5J9
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O5' | C5' | sing | 1.43Å | 1.44Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| N4T | C4T | sing | 1.37Å | 1.32Å | |
| N3T | C4T | doub | 1.33Å | 1.35Å | |
| N3T | C2T | sing | 1.33Å | 1.35Å | |
| O2T | C2T | doub | 1.22Å | 1.24Å | |
| C4T | C5T | sing | 1.41Å | 1.40Å | |
| C2T | N1T | sing | 1.35Å | 1.35Å | |
| C4' | C3' | sing | 1.54Å | 1.55Å | |
| C4' | O4' | sing | 1.44Å | 1.47Å | |
| C3' | N10 | sing | 1.47Å | 1.48Å | |
| C3' | C2' | sing | 1.54Å | 1.53Å | |
| O4' | C1' | sing | 1.44Å | 1.41Å | |
| C5T | C6T | doub | 1.35Å | 1.39Å | |
| C14 | N10 | sing | 1.35Å | 1.34Å | Aromatic |
| C14 | C13 | doub | 1.35Å | 1.33Å | Aromatic |
| N10 | N11 | sing | 1.29Å | 1.34Å | Aromatic |
| N1T | C6T | sing | 1.36Å | 1.42Å | |
| N1T | C15 | sing | 1.46Å | 1.48Å | |
| C2' | C1' | sing | 1.54Å | 1.53Å | |
| C2' | O2' | sing | 1.43Å | 1.44Å | |
| C13 | C15 | sing | 1.51Å | 1.53Å | |
| C13 | N12 | sing | 1.34Å | 1.32Å | Aromatic |
| N11 | N12 | doub | 1.29Å | 1.33Å | Aromatic |
| C1' | N9 | sing | 1.47Å | 1.51Å | |
| N9 | C8 | sing | 1.36Å | 1.33Å | Aromatic |
| N9 | C4 | sing | 1.37Å | 1.34Å | Aromatic |
| C8 | N7 | doub | 1.30Å | 1.32Å | Aromatic |
| N3 | C4 | doub | 1.33Å | 1.35Å | Aromatic |
| N3 | C2 | sing | 1.32Å | 1.38Å | Aromatic |
| C4 | C5 | sing | 1.40Å | 1.35Å | Aromatic |
| C2 | N1 | doub | 1.32Å | 1.39Å | Aromatic |
| N7 | C5 | sing | 1.35Å | 1.34Å | Aromatic |
| C5 | C6 | doub | 1.41Å | 1.36Å | Aromatic |
| N1 | C6 | sing | 1.33Å | 1.34Å | Aromatic |
| C6 | N6 | sing | 1.38Å | 1.35Å | |
| C14 | H1 | sing | 1.08Å | 1.08Å | |
| C8 | H2 | sing | 1.08Å | 1.08Å | |
| N4T | H3 | sing | 0.97Å | 1.00Å | |
| N4T | H4 | sing | 0.97Å | 1.00Å | |
| C5T | H5 | sing | 1.08Å | 1.08Å | |
| C6T | H6 | sing | 1.08Å | 1.08Å | |
| C15 | H7 | sing | 1.09Å | 1.10Å | |
| C15 | H8 | sing | 1.09Å | 1.10Å | |
| C3' | H9 | sing | 1.09Å | 1.10Å | |
| C2' | H10 | sing | 1.09Å | 1.10Å | |
| O2' | H11 | sing | 0.97Å | 0.95Å | |
| C4' | H12 | sing | 1.09Å | 1.10Å | |
| C5' | H13 | sing | 1.09Å | 1.10Å | |
| C5' | H14 | sing | 1.09Å | 1.10Å | |
| O5' | H15 | sing | 0.97Å | 0.95Å | |
| C1' | H16 | sing | 1.09Å | 1.10Å | |
| C2 | H17 | sing | 1.08Å | 1.08Å | |
| N6 | H18 | sing | 0.97Å | 1.00Å | |
| N6 | H19 | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O5' | C5' | C4' | 112.2° | 109.5° |
| O5' | C5' | H13 | 108.8° | 109.5° |
| O5' | C5' | H14 | 108.8° | 109.4° |
| C5' | O5' | H15 | 109.5° | 114.0° |
| C5' | C4' | C3' | 117.9° | 110.4° |
| C5' | C4' | O4' | 100.5° | 110.3° |
| C5' | C4' | H12 | 110.4° | 110.4° |
| C4' | C5' | H13 | 108.8° | 109.5° |
| C4' | C5' | H14 | 108.8° | 109.5° |
| N4T | C4T | N3T | 119.1° | 120.2° |
| N4T | C4T | C5T | 120.6° | 120.2° |
| C4T | N4T | H3 | 120.0° | 120.0° |
| C4T | N4T | H4 | 120.0° | 120.0° |
| C4T | N3T | C2T | 121.9° | 120.7° |
| N3T | C4T | C5T | 120.3° | 119.6° |
| N3T | C2T | O2T | 118.3° | 119.4° |
| N3T | C2T | N1T | 120.6° | 121.1° |
| O2T | C2T | N1T | 121.0° | 119.5° |
| C4T | C5T | C6T | 118.3° | 119.0° |
| C4T | C5T | H5 | 120.9° | 120.5° |
| C2T | N1T | C6T | 119.5° | 120.3° |
| C2T | N1T | C15 | 120.8° | 119.8° |
| C3' | C4' | O4' | 106.9° | 104.8° |
| C4' | C3' | N10 | 111.3° | 110.5° |
| C4' | C3' | C2' | 102.0° | 104.1° |
| C4' | C3' | H9 | 110.0° | 110.6° |
| C3' | C4' | H12 | 109.8° | 110.4° |
| C4' | O4' | C1' | 107.0° | 105.3° |
| O4' | C4' | H12 | 111.0° | 110.4° |
| N10 | C3' | C2' | 111.9° | 110.5° |
| C3' | N10 | C14 | 128.5° | 125.9° |
| C3' | N10 | N11 | 123.5° | 125.8° |
| N10 | C3' | H9 | 111.0° | 110.5° |
| C3' | C2' | C1' | 102.1° | 104.1° |
| C3' | C2' | O2' | 112.5° | 110.5° |
| C2' | C3' | H9 | 110.4° | 110.5° |
| C3' | C2' | H10 | 110.3° | 110.5° |
| O4' | C1' | C2' | 103.9° | 104.8° |
| O4' | C1' | N9 | 109.3° | 110.4° |
| O4' | C1' | H16 | 110.2° | 110.4° |
| C5T | C6T | N1T | 119.4° | 119.3° |
| C6T | C5T | H5 | 120.8° | 120.5° |
| C5T | C6T | H6 | 120.3° | 120.3° |
| N10 | C14 | C13 | 106.3° | 106.1° |
| C14 | N10 | N11 | 108.0° | 108.3° |
| N10 | C14 | H1 | 126.9° | 127.0° |
| C14 | C13 | C15 | 126.1° | 126.7° |
| C14 | C13 | N12 | 110.7° | 106.5° |
| C13 | C14 | H1 | 126.8° | 126.9° |
| N10 | N11 | N12 | 108.6° | 110.1° |
| C6T | N1T | C15 | 119.6° | 119.8° |
| N1T | C6T | H6 | 120.3° | 120.4° |
| N1T | C15 | C13 | 109.7° | 109.5° |
| N1T | C15 | H7 | 109.4° | 109.5° |
| N1T | C15 | H8 | 109.4° | 109.5° |
| C1' | C2' | O2' | 109.7° | 110.5° |
| C2' | C1' | N9 | 115.7° | 110.4° |
| C1' | C2' | H10 | 110.3° | 110.5° |
| C2' | C1' | H16 | 108.6° | 110.4° |
| O2' | C2' | H10 | 111.6° | 110.5° |
| C2' | O2' | H11 | 109.5° | 114.0° |
| C15 | C13 | N12 | 123.2° | 126.7° |
| C13 | C15 | H7 | 109.4° | 109.4° |
| C13 | C15 | H8 | 109.4° | 109.5° |
| C13 | N12 | N11 | 106.4° | 108.9° |
| C1' | N9 | C8 | 127.9° | 126.3° |
| C1' | N9 | C4 | 124.5° | 126.2° |
| N9 | C1' | H16 | 108.9° | 110.4° |
| C8 | N9 | C4 | 107.6° | 107.5° |
| N9 | C8 | N7 | 108.2° | 109.9° |
| N9 | C8 | H2 | 125.9° | 125.0° |
| N9 | C4 | N3 | 129.7° | 135.0° |
| N9 | C4 | C5 | 108.8° | 106.0° |
| C8 | N7 | C5 | 109.7° | 109.5° |
| N7 | C8 | H2 | 125.9° | 125.1° |
| C4 | N3 | C2 | 119.8° | 120.7° |
| N3 | C4 | C5 | 121.5° | 119.1° |
| N3 | C2 | N1 | 118.5° | 122.5° |
| N3 | C2 | H17 | 120.8° | 118.8° |
| C4 | C5 | N7 | 105.7° | 107.1° |
| C4 | C5 | C6 | 119.1° | 118.2° |
| C2 | N1 | C6 | 119.8° | 121.2° |
| N1 | C2 | H17 | 120.8° | 118.7° |
| N7 | C5 | C6 | 135.2° | 134.7° |
| C5 | C6 | N1 | 121.3° | 118.4° |
| C5 | C6 | N6 | 122.1° | 120.8° |
| N1 | C6 | N6 | 116.6° | 120.8° |
| C6 | N6 | H18 | 109.5° | 120.0° |
| C6 | N6 | H19 | 109.5° | 120.0° |
| H3 | N4T | H4 | 120.0° | 120.0° |
| H7 | C15 | H8 | 109.5° | 109.4° |
| H13 | C5' | H14 | 109.5° | 109.5° |
| H18 | N6 | H19 | 109.5° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O5' | C5' | C4' | H13 | 120.4° | 120.0° |
| O5' | C5' | C4' | H14 | 120.4° | 120.0° |
| O5' | C5' | C4' | C3' | 22.9° | 175.0° |
| O5' | C5' | C4' | O4' | 92.7° | 69.6° |
| O5' | C5' | C4' | H12 | 150.1° | 52.7° |
| O5' | C5' | H13 | H14 | 118.8° | 119.9° |
| C5' | C4' | C3' | O4' | 112.0° | 118.8° |
| C5' | C4' | C3' | H12 | 127.5° | 122.4° |
| C5' | C4' | O4' | H12 | 116.7° | 122.3° |
| C5' | C4' | C3' | N10 | 138.2° | 98.6° |
| C5' | C4' | C3' | C2' | 102.4° | 142.8° |
| C5' | C4' | O4' | C1' | 141.0° | 159.3° |
| C5' | C4' | C3' | H9 | 14.8° | 24.0° |
| C4' | C5' | H13 | H14 | 118.7° | 120.1° |
| C4' | C5' | O5' | H15 | 180.0° | 180.0° |
| N4T | C4T | N3T | C5T | 179.7° | 179.8° |
| N4T | C4T | N3T | C2T | 179.9° | 179.9° |
| N4T | C4T | C5T | C6T | 179.7° | 180.0° |
| C4T | N4T | H3 | H4 | 180.0° | 179.9° |
| N4T | C4T | C5T | H5 | 0.3° | 0.2° |
| C4T | N3T | C2T | O2T | 179.5° | 179.9° |
| C4T | N3T | C2T | N1T | 0.5° | 0.3° |
| N3T | C4T | C5T | C6T | 0.0° | 0.1° |
| N3T | C4T | N4T | H3 | 0.0° | 0.1° |
| N3T | C4T | N4T | H4 | 180.0° | 180.0° |
| N3T | C4T | C5T | H5 | 180.0° | 180.0° |
| N3T | C2T | O2T | N1T | 179.0° | 179.7° |
| C2T | N3T | C4T | C5T | 0.5° | 0.1° |
| N3T | C2T | N1T | C6T | 0.1° | 0.6° |
| N3T | C2T | N1T | C15 | 178.6° | 179.7° |
| O2T | C2T | N1T | C6T | 179.1° | 179.7° |
| O2T | C2T | N1T | C15 | 0.4° | 0.1° |
| C4T | C5T | C6T | H5 | 180.0° | 179.9° |
| C4T | C5T | C6T | N1T | 0.3° | 0.3° |
| C5T | C4T | N4T | H3 | 179.7° | 180.0° |
| C5T | C4T | N4T | H4 | 0.3° | 0.1° |
| C4T | C5T | C6T | H6 | 179.7° | 179.9° |
| C2T | N1T | C6T | C5T | 0.3° | 0.6° |
| C2T | N1T | C6T | C15 | 178.7° | 179.7° |
| C2T | N1T | C15 | C13 | 80.1° | 90.0° |
| C2T | N1T | C6T | H6 | 179.7° | 179.7° |
| C2T | N1T | C15 | H7 | 39.9° | 30.0° |
| C2T | N1T | C15 | H8 | 159.8° | 150.0° |
| C3' | C4' | O4' | H12 | 119.7° | 118.9° |
| C4' | C3' | N10 | C2' | 113.4° | 114.6° |
| C4' | C3' | N10 | H9 | 122.9° | 122.7° |
| C4' | C3' | C2' | H9 | 116.9° | 118.8° |
| C3' | C4' | O4' | C1' | 17.4° | 40.5° |
| C4' | C3' | N10 | C14 | 135.2° | 29.6° |
| C4' | C3' | N10 | N11 | 45.5° | 150.4° |
| C4' | C3' | C2' | C1' | 30.8° | 0.0° |
| C4' | C3' | C2' | O2' | 148.3° | 118.6° |
| C4' | C3' | C2' | H10 | 86.5° | 118.7° |
| C3' | C4' | C5' | H13 | 97.5° | 55.0° |
| C3' | C4' | C5' | H14 | 143.3° | 65.0° |
| O4' | C4' | C3' | N10 | 109.8° | 142.6° |
| O4' | C4' | C3' | C2' | 9.7° | 24.0° |
| C4' | O4' | C1' | C2' | 37.7° | 40.5° |
| C4' | O4' | C1' | N9 | 161.7° | 159.3° |
| O4' | C4' | C3' | H9 | 126.8° | 94.7° |
| O4' | C4' | C5' | H13 | 146.9° | 170.4° |
| O4' | C4' | C5' | H14 | 27.7° | 50.4° |
| C4' | O4' | C1' | H16 | 78.6° | 78.3° |
| N10 | C3' | C2' | H9 | 124.1° | 122.6° |
| C3' | N10 | C14 | N11 | 179.4° | 180.0° |
| C3' | N10 | C14 | C13 | 179.9° | 180.0° |
| N10 | C3' | C2' | C1' | 88.2° | 118.6° |
| N10 | C3' | C2' | O2' | 29.3° | 0.0° |
| C3' | N10 | N11 | N12 | 179.3° | 180.0° |
| C3' | N10 | C14 | H1 | 0.1° | 0.3° |
| N10 | C3' | C2' | H10 | 154.5° | 122.7° |
| N10 | C3' | C4' | H12 | 10.7° | 23.8° |
| C3' | C2' | C1' | O4' | 43.1° | 24.0° |
| C2' | C3' | N10 | C14 | 111.4° | 85.0° |
| C2' | C3' | N10 | N11 | 67.9° | 95.0° |
| C3' | C2' | C1' | O2' | 119.5° | 118.7° |
| C3' | C2' | C1' | H10 | 117.2° | 118.7° |
| C3' | C2' | O2' | H10 | 124.5° | 122.7° |
| C3' | C2' | C1' | N9 | 162.9° | 142.8° |
| C3' | C2' | O2' | H11 | 180.0° | 180.0° |
| C2' | C3' | C4' | H12 | 130.2° | 94.8° |
| C3' | C2' | C1' | H16 | 74.2° | 94.9° |
| O4' | C1' | C2' | N9 | 119.8° | 118.8° |
| O4' | C1' | C2' | H16 | 117.4° | 118.9° |
| O4' | C1' | C2' | O2' | 162.6° | 142.7° |
| O4' | C1' | N9 | H16 | 120.5° | 122.3° |
| O4' | C1' | N9 | C8 | 115.6° | 20.3° |
| O4' | C1' | N9 | C4 | 66.3° | 159.6° |
| O4' | C1' | C2' | H10 | 74.1° | 94.7° |
| C1' | O4' | C4' | H12 | 102.3° | 78.4° |
| C5T | C6T | N1T | H6 | 180.0° | 179.8° |
| C5T | C6T | N1T | C15 | 179.0° | 179.7° |
| N10 | C14 | C13 | H1 | 180.0° | 179.7° |
| N10 | C14 | C13 | C15 | 179.7° | 179.9° |
| N10 | C14 | C13 | N12 | 1.0° | 0.0° |
| C14 | N10 | N11 | N12 | 0.2° | 0.0° |
| C14 | N10 | C3' | H9 | 12.3° | 152.4° |
| C13 | C14 | N10 | N11 | 0.5° | 0.0° |
| C14 | C13 | C15 | N1T | 105.7° | 95.0° |
| C14 | C13 | C15 | N12 | 178.5° | 180.0° |
| C14 | C13 | N12 | N11 | 1.1° | 0.0° |
| C14 | C13 | C15 | H7 | 14.3° | 145.0° |
| C14 | C13 | C15 | H8 | 134.2° | 25.0° |
| N10 | N11 | N12 | C13 | 0.8° | 0.0° |
| N11 | N10 | C14 | H1 | 179.5° | 179.7° |
| N11 | N10 | C3' | H9 | 168.3° | 27.6° |
| C6T | N1T | C15 | C13 | 101.2° | 89.8° |
| N1T | C6T | C5T | H5 | 179.7° | 179.8° |
| C6T | N1T | C15 | H7 | 138.8° | 150.3° |
| C6T | N1T | C15 | H8 | 18.9° | 30.3° |
| N1T | C15 | C13 | H7 | 120.0° | 120.0° |
| N1T | C15 | C13 | H8 | 120.0° | 120.0° |
| N1T | C15 | C13 | N12 | 75.7° | 85.0° |
| C15 | N1T | C6T | H6 | 1.0° | 0.1° |
| N1T | C15 | H7 | H8 | 119.9° | 120.1° |
| C1' | C2' | O2' | H10 | 122.6° | 122.6° |
| C2' | C1' | N9 | H16 | 122.7° | 122.3° |
| C2' | C1' | N9 | C8 | 1.2° | 95.0° |
| C2' | C1' | N9 | C4 | 176.9° | 85.0° |
| C1' | C2' | C3' | H9 | 147.6° | 118.8° |
| C1' | C2' | O2' | H11 | 67.0° | 65.3° |
| O2' | C2' | C1' | N9 | 77.6° | 98.5° |
| O2' | C2' | C3' | H9 | 94.8° | 122.5° |
| O2' | C2' | C1' | H16 | 45.3° | 23.8° |
| C15 | C13 | N12 | N11 | 179.9° | 179.9° |
| C15 | C13 | C14 | H1 | 0.3° | 0.3° |
| C13 | C15 | H7 | H8 | 119.9° | 119.9° |
| N12 | C13 | C14 | H1 | 179.0° | 179.7° |
| N12 | C13 | C15 | H7 | 164.3° | 35.0° |
| N12 | C13 | C15 | H8 | 44.3° | 155.0° |
| C1' | N9 | C8 | C4 | 178.4° | 180.0° |
| C1' | N9 | C8 | N7 | 179.0° | 179.8° |
| C1' | N9 | C4 | N3 | 1.7° | 0.3° |
| C1' | N9 | C4 | C5 | 179.2° | 180.0° |
| C1' | N9 | C8 | H2 | 1.0° | 0.3° |
| N9 | C1' | C2' | H10 | 45.7° | 24.1° |
| N9 | C8 | N7 | H2 | 180.0° | 179.5° |
| C8 | N9 | C4 | N3 | 179.9° | 179.7° |
| C8 | N9 | C4 | C5 | 0.7° | 0.0° |
| N9 | C8 | N7 | C5 | 0.3° | 0.4° |
| C8 | N9 | C1' | H16 | 123.9° | 142.7° |
| C4 | N9 | C8 | N7 | 0.6° | 0.3° |
| N9 | C4 | N3 | C5 | 179.1° | 179.6° |
| N9 | C4 | N3 | C2 | 179.4° | 179.6° |
| N9 | C4 | C5 | N7 | 0.6° | 0.2° |
| N9 | C4 | C5 | C6 | 179.6° | 179.7° |
| C4 | N9 | C8 | H2 | 179.4° | 179.8° |
| C4 | N9 | C1' | H16 | 54.2° | 37.3° |
| C8 | N7 | C5 | C4 | 0.2° | 0.4° |
| C8 | N7 | C5 | C6 | 179.0° | 179.6° |
| C4 | N3 | C2 | N1 | 1.1° | 0.0° |
| N3 | C4 | C5 | N7 | 179.8° | 180.0° |
| N3 | C4 | C5 | C6 | 1.2° | 0.0° |
| C4 | N3 | C2 | H17 | 178.9° | 180.0° |
| C2 | N3 | C4 | C5 | 1.5° | 0.0° |
| N3 | C2 | N1 | H17 | 180.0° | 180.0° |
| N3 | C2 | N1 | C6 | 0.3° | 0.0° |
| C4 | C5 | N7 | C6 | 178.8° | 180.0° |
| C4 | C5 | C6 | N1 | 0.4° | 0.0° |
| C4 | C5 | C6 | N6 | 179.1° | 180.0° |
| C2 | N1 | C6 | C5 | 0.0° | 0.0° |
| C2 | N1 | C6 | N6 | 179.6° | 180.0° |
| N7 | C5 | C6 | N1 | 179.0° | 180.0° |
| N7 | C5 | C6 | N6 | 0.4° | 0.0° |
| C5 | N7 | C8 | H2 | 179.7° | 179.9° |
| C5 | C6 | N1 | N6 | 179.5° | 180.0° |
| C5 | C6 | N6 | H18 | 179.5° | 0.1° |
| C5 | C6 | N6 | H19 | 60.5° | 180.0° |
| C6 | N1 | C2 | H17 | 179.7° | 180.0° |
| N1 | C6 | N6 | H18 | 0.0° | 180.0° |
| N1 | C6 | N6 | H19 | 120.0° | 0.1° |
| C6 | N6 | H18 | H19 | 120.0° | 179.9° |
| H5 | C5T | C6T | H6 | 0.3° | 0.0° |
| H9 | C3' | C2' | H10 | 30.4° | 0.1° |
| H9 | C3' | C4' | H12 | 112.7° | 146.4° |
| H10 | C2' | O2' | H11 | 55.5° | 57.3° |
| H10 | C2' | C1' | H16 | 168.6° | 146.4° |
| H12 | C4' | C5' | H13 | 29.7° | 67.3° |
| H12 | C4' | C5' | H14 | 89.5° | 172.6° |
| H13 | C5' | O5' | H15 | 59.6° | 60.0° |
| H14 | C5' | O5' | H15 | 59.6° | 60.0° |
