PYA
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C1 | C2 | doub | 1.37Å | 1.37Å | Aromatic |
| C1 | C1A | sing | 1.41Å | 1.38Å | Aromatic |
| C1 | H1 | sing | 1.08Å | 1.10Å | |
| C2 | C3 | sing | 1.39Å | 1.38Å | Aromatic |
| C2 | HC2 | sing | 1.08Å | 1.10Å | |
| C3 | N4 | doub | 1.31Å | 1.30Å | Aromatic |
| C3 | H3 | sing | 1.08Å | 1.10Å | |
| N4 | C4A | sing | 1.33Å | 1.32Å | Aromatic |
| C4A | C4B | sing | 1.47Å | 1.41Å | Aromatic |
| C4A | C1A | doub | 1.41Å | 1.43Å | Aromatic |
| C4B | N5 | doub | 1.33Å | 1.32Å | Aromatic |
| C4B | C8A | sing | 1.41Å | 1.42Å | Aromatic |
| N5 | C6 | sing | 1.31Å | 1.31Å | Aromatic |
| C6 | C7 | doub | 1.39Å | 1.39Å | Aromatic |
| C6 | CB | sing | 1.51Å | 1.55Å | |
| C7 | C8 | sing | 1.37Å | 1.37Å | Aromatic |
| C7 | H7 | sing | 1.08Å | 1.10Å | |
| C8 | C8A | doub | 1.41Å | 1.38Å | Aromatic |
| C8 | H8 | sing | 1.08Å | 1.10Å | |
| C8A | C9 | sing | 1.41Å | 1.39Å | Aromatic |
| C9 | C10 | doub | 1.35Å | 1.37Å | Aromatic |
| C9 | H9 | sing | 1.08Å | 1.10Å | |
| C10 | C1A | sing | 1.41Å | 1.38Å | Aromatic |
| C10 | H10 | sing | 1.08Å | 1.10Å | |
| CB | CA | sing | 1.53Å | 1.58Å | |
| CB | HB3 | sing | 1.09Å | 1.12Å | |
| CB | HB2 | sing | 1.09Å | 1.12Å | |
| CA | N | sing | 1.47Å | 1.49Å | |
| CA | C | sing | 1.51Å | 1.55Å | |
| CA | HA | sing | 1.09Å | 1.11Å | |
| N | H | sing | 1.01Å | 1.02Å | |
| N | H2 | sing | 1.01Å | 1.02Å | |
| C | O | doub | 1.21Å | 1.24Å | |
| C | OXT | sing | 1.34Å | 1.35Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C2 | C1 | C1A | 118.8° | 118.2° |
| C2 | C1 | H1 | 120.2° | 120.9° |
| C1 | C2 | C3 | 119.1° | 119.9° |
| C1 | C2 | HC2 | 120.2° | 120.1° |
| C1A | C1 | H1 | 121.0° | 120.9° |
| C1 | C1A | C4A | 118.9° | 118.8° |
| C1 | C1A | C10 | 120.5° | 121.0° |
| C3 | C2 | HC2 | 120.7° | 120.0° |
| C2 | C3 | N4 | 122.0° | 121.5° |
| C2 | C3 | H3 | 122.0° | 119.3° |
| N4 | C3 | H3 | 116.0° | 119.3° |
| C3 | N4 | C4A | 122.2° | 121.4° |
| N4 | C4A | C4B | 122.4° | 121.2° |
| N4 | C4A | C1A | 119.0° | 120.2° |
| C4B | C4A | C1A | 118.6° | 118.6° |
| C4A | C4B | N5 | 122.4° | 121.3° |
| C4A | C4B | C8A | 119.0° | 118.5° |
| C4A | C1A | C10 | 120.6° | 120.2° |
| N5 | C4B | C8A | 118.7° | 120.2° |
| C4B | N5 | C6 | 123.6° | 121.3° |
| C4B | C8A | C8 | 118.7° | 118.8° |
| C4B | C8A | C9 | 120.5° | 120.2° |
| N5 | C6 | C7 | 120.1° | 121.6° |
| N5 | C6 | CB | 119.2° | 119.2° |
| C7 | C6 | CB | 120.5° | 119.2° |
| C6 | C7 | C8 | 119.5° | 119.9° |
| C6 | C7 | H7 | 120.8° | 120.1° |
| C6 | CB | CA | 118.0° | 109.5° |
| C6 | CB | HB3 | 109.1° | 109.5° |
| C6 | CB | HB2 | 109.2° | 109.5° |
| C8 | C7 | H7 | 119.7° | 120.0° |
| C7 | C8 | C8A | 119.4° | 118.2° |
| C7 | C8 | H8 | 120.0° | 120.9° |
| C8A | C8 | H8 | 120.7° | 120.9° |
| C8 | C8A | C9 | 120.7° | 121.0° |
| C8A | C9 | C10 | 120.6° | 121.2° |
| C8A | C9 | H9 | 120.1° | 119.4° |
| C10 | C9 | H9 | 119.3° | 119.4° |
| C9 | C10 | C1A | 120.7° | 121.3° |
| C9 | C10 | H10 | 119.3° | 119.3° |
| C1A | C10 | H10 | 120.0° | 119.4° |
| CA | CB | HB3 | 109.2° | 109.4° |
| CA | CB | HB2 | 109.1° | 109.5° |
| CB | CA | N | 114.8° | 109.5° |
| CB | CA | C | 114.7° | 109.5° |
| CB | CA | HA | 101.2° | 109.5° |
| HB3 | CB | HB2 | 100.9° | 109.4° |
| N | CA | C | 108.4° | 109.5° |
| N | CA | HA | 108.6° | 109.5° |
| CA | N | H | 114.9° | 106.7° |
| CA | N | H2 | 110.2° | 106.7° |
| C | CA | HA | 108.7° | 109.5° |
| CA | C | O | 121.7° | 120.0° |
| CA | C | OXT | 114.1° | 120.0° |
| H | N | H2 | 110.3° | 106.7° |
| O | C | OXT | 124.2° | 120.0° |
| C | OXT | HXT | 114.1° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C2 | C1 | C1A | H1 | 180.0° | 179.9° |
| C1 | C2 | C3 | HC2 | 180.0° | 180.0° |
| C1 | C2 | C3 | N4 | 0.1° | 0.0° |
| C1 | C2 | C3 | H3 | 179.9° | 180.0° |
| C2 | C1 | C1A | C4A | 0.1° | 0.0° |
| C2 | C1 | C1A | C10 | 179.8° | 179.9° |
| C1A | C1 | C2 | C3 | 0.2° | 0.0° |
| C1A | C1 | C2 | HC2 | 179.8° | 180.0° |
| C1 | C1A | C4A | N4 | 0.0° | 0.0° |
| C1 | C1A | C4A | C4B | 180.0° | 180.0° |
| C1 | C1A | C4A | C10 | 179.9° | 179.9° |
| C1 | C1A | C10 | C9 | 179.6° | 180.0° |
| C1 | C1A | C10 | H10 | 0.4° | 0.1° |
| H1 | C1 | C2 | C3 | 179.9° | 179.9° |
| H1 | C1 | C2 | HC2 | 0.2° | 0.0° |
| H1 | C1 | C1A | C4A | 180.0° | 179.9° |
| H1 | C1 | C1A | C10 | 0.1° | 0.0° |
| C2 | C3 | N4 | H3 | 180.0° | 180.0° |
| C2 | C3 | N4 | C4A | 0.0° | 0.0° |
| HC2 | C2 | C3 | N4 | 179.8° | 180.0° |
| HC2 | C2 | C3 | H3 | 0.2° | 0.1° |
| C3 | N4 | C4A | C4B | 179.9° | 180.0° |
| C3 | N4 | C4A | C1A | 0.1° | 0.0° |
| H3 | C3 | N4 | C4A | 180.0° | 180.0° |
| N4 | C4A | C4B | C1A | 180.0° | 180.0° |
| N4 | C4A | C4B | N5 | 0.0° | 0.3° |
| N4 | C4A | C4B | C8A | 179.7° | 179.9° |
| N4 | C4A | C1A | C10 | 179.9° | 179.9° |
| C4A | C4B | N5 | C8A | 179.7° | 179.8° |
| C4A | C4B | N5 | C6 | 178.0° | 179.7° |
| C4A | C4B | C8A | C8 | 179.9° | 180.0° |
| C4A | C4B | C8A | C9 | 0.1° | 0.1° |
| C4B | C4A | C1A | C10 | 0.1° | 0.0° |
| C1A | C4A | C4B | N5 | 180.0° | 179.7° |
| C1A | C4A | C4B | C8A | 0.3° | 0.1° |
| C4A | C1A | C10 | C9 | 0.3° | 0.1° |
| C4A | C1A | C10 | H10 | 179.7° | 180.0° |
| C4B | N5 | C6 | C7 | 2.7° | 0.5° |
| C4B | N5 | C6 | CB | 177.1° | 179.7° |
| N5 | C4B | C8A | C8 | 0.2° | 0.2° |
| N5 | C4B | C8A | C9 | 179.8° | 179.7° |
| C8A | C4B | N5 | C6 | 2.3° | 0.5° |
| C4B | C8A | C8 | C7 | 1.4° | 0.0° |
| C4B | C8A | C8 | C9 | 180.0° | 179.9° |
| C4B | C8A | C8 | H8 | 178.6° | 180.0° |
| C4B | C8A | C9 | C10 | 0.3° | 0.2° |
| C4B | C8A | C9 | H9 | 179.7° | 180.0° |
| N5 | C6 | C7 | CB | 174.3° | 179.7° |
| N5 | C6 | C7 | C8 | 0.9° | 0.3° |
| N5 | C6 | C7 | H7 | 179.0° | 179.8° |
| N5 | C6 | CB | CA | 62.3° | 60.2° |
| N5 | C6 | CB | HB3 | 63.0° | 179.8° |
| N5 | C6 | CB | HB2 | 172.4° | 59.8° |
| C6 | C7 | C8 | H7 | 179.9° | 179.9° |
| C6 | C7 | C8 | C8A | 1.0° | 0.0° |
| C6 | C7 | C8 | H8 | 178.9° | 180.0° |
| C7 | C6 | CB | CA | 123.3° | 120.0° |
| C7 | C6 | CB | HB3 | 111.4° | 0.0° |
| C7 | C6 | CB | HB2 | 1.9° | 119.9° |
| CB | C6 | C7 | C8 | 175.2° | 180.0° |
| CB | C6 | C7 | H7 | 4.7° | 0.1° |
| C6 | CB | CA | HB3 | 125.2° | 120.0° |
| C6 | CB | CA | HB2 | 125.3° | 120.0° |
| C6 | CB | HB3 | HB2 | 114.9° | 120.0° |
| C6 | CB | CA | N | 106.9° | 60.0° |
| C6 | CB | CA | C | 126.6° | 180.0° |
| C6 | CB | CA | HA | 9.8° | 60.0° |
| C7 | C8 | C8A | H8 | 179.9° | 180.0° |
| C7 | C8 | C8A | C9 | 178.6° | 179.9° |
| H7 | C7 | C8 | C8A | 179.0° | 179.9° |
| H7 | C7 | C8 | H8 | 1.0° | 0.1° |
| C8 | C8A | C9 | C10 | 179.7° | 180.0° |
| C8 | C8A | C9 | H9 | 0.3° | 0.1° |
| H8 | C8 | C8A | C9 | 1.5° | 0.1° |
| C8A | C9 | C10 | H9 | 180.0° | 179.8° |
| C8A | C9 | C10 | C1A | 0.5° | 0.1° |
| C8A | C9 | C10 | H10 | 179.5° | 179.9° |
| C9 | C10 | C1A | H10 | 180.0° | 179.9° |
| H9 | C9 | C10 | C1A | 179.5° | 179.9° |
| H9 | C9 | C10 | H10 | 0.5° | 0.1° |
| CA | CB | HB3 | HB2 | 114.9° | 120.0° |
| CB | CA | N | C | 129.7° | 120.0° |
| CB | CA | N | HA | 112.4° | 120.0° |
| CB | CA | C | HA | 112.4° | 120.0° |
| CB | CA | N | H | 180.0° | 60.0° |
| CB | CA | N | H2 | 54.7° | 53.7° |
| CB | CA | C | O | 36.4° | 90.0° |
| CB | CA | C | OXT | 141.7° | 90.0° |
| HB3 | CB | CA | N | 127.9° | 60.0° |
| HB3 | CB | CA | C | 1.3° | 60.0° |
| HB3 | CB | CA | HA | 115.4° | 180.0° |
| HB2 | CB | CA | N | 18.4° | 179.9° |
| HB2 | CB | CA | C | 108.1° | 59.9° |
| HB2 | CB | CA | HA | 135.1° | 60.1° |
| N | CA | C | HA | 117.8° | 120.0° |
| CA | N | H | H2 | 125.3° | 113.7° |
| N | CA | C | O | 93.4° | 30.0° |
| N | CA | C | OXT | 88.4° | 149.9° |
| C | CA | N | H | 50.2° | 60.0° |
| C | CA | N | H2 | 175.5° | 173.8° |
| CA | C | O | OXT | 177.9° | 180.0° |
| CA | C | OXT | HXT | 180.0° | 180.0° |
| HA | CA | N | H | 67.7° | 180.0° |
| HA | CA | N | H2 | 57.6° | 66.2° |
| HA | CA | C | O | 148.8° | 150.0° |
| HA | CA | C | OXT | 29.4° | 29.9° |
| O | C | OXT | HXT | 1.9° | 0.0° |
