PYD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N1' | C2' | doub | 1.32Å | 1.36Å | Aromatic |
| N1' | C6' | sing | 1.32Å | 1.37Å | Aromatic |
| C2' | CM2 | sing | 1.51Å | 1.46Å | |
| C2' | N3' | sing | 1.32Å | 1.32Å | Aromatic |
| CM2 | HM21 | sing | 1.09Å | 1.12Å | |
| CM2 | HM22 | sing | 1.09Å | 1.12Å | |
| CM2 | HM23 | sing | 1.09Å | 1.11Å | |
| N3' | C4' | doub | 1.33Å | 1.38Å | Aromatic |
| C4' | N4' | sing | 1.38Å | 1.30Å | |
| C4' | C5' | sing | 1.40Å | 1.44Å | Aromatic |
| N4' | HN41 | sing | 0.97Å | 1.02Å | |
| N4' | HN42 | sing | 0.97Å | 1.02Å | |
| C5' | C6' | doub | 1.38Å | 1.36Å | Aromatic |
| C5' | C7' | sing | 1.51Å | 1.52Å | |
| C6' | HC6' | sing | 1.08Å | 1.10Å | |
| C7' | HC71 | sing | 1.09Å | 1.11Å | |
| C7' | HC72 | sing | 1.09Å | 1.12Å | |
| C7' | HC73 | sing | 1.09Å | 1.11Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C2' | N1' | C6' | 120.3° | 121.1° |
| N1' | C2' | CM2 | 116.7° | 119.1° |
| N1' | C2' | N3' | 122.5° | 121.8° |
| N1' | C6' | C5' | 121.3° | 119.2° |
| N1' | C6' | HC6' | 119.9° | 120.4° |
| CM2 | C2' | N3' | 120.7° | 119.1° |
| C2' | CM2 | HM21 | 116.7° | 109.5° |
| C2' | CM2 | HM22 | 109.5° | 109.4° |
| C2' | CM2 | HM23 | 109.6° | 109.5° |
| C2' | N3' | C4' | 118.2° | 120.7° |
| HM21 | CM2 | HM22 | 109.6° | 109.4° |
| HM21 | CM2 | HM23 | 109.6° | 109.5° |
| HM22 | CM2 | HM23 | 100.6° | 109.5° |
| N3' | C4' | N4' | 116.5° | 120.6° |
| N3' | C4' | C5' | 121.6° | 118.9° |
| N4' | C4' | C5' | 121.9° | 120.5° |
| C4' | N4' | HN41 | 116.6° | 120.0° |
| C4' | N4' | HN42 | 109.7° | 120.0° |
| C4' | C5' | C6' | 116.1° | 118.3° |
| C4' | C5' | C7' | 122.2° | 120.9° |
| HN41 | N4' | HN42 | 109.7° | 119.9° |
| C6' | C5' | C7' | 121.7° | 120.8° |
| C5' | C6' | HC6' | 118.8° | 120.4° |
| C5' | C7' | HC71 | 122.2° | 109.4° |
| C5' | C7' | HC72 | 107.7° | 109.5° |
| C5' | C7' | HC73 | 107.7° | 109.5° |
| HC71 | C7' | HC72 | 107.7° | 109.4° |
| HC71 | C7' | HC73 | 107.7° | 109.4° |
| HC72 | C7' | HC73 | 102.1° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| N1' | C2' | CM2 | N3' | 180.0° | 179.8° |
| N1' | C2' | CM2 | HM21 | 180.0° | 90.0° |
| N1' | C2' | CM2 | HM22 | 54.8° | 150.1° |
| N1' | C2' | CM2 | HM23 | 54.7° | 30.1° |
| N1' | C2' | N3' | C4' | 0.9° | 0.5° |
| C2' | N1' | C6' | C5' | 0.6° | 0.0° |
| C2' | N1' | C6' | HC6' | 179.4° | 180.0° |
| C6' | N1' | C2' | CM2 | 178.8° | 180.0° |
| C6' | N1' | C2' | N3' | 1.3° | 0.2° |
| N1' | C6' | C5' | C4' | 0.3° | 0.0° |
| N1' | C6' | C5' | HC6' | 179.9° | 180.0° |
| N1' | C6' | C5' | C7' | 179.9° | 180.0° |
| C2' | CM2 | HM21 | HM22 | 125.2° | 120.0° |
| C2' | CM2 | HM21 | HM23 | 125.3° | 120.1° |
| C2' | CM2 | HM22 | HM23 | 115.4° | 120.0° |
| CM2 | C2' | N3' | C4' | 179.1° | 179.7° |
| N3' | C2' | CM2 | HM21 | 0.0° | 90.2° |
| N3' | C2' | CM2 | HM22 | 125.2° | 29.8° |
| N3' | C2' | CM2 | HM23 | 125.3° | 149.8° |
| C2' | N3' | C4' | N4' | 179.7° | 179.8° |
| C2' | N3' | C4' | C5' | 0.0° | 0.5° |
| HM21 | CM2 | HM22 | HM23 | 115.4° | 120.0° |
| N3' | C4' | N4' | C5' | 179.7° | 179.7° |
| N3' | C4' | N4' | HN41 | 179.9° | 0.3° |
| N3' | C4' | N4' | HN42 | 54.7° | 179.7° |
| N3' | C4' | C5' | C6' | 0.6° | 0.3° |
| N3' | C4' | C5' | C7' | 179.6° | 179.8° |
| C4' | N4' | HN41 | HN42 | 125.4° | 179.9° |
| N4' | C4' | C5' | C6' | 179.7° | 180.0° |
| N4' | C4' | C5' | C7' | 0.0° | 0.0° |
| C5' | C4' | N4' | HN41 | 0.2° | 180.0° |
| C5' | C4' | N4' | HN42 | 125.6° | 0.0° |
| C4' | C5' | C6' | C7' | 179.7° | 180.0° |
| C4' | C5' | C6' | HC6' | 179.7° | 180.0° |
| C4' | C5' | C7' | HC71 | 180.0° | 90.0° |
| C4' | C5' | C7' | HC72 | 54.7° | 29.9° |
| C4' | C5' | C7' | HC73 | 54.7° | 150.0° |
| C6' | C5' | C7' | HC71 | 0.3° | 90.0° |
| C6' | C5' | C7' | HC72 | 125.5° | 150.0° |
| C6' | C5' | C7' | HC73 | 125.0° | 29.9° |
| C7' | C5' | C6' | HC6' | 0.0° | 0.0° |
| C5' | C7' | HC71 | HC72 | 125.2° | 120.0° |
| C5' | C7' | HC71 | HC73 | 125.3° | 120.0° |
| C5' | C7' | HC72 | HC73 | 113.2° | 120.1° |
| HC71 | C7' | HC72 | HC73 | 113.2° | 119.9° |
