PYJ
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| CB | CX | sing | 1.53Å | 1.54Å | |
| CB | CG | sing | 1.51Å | 1.50Å | |
| CB | HCB1 | sing | 1.09Å | 1.10Å | |
| CB | HCB2 | sing | 1.09Å | 1.10Å | |
| CX | HCX1 | sing | 1.09Å | 1.10Å | |
| CX | HCX2 | sing | 1.09Å | 1.10Å | |
| CX | HCX3 | sing | 1.09Å | 1.10Å | |
| CG | CD1 | doub | 1.38Å | 1.39Å | Aromatic |
| CG | CD2 | sing | 1.38Å | 1.40Å | Aromatic |
| CD1 | CE1 | sing | 1.38Å | 1.40Å | Aromatic |
| CD1 | HCD1 | sing | 1.08Å | 1.08Å | |
| CD2 | CE2 | doub | 1.38Å | 1.39Å | Aromatic |
| CD2 | HCD2 | sing | 1.08Å | 1.08Å | |
| CE1 | CZ | doub | 1.38Å | 1.40Å | Aromatic |
| CE1 | HCE1 | sing | 1.08Å | 1.08Å | |
| CE2 | CZ | sing | 1.38Å | 1.39Å | Aromatic |
| CE2 | HCE2 | sing | 1.08Å | 1.08Å | |
| CZ | HCZ1 | sing | 1.08Å | 1.08Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CX | CB | CG | 117.0° | 109.5° |
| CX | CB | HCB1 | 107.6° | 109.5° |
| CX | CB | HCB2 | 107.6° | 109.5° |
| CB | CX | HCX1 | 109.5° | 109.5° |
| CB | CX | HCX2 | 109.5° | 109.5° |
| CB | CX | HCX3 | 109.5° | 109.5° |
| CG | CB | HCB1 | 107.6° | 109.5° |
| CG | CB | HCB2 | 107.6° | 109.4° |
| CB | CG | CD1 | 113.0° | 120.0° |
| CB | CG | CD2 | 126.3° | 120.0° |
| HCB1 | CB | HCB2 | 109.5° | 109.5° |
| HCX1 | CX | HCX2 | 109.5° | 109.5° |
| HCX1 | CX | HCX3 | 109.4° | 109.4° |
| HCX2 | CX | HCX3 | 109.5° | 109.5° |
| CD1 | CG | CD2 | 120.7° | 120.0° |
| CG | CD1 | CE1 | 123.3° | 120.0° |
| CG | CD1 | HCD1 | 118.4° | 120.0° |
| CG | CD2 | CE2 | 117.8° | 120.0° |
| CG | CD2 | HCD2 | 121.1° | 120.0° |
| CE1 | CD1 | HCD1 | 118.3° | 120.0° |
| CD1 | CE1 | CZ | 113.9° | 120.0° |
| CD1 | CE1 | HCE1 | 123.0° | 120.0° |
| CE2 | CD2 | HCD2 | 121.1° | 120.0° |
| CD2 | CE2 | CZ | 119.9° | 120.0° |
| CD2 | CE2 | HCE2 | 120.0° | 120.0° |
| CZ | CE1 | HCE1 | 123.0° | 120.0° |
| CE1 | CZ | CE2 | 124.4° | 120.0° |
| CE1 | CZ | HCZ1 | 117.8° | 120.0° |
| CZ | CE2 | HCE2 | 120.1° | 120.0° |
| CE2 | CZ | HCZ1 | 117.8° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CX | CB | CG | HCB1 | 121.1° | 120.0° |
| CX | CB | CG | HCB2 | 121.1° | 120.0° |
| CX | CB | HCB1 | HCB2 | 116.6° | 120.0° |
| CB | CX | HCX1 | HCX2 | 120.1° | 120.0° |
| CB | CX | HCX1 | HCX3 | 120.0° | 120.0° |
| CB | CX | HCX2 | HCX3 | 120.0° | 120.0° |
| CX | CB | CG | CD1 | 44.8° | 90.0° |
| CX | CB | CG | CD2 | 136.2° | 90.2° |
| CG | CB | HCB1 | HCB2 | 116.6° | 120.0° |
| CG | CB | CX | HCX1 | 180.0° | 180.0° |
| CG | CB | CX | HCX2 | 60.0° | 60.0° |
| CG | CB | CX | HCX3 | 60.0° | 60.0° |
| CB | CG | CD1 | CD2 | 179.1° | 179.8° |
| CB | CG | CD1 | CE1 | 179.0° | 179.9° |
| CB | CG | CD1 | HCD1 | 1.0° | 0.0° |
| CB | CG | CD2 | CE2 | 178.9° | 180.0° |
| CB | CG | CD2 | HCD2 | 1.1° | 0.1° |
| HCB1 | CB | CX | HCX1 | 59.0° | 60.0° |
| HCB1 | CB | CX | HCX2 | 61.1° | 60.0° |
| HCB1 | CB | CX | HCX3 | 178.9° | 179.9° |
| HCB1 | CB | CG | CD1 | 76.3° | 30.0° |
| HCB1 | CB | CG | CD2 | 102.7° | 149.8° |
| HCB2 | CB | CX | HCX1 | 58.9° | 60.0° |
| HCB2 | CB | CX | HCX2 | 178.9° | 180.0° |
| HCB2 | CB | CX | HCX3 | 61.1° | 59.9° |
| HCB2 | CB | CG | CD1 | 165.9° | 150.0° |
| HCB2 | CB | CG | CD2 | 15.1° | 29.8° |
| HCX1 | CX | HCX2 | HCX3 | 119.9° | 120.0° |
| CG | CD1 | CE1 | HCD1 | 180.0° | 179.9° |
| CD1 | CG | CD2 | CE2 | 0.1° | 0.2° |
| CD1 | CG | CD2 | HCD2 | 180.0° | 179.7° |
| CG | CD1 | CE1 | CZ | 0.0° | 0.1° |
| CG | CD1 | CE1 | HCE1 | 180.0° | 180.0° |
| CD2 | CG | CD1 | CE1 | 0.1° | 0.2° |
| CD2 | CG | CD1 | HCD1 | 179.9° | 179.8° |
| CG | CD2 | CE2 | HCD2 | 180.0° | 179.9° |
| CG | CD2 | CE2 | CZ | 0.1° | 0.1° |
| CG | CD2 | CE2 | HCE2 | 179.9° | 179.9° |
| CD1 | CE1 | CZ | HCE1 | 180.0° | 180.0° |
| CD1 | CE1 | CZ | CE2 | 0.2° | 0.2° |
| CD1 | CE1 | CZ | HCZ1 | 179.8° | 180.0° |
| HCD1 | CD1 | CE1 | CZ | 180.0° | 180.0° |
| HCD1 | CD1 | CE1 | HCE1 | 0.0° | 0.0° |
| CD2 | CE2 | CZ | CE1 | 0.3° | 0.2° |
| CD2 | CE2 | CZ | HCE2 | 180.0° | 180.0° |
| CD2 | CE2 | CZ | HCZ1 | 179.7° | 179.9° |
| HCD2 | CD2 | CE2 | CZ | 179.8° | 180.0° |
| HCD2 | CD2 | CE2 | HCE2 | 0.2° | 0.0° |
| CE1 | CZ | CE2 | HCZ1 | 180.0° | 179.8° |
| CE1 | CZ | CE2 | HCE2 | 179.7° | 179.7° |
| HCE1 | CE1 | CZ | CE2 | 179.8° | 179.8° |
| HCE1 | CE1 | CZ | HCZ1 | 0.2° | 0.1° |
| HCE2 | CE2 | CZ | HCZ1 | 0.3° | 0.1° |
