YDJ
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C1 | C2 | sing | 1.38Å | 1.38Å | Aromatic |
| C1 | C6 | doub | 1.38Å | 1.37Å | Aromatic |
| C2 | C3 | doub | 1.40Å | 1.38Å | Aromatic |
| C3 | C4 | sing | 1.40Å | 1.37Å | Aromatic |
| C3 | C7 | sing | 1.48Å | 1.45Å | Aromatic |
| C4 | C5 | doub | 1.38Å | 1.37Å | Aromatic |
| C5 | C6 | sing | 1.39Å | 1.38Å | Aromatic |
| C5 | F1 | sing | 1.35Å | 1.34Å | |
| C7 | C8 | doub | 1.36Å | 1.38Å | Aromatic |
| C7 | S1 | sing | 1.76Å | 1.72Å | Aromatic |
| C8 | C9 | sing | 1.37Å | 1.43Å | Aromatic |
| C9 | C10 | doub | 1.37Å | 1.38Å | Aromatic |
| C9 | N3 | sing | 1.40Å | 1.40Å | |
| C10 | S1 | sing | 1.76Å | 1.72Å | Aromatic |
| C10 | C11 | sing | 1.42Å | 1.45Å | |
| C11 | O1 | doub | 1.22Å | 1.23Å | |
| C11 | N1 | sing | 1.35Å | 1.36Å | |
| N1 | C12 | sing | 1.46Å | 1.44Å | |
| C12 | C13 | sing | 1.53Å | 1.51Å | |
| C12 | C16 | sing | 1.53Å | 1.51Å | |
| C13 | C14 | sing | 1.53Å | 1.53Å | |
| C14 | C15 | sing | 1.53Å | 1.51Å | |
| C15 | N2 | sing | 1.47Å | 1.49Å | |
| N2 | C16 | sing | 1.47Å | 1.49Å | |
| N3 | C17 | sing | 1.35Å | 1.38Å | |
| C17 | O2 | doub | 1.22Å | 1.22Å | |
| C17 | N4 | sing | 1.35Å | 1.38Å | |
| C1 | H1 | sing | 1.08Å | 1.08Å | |
| C2 | H2 | sing | 1.08Å | 1.08Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C4 | H4 | sing | 1.08Å | 1.08Å | |
| C8 | H8 | sing | 1.08Å | 1.08Å | |
| N3 | H3 | sing | 0.97Å | 1.00Å | |
| N1 | HA | sing | 0.97Å | 1.00Å | |
| C12 | H12 | sing | 1.09Å | 1.10Å | |
| C13 | H131 | sing | 1.09Å | 1.10Å | |
| C13 | H132 | sing | 1.09Å | 1.10Å | |
| C16 | H161 | sing | 1.09Å | 1.10Å | |
| C16 | H162 | sing | 1.09Å | 1.10Å | |
| C14 | H141 | sing | 1.09Å | 1.10Å | |
| C14 | H142 | sing | 1.09Å | 1.10Å | |
| C15 | H151 | sing | 1.09Å | 1.10Å | |
| C15 | H152 | sing | 1.09Å | 1.10Å | |
| N2 | HB | sing | 1.01Å | 1.00Å | |
| N4 | H41N | sing | 0.97Å | 1.00Å | |
| N4 | H42N | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C2 | C1 | C6 | 119.3° | 120.1° |
| C1 | C2 | C3 | 121.2° | 119.9° |
| C2 | C1 | H1 | 120.4° | 119.9° |
| C1 | C2 | H2 | 119.4° | 120.1° |
| C1 | C6 | C5 | 119.1° | 120.3° |
| C6 | C1 | H1 | 120.3° | 120.0° |
| C1 | C6 | H6 | 120.4° | 119.8° |
| C2 | C3 | C4 | 119.3° | 119.7° |
| C2 | C3 | C7 | 120.5° | 120.2° |
| C3 | C2 | H2 | 119.4° | 120.0° |
| C4 | C3 | C7 | 120.2° | 120.1° |
| C3 | C4 | C5 | 119.2° | 119.8° |
| C3 | C4 | H4 | 120.4° | 120.1° |
| C3 | C7 | C8 | 128.0° | 125.1° |
| C3 | C7 | S1 | 121.5° | 125.0° |
| C4 | C5 | C6 | 121.8° | 120.1° |
| C4 | C5 | F1 | 117.9° | 119.9° |
| C5 | C4 | H4 | 120.4° | 120.1° |
| C6 | C5 | F1 | 120.3° | 119.9° |
| C5 | C6 | H6 | 120.4° | 119.9° |
| C8 | C7 | S1 | 110.5° | 109.9° |
| C7 | C8 | C9 | 113.5° | 114.8° |
| C7 | C8 | H8 | 123.2° | 122.6° |
| C7 | S1 | C10 | 92.6° | 91.3° |
| C8 | C9 | C10 | 112.0° | 114.4° |
| C8 | C9 | N3 | 127.9° | 122.8° |
| C9 | C8 | H8 | 123.3° | 122.6° |
| C10 | C9 | N3 | 120.2° | 122.7° |
| C9 | C10 | S1 | 111.4° | 109.6° |
| C9 | C10 | C11 | 124.3° | 125.2° |
| C9 | N3 | C17 | 122.7° | 119.9° |
| C9 | N3 | H3 | 118.6° | 120.0° |
| S1 | C10 | C11 | 124.3° | 125.2° |
| C10 | C11 | O1 | 122.2° | 120.0° |
| C10 | C11 | N1 | 116.5° | 120.0° |
| O1 | C11 | N1 | 121.2° | 120.0° |
| C11 | N1 | C12 | 117.7° | 120.0° |
| C11 | N1 | HA | 121.1° | 120.0° |
| N1 | C12 | C13 | 110.5° | 109.5° |
| N1 | C12 | C16 | 107.4° | 109.5° |
| C12 | N1 | HA | 121.2° | 120.0° |
| N1 | C12 | H12 | 110.8° | 109.5° |
| C13 | C12 | C16 | 111.3° | 109.3° |
| C12 | C13 | C14 | 112.3° | 109.2° |
| C13 | C12 | H12 | 106.9° | 109.5° |
| C12 | C13 | H131 | 108.6° | 109.6° |
| C12 | C13 | H132 | 108.5° | 109.5° |
| C12 | C16 | N2 | 108.8° | 109.5° |
| C16 | C12 | H12 | 110.0° | 109.5° |
| C12 | C16 | H161 | 109.7° | 109.5° |
| C12 | C16 | H162 | 109.7° | 109.5° |
| C13 | C14 | C15 | 110.6° | 109.3° |
| C14 | C13 | H131 | 108.6° | 109.5° |
| C14 | C13 | H132 | 108.6° | 109.5° |
| C13 | C14 | H141 | 109.1° | 109.5° |
| C13 | C14 | H142 | 109.1° | 109.5° |
| C14 | C15 | N2 | 105.8° | 109.5° |
| C15 | C14 | H141 | 109.1° | 109.4° |
| C15 | C14 | H142 | 109.1° | 109.5° |
| C14 | C15 | H151 | 110.7° | 109.5° |
| C14 | C15 | H152 | 110.7° | 109.4° |
| C15 | N2 | C16 | 113.4° | 111.2° |
| N2 | C15 | H151 | 110.7° | 109.5° |
| N2 | C15 | H152 | 110.7° | 109.4° |
| C15 | N2 | HB | 108.2° | 110.9° |
| N2 | C16 | H161 | 109.7° | 109.5° |
| N2 | C16 | H162 | 109.7° | 109.4° |
| C16 | N2 | HB | 108.2° | 111.0° |
| N3 | C17 | O2 | 124.2° | 120.1° |
| N3 | C17 | N4 | 114.3° | 120.0° |
| C17 | N3 | H3 | 118.7° | 120.0° |
| O2 | C17 | N4 | 121.5° | 120.0° |
| C17 | N4 | H41N | 120.0° | 120.0° |
| C17 | N4 | H42N | 120.0° | 120.0° |
| H131 | C13 | H132 | 110.4° | 109.6° |
| H161 | C16 | H162 | 109.3° | 109.5° |
| H141 | C14 | H142 | 109.8° | 109.5° |
| H151 | C15 | H152 | 108.2° | 109.4° |
| H41N | N4 | H42N | 120.0° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C2 | C1 | C6 | H1 | 180.0° | 179.8° |
| C1 | C2 | C3 | H2 | 180.0° | 180.0° |
| C1 | C2 | C3 | C4 | 0.2° | 0.0° |
| C1 | C2 | C3 | C7 | 179.4° | 180.0° |
| C2 | C1 | C6 | C5 | 0.2° | 0.0° |
| C2 | C1 | C6 | H6 | 179.8° | 180.0° |
| C6 | C1 | C2 | C3 | 0.2° | 0.0° |
| C1 | C6 | C5 | C4 | 0.4° | 0.0° |
| C1 | C6 | C5 | H6 | 180.0° | 180.0° |
| C1 | C6 | C5 | F1 | 179.8° | 180.0° |
| C6 | C1 | C2 | H2 | 179.8° | 180.0° |
| C2 | C3 | C4 | C7 | 179.6° | 180.0° |
| C2 | C3 | C4 | C5 | 0.7° | 0.0° |
| C2 | C3 | C7 | C8 | 18.7° | 180.0° |
| C2 | C3 | C7 | S1 | 160.8° | 0.3° |
| C3 | C2 | C1 | H1 | 179.7° | 179.7° |
| C2 | C3 | C4 | H4 | 179.3° | 180.0° |
| C3 | C4 | C5 | H4 | 180.0° | 180.0° |
| C3 | C4 | C5 | C6 | 0.8° | 0.0° |
| C3 | C4 | C5 | F1 | 179.8° | 180.0° |
| C4 | C3 | C7 | C8 | 160.9° | 0.0° |
| C4 | C3 | C7 | S1 | 19.6° | 179.7° |
| C4 | C3 | C2 | H2 | 179.8° | 180.0° |
| C7 | C3 | C4 | C5 | 178.9° | 180.0° |
| C3 | C7 | C8 | S1 | 179.6° | 179.7° |
| C3 | C7 | C8 | C9 | 178.4° | 179.9° |
| C3 | C7 | S1 | C10 | 178.7° | 180.0° |
| C7 | C3 | C2 | H2 | 0.6° | 0.0° |
| C7 | C3 | C4 | H4 | 1.1° | 0.0° |
| C3 | C7 | C8 | H8 | 1.6° | 0.1° |
| C4 | C5 | C6 | F1 | 179.4° | 180.0° |
| C4 | C5 | C6 | H6 | 179.6° | 180.0° |
| C5 | C6 | C1 | H1 | 179.8° | 179.7° |
| C6 | C5 | C4 | H4 | 179.2° | 180.0° |
| F1 | C5 | C6 | H6 | 0.3° | 0.0° |
| F1 | C5 | C4 | H4 | 0.2° | 0.0° |
| C7 | C8 | C9 | H8 | 180.0° | 180.0° |
| C7 | C8 | C9 | C10 | 0.9° | 0.0° |
| C7 | C8 | C9 | N3 | 179.4° | 179.9° |
| C8 | C7 | S1 | C10 | 0.9° | 0.3° |
| S1 | C7 | C8 | C9 | 1.2° | 0.2° |
| C7 | S1 | C10 | C9 | 0.5° | 0.3° |
| C7 | S1 | C10 | C11 | 178.8° | 179.9° |
| S1 | C7 | C8 | H8 | 178.8° | 179.8° |
| C8 | C9 | C10 | N3 | 179.8° | 179.9° |
| C8 | C9 | C10 | S1 | 0.1° | 0.2° |
| C8 | C9 | C10 | C11 | 179.4° | 180.0° |
| C8 | C9 | N3 | C17 | 9.6° | 7.1° |
| C8 | C9 | N3 | H3 | 170.4° | 172.7° |
| C9 | C10 | S1 | C11 | 179.3° | 179.8° |
| C9 | C10 | C11 | O1 | 3.2° | 0.0° |
| C9 | C10 | C11 | N1 | 179.5° | 180.0° |
| C10 | C9 | N3 | C17 | 170.7° | 172.8° |
| C10 | C9 | C8 | H8 | 179.1° | 180.0° |
| C10 | C9 | N3 | H3 | 9.3° | 7.3° |
| N3 | C9 | C10 | S1 | 179.9° | 179.8° |
| N3 | C9 | C10 | C11 | 0.8° | 0.0° |
| C9 | N3 | C17 | H3 | 180.0° | 179.9° |
| C9 | N3 | C17 | O2 | 16.2° | 5.1° |
| C9 | N3 | C17 | N4 | 163.1° | 174.9° |
| N3 | C9 | C8 | H8 | 0.6° | 0.1° |
| S1 | C10 | C11 | O1 | 176.0° | 179.8° |
| S1 | C10 | C11 | N1 | 1.3° | 0.2° |
| C10 | C11 | O1 | N1 | 177.2° | 180.0° |
| C10 | C11 | N1 | C12 | 165.1° | 180.0° |
| C10 | C11 | N1 | HA | 14.8° | 0.0° |
| O1 | C11 | N1 | C12 | 12.2° | 0.1° |
| O1 | C11 | N1 | HA | 167.8° | 180.0° |
| C11 | N1 | C12 | HA | 180.0° | 179.9° |
| C11 | N1 | C12 | C13 | 146.2° | 155.0° |
| C11 | N1 | C12 | C16 | 92.2° | 85.2° |
| C11 | N1 | C12 | H12 | 28.0° | 34.9° |
| N1 | C12 | C13 | C16 | 119.3° | 119.9° |
| N1 | C12 | C13 | H12 | 120.6° | 120.1° |
| N1 | C12 | C16 | H12 | 120.6° | 120.1° |
| N1 | C12 | C13 | C14 | 170.8° | 177.6° |
| N1 | C12 | C16 | N2 | 173.8° | 179.1° |
| N1 | C12 | C13 | H131 | 69.2° | 62.5° |
| N1 | C12 | C13 | H132 | 50.8° | 57.7° |
| N1 | C12 | C16 | H161 | 53.8° | 59.1° |
| N1 | C12 | C16 | H162 | 66.2° | 60.9° |
| C13 | C12 | C16 | H12 | 118.3° | 120.0° |
| C12 | C13 | C14 | H131 | 120.0° | 120.0° |
| C12 | C13 | C14 | H132 | 120.0° | 119.9° |
| C12 | C13 | C14 | C15 | 55.5° | 57.6° |
| C13 | C12 | C16 | N2 | 52.7° | 59.2° |
| C13 | C12 | N1 | HA | 33.8° | 25.0° |
| C12 | C13 | H131 | H132 | 118.8° | 120.2° |
| C13 | C12 | C16 | H161 | 67.3° | 60.8° |
| C13 | C12 | C16 | H162 | 172.7° | 179.2° |
| C12 | C13 | C14 | H141 | 64.5° | 62.3° |
| C12 | C13 | C14 | H142 | 175.6° | 177.6° |
| C16 | C12 | C13 | C14 | 51.5° | 57.6° |
| C12 | C16 | N2 | C15 | 61.7° | 61.7° |
| C12 | C16 | N2 | H161 | 120.0° | 120.0° |
| C12 | C16 | N2 | H162 | 120.0° | 120.0° |
| C16 | C12 | N1 | HA | 87.8° | 94.9° |
| C16 | C12 | C13 | H131 | 171.5° | 177.6° |
| C16 | C12 | C13 | H132 | 68.5° | 62.2° |
| C12 | C16 | H161 | H162 | 120.3° | 120.0° |
| C12 | C16 | N2 | HB | 58.3° | 62.3° |
| C13 | C14 | C15 | H141 | 120.0° | 119.9° |
| C13 | C14 | C15 | H142 | 120.0° | 120.0° |
| C13 | C14 | C15 | N2 | 59.1° | 59.1° |
| C14 | C13 | C12 | H12 | 68.6° | 62.4° |
| C14 | C13 | H131 | H132 | 118.9° | 120.1° |
| C13 | C14 | H141 | H142 | 119.5° | 120.1° |
| C13 | C14 | C15 | H151 | 179.1° | 179.2° |
| C13 | C14 | C15 | H152 | 60.9° | 60.9° |
| C14 | C15 | N2 | H151 | 120.0° | 120.1° |
| C14 | C15 | N2 | H152 | 120.0° | 120.0° |
| C14 | C15 | N2 | C16 | 64.5° | 61.7° |
| C15 | C14 | C13 | H131 | 175.6° | 177.6° |
| C15 | C14 | C13 | H132 | 64.4° | 62.3° |
| C15 | C14 | H141 | H142 | 119.6° | 120.1° |
| C14 | C15 | H151 | H152 | 121.5° | 120.0° |
| C14 | C15 | N2 | HB | 55.5° | 62.4° |
| C15 | N2 | C16 | HB | 120.0° | 124.1° |
| C15 | N2 | C16 | H161 | 58.3° | 58.3° |
| C15 | N2 | C16 | H162 | 178.3° | 178.3° |
| N2 | C15 | C14 | H141 | 60.9° | 60.8° |
| N2 | C15 | C14 | H142 | 179.1° | 179.1° |
| N2 | C15 | H151 | H152 | 121.5° | 119.9° |
| N2 | C16 | C12 | H12 | 65.6° | 60.8° |
| N2 | C16 | H161 | H162 | 120.3° | 119.9° |
| C16 | N2 | C15 | H151 | 175.5° | 178.2° |
| C16 | N2 | C15 | H152 | 55.6° | 58.3° |
| N3 | C17 | O2 | N4 | 179.2° | 180.0° |
| N3 | C17 | N4 | H41N | 179.3° | 0.1° |
| N3 | C17 | N4 | H42N | 0.8° | 180.0° |
| O2 | C17 | N3 | H3 | 163.8° | 174.8° |
| O2 | C17 | N4 | H41N | 0.0° | 180.0° |
| O2 | C17 | N4 | H42N | 180.0° | 0.1° |
| N4 | C17 | N3 | H3 | 16.9° | 5.2° |
| C17 | N4 | H41N | H42N | 180.0° | 179.9° |
| H1 | C1 | C2 | H2 | 0.2° | 0.2° |
| H1 | C1 | C6 | H6 | 0.2° | 0.2° |
| HA | N1 | C12 | H12 | 152.1° | 145.0° |
| H12 | C12 | C13 | H131 | 51.4° | 57.6° |
| H12 | C12 | C13 | H132 | 171.4° | 177.8° |
| H12 | C12 | C16 | H161 | 174.4° | 179.2° |
| H12 | C12 | C16 | H162 | 54.4° | 59.2° |
| H131 | C13 | C14 | H141 | 55.6° | 57.7° |
| H131 | C13 | C14 | H142 | 64.4° | 62.5° |
| H132 | C13 | C14 | H141 | 175.5° | 177.8° |
| H132 | C13 | C14 | H142 | 55.6° | 57.7° |
| H161 | C16 | N2 | HB | 178.3° | 177.6° |
| H162 | C16 | N2 | HB | 61.7° | 57.7° |
| H141 | C14 | C15 | H151 | 59.1° | 59.3° |
| H141 | C14 | C15 | H152 | 179.1° | 179.2° |
| H142 | C14 | C15 | H151 | 60.9° | 60.8° |
| H142 | C14 | C15 | H152 | 59.1° | 59.1° |
| H151 | C15 | N2 | HB | 64.5° | 57.7° |
| H152 | C15 | N2 | HB | 175.5° | 177.6° |
