PM9
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N | C4A | sing | 1.32Å | 1.34Å | |
| N | CA | doub | 1.33Å | 1.34Å | |
| C | O1 | sing | 1.35Å | 1.25Å | |
| C | O2 | doub | 1.22Å | 1.26Å | |
| C | CA | sing | 1.40Å | 1.46Å | |
| CB | CG | sing | 1.53Å | 1.54Å | |
| CB | CA | sing | 1.51Å | 1.54Å | |
| CG | SD | sing | 1.81Å | 1.78Å | |
| SD | CE | sing | 1.81Å | 1.78Å | |
| C2 | C2A | sing | 1.51Å | 1.51Å | |
| C2 | C3 | doub | 1.36Å | 1.48Å | |
| C2 | N1 | sing | 1.36Å | 1.36Å | |
| C3 | C4 | sing | 1.42Å | 1.49Å | |
| C3 | O3 | sing | 1.36Å | 1.33Å | |
| C4 | C4A | doub | 1.41Å | 1.50Å | |
| C4 | C5 | sing | 1.41Å | 1.48Å | |
| C5 | C5A | sing | 1.51Å | 1.51Å | |
| C5 | C6 | doub | 1.35Å | 1.39Å | |
| C5A | O4P | sing | 1.43Å | 1.44Å | |
| C6 | N1 | sing | 1.35Å | 1.37Å | |
| O1P | P | doub | 1.48Å | 1.52Å | |
| O2P | P | sing | 1.61Å | 1.51Å | |
| O3P | P | sing | 1.61Å | 1.52Å | |
| O4P | P | sing | 1.61Å | 1.62Å | |
| C4A | H4 | sing | 1.08Å | 1.08Å | |
| O1 | H1 | sing | 0.97Å | 0.95Å | |
| CB | HBC1 | sing | 1.09Å | 1.10Å | |
| CB | HBC2 | sing | 1.09Å | 1.10Å | |
| CG | HGC1 | sing | 1.09Å | 1.10Å | |
| CG | HGC2 | sing | 1.09Å | 1.10Å | |
| CE | HEC1 | sing | 1.09Å | 1.10Å | |
| CE | HEC2 | sing | 1.09Å | 1.10Å | |
| CE | HEC3 | sing | 1.09Å | 1.10Å | |
| C2A | H2A1 | sing | 1.09Å | 1.10Å | |
| C2A | H2A2 | sing | 1.09Å | 1.10Å | |
| C2A | H2A3 | sing | 1.09Å | 1.10Å | |
| O3 | H3 | sing | 0.97Å | 0.95Å | |
| C5A | H5A1 | sing | 1.09Å | 1.10Å | |
| C5A | H5A2 | sing | 1.09Å | 1.10Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| O3P | H3P | sing | 0.97Å | 0.95Å | |
| O2P | H2P | sing | 0.97Å | 0.95Å | |
| N1 | HN | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C4A | N | CA | 128.2° | 120.0° |
| N | C4A | C4 | 118.6° | 120.0° |
| N | C4A | H4 | 120.7° | 120.0° |
| N | CA | C | 115.6° | 120.0° |
| N | CA | CB | 120.4° | 120.0° |
| O1 | C | O2 | 121.2° | 120.0° |
| O1 | C | CA | 120.5° | 120.0° |
| C | O1 | H1 | 109.5° | 114.1° |
| O2 | C | CA | 118.3° | 120.0° |
| C | CA | CB | 123.9° | 120.0° |
| CG | CB | CA | 113.6° | 109.4° |
| CB | CG | SD | 112.6° | 109.5° |
| CG | CB | HBC1 | 108.1° | 109.5° |
| CG | CB | HBC2 | 107.1° | 109.5° |
| CB | CG | HGC1 | 108.5° | 109.5° |
| CB | CG | HGC2 | 107.7° | 109.5° |
| CA | CB | HBC1 | 108.1° | 109.5° |
| CA | CB | HBC2 | 107.2° | 109.4° |
| CG | SD | CE | 105.5° | 103.0° |
| SD | CG | HGC1 | 108.4° | 109.5° |
| SD | CG | HGC2 | 107.7° | 109.4° |
| SD | CE | HEC1 | 109.5° | 109.4° |
| SD | CE | HEC2 | 109.4° | 109.5° |
| SD | CE | HEC3 | 109.5° | 109.5° |
| C2A | C2 | C3 | 119.0° | 119.7° |
| C2A | C2 | N1 | 121.2° | 119.7° |
| C2 | C2A | H2A1 | 109.5° | 109.5° |
| C2 | C2A | H2A2 | 109.5° | 109.5° |
| C2 | C2A | H2A3 | 109.5° | 109.5° |
| C3 | C2 | N1 | 119.7° | 120.6° |
| C2 | C3 | C4 | 117.4° | 119.1° |
| C2 | C3 | O3 | 121.4° | 120.5° |
| C2 | N1 | C6 | 124.1° | 121.5° |
| C2 | N1 | HN | 117.9° | 119.2° |
| C4 | C3 | O3 | 121.2° | 120.4° |
| C3 | C4 | C4A | 121.6° | 120.7° |
| C3 | C4 | C5 | 117.4° | 118.6° |
| C3 | O3 | H3 | 109.5° | 114.0° |
| C4A | C4 | C5 | 121.0° | 120.7° |
| C4 | C4A | H4 | 120.7° | 120.0° |
| C4 | C5 | C5A | 119.2° | 120.3° |
| C4 | C5 | C6 | 119.9° | 119.3° |
| C5A | C5 | C6 | 120.8° | 120.3° |
| C5 | C5A | O4P | 106.7° | 109.5° |
| C5 | C5A | H5A1 | 110.4° | 109.5° |
| C5 | C5A | H5A2 | 111.0° | 109.5° |
| C5 | C6 | N1 | 121.3° | 120.8° |
| C5 | C6 | H6 | 119.3° | 119.6° |
| C5A | O4P | P | 120.6° | 123.0° |
| O4P | C5A | H5A1 | 110.4° | 109.5° |
| O4P | C5A | H5A2 | 111.0° | 109.4° |
| N1 | C6 | H6 | 119.4° | 119.6° |
| C6 | N1 | HN | 118.0° | 119.3° |
| O1P | P | O2P | 110.3° | 109.4° |
| O1P | P | O3P | 114.1° | 109.5° |
| O1P | P | O4P | 108.3° | 109.5° |
| O2P | P | O3P | 114.1° | 109.5° |
| O2P | P | O4P | 106.3° | 109.4° |
| P | O2P | H2P | 109.5° | 114.0° |
| O3P | P | O4P | 103.1° | 109.5° |
| P | O3P | H3P | 109.5° | 114.0° |
| HBC1 | CB | HBC2 | 112.8° | 109.5° |
| HGC1 | CG | HGC2 | 111.9° | 109.5° |
| HEC1 | CE | HEC2 | 109.5° | 109.5° |
| HEC1 | CE | HEC3 | 109.5° | 109.4° |
| HEC2 | CE | HEC3 | 109.5° | 109.5° |
| H2A1 | C2A | H2A2 | 109.4° | 109.4° |
| H2A1 | C2A | H2A3 | 109.4° | 109.5° |
| H2A2 | C2A | H2A3 | 109.5° | 109.4° |
| H5A1 | C5A | H5A2 | 107.3° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C4A | N | CA | C | 176.3° | 174.4° |
| C4A | N | CA | CB | 6.4° | 5.6° |
| N | C4A | C4 | C3 | 2.8° | 0.1° |
| N | C4A | C4 | H4 | 180.0° | 179.9° |
| N | C4A | C4 | C5 | 175.6° | 180.0° |
| N | CA | C | O1 | 169.8° | 0.0° |
| N | CA | C | O2 | 10.4° | 180.0° |
| N | CA | C | CB | 177.2° | 180.0° |
| N | CA | CB | CG | 135.9° | 84.7° |
| CA | N | C4A | C4 | 168.2° | 174.3° |
| CA | N | C4A | H4 | 11.8° | 5.6° |
| N | CA | CB | HBC1 | 15.9° | 35.3° |
| N | CA | CB | HBC2 | 105.9° | 155.3° |
| O1 | C | O2 | CA | 179.8° | 180.0° |
| O1 | C | CA | CB | 7.4° | 180.0° |
| O2 | C | CA | CB | 172.4° | 0.0° |
| O2 | C | O1 | H1 | 0.0° | 0.0° |
| C | CA | CB | CG | 47.0° | 95.3° |
| CA | C | O1 | H1 | 179.8° | 180.0° |
| C | CA | CB | HBC1 | 167.0° | 144.7° |
| C | CA | CB | HBC2 | 71.1° | 24.7° |
| CG | CB | CA | HBC1 | 120.0° | 120.0° |
| CG | CB | CA | HBC2 | 118.2° | 120.0° |
| CB | CG | SD | HGC1 | 120.0° | 120.0° |
| CB | CG | SD | HGC2 | 118.7° | 120.0° |
| CB | CG | SD | CE | 52.1° | 180.0° |
| CG | CB | HBC1 | HBC2 | 118.3° | 120.0° |
| CB | CG | HGC1 | HGC2 | 118.7° | 120.0° |
| CA | CB | CG | SD | 55.7° | 180.0° |
| CA | CB | HBC1 | HBC2 | 118.3° | 120.0° |
| CA | CB | CG | HGC1 | 64.3° | 60.0° |
| CA | CB | CG | HGC2 | 174.3° | 60.0° |
| SD | CG | CB | HBC1 | 64.3° | 60.0° |
| SD | CG | CB | HBC2 | 173.8° | 60.0° |
| SD | CG | HGC1 | HGC2 | 118.7° | 120.0° |
| CG | SD | CE | HEC1 | 99.9° | 60.0° |
| CG | SD | CE | HEC2 | 140.1° | 60.0° |
| CG | SD | CE | HEC3 | 20.1° | 179.9° |
| CE | SD | CG | HGC1 | 172.1° | 60.0° |
| CE | SD | CG | HGC2 | 66.6° | 60.0° |
| SD | CE | HEC1 | HEC2 | 120.0° | 120.0° |
| SD | CE | HEC1 | HEC3 | 120.0° | 119.9° |
| SD | CE | HEC2 | HEC3 | 120.0° | 120.0° |
| C2A | C2 | C3 | N1 | 178.3° | 179.7° |
| C2A | C2 | C3 | C4 | 179.4° | 180.0° |
| C2A | C2 | C3 | O3 | 0.6° | 0.1° |
| C2A | C2 | N1 | C6 | 180.0° | 179.7° |
| C2 | C2A | H2A1 | H2A2 | 120.0° | 120.0° |
| C2 | C2A | H2A1 | H2A3 | 120.0° | 120.1° |
| C2 | C2A | H2A2 | H2A3 | 120.0° | 120.0° |
| C2A | C2 | N1 | HN | 0.0° | 0.0° |
| C2 | C3 | C4 | O3 | 180.0° | 180.0° |
| C2 | C3 | C4 | C4A | 179.3° | 180.0° |
| C2 | C3 | C4 | C5 | 0.9° | 0.0° |
| C3 | C2 | N1 | C6 | 1.8° | 0.6° |
| C3 | C2 | C2A | H2A1 | 31.0° | 90.1° |
| C3 | C2 | C2A | H2A2 | 150.9° | 150.0° |
| C3 | C2 | C2A | H2A3 | 89.0° | 30.0° |
| C2 | C3 | O3 | H3 | 158.2° | 0.0° |
| C3 | C2 | N1 | HN | 178.2° | 179.7° |
| N1 | C2 | C3 | C4 | 1.2° | 0.3° |
| N1 | C2 | C3 | O3 | 178.9° | 179.7° |
| C2 | N1 | C6 | C5 | 2.2° | 0.6° |
| C2 | N1 | C6 | HN | 180.0° | 179.7° |
| N1 | C2 | C2A | H2A1 | 147.3° | 90.3° |
| N1 | C2 | C2A | H2A2 | 27.3° | 29.7° |
| N1 | C2 | C2A | H2A3 | 92.8° | 149.7° |
| C2 | N1 | C6 | H6 | 177.8° | 179.7° |
| C3 | C4 | C4A | C5 | 178.4° | 179.9° |
| C3 | C4 | C5 | C5A | 179.3° | 180.0° |
| C3 | C4 | C5 | C6 | 1.3° | 0.1° |
| C3 | C4 | C4A | H4 | 177.2° | 180.0° |
| C4 | C3 | O3 | H3 | 21.8° | 180.0° |
| O3 | C3 | C4 | C4A | 0.7° | 0.0° |
| O3 | C3 | C4 | C5 | 179.1° | 179.9° |
| C4A | C4 | C5 | C5A | 2.3° | 0.1° |
| C4A | C4 | C5 | C6 | 179.7° | 180.0° |
| C4 | C5 | C5A | C6 | 178.0° | 179.9° |
| C4 | C5 | C5A | O4P | 77.5° | 180.0° |
| C4 | C5 | C6 | N1 | 1.8° | 0.2° |
| C5 | C4 | C4A | H4 | 4.4° | 0.1° |
| C4 | C5 | C5A | H5A1 | 162.5° | 60.0° |
| C4 | C5 | C5A | H5A2 | 43.6° | 60.0° |
| C4 | C5 | C6 | H6 | 178.1° | 180.0° |
| C5 | C5A | O4P | H5A1 | 120.0° | 120.0° |
| C5 | C5A | O4P | H5A2 | 121.1° | 120.0° |
| C5A | C5 | C6 | N1 | 179.8° | 179.7° |
| C5 | C5A | O4P | P | 145.9° | 180.0° |
| C5 | C5A | H5A1 | H5A2 | 121.2° | 120.0° |
| C5A | C5 | C6 | H6 | 0.2° | 0.1° |
| C6 | C5 | C5A | O4P | 100.5° | 0.1° |
| C5 | C6 | N1 | H6 | 180.0° | 179.8° |
| C6 | C5 | C5A | H5A1 | 19.5° | 120.1° |
| C6 | C5 | C5A | H5A2 | 138.4° | 119.9° |
| C5 | C6 | N1 | HN | 177.8° | 179.7° |
| C5A | O4P | P | O1P | 63.2° | 55.0° |
| C5A | O4P | P | O2P | 55.2° | 175.0° |
| C5A | O4P | P | O3P | 175.6° | 65.0° |
| O4P | C5A | H5A1 | H5A2 | 121.1° | 120.0° |
| O1P | P | O2P | O3P | 129.9° | 120.0° |
| O1P | P | O2P | O4P | 117.2° | 120.0° |
| O1P | P | O3P | O4P | 117.2° | 120.0° |
| O1P | P | O3P | H3P | 33.7° | 180.0° |
| O1P | P | O2P | H2P | 176.4° | 60.0° |
| O2P | P | O3P | O4P | 114.9° | 120.0° |
| O2P | P | O3P | H3P | 94.3° | 60.0° |
| O3P | P | O2P | H2P | 53.7° | 60.0° |
| P | O4P | C5A | H5A1 | 94.1° | 60.0° |
| P | O4P | C5A | H5A2 | 24.8° | 60.0° |
| O4P | P | O3P | H3P | 150.8° | 60.0° |
| O4P | P | O2P | H2P | 59.2° | 180.0° |
| HBC1 | CB | CG | HGC1 | 175.7° | 60.0° |
| HBC1 | CB | CG | HGC2 | 54.3° | 179.9° |
| HBC2 | CB | CG | HGC1 | 53.8° | 180.0° |
| HBC2 | CB | CG | HGC2 | 67.5° | 59.9° |
| HEC1 | CE | HEC2 | HEC3 | 120.0° | 120.0° |
| H2A1 | C2A | H2A2 | H2A3 | 120.0° | 120.0° |
| H6 | C6 | N1 | HN | 2.2° | 0.0° |
