P5E
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O2G | PG | doub | 1.48Å | 1.50Å | |
| O3B | PG | sing | 1.61Å | 1.65Å | |
| O3B | PB | sing | 1.61Å | 1.66Å | |
| O4 | C4 | doub | 1.22Å | 1.16Å | |
| PG | O3G | sing | 1.61Å | 1.45Å | |
| PG | O1G | sing | 1.61Å | 1.50Å | |
| S1A | PA | sing | 2.12Å | 1.50Å | |
| O3A | PB | sing | 1.61Å | 1.64Å | |
| O3A | PA | sing | 1.61Å | 1.64Å | |
| C5 | C4 | sing | 1.42Å | 1.39Å | |
| C5 | C6 | doub | 1.35Å | 1.32Å | |
| C4 | N3 | sing | 1.35Å | 1.30Å | |
| PB | O1B | doub | 1.48Å | 1.47Å | |
| PB | O2B | sing | 1.61Å | 1.48Å | |
| PA | O2A | doub | 1.48Å | 1.49Å | |
| PA | O5' | sing | 1.61Å | 1.65Å | |
| C6 | N1 | sing | 1.37Å | 1.33Å | |
| N3 | C2 | sing | 1.35Å | 1.34Å | |
| O5' | C5' | sing | 1.43Å | 1.37Å | |
| N1 | C2 | sing | 1.35Å | 1.35Å | |
| N1 | C1' | sing | 1.46Å | 1.48Å | |
| C2 | O2 | doub | 1.22Å | 1.18Å | |
| C5' | C4' | sing | 1.53Å | 1.58Å | |
| C2' | C1' | sing | 1.54Å | 1.33Å | |
| C2' | O2' | sing | 1.43Å | 1.43Å | |
| C2' | C3' | sing | 1.54Å | 1.61Å | |
| C1' | O4' | sing | 1.44Å | 1.52Å | |
| O4' | C4' | sing | 1.44Å | 1.57Å | |
| C4' | C3' | sing | 1.54Å | 1.30Å | |
| C3' | O3' | sing | 1.43Å | 1.46Å | |
| O2B | H1 | sing | 0.97Å | 0.95Å | |
| O1G | H2 | sing | 0.97Å | 0.95Å | |
| O3G | H3 | sing | 0.97Å | 0.95Å | |
| C5' | H4 | sing | 1.09Å | 1.10Å | |
| C5' | H5 | sing | 1.09Å | 1.10Å | |
| C4' | H6 | sing | 1.09Å | 1.10Å | |
| C1' | H7 | sing | 1.09Å | 1.10Å | |
| C2' | H8 | sing | 1.09Å | 1.10Å | |
| O2' | H9 | sing | 0.97Å | 0.95Å | |
| C3' | H10 | sing | 1.09Å | 1.10Å | |
| O3' | H11 | sing | 0.97Å | 0.95Å | |
| C6 | H12 | sing | 1.08Å | 1.08Å | |
| N3 | H13 | sing | 0.97Å | 1.00Å | |
| C5 | H14 | sing | 1.08Å | 1.08Å | |
| S1A | H15 | sing | 1.34Å | 1.30Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O2G | PG | O3B | 109.6° | 109.5° |
| O2G | PG | O3G | 109.6° | 109.5° |
| O2G | PG | O1G | 109.3° | 109.4° |
| PG | O3B | PB | 121.2° | 134.0° |
| O3B | PG | O3G | 109.0° | 109.5° |
| O3B | PG | O1G | 109.4° | 109.4° |
| O3B | PB | O3A | 110.1° | 109.5° |
| O3B | PB | O1B | 110.1° | 109.5° |
| O3B | PB | O2B | 108.0° | 109.5° |
| O4 | C4 | C5 | 119.8° | 120.3° |
| O4 | C4 | N3 | 119.8° | 120.3° |
| O3G | PG | O1G | 110.0° | 109.5° |
| PG | O3G | H3 | 109.5° | 114.0° |
| PG | O1G | H2 | 109.5° | 114.0° |
| S1A | PA | O3A | 105.0° | 109.5° |
| S1A | PA | O2A | 116.4° | 109.4° |
| S1A | PA | O5' | 110.3° | 109.5° |
| PA | S1A | H15 | 102.0° | 103.0° |
| PB | O3A | PA | 121.0° | 134.0° |
| O3A | PB | O1B | 110.0° | 109.5° |
| O3A | PB | O2B | 108.7° | 109.4° |
| O3A | PA | O2A | 108.1° | 109.5° |
| O3A | PA | O5' | 109.4° | 109.5° |
| C4 | C5 | C6 | 119.5° | 119.1° |
| C5 | C4 | N3 | 120.3° | 119.3° |
| C4 | C5 | H14 | 120.2° | 120.4° |
| C5 | C6 | N1 | 120.1° | 119.7° |
| C5 | C6 | H12 | 120.0° | 120.2° |
| C6 | C5 | H14 | 120.2° | 120.4° |
| C4 | N3 | C2 | 119.9° | 120.3° |
| C4 | N3 | H13 | 120.0° | 119.9° |
| O1B | PB | O2B | 109.8° | 109.5° |
| PB | O2B | H1 | 109.5° | 114.0° |
| O2A | PA | O5' | 107.5° | 109.5° |
| PA | O5' | C5' | 116.5° | 123.0° |
| C6 | N1 | C2 | 120.1° | 120.6° |
| C6 | N1 | C1' | 119.5° | 119.7° |
| N1 | C6 | H12 | 120.0° | 120.1° |
| N3 | C2 | N1 | 119.9° | 120.9° |
| N3 | C2 | O2 | 119.8° | 119.6° |
| C2 | N3 | H13 | 120.0° | 119.8° |
| O5' | C5' | C4' | 110.9° | 109.5° |
| O5' | C5' | H4 | 109.1° | 109.4° |
| O5' | C5' | H5 | 109.1° | 109.5° |
| C2 | N1 | C1' | 120.3° | 119.7° |
| N1 | C2 | O2 | 120.2° | 119.5° |
| N1 | C1' | C2' | 111.1° | 110.5° |
| N1 | C1' | O4' | 109.0° | 110.3° |
| N1 | C1' | H7 | 109.9° | 110.3° |
| C5' | C4' | O4' | 111.2° | 110.4° |
| C5' | C4' | C3' | 110.0° | 110.4° |
| C4' | C5' | H4 | 109.1° | 109.5° |
| C4' | C5' | H5 | 109.1° | 109.5° |
| C5' | C4' | H6 | 108.5° | 110.3° |
| C1' | C2' | O2' | 109.1° | 110.5° |
| C1' | C2' | C3' | 104.6° | 104.1° |
| C2' | C1' | O4' | 104.7° | 104.8° |
| C2' | C1' | H7 | 112.4° | 110.4° |
| C1' | C2' | H8 | 113.8° | 110.5° |
| O2' | C2' | C3' | 107.5° | 110.5° |
| O2' | C2' | H8 | 112.0° | 110.4° |
| C2' | O2' | H9 | 109.5° | 114.0° |
| C2' | C3' | C4' | 106.4° | 104.0° |
| C2' | C3' | O3' | 108.8° | 110.5° |
| C3' | C2' | H8 | 109.4° | 110.6° |
| C2' | C3' | H10 | 108.5° | 110.5° |
| C1' | O4' | C4' | 105.0° | 105.2° |
| O4' | C1' | H7 | 109.5° | 110.3° |
| O4' | C4' | C3' | 105.9° | 104.8° |
| O4' | C4' | H6 | 108.6° | 110.5° |
| C4' | C3' | O3' | 109.2° | 110.5° |
| C3' | C4' | H6 | 112.7° | 110.4° |
| C4' | C3' | H10 | 113.2° | 110.5° |
| O3' | C3' | H10 | 110.5° | 110.6° |
| C3' | O3' | H11 | 109.5° | 114.0° |
| H4 | C5' | H5 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O2G | PG | O3B | O3G | 119.9° | 120.1° |
| O2G | PG | O3B | O1G | 119.8° | 119.9° |
| O2G | PG | O3B | PB | 159.7° | 44.9° |
| O2G | PG | O3G | O1G | 120.2° | 120.0° |
| O2G | PG | O1G | H2 | 0.0° | 180.0° |
| O2G | PG | O3G | H3 | 0.0° | 60.0° |
| O3B | PG | O3G | O1G | 119.9° | 120.0° |
| PG | O3B | PB | O3A | 109.7° | 160.0° |
| PG | O3B | PB | O1B | 128.8° | 39.9° |
| PG | O3B | PB | O2B | 8.9° | 80.1° |
| O3B | PG | O1G | H2 | 120.0° | 60.0° |
| O3B | PG | O3G | H3 | 119.9° | 180.0° |
| PB | O3B | PG | O3G | 39.8° | 165.0° |
| PB | O3B | PG | O1G | 80.5° | 75.0° |
| O3B | PB | O3A | O1B | 121.5° | 120.1° |
| O3B | PB | O3A | O2B | 118.2° | 120.0° |
| O3B | PB | O3A | PA | 119.2° | 165.0° |
| O3B | PB | O1B | O2B | 118.8° | 120.0° |
| O3B | PB | O2B | H1 | 120.1° | 60.0° |
| O4 | C4 | C5 | N3 | 179.6° | 179.6° |
| O4 | C4 | C5 | C6 | 180.0° | 179.8° |
| O4 | C4 | N3 | C2 | 180.0° | 180.0° |
| O4 | C4 | N3 | H13 | 0.0° | 0.1° |
| O4 | C4 | C5 | H14 | 0.0° | 0.5° |
| O3G | PG | O1G | H2 | 120.4° | 60.0° |
| O1G | PG | O3G | H3 | 120.2° | 60.0° |
| S1A | PA | O3A | PB | 157.4° | 60.0° |
| S1A | PA | O3A | O2A | 124.9° | 120.0° |
| S1A | PA | O3A | O5' | 118.3° | 120.0° |
| S1A | PA | O2A | O5' | 124.2° | 120.0° |
| S1A | PA | O5' | C5' | 153.1° | 64.9° |
| O3A | PB | O1B | O2B | 119.6° | 120.0° |
| PB | O3A | PA | O2A | 32.5° | 59.9° |
| PB | O3A | PA | O5' | 84.3° | 179.9° |
| O3A | PB | O2B | H1 | 120.4° | 60.0° |
| PA | O3A | PB | O1B | 119.3° | 45.0° |
| PA | O3A | PB | O2B | 1.0° | 75.0° |
| O3A | PA | O2A | O5' | 118.0° | 120.0° |
| O3A | PA | O5' | C5' | 91.9° | 175.0° |
| O3A | PA | S1A | H15 | 119.5° | 60.0° |
| C4 | C5 | C6 | H14 | 180.0° | 179.3° |
| C4 | C5 | C6 | N1 | 0.1° | 0.4° |
| C5 | C4 | N3 | C2 | 0.4° | 0.4° |
| C4 | C5 | C6 | H12 | 179.9° | 179.5° |
| C5 | C4 | N3 | H13 | 179.7° | 179.5° |
| C6 | C5 | C4 | N3 | 0.3° | 0.6° |
| C5 | C6 | N1 | H12 | 180.0° | 179.9° |
| C5 | C6 | N1 | C2 | 0.4° | 0.1° |
| C5 | C6 | N1 | C1' | 179.8° | 179.7° |
| C4 | N3 | C2 | H13 | 180.0° | 179.9° |
| C4 | N3 | C2 | N1 | 0.0° | 0.1° |
| C4 | N3 | C2 | O2 | 179.9° | 180.0° |
| N3 | C4 | C5 | H14 | 179.7° | 180.0° |
| O1B | PB | O2B | H1 | 0.0° | 180.0° |
| O2A | PA | O5' | C5' | 25.2° | 55.0° |
| O2A | PA | S1A | H15 | 0.0° | 180.0° |
| PA | O5' | C5' | C4' | 173.0° | 180.0° |
| PA | O5' | C5' | H4 | 52.8° | 60.1° |
| PA | O5' | C5' | H5 | 66.8° | 59.9° |
| O5' | PA | S1A | H15 | 122.8° | 60.0° |
| C6 | N1 | C2 | N3 | 0.4° | 0.3° |
| C6 | N1 | C2 | C1' | 179.4° | 179.6° |
| C6 | N1 | C2 | O2 | 179.5° | 179.7° |
| C6 | N1 | C1' | C2' | 76.3° | 61.5° |
| C6 | N1 | C1' | O4' | 38.6° | 53.9° |
| C6 | N1 | C1' | H7 | 158.6° | 176.1° |
| N1 | C6 | C5 | H14 | 179.9° | 179.7° |
| N3 | C2 | N1 | O2 | 179.8° | 179.9° |
| N3 | C2 | N1 | C1' | 179.7° | 180.0° |
| O5' | C5' | C4' | H4 | 120.2° | 119.9° |
| O5' | C5' | C4' | H5 | 120.2° | 120.1° |
| O5' | C5' | C4' | O4' | 9.7° | 69.6° |
| O5' | C5' | C4' | C3' | 107.3° | 175.0° |
| O5' | C5' | H4 | H5 | 119.3° | 120.0° |
| O5' | C5' | C4' | H6 | 129.0° | 52.8° |
| C2 | N1 | C1' | C2' | 104.4° | 118.1° |
| C2 | N1 | C1' | O4' | 140.8° | 126.5° |
| C2 | N1 | C1' | H7 | 20.7° | 4.3° |
| C2 | N1 | C6 | H12 | 179.6° | 180.0° |
| N1 | C2 | N3 | H13 | 180.0° | 180.0° |
| C1' | N1 | C2 | O2 | 0.1° | 0.1° |
| N1 | C1' | C2' | O4' | 117.6° | 118.8° |
| N1 | C1' | C2' | H7 | 123.7° | 122.4° |
| N1 | C1' | C2' | O2' | 93.9° | 98.5° |
| N1 | C1' | C2' | C3' | 151.3° | 142.8° |
| N1 | C1' | O4' | H7 | 120.3° | 122.2° |
| N1 | C1' | O4' | C4' | 141.1° | 159.5° |
| N1 | C1' | C2' | H8 | 32.0° | 24.0° |
| C1' | N1 | C6 | H12 | 0.2° | 0.4° |
| O2 | C2 | N3 | H13 | 0.1° | 0.1° |
| C5' | C4' | C3' | C2' | 98.8° | 142.8° |
| C5' | C4' | O4' | C1' | 117.2° | 159.4° |
| C5' | C4' | O4' | C3' | 119.5° | 118.8° |
| C5' | C4' | O4' | H6 | 119.2° | 122.3° |
| C5' | C4' | C3' | H6 | 121.2° | 122.2° |
| C5' | C4' | C3' | O3' | 143.9° | 98.5° |
| C4' | C5' | H4 | H5 | 119.4° | 120.0° |
| C5' | C4' | C3' | H10 | 20.3° | 24.2° |
| C1' | C2' | O2' | C3' | 112.9° | 114.7° |
| C1' | C2' | O2' | H8 | 126.9° | 122.6° |
| C1' | C2' | C3' | H8 | 122.3° | 118.7° |
| C2' | C1' | O4' | H7 | 120.7° | 118.9° |
| C2' | C1' | O4' | C4' | 22.1° | 40.5° |
| C1' | C2' | C3' | C4' | 37.6° | 0.0° |
| C1' | C2' | C3' | O3' | 79.9° | 118.6° |
| C1' | C2' | O2' | H9 | 180.0° | 179.9° |
| C1' | C2' | C3' | H10 | 159.8° | 118.6° |
| O2' | C2' | C3' | H8 | 121.8° | 122.6° |
| O2' | C2' | C1' | O4' | 148.6° | 142.7° |
| O2' | C2' | C3' | C4' | 153.5° | 118.7° |
| O2' | C2' | C3' | O3' | 36.0° | 0.0° |
| O2' | C2' | C1' | H7 | 29.9° | 23.8° |
| O2' | C2' | C3' | H10 | 84.3° | 122.7° |
| C3' | C2' | C1' | O4' | 33.8° | 24.0° |
| C2' | C3' | C4' | O4' | 21.4° | 24.0° |
| C2' | C3' | C4' | O3' | 117.3° | 118.6° |
| C2' | C3' | C4' | H10 | 119.1° | 118.7° |
| C2' | C3' | O3' | H10 | 119.0° | 122.7° |
| C2' | C3' | C4' | H6 | 140.0° | 95.0° |
| C3' | C2' | C1' | H7 | 84.9° | 94.8° |
| C3' | C2' | O2' | H9 | 67.1° | 65.4° |
| C2' | C3' | O3' | H11 | 180.0° | 65.4° |
| C1' | O4' | C4' | C3' | 2.2° | 40.5° |
| C1' | O4' | C4' | H6 | 123.5° | 78.4° |
| O4' | C1' | C2' | H8 | 85.6° | 94.8° |
| O4' | C4' | C3' | H6 | 118.6° | 118.9° |
| O4' | C4' | C3' | O3' | 95.9° | 142.6° |
| O4' | C4' | C5' | H4 | 129.9° | 50.4° |
| O4' | C4' | C5' | H5 | 110.5° | 170.4° |
| C4' | O4' | C1' | H7 | 98.6° | 78.3° |
| O4' | C4' | C3' | H10 | 140.6° | 94.7° |
| C4' | C3' | O3' | H10 | 125.2° | 122.6° |
| C3' | C4' | C5' | H4 | 12.9° | 65.0° |
| C3' | C4' | C5' | H5 | 132.5° | 55.0° |
| C4' | C3' | C2' | H8 | 84.7° | 118.7° |
| C4' | C3' | O3' | H11 | 64.2° | 180.0° |
| O3' | C3' | C4' | H6 | 22.7° | 23.7° |
| O3' | C3' | C2' | H8 | 157.8° | 122.7° |
| H4 | C5' | C4' | H6 | 110.8° | 172.7° |
| H5 | C5' | C4' | H6 | 8.8° | 67.3° |
| H6 | C4' | C3' | H10 | 100.9° | 146.4° |
| H7 | C1' | C2' | H8 | 155.7° | 146.4° |
| H8 | C2' | O2' | H9 | 53.1° | 57.4° |
| H8 | C2' | C3' | H10 | 37.5° | 0.1° |
| H10 | C3' | O3' | H11 | 61.0° | 57.4° |
| H12 | C6 | C5 | H14 | 0.1° | 0.2° |
