| C5 | C5M | H5MA | 109.4° | 109.5° |
| C5 | C5M | H5MB | 109.5° | 109.5° |
| C2' | C1' | O4' | 107.6° | 107.3° |
| C2' | C1' | H1' | 112.0° | 109.9° |
| C1' | C2' | C3' | 104.6° | 104.2° |
| C1' | C2' | H2' | 111.1° | 110.5° |
| C1' | C2' | H2'A | 111.1° | 110.5° |
| O4' | C1' | H1' | 107.0° | 110.0° |
| C1' | O4' | C4' | 110.5° | 107.0° |
| C3' | C2' | H2' | 111.1° | 110.5° |
| C3' | C2' | H2'A | 111.1° | 110.4° |
| C2' | C3' | O3' | 111.1° | 110.9° |
| C2' | C3' | C4' | 103.2° | 102.1° |
| C2' | C3' | H3' | 112.9° | 110.9° |
| H2' | C2' | H2'A | 107.8° | 110.5° |
| O22 | C21 | H21 | 108.8° | 109.4° |
| O22 | C21 | H16 | 108.8° | 109.5° |
| C21 | O22 | H17 | 109.5° | 114.0° |
| H21 | C21 | H16 | 110.1° | 109.5° |
| O3' | C3' | C4' | 110.6° | 110.9° |
| O3' | C3' | H3' | 105.8° | 110.8° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| C4' | C3' | H3' | 113.4° | 111.0° |
| C3' | C4' | O4' | 107.6° | 103.4° |
| C3' | C4' | C5' | 114.6° | 110.6° |
| C3' | C4' | H4' | 107.2° | 110.6° |
| O4' | C4' | C5' | 109.0° | 110.6° |
| O4' | C4' | H4' | 113.0° | 110.6° |
| C5' | C4' | H4' | 105.7° | 110.7° |
| C4' | C5' | O5' | 107.9° | 109.4° |
| C4' | C5' | H5' | 110.0° | 109.5° |
| C4' | C5' | H5'A | 110.0° | 109.5° |
| O5' | C5' | H5' | 110.0° | 109.5° |
| O5' | C5' | H5'A | 110.0° | 109.5° |
| H5' | C5' | H5'A | 108.9° | 109.5° |
| H5M | C5M | H5MA | 109.5° | 109.4° |
| H5M | C5M | H5MB | 109.4° | 109.5° |
| H5MA | C5M | H5MB | 109.5° | 109.5° |
| P | O9 | H15 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1P | P | O2P | O5' | 118.3° | 120.0° |
| O1P | P | O2P | O9 | 119.3° | 120.0° |
| O1P | P | O5' | O9 | 119.8° | 120.0° |
| O1P | P | O5' | C5' | 129.1° | 65.0° |
| O1P | P | O9 | H15 | 119.5° | 59.9° |
| O2P | P | O5' | O9 | 121.2° | 120.0° |
| O2P | P | O1P | H14 | 0.0° | 180.0° |
| O2P | P | O5' | C5' | 112.0° | 55.0° |
| O2P | P | O9 | H15 | 0.0° | 60.0° |
| O5' | P | O1P | H14 | 118.9° | 60.0° |
| P | O5' | C5' | C4' | 150.0° | 180.0° |
| P | O5' | C5' | H5' | 90.0° | 60.0° |
| P | O5' | C5' | H5'A | 30.0° | 60.0° |
| O5' | P | O9 | H15 | 121.0° | 179.9° |
| C2 | N1 | C6 | C1' | 176.9° | 179.8° |
| N1 | C2 | O2 | N3 | 179.3° | 180.0° |
| N1 | C2 | N3 | C4 | 0.7° | 0.0° |
| N1 | C2 | N3 | C21 | 179.4° | 180.0° |
| C2 | N1 | C6 | C5 | 2.8° | 0.0° |
| C2 | N1 | C6 | H6 | 177.3° | 180.0° |
| C2 | N1 | C1' | C2' | 75.9° | 115.0° |
| C2 | N1 | C1' | O4' | 161.0° | 127.2° |
| C2 | N1 | C1' | H1' | 44.4° | 6.1° |
| C6 | N1 | C2 | O2 | 179.6° | 180.0° |
| C6 | N1 | C2 | N3 | 1.1° | 0.0° |
| N1 | C6 | C5 | C4 | 2.5° | 0.0° |
| N1 | C6 | C5 | H6 | 180.0° | 180.0° |
| N1 | C6 | C5 | C5M | 176.6° | 180.0° |
| C6 | N1 | C1' | C2' | 101.0° | 65.3° |
| C6 | N1 | C1' | O4' | 22.1° | 52.6° |
| C6 | N1 | C1' | H1' | 138.8° | 173.7° |
| C1' | N1 | C2 | O2 | 3.5° | 0.2° |
| C1' | N1 | C2 | N3 | 175.8° | 179.8° |
| C1' | N1 | C6 | C5 | 174.2° | 179.8° |
| C1' | N1 | C6 | H6 | 5.8° | 0.2° |
| N1 | C1' | C2' | O4' | 127.6° | 119.4° |
| N1 | C1' | C2' | H1' | 115.0° | 121.0° |
| N1 | C1' | O4' | H1' | 114.5° | 121.1° |
| N1 | C1' | C2' | C3' | 143.7° | 121.4° |
| N1 | C1' | C2' | H2' | 96.3° | 119.9° |
| N1 | C1' | C2' | H2'A | 23.7° | 2.8° |
| N1 | C1' | O4' | C4' | 125.5° | 146.0° |
| O2 | C2 | N3 | C4 | 178.6° | 179.9° |
| O2 | C2 | N3 | C21 | 0.2° | 0.0° |
| C2 | N3 | C4 | C21 | 178.8° | 179.9° |
| C2 | N3 | C4 | O4 | 178.9° | 180.0° |
| C2 | N3 | C4 | C5 | 0.9° | 0.1° |
| C2 | N3 | C21 | O22 | 118.3° | 105.0° |
| C2 | N3 | C21 | H21 | 121.7° | 135.0° |
| C2 | N3 | C21 | H16 | 1.7° | 15.1° |
| N3 | C4 | O4 | C5 | 179.8° | 179.9° |
| N3 | C4 | C5 | C6 | 0.6° | 0.1° |
| N3 | C4 | C5 | C5M | 178.5° | 180.0° |
| C4 | N3 | C21 | O22 | 63.0° | 74.9° |
| C4 | N3 | C21 | H21 | 57.1° | 45.0° |
| C4 | N3 | C21 | H16 | 177.0° | 165.0° |
| C21 | N3 | C4 | O4 | 0.1° | 0.0° |
| C21 | N3 | C4 | C5 | 179.7° | 180.0° |
| N3 | C21 | O22 | H21 | 120.0° | 120.0° |
| N3 | C21 | O22 | H16 | 120.0° | 120.1° |
| N3 | C21 | H21 | H16 | 119.1° | 120.0° |
| N3 | C21 | O22 | H17 | 48.9° | 180.0° |
| O4 | C4 | C5 | C6 | 179.6° | 180.0° |
| O4 | C4 | C5 | C5M | 1.3° | 0.0° |
| C4 | C5 | C6 | C5M | 179.1° | 180.0° |
| C4 | C5 | C6 | H6 | 177.6° | 180.0° |
| C4 | C5 | C5M | H5M | 180.0° | 0.0° |
| C4 | C5 | C5M | H5MA | 60.0° | 120.0° |
| C4 | C5 | C5M | H5MB | 60.0° | 120.0° |
| C6 | C5 | C5M | H5M | 1.0° | 180.0° |
| C6 | C5 | C5M | H5MA | 119.0° | 60.0° |
| C6 | C5 | C5M | H5MB | 121.0° | 60.0° |
| C5M | C5 | C6 | H6 | 3.3° | 0.0° |
| C5 | C5M | H5M | H5MA | 120.0° | 120.0° |
| C5 | C5M | H5M | H5MB | 120.0° | 120.0° |
| C5 | C5M | H5MA | H5MB | 120.0° | 120.0° |
| C2' | C1' | O4' | H1' | 120.6° | 119.5° |
| C1' | C2' | C3' | H2' | 120.0° | 118.7° |
| C1' | C2' | C3' | H2'A | 120.0° | 118.7° |
| C1' | C2' | H2' | H2'A | 122.0° | 122.6° |
| C1' | C2' | C3' | O3' | 94.5° | 139.1° |
| C1' | C2' | C3' | C4' | 24.1° | 20.9° |
| C1' | C2' | C3' | H3' | 146.9° | 97.3° |
| C2' | C1' | O4' | C4' | 0.6° | 26.5° |
| O4' | C1' | C2' | C3' | 16.1° | 2.0° |
| O4' | C1' | C2' | H2' | 136.1° | 120.7° |
| O4' | C1' | C2' | H2'A | 103.9° | 116.6° |
| C1' | O4' | C4' | C3' | 15.3° | 40.1° |
| C1' | O4' | C4' | C5' | 109.5° | 158.6° |
| C1' | O4' | C4' | H4' | 133.4° | 78.4° |
| H1' | C1' | C2' | C3' | 101.3° | 117.6° |
| H1' | C1' | C2' | H2' | 18.7° | 1.1° |
| H1' | C1' | C2' | H2'A | 138.7° | 123.8° |
| H1' | C1' | O4' | C4' | 120.0° | 93.0° |
| H14 | O1P | P | O9 | 119.7° | 60.0° |
| C3' | C2' | H2' | H2'A | 122.0° | 122.6° |
| C2' | C3' | O3' | C4' | 114.0° | 112.6° |
| C2' | C3' | O3' | H3' | 122.9° | 123.7° |
| C2' | C3' | C4' | H3' | 122.5° | 118.2° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.5° |
| C2' | C3' | C4' | O4' | 24.6° | 37.1° |
| C2' | C3' | C4' | C5' | 96.7° | 155.5° |
| C2' | C3' | C4' | H4' | 146.4° | 81.4° |
| H2' | C2' | C3' | O3' | 25.5° | 20.3° |
| H2' | C2' | C3' | C4' | 144.1° | 97.8° |
| H2' | C2' | C3' | H3' | 93.1° | 143.9° |
| H2'A | C2' | C3' | O3' | 145.5° | 102.3° |
| H2'A | C2' | C3' | C4' | 95.9° | 139.6° |
| H2'A | C2' | C3' | H3' | 26.9° | 21.3° |
| O22 | C21 | H21 | H16 | 119.2° | 120.0° |
| H21 | C21 | O22 | H17 | 71.1° | 60.1° |
| O3' | C3' | C4' | H3' | 118.6° | 123.6° |
| O3' | C3' | C4' | O4' | 94.3° | 155.2° |
| O3' | C3' | C4' | C5' | 144.4° | 86.3° |
| O3' | C3' | C4' | H4' | 27.5° | 36.7° |
| C4' | C3' | O3' | HO3' | 66.0° | 174.2° |
| C3' | C4' | O4' | C5' | 124.8° | 118.4° |
| C3' | C4' | O4' | H4' | 118.1° | 118.5° |
| C3' | C4' | C5' | H4' | 117.7° | 123.0° |
| C3' | C4' | C5' | O5' | 177.7° | 175.0° |
| C3' | C4' | C5' | H5' | 62.3° | 55.0° |
| C3' | C4' | C5' | H5'A | 57.7° | 65.0° |
| H3' | C3' | O3' | HO3' | 57.1° | 62.1° |
| H3' | C3' | C4' | O4' | 147.1° | 81.2° |
| H3' | C3' | C4' | C5' | 25.7° | 37.3° |
| H3' | C3' | C4' | H4' | 91.1° | 160.3° |
| O4' | C4' | C5' | H4' | 121.7° | 123.0° |
| O4' | C4' | C5' | O5' | 57.1° | 71.0° |
| O4' | C4' | C5' | H5' | 177.1° | 169.0° |
| O4' | C4' | C5' | H5'A | 62.9° | 49.0° |
| C4' | C5' | O5' | H5' | 120.0° | 120.0° |
| C4' | C5' | O5' | H5'A | 120.0° | 119.9° |
| C4' | C5' | H5' | H5'A | 120.7° | 120.0° |
| H4' | C4' | C5' | O5' | 64.6° | 52.0° |
| H4' | C4' | C5' | H5' | 55.4° | 68.0° |
| H4' | C4' | C5' | H5'A | 175.4° | 172.0° |
| O5' | C5' | H5' | H5'A | 120.6° | 120.0° |
| C5' | O5' | P | O9 | 9.2° | 175.0° |
| H5M | C5M | H5MA | H5MB | 120.0° | 120.0° |
| H16 | C21 | O22 | H17 | 168.9° | 59.9° |
