P5D
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C1 | CG | sing | 1.51Å | 1.50Å | |
| C1 | C2 | sing | 1.53Å | 1.54Å | |
| C1 | H1 | sing | 1.09Å | 1.10Å | |
| C1 | H1A | sing | 1.09Å | 1.10Å | |
| N1 | C2 | sing | 1.47Å | 1.48Å | |
| N1 | HN1 | sing | 1.01Å | 1.00Å | |
| N1 | HN1A | sing | 1.01Å | 1.00Å | |
| C2 | P3 | sing | 1.82Å | 1.82Å | |
| C2 | H2 | sing | 1.09Å | 1.10Å | |
| O32 | P3 | doub | 1.48Å | 1.58Å | |
| O31 | P3 | sing | 1.61Å | 1.50Å | |
| P3 | C4 | sing | 1.82Å | 1.80Å | |
| C4 | C5 | sing | 1.53Å | 1.56Å | |
| C4 | H4 | sing | 1.09Å | 1.10Å | |
| C4 | H4A | sing | 1.09Å | 1.10Å | |
| C6 | C5 | sing | 1.51Å | 1.54Å | |
| C5 | C7 | sing | 1.53Å | 1.53Å | |
| C5 | H5 | sing | 1.09Å | 1.10Å | |
| O62 | C6 | doub | 1.21Å | 1.26Å | |
| O61 | C6 | sing | 1.34Å | 1.23Å | |
| C7 | C8 | sing | 1.51Å | 1.53Å | |
| C7 | H7 | sing | 1.09Å | 1.10Å | |
| C7 | H7A | sing | 1.09Å | 1.10Å | |
| O81 | C8 | doub | 1.21Å | 1.24Å | |
| C8 | O82 | sing | 1.34Å | 1.24Å | |
| CD1 | CG | doub | 1.38Å | 1.39Å | Aromatic |
| CG | CD2 | sing | 1.38Å | 1.39Å | Aromatic |
| CE1 | CZ | doub | 1.38Å | 1.39Å | Aromatic |
| CZ | CE2 | sing | 1.38Å | 1.39Å | Aromatic |
| CZ | HZ | sing | 1.08Å | 1.08Å | |
| O31 | HO31 | sing | 0.97Å | 0.95Å | |
| O61 | HO61 | sing | 0.97Å | 0.95Å | |
| O82 | HO82 | sing | 0.97Å | 0.95Å | |
| CD1 | CE1 | sing | 1.38Å | 1.39Å | Aromatic |
| CD1 | HD1 | sing | 1.08Å | 1.08Å | |
| CD2 | CE2 | doub | 1.38Å | 1.39Å | Aromatic |
| CD2 | HD2 | sing | 1.08Å | 1.08Å | |
| CE1 | HE1 | sing | 1.08Å | 1.08Å | |
| CE2 | HE2 | sing | 1.08Å | 1.08Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CG | C1 | C2 | 115.3° | 109.5° |
| CG | C1 | H1 | 107.6° | 109.5° |
| CG | C1 | H1A | 107.6° | 109.5° |
| C1 | CG | CD1 | 119.8° | 119.9° |
| C1 | CG | CD2 | 120.9° | 120.0° |
| C2 | C1 | H1 | 107.6° | 109.5° |
| C2 | C1 | H1A | 107.6° | 109.5° |
| C1 | C2 | N1 | 111.0° | 109.4° |
| C1 | C2 | P3 | 112.4° | 109.4° |
| C1 | C2 | H2 | 105.0° | 109.5° |
| H1 | C1 | H1A | 111.3° | 109.4° |
| C2 | N1 | HN1 | 109.5° | 111.0° |
| C2 | N1 | HN1A | 109.5° | 111.0° |
| N1 | C2 | P3 | 104.8° | 109.5° |
| N1 | C2 | H2 | 112.6° | 109.5° |
| HN1 | N1 | HN1A | 109.5° | 111.0° |
| P3 | C2 | H2 | 111.2° | 109.5° |
| C2 | P3 | O32 | 109.0° | 109.5° |
| C2 | P3 | O31 | 106.2° | 109.5° |
| C2 | P3 | C4 | 108.9° | 109.4° |
| O32 | P3 | O31 | 109.5° | 109.5° |
| O32 | P3 | C4 | 111.9° | 109.4° |
| O31 | P3 | C4 | 111.1° | 109.4° |
| P3 | O31 | HO31 | 109.5° | 114.1° |
| P3 | C4 | C5 | 116.4° | 109.5° |
| P3 | C4 | H4 | 107.2° | 109.5° |
| P3 | C4 | H4A | 107.3° | 109.5° |
| C5 | C4 | H4 | 107.2° | 109.4° |
| C5 | C4 | H4A | 107.2° | 109.5° |
| C4 | C5 | C6 | 113.4° | 109.5° |
| C4 | C5 | C7 | 107.5° | 109.5° |
| C4 | C5 | H5 | 110.5° | 109.4° |
| H4 | C4 | H4A | 111.6° | 109.4° |
| C6 | C5 | C7 | 115.2° | 109.5° |
| C6 | C5 | H5 | 101.8° | 109.5° |
| C5 | C6 | O62 | 118.6° | 120.0° |
| C5 | C6 | O61 | 116.5° | 120.0° |
| C7 | C5 | H5 | 108.4° | 109.4° |
| C5 | C7 | C8 | 115.0° | 109.4° |
| C5 | C7 | H7 | 107.7° | 109.5° |
| C5 | C7 | H7A | 107.7° | 109.5° |
| O62 | C6 | O61 | 124.9° | 120.1° |
| C6 | O61 | HO61 | 109.5° | 117.0° |
| C8 | C7 | H7 | 107.7° | 109.5° |
| C8 | C7 | H7A | 107.7° | 109.5° |
| C7 | C8 | O81 | 117.5° | 120.0° |
| C7 | C8 | O82 | 116.3° | 120.0° |
| H7 | C7 | H7A | 111.2° | 109.5° |
| O81 | C8 | O82 | 126.2° | 120.0° |
| C8 | O82 | HO82 | 109.5° | 117.0° |
| CD1 | CG | CD2 | 119.3° | 120.0° |
| CG | CD1 | CE1 | 120.5° | 119.9° |
| CG | CD1 | HD1 | 119.7° | 120.0° |
| CG | CD2 | CE2 | 120.4° | 120.0° |
| CG | CD2 | HD2 | 119.8° | 120.0° |
| CE1 | CZ | CE2 | 120.2° | 120.0° |
| CE1 | CZ | HZ | 119.9° | 120.0° |
| CZ | CE1 | CD1 | 119.8° | 120.0° |
| CZ | CE1 | HE1 | 120.1° | 120.0° |
| CE2 | CZ | HZ | 119.9° | 120.1° |
| CZ | CE2 | CD2 | 119.8° | 120.0° |
| CZ | CE2 | HE2 | 120.1° | 120.0° |
| CE1 | CD1 | HD1 | 119.7° | 120.1° |
| CD1 | CE1 | HE1 | 120.1° | 120.0° |
| CE2 | CD2 | HD2 | 119.8° | 120.0° |
| CD2 | CE2 | HE2 | 120.1° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CG | C1 | C2 | H1 | 120.0° | 120.0° |
| CG | C1 | C2 | H1A | 120.0° | 120.0° |
| CG | C1 | H1 | H1A | 117.6° | 120.0° |
| CG | C1 | C2 | N1 | 82.6° | 180.0° |
| CG | C1 | C2 | P3 | 160.5° | 60.0° |
| CG | C1 | C2 | H2 | 39.4° | 60.0° |
| C1 | CG | CD1 | CD2 | 179.7° | 179.7° |
| C1 | CG | CD1 | CE1 | 180.0° | 180.0° |
| C1 | CG | CD1 | HD1 | 0.1° | 0.0° |
| C1 | CG | CD2 | CE2 | 180.0° | 180.0° |
| C1 | CG | CD2 | HD2 | 0.0° | 0.0° |
| C2 | C1 | H1 | H1A | 117.6° | 120.0° |
| C1 | C2 | N1 | P3 | 121.5° | 120.0° |
| C1 | C2 | N1 | H2 | 117.4° | 120.0° |
| C1 | C2 | N1 | HN1 | 180.0° | 60.0° |
| C1 | C2 | N1 | HN1A | 60.0° | 63.9° |
| C1 | C2 | P3 | H2 | 117.4° | 120.0° |
| C1 | C2 | P3 | O32 | 53.1° | 60.1° |
| C1 | C2 | P3 | O31 | 171.0° | 60.0° |
| C1 | C2 | P3 | C4 | 69.2° | 180.0° |
| C2 | C1 | CG | CD1 | 129.8° | 89.7° |
| C2 | C1 | CG | CD2 | 49.9° | 90.0° |
| H1 | C1 | C2 | N1 | 157.4° | 60.0° |
| H1 | C1 | C2 | P3 | 40.4° | 180.0° |
| H1 | C1 | C2 | H2 | 80.6° | 60.0° |
| H1 | C1 | CG | CD1 | 110.2° | 150.3° |
| H1 | C1 | CG | CD2 | 70.1° | 30.0° |
| H1A | C1 | C2 | N1 | 37.4° | 60.0° |
| H1A | C1 | C2 | P3 | 79.5° | 60.0° |
| H1A | C1 | C2 | H2 | 159.4° | 180.0° |
| H1A | C1 | CG | CD1 | 9.7° | 30.3° |
| H1A | C1 | CG | CD2 | 169.9° | 150.0° |
| C2 | N1 | HN1 | HN1A | 120.0° | 123.9° |
| N1 | C2 | P3 | H2 | 122.0° | 120.0° |
| N1 | C2 | P3 | O32 | 67.5° | 180.0° |
| N1 | C2 | P3 | O31 | 50.4° | 59.9° |
| N1 | C2 | P3 | C4 | 170.2° | 60.0° |
| HN1 | N1 | C2 | P3 | 58.5° | 60.0° |
| HN1 | N1 | C2 | H2 | 62.5° | 180.0° |
| HN1A | N1 | C2 | P3 | 61.5° | 176.1° |
| HN1A | N1 | C2 | H2 | 177.5° | 56.0° |
| C2 | P3 | O32 | O31 | 115.8° | 120.1° |
| C2 | P3 | O32 | C4 | 120.5° | 120.0° |
| C2 | P3 | O31 | C4 | 118.3° | 119.9° |
| C2 | P3 | C4 | C5 | 125.5° | 175.0° |
| C2 | P3 | C4 | H4 | 114.5° | 65.0° |
| C2 | P3 | C4 | H4A | 5.5° | 55.0° |
| C2 | P3 | O31 | HO31 | 117.6° | 59.9° |
| H2 | C2 | P3 | O32 | 170.6° | 60.0° |
| H2 | C2 | P3 | O31 | 71.5° | 180.0° |
| H2 | C2 | P3 | C4 | 48.2° | 60.0° |
| O32 | P3 | O31 | C4 | 124.1° | 120.0° |
| O32 | P3 | C4 | C5 | 4.9° | 55.0° |
| O32 | P3 | C4 | H4 | 124.9° | 175.0° |
| O32 | P3 | C4 | H4A | 115.1° | 65.0° |
| O32 | P3 | O31 | HO31 | 0.0° | 180.0° |
| O31 | P3 | C4 | C5 | 117.8° | 65.0° |
| O31 | P3 | C4 | H4 | 2.1° | 55.0° |
| O31 | P3 | C4 | H4A | 122.2° | 175.0° |
| P3 | C4 | C5 | H4 | 120.0° | 120.0° |
| P3 | C4 | C5 | H4A | 120.0° | 120.1° |
| P3 | C4 | H4 | H4A | 117.2° | 120.0° |
| P3 | C4 | C5 | C6 | 53.1° | 75.0° |
| P3 | C4 | C5 | C7 | 178.5° | 165.0° |
| P3 | C4 | C5 | H5 | 60.4° | 45.0° |
| C4 | P3 | O31 | HO31 | 124.1° | 60.0° |
| C5 | C4 | H4 | H4A | 117.1° | 119.9° |
| C4 | C5 | C6 | C7 | 124.4° | 120.0° |
| C4 | C5 | C6 | H5 | 118.6° | 120.0° |
| C4 | C5 | C7 | H5 | 119.4° | 119.9° |
| C4 | C5 | C6 | O62 | 9.5° | 0.0° |
| C4 | C5 | C6 | O61 | 170.2° | 179.9° |
| C4 | C5 | C7 | C8 | 70.9° | 174.9° |
| C4 | C5 | C7 | H7 | 169.0° | 65.1° |
| C4 | C5 | C7 | H7A | 49.1° | 55.0° |
| H4 | C4 | C5 | C6 | 66.9° | 45.1° |
| H4 | C4 | C5 | C7 | 61.5° | 75.0° |
| H4 | C4 | C5 | H5 | 179.6° | 165.1° |
| H4A | C4 | C5 | C6 | 173.1° | 164.9° |
| H4A | C4 | C5 | C7 | 58.4° | 44.9° |
| H4A | C4 | C5 | H5 | 59.6° | 75.0° |
| C6 | C5 | C7 | H5 | 113.2° | 120.1° |
| C5 | C6 | O62 | O61 | 179.7° | 180.0° |
| C6 | C5 | C7 | C8 | 161.7° | 65.0° |
| C6 | C5 | C7 | H7 | 41.6° | 55.0° |
| C6 | C5 | C7 | H7A | 78.3° | 175.0° |
| C5 | C6 | O61 | HO61 | 179.6° | 180.0° |
| C7 | C5 | C6 | O62 | 114.9° | 120.0° |
| C7 | C5 | C6 | O61 | 65.4° | 60.0° |
| C5 | C7 | C8 | H7 | 120.0° | 120.0° |
| C5 | C7 | C8 | H7A | 120.0° | 120.0° |
| C5 | C7 | H7 | H7A | 117.7° | 120.0° |
| C5 | C7 | C8 | O81 | 40.6° | 0.0° |
| C5 | C7 | C8 | O82 | 138.2° | 180.0° |
| H5 | C5 | C6 | O62 | 128.1° | 120.0° |
| H5 | C5 | C6 | O61 | 51.6° | 60.0° |
| H5 | C5 | C7 | C8 | 48.4° | 55.1° |
| H5 | C5 | C7 | H7 | 71.6° | 175.0° |
| H5 | C5 | C7 | H7A | 168.4° | 64.9° |
| O62 | C6 | O61 | HO61 | 0.0° | 0.1° |
| C8 | C7 | H7 | H7A | 117.7° | 120.0° |
| C7 | C8 | O81 | O82 | 178.6° | 180.0° |
| C7 | C8 | O82 | HO82 | 178.7° | 180.0° |
| H7 | C7 | C8 | O81 | 79.4° | 120.0° |
| H7 | C7 | C8 | O82 | 101.8° | 60.0° |
| H7A | C7 | C8 | O81 | 160.6° | 120.0° |
| H7A | C7 | C8 | O82 | 18.2° | 60.1° |
| O81 | C8 | O82 | HO82 | 0.0° | 0.0° |
| CG | CD1 | CE1 | CZ | 0.3° | 0.0° |
| CG | CD1 | CE1 | HD1 | 180.0° | 180.0° |
| CD1 | CG | CD2 | CE2 | 0.3° | 0.3° |
| CD1 | CG | CD2 | HD2 | 179.7° | 179.7° |
| CG | CD1 | CE1 | HE1 | 179.7° | 180.0° |
| CG | CD2 | CE2 | CZ | 0.2° | 0.0° |
| CD2 | CG | CD1 | CE1 | 0.4° | 0.3° |
| CD2 | CG | CD1 | HD1 | 179.6° | 179.7° |
| CG | CD2 | CE2 | HD2 | 180.0° | 180.0° |
| CG | CD2 | CE2 | HE2 | 179.8° | 179.7° |
| CE1 | CZ | CE2 | HZ | 180.0° | 179.7° |
| CZ | CE1 | CD1 | HE1 | 180.0° | 180.0° |
| CZ | CE1 | CD1 | HD1 | 179.7° | 180.0° |
| CE1 | CZ | CE2 | CD2 | 0.2° | 0.2° |
| CE1 | CZ | CE2 | HE2 | 179.9° | 180.0° |
| CE2 | CZ | CE1 | CD1 | 0.2° | 0.2° |
| CZ | CE2 | CD2 | HE2 | 180.0° | 179.8° |
| CZ | CE2 | CD2 | HD2 | 179.8° | 180.0° |
| CE2 | CZ | CE1 | HE1 | 179.8° | 179.7° |
| HZ | CZ | CE1 | CD1 | 179.8° | 180.0° |
| HZ | CZ | CE2 | CD2 | 179.8° | 180.0° |
| HZ | CZ | CE1 | HE1 | 0.2° | 0.0° |
| HZ | CZ | CE2 | HE2 | 0.1° | 0.3° |
| HD1 | CD1 | CE1 | HE1 | 0.3° | 0.0° |
| HD2 | CD2 | CE2 | HE2 | 0.2° | 0.3° |
