Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | OP1 | sing | 1.61Å | 1.48Å | |
| P | S2P | doub | 1.86Å | 2.13Å | |
| P | OP3 | sing | 1.61Å | 1.62Å | |
| P | O5' | sing | 1.61Å | 1.62Å | |
| OP1 | HOP1 | sing | 0.97Å | 0.95Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å | |
| O5' | C5' | sing | 1.43Å | 1.42Å | |
| C5' | C4' | sing | 1.53Å | 1.53Å | |
| C5' | H5' | sing | 1.09Å | 1.09Å | |
| C5' | H5'' | sing | 1.09Å | 1.09Å | |
| C4' | O4' | sing | 1.45Å | 1.42Å | |
| C4' | C3' | sing | 1.55Å | 1.53Å | |
| C4' | H4' | sing | 1.09Å | 1.09Å | |
| O4' | C1' | sing | 1.44Å | 1.42Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C3' | C2' | sing | 1.55Å | 1.52Å | |
| C3' | H3' | sing | 1.09Å | 1.09Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C2' | C1' | sing | 1.54Å | 1.53Å | |
| C2' | H2' | sing | 1.09Å | 1.08Å | |
| C2' | H2'' | sing | 1.09Å | 1.09Å | |
| C1' | N1 | sing | 1.47Å | 1.49Å | |
| C1' | H1' | sing | 1.09Å | 1.09Å | |
| N1 | C2 | sing | 1.34Å | 1.39Å | |
| N1 | C6 | sing | 1.37Å | 1.38Å | |
| C2 | O2 | doub | 1.22Å | 1.23Å | |
| C2 | N3 | sing | 1.35Å | 1.39Å | |
| N3 | C4 | sing | 1.35Å | 1.39Å | |
| N3 | HN3 | sing | 0.97Å | 1.01Å | |
| C4 | O4 | doub | 1.22Å | 1.23Å | |
| C4 | C5 | sing | 1.42Å | 1.45Å | |
| C5 | C5M | sing | 1.51Å | 1.52Å | |
| C5 | C6 | doub | 1.35Å | 1.36Å | |
| C5M | HM51 | sing | 1.09Å | 1.09Å | |
| C5M | HM52 | sing | 1.09Å | 1.09Å | |
| C5M | HM53 | sing | 1.09Å | 1.09Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | S2P | 120.0° | 109.4° |
| OP1 | P | OP3 | 107.6° | 109.4° |
| OP1 | P | O5' | 107.9° | 109.5° |
| P | OP1 | HOP1 | 120.0° | 106.8° |
| S2P | P | OP3 | 108.1° | 109.5° |
| S2P | P | O5' | 107.1° | 109.5° |
| OP3 | P | O5' | 105.2° | 109.5° |
| P | OP3 | HOP3 | 107.6° | 106.9° |
| P | O5' | C5' | 122.4° | 106.8° |
| O5' | C5' | C4' | 110.0° | 109.5° |
| O5' | C5' | H5' | 109.8° | 109.4° |
| O5' | C5' | H5'' | 109.9° | 109.5° |
| C4' | C5' | H5' | 108.8° | 109.5° |
| C4' | C5' | H5'' | 109.4° | 109.5° |
| C5' | C4' | O4' | 110.1° | 110.7° |
| C5' | C4' | C3' | 114.6° | 110.6° |
| C5' | C4' | H4' | 109.4° | 110.5° |
| H5' | C5' | H5'' | 109.0° | 109.5° |
| O4' | C4' | C3' | 105.7° | 103.6° |
| O4' | C4' | H4' | 108.2° | 110.5° |
| C4' | O4' | C1' | 109.3° | 106.8° |
| C3' | C4' | H4' | 108.6° | 110.6° |
| C4' | C3' | O3' | 112.5° | 110.9° |
| C4' | C3' | C2' | 99.8° | 102.1° |
| C4' | C3' | H3' | 110.1° | 110.9° |
| O4' | C1' | C2' | 106.8° | 107.5° |
| O4' | C1' | N1 | 111.1° | 109.9° |
| O4' | C1' | H1' | 107.6° | 109.9° |
| O3' | C3' | C2' | 111.1° | 110.9° |
| O3' | C3' | H3' | 112.2° | 110.8° |
| C3' | O3' | HO3' | 112.4° | 106.8° |
| C2' | C3' | H3' | 110.5° | 110.9° |
| C3' | C2' | C1' | 103.9° | 104.2° |
| C3' | C2' | H2' | 112.1° | 110.5° |
| C3' | C2' | H2'' | 109.8° | 110.5° |
| C1' | C2' | H2' | 111.8° | 110.5° |
| C1' | C2' | H2'' | 108.9° | 110.5° |
| C2' | C1' | N1 | 110.8° | 109.9° |
| C2' | C1' | H1' | 109.1° | 109.8° |
| H2' | C2' | H2'' | 110.1° | 110.5° |
| N1 | C1' | H1' | 111.3° | 109.9° |
| C1' | N1 | C2 | 118.0° | 119.7° |
| C1' | N1 | C6 | 121.6° | 119.6° |
| C2 | N1 | C6 | 120.4° | 120.6° |
| N1 | C2 | O2 | 123.1° | 119.5° |
| N1 | C2 | N3 | 116.2° | 120.9° |
| N1 | C6 | C5 | 122.2° | 119.7° |
| N1 | C6 | H6 | 119.2° | 120.2° |
| O2 | C2 | N3 | 120.7° | 119.5° |
| C2 | N3 | C4 | 126.5° | 120.2° |
| C2 | N3 | HN3 | 116.2° | 119.9° |
| C4 | N3 | HN3 | 117.4° | 119.9° |
| N3 | C4 | O4 | 120.0° | 120.3° |
| N3 | C4 | C5 | 114.0° | 119.4° |
| O4 | C4 | C5 | 126.0° | 120.3° |
| C4 | C5 | C5M | 119.8° | 120.4° |
| C4 | C5 | C6 | 120.4° | 119.1° |
| C5M | C5 | C6 | 119.7° | 120.5° |
| C5 | C5M | HM51 | 109.7° | 109.5° |
| C5 | C5M | HM52 | 110.5° | 109.5° |
| C5 | C5M | HM53 | 110.0° | 109.5° |
| C5 | C6 | H6 | 118.7° | 120.1° |
| HM51 | C5M | HM52 | 109.2° | 109.4° |
| HM51 | C5M | HM53 | 109.2° | 109.5° |
| HM52 | C5M | HM53 | 108.1° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | S2P | OP3 | 123.8° | 120.0° |
| OP1 | P | S2P | O5' | 123.3° | 120.0° |
| OP1 | P | OP3 | O5' | 114.9° | 120.0° |
| OP1 | P | OP3 | HOP3 | 180.0° | 60.0° |
| OP1 | P | O5' | C5' | 33.8° | 180.0° |
| S2P | P | OP3 | O5' | 114.2° | 120.1° |
| S2P | P | OP1 | HOP1 | 180.0° | 60.0° |
| S2P | P | OP3 | HOP3 | 49.0° | 180.0° |
| S2P | P | O5' | C5' | 164.2° | 60.0° |
| OP3 | P | OP1 | HOP1 | 56.0° | 60.0° |
| OP3 | P | O5' | C5' | 80.9° | 60.1° |
| O5' | P | OP1 | HOP1 | 57.1° | 180.0° |
| O5' | P | OP3 | HOP3 | 65.1° | 60.0° |
| P | O5' | C5' | C4' | 172.3° | 180.0° |
| P | O5' | C5' | H5' | 52.7° | 60.0° |
| P | O5' | C5' | H5'' | 67.2° | 60.0° |
| O5' | C5' | C4' | H5' | 120.3° | 120.0° |
| O5' | C5' | C4' | H5'' | 120.8° | 120.0° |
| O5' | C5' | H5' | H5'' | 120.4° | 120.0° |
| O5' | C5' | C4' | O4' | 56.7° | 65.7° |
| O5' | C5' | C4' | C3' | 62.3° | 180.0° |
| O5' | C5' | C4' | H4' | 175.5° | 57.1° |
| C4' | C5' | H5' | H5'' | 119.2° | 120.0° |
| C5' | C4' | O4' | C3' | 124.3° | 118.6° |
| C5' | C4' | O4' | H4' | 119.5° | 122.8° |
| C5' | C4' | C3' | H4' | 122.6° | 122.8° |
| C5' | C4' | O4' | C1' | 151.8° | 158.5° |
| C5' | C4' | C3' | O3' | 83.2° | 86.1° |
| C5' | C4' | C3' | C2' | 158.9° | 155.7° |
| C5' | C4' | C3' | H3' | 42.7° | 37.5° |
| H5' | C5' | C4' | O4' | 63.6° | 174.3° |
| H5' | C5' | C4' | C3' | 177.4° | 60.0° |
| H5' | C5' | C4' | H4' | 55.2° | 62.9° |
| H5'' | C5' | C4' | O4' | 177.5° | 54.3° |
| H5'' | C5' | C4' | C3' | 58.5° | 60.0° |
| H5'' | C5' | C4' | H4' | 63.7° | 177.1° |
| O4' | C4' | C3' | H4' | 116.0° | 118.5° |
| O4' | C4' | C3' | O3' | 155.3° | 155.2° |
| O4' | C4' | C3' | C2' | 37.5° | 37.0° |
| O4' | C4' | C3' | H3' | 78.7° | 81.2° |
| C4' | O4' | C1' | C2' | 5.3° | 26.3° |
| C4' | O4' | C1' | N1 | 126.2° | 145.8° |
| C4' | O4' | C1' | H1' | 111.7° | 93.2° |
| C3' | C4' | O4' | C1' | 27.5° | 39.9° |
| C4' | C3' | O3' | C2' | 110.9° | 112.7° |
| C4' | C3' | O3' | H3' | 124.8° | 123.7° |
| C4' | C3' | C2' | H3' | 115.9° | 118.2° |
| C4' | C3' | O3' | HO3' | 180.0° | 174.1° |
| C4' | C3' | C2' | C1' | 33.2° | 20.9° |
| C4' | C3' | C2' | H2' | 154.1° | 97.8° |
| C4' | C3' | C2' | H2'' | 83.2° | 139.5° |
| H4' | C4' | O4' | C1' | 88.7° | 78.7° |
| H4' | C4' | C3' | O3' | 39.4° | 36.7° |
| H4' | C4' | C3' | C2' | 78.4° | 81.5° |
| H4' | C4' | C3' | H3' | 165.3° | 160.4° |
| O4' | C1' | C2' | C3' | 18.9° | 1.9° |
| O4' | C1' | C2' | N1 | 121.1° | 119.5° |
| O4' | C1' | C2' | H1' | 116.0° | 119.5° |
| O4' | C1' | C2' | H2' | 140.0° | 120.6° |
| O4' | C1' | C2' | H2'' | 98.1° | 116.7° |
| O4' | C1' | N1 | H1' | 119.9° | 121.1° |
| O4' | C1' | N1 | C2 | 142.9° | 58.3° |
| O4' | C1' | N1 | C6 | 34.6° | 121.7° |
| O3' | C3' | C2' | H3' | 125.2° | 123.6° |
| O3' | C3' | C2' | C1' | 152.1° | 139.1° |
| O3' | C3' | C2' | H2' | 87.0° | 20.4° |
| O3' | C3' | C2' | H2'' | 35.7° | 102.2° |
| C2' | C3' | O3' | HO3' | 69.0° | 61.4° |
| C3' | C2' | C1' | H2' | 121.1° | 118.7° |
| C3' | C2' | C1' | H2'' | 117.0° | 118.6° |
| C3' | C2' | H2' | H2'' | 122.6° | 122.6° |
| C3' | C2' | C1' | N1 | 102.2° | 121.4° |
| C3' | C2' | C1' | H1' | 134.9° | 117.6° |
| H3' | C3' | O3' | HO3' | 55.2° | 62.2° |
| H3' | C3' | C2' | C1' | 82.7° | 97.3° |
| H3' | C3' | C2' | H2' | 38.2° | 144.0° |
| H3' | C3' | C2' | H2'' | 160.9° | 21.4° |
| C1' | C2' | H2' | H2'' | 121.2° | 122.6° |
| C2' | C1' | N1 | H1' | 121.6° | 120.9° |
| C2' | C1' | N1 | C2 | 98.6° | 59.7° |
| C2' | C1' | N1 | C6 | 83.9° | 120.2° |
| H2' | C2' | C1' | N1 | 18.9° | 119.9° |
| H2' | C2' | C1' | H1' | 104.0° | 1.1° |
| H2'' | C2' | C1' | N1 | 140.8° | 2.8° |
| H2'' | C2' | C1' | H1' | 17.9° | 123.8° |
| C1' | N1 | C2 | C6 | 177.6° | 180.0° |
| C1' | N1 | C2 | O2 | 8.5° | 0.1° |
| C1' | N1 | C2 | N3 | 171.4° | 180.0° |
| C1' | N1 | C6 | C5 | 170.5° | 180.0° |
| C1' | N1 | C6 | H6 | 8.2° | 0.1° |
| H1' | C1' | N1 | C2 | 23.0° | 179.4° |
| H1' | C1' | N1 | C6 | 154.5° | 0.7° |
| N1 | C2 | O2 | N3 | 180.0° | 179.9° |
| N1 | C2 | N3 | C4 | 0.8° | 0.2° |
| N1 | C2 | N3 | HN3 | 179.6° | 180.0° |
| C2 | N1 | C6 | C5 | 6.9° | 0.1° |
| C2 | N1 | C6 | H6 | 174.4° | 180.0° |
| C6 | N1 | C2 | O2 | 173.9° | 179.9° |
| C6 | N1 | C2 | N3 | 6.1° | 0.0° |
| N1 | C6 | C5 | C4 | 2.2° | 0.3° |
| N1 | C6 | C5 | C5M | 175.5° | 180.0° |
| N1 | C6 | C5 | H6 | 178.7° | 179.9° |
| O2 | C2 | N3 | C4 | 179.2° | 179.7° |
| O2 | C2 | N3 | HN3 | 0.4° | 0.1° |
| C2 | N3 | C4 | HN3 | 179.6° | 179.8° |
| C2 | N3 | C4 | O4 | 177.0° | 180.0° |
| C2 | N3 | C4 | C5 | 3.6° | 0.4° |
| N3 | C4 | O4 | C5 | 179.3° | 179.6° |
| N3 | C4 | C5 | C5M | 179.5° | 179.8° |
| N3 | C4 | C5 | C6 | 2.9° | 0.4° |
| HN3 | N3 | C4 | O4 | 3.4° | 0.2° |
| HN3 | N3 | C4 | C5 | 176.0° | 179.8° |
| O4 | C4 | C5 | C5M | 0.1° | 0.2° |
| O4 | C4 | C5 | C6 | 177.8° | 179.9° |
| C4 | C5 | C5M | C6 | 177.7° | 179.7° |
| C4 | C5 | C5M | HM51 | 86.1° | 0.3° |
| C4 | C5 | C5M | HM52 | 153.4° | 119.7° |
| C4 | C5 | C5M | HM53 | 34.0° | 120.3° |
| C4 | C5 | C6 | H6 | 179.1° | 179.8° |
| C5 | C5M | HM51 | HM52 | 121.3° | 120.0° |
| C5 | C5M | HM51 | HM53 | 120.6° | 120.0° |
| C5 | C5M | HM52 | HM53 | 120.4° | 120.0° |
| C5M | C5 | C6 | H6 | 3.2° | 0.1° |
| C6 | C5 | C5M | HM51 | 96.2° | 180.0° |
| C6 | C5 | C5M | HM52 | 24.3° | 60.0° |
| C6 | C5 | C5M | HM53 | 143.6° | 60.0° |
| HM51 | C5M | HM52 | HM53 | 118.8° | 120.0° |
