5DD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O2P | P | doub | 1.48Å | 1.52Å | |
| C5' | O5' | sing | 1.43Å | 1.42Å | |
| C5' | C4' | sing | 1.53Å | 1.53Å | |
| P | O5' | sing | 1.61Å | 1.62Å | |
| P | O1P | sing | 1.61Å | 1.52Å | |
| P | O3P | sing | 1.61Å | 1.51Å | |
| O4' | C4' | sing | 1.43Å | 1.44Å | |
| C4' | C3' | sing | 1.53Å | 1.53Å | |
| O2 | C2 | doub | 1.22Å | 1.25Å | |
| O3' | C3' | sing | 1.43Å | 1.43Å | |
| C3' | C2' | sing | 1.53Å | 1.54Å | |
| C2 | N1 | sing | 1.34Å | 1.34Å | |
| C2 | N3 | sing | 1.34Å | 1.34Å | |
| C1' | C2' | sing | 1.53Å | 1.52Å | |
| C1' | N10 | sing | 1.47Å | 1.45Å | |
| N1 | C10 | doub | 1.31Å | 1.35Å | |
| N3 | C4 | sing | 1.34Å | 1.34Å | |
| C2' | O2' | sing | 1.43Å | 1.43Å | |
| C10 | N10 | sing | 1.35Å | 1.39Å | |
| C10 | C4A | sing | 1.50Å | 1.52Å | |
| N10 | C9A | sing | 1.40Å | 1.39Å | |
| C4 | C4A | sing | 1.50Å | 1.49Å | |
| C4 | O4 | doub | 1.21Å | 1.25Å | |
| C9A | C9 | doub | 1.39Å | 1.39Å | Aromatic |
| C9A | C5A | sing | 1.39Å | 1.49Å | Aromatic |
| C4A | C1 | sing | 1.53Å | 1.52Å | |
| C1 | C5A | sing | 1.51Å | 1.52Å | |
| C9 | C8 | sing | 1.38Å | 1.39Å | Aromatic |
| C5A | C6 | doub | 1.38Å | 1.38Å | Aromatic |
| C8 | C8M | sing | 1.51Å | 1.50Å | |
| C8 | C7 | doub | 1.38Å | 1.48Å | Aromatic |
| C6 | C7 | sing | 1.38Å | 1.38Å | Aromatic |
| C7 | C7M | sing | 1.51Å | 1.50Å | |
| O3P | H1 | sing | 0.97Å | 0.95Å | |
| O1P | H2 | sing | 0.97Å | 0.95Å | |
| C5' | H3 | sing | 1.09Å | 1.10Å | |
| C5' | H4 | sing | 1.09Å | 1.10Å | |
| C4' | H5 | sing | 1.09Å | 1.10Å | |
| O4' | H6 | sing | 0.97Å | 0.95Å | |
| C3' | H7 | sing | 1.09Å | 1.10Å | |
| O3' | H8 | sing | 0.97Å | 0.95Å | |
| C2' | H9 | sing | 1.09Å | 1.10Å | |
| O2' | H10 | sing | 0.97Å | 0.95Å | |
| C1' | H11 | sing | 1.09Å | 1.10Å | |
| C1' | H12 | sing | 1.09Å | 1.10Å | |
| C9 | H13 | sing | 1.08Å | 1.08Å | |
| C8M | H14 | sing | 1.09Å | 1.10Å | |
| C8M | H15 | sing | 1.09Å | 1.10Å | |
| C8M | H16 | sing | 1.09Å | 1.10Å | |
| C7M | H17 | sing | 1.09Å | 1.10Å | |
| C7M | H18 | sing | 1.09Å | 1.10Å | |
| C7M | H19 | sing | 1.09Å | 1.10Å | |
| C6 | H20 | sing | 1.08Å | 1.08Å | |
| C4A | H21 | sing | 1.09Å | 1.10Å | |
| N3 | H22 | sing | 0.97Å | 1.00Å | |
| C1 | H23 | sing | 1.09Å | 1.10Å | |
| C1 | H24 | sing | 1.09Å | 1.10Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O2P | P | O5' | 109.3° | 109.4° |
| O2P | P | O1P | 109.7° | 109.5° |
| O2P | P | O3P | 109.4° | 109.4° |
| O5' | C5' | C4' | 110.3° | 109.5° |
| C5' | O5' | P | 123.1° | 123.0° |
| O5' | C5' | H3 | 109.3° | 109.5° |
| O5' | C5' | H4 | 109.3° | 109.5° |
| C5' | C4' | O4' | 110.1° | 109.4° |
| C5' | C4' | C3' | 110.1° | 109.5° |
| C4' | C5' | H3 | 109.2° | 109.5° |
| C4' | C5' | H4 | 109.2° | 109.4° |
| C5' | C4' | H5 | 108.2° | 109.4° |
| O5' | P | O1P | 109.9° | 109.5° |
| O5' | P | O3P | 107.9° | 109.5° |
| O1P | P | O3P | 110.6° | 109.5° |
| P | O1P | H2 | 109.5° | 114.0° |
| P | O3P | H1 | 109.5° | 114.1° |
| O4' | C4' | C3' | 110.7° | 109.5° |
| O4' | C4' | H5 | 109.5° | 109.5° |
| C4' | O4' | H6 | 109.5° | 114.0° |
| C4' | C3' | O3' | 107.7° | 109.5° |
| C4' | C3' | C2' | 112.5° | 109.4° |
| C3' | C4' | H5 | 108.2° | 109.5° |
| C4' | C3' | H7 | 108.4° | 109.5° |
| O2 | C2 | N1 | 118.2° | 119.0° |
| O2 | C2 | N3 | 120.5° | 119.1° |
| O3' | C3' | C2' | 110.3° | 109.5° |
| O3' | C3' | H7 | 109.7° | 109.5° |
| C3' | O3' | H8 | 109.5° | 114.0° |
| C3' | C2' | C1' | 109.4° | 109.4° |
| C3' | C2' | O2' | 111.5° | 109.5° |
| C2' | C3' | H7 | 108.3° | 109.4° |
| C3' | C2' | H9 | 108.3° | 109.4° |
| N1 | C2 | N3 | 121.3° | 121.9° |
| C2 | N1 | C10 | 121.0° | 122.4° |
| C2 | N3 | C4 | 122.6° | 121.0° |
| C2 | N3 | H22 | 118.7° | 119.5° |
| C2' | C1' | N10 | 112.2° | 109.5° |
| C1' | C2' | O2' | 109.5° | 109.5° |
| C1' | C2' | H9 | 108.4° | 109.5° |
| C2' | C1' | H11 | 108.8° | 109.5° |
| C2' | C1' | H12 | 108.8° | 109.5° |
| C1' | N10 | C10 | 119.4° | 119.9° |
| C1' | N10 | C9A | 120.0° | 119.9° |
| N10 | C1' | H11 | 108.8° | 109.5° |
| N10 | C1' | H12 | 108.8° | 109.4° |
| N1 | C10 | N10 | 114.9° | 119.7° |
| N1 | C10 | C4A | 123.0° | 121.1° |
| N3 | C4 | C4A | 122.2° | 120.8° |
| N3 | C4 | O4 | 121.1° | 119.6° |
| C4 | N3 | H22 | 118.7° | 119.6° |
| O2' | C2' | H9 | 109.7° | 109.5° |
| C2' | O2' | H10 | 109.5° | 114.0° |
| N10 | C10 | C4A | 122.1° | 119.2° |
| C10 | N10 | C9A | 119.1° | 120.2° |
| C10 | C4A | C4 | 109.2° | 111.1° |
| C10 | C4A | C1 | 108.6° | 109.6° |
| C10 | C4A | H21 | 107.8° | 108.4° |
| N10 | C9A | C9 | 121.0° | 119.9° |
| N10 | C9A | C5A | 118.0° | 120.4° |
| C4A | C4 | O4 | 116.1° | 119.6° |
| C4 | C4A | C1 | 115.0° | 111.3° |
| C4 | C4A | H21 | 108.2° | 107.9° |
| C9 | C9A | C5A | 120.8° | 119.7° |
| C9A | C9 | C8 | 119.1° | 120.0° |
| C9A | C9 | H13 | 120.4° | 120.1° |
| C9A | C5A | C1 | 121.4° | 119.9° |
| C9A | C5A | C6 | 119.3° | 120.1° |
| C4A | C1 | C5A | 108.6° | 108.6° |
| C1 | C4A | H21 | 107.7° | 108.4° |
| C4A | C1 | H23 | 109.7° | 109.7° |
| C4A | C1 | H24 | 109.7° | 109.6° |
| C1 | C5A | C6 | 119.3° | 120.0° |
| C5A | C1 | H23 | 109.7° | 109.7° |
| C5A | C1 | H24 | 109.7° | 109.5° |
| C9 | C8 | C8M | 120.8° | 119.9° |
| C9 | C8 | C7 | 120.3° | 120.1° |
| C8 | C9 | H13 | 120.5° | 120.0° |
| C5A | C6 | C7 | 120.4° | 120.0° |
| C5A | C6 | H20 | 119.8° | 120.0° |
| C8M | C8 | C7 | 118.9° | 119.9° |
| C8 | C8M | H14 | 109.5° | 109.5° |
| C8 | C8M | H15 | 109.5° | 109.5° |
| C8 | C8M | H16 | 109.5° | 109.5° |
| C8 | C7 | C6 | 120.0° | 120.1° |
| C8 | C7 | C7M | 120.0° | 119.9° |
| C6 | C7 | C7M | 120.0° | 120.0° |
| C7 | C6 | H20 | 119.8° | 120.0° |
| C7 | C7M | H17 | 109.5° | 109.4° |
| C7 | C7M | H18 | 109.5° | 109.4° |
| C7 | C7M | H19 | 109.5° | 109.5° |
| H3 | C5' | H4 | 109.5° | 109.5° |
| H11 | C1' | H12 | 109.5° | 109.5° |
| H14 | C8M | H15 | 109.5° | 109.4° |
| H14 | C8M | H16 | 109.4° | 109.5° |
| H15 | C8M | H16 | 109.5° | 109.5° |
| H17 | C7M | H18 | 109.4° | 109.5° |
| H17 | C7M | H19 | 109.5° | 109.5° |
| H18 | C7M | H19 | 109.5° | 109.5° |
| H23 | C1 | H24 | 109.5° | 109.8° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O2P | P | O5' | C5' | 66.9° | 55.0° |
| O2P | P | O5' | O1P | 120.5° | 120.0° |
| O2P | P | O5' | O3P | 118.9° | 120.0° |
| O2P | P | O1P | O3P | 120.8° | 120.0° |
| O2P | P | O3P | H1 | 0.0° | 60.0° |
| O2P | P | O1P | H2 | 0.0° | 180.0° |
| O5' | C5' | C4' | H3 | 120.1° | 120.0° |
| O5' | C5' | C4' | H4 | 120.1° | 120.0° |
| C5' | O5' | P | O1P | 53.6° | 65.0° |
| C5' | O5' | P | O3P | 174.3° | 175.0° |
| O5' | C5' | C4' | O4' | 64.0° | 65.0° |
| O5' | C5' | C4' | C3' | 58.3° | 175.0° |
| O5' | C5' | H3 | H4 | 119.6° | 120.0° |
| O5' | C5' | C4' | H5 | 176.4° | 55.0° |
| C4' | C5' | O5' | P | 80.2° | 180.0° |
| C5' | C4' | O4' | C3' | 121.9° | 120.0° |
| C5' | C4' | O4' | H5 | 118.9° | 120.0° |
| C5' | C4' | C3' | H5 | 118.1° | 120.0° |
| C5' | C4' | C3' | O3' | 50.4° | 60.0° |
| C5' | C4' | C3' | C2' | 172.1° | 180.0° |
| C4' | C5' | H3 | H4 | 119.6° | 120.0° |
| C5' | C4' | O4' | H6 | 180.0° | 60.0° |
| C5' | C4' | C3' | H7 | 68.2° | 60.0° |
| O5' | P | O1P | O3P | 119.0° | 120.1° |
| O5' | P | O3P | H1 | 118.8° | 180.0° |
| O5' | P | O1P | H2 | 120.2° | 60.0° |
| P | O5' | C5' | H3 | 159.7° | 60.0° |
| P | O5' | C5' | H4 | 39.9° | 60.0° |
| O1P | P | O3P | H1 | 121.0° | 60.0° |
| O3P | P | O1P | H2 | 120.8° | 60.0° |
| O4' | C4' | C3' | H5 | 120.0° | 120.1° |
| O4' | C4' | C3' | O3' | 172.3° | 180.0° |
| O4' | C4' | C3' | C2' | 65.9° | 60.0° |
| O4' | C4' | C5' | H3 | 175.9° | 55.0° |
| O4' | C4' | C5' | H4 | 56.1° | 175.0° |
| O4' | C4' | C3' | H7 | 53.7° | 59.9° |
| C4' | C3' | O3' | C2' | 123.1° | 120.0° |
| C4' | C3' | O3' | H7 | 117.7° | 120.0° |
| C4' | C3' | C2' | H7 | 119.7° | 120.0° |
| C4' | C3' | C2' | C1' | 55.9° | 180.0° |
| C4' | C3' | C2' | O2' | 177.1° | 60.0° |
| C3' | C4' | C5' | H3 | 61.8° | 65.0° |
| C3' | C4' | C5' | H4 | 178.4° | 55.0° |
| C3' | C4' | O4' | H6 | 58.1° | 60.0° |
| C4' | C3' | O3' | H8 | 180.0° | 60.0° |
| C4' | C3' | C2' | H9 | 62.1° | 60.0° |
| O2 | C2 | N1 | N3 | 179.8° | 180.0° |
| O2 | C2 | N1 | C10 | 178.7° | 174.2° |
| O2 | C2 | N3 | C4 | 178.5° | 172.7° |
| O2 | C2 | N3 | H22 | 1.5° | 7.2° |
| O3' | C3' | C2' | H7 | 120.0° | 120.0° |
| O3' | C3' | C2' | C1' | 64.4° | 60.0° |
| O3' | C3' | C2' | O2' | 56.9° | 180.0° |
| O3' | C3' | C4' | H5 | 67.7° | 60.0° |
| O3' | C3' | C2' | H9 | 177.6° | 60.0° |
| C3' | C2' | C1' | O2' | 122.5° | 120.0° |
| C3' | C2' | C1' | H9 | 117.9° | 120.0° |
| C3' | C2' | C1' | N10 | 155.3° | 178.7° |
| C3' | C2' | O2' | H9 | 119.9° | 120.0° |
| C2' | C3' | C4' | H5 | 54.0° | 60.0° |
| C2' | C3' | O3' | H8 | 56.9° | 60.0° |
| C3' | C2' | O2' | H10 | 180.0° | 59.7° |
| C3' | C2' | C1' | H11 | 34.9° | 61.3° |
| C3' | C2' | C1' | H12 | 84.4° | 58.7° |
| N1 | C2 | N3 | C4 | 1.7° | 7.3° |
| C2 | N1 | C10 | N10 | 176.1° | 174.3° |
| C2 | N1 | C10 | C4A | 1.9° | 5.3° |
| N1 | C2 | N3 | H22 | 178.3° | 172.8° |
| N3 | C2 | N1 | C10 | 1.0° | 5.8° |
| C2 | N3 | C4 | H22 | 180.0° | 179.9° |
| C2 | N3 | C4 | C4A | 7.5° | 2.2° |
| C2 | N3 | C4 | O4 | 179.0° | 177.7° |
| C2' | C1' | N10 | H11 | 120.4° | 120.0° |
| C2' | C1' | N10 | H12 | 120.4° | 120.0° |
| C1' | C2' | O2' | H9 | 118.9° | 120.0° |
| C2' | C1' | N10 | C10 | 111.0° | 95.5° |
| C2' | C1' | N10 | C9A | 83.4° | 84.3° |
| C1' | C2' | C3' | H7 | 175.6° | 60.0° |
| C1' | C2' | O2' | H10 | 58.8° | 60.3° |
| C2' | C1' | H11 | H12 | 118.8° | 120.1° |
| C1' | N10 | C10 | N1 | 1.5° | 8.8° |
| N10 | C1' | C2' | O2' | 32.8° | 61.3° |
| C1' | N10 | C10 | C9A | 165.8° | 179.7° |
| C1' | N10 | C10 | C4A | 176.5° | 171.6° |
| C1' | N10 | C9A | C9 | 25.1° | 15.3° |
| C1' | N10 | C9A | C5A | 151.5° | 164.6° |
| N10 | C1' | C2' | H9 | 86.9° | 58.7° |
| N10 | C1' | H11 | H12 | 118.8° | 119.9° |
| N1 | C10 | N10 | C4A | 178.0° | 179.6° |
| N1 | C10 | N10 | C9A | 167.3° | 170.9° |
| N1 | C10 | C4A | C4 | 6.5° | 13.1° |
| N1 | C10 | C4A | C1 | 132.7° | 136.6° |
| N1 | C10 | C4A | H21 | 110.8° | 105.3° |
| N3 | C4 | C4A | C10 | 9.1° | 11.5° |
| N3 | C4 | C4A | O4 | 171.9° | 180.0° |
| N3 | C4 | C4A | C1 | 131.5° | 134.1° |
| N3 | C4 | C4A | H21 | 108.0° | 107.1° |
| O2' | C2' | C3' | H7 | 63.2° | 60.0° |
| O2' | C2' | C1' | H11 | 87.6° | 58.7° |
| O2' | C2' | C1' | H12 | 153.2° | 178.7° |
| N10 | C10 | C4A | C4 | 171.3° | 166.5° |
| C10 | N10 | C9A | C9 | 169.2° | 164.9° |
| C10 | N10 | C9A | C5A | 14.2° | 15.2° |
| N10 | C10 | C4A | C1 | 45.1° | 43.0° |
| C10 | N10 | C1' | H11 | 128.6° | 24.5° |
| C10 | N10 | C1' | H12 | 9.4° | 144.5° |
| N10 | C10 | C4A | H21 | 71.3° | 75.1° |
| C4A | C10 | N10 | C9A | 10.7° | 8.7° |
| C10 | C4A | C4 | C1 | 122.4° | 122.5° |
| C10 | C4A | C4 | H21 | 117.1° | 118.6° |
| C10 | C4A | C4 | O4 | 179.0° | 168.4° |
| C10 | C4A | C1 | H21 | 116.5° | 118.1° |
| C10 | C4A | C1 | C5A | 50.7° | 51.7° |
| C10 | C4A | C1 | H23 | 69.2° | 171.5° |
| C10 | C4A | C1 | H24 | 170.6° | 67.9° |
| N10 | C9A | C9 | C5A | 176.6° | 179.9° |
| N10 | C9A | C5A | C1 | 2.4° | 1.4° |
| N10 | C9A | C9 | C8 | 178.9° | 179.5° |
| N10 | C9A | C5A | C6 | 179.1° | 179.2° |
| C9A | N10 | C1' | H11 | 37.1° | 155.7° |
| C9A | N10 | C1' | H12 | 156.3° | 35.8° |
| N10 | C9A | C9 | H13 | 1.1° | 0.5° |
| C4 | C4A | C1 | H21 | 120.8° | 118.5° |
| C4 | C4A | C1 | C5A | 173.5° | 175.0° |
| C4A | C4 | N3 | H22 | 172.5° | 177.6° |
| C4 | C4A | C1 | H23 | 53.6° | 65.1° |
| C4 | C4A | C1 | H24 | 66.7° | 55.5° |
| O4 | C4 | C4A | C1 | 56.5° | 45.9° |
| O4 | C4 | C4A | H21 | 64.0° | 72.9° |
| O4 | C4 | N3 | H22 | 1.0° | 2.4° |
| C9 | C9A | C5A | C1 | 179.0° | 178.7° |
| C9A | C9 | C8 | H13 | 180.0° | 180.0° |
| C9 | C9A | C5A | C6 | 2.4° | 0.7° |
| C9A | C9 | C8 | C8M | 179.0° | 179.9° |
| C9A | C9 | C8 | C7 | 1.1° | 0.0° |
| C9A | C5A | C1 | C4A | 31.5° | 32.5° |
| C9A | C5A | C1 | C6 | 178.5° | 179.4° |
| C5A | C9A | C9 | C8 | 2.3° | 0.4° |
| C9A | C5A | C6 | C7 | 1.3° | 0.5° |
| C5A | C9A | C9 | H13 | 177.7° | 179.6° |
| C9A | C5A | C6 | H20 | 178.7° | 179.5° |
| C9A | C5A | C1 | H23 | 88.3° | 152.3° |
| C9A | C5A | C1 | H24 | 151.4° | 87.1° |
| C4A | C1 | C5A | H23 | 119.9° | 119.8° |
| C4A | C1 | C5A | H24 | 119.9° | 119.6° |
| C4A | C1 | C5A | C6 | 147.0° | 146.9° |
| C4A | C1 | H23 | H24 | 120.4° | 120.5° |
| C1 | C5A | C6 | C7 | 179.9° | 178.9° |
| C1 | C5A | C6 | H20 | 0.1° | 1.1° |
| C5A | C1 | C4A | H21 | 65.8° | 66.4° |
| C5A | C1 | H23 | H24 | 120.4° | 120.4° |
| C9 | C8 | C8M | C7 | 179.9° | 180.0° |
| C9 | C8 | C7 | C6 | 0.0° | 0.2° |
| C9 | C8 | C7 | C7M | 179.9° | 179.8° |
| C9 | C8 | C8M | H14 | 89.9° | 90.0° |
| C9 | C8 | C8M | H15 | 150.0° | 150.0° |
| C9 | C8 | C8M | H16 | 30.0° | 30.0° |
| C5A | C6 | C7 | C8 | 0.2° | 0.1° |
| C5A | C6 | C7 | H20 | 180.0° | 179.9° |
| C5A | C6 | C7 | C7M | 179.8° | 179.9° |
| C6 | C5A | C1 | H23 | 93.1° | 27.0° |
| C6 | C5A | C1 | H24 | 27.1° | 93.5° |
| C8M | C8 | C7 | C6 | 180.0° | 179.8° |
| C8M | C8 | C7 | C7M | 0.1° | 0.2° |
| C8M | C8 | C9 | H13 | 1.1° | 0.1° |
| C8 | C8M | H14 | H15 | 120.0° | 120.0° |
| C8 | C8M | H14 | H16 | 120.0° | 120.0° |
| C8 | C8M | H15 | H16 | 120.0° | 120.1° |
| C8 | C7 | C6 | C7M | 179.9° | 180.0° |
| C7 | C8 | C9 | H13 | 178.9° | 179.9° |
| C7 | C8 | C8M | H14 | 90.0° | 90.0° |
| C7 | C8 | C8M | H15 | 30.0° | 30.0° |
| C7 | C8 | C8M | H16 | 150.0° | 150.0° |
| C8 | C7 | C7M | H17 | 90.0° | 90.0° |
| C8 | C7 | C7M | H18 | 150.0° | 150.0° |
| C8 | C7 | C7M | H19 | 30.0° | 30.0° |
| C8 | C7 | C6 | H20 | 179.8° | 180.0° |
| C6 | C7 | C7M | H17 | 89.9° | 90.0° |
| C6 | C7 | C7M | H18 | 30.1° | 30.0° |
| C6 | C7 | C7M | H19 | 150.1° | 150.0° |
| C7 | C7M | H17 | H18 | 120.0° | 119.9° |
| C7 | C7M | H17 | H19 | 120.0° | 120.0° |
| C7 | C7M | H18 | H19 | 120.0° | 120.0° |
| C7M | C7 | C6 | H20 | 0.3° | 0.0° |
| H3 | C5' | C4' | H5 | 56.3° | 175.0° |
| H4 | C5' | C4' | H5 | 63.5° | 65.0° |
| H5 | C4' | O4' | H6 | 61.2° | 180.0° |
| H5 | C4' | C3' | H7 | 173.7° | NaN° |
| H7 | C3' | O3' | H8 | 62.3° | 180.0° |
| H7 | C3' | C2' | H9 | 57.6° | 180.0° |
| H9 | C2' | O2' | H10 | 60.1° | 179.6° |
| H9 | C2' | C1' | H11 | 152.7° | 178.7° |
| H9 | C2' | C1' | H12 | 33.5° | 61.2° |
| H14 | C8M | H15 | H16 | 119.9° | 120.0° |
| H17 | C7M | H18 | H19 | 120.0° | 120.1° |
| H21 | C4A | C1 | H23 | 174.4° | 53.4° |
| H21 | C4A | C1 | H24 | 54.1° | 174.0° |
