TYD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| PA | O1A | doub | 1.48Å | 1.52Å | |
| PA | O2A | sing | 1.61Å | 1.45Å | |
| PA | O3A | sing | 1.61Å | 1.61Å | |
| PA | O5' | sing | 1.61Å | 1.60Å | |
| O2A | HOA2 | sing | 0.97Å | 0.95Å | |
| O3A | PB | sing | 1.61Å | 1.62Å | |
| PB | O1B | doub | 1.48Å | 1.47Å | |
| PB | O2B | sing | 1.61Å | 1.51Å | |
| PB | O3B | sing | 1.61Å | 1.46Å | |
| O2B | HOB2 | sing | 0.97Å | 0.95Å | |
| O3B | HOB3 | sing | 0.97Å | 0.95Å | |
| O5' | C5' | sing | 1.43Å | 1.44Å | |
| C5' | C4' | sing | 1.53Å | 1.50Å | |
| C5' | H5'1 | sing | 1.09Å | 1.12Å | |
| C5' | H5'2 | sing | 1.09Å | 1.11Å | |
| C4' | O4' | sing | 1.45Å | 1.41Å | |
| C4' | C3' | sing | 1.55Å | 1.52Å | |
| C4' | H4' | sing | 1.09Å | 1.12Å | |
| O4' | C1' | sing | 1.44Å | 1.45Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C3' | C2' | sing | 1.55Å | 1.51Å | |
| C3' | H3' | sing | 1.09Å | 1.12Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C2' | C1' | sing | 1.54Å | 1.55Å | |
| C2' | H2'1 | sing | 1.09Å | 1.12Å | |
| C2' | H2'2 | sing | 1.09Å | 1.11Å | |
| C1' | N1 | sing | 1.47Å | 1.48Å | |
| C1' | H1' | sing | 1.09Å | 1.12Å | |
| N1 | C2 | sing | 1.34Å | 1.39Å | Aromatic |
| N1 | C6 | sing | 1.37Å | 1.38Å | Aromatic |
| C2 | O2 | doub | 1.22Å | 1.23Å | |
| C2 | N3 | sing | 1.35Å | 1.41Å | Aromatic |
| N3 | C4 | sing | 1.35Å | 1.39Å | Aromatic |
| N3 | HN3 | sing | 0.97Å | 1.02Å | |
| C4 | O4 | doub | 1.22Å | 1.23Å | |
| C4 | C5 | sing | 1.41Å | 1.45Å | Aromatic |
| C5 | C5M | sing | 1.51Å | 1.52Å | |
| C5 | C6 | doub | 1.35Å | 1.34Å | Aromatic |
| C5M | H51 | sing | 1.09Å | 1.12Å | |
| C5M | H52 | sing | 1.09Å | 1.12Å | |
| C5M | H53 | sing | 1.09Å | 1.11Å | |
| C6 | H6 | sing | 1.08Å | 1.10Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O1A | PA | O2A | 120.3° | 109.5° |
| O1A | PA | O3A | 108.3° | 109.5° |
| O1A | PA | O5' | 109.4° | 109.5° |
| O2A | PA | O3A | 106.1° | 109.4° |
| O2A | PA | O5' | 108.0° | 109.5° |
| PA | O2A | HOA2 | 120.3° | 106.8° |
| O3A | PA | O5' | 103.3° | 109.5° |
| PA | O3A | PB | 134.8° | 106.8° |
| PA | O5' | C5' | 118.0° | 106.8° |
| O3A | PB | O1B | 103.0° | 109.5° |
| O3A | PB | O2B | 106.6° | 109.5° |
| O3A | PB | O3B | 103.9° | 109.5° |
| O1B | PB | O2B | 111.1° | 109.4° |
| O1B | PB | O3B | 115.2° | 109.5° |
| O2B | PB | O3B | 115.6° | 109.4° |
| PB | O2B | HOB2 | 106.5° | 106.8° |
| PB | O3B | HOB3 | 103.9° | 106.9° |
| O5' | C5' | C4' | 110.8° | 109.5° |
| O5' | C5' | H5'1 | 111.7° | 109.5° |
| O5' | C5' | H5'2 | 111.7° | 109.4° |
| C4' | C5' | H5'1 | 111.7° | 109.4° |
| C4' | C5' | H5'2 | 111.7° | 109.4° |
| C5' | C4' | O4' | 107.3° | 110.7° |
| C5' | C4' | C3' | 115.6° | 110.7° |
| C5' | C4' | H4' | 105.1° | 110.6° |
| H5'1 | C5' | H5'2 | 98.7° | 109.5° |
| O4' | C4' | C3' | 103.6° | 103.6° |
| O4' | C4' | H4' | 116.9° | 110.5° |
| C4' | O4' | C1' | 111.0° | 106.9° |
| C3' | C4' | H4' | 108.8° | 110.6° |
| C4' | C3' | O3' | 101.4° | 110.9° |
| C4' | C3' | C2' | 101.4° | 102.2° |
| C4' | C3' | H3' | 121.4° | 110.9° |
| O4' | C1' | C2' | 104.4° | 107.4° |
| O4' | C1' | N1 | 108.8° | 109.8° |
| O4' | C1' | H1' | 114.5° | 109.9° |
| O3' | C3' | C2' | 115.3° | 110.9° |
| O3' | C3' | H3' | 108.7° | 110.8° |
| C3' | O3' | HO3' | 101.5° | 106.8° |
| C2' | C3' | H3' | 108.8° | 110.9° |
| C3' | C2' | C1' | 102.4° | 104.2° |
| C3' | C2' | H2'1 | 114.9° | 110.4° |
| C3' | C2' | H2'2 | 114.9° | 110.6° |
| C1' | C2' | H2'1 | 114.9° | 110.5° |
| C1' | C2' | H2'2 | 115.0° | 110.5° |
| C2' | C1' | N1 | 113.0° | 109.9° |
| C2' | C1' | H1' | 110.3° | 109.9° |
| H2'1 | C2' | H2'2 | 95.5° | 110.5° |
| N1 | C1' | H1' | 106.0° | 109.9° |
| C1' | N1 | C2 | 119.2° | 119.7° |
| C1' | N1 | C6 | 120.4° | 119.6° |
| C2 | N1 | C6 | 120.2° | 120.7° |
| N1 | C2 | O2 | 121.2° | 119.6° |
| N1 | C2 | N3 | 117.1° | 120.9° |
| N1 | C6 | C5 | 121.9° | 119.6° |
| N1 | C6 | H6 | 120.4° | 120.2° |
| O2 | C2 | N3 | 121.7° | 119.5° |
| C2 | N3 | C4 | 124.6° | 120.2° |
| C2 | N3 | HN3 | 118.3° | 119.9° |
| C4 | N3 | HN3 | 117.1° | 119.9° |
| N3 | C4 | O4 | 119.4° | 120.3° |
| N3 | C4 | C5 | 114.4° | 119.4° |
| O4 | C4 | C5 | 126.2° | 120.3° |
| C4 | C5 | C5M | 120.4° | 120.4° |
| C4 | C5 | C6 | 121.5° | 119.1° |
| C5M | C5 | C6 | 118.0° | 120.4° |
| C5 | C5M | H51 | 120.4° | 109.5° |
| C5 | C5M | H52 | 108.3° | 109.5° |
| C5 | C5M | H53 | 108.3° | 109.5° |
| C5 | C6 | H6 | 117.6° | 120.2° |
| H51 | C5M | H52 | 108.2° | 109.4° |
| H51 | C5M | H53 | 108.3° | 109.5° |
| H52 | C5M | H53 | 101.7° | 109.4° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O1A | PA | O2A | O3A | 123.3° | 120.0° |
| O1A | PA | O2A | O5' | 126.5° | 120.0° |
| O1A | PA | O3A | O5' | 116.0° | 120.0° |
| O1A | PA | O2A | HOA2 | 179.9° | 180.0° |
| O1A | PA | O3A | PB | 3.6° | 60.0° |
| O1A | PA | O5' | C5' | 52.4° | 60.0° |
| O2A | PA | O3A | O5' | 113.6° | 120.0° |
| O2A | PA | O3A | PB | 134.1° | 60.0° |
| O2A | PA | O5' | C5' | 175.0° | 60.0° |
| O3A | PA | O2A | HOA2 | 56.7° | 60.0° |
| PA | O3A | PB | O1B | 104.9° | 60.0° |
| PA | O3A | PB | O2B | 12.1° | 180.0° |
| PA | O3A | PB | O3B | 134.7° | 60.1° |
| O3A | PA | O5' | C5' | 62.8° | 179.9° |
| O5' | PA | O2A | HOA2 | 53.6° | 60.0° |
| O5' | PA | O3A | PB | 112.3° | 180.0° |
| PA | O5' | C5' | C4' | 131.9° | 180.0° |
| PA | O5' | C5' | H5'1 | 6.7° | 60.0° |
| PA | O5' | C5' | H5'2 | 102.9° | 60.0° |
| O3A | PB | O1B | O2B | 113.7° | 120.0° |
| O3A | PB | O1B | O3B | 112.4° | 120.0° |
| O3A | PB | O2B | O3B | 114.9° | 120.0° |
| O3A | PB | O2B | HOB2 | 180.0° | 180.0° |
| O3A | PB | O3B | HOB3 | 180.0° | 60.0° |
| O1B | PB | O2B | O3B | 133.7° | 120.0° |
| O1B | PB | O2B | HOB2 | 68.6° | 60.0° |
| O1B | PB | O3B | HOB3 | 68.1° | 179.9° |
| O2B | PB | O3B | HOB3 | 63.6° | 60.0° |
| O3B | PB | O2B | HOB2 | 65.1° | 60.0° |
| O5' | C5' | C4' | H5'1 | 125.2° | 120.1° |
| O5' | C5' | C4' | H5'2 | 125.3° | 120.0° |
| O5' | C5' | H5'1 | H5'2 | 117.6° | 120.0° |
| O5' | C5' | C4' | O4' | 56.6° | 65.7° |
| O5' | C5' | C4' | C3' | 58.4° | 180.0° |
| O5' | C5' | C4' | H4' | 178.3° | 57.1° |
| C4' | C5' | H5'1 | H5'2 | 117.6° | 119.9° |
| C5' | C4' | O4' | C3' | 122.7° | 118.7° |
| C5' | C4' | O4' | H4' | 117.7° | 122.8° |
| C5' | C4' | C3' | H4' | 117.9° | 122.9° |
| C5' | C4' | O4' | C1' | 150.2° | 158.6° |
| C5' | C4' | C3' | O3' | 83.2° | 86.1° |
| C5' | C4' | C3' | C2' | 157.8° | 155.6° |
| C5' | C4' | C3' | H3' | 37.3° | 37.5° |
| H5'1 | C5' | C4' | O4' | 178.2° | 174.2° |
| H5'1 | C5' | C4' | C3' | 66.8° | 60.0° |
| H5'1 | C5' | C4' | H4' | 53.1° | 63.0° |
| H5'2 | C5' | C4' | O4' | 68.7° | 54.3° |
| H5'2 | C5' | C4' | C3' | 176.3° | 60.0° |
| H5'2 | C5' | C4' | H4' | 56.4° | 177.1° |
| O4' | C4' | C3' | H4' | 125.0° | 118.4° |
| O4' | C4' | C3' | O3' | 159.8° | 155.2° |
| O4' | C4' | C3' | C2' | 40.7° | 36.9° |
| O4' | C4' | C3' | H3' | 79.8° | 81.3° |
| C4' | O4' | C1' | C2' | 3.1° | 26.4° |
| C4' | O4' | C1' | N1 | 124.0° | 145.8° |
| C4' | O4' | C1' | H1' | 117.6° | 93.2° |
| C3' | C4' | O4' | C1' | 27.4° | 39.9° |
| C4' | C3' | O3' | C2' | 108.5° | 112.8° |
| C4' | C3' | O3' | H3' | 129.0° | 123.6° |
| C4' | C3' | C2' | H3' | 129.0° | 118.2° |
| C4' | C3' | O3' | HO3' | 180.0° | 174.3° |
| C4' | C3' | C2' | C1' | 38.0° | 20.8° |
| C4' | C3' | C2' | H2'1 | 163.2° | 97.8° |
| C4' | C3' | C2' | H2'2 | 87.4° | 139.6° |
| H4' | C4' | O4' | C1' | 92.1° | 78.6° |
| H4' | C4' | C3' | O3' | 34.7° | 36.8° |
| H4' | C4' | C3' | C2' | 84.3° | 81.5° |
| H4' | C4' | C3' | H3' | 155.2° | 160.4° |
| O4' | C1' | C2' | C3' | 22.6° | 2.0° |
| O4' | C1' | C2' | N1 | 118.1° | 119.5° |
| O4' | C1' | C2' | H1' | 123.4° | 119.5° |
| O4' | C1' | C2' | H2'1 | 147.9° | 120.6° |
| O4' | C1' | C2' | H2'2 | 102.6° | 116.8° |
| O4' | C1' | N1 | H1' | 123.6° | 121.0° |
| O4' | C1' | N1 | C2 | 155.7° | 58.3° |
| O4' | C1' | N1 | C6 | 30.4° | 121.7° |
| O3' | C3' | C2' | H3' | 122.4° | 123.5° |
| O3' | C3' | C2' | C1' | 146.5° | 139.1° |
| O3' | C3' | C2' | H2'1 | 88.2° | 20.5° |
| O3' | C3' | C2' | H2'2 | 21.2° | 102.2° |
| C2' | C3' | O3' | HO3' | 71.4° | 61.4° |
| C3' | C2' | C1' | H2'1 | 125.3° | 118.6° |
| C3' | C2' | C1' | H2'2 | 125.3° | 118.8° |
| C3' | C2' | H2'1 | H2'2 | 120.7° | 122.7° |
| C3' | C2' | C1' | N1 | 95.4° | 121.5° |
| C3' | C2' | C1' | H1' | 146.1° | 117.5° |
| H3' | C3' | O3' | HO3' | 51.0° | 62.1° |
| H3' | C3' | C2' | C1' | 91.0° | 97.4° |
| H3' | C3' | C2' | H2'1 | 34.2° | 144.0° |
| H3' | C3' | C2' | H2'2 | 143.6° | 21.4° |
| C1' | C2' | H2'1 | H2'2 | 120.8° | 122.6° |
| C2' | C1' | N1 | H1' | 121.0° | 121.1° |
| C2' | C1' | N1 | C2 | 88.9° | 59.6° |
| C2' | C1' | N1 | C6 | 85.1° | 120.3° |
| H2'1 | C2' | C1' | N1 | 29.8° | 119.9° |
| H2'1 | C2' | C1' | H1' | 88.7° | 1.1° |
| H2'2 | C2' | C1' | N1 | 139.3° | 2.7° |
| H2'2 | C2' | C1' | H1' | 20.8° | 123.7° |
| C1' | N1 | C2 | C6 | 173.9° | 179.9° |
| C1' | N1 | C2 | O2 | 4.0° | 0.1° |
| C1' | N1 | C2 | N3 | 177.1° | 179.9° |
| C1' | N1 | C6 | C5 | 179.9° | 180.0° |
| C1' | N1 | C6 | H6 | 0.2° | 0.1° |
| H1' | C1' | N1 | C2 | 32.1° | 179.3° |
| H1' | C1' | N1 | C6 | 154.0° | 0.8° |
| N1 | C2 | O2 | N3 | 178.9° | 180.0° |
| N1 | C2 | N3 | C4 | 0.8° | 0.2° |
| N1 | C2 | N3 | HN3 | 179.1° | 180.0° |
| C2 | N1 | C6 | C5 | 6.3° | 0.1° |
| C2 | N1 | C6 | H6 | 173.7° | 180.0° |
| C6 | N1 | C2 | O2 | 177.9° | 180.0° |
| C6 | N1 | C2 | N3 | 3.2° | 0.0° |
| N1 | C6 | C5 | C4 | 5.3° | 0.3° |
| N1 | C6 | C5 | C5M | 173.0° | 180.0° |
| N1 | C6 | C5 | H6 | 180.0° | 179.9° |
| O2 | C2 | N3 | C4 | 178.1° | 179.8° |
| O2 | C2 | N3 | HN3 | 2.0° | 0.0° |
| C2 | N3 | C4 | HN3 | 180.0° | 179.8° |
| C2 | N3 | C4 | O4 | 178.4° | 179.9° |
| C2 | N3 | C4 | C5 | 1.8° | 0.5° |
| N3 | C4 | O4 | C5 | 179.8° | 179.5° |
| N3 | C4 | C5 | C5M | 177.0° | 179.8° |
| N3 | C4 | C5 | C6 | 1.2° | 0.5° |
| HN3 | N3 | C4 | O4 | 1.6° | 0.3° |
| HN3 | N3 | C4 | C5 | 178.2° | 179.7° |
| O4 | C4 | C5 | C5M | 3.2° | 0.3° |
| O4 | C4 | C5 | C6 | 178.6° | 180.0° |
| C4 | C5 | C5M | C6 | 178.3° | 179.7° |
| C4 | C5 | C5M | H51 | 180.0° | 0.3° |
| C4 | C5 | C5M | H52 | 54.8° | 119.7° |
| C4 | C5 | C5M | H53 | 54.7° | 120.3° |
| C4 | C5 | C6 | H6 | 174.7° | 179.8° |
| C5 | C5M | H51 | H52 | 125.2° | 120.0° |
| C5 | C5M | H51 | H53 | 125.3° | 120.0° |
| C5 | C5M | H52 | H53 | 113.9° | 120.0° |
| C5M | C5 | C6 | H6 | 7.0° | 0.1° |
| C6 | C5 | C5M | H51 | 1.7° | 180.0° |
| C6 | C5 | C5M | H52 | 126.9° | 60.0° |
| C6 | C5 | C5M | H53 | 123.6° | 60.0° |
| H51 | C5M | H52 | H53 | 114.0° | 120.0° |
