3YM
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| CAI | CD1 | doub | 1.38Å | 1.39Å | Aromatic |
| CAI | CAK | sing | 1.39Å | 1.39Å | Aromatic |
| CD1 | CG | sing | 1.38Å | 1.39Å | Aromatic |
| O | C | doub | 1.21Å | 1.23Å | |
| CA | C | sing | 1.51Å | 1.53Å | |
| CA | N | sing | 1.47Å | 1.46Å | |
| CA | CB | sing | 1.53Å | 1.53Å | |
| OAL | CAK | sing | 1.36Å | 1.36Å | |
| CAK | CAJ | doub | 1.39Å | 1.39Å | Aromatic |
| CG | CB | sing | 1.51Å | 1.54Å | |
| CG | CD2 | doub | 1.38Å | 1.40Å | Aromatic |
| CAJ | CD2 | sing | 1.39Å | 1.39Å | Aromatic |
| CAJ | OAM | sing | 1.36Å | 1.36Å | |
| OAM | CAN | sing | 1.43Å | 1.42Å | |
| CAN | H1 | sing | 1.09Å | 1.10Å | |
| CAN | H11 | sing | 1.09Å | 1.10Å | |
| CAN | H3 | sing | 1.09Å | 1.10Å | |
| CD2 | H4 | sing | 1.08Å | 1.08Å | |
| OAL | H5 | sing | 0.97Å | 0.95Å | |
| CAI | H6 | sing | 1.08Å | 1.08Å | |
| CD1 | H7 | sing | 1.08Å | 1.08Å | |
| CB | H8 | sing | 1.09Å | 1.10Å | |
| CB | H9 | sing | 1.09Å | 1.10Å | |
| CA | HA | sing | 1.09Å | 1.10Å | |
| N | H | sing | 1.01Å | 1.00Å | |
| N | H2 | sing | 1.01Å | 1.00Å | |
| C | OXT | sing | 1.34Å | 32.03Å | |
| OXT | HXT | sing | 0.97Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CD1 | CAI | CAK | 120.3° | 120.0° |
| CAI | CD1 | CG | 120.2° | 120.2° |
| CD1 | CAI | H6 | 119.9° | 120.0° |
| CAI | CD1 | H7 | 119.9° | 119.9° |
| CAI | CAK | OAL | 119.7° | 120.0° |
| CAI | CAK | CAJ | 119.9° | 119.9° |
| CAK | CAI | H6 | 119.9° | 120.0° |
| CD1 | CG | CB | 121.2° | 120.0° |
| CD1 | CG | CD2 | 119.5° | 120.1° |
| CG | CD1 | H7 | 119.9° | 119.9° |
| O | C | CA | 121.8° | 120.0° |
| O | C | OXT | 30.2° | 120.1° |
| C | CA | N | 107.9° | 109.5° |
| C | CA | CB | 108.0° | 109.5° |
| C | CA | HA | 109.8° | 109.5° |
| CA | C | OXT | 95.1° | 120.0° |
| N | CA | CB | 110.5° | 109.5° |
| N | CA | HA | 110.8° | 109.4° |
| CA | N | H | 109.5° | 110.9° |
| CA | N | H2 | 109.4° | 111.0° |
| CA | CB | CG | 114.1° | 109.4° |
| CA | CB | H8 | 108.3° | 109.5° |
| CA | CB | H9 | 108.3° | 109.4° |
| CB | CA | HA | 109.8° | 109.4° |
| OAL | CAK | CAJ | 120.3° | 120.1° |
| CAK | OAL | H5 | 109.5° | 114.0° |
| CAK | CAJ | CD2 | 119.7° | 119.8° |
| CAK | CAJ | OAM | 120.3° | 120.1° |
| CB | CG | CD2 | 119.3° | 119.9° |
| CG | CB | H8 | 108.3° | 109.5° |
| CG | CB | H9 | 108.3° | 109.5° |
| CG | CD2 | CAJ | 120.5° | 120.0° |
| CG | CD2 | H4 | 119.8° | 120.0° |
| CD2 | CAJ | OAM | 120.0° | 120.1° |
| CAJ | CD2 | H4 | 119.8° | 120.0° |
| CAJ | OAM | CAN | 108.6° | 117.0° |
| OAM | CAN | H1 | 109.5° | 109.5° |
| OAM | CAN | H11 | 109.5° | 109.5° |
| OAM | CAN | H3 | 109.5° | 109.5° |
| H1 | CAN | H11 | 109.4° | 109.4° |
| H1 | CAN | H3 | 109.5° | 109.5° |
| H11 | CAN | H3 | 109.5° | 109.5° |
| H8 | CB | H9 | 109.4° | 109.5° |
| H | N | H2 | 109.5° | 111.0° |
| C | OXT | HXT | 90.0° | 117.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CD1 | CAI | CAK | H6 | 180.0° | 179.7° |
| CAI | CD1 | CG | H7 | 180.0° | 179.7° |
| CD1 | CAI | CAK | OAL | 179.7° | 180.0° |
| CD1 | CAI | CAK | CAJ | 0.3° | 0.0° |
| CAI | CD1 | CG | CB | 179.6° | 180.0° |
| CAI | CD1 | CG | CD2 | 0.4° | 0.6° |
| CAK | CAI | CD1 | CG | 0.3° | 0.3° |
| CAI | CAK | OAL | CAJ | 180.0° | 179.9° |
| CAI | CAK | CAJ | CD2 | 0.3° | 0.0° |
| CAI | CAK | CAJ | OAM | 179.8° | 179.7° |
| CAI | CAK | OAL | H5 | 180.0° | 90.0° |
| CAK | CAI | CD1 | H7 | 179.7° | 180.0° |
| CD1 | CG | CB | CA | 82.9° | 90.0° |
| CD1 | CG | CB | CD2 | 179.2° | 179.4° |
| CD1 | CG | CD2 | CAJ | 0.4° | 0.6° |
| CD1 | CG | CD2 | H4 | 179.6° | 179.4° |
| CG | CD1 | CAI | H6 | 179.7° | 180.0° |
| CD1 | CG | CB | H8 | 156.4° | 150.0° |
| CD1 | CG | CB | H9 | 37.8° | 29.9° |
| O | C | CA | OXT | 15.1° | 180.0° |
| O | C | CA | N | 120.1° | 20.0° |
| O | C | CA | CB | 120.4° | 100.0° |
| O | C | CA | HA | 0.7° | 140.0° |
| O | C | OXT | HXT | 90.0° | 0.0° |
| C | CA | N | CB | 117.9° | 120.1° |
| C | CA | N | HA | 120.3° | 120.0° |
| C | CA | CB | HA | 119.7° | 120.0° |
| C | CA | CB | CG | 176.9° | 175.0° |
| C | CA | CB | H8 | 56.2° | 55.0° |
| C | CA | CB | H9 | 62.4° | 65.0° |
| C | CA | N | H | 180.0° | 60.0° |
| C | CA | N | H2 | 60.0° | 176.0° |
| CA | C | OXT | HXT | 90.0° | 180.0° |
| N | CA | CB | HA | 122.5° | 120.0° |
| N | CA | CB | CG | 59.0° | 64.9° |
| N | CA | CB | H8 | 61.6° | 175.0° |
| N | CA | CB | H9 | 179.7° | 55.0° |
| CA | N | H | H2 | 120.0° | 124.0° |
| N | CA | C | OXT | 135.2° | 160.0° |
| CA | CB | CG | H8 | 120.7° | 120.0° |
| CA | CB | CG | H9 | 120.7° | 119.9° |
| CA | CB | CG | CD2 | 97.8° | 90.6° |
| CA | CB | H8 | H9 | 117.9° | 120.0° |
| CB | CA | N | H | 62.1° | 60.0° |
| CB | CA | N | H2 | 177.9° | 63.9° |
| CB | CA | C | OXT | 105.3° | 80.0° |
| OAL | CAK | CAJ | CD2 | 179.7° | 179.9° |
| OAL | CAK | CAJ | OAM | 0.2° | 0.3° |
| OAL | CAK | CAI | H6 | 0.2° | 0.4° |
| CAK | CAJ | CD2 | CG | 0.4° | 0.3° |
| CAK | CAJ | CD2 | OAM | 179.9° | 179.7° |
| CAK | CAJ | OAM | CAN | 89.0° | 179.7° |
| CAK | CAJ | CD2 | H4 | 179.6° | 179.7° |
| CAJ | CAK | OAL | H5 | 0.0° | 90.0° |
| CAJ | CAK | CAI | H6 | 179.8° | 179.7° |
| CB | CG | CD2 | CAJ | 179.6° | 180.0° |
| CB | CG | CD2 | H4 | 0.3° | 0.0° |
| CB | CG | CD1 | H7 | 0.4° | 0.3° |
| CG | CB | H8 | H9 | 117.9° | 120.0° |
| CG | CB | CA | HA | 63.4° | 55.0° |
| CG | CD2 | CAJ | H4 | 180.0° | 180.0° |
| CG | CD2 | CAJ | OAM | 179.7° | 180.0° |
| CD2 | CG | CD1 | H7 | 179.6° | 179.7° |
| CD2 | CG | CB | H8 | 22.9° | 29.4° |
| CD2 | CG | CB | H9 | 141.5° | 149.5° |
| CD2 | CAJ | OAM | CAN | 90.9° | 0.0° |
| CAJ | OAM | CAN | H1 | 180.0° | 60.0° |
| CAJ | OAM | CAN | H11 | 60.0° | 60.0° |
| CAJ | OAM | CAN | H3 | 60.0° | 180.0° |
| OAM | CAJ | CD2 | H4 | 0.3° | 0.0° |
| OAM | CAN | H1 | H11 | 120.0° | 120.0° |
| OAM | CAN | H1 | H3 | 120.0° | 120.0° |
| OAM | CAN | H11 | H3 | 120.0° | 120.0° |
| H1 | CAN | H11 | H3 | 120.0° | 120.0° |
| H6 | CAI | CD1 | H7 | 0.3° | 0.3° |
| H8 | CB | CA | HA | 175.9° | 65.0° |
| H9 | CB | CA | HA | 57.3° | 175.0° |
| HA | CA | N | H | 59.8° | 180.0° |
| HA | CA | N | H2 | 60.2° | 56.0° |
| HA | CA | C | OXT | 14.4° | 40.0° |
