PM3
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N | CA | sing | 1.47Å | 1.46Å | |
| N | H | sing | 1.01Å | 1.00Å | |
| N | H2 | sing | 1.01Å | 1.00Å | |
| CA | CB | sing | 1.53Å | 1.53Å | |
| CA | C | sing | 1.51Å | 1.52Å | |
| CA | HA | sing | 1.09Å | 1.10Å | |
| CB | CG | sing | 1.51Å | 1.51Å | |
| CB | HB2 | sing | 1.09Å | 1.10Å | |
| CB | HB3 | sing | 1.09Å | 1.10Å | |
| CG | CD1 | sing | 1.38Å | 1.39Å | Aromatic |
| CG | CD2 | doub | 1.38Å | 1.39Å | Aromatic |
| CD1 | CE1 | doub | 1.38Å | 1.39Å | Aromatic |
| CD1 | HD1 | sing | 1.08Å | 1.08Å | |
| CE1 | CZ | sing | 1.38Å | 1.39Å | Aromatic |
| CE1 | HE1 | sing | 1.08Å | 1.08Å | |
| CD2 | CE2 | sing | 1.38Å | 1.39Å | Aromatic |
| CD2 | HD2 | sing | 1.08Å | 1.08Å | |
| CE2 | CZ | doub | 1.38Å | 1.38Å | Aromatic |
| CE2 | HE2 | sing | 1.08Å | 1.08Å | |
| CZ | CH4 | sing | 1.51Å | 1.51Å | |
| CH4 | P | sing | 1.82Å | 1.78Å | |
| CH4 | HH42 | sing | 1.09Å | 1.10Å | |
| CH4 | HH43 | sing | 1.09Å | 1.10Å | |
| P | O1 | sing | 1.61Å | 1.49Å | |
| P | O2 | doub | 1.48Å | 1.48Å | |
| P | O3 | sing | 1.61Å | 1.48Å | |
| O1 | HO1 | sing | 0.97Å | 0.95Å | |
| O3 | HO3 | sing | 0.97Å | 0.95Å | |
| C | OXT | sing | 1.34Å | 1.23Å | |
| C | O | doub | 1.21Å | 1.33Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CA | N | H | 109.5° | 106.7° |
| CA | N | H2 | 109.5° | 106.7° |
| N | CA | CB | 110.4° | 109.5° |
| N | CA | C | 110.7° | 109.5° |
| N | CA | HA | 107.6° | 109.4° |
| H | N | H2 | 109.5° | 106.7° |
| CB | CA | C | 108.1° | 109.5° |
| CB | CA | HA | 110.2° | 109.5° |
| CA | CB | CG | 115.0° | 109.5° |
| CA | CB | HB2 | 106.4° | 109.5° |
| CA | CB | HB3 | 107.7° | 109.5° |
| C | CA | HA | 109.9° | 109.4° |
| CA | C | OXT | 121.5° | 120.0° |
| CA | C | O | 115.4° | 120.0° |
| CG | CB | HB2 | 106.4° | 109.5° |
| CG | CB | HB3 | 107.7° | 109.5° |
| CB | CG | CD1 | 120.9° | 120.0° |
| CB | CG | CD2 | 120.7° | 120.0° |
| HB2 | CB | HB3 | 113.9° | 109.5° |
| CD1 | CG | CD2 | 118.4° | 120.0° |
| CG | CD1 | CE1 | 121.0° | 120.0° |
| CG | CD1 | HD1 | 119.5° | 120.0° |
| CG | CD2 | CE2 | 121.2° | 120.0° |
| CG | CD2 | HD2 | 119.4° | 120.0° |
| CE1 | CD1 | HD1 | 119.5° | 120.0° |
| CD1 | CE1 | CZ | 119.4° | 120.0° |
| CD1 | CE1 | HE1 | 120.3° | 120.1° |
| CZ | CE1 | HE1 | 120.3° | 119.9° |
| CE1 | CZ | CE2 | 120.5° | 120.0° |
| CE1 | CZ | CH4 | 119.9° | 120.0° |
| CE2 | CD2 | HD2 | 119.4° | 120.0° |
| CD2 | CE2 | CZ | 119.6° | 120.0° |
| CD2 | CE2 | HE2 | 120.2° | 120.0° |
| CZ | CE2 | HE2 | 120.2° | 120.0° |
| CE2 | CZ | CH4 | 119.6° | 120.0° |
| CZ | CH4 | P | 118.0° | 109.5° |
| CZ | CH4 | HH42 | 104.8° | 109.5° |
| CZ | CH4 | HH43 | 106.7° | 109.4° |
| P | CH4 | HH42 | 104.8° | 109.5° |
| P | CH4 | HH43 | 106.7° | 109.5° |
| CH4 | P | O1 | 105.5° | 109.5° |
| CH4 | P | O2 | 104.6° | 109.5° |
| CH4 | P | O3 | 105.7° | 109.5° |
| HH42 | CH4 | HH43 | 116.4° | 109.4° |
| O1 | P | O2 | 113.3° | 109.5° |
| O1 | P | O3 | 113.4° | 109.5° |
| P | O1 | HO1 | 109.5° | 106.8° |
| O2 | P | O3 | 113.3° | 109.5° |
| P | O3 | HO3 | 109.5° | 106.8° |
| OXT | C | O | 123.1° | 120.0° |
| C | OXT | HXT | 109.5° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CA | N | H | H2 | 120.0° | 113.8° |
| N | CA | CB | C | 121.2° | 120.0° |
| N | CA | CB | HA | 118.7° | 120.0° |
| N | CA | C | HA | 118.7° | 119.9° |
| N | CA | CB | CG | 71.4° | 65.0° |
| N | CA | CB | HB2 | 171.1° | 55.0° |
| N | CA | CB | HB3 | 48.6° | 175.0° |
| N | CA | C | OXT | 134.0° | 160.0° |
| N | CA | C | O | 46.7° | 20.0° |
| H | N | CA | CB | 39.5° | 60.0° |
| H | N | CA | C | 159.1° | 60.0° |
| H | N | CA | HA | 80.8° | 180.0° |
| H2 | N | CA | CB | 80.6° | 53.7° |
| H2 | N | CA | C | 39.1° | 173.8° |
| H2 | N | CA | HA | 159.1° | 66.3° |
| CB | CA | C | HA | 120.3° | 120.0° |
| CA | CB | CG | HB2 | 117.5° | 120.0° |
| CA | CB | CG | HB3 | 120.0° | 120.0° |
| CA | CB | HB2 | HB3 | 118.4° | 120.0° |
| CA | CB | CG | CD1 | 123.9° | 90.3° |
| CA | CB | CG | CD2 | 58.5° | 90.0° |
| CB | CA | C | OXT | 104.9° | 80.0° |
| CB | CA | C | O | 74.3° | 100.0° |
| C | CA | CB | CG | 167.4° | 175.0° |
| C | CA | CB | HB2 | 49.9° | 65.0° |
| C | CA | CB | HB3 | 72.5° | 55.0° |
| CA | C | OXT | O | 179.2° | 180.0° |
| CA | C | OXT | HXT | 179.2° | 180.0° |
| HA | CA | CB | CG | 47.3° | 55.0° |
| HA | CA | CB | HB2 | 70.2° | 175.0° |
| HA | CA | CB | HB3 | 167.3° | 65.0° |
| HA | CA | C | OXT | 15.4° | 40.0° |
| HA | CA | C | O | 165.4° | 140.0° |
| CG | CB | HB2 | HB3 | 118.5° | 120.0° |
| CB | CG | CD1 | CD2 | 177.7° | 179.7° |
| CB | CG | CD1 | CE1 | 177.3° | 179.8° |
| CB | CG | CD1 | HD1 | 2.7° | 0.2° |
| CB | CG | CD2 | CE2 | 177.5° | 180.0° |
| CB | CG | CD2 | HD2 | 2.4° | 0.1° |
| HB2 | CB | CG | CD1 | 118.5° | 149.7° |
| HB2 | CB | CG | CD2 | 59.1° | 30.0° |
| HB3 | CB | CG | CD1 | 3.9° | 29.7° |
| HB3 | CB | CG | CD2 | 178.5° | 150.0° |
| CG | CD1 | CE1 | HD1 | 180.0° | 179.6° |
| CG | CD1 | CE1 | CZ | 0.2° | 0.4° |
| CG | CD1 | CE1 | HE1 | 179.7° | 179.8° |
| CD1 | CG | CD2 | CE2 | 0.1° | 0.3° |
| CD1 | CG | CD2 | HD2 | 179.9° | 179.8° |
| CD2 | CG | CD1 | CE1 | 0.3° | 0.5° |
| CD2 | CG | CD1 | HD1 | 179.7° | 179.9° |
| CG | CD2 | CE2 | HD2 | 180.0° | 179.9° |
| CG | CD2 | CE2 | CZ | 0.2° | 0.0° |
| CG | CD2 | CE2 | HE2 | 179.8° | 179.9° |
| CD1 | CE1 | CZ | HE1 | 180.0° | 179.8° |
| CD1 | CE1 | CZ | CE2 | 0.0° | 0.1° |
| CD1 | CE1 | CZ | CH4 | 179.7° | 179.8° |
| HD1 | CD1 | CE1 | CZ | 179.8° | 180.0° |
| HD1 | CD1 | CE1 | HE1 | 0.3° | 0.2° |
| CE1 | CZ | CE2 | CD2 | 0.2° | 0.1° |
| CE1 | CZ | CE2 | CH4 | 179.7° | 179.9° |
| CE1 | CZ | CE2 | HE2 | 179.8° | 180.0° |
| CE1 | CZ | CH4 | P | 86.8° | 90.0° |
| CE1 | CZ | CH4 | HH42 | 157.1° | 30.1° |
| CE1 | CZ | CH4 | HH43 | 33.2° | 150.0° |
| HE1 | CE1 | CZ | CE2 | 180.0° | 179.9° |
| HE1 | CE1 | CZ | CH4 | 0.3° | 0.0° |
| CD2 | CE2 | CZ | HE2 | 180.0° | 179.9° |
| CD2 | CE2 | CZ | CH4 | 180.0° | 180.0° |
| HD2 | CD2 | CE2 | CZ | 179.8° | 179.9° |
| HD2 | CD2 | CE2 | HE2 | 0.2° | 0.0° |
| CE2 | CZ | CH4 | P | 92.9° | 89.9° |
| CE2 | CZ | CH4 | HH42 | 23.2° | 150.0° |
| CE2 | CZ | CH4 | HH43 | 147.1° | 30.1° |
| HE2 | CE2 | CZ | CH4 | 0.1° | 0.1° |
| CZ | CH4 | P | HH42 | 116.0° | 120.0° |
| CZ | CH4 | P | HH43 | 120.0° | 120.0° |
| CZ | CH4 | HH42 | HH43 | 117.6° | 119.9° |
| CZ | CH4 | P | O1 | 57.6° | 175.0° |
| CZ | CH4 | P | O2 | 62.2° | 55.0° |
| CZ | CH4 | P | O3 | 177.9° | 65.0° |
| P | CH4 | HH42 | HH43 | 117.6° | 120.0° |
| CH4 | P | O1 | O2 | 113.8° | 120.0° |
| CH4 | P | O1 | O3 | 115.2° | 120.0° |
| CH4 | P | O2 | O3 | 114.6° | 120.0° |
| CH4 | P | O1 | HO1 | 89.8° | 180.0° |
| CH4 | P | O3 | HO3 | 87.6° | 60.0° |
| HH42 | CH4 | P | O1 | 58.5° | 55.0° |
| HH42 | CH4 | P | O2 | 178.2° | 65.0° |
| HH42 | CH4 | P | O3 | 61.9° | 175.0° |
| HH43 | CH4 | P | O1 | 177.5° | 65.0° |
| HH43 | CH4 | P | O2 | 57.8° | 175.0° |
| HH43 | CH4 | P | O3 | 62.1° | 55.0° |
| O1 | P | O2 | O3 | 131.0° | 120.0° |
| O1 | P | O3 | HO3 | 27.4° | 60.0° |
| O2 | P | O1 | HO1 | 24.0° | 60.0° |
| O2 | P | O3 | HO3 | 158.4° | 180.0° |
| O3 | P | O1 | HO1 | 155.0° | 60.0° |
| O | C | OXT | HXT | 0.0° | 0.0° |
