PYP
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | O1P | doub | 1.48Å | 1.48Å | |
| P | O2P | sing | 1.61Å | 1.48Å | |
| P | O5' | sing | 1.61Å | 1.62Å | |
| P | O3P | sing | 1.61Å | 11.64Å | |
| O2P | HOP2 | sing | 0.97Å | 0.95Å | |
| O5' | C5' | sing | 1.43Å | 1.44Å | |
| C5' | C4' | sing | 1.53Å | 1.53Å | |
| C5' | H5'1 | sing | 1.09Å | 1.10Å | |
| C5' | H5'2 | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.45Å | |
| C4' | C3' | sing | 1.54Å | 1.53Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.44Å | 1.44Å | |
| C1' | C10 | sing | 1.51Å | 1.54Å | |
| C1' | C2' | sing | 1.55Å | 1.53Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C1 | C2 | doub | 1.32Å | 1.41Å | Aromatic |
| C1 | C10 | sing | 1.47Å | 1.45Å | Aromatic |
| C1 | H1 | sing | 1.08Å | 1.08Å | |
| C2 | C12 | sing | 1.47Å | 1.44Å | Aromatic |
| C2 | H2 | sing | 1.08Å | 1.08Å | |
| C3 | C4 | doub | 1.32Å | 1.41Å | Aromatic |
| C3 | C12 | sing | 1.47Å | 1.44Å | Aromatic |
| C3 | H3 | sing | 1.08Å | 1.08Å | |
| C4 | C13 | sing | 1.47Å | 1.45Å | Aromatic |
| C4 | H4 | sing | 1.08Å | 1.08Å | |
| C5 | C6 | doub | 1.32Å | 1.41Å | Aromatic |
| C5 | C13 | sing | 1.47Å | 1.45Å | Aromatic |
| C5 | H5 | sing | 1.08Å | 1.08Å | |
| C6 | C7 | sing | 1.47Å | 1.41Å | Aromatic |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C7 | C14 | doub | 1.31Å | 1.45Å | Aromatic |
| C7 | H7 | sing | 1.08Å | 1.08Å | |
| C8 | C9 | doub | 1.31Å | 1.41Å | Aromatic |
| C8 | C14 | sing | 1.47Å | 1.44Å | Aromatic |
| C8 | H8 | sing | 1.08Å | 1.08Å | |
| C9 | C11 | sing | 1.47Å | 1.46Å | Aromatic |
| C9 | H9 | sing | 1.08Å | 1.08Å | |
| C10 | C11 | doub | 1.31Å | 1.39Å | Aromatic |
| C11 | C15 | sing | 1.47Å | 1.40Å | Aromatic |
| C12 | C15 | doub | 1.31Å | 1.39Å | Aromatic |
| C13 | C16 | doub | 1.31Å | 1.39Å | Aromatic |
| C14 | C16 | sing | 1.47Å | 1.39Å | Aromatic |
| C15 | C16 | sing | 1.47Å | 1.40Å | Aromatic |
| C2' | C3' | sing | 1.55Å | 1.56Å | |
| C2' | H2'2 | sing | 1.09Å | 1.10Å | |
| C2' | H2'1 | sing | 1.09Å | 1.10Å | |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | H3T | sing | 0.97Å | 0.95Å | |
| O3P | HOP3 | sing | 0.97Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O1P | P | O2P | 119.6° | 109.5° |
| O1P | P | O5' | 108.9° | 109.5° |
| O1P | P | O3P | 93.8° | 109.5° |
| O2P | P | O5' | 108.0° | 109.5° |
| O2P | P | O3P | 130.7° | 109.5° |
| P | O2P | HOP2 | 109.5° | 114.0° |
| O5' | P | O3P | 91.7° | 109.4° |
| P | O5' | C5' | 125.7° | 123.0° |
| P | O3P | HOP3 | 90.0° | 114.0° |
| O5' | C5' | C4' | 112.7° | 109.4° |
| O5' | C5' | H5'1 | 108.4° | 109.5° |
| O5' | C5' | H5'2 | 107.7° | 109.5° |
| C4' | C5' | H5'1 | 108.4° | 109.5° |
| C4' | C5' | H5'2 | 107.7° | 109.5° |
| C5' | C4' | O4' | 109.3° | 109.9° |
| C5' | C4' | C3' | 112.8° | 109.8° |
| C5' | C4' | H4' | 106.2° | 109.9° |
| H5'1 | C5' | H5'2 | 112.0° | 109.5° |
| O4' | C4' | C3' | 105.8° | 107.3° |
| O4' | C4' | H4' | 113.2° | 109.9° |
| C4' | O4' | C1' | 108.4° | 107.0° |
| C3' | C4' | H4' | 109.7° | 110.0° |
| C4' | C3' | C2' | 100.2° | 104.1° |
| C4' | C3' | O3' | 110.3° | 110.5° |
| C4' | C3' | H3' | 114.9° | 110.5° |
| O4' | C1' | C10 | 114.4° | 110.7° |
| O4' | C1' | C2' | 104.5° | 103.5° |
| O4' | C1' | H1' | 111.4° | 110.6° |
| C10 | C1' | C2' | 114.2° | 110.6° |
| C10 | C1' | H1' | 101.1° | 110.5° |
| C1' | C10 | C1 | 117.7° | 120.0° |
| C1' | C10 | C11 | 122.8° | 120.1° |
| C2' | C1' | H1' | 111.6° | 110.7° |
| C1' | C2' | C3' | 97.8° | 102.1° |
| C1' | C2' | H2'2 | 113.6° | 110.9° |
| C1' | C2' | H2'1 | 115.9° | 110.9° |
| C2 | C1 | C10 | 119.4° | 120.6° |
| C2 | C1 | H1 | 120.3° | 119.7° |
| C1 | C2 | C12 | 118.7° | 119.7° |
| C1 | C2 | H2 | 120.6° | 120.1° |
| C10 | C1 | H1 | 120.3° | 119.7° |
| C1 | C10 | C11 | 119.5° | 119.8° |
| C12 | C2 | H2 | 120.7° | 120.2° |
| C2 | C12 | C3 | 116.8° | 121.0° |
| C2 | C12 | C15 | 121.3° | 119.4° |
| C4 | C3 | C12 | 118.6° | 120.1° |
| C4 | C3 | H3 | 120.7° | 119.9° |
| C3 | C4 | C13 | 118.5° | 120.1° |
| C3 | C4 | H4 | 120.7° | 119.9° |
| C12 | C3 | H3 | 120.7° | 119.9° |
| C3 | C12 | C15 | 121.9° | 119.6° |
| C13 | C4 | H4 | 120.7° | 119.9° |
| C4 | C13 | C5 | 117.8° | 121.0° |
| C4 | C13 | C16 | 120.8° | 119.5° |
| C6 | C5 | C13 | 119.7° | 119.7° |
| C6 | C5 | H5 | 120.2° | 120.2° |
| C5 | C6 | C7 | 118.9° | 120.6° |
| C5 | C6 | H6 | 120.6° | 119.7° |
| C13 | C5 | H5 | 120.1° | 120.1° |
| C5 | C13 | C16 | 121.5° | 119.4° |
| C7 | C6 | H6 | 120.5° | 119.8° |
| C6 | C7 | C14 | 119.5° | 119.8° |
| C6 | C7 | H7 | 120.3° | 120.0° |
| C14 | C7 | H7 | 120.3° | 120.2° |
| C7 | C14 | C8 | 117.0° | 121.4° |
| C7 | C14 | C16 | 122.1° | 119.3° |
| C9 | C8 | C14 | 118.6° | 122.2° |
| C9 | C8 | H8 | 120.7° | 119.0° |
| C8 | C9 | C11 | 120.0° | 122.2° |
| C8 | C9 | H9 | 120.0° | 119.0° |
| C14 | C8 | H8 | 120.7° | 118.9° |
| C8 | C14 | C16 | 120.9° | 119.3° |
| C11 | C9 | H9 | 120.0° | 118.8° |
| C9 | C11 | C10 | 119.8° | 121.4° |
| C9 | C11 | C15 | 118.7° | 119.4° |
| C10 | C11 | C15 | 121.5° | 119.3° |
| C11 | C15 | C12 | 119.7° | 121.3° |
| C11 | C15 | C16 | 121.3° | 118.5° |
| C12 | C15 | C16 | 119.0° | 120.3° |
| C13 | C16 | C14 | 118.4° | 121.2° |
| C13 | C16 | C15 | 121.2° | 120.3° |
| C14 | C16 | C15 | 120.5° | 118.5° |
| C3' | C2' | H2'2 | 113.6° | 110.8° |
| C3' | C2' | H2'1 | 115.9° | 110.9° |
| C2' | C3' | O3' | 109.7° | 110.5° |
| C2' | C3' | H3' | 115.5° | 110.5° |
| H2'2 | C2' | H2'1 | 100.9° | 110.9° |
| O3' | C3' | H3' | 106.2° | 110.6° |
| C3' | O3' | H3T | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1P | P | O2P | O5' | 125.1° | 120.0° |
| O1P | P | O2P | O3P | 126.2° | 120.1° |
| O1P | P | O5' | O3P | 94.6° | 120.0° |
| O1P | P | O2P | HOP2 | 15.6° | 180.0° |
| O1P | P | O5' | C5' | 16.2° | 55.0° |
| O1P | P | O3P | HOP3 | 90.0° | 60.0° |
| O2P | P | O5' | O3P | 134.1° | 120.0° |
| O2P | P | O5' | C5' | 115.1° | 65.0° |
| O2P | P | O3P | HOP3 | 90.0° | 60.0° |
| O5' | P | O2P | HOP2 | 109.6° | 60.1° |
| P | O5' | C5' | C4' | 61.3° | 180.0° |
| P | O5' | C5' | H5'1 | 178.7° | 60.0° |
| P | O5' | C5' | H5'2 | 57.3° | 60.0° |
| O5' | P | O3P | HOP3 | 90.0° | 180.0° |
| O3P | P | O2P | HOP2 | 141.8° | 59.9° |
| O3P | P | O5' | C5' | 110.8° | 175.0° |
| O5' | C5' | C4' | H5'1 | 120.0° | 120.0° |
| O5' | C5' | C4' | H5'2 | 118.6° | 120.0° |
| O5' | C5' | H5'1 | H5'2 | 118.7° | 120.0° |
| O5' | C5' | C4' | O4' | 58.5° | 66.5° |
| O5' | C5' | C4' | C3' | 175.8° | 175.7° |
| O5' | C5' | C4' | H4' | 64.0° | 54.6° |
| C4' | C5' | H5'1 | H5'2 | 118.7° | 120.0° |
| C5' | C4' | O4' | C3' | 121.7° | 119.4° |
| C5' | C4' | O4' | H4' | 118.2° | 121.1° |
| C5' | C4' | C3' | H4' | 118.2° | 121.1° |
| C5' | C4' | O4' | C1' | 117.9° | 145.9° |
| C5' | C4' | C3' | C2' | 88.0° | 121.5° |
| C5' | C4' | C3' | O3' | 156.4° | 119.9° |
| C5' | C4' | C3' | H3' | 36.4° | 2.8° |
| H5'1 | C5' | C4' | O4' | 61.5° | 53.5° |
| H5'1 | C5' | C4' | C3' | 55.9° | 64.3° |
| H5'1 | C5' | C4' | H4' | 176.0° | 174.6° |
| H5'2 | C5' | C4' | O4' | 177.1° | 173.5° |
| H5'2 | C5' | C4' | C3' | 65.5° | 55.7° |
| H5'2 | C5' | C4' | H4' | 54.6° | 65.4° |
| O4' | C4' | C3' | H4' | 122.4° | 119.5° |
| C4' | O4' | C1' | C10 | 151.9° | 158.6° |
| C4' | O4' | C1' | C2' | 26.3° | 40.0° |
| C4' | O4' | C1' | H1' | 94.2° | 78.6° |
| O4' | C4' | C3' | C2' | 31.4° | 2.0° |
| O4' | C4' | C3' | O3' | 84.2° | 120.7° |
| O4' | C4' | C3' | H3' | 155.8° | 116.6° |
| C3' | C4' | O4' | C1' | 3.8° | 26.5° |
| C4' | C3' | C2' | C1' | 44.9° | 20.9° |
| C4' | C3' | C2' | O3' | 116.1° | 118.7° |
| C4' | C3' | C2' | H3' | 124.0° | 118.6° |
| C4' | C3' | C2' | H2'2 | 164.9° | 139.1° |
| C4' | C3' | C2' | H2'1 | 79.0° | 97.3° |
| C4' | C3' | O3' | H3' | 125.1° | 122.6° |
| C4' | C3' | O3' | H3T | 94.2° | 180.0° |
| H4' | C4' | O4' | C1' | 123.9° | 93.1° |
| H4' | C4' | C3' | C2' | 153.8° | 117.5° |
| H4' | C4' | C3' | O3' | 38.2° | 1.2° |
| H4' | C4' | C3' | H3' | 81.8° | 123.9° |
| O4' | C1' | C10 | C2' | 120.3° | 114.1° |
| O4' | C1' | C10 | H1' | 119.8° | 122.8° |
| O4' | C1' | C2' | H1' | 120.5° | 118.5° |
| O4' | C1' | C10 | C1 | 46.5° | 23.6° |
| O4' | C1' | C10 | C11 | 132.4° | 156.4° |
| O4' | C1' | C2' | C3' | 44.5° | 37.0° |
| O4' | C1' | C2' | H2'2 | 164.4° | 155.2° |
| O4' | C1' | C2' | H2'1 | 79.4° | 81.2° |
| C10 | C1' | C2' | H1' | 113.8° | 122.9° |
| C1' | C10 | C1 | C2 | 178.9° | 180.0° |
| C1' | C10 | C1 | C11 | 179.0° | 180.0° |
| C1' | C10 | C1 | H1 | 1.2° | 0.2° |
| C1' | C10 | C11 | C9 | 1.4° | 0.0° |
| C1' | C10 | C11 | C15 | 178.7° | 180.0° |
| C10 | C1' | C2' | C3' | 170.2° | 155.6° |
| C10 | C1' | C2' | H2'2 | 69.8° | 86.3° |
| C10 | C1' | C2' | H2'1 | 46.3° | 37.4° |
| C2' | C1' | C10 | C1 | 73.8° | 90.5° |
| C2' | C1' | C10 | C11 | 107.3° | 89.5° |
| C1' | C2' | C3' | H2'2 | 120.0° | 118.2° |
| C1' | C2' | C3' | H2'1 | 123.9° | 118.2° |
| C1' | C2' | H2'2 | H2'1 | 124.7° | 123.7° |
| C1' | C2' | C3' | O3' | 71.2° | 97.8° |
| C1' | C2' | C3' | H3' | 168.9° | 139.5° |
| H1' | C1' | C10 | C1 | 166.3° | 146.4° |
| H1' | C1' | C10 | C11 | 12.6° | 33.6° |
| H1' | C1' | C2' | C3' | 76.0° | 81.5° |
| H1' | C1' | C2' | H2'2 | 44.0° | 36.6° |
| H1' | C1' | C2' | H2'1 | 160.1° | 160.3° |
| C2 | C1 | C10 | H1 | 180.0° | 179.7° |
| C1 | C2 | C12 | H2 | 180.0° | 179.9° |
| C1 | C2 | C12 | C3 | 179.9° | 180.0° |
| C2 | C1 | C10 | C11 | 0.1° | 0.0° |
| C1 | C2 | C12 | C15 | 0.1° | 0.0° |
| C10 | C1 | C2 | C12 | 0.0° | 0.0° |
| C10 | C1 | C2 | H2 | 180.0° | 179.9° |
| C1 | C10 | C11 | C9 | 179.7° | 180.0° |
| C1 | C10 | C11 | C15 | 0.2° | 0.0° |
| H1 | C1 | C2 | C12 | 180.0° | 179.8° |
| H1 | C1 | C2 | H2 | 0.0° | 0.4° |
| H1 | C1 | C10 | C11 | 179.9° | 179.8° |
| C2 | C12 | C3 | C4 | 179.9° | 180.0° |
| C2 | C12 | C3 | C15 | 180.0° | 180.0° |
| C2 | C12 | C3 | H3 | 0.1° | 0.1° |
| C2 | C12 | C15 | C11 | 0.0° | 0.0° |
| C2 | C12 | C15 | C16 | 179.9° | 180.0° |
| H2 | C2 | C12 | C3 | 0.1° | 0.1° |
| H2 | C2 | C12 | C15 | 179.9° | 179.9° |
| C4 | C3 | C12 | H3 | 180.0° | 179.9° |
| C3 | C4 | C13 | H4 | 180.0° | 180.0° |
| C3 | C4 | C13 | C5 | 179.8° | 180.0° |
| C4 | C3 | C12 | C15 | 0.1° | 0.1° |
| C3 | C4 | C13 | C16 | 0.2° | 0.1° |
| C12 | C3 | C4 | C13 | 0.1° | 0.1° |
| C12 | C3 | C4 | H4 | 179.9° | 180.0° |
| C3 | C12 | C15 | C11 | 179.9° | 180.0° |
| C3 | C12 | C15 | C16 | 0.1° | 0.0° |
| H3 | C3 | C4 | C13 | 179.9° | 180.0° |
| H3 | C3 | C4 | H4 | 0.1° | 0.1° |
| H3 | C3 | C12 | C15 | 179.9° | 179.9° |
| C4 | C13 | C5 | C6 | 179.8° | 180.0° |
| C4 | C13 | C5 | C16 | 180.0° | 179.9° |
| C4 | C13 | C5 | H5 | 0.1° | 0.0° |
| C4 | C13 | C16 | C14 | 179.9° | 180.0° |
| C4 | C13 | C16 | C15 | 0.2° | 0.0° |
| H4 | C4 | C13 | C5 | 0.2° | 0.0° |
| H4 | C4 | C13 | C16 | 179.8° | 180.0° |
| C6 | C5 | C13 | H5 | 180.0° | 179.9° |
| C5 | C6 | C7 | H6 | 180.0° | 180.0° |
| C5 | C6 | C7 | C14 | 0.0° | 0.0° |
| C5 | C6 | C7 | H7 | 180.0° | 180.0° |
| C6 | C5 | C13 | C16 | 0.2° | 0.1° |
| C13 | C5 | C6 | C7 | 0.1° | 0.1° |
| C13 | C5 | C6 | H6 | 179.8° | 180.0° |
| C5 | C13 | C16 | C14 | 0.1° | 0.0° |
| C5 | C13 | C16 | C15 | 179.8° | 180.0° |
| H5 | C5 | C6 | C7 | 179.9° | 180.0° |
| H5 | C5 | C6 | H6 | 0.1° | 0.1° |
| H5 | C5 | C13 | C16 | 179.9° | 180.0° |
| C6 | C7 | C14 | H7 | 180.0° | 180.0° |
| C6 | C7 | C14 | C8 | 179.9° | 179.9° |
| C6 | C7 | C14 | C16 | 0.1° | 0.1° |
| H6 | C6 | C7 | C14 | 180.0° | 179.9° |
| H6 | C6 | C7 | H7 | 0.0° | 0.0° |
| C7 | C14 | C8 | C9 | 180.0° | 180.0° |
| C7 | C14 | C8 | C16 | 179.9° | 179.9° |
| C7 | C14 | C8 | H8 | 0.0° | 0.1° |
| C7 | C14 | C16 | C13 | 0.1° | 0.0° |
| C7 | C14 | C16 | C15 | 179.9° | 180.0° |
| H7 | C7 | C14 | C8 | 0.0° | 0.1° |
| H7 | C7 | C14 | C16 | 179.9° | 180.0° |
| C9 | C8 | C14 | H8 | 180.0° | 179.9° |
| C8 | C9 | C11 | H9 | 180.0° | 179.9° |
| C8 | C9 | C11 | C10 | 179.9° | 179.9° |
| C8 | C9 | C11 | C15 | 0.2° | 0.0° |
| C9 | C8 | C14 | C16 | 0.1° | 0.1° |
| C14 | C8 | C9 | C11 | 0.1° | 0.1° |
| C14 | C8 | C9 | H9 | 179.9° | 180.0° |
| C8 | C14 | C16 | C13 | 180.0° | 179.9° |
| C8 | C14 | C16 | C15 | 0.1° | 0.1° |
| H8 | C8 | C9 | C11 | 179.9° | 180.0° |
| H8 | C8 | C9 | H9 | 0.1° | 0.1° |
| H8 | C8 | C14 | C16 | 180.0° | 180.0° |
| C9 | C11 | C10 | C15 | 179.9° | 179.9° |
| C9 | C11 | C15 | C12 | 179.8° | 180.0° |
| C9 | C11 | C15 | C16 | 0.2° | 0.0° |
| H9 | C9 | C11 | C10 | 0.1° | 0.0° |
| H9 | C9 | C11 | C15 | 179.8° | 180.0° |
| C10 | C11 | C15 | C12 | 0.1° | 0.0° |
| C10 | C11 | C15 | C16 | 179.9° | 180.0° |
| C11 | C15 | C12 | C16 | 180.0° | 180.0° |
| C11 | C15 | C16 | C13 | 179.9° | 180.0° |
| C11 | C15 | C16 | C14 | 0.0° | 0.0° |
| C12 | C15 | C16 | C13 | 0.2° | 0.0° |
| C12 | C15 | C16 | C14 | 180.0° | 180.0° |
| C13 | C16 | C14 | C15 | 179.9° | 180.0° |
| C3' | C2' | H2'2 | H2'1 | 124.7° | 123.6° |
| C2' | C3' | O3' | H3' | 125.4° | 122.7° |
| C2' | C3' | O3' | H3T | 15.4° | 65.2° |
| H2'2 | C2' | C3' | O3' | 48.8° | 20.4° |
| H2'2 | C2' | C3' | H3' | 71.1° | 102.3° |
| H2'1 | C2' | C3' | O3' | 165.0° | 144.0° |
| H2'1 | C2' | C3' | H3' | 45.0° | 21.3° |
| H3' | C3' | O3' | H3T | 140.8° | 57.4° |
