APD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C | O | doub | 1.21Å | 1.23Å | |
| C | CA | sing | 1.51Å | 1.51Å | |
| C | OXT | sing | 1.34Å | 1.33Å | |
| CA | N | sing | 1.47Å | 1.45Å | |
| CA | CB | sing | 1.53Å | 1.53Å | |
| CA | HA | sing | 1.09Å | 1.11Å | |
| N | H | sing | 1.01Å | 1.02Å | |
| N | H2 | sing | 1.01Å | 1.02Å | |
| CB | CG | sing | 1.51Å | 1.51Å | |
| CB | HBC1 | sing | 1.09Å | 1.11Å | |
| CB | HBC2 | sing | 1.09Å | 1.11Å | |
| CG | CD1 | doub | 1.38Å | 1.40Å | Aromatic |
| CG | CD2 | sing | 1.38Å | 1.39Å | Aromatic |
| CD1 | CE1 | sing | 1.38Å | 1.40Å | Aromatic |
| CD1 | HD1 | sing | 1.08Å | 1.10Å | |
| CD2 | CE2 | doub | 1.38Å | 1.40Å | Aromatic |
| CD2 | HD2 | sing | 1.08Å | 1.10Å | |
| CE1 | CZ | doub | 1.38Å | 1.39Å | Aromatic |
| CE1 | HE1 | sing | 1.08Å | 1.10Å | |
| CE2 | CZ | sing | 1.38Å | 1.40Å | Aromatic |
| CE2 | C5 | sing | 1.51Å | 1.50Å | |
| CZ | HZ | sing | 1.08Å | 1.10Å | |
| C5 | H5C1 | sing | 1.09Å | 1.12Å | |
| C5 | H5C2 | sing | 1.09Å | 1.11Å | |
| C5 | H5C3 | sing | 1.09Å | 1.12Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O | C | CA | 119.8° | 120.0° |
| O | C | OXT | 124.1° | 120.0° |
| CA | C | OXT | 116.1° | 120.0° |
| C | CA | N | 110.0° | 109.5° |
| C | CA | CB | 110.8° | 109.5° |
| C | CA | HA | 108.7° | 109.5° |
| C | OXT | HXT | 124.1° | 120.0° |
| N | CA | CB | 110.0° | 109.4° |
| N | CA | HA | 108.7° | 109.4° |
| CA | N | H | 110.0° | 106.6° |
| CA | N | H2 | 112.0° | 106.7° |
| CB | CA | HA | 108.7° | 109.5° |
| CA | CB | CG | 111.3° | 109.5° |
| CA | CB | HBC1 | 111.5° | 109.4° |
| CA | CB | HBC2 | 111.5° | 109.5° |
| H | N | H2 | 112.0° | 106.7° |
| CG | CB | HBC1 | 111.5° | 109.4° |
| CG | CB | HBC2 | 111.5° | 109.6° |
| CB | CG | CD1 | 120.9° | 119.9° |
| CB | CG | CD2 | 120.4° | 120.1° |
| HBC1 | CB | HBC2 | 98.8° | 109.4° |
| CD1 | CG | CD2 | 118.6° | 120.0° |
| CG | CD1 | CE1 | 120.8° | 120.0° |
| CG | CD1 | HD1 | 119.6° | 120.0° |
| CG | CD2 | CE2 | 121.6° | 120.0° |
| CG | CD2 | HD2 | 119.2° | 120.0° |
| CE1 | CD1 | HD1 | 119.6° | 120.0° |
| CD1 | CE1 | CZ | 119.3° | 120.0° |
| CD1 | CE1 | HE1 | 120.4° | 120.0° |
| CE2 | CD2 | HD2 | 119.2° | 120.0° |
| CD2 | CE2 | CZ | 118.8° | 120.0° |
| CD2 | CE2 | C5 | 120.3° | 120.0° |
| CZ | CE1 | HE1 | 120.3° | 120.0° |
| CE1 | CZ | CE2 | 120.8° | 120.0° |
| CE1 | CZ | HZ | 119.6° | 120.0° |
| CZ | CE2 | C5 | 120.9° | 120.0° |
| CE2 | CZ | HZ | 119.6° | 120.0° |
| CE2 | C5 | H5C1 | 120.9° | 109.5° |
| CE2 | C5 | H5C2 | 108.1° | 109.4° |
| CE2 | C5 | H5C3 | 108.1° | 109.5° |
| H5C1 | C5 | H5C2 | 108.1° | 109.5° |
| H5C1 | C5 | H5C3 | 108.1° | 109.5° |
| H5C2 | C5 | H5C3 | 101.8° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O | C | CA | OXT | 179.9° | 180.0° |
| O | C | CA | N | 37.7° | 30.0° |
| O | C | CA | CB | 84.1° | 90.0° |
| O | C | CA | HA | 156.5° | 150.0° |
| O | C | OXT | HXT | 180.0° | 0.1° |
| C | CA | N | CB | 122.3° | 120.1° |
| C | CA | N | HA | 118.8° | 120.0° |
| C | CA | CB | HA | 119.3° | 120.0° |
| C | CA | N | H | 180.0° | 60.0° |
| C | CA | N | H2 | 54.7° | 173.8° |
| C | CA | CB | CG | 175.3° | 179.9° |
| C | CA | CB | HBC1 | 50.1° | 60.0° |
| C | CA | CB | HBC2 | 59.4° | 59.9° |
| CA | C | OXT | HXT | 0.1° | 180.0° |
| OXT | C | CA | N | 142.4° | 149.9° |
| OXT | C | CA | CB | 95.8° | 90.1° |
| OXT | C | CA | HA | 23.6° | 30.0° |
| N | CA | CB | HA | 118.9° | 119.9° |
| CA | N | H | H2 | 125.3° | 113.8° |
| N | CA | CB | CG | 62.9° | 60.0° |
| N | CA | CB | HBC1 | 171.9° | 179.9° |
| N | CA | CB | HBC2 | 62.4° | 60.1° |
| CB | CA | N | H | 57.7° | 60.1° |
| CB | CA | N | H2 | 67.6° | 53.7° |
| CA | CB | CG | HBC1 | 125.3° | 119.9° |
| CA | CB | CG | HBC2 | 125.3° | 120.1° |
| CA | CB | HBC1 | HBC2 | 117.4° | 120.0° |
| CA | CB | CG | CD1 | 87.2° | 90.0° |
| CA | CB | CG | CD2 | 89.9° | 89.8° |
| HA | CA | N | H | 61.2° | 180.0° |
| HA | CA | N | H2 | 173.6° | 66.2° |
| HA | CA | CB | CG | 56.0° | 59.9° |
| HA | CA | CB | HBC1 | 69.3° | 60.0° |
| HA | CA | CB | HBC2 | 178.7° | 180.0° |
| CG | CB | HBC1 | HBC2 | 117.4° | 120.0° |
| CB | CG | CD1 | CD2 | 177.1° | 179.8° |
| CB | CG | CD1 | CE1 | 176.7° | 180.0° |
| CB | CG | CD1 | HD1 | 3.3° | 0.0° |
| CB | CG | CD2 | CE2 | 176.8° | 179.7° |
| CB | CG | CD2 | HD2 | 3.3° | 0.2° |
| HBC1 | CB | CG | CD1 | 38.1° | 150.0° |
| HBC1 | CB | CG | CD2 | 144.8° | 30.2° |
| HBC2 | CB | CG | CD1 | 147.6° | 30.1° |
| HBC2 | CB | CG | CD2 | 35.3° | 150.1° |
| CG | CD1 | CE1 | HD1 | 180.0° | 180.0° |
| CD1 | CG | CD2 | CE2 | 0.4° | 0.5° |
| CD1 | CG | CD2 | HD2 | 179.6° | 180.0° |
| CG | CD1 | CE1 | CZ | 0.2° | 0.0° |
| CG | CD1 | CE1 | HE1 | 179.8° | 180.0° |
| CD2 | CG | CD1 | CE1 | 0.4° | 0.2° |
| CD2 | CG | CD1 | HD1 | 179.6° | 179.8° |
| CG | CD2 | CE2 | HD2 | 180.0° | 179.5° |
| CG | CD2 | CE2 | CZ | 0.1° | 0.5° |
| CG | CD2 | CE2 | C5 | 179.7° | 179.8° |
| CD1 | CE1 | CZ | HE1 | 180.0° | 180.0° |
| CD1 | CE1 | CZ | CE2 | 0.2° | 0.0° |
| CD1 | CE1 | CZ | HZ | 179.8° | 180.0° |
| HD1 | CD1 | CE1 | CZ | 179.9° | 179.9° |
| HD1 | CD1 | CE1 | HE1 | 0.1° | 0.0° |
| CD2 | CE2 | CZ | CE1 | 0.2° | 0.3° |
| CD2 | CE2 | CZ | C5 | 179.8° | 179.7° |
| CD2 | CE2 | CZ | HZ | 179.8° | 179.7° |
| CD2 | CE2 | C5 | H5C1 | 0.2° | 90.3° |
| CD2 | CE2 | C5 | H5C2 | 125.0° | 29.7° |
| CD2 | CE2 | C5 | H5C3 | 125.5° | 149.7° |
| HD2 | CD2 | CE2 | CZ | 179.9° | 180.0° |
| HD2 | CD2 | CE2 | C5 | 0.3° | 0.3° |
| CE1 | CZ | CE2 | HZ | 180.0° | 180.0° |
| CE1 | CZ | CE2 | C5 | 180.0° | 180.0° |
| HE1 | CE1 | CZ | CE2 | 179.8° | 180.0° |
| HE1 | CE1 | CZ | HZ | 0.2° | 0.0° |
| CZ | CE2 | C5 | H5C1 | 180.0° | 90.0° |
| CZ | CE2 | C5 | H5C2 | 54.8° | 150.0° |
| CZ | CE2 | C5 | H5C3 | 54.7° | 30.0° |
| C5 | CE2 | CZ | HZ | 0.0° | 0.0° |
| CE2 | C5 | H5C1 | H5C2 | 125.3° | 119.9° |
| CE2 | C5 | H5C1 | H5C3 | 125.3° | 120.0° |
| CE2 | C5 | H5C2 | H5C3 | 113.7° | 120.0° |
| H5C1 | C5 | H5C2 | H5C3 | 113.8° | 120.0° |
