5PD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| S06 | C05 | sing | 1.81Å | 1.81Å | |
| C05 | C04 | sing | 1.53Å | 1.49Å | |
| C04 | N03 | sing | 1.47Å | 1.44Å | |
| N03 | C02 | sing | 1.35Å | 1.33Å | |
| C02 | O01 | doub | 1.21Å | 1.20Å | |
| C02 | C07 | sing | 1.51Å | 1.51Å | |
| C07 | C08 | sing | 1.53Å | 1.52Å | |
| C08 | N09 | sing | 1.47Å | 1.39Å | |
| N09 | C10 | sing | 1.35Å | 1.29Å | |
| C10 | O11 | doub | 1.21Å | 1.24Å | |
| C10 | C12 | sing | 1.51Å | 1.52Å | |
| C12 | O13 | sing | 1.43Å | 1.48Å | |
| C12 | C14 | sing | 1.53Å | 1.56Å | |
| C14 | C15 | sing | 1.53Å | 1.49Å | |
| C14 | C17 | sing | 1.53Å | 1.60Å | |
| C14 | C16 | sing | 1.53Å | 1.54Å | |
| O21 | P19 | doub | 1.48Å | 1.51Å | |
| O18 | P19 | sing | 1.61Å | 1.63Å | |
| O18 | C17 | sing | 1.43Å | 1.42Å | |
| P19 | O20 | sing | 1.61Å | 1.48Å | |
| C15 | H1 | sing | 1.09Å | 1.10Å | |
| C15 | H2 | sing | 1.09Å | 1.10Å | |
| C15 | H3 | sing | 1.09Å | 1.10Å | |
| C17 | H4 | sing | 1.09Å | 1.10Å | |
| C17 | H5 | sing | 1.09Å | 1.10Å | |
| O20 | H6 | sing | 0.97Å | 0.95Å | |
| C16 | H7 | sing | 1.09Å | 1.10Å | |
| C16 | H8 | sing | 1.09Å | 1.10Å | |
| C16 | H9 | sing | 1.09Å | 1.10Å | |
| C12 | H10 | sing | 1.09Å | 1.10Å | |
| O13 | H11 | sing | 0.97Å | 0.95Å | |
| N09 | H12 | sing | 0.97Å | 1.00Å | |
| C08 | H13 | sing | 1.09Å | 1.10Å | |
| C08 | H14 | sing | 1.09Å | 1.10Å | |
| C07 | H15 | sing | 1.09Å | 1.10Å | |
| C07 | H16 | sing | 1.09Å | 1.10Å | |
| N03 | H17 | sing | 0.97Å | 1.00Å | |
| C04 | H18 | sing | 1.09Å | 1.10Å | |
| C04 | H19 | sing | 1.09Å | 1.10Å | |
| C05 | H20 | sing | 1.09Å | 1.10Å | |
| C05 | H21 | sing | 1.09Å | 1.10Å | |
| S06 | H22 | sing | 1.35Å | 1.30Å | |
| P19 | H23 | sing | 1.42Å | 1.42Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| S06 | C05 | C04 | 110.5° | 109.5° |
| S06 | C05 | H20 | 109.2° | 109.5° |
| S06 | C05 | H21 | 109.2° | 109.4° |
| C05 | S06 | H22 | 102.0° | 103.0° |
| C05 | C04 | N03 | 112.6° | 109.5° |
| C05 | C04 | H18 | 108.7° | 109.5° |
| C05 | C04 | H19 | 108.7° | 109.5° |
| C04 | C05 | H20 | 109.2° | 109.5° |
| C04 | C05 | H21 | 109.2° | 109.5° |
| C04 | N03 | C02 | 124.5° | 120.0° |
| C04 | N03 | H17 | 117.7° | 120.0° |
| N03 | C04 | H18 | 108.7° | 109.4° |
| N03 | C04 | H19 | 108.7° | 109.5° |
| N03 | C02 | O01 | 124.8° | 120.0° |
| N03 | C02 | C07 | 116.5° | 120.1° |
| C02 | N03 | H17 | 117.8° | 120.0° |
| O01 | C02 | C07 | 118.5° | 120.0° |
| C02 | C07 | C08 | 118.5° | 109.5° |
| C02 | C07 | H15 | 107.2° | 109.4° |
| C02 | C07 | H16 | 107.2° | 109.4° |
| C07 | C08 | N09 | 110.3° | 109.5° |
| C07 | C08 | H13 | 109.2° | 109.5° |
| C07 | C08 | H14 | 109.3° | 109.5° |
| C08 | C07 | H15 | 107.2° | 109.5° |
| C08 | C07 | H16 | 107.2° | 109.5° |
| C08 | N09 | C10 | 135.6° | 120.0° |
| C08 | N09 | H12 | 112.2° | 120.0° |
| N09 | C08 | H13 | 109.3° | 109.5° |
| N09 | C08 | H14 | 109.2° | 109.5° |
| N09 | C10 | O11 | 103.2° | 120.0° |
| N09 | C10 | C12 | 135.8° | 120.0° |
| C10 | N09 | H12 | 112.2° | 120.0° |
| O11 | C10 | C12 | 120.6° | 120.0° |
| C10 | C12 | O13 | 104.7° | 109.5° |
| C10 | C12 | C14 | 105.0° | 109.5° |
| C10 | C12 | H10 | 112.6° | 109.5° |
| O13 | C12 | C14 | 108.9° | 109.5° |
| O13 | C12 | H10 | 113.1° | 109.5° |
| C12 | O13 | H11 | 109.5° | 114.0° |
| C12 | C14 | C15 | 118.6° | 109.5° |
| C12 | C14 | C17 | 102.9° | 109.4° |
| C12 | C14 | C16 | 119.4° | 109.5° |
| C14 | C12 | H10 | 111.9° | 109.4° |
| C15 | C14 | C17 | 91.5° | 109.5° |
| C15 | C14 | C16 | 120.2° | 109.5° |
| C14 | C15 | H1 | 109.5° | 109.5° |
| C14 | C15 | H2 | 109.4° | 109.5° |
| C14 | C15 | H3 | 109.5° | 109.4° |
| C17 | C14 | C16 | 89.2° | 109.4° |
| C14 | C17 | O18 | 115.2° | 109.5° |
| C14 | C17 | H4 | 108.0° | 109.4° |
| C14 | C17 | H5 | 108.0° | 109.5° |
| C14 | C16 | H7 | 109.5° | 109.5° |
| C14 | C16 | H8 | 109.4° | 109.5° |
| C14 | C16 | H9 | 109.4° | 109.4° |
| O21 | P19 | O18 | 112.5° | 109.5° |
| O21 | P19 | O20 | 116.2° | 109.5° |
| O21 | P19 | H23 | 102.5° | 109.5° |
| P19 | O18 | C17 | 128.8° | 123.0° |
| O18 | P19 | O20 | 118.1° | 109.4° |
| O18 | P19 | H23 | 101.6° | 109.4° |
| O18 | C17 | H4 | 108.0° | 109.5° |
| O18 | C17 | H5 | 108.0° | 109.5° |
| P19 | O20 | H6 | 109.5° | 113.9° |
| O20 | P19 | H23 | 102.8° | 109.5° |
| H1 | C15 | H2 | 109.5° | 109.5° |
| H1 | C15 | H3 | 109.4° | 109.4° |
| H2 | C15 | H3 | 109.5° | 109.5° |
| H4 | C17 | H5 | 109.4° | 109.5° |
| H7 | C16 | H8 | 109.5° | 109.4° |
| H7 | C16 | H9 | 109.5° | 109.5° |
| H8 | C16 | H9 | 109.5° | 109.5° |
| H13 | C08 | H14 | 109.5° | 109.4° |
| H15 | C07 | H16 | 109.5° | 109.4° |
| H18 | C04 | H19 | 109.5° | 109.5° |
| H20 | C05 | H21 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| S06 | C05 | C04 | H20 | 120.2° | 120.0° |
| S06 | C05 | C04 | H21 | 120.1° | 120.0° |
| S06 | C05 | C04 | N03 | 140.1° | 180.0° |
| S06 | C05 | C04 | H18 | 19.7° | 60.0° |
| S06 | C05 | C04 | H19 | 99.4° | 60.0° |
| S06 | C05 | H20 | H21 | 119.5° | 120.0° |
| C05 | C04 | N03 | H18 | 120.5° | 120.0° |
| C05 | C04 | N03 | H19 | 120.5° | 120.0° |
| C05 | C04 | N03 | C02 | 65.7° | 180.0° |
| C05 | C04 | N03 | H17 | 114.3° | 0.0° |
| C05 | C04 | H18 | H19 | 118.5° | 120.0° |
| C04 | C05 | H20 | H21 | 119.5° | 120.0° |
| C04 | C05 | S06 | H22 | 180.0° | 180.0° |
| C04 | N03 | C02 | H17 | 180.0° | 180.0° |
| C04 | N03 | C02 | O01 | 5.4° | 0.0° |
| C04 | N03 | C02 | C07 | 179.9° | 180.0° |
| N03 | C04 | H18 | H19 | 118.6° | 120.0° |
| N03 | C04 | C05 | H20 | 99.7° | 60.0° |
| N03 | C04 | C05 | H21 | 20.0° | 60.0° |
| N03 | C02 | O01 | C07 | 174.5° | 179.9° |
| N03 | C02 | C07 | C08 | 108.8° | 180.0° |
| N03 | C02 | C07 | H15 | 129.9° | 59.9° |
| N03 | C02 | C07 | H16 | 12.5° | 60.0° |
| C02 | N03 | C04 | H18 | 173.8° | 60.0° |
| C02 | N03 | C04 | H19 | 54.8° | 60.0° |
| O01 | C02 | C07 | C08 | 76.3° | 0.0° |
| O01 | C02 | C07 | H15 | 45.0° | 120.0° |
| O01 | C02 | C07 | H16 | 162.5° | 120.1° |
| O01 | C02 | N03 | H17 | 174.6° | 180.0° |
| C02 | C07 | C08 | H15 | 121.3° | 120.0° |
| C02 | C07 | C08 | H16 | 121.3° | 120.0° |
| C02 | C07 | C08 | N09 | 85.0° | 180.0° |
| C02 | C07 | C08 | H13 | 154.9° | 60.0° |
| C02 | C07 | C08 | H14 | 35.2° | 60.0° |
| C02 | C07 | H15 | H16 | 115.9° | 119.9° |
| C07 | C02 | N03 | H17 | 0.1° | 0.0° |
| C07 | C08 | N09 | H13 | 120.1° | 120.0° |
| C07 | C08 | N09 | H14 | 120.1° | 120.0° |
| C07 | C08 | N09 | C10 | 135.9° | 180.0° |
| C07 | C08 | N09 | H12 | 44.2° | 0.1° |
| C07 | C08 | H13 | H14 | 119.6° | 120.0° |
| C08 | C07 | H15 | H16 | 115.9° | 120.0° |
| C08 | N09 | C10 | H12 | 180.0° | 179.9° |
| C08 | N09 | C10 | O11 | 176.7° | 4.5° |
| C08 | N09 | C10 | C12 | 4.3° | 175.2° |
| N09 | C08 | H13 | H14 | 119.6° | 120.0° |
| N09 | C08 | C07 | H15 | 36.3° | 60.0° |
| N09 | C08 | C07 | H16 | 153.8° | 60.0° |
| N09 | C10 | O11 | C12 | 173.8° | 179.7° |
| N09 | C10 | C12 | O13 | 160.2° | 171.9° |
| N09 | C10 | C12 | C14 | 85.1° | 68.1° |
| N09 | C10 | C12 | H10 | 37.0° | 51.9° |
| C10 | N09 | C08 | H13 | 15.8° | 60.0° |
| C10 | N09 | C08 | H14 | 104.0° | 60.0° |
| O11 | C10 | C12 | O13 | 28.4° | 8.4° |
| O11 | C10 | C12 | C14 | 86.3° | 111.6° |
| O11 | C10 | C12 | H10 | 151.7° | 128.4° |
| O11 | C10 | N09 | H12 | 3.3° | 175.6° |
| C10 | C12 | O13 | C14 | 111.9° | 120.0° |
| C10 | C12 | O13 | H10 | 123.0° | 120.0° |
| C10 | C12 | C14 | H10 | 122.5° | 120.0° |
| C10 | C12 | C14 | C15 | 96.6° | 174.1° |
| C10 | C12 | C14 | C17 | 164.4° | 54.0° |
| C10 | C12 | C14 | C16 | 68.0° | 65.9° |
| C10 | C12 | O13 | H11 | 12.3° | 60.0° |
| C12 | C10 | N09 | H12 | 175.6° | 4.7° |
| O13 | C12 | C14 | H10 | 125.8° | 120.0° |
| O13 | C12 | C14 | C15 | 151.7° | 54.0° |
| O13 | C12 | C14 | C17 | 52.8° | 66.0° |
| O13 | C12 | C14 | C16 | 43.6° | 174.1° |
| C12 | C14 | C15 | C17 | 105.5° | 120.0° |
| C12 | C14 | C15 | C16 | 164.5° | 120.0° |
| C12 | C14 | C17 | C16 | 120.0° | 120.0° |
| C12 | C14 | C17 | O18 | 44.6° | 180.0° |
| C12 | C14 | C15 | H1 | 180.0° | 65.6° |
| C12 | C14 | C15 | H2 | 60.0° | 54.4° |
| C12 | C14 | C15 | H3 | 60.0° | 174.4° |
| C12 | C14 | C17 | H4 | 165.4° | 60.0° |
| C12 | C14 | C17 | H5 | 76.3° | 60.0° |
| C12 | C14 | C16 | H7 | 180.0° | 53.5° |
| C12 | C14 | C16 | H8 | 60.0° | 66.4° |
| C12 | C14 | C16 | H9 | 60.0° | 173.5° |
| C14 | C12 | O13 | H11 | 99.6° | 60.1° |
| C15 | C14 | C17 | C16 | 120.2° | 120.0° |
| C15 | C14 | C17 | O18 | 75.2° | 60.0° |
| C14 | C15 | H1 | H2 | 120.0° | 120.0° |
| C14 | C15 | H1 | H3 | 120.0° | 120.0° |
| C14 | C15 | H2 | H3 | 120.0° | 120.0° |
| C15 | C14 | C17 | H4 | 45.6° | 60.0° |
| C15 | C14 | C17 | H5 | 163.9° | 180.0° |
| C15 | C14 | C16 | H7 | 15.6° | 66.5° |
| C15 | C14 | C16 | H8 | 104.4° | 173.5° |
| C15 | C14 | C16 | H9 | 135.6° | 53.5° |
| C15 | C14 | C12 | H10 | 25.9° | 65.9° |
| C14 | C17 | O18 | P19 | 177.0° | 180.0° |
| C14 | C17 | O18 | H4 | 120.9° | 120.0° |
| C14 | C17 | O18 | H5 | 120.9° | 120.0° |
| C17 | C14 | C15 | H1 | 74.5° | 54.3° |
| C17 | C14 | C15 | H2 | 45.6° | 174.4° |
| C17 | C14 | C15 | H3 | 165.5° | 65.6° |
| C14 | C17 | H4 | H5 | 117.4° | 120.0° |
| C17 | C14 | C16 | H7 | 75.7° | 173.5° |
| C17 | C14 | C16 | H8 | 164.3° | 53.5° |
| C17 | C14 | C16 | H9 | 44.3° | 66.5° |
| C17 | C14 | C12 | H10 | 73.0° | 174.0° |
| C16 | C14 | C17 | O18 | 164.6° | 60.1° |
| C16 | C14 | C15 | H1 | 15.5° | 174.4° |
| C16 | C14 | C15 | H2 | 135.5° | 65.6° |
| C16 | C14 | C15 | H3 | 104.5° | 54.4° |
| C16 | C14 | C17 | H4 | 74.6° | 180.0° |
| C16 | C14 | C17 | H5 | 43.7° | 60.0° |
| C14 | C16 | H7 | H8 | 120.0° | 120.0° |
| C14 | C16 | H7 | H9 | 120.0° | 119.9° |
| C14 | C16 | H8 | H9 | 120.0° | 120.0° |
| C16 | C14 | C12 | H10 | 169.5° | 54.1° |
| O21 | P19 | O18 | O20 | 139.7° | 120.0° |
| O21 | P19 | O18 | H23 | 108.9° | 120.0° |
| O21 | P19 | O18 | C17 | 167.3° | 45.0° |
| O21 | P19 | O20 | H23 | 111.0° | 120.1° |
| O21 | P19 | O20 | H6 | 0.0° | 60.0° |
| O18 | P19 | O20 | H23 | 110.8° | 119.9° |
| P19 | O18 | C17 | H4 | 62.1° | 60.0° |
| P19 | O18 | C17 | H5 | 56.1° | 60.0° |
| O18 | P19 | O20 | H6 | 138.2° | 180.0° |
| C17 | O18 | P19 | O20 | 27.7° | 165.0° |
| O18 | C17 | H4 | H5 | 117.3° | 120.0° |
| C17 | O18 | P19 | H23 | 83.8° | 75.0° |
| H1 | C15 | H2 | H3 | 120.0° | 120.0° |
| H6 | O20 | P19 | H23 | 111.0° | 60.1° |
| H7 | C16 | H8 | H9 | 120.0° | 120.1° |
| H10 | C12 | O13 | H11 | 135.3° | 180.0° |
| H12 | N09 | C08 | H13 | 164.3° | 120.1° |
| H12 | N09 | C08 | H14 | 76.0° | 119.9° |
| H13 | C08 | C07 | H15 | 83.8° | 180.0° |
| H13 | C08 | C07 | H16 | 33.7° | 60.0° |
| H14 | C08 | C07 | H15 | 156.4° | 60.0° |
| H14 | C08 | C07 | H16 | 86.1° | 180.0° |
| H17 | N03 | C04 | H18 | 6.2° | 120.0° |
| H17 | N03 | C04 | H19 | 125.2° | 120.0° |
| H18 | C04 | C05 | H20 | 139.8° | 180.0° |
| H18 | C04 | C05 | H21 | 100.4° | 59.9° |
| H19 | C04 | C05 | H20 | 20.8° | 60.0° |
| H19 | C04 | C05 | H21 | 140.5° | 180.0° |
| H20 | C05 | S06 | H22 | 59.8° | 60.0° |
| H21 | C05 | S06 | H22 | 59.9° | 60.1° |
