5VD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O19 | C4 | sing | 1.36Å | 1.35Å | |
| C3 | C4 | doub | 1.39Å | 1.38Å | Aromatic |
| C3 | C2 | sing | 1.38Å | 1.39Å | Aromatic |
| C4 | CE2 | sing | 1.40Å | 1.46Å | Aromatic |
| C2 | C1 | doub | 1.39Å | 1.38Å | Aromatic |
| O17 | CZ | doub | 1.22Å | 1.26Å | |
| CE2 | CZ | sing | 1.47Å | 1.48Å | |
| CE2 | CD2 | doub | 1.41Å | 1.48Å | Aromatic |
| C1 | CD2 | sing | 1.40Å | 1.48Å | Aromatic |
| C1 | O18 | sing | 1.36Å | 1.35Å | |
| CZ | CE1 | sing | 1.48Å | 1.47Å | |
| CD2 | CG | sing | 1.47Å | 1.48Å | |
| CE1 | C5 | sing | 1.39Å | 1.38Å | Aromatic |
| CE1 | CD1 | doub | 1.41Å | 1.48Å | Aromatic |
| C22 | O21 | sing | 1.45Å | 1.42Å | |
| CG | CD1 | sing | 1.47Å | 1.48Å | |
| CG | O16 | doub | 1.22Å | 1.25Å | |
| C5 | C6 | doub | 1.39Å | 1.38Å | Aromatic |
| CD1 | C8 | sing | 1.39Å | 1.46Å | Aromatic |
| O21 | C14 | sing | 1.34Å | 1.43Å | |
| O20 | C14 | doub | 1.21Å | 1.21Å | |
| C14 | C12 | sing | 1.51Å | 1.45Å | |
| C6 | C12 | sing | 1.51Å | 1.46Å | |
| C6 | C7 | sing | 1.38Å | 1.47Å | Aromatic |
| C12 | C11 | sing | 1.53Å | 1.55Å | |
| C8 | C7 | doub | 1.40Å | 1.45Å | Aromatic |
| C8 | O2 | sing | 1.36Å | 1.34Å | |
| C7 | C9 | sing | 1.51Å | 1.46Å | |
| C11 | C13 | sing | 1.53Å | 1.53Å | |
| C11 | C10 | sing | 1.54Å | 1.53Å | |
| C11 | O14 | sing | 1.43Å | 1.45Å | |
| C9 | C10 | sing | 1.53Å | 1.52Å | |
| C9 | O1 | sing | 1.43Å | 1.43Å | |
| C2 | H1 | sing | 1.08Å | 1.08Å | |
| O14 | H2 | sing | 0.97Å | 0.95Å | |
| C3 | H3 | sing | 1.08Å | 1.08Å | |
| C5 | H4 | sing | 1.08Å | 1.08Å | |
| C10 | H5 | sing | 1.09Å | 1.10Å | |
| C10 | H6 | sing | 1.09Å | 1.10Å | |
| C9 | H7 | sing | 1.09Å | 1.10Å | |
| C12 | H8 | sing | 1.09Å | 1.10Å | |
| O18 | H9 | sing | 0.97Å | 0.95Å | |
| O19 | H10 | sing | 0.97Å | 0.95Å | |
| C13 | H11 | sing | 1.09Å | 1.10Å | |
| C13 | H12 | sing | 1.09Å | 1.10Å | |
| C13 | H13 | sing | 1.09Å | 1.10Å | |
| C22 | H14 | sing | 1.09Å | 1.10Å | |
| C22 | H15 | sing | 1.09Å | 1.10Å | |
| C22 | H16 | sing | 1.09Å | 1.10Å | |
| O1 | H17 | sing | 0.97Å | 0.95Å | |
| O2 | H18 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O19 | C4 | C3 | 121.7° | 120.0° |
| O19 | C4 | CE2 | 118.9° | 120.0° |
| C4 | O19 | H10 | 109.5° | 114.0° |
| C4 | C3 | C2 | 123.2° | 120.5° |
| C3 | C4 | CE2 | 119.3° | 119.9° |
| C4 | C3 | H3 | 118.4° | 119.7° |
| C3 | C2 | C1 | 121.2° | 120.5° |
| C3 | C2 | H1 | 119.4° | 119.7° |
| C2 | C3 | H3 | 118.4° | 119.8° |
| C4 | CE2 | CZ | 119.4° | 120.3° |
| C4 | CE2 | CD2 | 118.1° | 119.6° |
| C2 | C1 | CD2 | 119.7° | 119.9° |
| C2 | C1 | O18 | 121.1° | 120.1° |
| C1 | C2 | H1 | 119.4° | 119.8° |
| O17 | CZ | CE2 | 121.6° | 120.1° |
| O17 | CZ | CE1 | 120.9° | 120.0° |
| CZ | CE2 | CD2 | 122.5° | 120.1° |
| CE2 | CZ | CE1 | 117.5° | 119.9° |
| CE2 | CD2 | C1 | 118.3° | 119.6° |
| CE2 | CD2 | CG | 120.1° | 120.1° |
| CD2 | C1 | O18 | 119.2° | 120.0° |
| C1 | CD2 | CG | 121.6° | 120.3° |
| C1 | O18 | H9 | 109.5° | 114.0° |
| CZ | CE1 | C5 | 118.8° | 120.6° |
| CZ | CE1 | CD1 | 120.1° | 120.0° |
| CD2 | CG | CD1 | 117.3° | 119.9° |
| CD2 | CG | O16 | 122.2° | 120.0° |
| C5 | CE1 | CD1 | 121.1° | 119.4° |
| CE1 | C5 | C6 | 120.6° | 120.7° |
| CE1 | C5 | H4 | 119.7° | 119.6° |
| CE1 | CD1 | CG | 122.5° | 120.1° |
| CE1 | CD1 | C8 | 119.1° | 119.4° |
| C22 | O21 | C14 | 117.0° | 117.0° |
| O21 | C22 | H14 | 109.5° | 109.5° |
| O21 | C22 | H15 | 109.5° | 109.4° |
| O21 | C22 | H16 | 109.5° | 109.5° |
| CD1 | CG | O16 | 120.4° | 120.1° |
| CG | CD1 | C8 | 118.5° | 120.5° |
| C5 | C6 | C12 | 118.7° | 117.4° |
| C5 | C6 | C7 | 122.2° | 120.1° |
| C6 | C5 | H4 | 119.7° | 119.7° |
| CD1 | C8 | C7 | 118.0° | 120.3° |
| CD1 | C8 | O2 | 121.5° | 119.8° |
| O21 | C14 | O20 | 124.3° | 120.0° |
| O21 | C14 | C12 | 112.5° | 120.0° |
| O20 | C14 | C12 | 123.2° | 120.0° |
| C14 | C12 | C6 | 115.5° | 109.3° |
| C14 | C12 | C11 | 116.4° | 109.2° |
| C14 | C12 | H8 | 104.2° | 109.2° |
| C12 | C6 | C7 | 119.0° | 122.5° |
| C6 | C12 | C11 | 111.3° | 110.7° |
| C6 | C12 | H8 | 104.1° | 109.2° |
| C6 | C7 | C8 | 118.9° | 120.0° |
| C6 | C7 | C9 | 123.8° | 122.6° |
| C12 | C11 | C13 | 111.5° | 109.7° |
| C12 | C11 | C10 | 107.4° | 108.3° |
| C12 | C11 | O14 | 111.6° | 109.8° |
| C11 | C12 | H8 | 103.4° | 109.2° |
| C7 | C8 | O2 | 120.5° | 119.8° |
| C8 | C7 | C9 | 117.2° | 117.4° |
| C8 | O2 | H18 | 109.5° | 114.0° |
| C7 | C9 | C10 | 112.8° | 110.6° |
| C7 | C9 | O1 | 102.9° | 109.2° |
| C7 | C9 | H7 | 111.0° | 109.2° |
| C13 | C11 | C10 | 109.9° | 109.6° |
| C13 | C11 | O14 | 105.6° | 109.7° |
| C11 | C13 | H11 | 109.5° | 109.5° |
| C11 | C13 | H12 | 109.5° | 109.4° |
| C11 | C13 | H13 | 109.5° | 109.5° |
| C10 | C11 | O14 | 110.9° | 109.7° |
| C11 | C10 | C9 | 111.8° | 108.3° |
| C11 | C10 | H5 | 108.9° | 109.7° |
| C11 | C10 | H6 | 108.9° | 109.8° |
| C11 | O14 | H2 | 109.5° | 114.0° |
| C10 | C9 | O1 | 108.4° | 109.3° |
| C9 | C10 | H5 | 108.9° | 109.7° |
| C9 | C10 | H6 | 108.9° | 109.7° |
| C10 | C9 | H7 | 110.2° | 109.2° |
| O1 | C9 | H7 | 111.5° | 109.2° |
| C9 | O1 | H17 | 109.5° | 114.0° |
| H5 | C10 | H6 | 109.4° | 109.7° |
| H11 | C13 | H12 | 109.5° | 109.5° |
| H11 | C13 | H13 | 109.5° | 109.5° |
| H12 | C13 | H13 | 109.4° | 109.5° |
| H14 | C22 | H15 | 109.5° | 109.5° |
| H14 | C22 | H16 | 109.4° | 109.5° |
| H15 | C22 | H16 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O19 | C4 | C3 | CE2 | 177.0° | 179.9° |
| O19 | C4 | C3 | C2 | 179.2° | 180.0° |
| O19 | C4 | CE2 | CZ | 0.2° | 0.1° |
| O19 | C4 | CE2 | CD2 | 179.9° | 180.0° |
| O19 | C4 | C3 | H3 | 0.9° | 0.0° |
| C4 | C3 | C2 | H3 | 180.0° | 179.9° |
| C4 | C3 | C2 | C1 | 3.6° | 0.0° |
| C3 | C4 | CE2 | CZ | 177.3° | 180.0° |
| C3 | C4 | CE2 | CD2 | 2.7° | 0.0° |
| C4 | C3 | C2 | H1 | 176.4° | 180.0° |
| C3 | C4 | O19 | H10 | 177.3° | 90.0° |
| C2 | C3 | C4 | CE2 | 3.8° | 0.0° |
| C3 | C2 | C1 | H1 | 180.0° | 180.0° |
| C3 | C2 | C1 | CD2 | 2.3° | 0.1° |
| C3 | C2 | C1 | O18 | 177.9° | 179.7° |
| C4 | CE2 | CZ | O17 | 0.1° | 0.0° |
| C4 | CE2 | CZ | CD2 | 179.9° | 180.0° |
| C4 | CE2 | CD2 | C1 | 1.6° | 0.0° |
| C4 | CE2 | CZ | CE1 | 179.1° | 180.0° |
| C4 | CE2 | CD2 | CG | 179.6° | 179.8° |
| CE2 | C4 | C3 | H3 | 176.2° | 179.9° |
| CE2 | C4 | O19 | H10 | 0.2° | 90.1° |
| C2 | C1 | CD2 | CE2 | 1.4° | 0.1° |
| C2 | C1 | CD2 | O18 | 179.8° | 179.8° |
| C2 | C1 | CD2 | CG | 179.8° | 179.8° |
| C1 | C2 | C3 | H3 | 176.3° | 180.0° |
| C2 | C1 | O18 | H9 | 178.7° | 89.7° |
| O17 | CZ | CE2 | CE1 | 179.2° | 180.0° |
| O17 | CZ | CE2 | CD2 | 179.9° | 179.9° |
| O17 | CZ | CE1 | C5 | 1.5° | 0.1° |
| O17 | CZ | CE1 | CD1 | 178.9° | 179.6° |
| CZ | CE2 | CD2 | C1 | 178.5° | 180.0° |
| CZ | CE2 | CD2 | CG | 0.3° | 0.2° |
| CE2 | CZ | CE1 | C5 | 177.7° | 179.9° |
| CE2 | CZ | CE1 | CD1 | 1.9° | 0.3° |
| CE2 | CD2 | C1 | CG | 178.8° | 179.7° |
| CE2 | CD2 | C1 | O18 | 178.8° | 179.7° |
| CD2 | CE2 | CZ | CE1 | 1.0° | 0.0° |
| CE2 | CD2 | CG | CD1 | 0.6° | 0.2° |
| CE2 | CD2 | CG | O16 | 178.3° | 179.8° |
| C1 | CD2 | CG | CD1 | 178.1° | 179.9° |
| C1 | CD2 | CG | O16 | 2.9° | 0.0° |
| CD2 | C1 | C2 | H1 | 177.7° | 180.0° |
| CD2 | C1 | O18 | H9 | 1.1° | 90.0° |
| O18 | C1 | CD2 | CG | 0.0° | 0.0° |
| O18 | C1 | C2 | H1 | 2.1° | 0.3° |
| CZ | CE1 | C5 | CD1 | 179.5° | 179.8° |
| CZ | CE1 | CD1 | CG | 1.6° | 0.4° |
| CZ | CE1 | C5 | C6 | 179.2° | 179.7° |
| CZ | CE1 | CD1 | C8 | 179.7° | 179.7° |
| CZ | CE1 | C5 | H4 | 0.9° | 0.2° |
| CD2 | CG | CD1 | CE1 | 0.3° | 0.1° |
| CD2 | CG | CD1 | O16 | 179.0° | 180.0° |
| CD2 | CG | CD1 | C8 | 179.0° | 179.9° |
| C5 | CE1 | CD1 | CG | 177.9° | 179.9° |
| CE1 | C5 | C6 | H4 | 180.0° | 179.9° |
| C5 | CE1 | CD1 | C8 | 0.8° | 0.1° |
| CE1 | C5 | C6 | C12 | 176.9° | 179.8° |
| CE1 | C5 | C6 | C7 | 0.5° | 0.1° |
| CE1 | CD1 | CG | C8 | 178.7° | 180.0° |
| CE1 | CD1 | CG | O16 | 179.3° | 179.9° |
| CD1 | CE1 | C5 | C6 | 1.3° | 0.1° |
| CE1 | CD1 | C8 | C7 | 0.6° | 0.1° |
| CE1 | CD1 | C8 | O2 | 179.4° | 179.9° |
| CD1 | CE1 | C5 | H4 | 178.7° | 180.0° |
| C22 | O21 | C14 | O20 | 4.1° | 0.0° |
| C22 | O21 | C14 | C12 | 177.3° | 180.0° |
| O21 | C22 | H14 | H15 | 120.0° | 120.0° |
| O21 | C22 | H14 | H16 | 120.0° | 120.0° |
| O21 | C22 | H15 | H16 | 120.0° | 120.0° |
| CG | CD1 | C8 | C7 | 179.3° | 180.0° |
| CG | CD1 | C8 | O2 | 1.9° | 0.0° |
| O16 | CG | CD1 | C8 | 2.0° | 0.0° |
| C5 | C6 | C12 | C14 | 73.8° | 41.9° |
| C5 | C6 | C12 | C7 | 176.5° | 179.8° |
| C5 | C6 | C12 | C11 | 150.6° | 162.3° |
| C5 | C6 | C7 | C8 | 0.9° | 0.2° |
| C5 | C6 | C7 | C9 | 177.6° | 179.3° |
| C5 | C6 | C12 | H8 | 39.9° | 77.5° |
| CD1 | C8 | C7 | C6 | 1.3° | 0.2° |
| CD1 | C8 | C7 | O2 | 178.8° | 180.0° |
| CD1 | C8 | C7 | C9 | 178.3° | 179.3° |
| CD1 | C8 | O2 | H18 | 0.9° | 90.0° |
| O21 | C14 | O20 | C12 | 178.4° | 180.0° |
| O21 | C14 | C12 | C6 | 128.7° | 146.9° |
| O21 | C14 | C12 | C11 | 98.0° | 91.9° |
| O21 | C14 | C12 | H8 | 15.1° | 27.5° |
| C14 | O21 | C22 | H14 | 180.0° | 60.0° |
| C14 | O21 | C22 | H15 | 60.0° | 180.0° |
| C14 | O21 | C22 | H16 | 60.0° | 60.0° |
| O20 | C14 | C12 | C6 | 49.9° | 33.2° |
| O20 | C14 | C12 | C11 | 83.4° | 88.0° |
| O20 | C14 | C12 | H8 | 163.5° | 152.6° |
| C14 | C12 | C6 | C11 | 135.6° | 120.4° |
| C14 | C12 | C6 | H8 | 113.7° | 119.4° |
| C14 | C12 | C6 | C7 | 109.7° | 138.3° |
| C14 | C12 | C11 | H8 | 113.6° | 119.3° |
| C14 | C12 | C11 | C13 | 43.1° | 51.9° |
| C14 | C12 | C11 | C10 | 77.4° | 171.6° |
| C14 | C12 | C11 | O14 | 160.9° | 68.7° |
| C6 | C12 | C11 | H8 | 111.2° | 120.3° |
| C12 | C6 | C7 | C8 | 175.5° | 179.6° |
| C12 | C6 | C7 | C9 | 1.2° | 0.8° |
| C6 | C12 | C11 | C13 | 178.3° | 68.4° |
| C6 | C12 | C11 | C10 | 57.8° | 51.2° |
| C6 | C12 | C11 | O14 | 63.9° | 170.9° |
| C12 | C6 | C5 | H4 | 3.1° | 0.3° |
| C7 | C6 | C12 | C11 | 25.9° | 17.9° |
| C6 | C7 | C8 | C9 | 176.9° | 179.6° |
| C6 | C7 | C8 | O2 | 179.8° | 179.8° |
| C6 | C7 | C9 | C10 | 4.8° | 17.9° |
| C6 | C7 | C9 | O1 | 111.7° | 138.2° |
| C7 | C6 | C5 | H4 | 179.5° | 179.8° |
| C6 | C7 | C9 | H7 | 129.0° | 102.4° |
| C7 | C6 | C12 | H8 | 136.6° | 102.4° |
| C12 | C11 | C13 | C10 | 119.0° | 118.8° |
| C12 | C11 | C13 | O14 | 121.3° | 120.7° |
| C12 | C11 | C10 | O14 | 122.1° | 119.8° |
| C12 | C11 | C10 | C9 | 65.4° | 69.9° |
| C12 | C11 | O14 | H2 | 180.0° | 179.4° |
| C12 | C11 | C10 | H5 | 174.2° | 170.4° |
| C12 | C11 | C10 | H6 | 54.9° | 49.8° |
| C12 | C11 | C13 | H11 | 180.0° | 171.7° |
| C12 | C11 | C13 | H12 | 60.0° | 68.4° |
| C12 | C11 | C13 | H13 | 60.0° | 51.6° |
| C8 | C7 | C9 | C10 | 178.4° | 162.5° |
| C8 | C7 | C9 | O1 | 65.1° | 42.2° |
| C8 | C7 | C9 | H7 | 54.2° | 77.2° |
| C7 | C8 | O2 | H18 | 179.7° | 90.0° |
| O2 | C8 | C7 | C9 | 2.9° | 0.6° |
| C7 | C9 | C10 | C11 | 38.5° | 51.2° |
| C7 | C9 | C10 | O1 | 113.2° | 120.3° |
| C7 | C9 | C10 | H7 | 124.6° | 120.3° |
| C7 | C9 | O1 | H7 | 119.0° | 119.4° |
| C7 | C9 | C10 | H5 | 158.8° | 170.9° |
| C7 | C9 | C10 | H6 | 81.9° | 68.6° |
| C7 | C9 | O1 | H17 | 180.0° | 175.9° |
| C13 | C11 | C10 | O14 | 116.4° | 120.5° |
| C13 | C11 | C10 | C9 | 173.1° | 49.8° |
| C13 | C11 | O14 | H2 | 58.7° | 60.0° |
| C13 | C11 | C10 | H5 | 52.7° | 69.9° |
| C13 | C11 | C10 | H6 | 66.5° | 169.5° |
| C13 | C11 | C12 | H8 | 70.5° | 171.3° |
| C11 | C13 | H11 | H12 | 120.0° | 120.0° |
| C11 | C13 | H11 | H13 | 120.0° | 120.0° |
| C11 | C13 | H12 | H13 | 120.0° | 120.0° |
| C11 | C10 | C9 | H5 | 120.4° | 119.7° |
| C11 | C10 | C9 | H6 | 120.3° | 119.8° |
| C11 | C10 | C9 | O1 | 74.7° | 171.5° |
| C10 | C11 | O14 | H2 | 60.4° | 60.5° |
| C11 | C10 | H5 | H6 | 118.9° | 120.6° |
| C11 | C10 | C9 | H7 | 163.1° | 69.1° |
| C10 | C11 | C12 | H8 | 169.0° | 69.1° |
| C10 | C11 | C13 | H11 | 61.0° | 52.8° |
| C10 | C11 | C13 | H12 | 179.0° | 172.8° |
| C10 | C11 | C13 | H13 | 59.0° | 67.2° |
| O14 | C11 | C10 | C9 | 56.7° | 170.3° |
| O14 | C11 | C10 | H5 | 63.7° | 50.6° |
| O14 | C11 | C10 | H6 | 177.1° | 70.0° |
| O14 | C11 | C12 | H8 | 47.3° | 50.6° |
| O14 | C11 | C13 | H11 | 58.7° | 67.7° |
| O14 | C11 | C13 | H12 | 61.3° | 52.3° |
| O14 | C11 | C13 | H13 | 178.7° | 172.3° |
| C10 | C9 | O1 | H7 | 121.4° | 119.4° |
| C9 | C10 | H5 | H6 | 118.9° | 120.5° |
| C10 | C9 | O1 | H17 | 60.4° | 54.7° |
| O1 | C9 | C10 | H5 | 45.7° | 68.8° |
| O1 | C9 | C10 | H6 | 164.9° | 51.7° |
| H1 | C2 | C3 | H3 | 3.7° | 0.1° |
| H5 | C10 | C9 | H7 | 76.5° | 50.6° |
| H6 | C10 | C9 | H7 | 42.8° | 171.1° |
| H7 | C9 | O1 | H17 | 61.0° | 64.7° |
| H11 | C13 | H12 | H13 | 120.0° | 120.0° |
| H14 | C22 | H15 | H16 | 120.0° | 120.0° |
