YBJ
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C | C5 | sing | 1.53Å | 1.52Å | |
| O | C5 | sing | 1.43Å | 1.43Å | |
| O | C1 | sing | 1.43Å | 1.43Å | |
| C5 | C4 | sing | 1.53Å | 1.52Å | |
| C6 | O2 | sing | 1.43Å | 1.43Å | |
| C4 | O2 | sing | 1.43Å | 1.42Å | |
| C4 | C3 | sing | 1.53Å | 1.52Å | |
| C1 | C2 | sing | 1.53Å | 1.52Å | |
| C2 | C3 | sing | 1.53Å | 1.52Å | |
| C3 | N | sing | 1.47Å | 1.48Å | |
| C1 | H9 | sing | 1.09Å | 1.10Å | |
| C2 | H8 | sing | 1.09Å | 1.10Å | |
| C2 | H7 | sing | 1.09Å | 1.10Å | |
| C3 | H2 | sing | 1.09Å | 1.10Å | |
| C4 | H1 | sing | 1.09Å | 1.10Å | |
| C5 | H | sing | 1.09Å | 1.10Å | |
| N | H10 | sing | 1.01Å | 1.00Å | |
| N | H11 | sing | 1.01Å | 1.00Å | |
| C | H4 | sing | 1.09Å | 1.10Å | |
| C | H6 | sing | 1.09Å | 1.10Å | |
| C | H5 | sing | 1.09Å | 1.10Å | |
| C6 | H13 | sing | 1.09Å | 1.10Å | |
| C6 | H12 | sing | 1.09Å | 1.10Å | |
| C6 | H14 | sing | 1.09Å | 1.10Å | |
| C1 | O1 | sing | 1.43Å | 1.38Å | |
| O1 | H3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C | C5 | O | 107.2° | 109.5° |
| C | C5 | C4 | 112.1° | 109.5° |
| C | C5 | H | 108.9° | 109.5° |
| C5 | C | H4 | 109.5° | 109.4° |
| C5 | C | H6 | 109.5° | 109.4° |
| C5 | C | H5 | 109.5° | 109.5° |
| C5 | O | C1 | 113.9° | 114.1° |
| O | C5 | C4 | 109.6° | 109.4° |
| O | C5 | H | 110.2° | 109.5° |
| O | C1 | C2 | 111.0° | 109.4° |
| O | C1 | H9 | 108.6° | 109.5° |
| O | C1 | O1 | 112.8° | 109.5° |
| C5 | C4 | O2 | 110.6° | 109.5° |
| C5 | C4 | C3 | 109.9° | 109.2° |
| C5 | C4 | H1 | 108.9° | 109.6° |
| C4 | C5 | H | 108.8° | 109.5° |
| C6 | O2 | C4 | 112.6° | 114.0° |
| O2 | C6 | H13 | 109.5° | 109.5° |
| O2 | C6 | H12 | 109.5° | 109.5° |
| O2 | C6 | H14 | 109.5° | 109.5° |
| O2 | C4 | C3 | 108.2° | 109.5° |
| O2 | C4 | H1 | 110.3° | 109.5° |
| C4 | C3 | C2 | 111.1° | 109.0° |
| C4 | C3 | N | 108.4° | 109.6° |
| C4 | C3 | H2 | 109.0° | 109.7° |
| C3 | C4 | H1 | 108.9° | 109.5° |
| C1 | C2 | C3 | 110.2° | 109.2° |
| C2 | C1 | H9 | 107.4° | 109.5° |
| C1 | C2 | H8 | 109.3° | 109.5° |
| C1 | C2 | H7 | 109.3° | 109.5° |
| C2 | C1 | O1 | 107.6° | 109.5° |
| C2 | C3 | N | 109.8° | 109.5° |
| C3 | C2 | H8 | 109.3° | 109.5° |
| C3 | C2 | H7 | 109.3° | 109.5° |
| C2 | C3 | H2 | 109.0° | 109.5° |
| N | C3 | H2 | 109.5° | 109.5° |
| C3 | N | H10 | 109.5° | 111.0° |
| C3 | N | H11 | 109.5° | 111.0° |
| H9 | C1 | O1 | 109.3° | 109.5° |
| H8 | C2 | H7 | 109.5° | 109.6° |
| H10 | N | H11 | 109.5° | 111.1° |
| H4 | C | H6 | 109.4° | 109.5° |
| H4 | C | H5 | 109.5° | 109.5° |
| H6 | C | H5 | 109.5° | 109.5° |
| H13 | C6 | H12 | 109.4° | 109.4° |
| H13 | C6 | H14 | 109.5° | 109.5° |
| H12 | C6 | H14 | 109.5° | 109.5° |
| C1 | O1 | H3 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C | C5 | O | C4 | 121.9° | 120.0° |
| C | C5 | O | H | 118.4° | 120.0° |
| C | C5 | O | C1 | 177.2° | 178.8° |
| C | C5 | C4 | H | 120.6° | 120.0° |
| C | C5 | C4 | O2 | 64.8° | 62.5° |
| C | C5 | C4 | C3 | 175.8° | 177.6° |
| C | C5 | C4 | H1 | 56.6° | 57.6° |
| C5 | C | H4 | H6 | 120.0° | 119.9° |
| C5 | C | H4 | H5 | 120.0° | 120.0° |
| C5 | C | H6 | H5 | 120.0° | 120.0° |
| O | C5 | C4 | H | 120.5° | 120.0° |
| O | C5 | C4 | O2 | 176.3° | 177.5° |
| O | C5 | C4 | C3 | 56.9° | 57.7° |
| C5 | O | C1 | C2 | 59.3° | 61.2° |
| C5 | O | C1 | H9 | 177.2° | 178.9° |
| O | C5 | C4 | H1 | 62.3° | 62.3° |
| O | C5 | C | H4 | 180.0° | 175.0° |
| O | C5 | C | H6 | 60.0° | 55.0° |
| O | C5 | C | H5 | 60.0° | 65.0° |
| C5 | O | C1 | O1 | 61.5° | 58.8° |
| C1 | O | C5 | C4 | 60.9° | 61.2° |
| O | C1 | C2 | H9 | 118.6° | 120.0° |
| O | C1 | C2 | O1 | 123.8° | 120.0° |
| O | C1 | C2 | C3 | 53.4° | 57.6° |
| O | C1 | H9 | O1 | 123.4° | 120.0° |
| O | C1 | C2 | H8 | 66.7° | 62.3° |
| O | C1 | C2 | H7 | 173.5° | 177.5° |
| C1 | O | C5 | H | 58.8° | 58.8° |
| O | C1 | O1 | H3 | 180.0° | 60.0° |
| C5 | C4 | O2 | C6 | 110.6° | 141.8° |
| C5 | C4 | O2 | C3 | 120.4° | 119.7° |
| C5 | C4 | O2 | H1 | 120.6° | 120.2° |
| C5 | C4 | C3 | H1 | 119.3° | 120.0° |
| C5 | C4 | C3 | C2 | 54.2° | 57.0° |
| C5 | C4 | C3 | N | 174.9° | 176.9° |
| C5 | C4 | C3 | H2 | 66.0° | 62.9° |
| C4 | C5 | C | H4 | 59.7° | 65.1° |
| C4 | C5 | C | H6 | 179.7° | 174.9° |
| C4 | C5 | C | H5 | 60.3° | 54.9° |
| C6 | O2 | C4 | C3 | 129.0° | 98.5° |
| C6 | O2 | C4 | H1 | 9.9° | 21.6° |
| O2 | C6 | H13 | H12 | 120.0° | 120.0° |
| O2 | C6 | H13 | H14 | 120.0° | 120.1° |
| O2 | C6 | H12 | H14 | 120.0° | 120.0° |
| O2 | C4 | C3 | H1 | 119.9° | 120.1° |
| O2 | C4 | C3 | C2 | 175.0° | 176.9° |
| O2 | C4 | C3 | N | 64.3° | 63.3° |
| O2 | C4 | C3 | H2 | 54.8° | 57.0° |
| O2 | C4 | C5 | H | 55.8° | 57.5° |
| C4 | O2 | C6 | H13 | 180.0° | 65.3° |
| C4 | O2 | C6 | H12 | 60.0° | 54.6° |
| C4 | O2 | C6 | H14 | 60.0° | 174.6° |
| C4 | C3 | C2 | C1 | 52.1° | 57.0° |
| C4 | C3 | C2 | N | 119.9° | 119.9° |
| C4 | C3 | C2 | H2 | 120.1° | 120.0° |
| C4 | C3 | N | H2 | 118.8° | 120.3° |
| C4 | C3 | C2 | H8 | 68.0° | 62.9° |
| C4 | C3 | C2 | H7 | 172.2° | 176.9° |
| C3 | C4 | C5 | H | 63.6° | 62.3° |
| C4 | C3 | N | H10 | 180.0° | 173.6° |
| C4 | C3 | N | H11 | 60.0° | 62.4° |
| C1 | C2 | C3 | H8 | 120.1° | 119.9° |
| C1 | C2 | C3 | H7 | 120.1° | 120.0° |
| C1 | C2 | C3 | N | 172.0° | 176.8° |
| C2 | C1 | H9 | O1 | 116.4° | 120.0° |
| C1 | C2 | H8 | H7 | 119.7° | 120.2° |
| C1 | C2 | C3 | H2 | 68.0° | 63.0° |
| C2 | C1 | O1 | H3 | 57.3° | 180.0° |
| C2 | C3 | N | H2 | 119.7° | 120.1° |
| C3 | C2 | C1 | H9 | 172.0° | 177.6° |
| C3 | C2 | H8 | H7 | 119.6° | 120.2° |
| C2 | C3 | C4 | H1 | 65.1° | 63.0° |
| C2 | C3 | N | H10 | 58.4° | 54.1° |
| C2 | C3 | N | H11 | 178.4° | 178.1° |
| C3 | C2 | C1 | O1 | 70.4° | 62.4° |
| N | C3 | C2 | H8 | 51.9° | 57.0° |
| N | C3 | C2 | H7 | 67.8° | 63.2° |
| N | C3 | C4 | H1 | 55.7° | 56.8° |
| C3 | N | H10 | H11 | 120.0° | 124.0° |
| H9 | C1 | C2 | H8 | 51.9° | 57.7° |
| H9 | C1 | C2 | H7 | 67.9° | 62.5° |
| H9 | C1 | O1 | H3 | 59.1° | 60.0° |
| H8 | C2 | C3 | H2 | 171.9° | 177.1° |
| H8 | C2 | C1 | O1 | 169.5° | 177.7° |
| H7 | C2 | C3 | H2 | 52.1° | 57.0° |
| H7 | C2 | C1 | O1 | 49.7° | 57.5° |
| H2 | C3 | C4 | H1 | 174.8° | 177.1° |
| H2 | C3 | N | H10 | 61.3° | 66.1° |
| H2 | C3 | N | H11 | 58.8° | 57.9° |
| H1 | C4 | C5 | H | 177.1° | 177.7° |
| H | C5 | C | H4 | 60.8° | 54.9° |
| H | C5 | C | H6 | 59.2° | 65.0° |
| H | C5 | C | H5 | 179.2° | 175.0° |
| H4 | C | H6 | H5 | 120.0° | 120.1° |
| H13 | C6 | H12 | H14 | 120.0° | 120.0° |
