DYJ
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O | C | doub | 1.21Å | 1.21Å | |
| C | CA | sing | 1.51Å | 1.56Å | |
| CG | CB | sing | 1.55Å | 1.54Å | |
| CG | CD | sing | 1.55Å | 1.54Å | |
| CB | CA | sing | 1.54Å | 1.30Å | |
| CA | N | sing | 1.47Å | 1.63Å | |
| CD | N | sing | 1.47Å | 1.28Å | |
| N | C06 | sing | 1.36Å | 1.42Å | |
| C06 | C07 | sing | 1.51Å | 1.50Å | |
| C06 | C08 | doub | 1.36Å | 1.35Å | |
| C08 | C09 | sing | 1.41Å | 1.52Å | |
| C09 | O11 | doub | 1.22Å | 1.21Å | |
| C09 | C10 | sing | 1.49Å | 1.51Å | |
| C10 | O13 | doub | 1.21Å | 1.26Å | |
| C10 | O12 | sing | 1.35Å | 1.26Å | |
| C | OXT | sing | 1.34Å | 1.33Å | |
| CA | H1 | sing | 1.09Å | 1.10Å | |
| CB | H2 | sing | 1.09Å | 1.10Å | |
| CB | H3 | sing | 1.09Å | 1.10Å | |
| CG | H4 | sing | 1.09Å | 1.10Å | |
| CG | H5 | sing | 1.09Å | 1.10Å | |
| CD | H6 | sing | 1.09Å | 1.10Å | |
| CD | H7 | sing | 1.09Å | 1.10Å | |
| C07 | H8 | sing | 1.09Å | 1.10Å | |
| C07 | H9 | sing | 1.09Å | 1.10Å | |
| C07 | H10 | sing | 1.09Å | 1.10Å | |
| C08 | H11 | sing | 1.08Å | 1.08Å | |
| O12 | H12 | sing | 0.97Å | 0.95Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O | C | CA | 120.2° | 120.0° |
| O | C | OXT | 123.3° | 120.0° |
| C | CA | CB | 113.1° | 109.9° |
| C | CA | N | 115.0° | 109.9° |
| CA | C | OXT | 116.6° | 120.0° |
| C | CA | H1 | 106.4° | 109.8° |
| CB | CG | CD | 105.2° | 101.7° |
| CG | CB | CA | 105.3° | 102.9° |
| CG | CB | H2 | 110.5° | 110.7° |
| CG | CB | H3 | 110.5° | 110.9° |
| CB | CG | H4 | 110.5° | 111.0° |
| CB | CG | H5 | 110.5° | 110.9° |
| CG | CD | N | 107.1° | 105.0° |
| CD | CG | H4 | 110.5° | 111.1° |
| CD | CG | H5 | 110.5° | 110.9° |
| CG | CD | H6 | 110.0° | 110.3° |
| CG | CD | H7 | 110.0° | 110.4° |
| CB | CA | N | 106.2° | 107.3° |
| CB | CA | H1 | 110.0° | 110.0° |
| CA | CB | H2 | 110.5° | 110.7° |
| CA | CB | H3 | 110.5° | 110.7° |
| CA | N | CD | 108.7° | 108.7° |
| CA | N | C06 | 126.4° | 125.6° |
| N | CA | H1 | 105.8° | 110.0° |
| CD | N | C06 | 125.0° | 125.7° |
| N | CD | H6 | 110.1° | 110.5° |
| N | CD | H7 | 110.1° | 110.1° |
| N | C06 | C07 | 118.9° | 120.0° |
| N | C06 | C08 | 118.5° | 120.0° |
| C07 | C06 | C08 | 122.6° | 120.0° |
| C06 | C07 | H8 | 109.5° | 109.5° |
| C06 | C07 | H9 | 109.5° | 109.5° |
| C06 | C07 | H10 | 109.5° | 109.5° |
| C06 | C08 | C09 | 128.5° | 120.0° |
| C06 | C08 | H11 | 115.8° | 120.0° |
| C08 | C09 | O11 | 123.2° | 119.9° |
| C08 | C09 | C10 | 117.8° | 120.0° |
| C09 | C08 | H11 | 115.7° | 120.0° |
| O11 | C09 | C10 | 119.0° | 120.1° |
| C09 | C10 | O13 | 120.3° | 120.0° |
| C09 | C10 | O12 | 119.4° | 120.0° |
| O13 | C10 | O12 | 120.3° | 120.0° |
| C10 | O12 | H12 | 109.5° | 117.0° |
| C | OXT | HXT | 109.5° | 117.0° |
| H2 | CB | H3 | 109.5° | 110.6° |
| H4 | CG | H5 | 109.5° | 111.0° |
| H6 | CD | H7 | 109.5° | 110.4° |
| H8 | C07 | H9 | 109.5° | 109.5° |
| H8 | C07 | H10 | 109.5° | 109.5° |
| H9 | C07 | H10 | 109.4° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O | C | CA | OXT | 178.2° | 179.7° |
| O | C | CA | CB | 87.2° | 117.8° |
| O | C | CA | N | 35.0° | 0.0° |
| O | C | CA | H1 | 151.8° | 121.1° |
| O | C | OXT | HXT | 0.0° | 0.0° |
| C | CA | CB | CG | 100.3° | 141.6° |
| C | CA | CB | N | 127.1° | 119.4° |
| C | CA | CB | H1 | 118.9° | 121.0° |
| C | CA | N | H1 | 117.2° | 121.0° |
| C | CA | N | CD | 105.1° | 118.6° |
| C | CA | N | C06 | 74.4° | 61.7° |
| C | CA | CB | H2 | 140.4° | 23.3° |
| C | CA | CB | H3 | 19.1° | 99.8° |
| CA | C | OXT | HXT | 178.2° | 179.7° |
| CB | CG | CD | H4 | 119.3° | 118.1° |
| CB | CG | CD | H5 | 119.3° | 118.0° |
| CG | CB | CA | H2 | 119.3° | 118.3° |
| CG | CB | CA | H3 | 119.3° | 118.6° |
| CG | CB | CA | N | 26.8° | 22.2° |
| CB | CG | CD | N | 12.0° | 36.7° |
| CG | CB | CA | H1 | 140.9° | 97.4° |
| CG | CB | H2 | H3 | 122.0° | 123.4° |
| CB | CG | H4 | H5 | 122.0° | 123.8° |
| CB | CG | CD | H6 | 131.7° | 155.8° |
| CB | CG | CD | H7 | 107.6° | 81.9° |
| CD | CG | CB | CA | 25.7° | 35.3° |
| CG | CD | N | CA | 3.4° | 23.8° |
| CG | CD | N | H6 | 119.6° | 118.9° |
| CG | CD | N | H7 | 119.6° | 118.8° |
| CG | CD | N | C06 | 177.1° | 155.9° |
| CD | CG | CB | H2 | 93.7° | 83.0° |
| CD | CG | CB | H3 | 145.0° | 153.8° |
| CD | CG | H4 | H5 | 122.0° | 123.8° |
| CG | CD | H6 | H7 | 121.1° | 122.3° |
| CB | CA | N | H1 | 116.9° | 119.6° |
| CB | CA | N | CD | 20.8° | 0.8° |
| CB | CA | N | C06 | 159.7° | 178.9° |
| CB | CA | C | OXT | 94.5° | 61.8° |
| CA | CB | H2 | H3 | 121.9° | 123.1° |
| CA | CB | CG | H4 | 93.7° | 153.5° |
| CA | CB | CG | H5 | 145.0° | 82.6° |
| CA | N | CD | C06 | 179.5° | 179.7° |
| CA | N | C06 | C07 | 18.8° | 0.0° |
| CA | N | C06 | C08 | 160.8° | 180.0° |
| N | CA | C | OXT | 143.2° | 179.7° |
| N | CA | CB | H2 | 92.5° | 96.2° |
| N | CA | CB | H3 | 146.2° | 140.8° |
| CA | N | CD | H6 | 116.3° | 142.8° |
| CA | N | CD | H7 | 123.0° | 95.0° |
| CD | N | C06 | C07 | 160.6° | 179.7° |
| CD | N | C06 | C08 | 19.7° | 0.3° |
| CD | N | CA | H1 | 137.7° | 120.4° |
| N | CD | CG | H4 | 107.3° | 154.9° |
| N | CD | CG | H5 | 131.3° | 81.2° |
| N | CD | H6 | H7 | 121.1° | 122.1° |
| N | C06 | C07 | C08 | 179.6° | 180.0° |
| N | C06 | C08 | C09 | 179.9° | 173.5° |
| C06 | N | CA | H1 | 42.8° | 59.3° |
| C06 | N | CD | H6 | 63.3° | 37.0° |
| C06 | N | CD | H7 | 57.5° | 85.3° |
| N | C06 | C07 | H8 | 180.0° | 95.7° |
| N | C06 | C07 | H9 | 60.0° | 144.3° |
| N | C06 | C07 | H10 | 60.0° | 24.3° |
| N | C06 | C08 | H11 | 0.1° | 6.5° |
| C07 | C06 | C08 | C09 | 0.3° | 6.6° |
| C06 | C07 | H8 | H9 | 120.0° | 120.0° |
| C06 | C07 | H8 | H10 | 120.0° | 120.0° |
| C06 | C07 | H9 | H10 | 120.0° | 120.0° |
| C07 | C06 | C08 | H11 | 179.7° | 173.4° |
| C06 | C08 | C09 | H11 | 180.0° | 180.0° |
| C06 | C08 | C09 | O11 | 10.8° | 5.3° |
| C06 | C08 | C09 | C10 | 169.4° | 174.7° |
| C08 | C06 | C07 | H8 | 0.4° | 84.3° |
| C08 | C06 | C07 | H9 | 119.7° | 35.7° |
| C08 | C06 | C07 | H10 | 120.4° | 155.7° |
| C08 | C09 | O11 | C10 | 179.8° | 180.0° |
| C08 | C09 | C10 | O13 | 132.0° | 0.0° |
| C08 | C09 | C10 | O12 | 47.6° | 180.0° |
| O11 | C09 | C10 | O13 | 48.2° | 180.0° |
| O11 | C09 | C10 | O12 | 132.2° | 0.0° |
| O11 | C09 | C08 | H11 | 169.2° | 174.7° |
| C09 | C10 | O13 | O12 | 179.6° | 180.0° |
| C10 | C09 | C08 | H11 | 10.6° | 5.3° |
| C09 | C10 | O12 | H12 | 179.6° | 180.0° |
| O13 | C10 | O12 | H12 | 0.0° | 0.0° |
| OXT | C | CA | H1 | 26.4° | 59.3° |
| H1 | CA | CB | H2 | 21.5° | 144.3° |
| H1 | CA | CB | H3 | 99.8° | 21.2° |
| H2 | CB | CG | H4 | 147.0° | 35.2° |
| H2 | CB | CG | H5 | 25.7° | 159.1° |
| H3 | CB | CG | H4 | 25.7° | 88.0° |
| H3 | CB | CG | H5 | 95.7° | 35.9° |
| H4 | CG | CD | H6 | 12.3° | 86.0° |
| H4 | CG | CD | H7 | 133.0° | 36.3° |
| H5 | CG | CD | H6 | 109.0° | 37.9° |
| H5 | CG | CD | H7 | 11.7° | 160.2° |
| H8 | C07 | H9 | H10 | 120.0° | 120.0° |
