T5S
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | OP3 | sing | 1.61Å | 1.60Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å | |
| OP1 | P | doub | 1.48Å | 1.49Å | |
| P | OP2 | sing | 1.61Å | 1.47Å | |
| P | O5' | sing | 1.61Å | 1.59Å | |
| OP2 | HOP2 | sing | 0.97Å | 0.95Å | |
| C5' | O5' | sing | 1.43Å | 1.42Å | |
| C1' | N1 | sing | 1.47Å | 1.50Å | |
| C6 | N1 | sing | 1.37Å | 1.39Å | |
| N1 | C2 | sing | 1.35Å | 1.39Å | |
| C6 | C5 | doub | 1.35Å | 1.39Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C2 | O2 | doub | 1.22Å | 1.21Å | |
| C2 | N3 | sing | 1.35Å | 1.39Å | |
| C4 | N3 | sing | 1.35Å | 1.39Å | |
| N3 | HN3 | sing | 0.97Å | 1.00Å | |
| C5 | C4 | sing | 1.42Å | 1.47Å | |
| C4 | O4 | doub | 1.22Å | 1.23Å | |
| SE | C5 | sing | 1.96Å | 1.92Å | |
| CH3 | SE | sing | 1.96Å | 1.47Å | |
| CH3 | HH3 | sing | 1.09Å | 1.10Å | |
| CH3 | HH3A | sing | 1.09Å | 1.10Å | |
| CH3 | HH3B | sing | 1.09Å | 1.10Å | |
| C3' | C2' | sing | 1.54Å | 1.52Å | |
| C2' | C1' | sing | 1.54Å | 1.52Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C2' | H2'A | sing | 1.09Å | 1.10Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'A | sing | 1.09Å | 1.10Å | |
| C3' | C4' | sing | 1.54Å | 1.53Å | |
| C4' | O4' | sing | 1.44Å | 1.45Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.44Å | 1.43Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| O3' | C3' | sing | 1.43Å | 1.41Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| P | OP3 | HOP3 | 109.5° | 114.0° |
| OP3 | P | OP1 | 105.7° | 109.5° |
| OP3 | P | OP2 | 111.1° | 109.5° |
| OP3 | P | O5' | 102.3° | 109.5° |
| OP1 | P | OP2 | 119.6° | 109.5° |
| OP1 | P | O5' | 110.0° | 109.5° |
| OP2 | P | O5' | 106.8° | 109.4° |
| P | OP2 | HOP2 | 109.5° | 114.1° |
| P | O5' | C5' | 120.8° | 123.0° |
| O5' | C5' | C4' | 109.8° | 109.5° |
| O5' | C5' | H5' | 109.4° | 109.5° |
| O5' | C5' | H5'A | 109.3° | 109.4° |
| C1' | N1 | C6 | 121.0° | 119.7° |
| C1' | N1 | C2 | 117.7° | 119.7° |
| N1 | C1' | C2' | 103.1° | 110.4° |
| N1 | C1' | O4' | 100.3° | 110.3° |
| N1 | C1' | H1' | 117.8° | 110.4° |
| C6 | N1 | C2 | 121.1° | 120.6° |
| N1 | C6 | C5 | 123.2° | 119.7° |
| N1 | C6 | H6 | 118.4° | 120.1° |
| N1 | C2 | O2 | 122.7° | 119.5° |
| N1 | C2 | N3 | 115.5° | 121.0° |
| C5 | C6 | H6 | 118.4° | 120.2° |
| C6 | C5 | C4 | 117.7° | 119.1° |
| C6 | C5 | SE | 124.4° | 120.5° |
| O2 | C2 | N3 | 121.7° | 119.5° |
| C2 | N3 | C4 | 127.3° | 120.3° |
| C2 | N3 | HN3 | 116.3° | 119.9° |
| C4 | N3 | HN3 | 116.3° | 119.8° |
| N3 | C4 | C5 | 115.0° | 119.4° |
| N3 | C4 | O4 | 121.2° | 120.3° |
| C5 | C4 | O4 | 123.8° | 120.3° |
| C4 | C5 | SE | 117.9° | 120.4° |
| C5 | SE | CH3 | 111.3° | 101.0° |
| SE | CH3 | HH3 | 109.5° | 109.5° |
| SE | CH3 | HH3A | 109.5° | 109.4° |
| SE | CH3 | HH3B | 109.5° | 109.5° |
| HH3 | CH3 | HH3A | 109.5° | 109.5° |
| HH3 | CH3 | HH3B | 109.4° | 109.5° |
| HH3A | CH3 | HH3B | 109.5° | 109.4° |
| C3' | C2' | C1' | 106.4° | 104.1° |
| C3' | C2' | H2' | 110.5° | 110.5° |
| C3' | C2' | H2'A | 111.1° | 110.6° |
| C2' | C3' | C4' | 105.2° | 104.1° |
| C2' | C3' | O3' | 105.4° | 110.5° |
| C2' | C3' | H3' | 117.0° | 110.5° |
| C1' | C2' | H2' | 110.5° | 110.5° |
| C1' | C2' | H2'A | 111.2° | 110.5° |
| C2' | C1' | O4' | 106.5° | 104.8° |
| C2' | C1' | H1' | 112.6° | 110.4° |
| H2' | C2' | H2'A | 107.1° | 110.4° |
| C4' | C5' | H5' | 109.4° | 109.4° |
| C4' | C5' | H5'A | 109.3° | 109.5° |
| C5' | C4' | C3' | 111.6° | 110.4° |
| C5' | C4' | O4' | 107.9° | 110.4° |
| C5' | C4' | H4' | 107.8° | 110.3° |
| H5' | C5' | H5'A | 109.7° | 109.4° |
| C3' | C4' | O4' | 105.2° | 104.8° |
| C3' | C4' | H4' | 110.4° | 110.5° |
| C4' | C3' | O3' | 115.4° | 110.5° |
| C4' | C3' | H3' | 107.2° | 110.5° |
| O4' | C4' | H4' | 114.0° | 110.3° |
| C4' | O4' | C1' | 109.6° | 105.3° |
| O4' | C1' | H1' | 115.0° | 110.4° |
| O3' | C3' | H3' | 107.0° | 110.6° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP3 | P | OP1 | OP2 | 126.1° | 120.0° |
| OP3 | P | OP1 | O5' | 109.8° | 120.0° |
| OP3 | P | OP2 | O5' | 110.8° | 120.0° |
| OP3 | P | OP2 | HOP2 | 56.4° | 60.0° |
| OP3 | P | O5' | C5' | 59.7° | 175.0° |
| HOP3 | OP3 | P | OP1 | 153.9° | 60.0° |
| HOP3 | OP3 | P | OP2 | 75.0° | 60.0° |
| HOP3 | OP3 | P | O5' | 38.7° | 180.0° |
| OP1 | P | OP2 | O5' | 125.7° | 120.0° |
| OP1 | P | OP2 | HOP2 | 179.9° | 180.0° |
| OP1 | P | O5' | C5' | 52.2° | 55.0° |
| OP2 | P | O5' | C5' | 176.5° | 65.0° |
| O5' | P | OP2 | HOP2 | 54.4° | 60.0° |
| P | O5' | C5' | C4' | 163.7° | 180.0° |
| P | O5' | C5' | H5' | 43.7° | 59.9° |
| P | O5' | C5' | H5'A | 76.4° | 60.0° |
| O5' | C5' | C4' | H5' | 120.0° | 120.1° |
| O5' | C5' | C4' | H5'A | 119.9° | 120.0° |
| O5' | C5' | H5' | H5'A | 119.9° | 120.0° |
| O5' | C5' | C4' | C3' | 35.9° | 178.1° |
| O5' | C5' | C4' | O4' | 79.3° | 66.4° |
| O5' | C5' | C4' | H4' | 157.3° | 55.8° |
| C1' | N1 | C6 | C2 | 176.5° | 179.7° |
| C1' | N1 | C6 | C5 | 172.7° | 179.8° |
| C1' | N1 | C6 | H6 | 7.3° | 0.3° |
| C1' | N1 | C2 | O2 | 6.4° | 0.3° |
| C1' | N1 | C2 | N3 | 173.6° | 179.7° |
| N1 | C1' | C2' | C3' | 115.3° | 142.8° |
| N1 | C1' | C2' | O4' | 105.0° | 118.8° |
| N1 | C1' | C2' | H1' | 128.0° | 122.4° |
| N1 | C1' | C2' | H2' | 4.7° | 98.6° |
| N1 | C1' | C2' | H2'A | 123.5° | 24.0° |
| N1 | C1' | O4' | C4' | 131.2° | 159.3° |
| N1 | C1' | O4' | H1' | 127.4° | 122.3° |
| N1 | C6 | C5 | H6 | 180.0° | 179.9° |
| C6 | N1 | C2 | O2 | 177.0° | 180.0° |
| C6 | N1 | C2 | N3 | 3.0° | 0.0° |
| N1 | C6 | C5 | C4 | 1.8° | 0.1° |
| N1 | C6 | C5 | SE | 177.1° | 180.0° |
| C6 | N1 | C1' | C2' | 74.5° | 115.3° |
| C6 | N1 | C1' | O4' | 35.3° | 129.3° |
| C6 | N1 | C1' | H1' | 160.8° | 7.1° |
| C2 | N1 | C6 | C5 | 3.8° | 0.1° |
| C2 | N1 | C6 | H6 | 176.2° | 180.0° |
| N1 | C2 | O2 | N3 | 180.0° | 179.9° |
| N1 | C2 | N3 | C4 | 0.6° | 0.0° |
| N1 | C2 | N3 | HN3 | 179.4° | 180.0° |
| C2 | N1 | C1' | C2' | 102.1° | 65.0° |
| C2 | N1 | C1' | O4' | 148.1° | 50.4° |
| C2 | N1 | C1' | H1' | 22.6° | 172.6° |
| C6 | C5 | C4 | N3 | 0.6° | 0.1° |
| C6 | C5 | C4 | SE | 179.0° | 179.9° |
| C6 | C5 | C4 | O4 | 179.1° | 179.9° |
| C6 | C5 | SE | CH3 | 49.8° | 180.0° |
| H6 | C6 | C5 | C4 | 178.2° | 180.0° |
| H6 | C6 | C5 | SE | 2.9° | 0.1° |
| O2 | C2 | N3 | C4 | 179.5° | 180.0° |
| O2 | C2 | N3 | HN3 | 0.5° | 0.1° |
| C2 | N3 | C4 | HN3 | 180.0° | 180.0° |
| C2 | N3 | C4 | C5 | 1.3° | 0.1° |
| C2 | N3 | C4 | O4 | 178.5° | 180.0° |
| N3 | C4 | C5 | O4 | 179.7° | 180.0° |
| N3 | C4 | C5 | SE | 179.6° | 180.0° |
| HN3 | N3 | C4 | C5 | 178.8° | 180.0° |
| HN3 | N3 | C4 | O4 | 1.5° | 0.0° |
| C4 | C5 | SE | CH3 | 129.0° | 0.0° |
| O4 | C4 | C5 | SE | 0.1° | 0.0° |
| C5 | SE | CH3 | HH3 | 131.4° | 180.0° |
| C5 | SE | CH3 | HH3A | 108.6° | 60.0° |
| C5 | SE | CH3 | HH3B | 11.4° | 59.9° |
| SE | CH3 | HH3 | HH3A | 120.0° | 120.0° |
| SE | CH3 | HH3 | HH3B | 120.0° | 120.0° |
| SE | CH3 | HH3A | HH3B | 120.0° | 119.9° |
| HH3 | CH3 | HH3A | HH3B | 119.9° | 120.1° |
| C3' | C2' | C1' | H2' | 120.0° | 118.7° |
| C3' | C2' | C1' | H2'A | 121.2° | 118.8° |
| C3' | C2' | H2' | H2'A | 121.2° | 122.7° |
| C2' | C3' | C4' | C5' | 137.0° | 142.8° |
| C2' | C3' | C4' | O3' | 115.7° | 118.7° |
| C2' | C3' | C4' | H3' | 125.2° | 118.6° |
| C2' | C3' | C4' | O4' | 20.1° | 23.9° |
| C2' | C3' | C4' | H4' | 103.2° | 94.9° |
| C3' | C2' | C1' | O4' | 10.2° | 24.0° |
| C3' | C2' | C1' | H1' | 116.7° | 94.8° |
| C2' | C3' | O3' | H3' | 125.2° | 122.6° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.5° |
| C1' | C2' | H2' | H2'A | 121.2° | 122.6° |
| C1' | C2' | C3' | C4' | 6.2° | 0.0° |
| C2' | C1' | O4' | C4' | 24.0° | 40.5° |
| C2' | C1' | O4' | H1' | 125.4° | 118.9° |
| C1' | C2' | C3' | O3' | 128.6° | 118.6° |
| C1' | C2' | C3' | H3' | 112.6° | 118.7° |
| H2' | C2' | C3' | C4' | 126.2° | 118.7° |
| H2' | C2' | C1' | O4' | 109.8° | 142.7° |
| H2' | C2' | C1' | H1' | 123.3° | 23.8° |
| H2' | C2' | C3' | O3' | 111.4° | 0.0° |
| H2' | C2' | C3' | H3' | 7.4° | 122.7° |
| H2'A | C2' | C3' | C4' | 115.0° | 118.7° |
| H2'A | C2' | C1' | O4' | 131.4° | 94.8° |
| H2'A | C2' | C1' | H1' | 4.5° | 146.4° |
| H2'A | C2' | C3' | O3' | 7.4° | 122.6° |
| H2'A | C2' | C3' | H3' | 126.2° | 0.0° |
| C4' | C5' | H5' | H5'A | 119.9° | 120.0° |
| C5' | C4' | C3' | O4' | 116.8° | 118.9° |
| C5' | C4' | C3' | H4' | 119.8° | 122.3° |
| C5' | C4' | O4' | H4' | 119.6° | 122.2° |
| C5' | C4' | O4' | C1' | 147.2° | 159.4° |
| C5' | C4' | C3' | O3' | 107.4° | 98.5° |
| C5' | C4' | C3' | H3' | 11.8° | 24.2° |
| H5' | C5' | C4' | C3' | 84.1° | 61.8° |
| H5' | C5' | C4' | O4' | 160.7° | 53.6° |
| H5' | C5' | C4' | H4' | 37.2° | 175.8° |
| H5'A | C5' | C4' | C3' | 155.8° | 58.1° |
| H5'A | C5' | C4' | O4' | 40.6° | 173.5° |
| H5'A | C5' | C4' | H4' | 82.9° | 64.2° |
| C3' | C4' | O4' | H4' | 121.0° | 118.9° |
| C3' | C4' | O4' | C1' | 27.9° | 40.5° |
| C4' | C3' | O3' | H3' | 119.2° | 122.7° |
| C4' | C3' | O3' | HO3' | 64.4° | 176.1° |
| C4' | O4' | C1' | H1' | 101.4° | 78.4° |
| O4' | C4' | C3' | O3' | 135.8° | 142.6° |
| O4' | C4' | C3' | H3' | 105.1° | 94.7° |
| H4' | C4' | O4' | C1' | 93.1° | 78.4° |
| H4' | C4' | C3' | O3' | 12.5° | 23.8° |
| H4' | C4' | C3' | H3' | 131.6° | 146.5° |
| H3' | C3' | O3' | HO3' | 54.8° | 61.2° |
