LYS
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 | 1.02Å | |
| N | H2 | sing | 1.01Å | 1.02Å | |
| CA | C | sing | 1.51Å | 1.53Å | |
| CA | CB | sing | 1.53Å | 1.52Å | |
| CA | HA | sing | 1.09Å | 1.11Å | |
| C | O | doub | 1.21Å | 1.25Å | |
| C | OXT | sing | 1.34Å | 1.26Å | |
| CB | CG | sing | 1.53Å | 1.51Å | |
| CB | HB2 | sing | 1.09Å | 1.12Å | |
| CB | HB3 | sing | 1.09Å | 1.12Å | |
| CG | CD | sing | 1.53Å | 1.53Å | |
| CG | HG2 | sing | 1.09Å | 1.12Å | |
| CG | HG3 | sing | 1.09Å | 1.12Å | |
| CD | CE | sing | 1.53Å | 1.54Å | |
| CD | HD2 | sing | 1.09Å | 1.11Å | |
| CD | HD3 | sing | 1.09Å | 1.12Å | |
| CE | NZ | sing | 1.47Å | 1.48Å | |
| CE | HE2 | sing | 1.09Å | 1.12Å | |
| CE | HE3 | sing | 1.09Å | 1.12Å | |
| NZ | HZ1 | sing | 1.01Å | 1.02Å | |
| NZ | HZ2 | sing | 1.01Å | 1.02Å | |
| NZ | HZ3 | sing | 1.01Å | 1.02Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CA | N | H | 112.0° | 106.7° |
| CA | N | H2 | 111.3° | 106.7° |
| N | CA | C | 112.0° | 109.5° |
| N | CA | CB | 111.4° | 109.5° |
| N | CA | HA | 106.7° | 109.5° |
| H | N | H2 | 111.2° | 106.7° |
| C | CA | CB | 110.4° | 109.5° |
| C | CA | HA | 107.8° | 109.5° |
| CA | C | O | 120.4° | 120.0° |
| CA | C | OXT | 115.5° | 120.0° |
| CB | CA | HA | 108.3° | 109.5° |
| CA | CB | CG | 114.8° | 109.4° |
| CA | CB | HB2 | 110.3° | 109.5° |
| CA | CB | HB3 | 110.3° | 109.5° |
| O | C | OXT | 121.5° | 120.0° |
| C | OXT | HXT | 115.4° | 120.0° |
| CG | CB | HB2 | 110.2° | 109.5° |
| CG | CB | HB3 | 110.2° | 109.4° |
| CB | CG | CD | 110.7° | 109.4° |
| CB | CG | HG2 | 111.8° | 109.5° |
| CB | CG | HG3 | 111.8° | 109.5° |
| HB2 | CB | HB3 | 100.0° | 109.5° |
| CD | CG | HG2 | 111.7° | 109.5° |
| CD | CG | HG3 | 111.7° | 109.4° |
| CG | CD | CE | 110.2° | 109.5° |
| CG | CD | HD2 | 112.0° | 109.5° |
| CG | CD | HD3 | 112.0° | 109.4° |
| HG2 | CG | HG3 | 98.6° | 109.5° |
| CE | CD | HD2 | 111.9° | 109.5° |
| CE | CD | HD3 | 111.9° | 109.5° |
| CD | CE | NZ | 106.5° | 109.5° |
| CD | CE | HE2 | 113.3° | 109.5° |
| CD | CE | HE3 | 113.4° | 109.5° |
| HD2 | CD | HD3 | 98.5° | 109.5° |
| NZ | CE | HE2 | 113.3° | 109.4° |
| NZ | CE | HE3 | 113.3° | 109.5° |
| CE | NZ | HZ1 | 106.5° | 109.4° |
| CE | NZ | HZ2 | 113.3° | 109.5° |
| CE | NZ | HZ3 | 113.4° | 109.5° |
| HE2 | CE | HE3 | 97.2° | 109.4° |
| HZ1 | NZ | HZ2 | 113.3° | 109.5° |
| HZ1 | NZ | HZ3 | 113.3° | 109.5° |
| HZ2 | NZ | HZ3 | 97.1° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CA | N | H | H2 | 125.3° | 113.8° |
| N | CA | C | CB | 124.8° | 120.0° |
| N | CA | C | HA | 117.0° | 120.0° |
| N | CA | CB | HA | 117.1° | 120.0° |
| N | CA | C | O | 0.5° | 20.0° |
| N | CA | C | OXT | 161.3° | 160.0° |
| N | CA | CB | CG | 62.5° | 65.0° |
| N | CA | CB | HB2 | 172.2° | 55.0° |
| N | CA | CB | HB3 | 62.7° | 175.0° |
| H | N | CA | C | 180.0° | 60.0° |
| H | N | CA | CB | 55.7° | 60.0° |
| H | N | CA | HA | 62.4° | 180.0° |
| H2 | N | CA | C | 54.7° | 173.8° |
| H2 | N | CA | CB | 69.5° | 53.8° |
| H2 | N | CA | HA | 172.4° | 66.2° |
| C | CA | CB | HA | 117.8° | 120.0° |
| CA | C | O | OXT | 160.7° | 180.0° |
| C | CA | CB | CG | 62.6° | 175.0° |
| C | CA | CB | HB2 | 62.7° | 65.0° |
| C | CA | CB | HB3 | 172.2° | 55.1° |
| CA | C | OXT | HXT | 180.0° | 180.0° |
| CB | CA | C | O | 124.3° | 100.0° |
| CB | CA | C | OXT | 73.9° | 80.0° |
| CA | CB | CG | HB2 | 125.3° | 120.0° |
| CA | CB | CG | HB3 | 125.3° | 120.0° |
| CA | CB | HB2 | HB3 | 116.1° | 120.0° |
| CA | CB | CG | CD | 127.4° | 180.0° |
| CA | CB | CG | HG2 | 107.4° | 60.0° |
| CA | CB | CG | HG3 | 2.1° | 60.1° |
| HA | CA | C | O | 117.6° | 140.0° |
| HA | CA | C | OXT | 44.2° | 40.1° |
| HA | CA | CB | CG | 179.6° | 55.0° |
| HA | CA | CB | HB2 | 55.1° | 175.0° |
| HA | CA | CB | HB3 | 54.4° | 65.0° |
| O | C | OXT | HXT | 18.5° | 0.1° |
| CG | CB | HB2 | HB3 | 116.0° | 120.0° |
| CB | CG | CD | HG2 | 125.3° | 120.0° |
| CB | CG | CD | HG3 | 125.3° | 120.0° |
| CB | CG | HG2 | HG3 | 117.7° | 120.1° |
| CB | CG | CD | CE | 159.2° | 180.0° |
| CB | CG | CD | HD2 | 34.0° | 60.0° |
| CB | CG | CD | HD3 | 75.5° | 60.0° |
| HB2 | CB | CG | CD | 2.1° | 60.0° |
| HB2 | CB | CG | HG2 | 127.4° | 180.0° |
| HB2 | CB | CG | HG3 | 123.2° | 60.0° |
| HB3 | CB | CG | CD | 107.3° | 60.0° |
| HB3 | CB | CG | HG2 | 17.9° | 59.9° |
| HB3 | CB | CG | HG3 | 127.4° | 180.0° |
| CD | CG | HG2 | HG3 | 117.6° | 120.0° |
| CG | CD | CE | HD2 | 125.3° | 120.0° |
| CG | CD | CE | HD3 | 125.3° | 119.9° |
| CG | CD | HD2 | HD3 | 117.9° | 120.0° |
| CG | CD | CE | NZ | 35.8° | 180.0° |
| CG | CD | CE | HE2 | 89.4° | 60.0° |
| CG | CD | CE | HE3 | 161.1° | 60.0° |
| HG2 | CG | CD | CE | 75.5° | 60.0° |
| HG2 | CG | CD | HD2 | 159.3° | 179.9° |
| HG2 | CG | CD | HD3 | 49.8° | 60.0° |
| HG3 | CG | CD | CE | 33.9° | 60.0° |
| HG3 | CG | CD | HD2 | 91.3° | 60.0° |
| HG3 | CG | CD | HD3 | 159.2° | 180.0° |
| CE | CD | HD2 | HD3 | 117.8° | 120.0° |
| CD | CE | NZ | HE2 | 125.3° | 120.1° |
| CD | CE | NZ | HE3 | 125.3° | 120.1° |
| CD | CE | HE2 | HE3 | 119.3° | 120.0° |
| CD | CE | NZ | HZ1 | 180.0° | 60.0° |
| CD | CE | NZ | HZ2 | 54.7° | 60.0° |
| CD | CE | NZ | HZ3 | 54.8° | 180.0° |
| HD2 | CD | CE | NZ | 161.1° | 60.0° |
| HD2 | CD | CE | HE2 | 35.9° | 180.0° |
| HD2 | CD | CE | HE3 | 73.7° | 60.0° |
| HD3 | CD | CE | NZ | 89.4° | 60.0° |
| HD3 | CD | CE | HE2 | 145.3° | 60.0° |
| HD3 | CD | CE | HE3 | 35.8° | 180.0° |
| NZ | CE | HE2 | HE3 | 119.2° | 119.9° |
| CE | NZ | HZ1 | HZ2 | 125.3° | 119.9° |
| CE | NZ | HZ1 | HZ3 | 125.3° | 120.0° |
| CE | NZ | HZ2 | HZ3 | 119.3° | 120.1° |
| HE2 | CE | NZ | HZ1 | 54.7° | 179.9° |
| HE2 | CE | NZ | HZ2 | 180.0° | 60.1° |
| HE2 | CE | NZ | HZ3 | 70.5° | 60.0° |
| HE3 | CE | NZ | HZ1 | 54.7° | 60.1° |
| HE3 | CE | NZ | HZ2 | 70.6° | 180.0° |
| HE3 | CE | NZ | HZ3 | 180.0° | 59.9° |
| HZ1 | NZ | HZ2 | HZ3 | 119.2° | 120.0° |
