YD5
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C32 | C33 | sing | 1.53Å | 1.55Å | |
| C32 | C4 | sing | 1.51Å | 1.53Å | |
| C33 | N | sing | 1.47Å | 1.48Å | |
| N | CA | sing | 1.47Å | 1.49Å | |
| C4 | O5 | doub | 1.21Å | 1.23Å | |
| CA | C | sing | 1.51Å | 1.53Å | |
| CA | C41 | sing | 1.53Å | 1.55Å | |
| C | O | doub | 1.21Å | 1.23Å | |
| CA | HA | sing | 1.09Å | 1.10Å | |
| C41 | H4 | sing | 1.09Å | 1.10Å | |
| C41 | H5 | sing | 1.09Å | 1.10Å | |
| C41 | H6 | sing | 1.09Å | 1.10Å | |
| N | H | sing | 1.01Å | 1.00Å | |
| C32 | H9 | sing | 1.09Å | 1.10Å | |
| C32 | H10 | sing | 1.09Å | 1.10Å | |
| C33 | H11 | sing | 1.09Å | 1.10Å | |
| C33 | H12 | sing | 1.09Å | 1.10Å | |
| C | OXT | sing | 1.34Å | 1.34Å | |
| C4 | O3 | sing | 1.34Å | 1.34Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å | |
| O3 | H3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C33 | C32 | C4 | 111.5° | 109.5° |
| C32 | C33 | N | 113.9° | 109.5° |
| C33 | C32 | H9 | 109.0° | 109.4° |
| C33 | C32 | H10 | 109.0° | 109.5° |
| C32 | C33 | H11 | 108.3° | 109.5° |
| C32 | C33 | H12 | 108.3° | 109.4° |
| C32 | C4 | O5 | 119.8° | 120.0° |
| C4 | C32 | H9 | 109.0° | 109.5° |
| C4 | C32 | H10 | 108.9° | 109.5° |
| C32 | C4 | O3 | 117.7° | 120.0° |
| C33 | N | CA | 115.8° | 111.0° |
| C33 | N | H | 107.9° | 111.0° |
| N | C33 | H11 | 108.3° | 109.5° |
| N | C33 | H12 | 108.4° | 109.5° |
| N | CA | C | 114.1° | 109.4° |
| N | CA | C41 | 115.9° | 109.5° |
| N | CA | HA | 103.4° | 109.4° |
| CA | N | H | 107.9° | 111.0° |
| O5 | C4 | O3 | 122.5° | 120.0° |
| C | CA | C41 | 115.1° | 109.5° |
| CA | C | O | 120.9° | 120.0° |
| C | CA | HA | 103.0° | 109.5° |
| CA | C | OXT | 115.9° | 120.0° |
| C41 | CA | HA | 102.8° | 109.5° |
| CA | C41 | H4 | 109.5° | 109.5° |
| CA | C41 | H5 | 109.5° | 109.5° |
| CA | C41 | H6 | 109.5° | 109.5° |
| O | C | OXT | 123.2° | 120.0° |
| H4 | C41 | H5 | 109.5° | 109.5° |
| H4 | C41 | H6 | 109.5° | 109.5° |
| H5 | C41 | H6 | 109.5° | 109.4° |
| H9 | C32 | H10 | 109.5° | 109.5° |
| H11 | C33 | H12 | 109.5° | 109.5° |
| C | OXT | HXT | 109.5° | 117.0° |
| C4 | O3 | H3 | 109.5° | 117.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C33 | C32 | C4 | H9 | 120.3° | 119.9° |
| C33 | C32 | C4 | H10 | 120.3° | 120.0° |
| C32 | C33 | N | H11 | 120.7° | 120.1° |
| C32 | C33 | N | H12 | 120.7° | 119.9° |
| C32 | C33 | N | CA | 74.9° | 180.0° |
| C33 | C32 | C4 | O5 | 52.1° | 0.0° |
| C32 | C33 | N | H | 164.2° | 56.1° |
| C33 | C32 | H9 | H10 | 119.1° | 120.0° |
| C32 | C33 | H11 | H12 | 117.9° | 119.9° |
| C33 | C32 | C4 | O3 | 128.0° | 179.7° |
| C4 | C32 | C33 | N | 93.7° | 180.0° |
| C32 | C4 | O5 | O3 | 180.0° | 179.7° |
| C4 | C32 | H9 | H10 | 119.1° | 120.1° |
| C4 | C32 | C33 | H11 | 27.0° | 59.9° |
| C4 | C32 | C33 | H12 | 145.6° | 60.0° |
| C32 | C4 | O3 | H3 | 180.0° | 179.7° |
| C33 | N | CA | H | 120.9° | 123.9° |
| C33 | N | CA | C | 143.2° | 155.0° |
| C33 | N | CA | C41 | 79.5° | 85.0° |
| C33 | N | CA | HA | 32.2° | 35.1° |
| N | C33 | C32 | H9 | 26.6° | 60.0° |
| N | C33 | C32 | H10 | 146.0° | 59.9° |
| N | C33 | H11 | H12 | 118.0° | 120.0° |
| N | CA | C | C41 | 137.6° | 120.0° |
| N | CA | C | HA | 111.3° | 119.9° |
| N | CA | C41 | HA | 112.0° | 120.0° |
| N | CA | C | O | 123.4° | 0.0° |
| N | CA | C41 | H4 | 180.0° | 180.0° |
| N | CA | C41 | H5 | 60.0° | 60.0° |
| N | CA | C41 | H6 | 60.0° | 60.0° |
| CA | N | C33 | H11 | 45.8° | 60.0° |
| CA | N | C33 | H12 | 164.5° | 60.1° |
| N | CA | C | OXT | 56.7° | 180.0° |
| O5 | C4 | C32 | H9 | 172.4° | 120.0° |
| O5 | C4 | C32 | H10 | 68.2° | 120.0° |
| O5 | C4 | O3 | H3 | 0.0° | 0.0° |
| C | CA | C41 | HA | 111.2° | 120.0° |
| CA | C | O | OXT | 179.9° | 180.0° |
| C | CA | C41 | H4 | 43.2° | 60.0° |
| C | CA | C41 | H5 | 163.2° | 179.9° |
| C | CA | C41 | H6 | 76.9° | 60.0° |
| C | CA | N | H | 95.9° | 81.1° |
| CA | C | OXT | HXT | 179.9° | 180.0° |
| C41 | CA | C | O | 14.2° | 120.0° |
| CA | C41 | H4 | H5 | 120.0° | 120.0° |
| CA | C41 | H4 | H6 | 120.0° | 120.1° |
| CA | C41 | H5 | H6 | 120.0° | 120.0° |
| C41 | CA | N | H | 41.4° | 38.9° |
| C41 | CA | C | OXT | 165.7° | 60.0° |
| O | C | CA | HA | 125.3° | 120.0° |
| O | C | OXT | HXT | 0.0° | 0.0° |
| HA | CA | C41 | H4 | 68.0° | 60.0° |
| HA | CA | C41 | H5 | 52.0° | 60.0° |
| HA | CA | C41 | H6 | 172.0° | 179.9° |
| HA | CA | N | H | 153.1° | 159.0° |
| HA | CA | C | OXT | 54.6° | 60.0° |
| H4 | C41 | H5 | H6 | 120.0° | 120.0° |
| H | N | C33 | H11 | 75.1° | 64.0° |
| H | N | C33 | H12 | 43.6° | 176.0° |
| H9 | C32 | C33 | H11 | 147.3° | 60.0° |
| H9 | C32 | C33 | H12 | 94.1° | NaN° |
| H9 | C32 | C4 | O3 | 7.7° | 59.8° |
| H10 | C32 | C33 | H11 | 93.3° | 180.0° |
| H10 | C32 | C33 | H12 | 25.4° | 60.0° |
| H10 | C32 | C4 | O3 | 111.8° | 60.3° |
