YB7
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| F1 | C5' | sing | 1.40Å | 1.36Å | |
| F2 | C5' | sing | 1.40Å | 1.37Å | |
| C5' | F3 | sing | 1.40Å | 1.36Å | |
| C5' | C4' | sing | 1.51Å | 1.53Å | |
| C3' | C4' | doub | 1.39Å | 1.36Å | Aromatic |
| C3' | C2' | sing | 1.38Å | 1.37Å | Aromatic |
| C4' | C18 | sing | 1.38Å | 1.38Å | Aromatic |
| C2' | C1' | doub | 1.40Å | 1.39Å | Aromatic |
| C18 | N9 | doub | 1.32Å | 1.34Å | Aromatic |
| C1' | N9 | sing | 1.33Å | 1.34Å | Aromatic |
| C1' | CAA | sing | 1.48Å | 1.53Å | |
| CAA | C7 | doub | 1.38Å | 1.38Å | Aromatic |
| CAA | N7 | sing | 1.36Å | 1.41Å | Aromatic |
| C7 | C8 | sing | 1.39Å | 1.43Å | Aromatic |
| N7 | C5 | sing | 1.37Å | 1.42Å | Aromatic |
| C8 | C9 | sing | 1.51Å | 1.53Å | |
| C8 | C5 | doub | 1.38Å | 1.41Å | Aromatic |
| C5 | C6 | sing | 1.47Å | 1.53Å | |
| C6 | O6 | doub | 1.22Å | 1.18Å | |
| C6 | N1 | sing | 1.35Å | 1.45Å | |
| N2 | C14 | sing | 1.32Å | 1.59Å | Aromatic |
| N2 | C13 | doub | 1.29Å | 1.41Å | Aromatic |
| N1 | C12 | sing | 1.46Å | 1.45Å | |
| C14 | C15 | doub | 1.34Å | 1.47Å | Aromatic |
| C13 | C12 | sing | 1.51Å | 1.53Å | |
| C13 | S1 | sing | 1.71Å | 1.60Å | Aromatic |
| OP3 | C16 | sing | 1.43Å | 1.40Å | |
| C12 | C17 | sing | 1.53Å | 1.53Å | |
| C15 | C16 | sing | 1.51Å | 1.53Å | |
| C15 | S1 | sing | 1.76Å | 1.60Å | Aromatic |
| N3 | C17 | sing | 1.47Å | 1.45Å | |
| N1 | H1 | sing | 0.97Å | 1.00Å | |
| C7 | H2 | sing | 1.08Å | 1.08Å | |
| N3 | H3 | sing | 1.01Å | 1.00Å | |
| N3 | H4 | sing | 1.01Å | 1.00Å | |
| C12 | H6 | sing | 1.09Å | 1.10Å | |
| C14 | H7 | sing | 1.08Å | 1.08Å | |
| C16 | H8 | sing | 1.09Å | 1.10Å | |
| C16 | H9 | sing | 1.09Å | 1.10Å | |
| C17 | H10 | sing | 1.09Å | 1.10Å | |
| C17 | H11 | sing | 1.09Å | 1.10Å | |
| C18 | H12 | sing | 1.08Å | 1.08Å | |
| C2' | H13 | sing | 1.08Å | 1.08Å | |
| C3' | H14 | sing | 1.08Å | 1.08Å | |
| C9 | H15 | sing | 1.09Å | 1.10Å | |
| C9 | H16 | sing | 1.09Å | 1.10Å | |
| C9 | H17 | sing | 1.09Å | 1.10Å | |
| N7 | H18 | sing | 0.97Å | 1.00Å | |
| OP3 | H19 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| F1 | C5' | F2 | 109.5° | 109.5° |
| F1 | C5' | F3 | 109.5° | 109.5° |
| F1 | C5' | C4' | 109.5° | 109.4° |
| F2 | C5' | F3 | 109.4° | 109.5° |
| F2 | C5' | C4' | 109.5° | 109.5° |
| F3 | C5' | C4' | 109.4° | 109.5° |
| C5' | C4' | C3' | 120.2° | 120.3° |
| C5' | C4' | C18 | 120.2° | 120.4° |
| C4' | C3' | C2' | 119.7° | 118.5° |
| C3' | C4' | C18 | 119.7° | 119.4° |
| C4' | C3' | H14 | 120.1° | 120.7° |
| C3' | C2' | C1' | 119.8° | 119.0° |
| C3' | C2' | H13 | 120.1° | 120.5° |
| C2' | C3' | H14 | 120.2° | 120.7° |
| C4' | C18 | N9 | 120.1° | 120.9° |
| C4' | C18 | H12 | 119.9° | 119.5° |
| C2' | C1' | N9 | 118.8° | 120.5° |
| C2' | C1' | CAA | 120.6° | 119.7° |
| C1' | C2' | H13 | 120.1° | 120.5° |
| C18 | N9 | C1' | 122.0° | 121.6° |
| N9 | C18 | H12 | 120.0° | 119.5° |
| N9 | C1' | CAA | 120.6° | 119.7° |
| C1' | CAA | C7 | 125.2° | 125.9° |
| C1' | CAA | N7 | 125.2° | 125.9° |
| C7 | CAA | N7 | 109.6° | 108.3° |
| CAA | C7 | C8 | 107.7° | 107.7° |
| CAA | C7 | H2 | 126.2° | 126.2° |
| CAA | N7 | C5 | 107.3° | 108.6° |
| CAA | N7 | H18 | 126.4° | 125.7° |
| C7 | C8 | C9 | 126.1° | 126.3° |
| C7 | C8 | C5 | 107.7° | 107.4° |
| C8 | C7 | H2 | 126.1° | 126.2° |
| N7 | C5 | C8 | 107.7° | 108.0° |
| N7 | C5 | C6 | 126.2° | 126.0° |
| C5 | N7 | H18 | 126.3° | 125.7° |
| C9 | C8 | C5 | 126.1° | 126.3° |
| C8 | C9 | H15 | 109.5° | 109.4° |
| C8 | C9 | H16 | 109.5° | 109.5° |
| C8 | C9 | H17 | 109.5° | 109.4° |
| C8 | C5 | C6 | 126.1° | 126.0° |
| C5 | C6 | O6 | 120.0° | 120.0° |
| C5 | C6 | N1 | 120.0° | 120.0° |
| O6 | C6 | N1 | 120.0° | 120.0° |
| C6 | N1 | C12 | 119.9° | 120.0° |
| C6 | N1 | H1 | 120.1° | 120.0° |
| C14 | N2 | C13 | 111.6° | 117.1° |
| N2 | C14 | C15 | 107.7° | 114.5° |
| N2 | C14 | H7 | 126.2° | 122.7° |
| N2 | C13 | C12 | 126.4° | 124.9° |
| N2 | C13 | S1 | 107.2° | 110.1° |
| N1 | C12 | C13 | 109.5° | 109.5° |
| N1 | C12 | C17 | 109.5° | 109.5° |
| C12 | N1 | H1 | 120.0° | 119.9° |
| N1 | C12 | H6 | 110.1° | 109.4° |
| C14 | C15 | C16 | 126.4° | 126.0° |
| C14 | C15 | S1 | 107.2° | 107.9° |
| C15 | C14 | H7 | 126.2° | 122.8° |
| C12 | C13 | S1 | 126.4° | 124.9° |
| C13 | C12 | C17 | 109.5° | 109.5° |
| C13 | C12 | H6 | 109.1° | 109.5° |
| C13 | S1 | C15 | 106.4° | 90.3° |
| OP3 | C16 | C15 | 109.5° | 109.5° |
| OP3 | C16 | H8 | 109.5° | 109.5° |
| OP3 | C16 | H9 | 109.5° | 109.5° |
| C16 | OP3 | H19 | 109.5° | 114.0° |
| C12 | C17 | N3 | 109.5° | 109.5° |
| C17 | C12 | H6 | 109.1° | 109.4° |
| C12 | C17 | H10 | 109.4° | 109.5° |
| C12 | C17 | H11 | 109.5° | 109.4° |
| C16 | C15 | S1 | 126.4° | 126.0° |
| C15 | C16 | H8 | 109.5° | 109.5° |
| C15 | C16 | H9 | 109.5° | 109.5° |
| C17 | N3 | H3 | 109.5° | 111.0° |
| C17 | N3 | H4 | 109.5° | 111.0° |
| N3 | C17 | H10 | 109.4° | 109.5° |
| N3 | C17 | H11 | 109.5° | 109.5° |
| H3 | N3 | H4 | 109.5° | 111.0° |
| H8 | C16 | H9 | 109.5° | 109.4° |
| H10 | C17 | H11 | 109.5° | 109.5° |
| H15 | C9 | H16 | 109.4° | 109.4° |
| H15 | C9 | H17 | 109.5° | 109.5° |
| H16 | C9 | H17 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| F1 | C5' | F2 | F3 | 120.0° | 120.0° |
| F1 | C5' | F2 | C4' | 120.1° | 120.0° |
| F1 | C5' | F3 | C4' | 120.0° | 119.9° |
| F1 | C5' | C4' | C3' | 22.4° | 150.0° |
| F1 | C5' | C4' | C18 | 157.6° | 30.0° |
| F2 | C5' | F3 | C4' | 119.9° | 120.0° |
| F2 | C5' | C4' | C3' | 97.7° | 30.0° |
| F2 | C5' | C4' | C18 | 82.3° | 150.0° |
| F3 | C5' | C4' | C3' | 142.4° | 90.0° |
| F3 | C5' | C4' | C18 | 37.6° | 89.9° |
| C5' | C4' | C3' | C18 | 180.0° | 180.0° |
| C5' | C4' | C3' | C2' | 180.0° | 180.0° |
| C5' | C4' | C18 | N9 | 180.0° | 180.0° |
| C5' | C4' | C18 | H12 | 0.0° | 0.1° |
| C5' | C4' | C3' | H14 | 0.0° | 0.0° |
| C4' | C3' | C2' | H14 | 180.0° | 180.0° |
| C4' | C3' | C2' | C1' | 0.1° | 0.0° |
| C3' | C4' | C18 | N9 | 0.1° | 0.0° |
| C3' | C4' | C18 | H12 | 180.0° | 180.0° |
| C4' | C3' | C2' | H13 | 180.0° | 180.0° |
| C2' | C3' | C4' | C18 | 0.0° | 0.0° |
| C3' | C2' | C1' | H13 | 180.0° | 180.0° |
| C3' | C2' | C1' | N9 | 0.1° | 0.0° |
| C3' | C2' | C1' | CAA | 180.0° | 179.7° |
| C4' | C18 | N9 | H12 | 180.0° | 179.9° |
| C4' | C18 | N9 | C1' | 0.1° | 0.0° |
| C18 | C4' | C3' | H14 | 180.0° | 180.0° |
| C2' | C1' | N9 | C18 | 0.0° | 0.0° |
| C2' | C1' | N9 | CAA | 180.0° | 179.7° |
| C2' | C1' | CAA | C7 | 48.2° | 179.7° |
| C2' | C1' | CAA | N7 | 131.9° | 0.4° |
| C1' | C2' | C3' | H14 | 179.9° | 180.0° |
| C18 | N9 | C1' | CAA | 180.0° | 179.7° |
| N9 | C1' | CAA | C7 | 131.8° | 0.0° |
| N9 | C1' | CAA | N7 | 48.1° | 180.0° |
| C1' | N9 | C18 | H12 | 180.0° | 180.0° |
| N9 | C1' | C2' | H13 | 180.0° | 180.0° |
| C1' | CAA | C7 | N7 | 179.9° | 179.9° |
| C1' | CAA | C7 | C8 | 180.0° | 180.0° |
| C1' | CAA | N7 | C5 | 180.0° | 179.8° |
| C1' | CAA | C7 | H2 | 0.0° | 0.2° |
| CAA | C1' | C2' | H13 | 0.0° | 0.3° |
| C1' | CAA | N7 | H18 | 0.0° | 0.1° |
| CAA | C7 | C8 | H2 | 180.0° | 179.8° |
| C7 | CAA | N7 | C5 | 0.1° | 0.1° |
| CAA | C7 | C8 | C9 | 180.0° | 179.8° |
| CAA | C7 | C8 | C5 | 0.0° | 0.2° |
| C7 | CAA | N7 | H18 | 180.0° | 180.0° |
| N7 | CAA | C7 | C8 | 0.0° | 0.0° |
| CAA | N7 | C5 | H18 | 180.0° | 180.0° |
| CAA | N7 | C5 | C8 | 0.1° | 0.2° |
| CAA | N7 | C5 | C6 | 180.0° | 180.0° |
| N7 | CAA | C7 | H2 | 179.9° | 179.9° |
| C7 | C8 | C5 | N7 | 0.0° | 0.2° |
| C7 | C8 | C9 | C5 | 180.0° | 180.0° |
| C7 | C8 | C5 | C6 | 180.0° | 180.0° |
| C7 | C8 | C9 | H15 | 90.0° | 90.0° |
| C7 | C8 | C9 | H16 | 150.0° | 150.0° |
| C7 | C8 | C9 | H17 | 30.0° | 30.0° |
| N7 | C5 | C8 | C9 | 180.0° | 179.7° |
| N7 | C5 | C8 | C6 | 180.0° | 179.8° |
| N7 | C5 | C6 | O6 | 150.2° | 179.7° |
| N7 | C5 | C6 | N1 | 29.8° | 0.2° |
| C9 | C8 | C5 | C6 | 0.0° | 0.1° |
| C9 | C8 | C7 | H2 | 0.0° | 0.0° |
| C8 | C9 | H15 | H16 | 120.0° | 120.0° |
| C8 | C9 | H15 | H17 | 120.0° | 119.9° |
| C8 | C9 | H16 | H17 | 120.0° | 120.0° |
| C8 | C5 | C6 | O6 | 29.9° | 0.1° |
| C8 | C5 | C6 | N1 | 150.2° | 180.0° |
| C5 | C8 | C7 | H2 | 180.0° | 180.0° |
| C5 | C8 | C9 | H15 | 90.0° | 90.0° |
| C5 | C8 | C9 | H16 | 30.0° | 29.9° |
| C5 | C8 | C9 | H17 | 150.0° | 150.0° |
| C8 | C5 | N7 | H18 | 180.0° | 179.9° |
| C5 | C6 | O6 | N1 | 180.0° | 179.9° |
| C5 | C6 | N1 | C12 | 180.0° | 180.0° |
| C5 | C6 | N1 | H1 | 0.0° | 0.4° |
| C6 | C5 | N7 | H18 | 0.0° | 0.1° |
| O6 | C6 | N1 | C12 | 0.0° | 0.1° |
| O6 | C6 | N1 | H1 | 179.9° | 179.7° |
| C6 | N1 | C12 | H1 | 180.0° | 179.6° |
| C6 | N1 | C12 | C13 | 119.5° | 155.3° |
| C6 | N1 | C12 | C17 | 120.4° | 84.7° |
| C6 | N1 | C12 | H6 | 0.5° | 35.3° |
| N2 | C14 | C15 | H7 | 180.0° | 180.0° |
| C14 | N2 | C13 | C12 | 180.0° | 179.9° |
| C14 | N2 | C13 | S1 | 0.0° | 0.0° |
| N2 | C14 | C15 | C16 | 180.0° | 180.0° |
| N2 | C14 | C15 | S1 | 0.0° | 0.0° |
| N2 | C13 | C12 | N1 | 1.3° | 45.0° |
| C13 | N2 | C14 | C15 | 0.0° | 0.0° |
| N2 | C13 | C12 | S1 | 180.0° | 180.0° |
| N2 | C13 | C12 | C17 | 121.3° | 75.0° |
| N2 | C13 | S1 | C15 | 0.0° | 0.0° |
| N2 | C13 | C12 | H6 | 119.3° | 165.0° |
| C13 | N2 | C14 | H7 | 180.0° | 180.0° |
| N1 | C12 | C13 | C17 | 120.1° | 120.0° |
| N1 | C12 | C13 | H6 | 120.6° | 120.0° |
| N1 | C12 | C13 | S1 | 178.7° | 135.0° |
| N1 | C12 | C17 | H6 | 120.6° | 120.0° |
| N1 | C12 | C17 | N3 | 36.5° | 55.0° |
| N1 | C12 | C17 | H10 | 83.4° | 175.0° |
| N1 | C12 | C17 | H11 | 156.5° | 65.0° |
| C14 | C15 | S1 | C13 | 0.0° | 0.0° |
| C14 | C15 | C16 | OP3 | 0.8° | 90.0° |
| C14 | C15 | C16 | S1 | 180.0° | 180.0° |
| C14 | C15 | C16 | H8 | 119.2° | 150.0° |
| C14 | C15 | C16 | H9 | 120.8° | 30.0° |
| C13 | C12 | C17 | H6 | 119.3° | 120.0° |
| C12 | C13 | S1 | C15 | 180.0° | 180.0° |
| C13 | C12 | C17 | N3 | 156.6° | 175.0° |
| C13 | C12 | N1 | H1 | 60.5° | 25.0° |
| C13 | C12 | C17 | H10 | 36.7° | 65.0° |
| C13 | C12 | C17 | H11 | 83.3° | 55.0° |
| S1 | C13 | C12 | C17 | 58.6° | 105.0° |
| C13 | S1 | C15 | C16 | 180.0° | 180.0° |
| S1 | C13 | C12 | H6 | 60.7° | 15.0° |
| OP3 | C16 | C15 | H8 | 120.0° | 120.0° |
| OP3 | C16 | C15 | H9 | 120.0° | 120.0° |
| OP3 | C16 | C15 | S1 | 179.2° | 90.1° |
| OP3 | C16 | H8 | H9 | 120.0° | 120.0° |
| C12 | C17 | N3 | H10 | 120.0° | 120.0° |
| C12 | C17 | N3 | H11 | 120.0° | 120.0° |
| C17 | C12 | N1 | H1 | 59.6° | 95.0° |
| C12 | C17 | N3 | H3 | 180.0° | 180.0° |
| C12 | C17 | N3 | H4 | 60.0° | 56.1° |
| C12 | C17 | H10 | H11 | 120.0° | 120.0° |
| C16 | C15 | C14 | H7 | 0.0° | 0.0° |
| C15 | C16 | H8 | H9 | 120.0° | 120.0° |
| C15 | C16 | OP3 | H19 | 180.0° | 180.0° |
| S1 | C15 | C14 | H7 | 180.0° | 180.0° |
| S1 | C15 | C16 | H8 | 60.8° | 30.0° |
| S1 | C15 | C16 | H9 | 59.2° | 149.9° |
| C17 | N3 | H3 | H4 | 120.0° | 123.9° |
| N3 | C17 | C12 | H6 | 84.0° | 65.0° |
| N3 | C17 | H10 | H11 | 120.0° | 120.0° |
| H1 | N1 | C12 | H6 | 179.6° | 145.1° |
| H3 | N3 | C17 | H10 | 60.0° | 60.0° |
| H3 | N3 | C17 | H11 | 60.0° | 60.0° |
| H4 | N3 | C17 | H10 | 180.0° | 63.9° |
| H4 | N3 | C17 | H11 | 60.0° | 176.1° |
| H6 | C12 | C17 | H10 | 156.0° | 55.0° |
| H6 | C12 | C17 | H11 | 36.0° | 175.0° |
| H8 | C16 | OP3 | H19 | 60.0° | 60.0° |
| H9 | C16 | OP3 | H19 | 60.0° | 60.0° |
| H13 | C2' | C3' | H14 | 0.1° | 0.1° |
| H15 | C9 | H16 | H17 | 120.0° | 120.0° |
