5JO
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP1 | P | doub | 1.48Å | 1.49Å | |
| P | OP2 | sing | 1.61Å | 1.48Å | |
| P | O5' | sing | 1.61Å | 1.59Å | |
| C5' | O5' | sing | 1.43Å | 1.43Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| O4' | C4' | sing | 1.44Å | 1.45Å | |
| O4' | C1' | sing | 1.44Å | 1.42Å | |
| C4' | C3' | sing | 1.54Å | 1.52Å | |
| C8 | N7 | doub | 1.30Å | 1.31Å | Aromatic |
| C8 | N9 | sing | 1.36Å | 1.37Å | Aromatic |
| C1' | N9 | sing | 1.46Å | 1.47Å | |
| C1' | C2' | sing | 1.54Å | 1.53Å | |
| N7 | C5 | sing | 1.36Å | 1.39Å | Aromatic |
| N9 | C4 | sing | 1.37Å | 1.37Å | Aromatic |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | C2' | sing | 1.55Å | 1.52Å | |
| C5 | C4 | doub | 1.40Å | 1.38Å | Aromatic |
| C5 | C6 | sing | 1.41Å | 1.41Å | Aromatic |
| C4 | N3 | sing | 1.33Å | 1.34Å | Aromatic |
| C2' | O2' | sing | 1.43Å | 1.42Å | |
| O2' | C6' | sing | 1.43Å | 1.41Å | |
| C6 | N6 | sing | 1.38Å | 1.34Å | |
| C6 | N1 | doub | 1.33Å | 1.35Å | Aromatic |
| N3 | C2 | doub | 1.32Å | 1.33Å | Aromatic |
| C6' | C7' | sing | 1.47Å | 1.41Å | |
| C2 | N1 | sing | 1.32Å | 1.34Å | Aromatic |
| C7' | C8' | trip | 1.17Å | 1.25Å | |
| C5' | H1 | sing | 1.09Å | 1.10Å | |
| C5' | H2 | sing | 1.09Å | 1.10Å | |
| C4' | H3 | sing | 1.09Å | 1.10Å | |
| C3' | H4 | sing | 1.09Å | 1.10Å | |
| O3' | H5 | sing | 0.97Å | 0.95Å | |
| C2' | H6 | sing | 1.09Å | 1.10Å | |
| C1' | H7 | sing | 1.09Å | 1.10Å | |
| C8 | H8 | sing | 1.08Å | 1.08Å | |
| N6 | H9 | sing | 0.97Å | 1.00Å | |
| N6 | H10 | sing | 0.97Å | 1.00Å | |
| C2 | H11 | sing | 1.08Å | 1.08Å | |
| OP2 | H13 | sing | 0.97Å | 0.95Å | |
| C6' | H14 | sing | 1.09Å | 1.10Å | |
| C6' | H15 | sing | 1.09Å | 1.10Å | |
| C8' | H16 | sing | 1.05Å | 1.06Å | |
| P | OP3 | sing | 1.61Å | 1.60Å | |
| OP3 | H12 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | OP2 | 119.1° | 109.4° |
| OP1 | P | O5' | 110.7° | 109.5° |
| OP1 | P | OP3 | 107.7° | 109.5° |
| OP2 | P | O5' | 106.6° | 109.5° |
| P | OP2 | H13 | 109.5° | 114.0° |
| OP2 | P | OP3 | 108.3° | 109.5° |
| P | O5' | C5' | 121.1° | 123.0° |
| O5' | P | OP3 | 103.2° | 109.5° |
| O5' | C5' | C4' | 110.2° | 109.4° |
| O5' | C5' | H1 | 109.3° | 109.5° |
| O5' | C5' | H2 | 109.3° | 109.5° |
| C5' | C4' | O4' | 110.1° | 110.4° |
| C5' | C4' | C3' | 116.5° | 110.4° |
| C4' | C5' | H1 | 109.3° | 109.4° |
| C4' | C5' | H2 | 109.3° | 109.5° |
| C5' | C4' | H3 | 108.7° | 110.3° |
| C4' | O4' | C1' | 109.4° | 105.3° |
| O4' | C4' | C3' | 103.4° | 104.8° |
| O4' | C4' | H3 | 109.4° | 110.4° |
| O4' | C1' | N9 | 108.5° | 110.4° |
| O4' | C1' | C2' | 106.7° | 104.8° |
| O4' | C1' | H7 | 110.2° | 110.4° |
| C4' | C3' | O3' | 111.5° | 110.5° |
| C4' | C3' | C2' | 100.8° | 104.1° |
| C3' | C4' | H3 | 108.5° | 110.4° |
| C4' | C3' | H4 | 109.4° | 110.5° |
| N7 | C8 | N9 | 113.8° | 110.0° |
| C8 | N7 | C5 | 103.9° | 109.4° |
| N7 | C8 | H8 | 123.1° | 125.0° |
| C8 | N9 | C1' | 128.2° | 126.3° |
| C8 | N9 | C4 | 105.8° | 107.5° |
| N9 | C8 | H8 | 123.1° | 125.0° |
| N9 | C1' | C2' | 113.3° | 110.3° |
| C1' | N9 | C4 | 126.0° | 126.2° |
| N9 | C1' | H7 | 109.5° | 110.4° |
| C1' | C2' | C3' | 101.0° | 104.1° |
| C1' | C2' | O2' | 111.9° | 110.5° |
| C1' | C2' | H6 | 110.1° | 110.7° |
| C2' | C1' | H7 | 108.7° | 110.5° |
| N7 | C5 | C4 | 110.6° | 107.1° |
| N7 | C5 | C6 | 132.3° | 134.7° |
| N9 | C4 | C5 | 105.9° | 106.0° |
| N9 | C4 | N3 | 127.3° | 135.0° |
| O3' | C3' | C2' | 114.4° | 110.6° |
| O3' | C3' | H4 | 110.8° | 110.5° |
| C3' | O3' | H5 | 109.5° | 114.0° |
| C3' | C2' | O2' | 111.4° | 110.5° |
| C2' | C3' | H4 | 109.5° | 110.6° |
| C3' | C2' | H6 | 110.2° | 110.5° |
| C4 | C5 | C6 | 117.1° | 118.2° |
| C5 | C4 | N3 | 126.8° | 119.0° |
| C5 | C6 | N6 | 123.7° | 120.8° |
| C5 | C6 | N1 | 117.7° | 118.4° |
| C4 | N3 | C2 | 110.6° | 120.6° |
| C2' | O2' | C6' | 111.4° | 114.0° |
| O2' | C2' | H6 | 111.8° | 110.4° |
| O2' | C6' | C7' | 103.0° | 109.5° |
| O2' | C6' | H14 | 111.0° | 109.4° |
| O2' | C6' | H15 | 111.0° | 109.5° |
| N6 | C6 | N1 | 118.7° | 120.8° |
| C6 | N6 | H9 | 109.5° | 120.0° |
| C6 | N6 | H10 | 109.5° | 120.0° |
| C6 | N1 | C2 | 118.6° | 121.2° |
| N3 | C2 | N1 | 129.3° | 122.4° |
| N3 | C2 | H11 | 115.4° | 118.8° |
| C6' | C7' | C8' | 177.6° | 180.0° |
| C7' | C6' | H14 | 111.0° | 109.5° |
| C7' | C6' | H15 | 111.1° | 109.5° |
| N1 | C2 | H11 | 115.4° | 118.8° |
| C7' | C8' | H16 | 180.0° | 179.9° |
| H1 | C5' | H2 | 109.5° | 109.5° |
| H9 | N6 | H10 | 109.4° | 120.0° |
| H14 | C6' | H15 | 109.5° | 109.5° |
| P | OP3 | H12 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | OP2 | O5' | 126.0° | 120.0° |
| OP1 | P | OP2 | OP3 | 123.5° | 120.0° |
| OP1 | P | O5' | OP3 | 115.0° | 120.0° |
| OP1 | P | O5' | C5' | 42.2° | 55.0° |
| OP1 | P | OP2 | H13 | 0.0° | 179.9° |
| OP1 | P | OP3 | H12 | 0.0° | 60.0° |
| OP2 | P | O5' | OP3 | 114.0° | 120.0° |
| OP2 | P | O5' | C5' | 173.2° | 65.0° |
| OP2 | P | OP3 | H12 | 130.1° | 60.0° |
| P | O5' | C5' | C4' | 178.5° | 179.9° |
| P | O5' | C5' | H1 | 61.4° | 60.0° |
| P | O5' | C5' | H2 | 58.3° | 60.1° |
| O5' | P | OP2 | H13 | 126.1° | 60.1° |
| O5' | P | OP3 | H12 | 117.2° | 180.0° |
| O5' | C5' | C4' | H1 | 120.1° | 120.0° |
| O5' | C5' | C4' | H2 | 120.1° | 120.0° |
| O5' | C5' | C4' | O4' | 65.0° | 69.6° |
| O5' | C5' | C4' | C3' | 52.3° | 175.0° |
| O5' | C5' | H1 | H2 | 119.7° | 120.0° |
| O5' | C5' | C4' | H3 | 175.2° | 52.7° |
| C5' | O5' | P | OP3 | 72.8° | 175.0° |
| C5' | C4' | O4' | C3' | 125.2° | 118.9° |
| C5' | C4' | O4' | H3 | 119.4° | 122.2° |
| C5' | C4' | O4' | C1' | 149.1° | 159.4° |
| C5' | C4' | C3' | H3 | 123.0° | 122.2° |
| C5' | C4' | C3' | O3' | 76.8° | 98.5° |
| C5' | C4' | C3' | C2' | 161.4° | 142.8° |
| C4' | C5' | H1 | H2 | 119.7° | 120.0° |
| C5' | C4' | C3' | H4 | 46.1° | 24.1° |
| O4' | C4' | C3' | H3 | 116.0° | 118.9° |
| C4' | O4' | C1' | N9 | 119.7° | 159.3° |
| C4' | O4' | C1' | C2' | 2.6° | 40.5° |
| O4' | C4' | C3' | O3' | 162.2° | 142.6° |
| O4' | C4' | C3' | C2' | 40.4° | 23.9° |
| O4' | C4' | C5' | H1 | 174.9° | 50.4° |
| O4' | C4' | C5' | H2 | 55.1° | 170.4° |
| O4' | C4' | C3' | H4 | 74.8° | 94.8° |
| C4' | O4' | C1' | H7 | 120.4° | 78.5° |
| C1' | O4' | C4' | C3' | 23.9° | 40.5° |
| O4' | C1' | N9 | C8 | 25.2° | 23.8° |
| O4' | C1' | N9 | C2' | 118.2° | 115.3° |
| O4' | C1' | N9 | H7 | 120.3° | 122.3° |
| O4' | C1' | C2' | H7 | 118.8° | 118.9° |
| O4' | C1' | N9 | C4 | 155.5° | 156.4° |
| O4' | C1' | C2' | C3' | 27.9° | 24.0° |
| O4' | C1' | C2' | O2' | 90.7° | 142.6° |
| C1' | O4' | C4' | H3 | 91.5° | 78.4° |
| O4' | C1' | C2' | H6 | 144.3° | 94.7° |
| C4' | C3' | C2' | C1' | 40.9° | 0.0° |
| C4' | C3' | O3' | C2' | 113.6° | 114.7° |
| C4' | C3' | O3' | H4 | 122.2° | 122.6° |
| C4' | C3' | C2' | H4 | 115.2° | 118.7° |
| C4' | C3' | C2' | O2' | 78.0° | 118.7° |
| C3' | C4' | C5' | H1 | 67.8° | 65.0° |
| C3' | C4' | C5' | H2 | 172.4° | 55.0° |
| C4' | C3' | O3' | H5 | 180.0° | 61.5° |
| C4' | C3' | C2' | H6 | 157.3° | 118.8° |
| N7 | C8 | N9 | H8 | 180.0° | 180.0° |
| N7 | C8 | N9 | C1' | 179.6° | 179.9° |
| N7 | C8 | N9 | C4 | 0.2° | 0.3° |
| C8 | N7 | C5 | C4 | 0.3° | 0.2° |
| C8 | N7 | C5 | C6 | 179.9° | 180.0° |
| C8 | N9 | C1' | C4 | 179.3° | 179.8° |
| C8 | N9 | C1' | C2' | 93.0° | 91.5° |
| N9 | C8 | N7 | C5 | 0.0° | 0.0° |
| C8 | N9 | C4 | C5 | 0.4° | 0.4° |
| C8 | N9 | C4 | N3 | 179.8° | 179.4° |
| C8 | N9 | C1' | H7 | 145.5° | 146.1° |
| N9 | C1' | C2' | H7 | 122.0° | 122.3° |
| N9 | C1' | C2' | C3' | 91.4° | 142.8° |
| C1' | N9 | C4 | C5 | 179.8° | 179.8° |
| C1' | N9 | C4 | N3 | 0.3° | 0.8° |
| N9 | C1' | C2' | O2' | 150.1° | 98.6° |
| N9 | C1' | C2' | H6 | 25.1° | 24.1° |
| C1' | N9 | C8 | H8 | 0.3° | 0.0° |
| C2' | C1' | N9 | C4 | 86.3° | 88.2° |
| C1' | C2' | C3' | O3' | 160.7° | 118.6° |
| C1' | C2' | C3' | O2' | 119.0° | 118.6° |
| C1' | C2' | C3' | H6 | 116.4° | 118.8° |
| C1' | C2' | O2' | H6 | 124.0° | 122.8° |
| C1' | C2' | O2' | C6' | 71.8° | 153.9° |
| C1' | C2' | C3' | H4 | 74.3° | 118.7° |
| N7 | C5 | C4 | N9 | 0.4° | 0.4° |
| N7 | C5 | C4 | C6 | 179.8° | 179.8° |
| N7 | C5 | C4 | N3 | 179.7° | 179.6° |
| N7 | C5 | C6 | N6 | 0.1° | 0.0° |
| N7 | C5 | C6 | N1 | 179.5° | 179.9° |
| C5 | N7 | C8 | H8 | 180.0° | 180.0° |
| N9 | C4 | C5 | N3 | 179.9° | 179.2° |
| N9 | C4 | C5 | C6 | 179.8° | 179.8° |
| N9 | C4 | N3 | C2 | 179.7° | 179.5° |
| C4 | N9 | C1' | H7 | 35.2° | 34.2° |
| C4 | N9 | C8 | H8 | 179.8° | 179.8° |
| O3' | C3' | C2' | H4 | 125.0° | 122.7° |
| O3' | C3' | C2' | O2' | 41.7° | 0.0° |
| O3' | C3' | C4' | H3 | 46.2° | 23.7° |
| O3' | C3' | C2' | H6 | 82.9° | 122.5° |
| C3' | C2' | O2' | H6 | 123.8° | 122.6° |
| C3' | C2' | O2' | C6' | 176.0° | 91.4° |
| C2' | C3' | C4' | H3 | 75.6° | 95.0° |
| C2' | C3' | O3' | H5 | 66.4° | 176.1° |
| C3' | C2' | C1' | H7 | 146.6° | 94.9° |
| C4 | C5 | C6 | N6 | 179.7° | 179.7° |
| C4 | C5 | C6 | N1 | 0.3° | 0.3° |
| C5 | C4 | N3 | C2 | 0.1° | 0.6° |
| C6 | C5 | C4 | N3 | 0.1° | 0.6° |
| C5 | C6 | N6 | N1 | 179.3° | 179.9° |
| C5 | C6 | N1 | C2 | 0.6° | 0.0° |
| C5 | C6 | N6 | H9 | 179.3° | 0.1° |
| C5 | C6 | N6 | H10 | 60.7° | 180.0° |
| C4 | N3 | C2 | N1 | 0.4° | 0.3° |
| C4 | N3 | C2 | H11 | 179.6° | 179.7° |
| C2' | O2' | C6' | C7' | 149.3° | 180.0° |
| O2' | C2' | C3' | H4 | 166.7° | 122.7° |
| O2' | C2' | C1' | H7 | 28.1° | 23.8° |
| C2' | O2' | C6' | H14 | 91.8° | 60.0° |
| C2' | O2' | C6' | H15 | 30.3° | 60.0° |
| O2' | C6' | C7' | H14 | 118.9° | 119.9° |
| O2' | C6' | C7' | H15 | 118.9° | 120.0° |
| O2' | C6' | C7' | C8' | 147.3° | 17.6° |
| C6' | O2' | C2' | H6 | 52.2° | 31.2° |
| O2' | C6' | H14 | H15 | 123.0° | 120.0° |
| N6 | C6 | N1 | C2 | 179.9° | 180.0° |
| C6 | N6 | H9 | H10 | 120.0° | 180.0° |
| C6 | N1 | C2 | N3 | 0.7° | 0.0° |
| N1 | C6 | N6 | H9 | 0.0° | 180.0° |
| N1 | C6 | N6 | H10 | 120.0° | 0.0° |
| C6 | N1 | C2 | H11 | 179.3° | 180.0° |
| N3 | C2 | N1 | H11 | 180.0° | 180.0° |
| C7' | C6' | H14 | H15 | 123.0° | 120.0° |
| C6' | C7' | C8' | H16 | 30.4° | 173.5° |
| C8' | C7' | C6' | H14 | 28.4° | 102.3° |
| C8' | C7' | C6' | H15 | 93.7° | 137.6° |
| H1 | C5' | C4' | H3 | 55.1° | 172.7° |
| H2 | C5' | C4' | H3 | 64.7° | 67.2° |
| H3 | C4' | C3' | H4 | 169.1° | 146.3° |
| H4 | C3' | O3' | H5 | 57.9° | 61.1° |
| H4 | C3' | C2' | H6 | 42.1° | 0.1° |
| H6 | C2' | C1' | H7 | 96.9° | 146.4° |
| H13 | OP2 | P | OP3 | 123.4° | 59.9° |
