UDP
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N1 | C2 | sing | 1.35Å | 1.43Å | |
| N1 | C6 | sing | 1.37Å | 1.41Å | |
| N1 | C1' | sing | 1.46Å | 1.48Å | |
| C2 | N3 | sing | 1.35Å | 1.39Å | |
| C2 | O2 | doub | 1.22Å | 1.21Å | |
| N3 | C4 | sing | 1.35Å | 1.42Å | |
| N3 | HN3 | sing | 0.97Å | 1.00Å | |
| C4 | C5 | sing | 1.42Å | 1.46Å | |
| C4 | O4 | doub | 1.22Å | 1.23Å | |
| C5 | C6 | doub | 1.35Å | 1.32Å | |
| C5 | H5 | sing | 1.08Å | 1.08Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C1' | C2' | sing | 1.55Å | 1.53Å | |
| C1' | O4' | sing | 1.44Å | 1.40Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C2' | O2' | sing | 1.43Å | 1.47Å | |
| C2' | C3' | sing | 1.55Å | 1.57Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| O2' | HO2' | sing | 0.97Å | 0.95Å | |
| C3' | C4' | sing | 1.54Å | 1.49Å | |
| C3' | O3' | sing | 1.43Å | 1.41Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.48Å | |
| C4' | C5' | sing | 1.53Å | 1.48Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C5' | O5' | sing | 1.43Å | 1.44Å | |
| C5' | H5'1 | sing | 1.09Å | 1.10Å | |
| C5' | H5'2 | sing | 1.09Å | 1.10Å | |
| O5' | PA | sing | 1.61Å | 1.61Å | |
| PA | O1A | doub | 1.48Å | 1.51Å | |
| PA | O2A | sing | 1.61Å | 1.50Å | |
| PA | O3A | sing | 1.61Å | 1.64Å | |
| O2A | HOA2 | sing | 0.97Å | 0.95Å | |
| O3A | PB | sing | 1.61Å | 1.57Å | |
| PB | O1B | doub | 1.48Å | 1.59Å | |
| PB | O2B | sing | 1.61Å | 1.51Å | |
| PB | O3B | sing | 1.61Å | 1.51Å | |
| O2B | HOB2 | sing | 0.97Å | 0.95Å | |
| O3B | HOB3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C2 | N1 | C6 | 121.7° | 120.6° |
| C2 | N1 | C1' | 118.2° | 119.7° |
| N1 | C2 | N3 | 114.3° | 121.0° |
| N1 | C2 | O2 | 124.2° | 119.5° |
| C6 | N1 | C1' | 120.0° | 119.7° |
| N1 | C6 | C5 | 122.5° | 119.7° |
| N1 | C6 | H6 | 118.7° | 120.2° |
| N1 | C1' | C2' | 114.8° | 110.6° |
| N1 | C1' | O4' | 109.2° | 110.6° |
| N1 | C1' | H1' | 104.2° | 110.6° |
| N3 | C2 | O2 | 121.5° | 119.5° |
| C2 | N3 | C4 | 125.7° | 120.2° |
| C2 | N3 | HN3 | 117.2° | 119.9° |
| C4 | N3 | HN3 | 117.1° | 119.8° |
| N3 | C4 | C5 | 116.0° | 119.4° |
| N3 | C4 | O4 | 117.3° | 120.4° |
| C5 | C4 | O4 | 126.6° | 120.3° |
| C4 | C5 | C6 | 119.8° | 119.1° |
| C4 | C5 | H5 | 120.1° | 120.5° |
| C6 | C5 | H5 | 120.1° | 120.4° |
| C5 | C6 | H6 | 118.8° | 120.1° |
| C2' | C1' | O4' | 103.4° | 103.5° |
| C2' | C1' | H1' | 110.0° | 110.6° |
| C1' | C2' | O2' | 108.3° | 110.9° |
| C1' | C2' | C3' | 102.5° | 102.1° |
| C1' | C2' | H2' | 115.3° | 110.9° |
| O4' | C1' | H1' | 115.5° | 110.8° |
| C1' | O4' | C4' | 113.0° | 107.0° |
| O2' | C2' | C3' | 111.3° | 110.9° |
| O2' | C2' | H2' | 107.0° | 110.8° |
| C2' | O2' | HO2' | 109.5° | 114.0° |
| C3' | C2' | H2' | 112.4° | 110.9° |
| C2' | C3' | C4' | 102.2° | 104.1° |
| C2' | C3' | O3' | 112.9° | 110.5° |
| C2' | C3' | H3' | 111.4° | 110.5° |
| C4' | C3' | O3' | 107.4° | 110.5° |
| C4' | C3' | H3' | 116.5° | 110.5° |
| C3' | C4' | O4' | 104.8° | 107.3° |
| C3' | C4' | C5' | 116.7° | 109.9° |
| C3' | C4' | H4' | 107.7° | 109.8° |
| O3' | C3' | H3' | 106.5° | 110.5° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| O4' | C4' | C5' | 108.7° | 109.9° |
| O4' | C4' | H4' | 115.7° | 109.9° |
| C5' | C4' | H4' | 103.7° | 110.0° |
| C4' | C5' | O5' | 104.4° | 109.5° |
| C4' | C5' | H5'1 | 111.2° | 109.4° |
| C4' | C5' | H5'2 | 111.2° | 109.5° |
| O5' | C5' | H5'1 | 111.2° | 109.5° |
| O5' | C5' | H5'2 | 111.2° | 109.5° |
| C5' | O5' | PA | 118.2° | 123.0° |
| H5'1 | C5' | H5'2 | 107.7° | 109.5° |
| O5' | PA | O1A | 107.4° | 109.5° |
| O5' | PA | O2A | 114.5° | 109.5° |
| O5' | PA | O3A | 111.9° | 109.5° |
| O1A | PA | O2A | 112.1° | 109.5° |
| O1A | PA | O3A | 107.1° | 109.5° |
| O2A | PA | O3A | 103.6° | 109.5° |
| PA | O2A | HOA2 | 109.5° | 114.0° |
| PA | O3A | PB | 131.1° | 134.0° |
| O3A | PB | O1B | 102.3° | 109.4° |
| O3A | PB | O2B | 108.1° | 109.5° |
| O3A | PB | O3B | 109.8° | 109.5° |
| O1B | PB | O2B | 114.6° | 109.5° |
| O1B | PB | O3B | 108.5° | 109.5° |
| O2B | PB | O3B | 112.9° | 109.5° |
| PB | O2B | HOB2 | 109.5° | 113.9° |
| PB | O3B | HOB3 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C2 | N1 | C6 | C1' | 175.9° | 179.7° |
| N1 | C2 | N3 | O2 | 178.1° | 179.9° |
| N1 | C2 | N3 | C4 | 1.1° | 0.1° |
| N1 | C2 | N3 | HN3 | 178.9° | 179.9° |
| C2 | N1 | C6 | C5 | 1.1° | 0.0° |
| C2 | N1 | C6 | H6 | 178.9° | 180.0° |
| C2 | N1 | C1' | C2' | 119.6° | 115.0° |
| C2 | N1 | C1' | O4' | 124.9° | 130.9° |
| C2 | N1 | C1' | H1' | 0.9° | 7.8° |
| C6 | N1 | C2 | N3 | 1.6° | 0.1° |
| C6 | N1 | C2 | O2 | 179.6° | 179.9° |
| N1 | C6 | C5 | C4 | 0.0° | 0.1° |
| N1 | C6 | C5 | H6 | 180.0° | 180.0° |
| N1 | C6 | C5 | H5 | 180.0° | 180.0° |
| C6 | N1 | C1' | C2' | 64.4° | 65.3° |
| C6 | N1 | C1' | O4' | 51.1° | 48.8° |
| C6 | N1 | C1' | H1' | 175.2° | 171.9° |
| C1' | N1 | C2 | N3 | 177.5° | 179.8° |
| C1' | N1 | C2 | O2 | 4.5° | 0.3° |
| C1' | N1 | C6 | C5 | 177.0° | 179.7° |
| C1' | N1 | C6 | H6 | 3.0° | 0.3° |
| N1 | C1' | C2' | O4' | 118.9° | 118.5° |
| N1 | C1' | C2' | H1' | 117.2° | 122.8° |
| N1 | C1' | O4' | H1' | 117.1° | 123.0° |
| N1 | C1' | C2' | O2' | 89.0° | 86.3° |
| N1 | C1' | C2' | C3' | 153.2° | 155.5° |
| N1 | C1' | C2' | H2' | 30.8° | 37.3° |
| N1 | C1' | O4' | C4' | 142.7° | 158.5° |
| C2 | N3 | C4 | HN3 | 180.0° | 180.0° |
| C2 | N3 | C4 | C5 | 0.2° | 0.0° |
| C2 | N3 | C4 | O4 | 178.2° | 180.0° |
| O2 | C2 | N3 | C4 | 179.2° | 179.9° |
| O2 | C2 | N3 | HN3 | 0.8° | 0.1° |
| N3 | C4 | C5 | O4 | 177.8° | 180.0° |
| N3 | C4 | C5 | C6 | 0.4° | 0.1° |
| N3 | C4 | C5 | H5 | 179.5° | 180.0° |
| HN3 | N3 | C4 | C5 | 179.8° | 180.0° |
| HN3 | N3 | C4 | O4 | 1.8° | 0.0° |
| C4 | C5 | C6 | H5 | 180.0° | 179.9° |
| C4 | C5 | C6 | H6 | 180.0° | 179.9° |
| O4 | C4 | C5 | C6 | 177.4° | 180.0° |
| O4 | C4 | C5 | H5 | 2.7° | 0.1° |
| H5 | C5 | C6 | H6 | 0.0° | 0.0° |
| C2' | C1' | O4' | H1' | 120.2° | 118.6° |
| C1' | C2' | O2' | C3' | 111.9° | 112.7° |
| C1' | C2' | O2' | H2' | 124.8° | 123.6° |
| C1' | C2' | C3' | H2' | 124.4° | 118.2° |
| C1' | C2' | O2' | HO2' | 180.0° | 180.0° |
| C1' | C2' | C3' | C4' | 36.5° | 20.9° |
| C1' | C2' | C3' | O3' | 78.6° | 97.8° |
| C1' | C2' | C3' | H3' | 161.6° | 139.6° |
| C2' | C1' | O4' | C4' | 20.0° | 40.1° |
| O4' | C1' | C2' | O2' | 152.1° | 155.2° |
| O4' | C1' | C2' | C3' | 34.4° | 37.0° |
| O4' | C1' | C2' | H2' | 88.1° | 81.2° |
| C1' | O4' | C4' | C3' | 3.6° | 26.5° |
| C1' | O4' | C4' | C5' | 121.8° | 146.0° |
| C1' | O4' | C4' | H4' | 122.0° | 92.9° |
| H1' | C1' | C2' | O2' | 28.2° | 36.6° |
| H1' | C1' | C2' | C3' | 89.6° | 81.7° |
| H1' | C1' | C2' | H2' | 148.0° | 160.1° |
| H1' | C1' | O4' | C4' | 100.2° | 78.5° |
| O2' | C2' | C3' | H2' | 120.1° | 123.5° |
| O2' | C2' | C3' | C4' | 152.0° | 139.1° |
| O2' | C2' | C3' | O3' | 37.0° | 20.4° |
| O2' | C2' | C3' | H3' | 82.8° | 102.2° |
| C3' | C2' | O2' | HO2' | 68.1° | 67.3° |
| C2' | C3' | C4' | O3' | 119.0° | 118.7° |
| C2' | C3' | C4' | H3' | 121.7° | 118.6° |
| C2' | C3' | O3' | H3' | 122.6° | 122.6° |
| C2' | C3' | C4' | O4' | 24.8° | 2.0° |
| C2' | C3' | C4' | C5' | 95.5° | 121.5° |
| C2' | C3' | C4' | H4' | 148.5° | 117.4° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.4° |
| H2' | C2' | O2' | HO2' | 55.2° | 56.3° |
| H2' | C2' | C3' | C4' | 87.9° | 97.3° |
| H2' | C2' | C3' | O3' | 157.0° | 144.0° |
| H2' | C2' | C3' | H3' | 37.3° | 21.3° |
| C4' | C3' | O3' | H3' | 125.6° | 122.7° |
| C3' | C4' | O4' | C5' | 125.5° | 119.4° |
| C3' | C4' | O4' | H4' | 118.4° | 119.4° |
| C3' | C4' | C5' | H4' | 118.1° | 121.0° |
| C4' | C3' | O3' | HO3' | 68.2° | 176.2° |
| C3' | C4' | C5' | O5' | 58.0° | 175.0° |
| C3' | C4' | C5' | H5'1 | 178.0° | 55.0° |
| C3' | C4' | C5' | H5'2 | 62.0° | 65.0° |
| O3' | C3' | C4' | O4' | 94.2° | 120.7° |
| O3' | C3' | C4' | C5' | 145.5° | 119.9° |
| O3' | C3' | C4' | H4' | 29.6° | 1.3° |
| H3' | C3' | C4' | O4' | 146.5° | 116.6° |
| H3' | C3' | C4' | C5' | 26.2° | 2.8° |
| H3' | C3' | C4' | H4' | 89.8° | 123.9° |
| H3' | C3' | O3' | HO3' | 57.4° | 61.2° |
| O4' | C4' | C5' | H4' | 123.7° | 121.1° |
| O4' | C4' | C5' | O5' | 60.2° | 67.2° |
| O4' | C4' | C5' | H5'1 | 59.8° | 172.9° |
| O4' | C4' | C5' | H5'2 | 179.8° | 52.8° |
| C4' | C5' | O5' | H5'1 | 120.0° | 120.0° |
| C4' | C5' | O5' | H5'2 | 120.0° | 120.0° |
| C4' | C5' | H5'1 | H5'2 | 122.1° | 120.0° |
| C4' | C5' | O5' | PA | 176.5° | 180.0° |
| H4' | C4' | C5' | O5' | 176.2° | 53.9° |
| H4' | C4' | C5' | H5'1 | 63.8° | 66.1° |
| H4' | C4' | C5' | H5'2 | 56.2° | 173.9° |
| O5' | C5' | H5'1 | H5'2 | 122.1° | 120.0° |
| C5' | O5' | PA | O1A | 171.1° | 55.0° |
| C5' | O5' | PA | O2A | 63.7° | 65.0° |
| C5' | O5' | PA | O3A | 53.8° | 175.0° |
| H5'1 | C5' | O5' | PA | 56.5° | 60.0° |
| H5'2 | C5' | O5' | PA | 63.5° | 60.0° |
| O5' | PA | O1A | O2A | 126.7° | 120.0° |
| O5' | PA | O1A | O3A | 120.4° | 120.0° |
| O5' | PA | O2A | O3A | 122.2° | 120.0° |
| O5' | PA | O2A | HOA2 | 122.7° | 59.9° |
| O5' | PA | O3A | PB | 43.1° | 165.0° |
| O1A | PA | O2A | O3A | 115.1° | 120.1° |
| O1A | PA | O2A | HOA2 | 0.0° | 179.9° |
| O1A | PA | O3A | PB | 74.3° | 45.0° |
| O2A | PA | O3A | PB | 167.0° | 75.0° |
| O3A | PA | O2A | HOA2 | 115.1° | 60.0° |
| PA | O3A | PB | O1B | 160.8° | 40.0° |
| PA | O3A | PB | O2B | 39.5° | 80.0° |
| PA | O3A | PB | O3B | 84.1° | 160.0° |
| O3A | PB | O1B | O2B | 116.7° | 120.0° |
| O3A | PB | O1B | O3B | 116.0° | 120.0° |
| O3A | PB | O2B | O3B | 121.6° | 120.0° |
| O3A | PB | O2B | HOB2 | 113.4° | 60.1° |
| O3A | PB | O3B | HOB3 | 111.1° | 180.0° |
| O1B | PB | O2B | O3B | 125.0° | 120.0° |
| O1B | PB | O2B | HOB2 | 0.0° | 180.0° |
| O1B | PB | O3B | HOB3 | 0.0° | 60.0° |
| O2B | PB | O3B | HOB3 | 128.2° | 60.0° |
| O3B | PB | O2B | HOB2 | 125.0° | 60.0° |
