YDB
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O6 | B1 | sing | 1.42Å | 1.35Å | |
| B1 | O5 | sing | 1.42Å | 1.35Å | |
| B1 | C5 | sing | 1.57Å | 1.57Å | |
| C6 | C5 | sing | 1.53Å | 1.53Å | |
| C6 | N5 | sing | 1.46Å | 1.45Å | |
| C5 | N4 | sing | 1.46Å | 1.45Å | |
| C7 | N5 | sing | 1.35Å | 1.40Å | Aromatic |
| C7 | C8 | doub | 1.37Å | 1.39Å | Aromatic |
| N5 | N7 | sing | 1.40Å | 1.38Å | Aromatic |
| O2 | C9 | doub | 1.21Å | 1.27Å | |
| N4 | C4 | sing | 1.35Å | 1.45Å | |
| C8 | C9 | sing | 1.47Å | 1.53Å | |
| C8 | N6 | sing | 1.34Å | 1.38Å | Aromatic |
| C9 | O3 | sing | 1.35Å | 1.27Å | |
| O1 | C4 | doub | 1.21Å | 1.19Å | |
| N7 | N6 | doub | 1.29Å | 1.40Å | Aromatic |
| C4 | C3 | sing | 1.51Å | 1.52Å | |
| C3 | S1 | sing | 1.81Å | 1.81Å | |
| S1 | C2 | sing | 1.76Å | 1.81Å | |
| C2 | N3 | doub | 1.30Å | 1.37Å | Aromatic |
| C2 | S2 | sing | 1.76Å | 1.80Å | Aromatic |
| N3 | N2 | sing | 1.38Å | 1.41Å | Aromatic |
| S2 | C1 | sing | 1.76Å | 1.76Å | Aromatic |
| N2 | C1 | doub | 1.30Å | 1.32Å | Aromatic |
| C1 | N1 | sing | 1.39Å | 1.45Å | |
| N1 | H1 | sing | 0.97Å | 1.00Å | |
| N1 | H2 | sing | 0.97Å | 1.00Å | |
| C3 | H3 | sing | 1.09Å | 1.10Å | |
| C3 | H4 | sing | 1.09Å | 1.10Å | |
| N4 | H5 | sing | 0.97Å | 1.00Å | |
| C5 | H6 | sing | 1.09Å | 1.10Å | |
| C6 | H7 | sing | 1.09Å | 1.10Å | |
| C6 | H8 | sing | 1.09Å | 1.10Å | |
| C7 | H9 | sing | 1.08Å | 1.08Å | |
| O3 | H10 | sing | 0.97Å | 0.95Å | |
| O5 | H11 | sing | 0.97Å | 0.95Å | |
| O6 | H12 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O6 | B1 | O5 | 109.5° | 120.0° |
| O6 | B1 | C5 | 110.4° | 120.0° |
| B1 | O6 | H12 | 109.5° | 114.0° |
| O5 | B1 | C5 | 109.3° | 120.0° |
| B1 | O5 | H11 | 109.5° | 114.0° |
| B1 | C5 | C6 | 111.1° | 109.5° |
| B1 | C5 | N4 | 107.5° | 109.5° |
| B1 | C5 | H6 | 107.7° | 109.5° |
| C5 | C6 | N5 | 112.0° | 109.5° |
| C6 | C5 | N4 | 113.0° | 109.5° |
| C6 | C5 | H6 | 108.2° | 109.4° |
| C5 | C6 | H7 | 108.9° | 109.4° |
| C5 | C6 | H8 | 108.8° | 109.4° |
| C6 | N5 | C7 | 126.2° | 126.6° |
| C6 | N5 | N7 | 125.5° | 126.6° |
| N5 | C6 | H7 | 108.8° | 109.5° |
| N5 | C6 | H8 | 108.8° | 109.5° |
| C5 | N4 | C4 | 121.0° | 120.0° |
| C5 | N4 | H5 | 119.5° | 120.0° |
| N4 | C5 | H6 | 109.2° | 109.5° |
| N5 | C7 | C8 | 107.6° | 106.8° |
| C7 | N5 | N7 | 108.3° | 106.8° |
| N5 | C7 | H9 | 126.2° | 126.6° |
| C7 | C8 | C9 | 126.2° | 125.7° |
| C7 | C8 | N6 | 108.4° | 108.5° |
| C8 | C7 | H9 | 126.2° | 126.6° |
| N5 | N7 | N6 | 107.9° | 108.4° |
| O2 | C9 | C8 | 119.5° | 120.0° |
| O2 | C9 | O3 | 120.9° | 120.0° |
| N4 | C4 | O1 | 121.9° | 120.0° |
| N4 | C4 | C3 | 118.4° | 120.0° |
| C4 | N4 | H5 | 119.5° | 119.9° |
| C9 | C8 | N6 | 125.5° | 125.8° |
| C8 | C9 | O3 | 119.5° | 120.0° |
| C8 | N6 | N7 | 107.9° | 109.5° |
| C9 | O3 | H10 | 109.5° | 116.9° |
| O1 | C4 | C3 | 119.7° | 120.0° |
| C4 | C3 | S1 | 106.3° | 109.5° |
| C4 | C3 | H3 | 110.2° | 109.5° |
| C4 | C3 | H4 | 110.3° | 109.5° |
| C3 | S1 | C2 | 105.6° | 103.0° |
| S1 | C3 | H3 | 110.3° | 109.4° |
| S1 | C3 | H4 | 110.3° | 109.4° |
| S1 | C2 | N3 | 125.4° | 125.4° |
| S1 | C2 | S2 | 123.3° | 125.4° |
| N3 | C2 | S2 | 111.3° | 109.2° |
| C2 | N3 | N2 | 111.9° | 115.6° |
| C2 | S2 | C1 | 89.0° | 90.4° |
| N3 | N2 | C1 | 115.3° | 115.6° |
| S2 | C1 | N2 | 112.5° | 109.2° |
| S2 | C1 | N1 | 123.1° | 125.3° |
| N2 | C1 | N1 | 124.4° | 125.4° |
| C1 | N1 | H1 | 109.5° | 120.0° |
| C1 | N1 | H2 | 109.5° | 120.0° |
| H1 | N1 | H2 | 109.4° | 120.0° |
| H3 | C3 | H4 | 109.5° | 109.4° |
| H7 | C6 | H8 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O6 | B1 | O5 | C5 | 121.1° | 180.0° |
| O6 | B1 | C5 | C6 | 22.4° | 90.0° |
| O6 | B1 | C5 | N4 | 146.4° | 30.0° |
| O6 | B1 | C5 | H6 | 96.0° | 150.0° |
| O6 | B1 | O5 | H11 | 180.0° | 180.0° |
| O5 | B1 | C5 | C6 | 98.1° | 90.0° |
| O5 | B1 | C5 | N4 | 25.9° | 150.0° |
| O5 | B1 | C5 | H6 | 143.5° | 30.0° |
| O5 | B1 | O6 | H12 | 180.0° | 180.0° |
| B1 | C5 | C6 | N4 | 120.8° | 120.0° |
| B1 | C5 | C6 | H6 | 118.1° | 120.0° |
| B1 | C5 | C6 | N5 | 87.0° | 60.0° |
| B1 | C5 | N4 | H6 | 116.6° | 120.0° |
| B1 | C5 | N4 | C4 | 158.8° | 105.0° |
| B1 | C5 | N4 | H5 | 21.2° | 75.1° |
| B1 | C5 | C6 | H7 | 33.3° | 180.0° |
| B1 | C5 | C6 | H8 | 152.6° | 60.0° |
| C5 | B1 | O5 | H11 | 58.9° | 0.0° |
| C5 | B1 | O6 | H12 | 59.6° | 0.0° |
| C5 | C6 | N5 | H7 | 120.4° | 120.0° |
| C5 | C6 | N5 | H8 | 120.4° | 120.0° |
| C6 | C5 | N4 | H6 | 120.5° | 120.0° |
| C5 | C6 | N5 | C7 | 102.6° | 125.3° |
| C5 | C6 | N5 | N7 | 78.3° | 55.0° |
| C6 | C5 | N4 | C4 | 78.3° | 135.0° |
| C6 | C5 | N4 | H5 | 101.7° | 45.0° |
| C5 | C6 | H7 | H8 | 118.9° | 120.0° |
| N5 | C6 | C5 | N4 | 33.8° | 180.0° |
| C6 | N5 | C7 | N7 | 179.2° | 179.8° |
| C6 | N5 | C7 | C8 | 179.5° | 180.0° |
| C6 | N5 | N7 | N6 | 179.5° | 179.8° |
| N5 | C6 | C5 | H6 | 154.9° | 60.0° |
| N5 | C6 | H7 | H8 | 118.8° | 120.0° |
| C6 | N5 | C7 | H9 | 0.5° | 0.0° |
| C5 | N4 | C4 | H5 | 180.0° | 180.0° |
| C5 | N4 | C4 | O1 | 1.0° | 0.0° |
| C5 | N4 | C4 | C3 | 179.4° | 180.0° |
| N4 | C5 | C6 | H7 | 154.2° | 60.0° |
| N4 | C5 | C6 | H8 | 86.5° | 60.0° |
| N5 | C7 | C8 | H9 | 180.0° | 180.0° |
| N5 | C7 | C8 | C9 | 179.8° | 180.0° |
| N5 | C7 | C8 | N6 | 0.3° | 0.0° |
| C7 | N5 | N7 | N6 | 0.3° | 0.5° |
| C7 | N5 | C6 | H7 | 17.8° | 5.3° |
| C7 | N5 | C6 | H8 | 137.0° | 114.7° |
| C8 | C7 | N5 | N7 | 0.4° | 0.2° |
| C7 | C8 | C9 | O2 | 19.2° | 0.1° |
| C7 | C8 | C9 | N6 | 179.4° | 180.0° |
| C7 | C8 | C9 | O3 | 161.5° | 180.0° |
| C7 | C8 | N6 | N7 | 0.1° | 0.3° |
| N5 | N7 | N6 | C8 | 0.1° | 0.5° |
| N7 | N5 | C6 | H7 | 161.3° | 175.0° |
| N7 | N5 | C6 | H8 | 42.0° | 65.0° |
| N7 | N5 | C7 | H9 | 179.6° | 179.7° |
| O2 | C9 | C8 | O3 | 179.3° | 179.9° |
| O2 | C9 | C8 | N6 | 160.2° | 180.0° |
| O2 | C9 | O3 | H10 | 0.0° | 0.1° |
| N4 | C4 | O1 | C3 | 179.6° | 180.0° |
| N4 | C4 | C3 | S1 | 176.8° | 180.0° |
| N4 | C4 | C3 | H3 | 63.7° | 60.0° |
| N4 | C4 | C3 | H4 | 57.3° | 60.0° |
| C4 | N4 | C5 | H6 | 42.2° | 15.0° |
| C9 | C8 | N6 | N7 | 179.6° | 179.7° |
| C9 | C8 | C7 | H9 | 0.2° | 0.0° |
| C8 | C9 | O3 | H10 | 179.3° | 180.0° |
| N6 | C8 | C9 | O3 | 19.1° | 0.1° |
| N6 | C8 | C7 | H9 | 179.7° | 180.0° |
| O1 | C4 | C3 | S1 | 2.8° | 0.0° |
| O1 | C4 | C3 | H3 | 116.6° | 119.9° |
| O1 | C4 | C3 | H4 | 122.3° | 120.0° |
| O1 | C4 | N4 | H5 | 179.0° | 179.9° |
| C4 | C3 | S1 | H3 | 119.5° | 120.0° |
| C4 | C3 | S1 | H4 | 119.5° | 120.0° |
| C4 | C3 | S1 | C2 | 171.9° | 180.0° |
| C4 | C3 | H3 | H4 | 121.5° | 120.1° |
| C3 | C4 | N4 | H5 | 0.7° | 0.0° |
| C3 | S1 | C2 | N3 | 16.3° | 0.0° |
| C3 | S1 | C2 | S2 | 163.0° | 179.8° |
| S1 | C3 | H3 | H4 | 121.5° | 119.9° |
| S1 | C2 | N3 | S2 | 179.4° | 179.7° |
| S1 | C2 | N3 | N2 | 179.7° | 180.0° |
| S1 | C2 | S2 | C1 | 179.7° | 179.9° |
| C2 | S1 | C3 | H3 | 68.7° | 60.0° |
| C2 | S1 | C3 | H4 | 52.4° | 60.0° |
| N3 | C2 | S2 | C1 | 0.3° | 0.3° |
| C2 | N3 | N2 | C1 | 0.1° | 0.0° |
| S2 | C2 | N3 | N2 | 0.3° | 0.2° |
| C2 | S2 | C1 | N2 | 0.3° | 0.3° |
| C2 | S2 | C1 | N1 | 179.8° | 179.9° |
| N3 | N2 | C1 | S2 | 0.2° | 0.2° |
| N3 | N2 | C1 | N1 | 180.0° | 180.0° |
| S2 | C1 | N2 | N1 | 179.9° | 179.7° |
| S2 | C1 | N1 | H1 | 0.0° | 179.8° |
| S2 | C1 | N1 | H2 | 120.0° | 0.5° |
| N2 | C1 | N1 | H1 | 179.9° | 0.1° |
| N2 | C1 | N1 | H2 | 59.9° | 179.8° |
| C1 | N1 | H1 | H2 | 120.0° | 179.7° |
| H5 | N4 | C5 | H6 | 137.8° | 164.9° |
| H6 | C5 | C6 | H7 | 84.7° | 60.0° |
| H6 | C5 | C6 | H8 | 34.6° | 180.0° |
