YDX
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N02 | C01 | sing | 1.46Å | 1.47Å | |
| C03 | N02 | sing | 1.35Å | 1.33Å | Aromatic |
| C04 | C03 | doub | 1.35Å | 1.38Å | Aromatic |
| C05 | C04 | sing | 1.40Å | 1.39Å | Aromatic |
| C07 | N06 | sing | 1.35Å | 1.45Å | |
| O08 | C07 | doub | 1.21Å | 1.19Å | |
| C09 | C07 | sing | 1.51Å | 1.51Å | |
| N10 | C09 | sing | 1.46Å | 1.46Å | |
| C11 | N10 | sing | 1.35Å | 1.31Å | Aromatic |
| C12 | C11 | doub | 1.35Å | 1.37Å | Aromatic |
| C13 | C12 | sing | 1.40Å | 1.40Å | Aromatic |
| N14 | C13 | doub | 1.31Å | 1.32Å | Aromatic |
| N06 | C05 | sing | 1.40Å | 1.45Å | |
| N15 | C05 | doub | 1.31Å | 1.34Å | Aromatic |
| N02 | N15 | sing | 1.40Å | 1.38Å | Aromatic |
| N10 | N14 | sing | 1.40Å | 1.38Å | Aromatic |
| C13 | H131 | sing | 1.08Å | 1.08Å | |
| C01 | H012 | sing | 1.09Å | 1.10Å | |
| C01 | H011 | sing | 1.09Å | 1.10Å | |
| C01 | H013 | sing | 1.09Å | 1.10Å | |
| C03 | H031 | sing | 1.08Å | 1.08Å | |
| C04 | H041 | sing | 1.08Å | 1.08Å | |
| N06 | H061 | sing | 0.97Å | 1.00Å | |
| C09 | H092 | sing | 1.09Å | 1.10Å | |
| C09 | H091 | sing | 1.09Å | 1.10Å | |
| C11 | H111 | sing | 1.08Å | 1.08Å | |
| C12 | H121 | sing | 1.08Å | 1.08Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C01 | N02 | C03 | 127.2° | 126.0° |
| C01 | N02 | N15 | 124.3° | 125.9° |
| N02 | C01 | H012 | 109.5° | 109.5° |
| N02 | C01 | H011 | 109.5° | 109.5° |
| N02 | C01 | H013 | 109.4° | 109.5° |
| N02 | C03 | C04 | 107.9° | 107.9° |
| C03 | N02 | N15 | 108.4° | 108.0° |
| N02 | C03 | H031 | 126.0° | 126.0° |
| C03 | C04 | C05 | 107.8° | 107.8° |
| C04 | C03 | H031 | 126.0° | 126.1° |
| C03 | C04 | H041 | 126.1° | 126.1° |
| C04 | C05 | N06 | 130.1° | 125.9° |
| C04 | C05 | N15 | 106.8° | 108.1° |
| C05 | C04 | H041 | 126.1° | 126.1° |
| N06 | C07 | O08 | 124.5° | 120.0° |
| N06 | C07 | C09 | 117.7° | 120.0° |
| C07 | N06 | C05 | 123.3° | 120.0° |
| C07 | N06 | H061 | 118.3° | 120.0° |
| O08 | C07 | C09 | 117.8° | 120.0° |
| C07 | C09 | N10 | 108.4° | 109.5° |
| C07 | C09 | H092 | 109.7° | 109.4° |
| C07 | C09 | H091 | 109.7° | 109.4° |
| C09 | N10 | C11 | 124.5° | 126.1° |
| C09 | N10 | N14 | 123.6° | 126.0° |
| N10 | C09 | H092 | 109.7° | 109.5° |
| N10 | C09 | H091 | 109.7° | 109.5° |
| N10 | C11 | C12 | 105.2° | 107.7° |
| C11 | N10 | N14 | 111.9° | 107.9° |
| N10 | C11 | H111 | 127.4° | 126.1° |
| C11 | C12 | C13 | 109.2° | 107.9° |
| C12 | C11 | H111 | 127.4° | 126.2° |
| C11 | C12 | H121 | 125.4° | 126.0° |
| C12 | C13 | N14 | 107.0° | 108.2° |
| C12 | C13 | H131 | 126.5° | 125.9° |
| C13 | C12 | H121 | 125.4° | 126.1° |
| C13 | N14 | N10 | 106.7° | 108.2° |
| N14 | C13 | H131 | 126.5° | 125.9° |
| N06 | C05 | N15 | 123.1° | 126.0° |
| C05 | N06 | H061 | 118.3° | 120.0° |
| C05 | N15 | N02 | 109.1° | 108.2° |
| H012 | C01 | H011 | 109.4° | 109.5° |
| H012 | C01 | H013 | 109.5° | 109.5° |
| H011 | C01 | H013 | 109.5° | 109.4° |
| H092 | C09 | H091 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C01 | N02 | C03 | N15 | 179.7° | 179.8° |
| C01 | N02 | C03 | C04 | 179.9° | 180.0° |
| C01 | N02 | N15 | C05 | 180.0° | 179.8° |
| N02 | C01 | H012 | H011 | 120.0° | 120.0° |
| N02 | C01 | H012 | H013 | 120.0° | 120.1° |
| N02 | C01 | H011 | H013 | 120.0° | 120.0° |
| C01 | N02 | C03 | H031 | 0.0° | 0.0° |
| N02 | C03 | C04 | H031 | 180.0° | 180.0° |
| N02 | C03 | C04 | C05 | 0.1° | 0.0° |
| C03 | N02 | N15 | C05 | 0.3° | 0.4° |
| C03 | N02 | C01 | H012 | 179.6° | 89.7° |
| C03 | N02 | C01 | H011 | 59.6° | 30.3° |
| C03 | N02 | C01 | H013 | 60.4° | 150.3° |
| N02 | C03 | C04 | H041 | 179.9° | 180.0° |
| C03 | C04 | C05 | H041 | 180.0° | 179.9° |
| C03 | C04 | C05 | N06 | 179.2° | 179.9° |
| C03 | C04 | C05 | N15 | 0.1° | 0.2° |
| C04 | C03 | N02 | N15 | 0.3° | 0.3° |
| C04 | C05 | N06 | C07 | 6.1° | 0.0° |
| C04 | C05 | N06 | N15 | 179.0° | 179.6° |
| C04 | C05 | N15 | N02 | 0.2° | 0.4° |
| C05 | C04 | C03 | H031 | 179.9° | 180.0° |
| C04 | C05 | N06 | H061 | 173.8° | 180.0° |
| N06 | C07 | O08 | C09 | 179.7° | 179.9° |
| N06 | C07 | C09 | N10 | 167.4° | 180.0° |
| C07 | N06 | C05 | H061 | 180.0° | 180.0° |
| C07 | N06 | C05 | N15 | 172.8° | 179.6° |
| N06 | C07 | C09 | H092 | 47.5° | 60.0° |
| N06 | C07 | C09 | H091 | 72.8° | 59.9° |
| O08 | C07 | C09 | N10 | 12.9° | 0.1° |
| O08 | C07 | N06 | C05 | 0.8° | 0.1° |
| O08 | C07 | N06 | H061 | 179.2° | 180.0° |
| O08 | C07 | C09 | H092 | 132.7° | 120.0° |
| O08 | C07 | C09 | H091 | 107.0° | 120.0° |
| C07 | C09 | N10 | H092 | 119.8° | 120.0° |
| C07 | C09 | N10 | H091 | 119.8° | 120.0° |
| C07 | C09 | N10 | C11 | 94.8° | 125.3° |
| C09 | C07 | N06 | C05 | 179.5° | 180.0° |
| C07 | C09 | N10 | N14 | 86.0° | 55.1° |
| C09 | C07 | N06 | H061 | 0.6° | 0.0° |
| C07 | C09 | H092 | H091 | 120.5° | 119.9° |
| C09 | N10 | C11 | N14 | 179.2° | 179.7° |
| C09 | N10 | C11 | C12 | 179.2° | 179.9° |
| C09 | N10 | N14 | C13 | 179.0° | 180.0° |
| N10 | C09 | H092 | H091 | 120.5° | 120.1° |
| C09 | N10 | C11 | H111 | 0.8° | 0.0° |
| N10 | C11 | C12 | H111 | 180.0° | 179.8° |
| N10 | C11 | C12 | C13 | 0.1° | 0.4° |
| C11 | N10 | N14 | C13 | 0.3° | 0.3° |
| C11 | N10 | C09 | H092 | 25.0° | 5.3° |
| C11 | N10 | C09 | H091 | 145.4° | 114.7° |
| N10 | C11 | C12 | H121 | 179.9° | 179.6° |
| C11 | C12 | C13 | H121 | 180.0° | 180.0° |
| C11 | C12 | C13 | N14 | 0.3° | 0.2° |
| C12 | C11 | N10 | N14 | 0.1° | 0.4° |
| C11 | C12 | C13 | H131 | 179.7° | 180.0° |
| C12 | C13 | N14 | H131 | 180.0° | 179.8° |
| C12 | C13 | N14 | N10 | 0.3° | 0.1° |
| C13 | C12 | C11 | H111 | 179.9° | 179.8° |
| N14 | C13 | C12 | H121 | 179.8° | 179.8° |
| N06 | C05 | N15 | N02 | 179.4° | 179.9° |
| N06 | C05 | C04 | H041 | 0.9° | 0.0° |
| N15 | C05 | C04 | H041 | 179.9° | 179.7° |
| N15 | C05 | N06 | H061 | 7.2° | 0.4° |
| N15 | N02 | C01 | H012 | 0.0° | 90.0° |
| N15 | N02 | C01 | H011 | 120.0° | 150.0° |
| N15 | N02 | C01 | H013 | 120.0° | 30.0° |
| N15 | N02 | C03 | H031 | 179.7° | 179.8° |
| N10 | N14 | C13 | H131 | 179.7° | 179.8° |
| N14 | N10 | C09 | H092 | 154.1° | 175.0° |
| N14 | N10 | C09 | H091 | 33.8° | 64.9° |
| N14 | N10 | C11 | H111 | 179.9° | 179.8° |
| H131 | C13 | C12 | H121 | 0.2° | 0.0° |
| H012 | C01 | H011 | H013 | 120.0° | 120.0° |
| H031 | C03 | C04 | H041 | 0.2° | 0.1° |
| H111 | C11 | C12 | H121 | 0.1° | 0.2° |
