9V9
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP1 | P | doub | 1.48Å | 1.52Å | |
| P | OP2 | sing | 1.61Å | 1.49Å | |
| P | O5' | sing | 1.61Å | 1.61Å | |
| C5' | O5' | sing | 1.43Å | 1.43Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| O4' | C4' | sing | 1.46Å | 1.42Å | |
| O4' | C1' | sing | 1.44Å | 1.46Å | |
| C6' | C4' | sing | 1.56Å | 1.51Å | |
| C6' | O2' | sing | 1.47Å | 1.43Å | |
| C4' | C3' | sing | 1.57Å | 1.51Å | |
| C5M | C5 | sing | 1.51Å | 1.52Å | |
| C6 | C5 | doub | 1.35Å | 1.38Å | |
| C6 | N1 | sing | 1.37Å | 1.35Å | |
| C5 | C4 | sing | 1.42Å | 1.48Å | |
| C1' | N1 | sing | 1.47Å | 1.50Å | |
| C1' | C2' | sing | 1.56Å | 1.51Å | |
| N1 | C2 | sing | 1.35Å | 1.42Å | |
| C4 | O4 | doub | 1.22Å | 1.25Å | |
| C4 | N3 | sing | 1.35Å | 1.35Å | |
| O2' | C2' | sing | 1.46Å | 1.46Å | |
| C2 | N3 | sing | 1.35Å | 1.35Å | |
| C2 | S1 | doub | 1.71Å | 1.61Å | |
| C3' | C2' | sing | 1.57Å | 1.48Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C6 | H1 | sing | 1.08Å | 1.08Å | |
| OP2 | H2 | sing | 0.97Å | 0.95Å | |
| C5' | H4 | sing | 1.09Å | 1.10Å | |
| C5' | H5 | sing | 1.09Å | 1.10Å | |
| C1' | H6 | sing | 1.09Å | 1.10Å | |
| N3 | H7 | sing | 0.97Å | 1.00Å | |
| C5M | H8 | sing | 1.09Å | 1.10Å | |
| C5M | H9 | sing | 1.09Å | 1.10Å | |
| C5M | H10 | sing | 1.09Å | 1.10Å | |
| C2' | H11 | sing | 1.09Å | 1.10Å | |
| C6' | H12 | sing | 1.09Å | 1.10Å | |
| C6' | H13 | sing | 1.09Å | 1.10Å | |
| C3' | H14 | sing | 1.09Å | 1.10Å | |
| O3' | H15 | sing | 0.97Å | 0.95Å | |
| P | OP3 | sing | 1.61Å | 1.60Å | |
| OP3 | H3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | OP2 | 123.2° | 109.5° |
| OP1 | P | O5' | 109.1° | 109.4° |
| OP1 | P | OP3 | 107.3° | 109.5° |
| OP2 | P | O5' | 104.9° | 109.5° |
| P | OP2 | H2 | 109.5° | 114.0° |
| OP2 | P | OP3 | 107.5° | 109.5° |
| P | O5' | C5' | 113.2° | 123.0° |
| O5' | P | OP3 | 102.9° | 109.5° |
| O5' | C5' | C4' | 108.8° | 109.5° |
| O5' | C5' | H4 | 109.6° | 109.5° |
| O5' | C5' | H5 | 109.6° | 109.4° |
| C5' | C4' | O4' | 110.5° | 116.3° |
| C5' | C4' | C6' | 119.8° | 116.4° |
| C5' | C4' | C3' | 114.7° | 116.7° |
| C4' | C5' | H4 | 109.6° | 109.5° |
| C4' | C5' | H5 | 109.6° | 109.4° |
| C4' | O4' | C1' | 107.2° | 106.9° |
| O4' | C4' | C6' | 106.8° | 104.7° |
| O4' | C4' | C3' | 103.3° | 101.2° |
| O4' | C1' | N1 | 108.7° | 110.2° |
| O4' | C1' | C2' | 100.7° | 105.4° |
| O4' | C1' | H6 | 105.8° | 110.3° |
| C4' | C6' | O2' | 99.9° | 105.0° |
| C6' | C4' | C3' | 100.2° | 99.1° |
| C4' | C6' | H12 | 111.8° | 110.3° |
| C4' | C6' | H13 | 111.8° | 110.3° |
| C6' | O2' | C2' | 108.9° | 106.2° |
| O2' | C6' | H12 | 111.8° | 111.7° |
| O2' | C6' | H13 | 111.8° | 109.2° |
| C4' | C3' | C2' | 93.0° | 93.2° |
| C4' | C3' | O3' | 113.9° | 112.6° |
| C4' | C3' | H14 | 113.6° | 112.6° |
| C5M | C5 | C6 | 123.1° | 120.4° |
| C5M | C5 | C4 | 120.0° | 120.5° |
| C5 | C5M | H8 | 109.5° | 109.5° |
| C5 | C5M | H9 | 109.5° | 109.5° |
| C5 | C5M | H10 | 109.5° | 109.5° |
| C5 | C6 | N1 | 122.2° | 119.7° |
| C6 | C5 | C4 | 116.9° | 119.1° |
| C5 | C6 | H1 | 118.9° | 120.1° |
| C6 | N1 | C1' | 121.6° | 119.7° |
| C6 | N1 | C2 | 119.5° | 120.7° |
| N1 | C6 | H1 | 118.9° | 120.2° |
| C5 | C4 | O4 | 120.2° | 120.3° |
| C5 | C4 | N3 | 119.0° | 119.4° |
| N1 | C1' | C2' | 129.0° | 110.3° |
| C1' | N1 | C2 | 118.9° | 119.7° |
| N1 | C1' | H6 | 105.4° | 110.2° |
| C1' | C2' | O2' | 104.6° | 103.8° |
| C1' | C2' | C3' | 105.5° | 99.0° |
| C2' | C1' | H6 | 105.3° | 110.4° |
| C1' | C2' | H11 | 115.3° | 116.4° |
| N1 | C2 | N3 | 120.0° | 120.9° |
| N1 | C2 | S1 | 119.9° | 119.6° |
| O4 | C4 | N3 | 120.8° | 120.3° |
| C4 | N3 | C2 | 122.3° | 120.3° |
| C4 | N3 | H7 | 118.8° | 119.9° |
| O2' | C2' | C3' | 97.4° | 102.0° |
| O2' | C2' | H11 | 116.1° | 116.3° |
| N3 | C2 | S1 | 120.1° | 119.5° |
| C2 | N3 | H7 | 118.8° | 119.9° |
| C2' | C3' | O3' | 104.6° | 113.3° |
| C3' | C2' | H11 | 115.8° | 116.7° |
| C2' | C3' | H14 | 114.1° | 111.8° |
| O3' | C3' | H14 | 115.2° | 112.1° |
| C3' | O3' | H15 | 109.5° | 114.0° |
| H4 | C5' | H5 | 109.5° | 109.4° |
| H8 | C5M | H9 | 109.4° | 109.5° |
| H8 | C5M | H10 | 109.5° | 109.5° |
| H9 | C5M | H10 | 109.5° | 109.5° |
| H12 | C6' | H13 | 109.5° | 110.4° |
| P | OP3 | H3 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | OP2 | O5' | 125.4° | 120.0° |
| OP1 | P | OP2 | OP3 | 125.5° | 120.0° |
| OP1 | P | O5' | OP3 | 113.8° | 119.9° |
| OP1 | P | O5' | C5' | 45.4° | 55.1° |
| OP1 | P | OP2 | H2 | 0.0° | 180.0° |
| OP1 | P | OP3 | H3 | 0.0° | 60.0° |
| OP2 | P | O5' | OP3 | 112.4° | 120.1° |
| OP2 | P | O5' | C5' | 179.2° | 64.9° |
| OP2 | P | OP3 | H3 | 134.5° | 60.0° |
| P | O5' | C5' | C4' | 164.9° | 180.0° |
| O5' | P | OP2 | H2 | 125.5° | 60.0° |
| P | O5' | C5' | H4 | 75.2° | 59.9° |
| P | O5' | C5' | H5 | 45.1° | 60.1° |
| O5' | P | OP3 | H3 | 115.0° | 180.0° |
| O5' | C5' | C4' | H4 | 119.9° | 120.1° |
| O5' | C5' | C4' | H5 | 119.9° | 119.9° |
| O5' | C5' | C4' | O4' | 63.3° | 65.7° |
| O5' | C5' | C4' | C6' | 172.1° | 58.4° |
| O5' | C5' | C4' | C3' | 52.9° | 174.9° |
| O5' | C5' | H4 | H5 | 120.3° | 120.0° |
| C5' | O5' | P | OP3 | 68.4° | 175.0° |
| C5' | C4' | O4' | C6' | 131.8° | 130.0° |
| C5' | C4' | O4' | C3' | 123.1° | 127.5° |
| C5' | C4' | O4' | C1' | 159.3° | 165.3° |
| C5' | C4' | C6' | C3' | 126.3° | 125.9° |
| C5' | C4' | C6' | O2' | 161.4° | 159.5° |
| C5' | C4' | C3' | C2' | 171.9° | 177.7° |
| C5' | C4' | C3' | O3' | 80.7° | 60.8° |
| C4' | C5' | H4 | H5 | 120.3° | 120.0° |
| C5' | C4' | C6' | H12 | 43.0° | 39.1° |
| C5' | C4' | C6' | H13 | 80.2° | 83.0° |
| C5' | C4' | C3' | H14 | 53.9° | 67.1° |
| O4' | C4' | C6' | C3' | 107.3° | 104.2° |
| O4' | C4' | C6' | O2' | 72.2° | 70.6° |
| C4' | O4' | C1' | N1 | 141.6° | 122.3° |
| C4' | O4' | C1' | C2' | 4.0° | 3.3° |
| O4' | C4' | C3' | C2' | 51.6° | 55.1° |
| O4' | C4' | C3' | O3' | 159.1° | 172.0° |
| O4' | C4' | C5' | H4 | 176.8° | 54.4° |
| O4' | C4' | C5' | H5 | 56.6° | 174.4° |
| C4' | O4' | C1' | H6 | 105.5° | 115.8° |
| O4' | C4' | C6' | H12 | 169.4° | 169.0° |
| O4' | C4' | C6' | H13 | 46.3° | 46.9° |
| O4' | C4' | C3' | H14 | 66.4° | 60.1° |
| C1' | O4' | C4' | C6' | 68.9° | 64.8° |
| C1' | O4' | C4' | C3' | 36.2° | 37.8° |
| O4' | C1' | N1 | C6 | 32.0° | 20.9° |
| O4' | C1' | N1 | C2' | 121.7° | 115.9° |
| O4' | C1' | N1 | H6 | 113.1° | 121.9° |
| O4' | C1' | C2' | H6 | 109.9° | 119.0° |
| O4' | C1' | N1 | C2 | 147.9° | 159.2° |
| O4' | C1' | C2' | O2' | 71.5° | 72.7° |
| O4' | C1' | C2' | C3' | 30.6° | 32.1° |
| O4' | C1' | C2' | H11 | 159.8° | 158.1° |
| C4' | C6' | O2' | H12 | 118.4° | 119.5° |
| C4' | C6' | O2' | H13 | 118.5° | 118.2° |
| C4' | C6' | O2' | C2' | 2.1° | 1.6° |
| C6' | C4' | C3' | C2' | 58.5° | 51.9° |
| C6' | C4' | C3' | O3' | 49.0° | 64.9° |
| C6' | C4' | C5' | H4 | 52.2° | 178.5° |
| C6' | C4' | C5' | H5 | 68.1° | 61.5° |
| C4' | C6' | H12 | H13 | 124.5° | 122.1° |
| C6' | C4' | C3' | H14 | 176.5° | 167.1° |
| O2' | C6' | C4' | C3' | 35.1° | 33.6° |
| C6' | O2' | C2' | C1' | 68.9° | 66.0° |
| C6' | O2' | C2' | C3' | 39.3° | 36.6° |
| C6' | O2' | C2' | H11 | 162.8° | 164.7° |
| O2' | C6' | H12 | H13 | 124.5° | 121.7° |
| C4' | C3' | C2' | C1' | 49.7° | 51.0° |
| C4' | C3' | C2' | O2' | 57.7° | 55.2° |
| C4' | C3' | C2' | O3' | 115.7° | 116.3° |
| C4' | C3' | C2' | H14 | 117.5° | 115.9° |
| C4' | C3' | O3' | H14 | 133.8° | 128.2° |
| C3' | C4' | C5' | H4 | 67.0° | 65.0° |
| C3' | C4' | C5' | H5 | 172.8° | 55.0° |
| C4' | C3' | C2' | H11 | 178.5° | 176.8° |
| C3' | C4' | C6' | H12 | 83.3° | 86.8° |
| C3' | C4' | C6' | H13 | 153.6° | 151.1° |
| C4' | C3' | O3' | H15 | 180.0° | 180.0° |
| C5M | C5 | C6 | C4 | 180.0° | 180.0° |
| C5M | C5 | C6 | N1 | 180.0° | 180.0° |
| C5M | C5 | C4 | O4 | 0.1° | 0.0° |
| C5M | C5 | C4 | N3 | 180.0° | 179.8° |
| C5M | C5 | C6 | H1 | 0.0° | 0.0° |
| C5 | C5M | H8 | H9 | 120.0° | 120.0° |
| C5 | C5M | H8 | H10 | 120.0° | 120.0° |
| C5 | C5M | H9 | H10 | 120.0° | 120.0° |
| C5 | C6 | N1 | H1 | 180.0° | 180.0° |
| C5 | C6 | N1 | C1' | 180.0° | 179.9° |
| C5 | C6 | N1 | C2 | 0.0° | 0.0° |
| C6 | C5 | C4 | O4 | 179.9° | 180.0° |
| C6 | C5 | C4 | N3 | 0.0° | 0.2° |
| C6 | C5 | C5M | H8 | 180.0° | 180.0° |
| C6 | C5 | C5M | H9 | 60.0° | 60.0° |
| C6 | C5 | C5M | H10 | 60.0° | 60.0° |
| N1 | C6 | C5 | C4 | 0.0° | 0.0° |
| C6 | N1 | C1' | C2 | 180.0° | 179.9° |
| C6 | N1 | C1' | C2' | 89.7° | 95.1° |
| C6 | N1 | C2 | N3 | 0.0° | 0.3° |
| C6 | N1 | C2 | S1 | 180.0° | 180.0° |
| C6 | N1 | C1' | H6 | 145.1° | 142.8° |
| C5 | C4 | O4 | N3 | 179.9° | 179.8° |
| C5 | C4 | N3 | C2 | 0.0° | 0.5° |
| C4 | C5 | C6 | H1 | 180.0° | 180.0° |
| C5 | C4 | N3 | H7 | 180.0° | 179.8° |
| C4 | C5 | C5M | H8 | 0.0° | 0.1° |
| C4 | C5 | C5M | H9 | 120.0° | 119.9° |
| C4 | C5 | C5M | H10 | 120.0° | 120.0° |
| N1 | C1' | C2' | H6 | 125.2° | 122.0° |
| N1 | C1' | C2' | O2' | 163.6° | 168.3° |
| C1' | N1 | C2 | N3 | 180.0° | 179.8° |
| C1' | N1 | C2 | S1 | 0.0° | 0.1° |
| N1 | C1' | C2' | C3' | 94.3° | 86.9° |
| C1' | N1 | C6 | H1 | 0.0° | 0.0° |
| N1 | C1' | C2' | H11 | 34.9° | 39.1° |
| C2' | C1' | N1 | C2 | 90.3° | 84.8° |
| C1' | C2' | O2' | C3' | 108.2° | 102.5° |
| C1' | C2' | O2' | H11 | 128.2° | 129.3° |
| C1' | C2' | C3' | H11 | 128.8° | 125.8° |
| C1' | C2' | C3' | O3' | 165.3° | 167.3° |
| C1' | C2' | C3' | H14 | 67.8° | 64.8° |
| N1 | C2 | N3 | C4 | 0.0° | 0.5° |
| N1 | C2 | N3 | S1 | 180.0° | 179.7° |
| C2 | N1 | C6 | H1 | 180.0° | 179.9° |
| C2 | N1 | C1' | H6 | 34.9° | 37.3° |
| N1 | C2 | N3 | H7 | 180.0° | 179.7° |
| O4 | C4 | N3 | C2 | 179.9° | 179.7° |
| O4 | C4 | N3 | H7 | 0.1° | 0.0° |
| C4 | N3 | C2 | H7 | 180.0° | 179.8° |
| C4 | N3 | C2 | S1 | 180.0° | 179.8° |
| O2' | C2' | C3' | H11 | 123.7° | 127.9° |
| O2' | C2' | C3' | O3' | 57.9° | 61.0° |
| O2' | C2' | C1' | H6 | 38.3° | 46.3° |
| C2' | O2' | C6' | H12 | 120.5° | 121.1° |
| C2' | O2' | C6' | H13 | 116.3° | 116.6° |
| O2' | C2' | C3' | H14 | 175.2° | 171.1° |
| S1 | C2 | N3 | H7 | 0.0° | 0.0° |
| C2' | C3' | O3' | H14 | 126.2° | 127.7° |
| C3' | C2' | C1' | H6 | 140.5° | 151.1° |
| C2' | C3' | O3' | H15 | 80.0° | 75.9° |
| O3' | C3' | C2' | H11 | 65.8° | 66.9° |
| H2 | OP2 | P | OP3 | 125.4° | 60.0° |
| H6 | C1' | C2' | H11 | 90.4° | 82.9° |
| H8 | C5M | H9 | H10 | 120.0° | 120.0° |
| H11 | C2' | C3' | H14 | 61.0° | 61.0° |
| H14 | C3' | O3' | H15 | 46.2° | 51.8° |
