4PD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | OP1 | doub | 1.50Å | 1.51Å | |
| P | OP2 | sing | 1.62Å | 1.51Å | |
| P | O5' | sing | 1.62Å | 1.63Å | |
| P | OP3 | sing | 1.62Å | 10.14Å | |
| OP2 | HOP2 | sing | 0.98Å | 0.95Å | |
| O5' | C5' | sing | 1.42Å | 1.42Å | |
| C5' | C4' | sing | 1.52Å | 1.54Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.44Å | |
| C4' | C3' | sing | 1.52Å | 1.53Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.43Å | 1.44Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C3' | C2' | sing | 1.51Å | 1.52Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C2' | C1' | sing | 1.52Å | 1.52Å | |
| C2' | H2' | sing | 1.10Å | 1.10Å | |
| C2' | H2'' | sing | 1.09Å | 1.10Å | |
| C1' | N1 | sing | 1.43Å | 1.47Å | |
| C1' | H1' | sing | 1.10Å | 1.10Å | |
| N1 | C2 | sing | 1.42Å | 1.41Å | |
| N1 | C6 | sing | 1.39Å | 1.39Å | |
| C2 | O2 | doub | 1.23Å | 1.23Å | |
| C2 | N3 | sing | 1.40Å | 1.38Å | |
| N3 | C4 | sing | 1.36Å | 1.35Å | |
| N3 | H19 | sing | 1.01Å | 1.00Å | |
| C4 | C5 | sing | 1.46Å | 1.46Å | |
| C4 | N17 | doub | 1.30Å | 1.30Å | |
| C5 | C6 | doub | 1.33Å | 1.33Å | |
| C5 | C14 | sing | 1.42Å | 1.42Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C14 | C15 | doub | 1.35Å | 1.35Å | |
| C14 | H14 | sing | 1.08Å | 1.08Å | |
| C15 | C16 | sing | 1.49Å | 1.49Å | |
| C15 | N17 | sing | 1.40Å | 1.40Å | |
| C16 | H161 | sing | 1.09Å | 1.10Å | |
| C16 | H162 | sing | 1.09Å | 1.10Å | |
| C16 | H163 | sing | 1.09Å | 1.10Å | |
| OP3 | HOP3 | sing | 0.98Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | OP2 | 121.3° | 115.3° |
| OP1 | P | O5' | 107.5° | 115.0° |
| OP1 | P | OP3 | 96.3° | 115.0° |
| OP2 | P | O5' | 108.8° | 103.7° |
| OP2 | P | OP3 | 134.0° | 103.3° |
| P | OP2 | HOP2 | 109.5° | 118.9° |
| O5' | P | OP3 | 27.9° | 102.9° |
| P | O5' | C5' | 118.4° | 118.5° |
| P | OP3 | HOP3 | 96.3° | 118.9° |
| O5' | C5' | C4' | 111.9° | 108.9° |
| O5' | C5' | H5' | 108.1° | 109.0° |
| O5' | C5' | H5'' | 108.6° | 108.9° |
| C4' | C5' | H5' | 108.1° | 110.3° |
| C4' | C5' | H5'' | 108.7° | 110.3° |
| C5' | C4' | O4' | 110.0° | 107.9° |
| C5' | C4' | C3' | 115.6° | 112.9° |
| C5' | C4' | H4' | 104.4° | 109.5° |
| H5' | C5' | H5'' | 111.4° | 109.3° |
| O4' | C4' | C3' | 108.1° | 106.2° |
| O4' | C4' | H4' | 112.4° | 107.9° |
| C4' | O4' | C1' | 108.8° | 109.3° |
| C3' | C4' | H4' | 106.5° | 112.2° |
| C4' | C3' | O3' | 109.8° | 109.9° |
| C4' | C3' | C2' | 102.6° | 103.1° |
| C4' | C3' | H3' | 114.1° | 113.5° |
| O4' | C1' | C2' | 108.3° | 107.4° |
| O4' | C1' | N1 | 109.3° | 109.3° |
| O4' | C1' | H1' | 112.4° | 108.0° |
| O3' | C3' | C2' | 110.8° | 109.7° |
| O3' | C3' | H3' | 106.4° | 107.4° |
| C3' | O3' | HO3' | 109.5° | 107.3° |
| C2' | C3' | H3' | 113.2° | 113.2° |
| C3' | C2' | C1' | 105.1° | 102.5° |
| C3' | C2' | H2' | 111.9° | 109.7° |
| C3' | C2' | H2'' | 111.0° | 114.1° |
| C1' | C2' | H2' | 111.9° | 110.6° |
| C1' | C2' | H2'' | 110.9° | 111.7° |
| C2' | C1' | N1 | 114.9° | 112.8° |
| C2' | C1' | H1' | 106.5° | 111.5° |
| H2' | C2' | H2'' | 106.1° | 108.3° |
| N1 | C1' | H1' | 105.5° | 107.8° |
| C1' | N1 | C2 | 118.8° | 118.8° |
| C1' | N1 | C6 | 119.4° | 118.7° |
| C2 | N1 | C6 | 121.7° | 122.5° |
| N1 | C2 | O2 | 124.6° | 124.2° |
| N1 | C2 | N3 | 116.2° | 115.0° |
| N1 | C6 | C5 | 120.6° | 121.0° |
| N1 | C6 | H6 | 119.7° | 116.9° |
| O2 | C2 | N3 | 119.2° | 120.8° |
| C2 | N3 | C4 | 123.1° | 123.8° |
| C2 | N3 | H19 | 118.4° | 118.1° |
| C4 | N3 | H19 | 118.5° | 118.1° |
| N3 | C4 | C5 | 118.7° | 118.1° |
| N3 | C4 | N17 | 128.6° | 129.1° |
| C5 | C4 | N17 | 112.7° | 112.9° |
| C4 | C5 | C6 | 119.2° | 119.6° |
| C4 | C5 | C14 | 104.3° | 103.9° |
| C4 | N17 | C15 | 103.5° | 103.5° |
| C6 | C5 | C14 | 136.4° | 136.5° |
| C5 | C6 | H6 | 119.7° | 122.1° |
| C5 | C14 | C15 | 104.7° | 104.9° |
| C5 | C14 | H14 | 127.6° | 127.1° |
| C15 | C14 | H14 | 127.7° | 128.0° |
| C14 | C15 | C16 | 125.8° | 126.0° |
| C14 | C15 | N17 | 114.8° | 114.9° |
| C16 | C15 | N17 | 119.3° | 119.1° |
| C15 | C16 | H161 | 109.5° | 110.1° |
| C15 | C16 | H162 | 109.5° | 110.1° |
| C15 | C16 | H163 | 109.5° | 110.1° |
| H161 | C16 | H162 | 109.5° | 109.0° |
| H161 | C16 | H163 | 109.4° | 109.0° |
| H162 | C16 | H163 | 109.5° | 108.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | OP2 | O5' | 125.5° | 126.6° |
| OP1 | P | OP2 | OP3 | 139.9° | 126.3° |
| OP1 | P | O5' | OP3 | 69.4° | 125.8° |
| OP1 | P | OP2 | HOP2 | 96.5° | 48.8° |
| OP1 | P | O5' | C5' | 170.0° | 179.9° |
| OP1 | P | OP3 | HOP3 | 180.0° | 48.0° |
| OP2 | P | O5' | OP3 | 157.5° | 107.4° |
| OP2 | P | O5' | C5' | 36.9° | 53.2° |
| OP2 | P | OP3 | HOP3 | 33.6° | 78.5° |
| O5' | P | OP2 | HOP2 | 29.0° | 175.4° |
| P | O5' | C5' | C4' | 171.8° | 180.0° |
| P | O5' | C5' | H5' | 52.9° | 59.6° |
| P | O5' | C5' | H5'' | 68.1° | 59.6° |
| O5' | P | OP3 | HOP3 | 63.9° | 173.8° |
| OP3 | P | OP2 | HOP2 | 43.4° | 77.5° |
| OP3 | P | O5' | C5' | 120.6° | 54.2° |
| O5' | C5' | C4' | H5' | 119.0° | 119.6° |
| O5' | C5' | C4' | H5'' | 120.0° | 119.5° |
| O5' | C5' | H5' | H5'' | 119.3° | 119.0° |
| O5' | C5' | C4' | O4' | 52.7° | 62.4° |
| O5' | C5' | C4' | C3' | 69.9° | 179.5° |
| O5' | C5' | C4' | H4' | 173.5° | 54.7° |
| C4' | C5' | H5' | H5'' | 119.3° | 121.5° |
| C5' | C4' | O4' | C3' | 127.0° | 121.4° |
| C5' | C4' | O4' | H4' | 115.8° | 118.2° |
| C5' | C4' | C3' | H4' | 115.3° | 124.3° |
| C5' | C4' | O4' | C1' | 142.6° | 108.6° |
| C5' | C4' | C3' | O3' | 92.7° | 154.2° |
| C5' | C4' | C3' | C2' | 149.4° | 88.8° |
| C5' | C4' | C3' | H3' | 26.6° | 34.0° |
| H5' | C5' | C4' | O4' | 66.2° | 57.1° |
| H5' | C5' | C4' | C3' | 171.1° | 60.0° |
| H5' | C5' | C4' | H4' | 54.6° | 174.3° |
| H5'' | C5' | C4' | O4' | 172.7° | 178.1° |
| H5'' | C5' | C4' | C3' | 50.0° | 61.0° |
| H5'' | C5' | C4' | H4' | 66.5° | 64.8° |
| O4' | C4' | C3' | H4' | 120.9° | 117.6° |
| O4' | C4' | C3' | O3' | 143.6° | 87.7° |
| O4' | C4' | C3' | C2' | 25.7° | 29.2° |
| O4' | C4' | C3' | H3' | 97.1° | 152.1° |
| C4' | O4' | C1' | C2' | 1.2° | 9.0° |
| C4' | O4' | C1' | N1 | 124.7° | 131.7° |
| C4' | O4' | C1' | H1' | 118.6° | 111.3° |
| C3' | C4' | O4' | C1' | 15.6° | 12.7° |
| C4' | C3' | O3' | C2' | 112.7° | 112.7° |
| C4' | C3' | O3' | H3' | 123.9° | 123.9° |
| C4' | C3' | C2' | H3' | 123.4° | 123.0° |
| C4' | C3' | O3' | HO3' | 10.1° | 104.8° |
| C4' | C3' | C2' | C1' | 25.4° | 33.4° |
| C4' | C3' | C2' | H2' | 96.2° | 84.1° |
| C4' | C3' | C2' | H2'' | 145.4° | 154.3° |
| H4' | C4' | O4' | C1' | 101.6° | 133.2° |
| H4' | C4' | C3' | O3' | 22.6° | 29.9° |
| H4' | C4' | C3' | C2' | 95.2° | 146.9° |
| H4' | C4' | C3' | H3' | 142.0° | 90.3° |
| O4' | C1' | C2' | C3' | 17.5° | 26.9° |
| O4' | C1' | C2' | N1 | 122.5° | 120.5° |
| O4' | C1' | C2' | H1' | 121.1° | 118.1° |
| O4' | C1' | C2' | H2' | 104.2° | 90.0° |
| O4' | C1' | C2' | H2'' | 137.5° | 149.4° |
| O4' | C1' | N1 | H1' | 121.1° | 117.1° |
| O4' | C1' | N1 | C2 | 123.2° | 147.1° |
| O4' | C1' | N1 | C6 | 55.6° | 32.9° |
| O3' | C3' | C2' | H3' | 119.4° | 119.9° |
| O3' | C3' | C2' | C1' | 142.6° | 83.6° |
| O3' | C3' | C2' | H2' | 21.0° | 158.9° |
| O3' | C3' | C2' | H2'' | 97.4° | 37.2° |
| C2' | C3' | O3' | HO3' | 102.6° | 142.5° |
| C3' | C2' | C1' | H2' | 121.7° | 116.9° |
| C3' | C2' | C1' | H2'' | 120.0° | 122.5° |
| C3' | C2' | H2' | H2'' | 121.2° | 125.1° |
| C3' | C2' | C1' | N1 | 105.0° | 147.4° |
| C3' | C2' | C1' | H1' | 138.6° | 91.2° |
| H3' | C3' | O3' | HO3' | 134.0° | 19.0° |
| H3' | C3' | C2' | C1' | 98.0° | 156.4° |
| H3' | C3' | C2' | H2' | 140.3° | 38.9° |
| H3' | C3' | C2' | H2'' | 22.0° | 82.7° |
| C1' | C2' | H2' | H2'' | 121.2° | 122.7° |
| C2' | C1' | N1 | H1' | 116.9° | 123.5° |
| C2' | C1' | N1 | C2 | 114.8° | 93.5° |
| C2' | C1' | N1 | C6 | 66.4° | 86.5° |
| H2' | C2' | C1' | N1 | 133.3° | 30.6° |
| H2' | C2' | C1' | H1' | 17.0° | 151.9° |
| H2'' | C2' | C1' | N1 | 15.0° | 90.1° |
| H2'' | C2' | C1' | H1' | 101.4° | 31.3° |
| C1' | N1 | C2 | C6 | 178.7° | 180.0° |
| C1' | N1 | C2 | O2 | 5.6° | 0.0° |
| C1' | N1 | C2 | N3 | 176.1° | 180.0° |
| C1' | N1 | C6 | C5 | 179.4° | 180.0° |
| C1' | N1 | C6 | H6 | 0.6° | 0.1° |
| H1' | C1' | N1 | C2 | 2.1° | 30.0° |
| H1' | C1' | N1 | C6 | 176.7° | 150.0° |
| N1 | C2 | O2 | N3 | 178.2° | 180.0° |
| N1 | C2 | N3 | C4 | 6.5° | 0.0° |
| N1 | C2 | N3 | H19 | 173.5° | 180.0° |
| C2 | N1 | C6 | C5 | 0.7° | 0.0° |
| C2 | N1 | C6 | H6 | 179.3° | 180.0° |
| C6 | N1 | C2 | O2 | 173.2° | 180.0° |
| C6 | N1 | C2 | N3 | 5.1° | 0.1° |
| N1 | C6 | C5 | C4 | 2.6° | 0.0° |
| N1 | C6 | C5 | H6 | 180.0° | 179.9° |
| N1 | C6 | C5 | C14 | 178.0° | 180.0° |
| O2 | C2 | N3 | C4 | 171.9° | 180.0° |
| O2 | C2 | N3 | H19 | 8.1° | 0.0° |
| C2 | N3 | C4 | H19 | 180.0° | 180.0° |
| C2 | N3 | C4 | C5 | 3.4° | 0.0° |
| C2 | N3 | C4 | N17 | 176.5° | 180.0° |
| N3 | C4 | C5 | N17 | 179.9° | 179.9° |
| N3 | C4 | C5 | C6 | 1.4° | 0.0° |
| N3 | C4 | C5 | C14 | 179.1° | 180.0° |
| N3 | C4 | N17 | C15 | 179.3° | 180.0° |
| H19 | N3 | C4 | C5 | 176.5° | 180.0° |
| H19 | N3 | C4 | N17 | 3.5° | 0.0° |
| C4 | C5 | C6 | C14 | 179.4° | 180.0° |
| C4 | C5 | C6 | H6 | 177.3° | 180.0° |
| C4 | C5 | C14 | C15 | 0.7° | 0.0° |
| C4 | C5 | C14 | H14 | 179.3° | 180.0° |
| C5 | C4 | N17 | C15 | 0.6° | 0.1° |
| N17 | C4 | C5 | C6 | 178.7° | 180.0° |
| N17 | C4 | C5 | C14 | 0.8° | 0.0° |
| C4 | N17 | C15 | C14 | 0.2° | 0.1° |
| C4 | N17 | C15 | C16 | 179.6° | 180.0° |
| C6 | C5 | C14 | C15 | 178.7° | 180.0° |
| C6 | C5 | C14 | H14 | 1.2° | 0.0° |
| C14 | C5 | C6 | H6 | 2.0° | 0.0° |
| C5 | C14 | C15 | H14 | 180.0° | 180.0° |
| C5 | C14 | C15 | C16 | 179.9° | 179.9° |
| C5 | C14 | C15 | N17 | 0.4° | 0.1° |
| C14 | C15 | C16 | N17 | 179.7° | 179.9° |
| C14 | C15 | C16 | H161 | 31.8° | 42.6° |
| C14 | C15 | C16 | H162 | 151.8° | 162.8° |
| C14 | C15 | C16 | H163 | 88.2° | 77.5° |
| H14 | C14 | C15 | C16 | 0.1° | 0.1° |
| H14 | C14 | C15 | N17 | 179.6° | 179.9° |
| C15 | C16 | H161 | H162 | 120.0° | 120.9° |
| C15 | C16 | H161 | H163 | 120.0° | 120.9° |
| C15 | C16 | H162 | H163 | 120.0° | 120.6° |
| N17 | C15 | C16 | H161 | 148.0° | 137.5° |
| N17 | C15 | C16 | H162 | 28.0° | 17.3° |
| N17 | C15 | C16 | H163 | 92.1° | 102.3° |
| H161 | C16 | H162 | H163 | 120.0° | 118.5° |
