PPD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N1 | C2 | doub | 1.32Å | 1.33Å | Aromatic |
| N1 | C6 | sing | 1.32Å | 1.35Å | Aromatic |
| C2 | C2A | sing | 1.51Å | 1.51Å | |
| C2 | C3 | sing | 1.39Å | 1.40Å | Aromatic |
| C2A | H2A1 | sing | 1.09Å | 1.11Å | |
| C2A | H2A2 | sing | 1.09Å | 1.11Å | |
| C2A | H2A3 | sing | 1.09Å | 1.12Å | |
| C3 | O3 | sing | 1.36Å | 1.34Å | |
| C3 | C4 | doub | 1.39Å | 1.39Å | Aromatic |
| O3 | HO3 | sing | 0.97Å | 0.95Å | |
| C4 | C4A | sing | 1.51Å | 1.43Å | |
| C4 | C5 | sing | 1.38Å | 1.41Å | Aromatic |
| C4A | N | sing | 1.47Å | 1.48Å | |
| C4A | H4A1 | sing | 1.09Å | 1.12Å | |
| C4A | H4A2 | sing | 1.09Å | 1.11Å | |
| C5 | C6 | doub | 1.38Å | 1.36Å | Aromatic |
| C5 | C5A | sing | 1.51Å | 1.55Å | |
| C6 | H6 | sing | 1.08Å | 1.10Å | |
| C5A | O4P | sing | 1.43Å | 1.41Å | |
| C5A | H5A1 | sing | 1.09Å | 1.11Å | |
| C5A | H5A2 | sing | 1.09Å | 1.11Å | |
| O4P | P | sing | 1.61Å | 1.58Å | |
| P | O1P | doub | 1.48Å | 1.47Å | |
| P | O2P | sing | 1.61Å | 1.54Å | |
| P | O3P | sing | 1.61Å | 1.47Å | |
| O2P | HOP2 | sing | 0.97Å | 0.95Å | |
| O3P | HOP3 | sing | 0.97Å | 0.95Å | |
| N | CA | sing | 1.47Å | 1.47Å | |
| N | HN | sing | 1.01Å | 1.02Å | |
| CA | CB | sing | 1.53Å | 1.50Å | |
| CA | C | sing | 1.51Å | 1.48Å | |
| CA | HA | sing | 1.09Å | 1.12Å | |
| CB | CG | sing | 1.51Å | 1.51Å | |
| CB | HB1 | sing | 1.09Å | 1.11Å | |
| CB | HB2 | sing | 1.09Å | 1.12Å | |
| CG | OD1 | doub | 1.21Å | 1.26Å | |
| CG | OD2 | sing | 1.34Å | 1.27Å | |
| OD2 | HOD | sing | 0.97Å | 0.95Å | |
| C | O | doub | 1.21Å | 1.25Å | |
| C | OXT | sing | 1.34Å | 1.27Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C2 | N1 | C6 | 125.6° | 121.8° |
| N1 | C2 | C2A | 118.2° | 119.7° |
| N1 | C2 | C3 | 116.6° | 120.7° |
| N1 | C6 | C5 | 118.0° | 120.9° |
| N1 | C6 | H6 | 120.7° | 119.6° |
| C2A | C2 | C3 | 125.2° | 119.6° |
| C2 | C2A | H2A1 | 118.3° | 109.5° |
| C2 | C2A | H2A2 | 109.1° | 109.5° |
| C2 | C2A | H2A3 | 109.1° | 109.5° |
| C2 | C3 | O3 | 115.6° | 120.5° |
| C2 | C3 | C4 | 121.2° | 119.1° |
| H2A1 | C2A | H2A2 | 109.1° | 109.5° |
| H2A1 | C2A | H2A3 | 109.0° | 109.5° |
| H2A2 | C2A | H2A3 | 101.0° | 109.4° |
| O3 | C3 | C4 | 123.2° | 120.4° |
| C3 | O3 | HO3 | 115.7° | 106.8° |
| C3 | C4 | C4A | 122.6° | 120.9° |
| C3 | C4 | C5 | 117.4° | 118.3° |
| C4A | C4 | C5 | 120.0° | 120.8° |
| C4 | C4A | N | 108.3° | 109.5° |
| C4 | C4A | H4A1 | 112.6° | 109.5° |
| C4 | C4A | H4A2 | 112.7° | 109.4° |
| C4 | C5 | C6 | 121.2° | 119.3° |
| C4 | C5 | C5A | 118.2° | 120.4° |
| N | C4A | H4A1 | 112.7° | 109.5° |
| N | C4A | H4A2 | 112.6° | 109.6° |
| C4A | N | CA | 121.6° | 106.7° |
| C4A | N | HN | 107.8° | 106.7° |
| H4A1 | C4A | H4A2 | 97.8° | 109.4° |
| C6 | C5 | C5A | 120.3° | 120.3° |
| C5 | C6 | H6 | 121.2° | 119.6° |
| C5 | C5A | O4P | 111.1° | 109.5° |
| C5 | C5A | H5A1 | 111.6° | 109.5° |
| C5 | C5A | H5A2 | 111.6° | 109.5° |
| O4P | C5A | H5A1 | 111.6° | 109.5° |
| O4P | C5A | H5A2 | 111.6° | 109.4° |
| C5A | O4P | P | 124.5° | 106.9° |
| H5A1 | C5A | H5A2 | 98.9° | 109.4° |
| O4P | P | O1P | 104.6° | 109.4° |
| O4P | P | O2P | 104.1° | 109.5° |
| O4P | P | O3P | 110.8° | 109.5° |
| O1P | P | O2P | 114.6° | 109.5° |
| O1P | P | O3P | 114.0° | 109.4° |
| O2P | P | O3P | 108.3° | 109.5° |
| P | O2P | HOP2 | 104.1° | 106.8° |
| P | O3P | HOP3 | 110.8° | 106.7° |
| CA | N | HN | 107.9° | 106.7° |
| N | CA | CB | 112.6° | 109.5° |
| N | CA | C | 109.7° | 109.5° |
| N | CA | HA | 107.8° | 109.5° |
| CB | CA | C | 111.4° | 109.4° |
| CB | CA | HA | 106.0° | 109.5° |
| CA | CB | CG | 115.1° | 109.5° |
| CA | CB | HB1 | 110.2° | 109.5° |
| CA | CB | HB2 | 110.1° | 109.5° |
| C | CA | HA | 109.1° | 109.5° |
| CA | C | O | 118.6° | 120.0° |
| CA | C | OXT | 117.5° | 120.0° |
| CG | CB | HB1 | 110.2° | 109.4° |
| CG | CB | HB2 | 110.2° | 109.5° |
| CB | CG | OD1 | 117.6° | 120.0° |
| CB | CG | OD2 | 121.4° | 120.0° |
| HB1 | CB | HB2 | 100.0° | 109.5° |
| OD1 | CG | OD2 | 121.0° | 120.0° |
| CG | OD2 | HOD | 121.4° | 120.0° |
| O | C | OXT | 123.8° | 120.0° |
| C | OXT | HXT | 117.5° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| N1 | C2 | C2A | C3 | 179.0° | 179.6° |
| N1 | C2 | C2A | H2A1 | 179.9° | 90.0° |
| N1 | C2 | C2A | H2A2 | 54.7° | 150.0° |
| N1 | C2 | C2A | H2A3 | 54.7° | 30.0° |
| N1 | C2 | C3 | O3 | 179.0° | 180.0° |
| N1 | C2 | C3 | C4 | 1.4° | 0.6° |
| C2 | N1 | C6 | C5 | 0.1° | 0.0° |
| C2 | N1 | C6 | H6 | 179.9° | 179.9° |
| C6 | N1 | C2 | C2A | 179.1° | 180.0° |
| C6 | N1 | C2 | C3 | 0.1° | 0.3° |
| N1 | C6 | C5 | C4 | 1.2° | 0.0° |
| N1 | C6 | C5 | H6 | 180.0° | 179.9° |
| N1 | C6 | C5 | C5A | 175.5° | 180.0° |
| C2 | C2A | H2A1 | H2A2 | 125.4° | 120.0° |
| C2 | C2A | H2A1 | H2A3 | 125.3° | 120.0° |
| C2 | C2A | H2A2 | H2A3 | 114.8° | 120.0° |
| C2A | C2 | C3 | O3 | 2.0° | 0.3° |
| C2A | C2 | C3 | C4 | 179.6° | 179.7° |
| C3 | C2 | C2A | H2A1 | 1.0° | 90.3° |
| C3 | C2 | C2A | H2A2 | 126.4° | 29.7° |
| C3 | C2 | C2A | H2A3 | 124.2° | 149.6° |
| C2 | C3 | O3 | C4 | 177.5° | 179.4° |
| C2 | C3 | O3 | HO3 | 179.9° | 90.6° |
| C2 | C3 | C4 | C4A | 179.6° | 179.7° |
| C2 | C3 | C4 | C5 | 2.6° | 0.6° |
| H2A1 | C2A | H2A2 | H2A3 | 114.7° | 120.0° |
| O3 | C3 | C4 | C4A | 2.2° | 0.3° |
| O3 | C3 | C4 | C5 | 180.0° | 180.0° |
| C4 | C3 | O3 | HO3 | 2.6° | 90.0° |
| C3 | C4 | C4A | C5 | 177.8° | 179.7° |
| C3 | C4 | C4A | N | 33.8° | 89.7° |
| C3 | C4 | C4A | H4A1 | 91.4° | 30.3° |
| C3 | C4 | C4A | H4A2 | 159.1° | 150.2° |
| C3 | C4 | C5 | C6 | 2.5° | 0.3° |
| C3 | C4 | C5 | C5A | 176.9° | 179.7° |
| C4 | C4A | N | H4A1 | 125.2° | 120.0° |
| C4 | C4A | N | H4A2 | 125.3° | 120.0° |
| C4 | C4A | H4A1 | H4A2 | 118.6° | 119.9° |
| C4A | C4 | C5 | C6 | 179.6° | 180.0° |
| C4A | C4 | C5 | C5A | 5.2° | 0.0° |
| C4 | C4A | N | CA | 166.5° | 180.0° |
| C4 | C4A | N | HN | 41.2° | 66.2° |
| C5 | C4 | C4A | N | 148.4° | 90.0° |
| C5 | C4 | C4A | H4A1 | 86.3° | 150.0° |
| C5 | C4 | C4A | H4A2 | 23.1° | 30.1° |
| C4 | C5 | C6 | C5A | 174.3° | 180.0° |
| C4 | C5 | C6 | H6 | 178.8° | 179.9° |
| C4 | C5 | C5A | O4P | 77.9° | 179.9° |
| C4 | C5 | C5A | H5A1 | 156.9° | 59.9° |
| C4 | C5 | C5A | H5A2 | 47.3° | 60.0° |
| N | C4A | H4A1 | H4A2 | 118.6° | 120.1° |
| C4A | N | CA | HN | 125.2° | 113.8° |
| C4A | N | CA | CB | 56.7° | 150.0° |
| C4A | N | CA | C | 178.6° | 90.0° |
| C4A | N | CA | HA | 59.9° | 30.0° |
| H4A1 | C4A | N | CA | 41.2° | 60.0° |
| H4A1 | C4A | N | HN | 84.0° | 173.8° |
| H4A2 | C4A | N | CA | 68.2° | 60.0° |
| H4A2 | C4A | N | HN | 166.5° | 53.8° |
| C6 | C5 | C5A | O4P | 107.6° | 0.0° |
| C6 | C5 | C5A | H5A1 | 17.6° | 120.1° |
| C6 | C5 | C5A | H5A2 | 127.2° | 120.0° |
| C5A | C5 | C6 | H6 | 4.5° | 0.0° |
| C5 | C5A | O4P | H5A1 | 125.2° | 120.1° |
| C5 | C5A | O4P | H5A2 | 125.2° | 120.0° |
| C5 | C5A | H5A1 | H5A2 | 117.6° | 120.0° |
| C5 | C5A | O4P | P | 178.7° | 180.0° |
| O4P | C5A | H5A1 | H5A2 | 117.5° | 119.9° |
| C5A | O4P | P | O1P | 145.3° | 60.0° |
| C5A | O4P | P | O2P | 94.0° | 180.0° |
| C5A | O4P | P | O3P | 22.1° | 59.9° |
| H5A1 | C5A | O4P | P | 53.5° | 59.9° |
| H5A2 | C5A | O4P | P | 56.1° | 60.1° |
| O4P | P | O1P | O2P | 113.3° | 120.0° |
| O4P | P | O1P | O3P | 121.1° | 120.0° |
| O4P | P | O2P | O3P | 117.9° | 120.1° |
| O4P | P | O2P | HOP2 | 180.0° | 180.0° |
| O4P | P | O3P | HOP3 | 180.0° | 60.1° |
| O1P | P | O2P | O3P | 128.4° | 120.0° |
| O1P | P | O2P | HOP2 | 66.3° | 60.1° |
| O1P | P | O3P | HOP3 | 62.3° | 180.0° |
| O2P | P | O3P | HOP3 | 66.5° | 60.0° |
| O3P | P | O2P | HOP2 | 62.1° | 59.9° |
| N | CA | CB | C | 123.8° | 120.0° |
| N | CA | CB | HA | 117.7° | 120.0° |
| N | CA | C | HA | 117.9° | 120.0° |
| N | CA | CB | CG | 56.3° | 60.0° |
| N | CA | CB | HB1 | 178.4° | 60.0° |
| N | CA | CB | HB2 | 69.0° | 180.0° |
| N | CA | C | O | 7.6° | 150.0° |
| N | CA | C | OXT | 175.0° | 30.0° |
| HN | N | CA | CB | 178.1° | 36.2° |
| HN | N | CA | C | 53.4° | 156.2° |
| HN | N | CA | HA | 65.3° | 83.8° |
| CB | CA | C | HA | 116.7° | 120.0° |
| CA | CB | CG | HB1 | 125.3° | 120.0° |
| CA | CB | CG | HB2 | 125.2° | 120.1° |
| CA | CB | HB1 | HB2 | 115.9° | 120.1° |
| CA | CB | CG | OD1 | 159.0° | 0.0° |
| CA | CB | CG | OD2 | 23.9° | 180.0° |
| CB | CA | C | O | 133.0° | 90.0° |
| CB | CA | C | OXT | 49.6° | 90.1° |
| C | CA | CB | CG | 67.4° | 180.0° |
| C | CA | CB | HB1 | 57.9° | 60.0° |
| C | CA | CB | HB2 | 167.3° | 60.0° |
| CA | C | O | OXT | 177.1° | 179.9° |
| CA | C | OXT | HXT | 179.9° | 180.0° |
| HA | CA | CB | CG | 174.0° | 60.1° |
| HA | CA | CB | HB1 | 60.7° | 180.0° |
| HA | CA | CB | HB2 | 48.7° | 59.9° |
| HA | CA | C | O | 110.3° | 30.0° |
| HA | CA | C | OXT | 67.0° | 150.0° |
| CG | CB | HB1 | HB2 | 116.0° | 120.0° |
| CB | CG | OD1 | OD2 | 177.1° | 179.9° |
| CB | CG | OD2 | HOD | 180.0° | 180.0° |
| HB1 | CB | CG | OD1 | 75.7° | 120.0° |
| HB1 | CB | CG | OD2 | 101.4° | 60.1° |
| HB2 | CB | CG | OD1 | 33.8° | 120.0° |
| HB2 | CB | CG | OD2 | 149.2° | 59.9° |
| OD1 | CG | OD2 | HOD | 3.1° | 0.1° |
| O | C | OXT | HXT | 2.8° | 0.0° |
