UPE
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP1 | P | doub | 1.48Å | 1.51Å | |
| O5' | P | sing | 1.61Å | 1.62Å | |
| OP3 | P | sing | 1.61Å | 1.58Å | |
| P | OP2 | sing | 1.61Å | 1.51Å | |
| C1' | N1 | sing | 1.46Å | 1.47Å | |
| C2 | N1 | sing | 1.34Å | 1.42Å | |
| N1 | C6 | sing | 1.36Å | 1.33Å | |
| O2 | C2 | doub | 1.22Å | 1.24Å | |
| C2 | N3 | sing | 1.34Å | 1.34Å | |
| N3 | C4 | sing | 1.35Å | 1.34Å | |
| N3 | HN3 | sing | 0.97Å | 1.00Å | |
| C4 | O4 | doub | 1.22Å | 1.25Å | |
| C4 | C5 | sing | 1.47Å | 1.49Å | |
| C6 | C5 | doub | 1.38Å | 1.39Å | |
| C5 | C21 | sing | 1.47Å | 1.51Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C2' | C1' | sing | 1.55Å | 1.52Å | |
| C1' | O4' | sing | 1.44Å | 1.43Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C2' | C3' | sing | 1.54Å | 1.51Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C2' | H2'A | sing | 1.09Å | 1.10Å | |
| C21 | O22 | doub | 1.22Å | 1.23Å | |
| C21 | N23 | sing | 1.35Å | 1.34Å | |
| N23 | C24 | sing | 1.46Å | 1.46Å | |
| N23 | HN23 | sing | 0.97Å | 1.00Å | |
| C24 | C25 | sing | 1.53Å | 1.52Å | |
| C24 | H24 | sing | 1.09Å | 1.10Å | |
| C24 | H24A | sing | 1.09Å | 1.10Å | |
| C25 | C26 | sing | 1.51Å | 1.51Å | |
| C25 | H25 | sing | 1.09Å | 1.10Å | |
| C25 | H25A | sing | 1.09Å | 1.10Å | |
| C31 | C26 | doub | 1.38Å | 1.39Å | Aromatic |
| C26 | C27 | sing | 1.38Å | 1.40Å | Aromatic |
| C27 | C28 | doub | 1.38Å | 1.39Å | Aromatic |
| C27 | H27 | sing | 1.08Å | 1.08Å | |
| C29 | C28 | sing | 1.38Å | 1.39Å | Aromatic |
| C28 | H28 | sing | 1.08Å | 1.08Å | |
| C30 | C29 | doub | 1.38Å | 1.40Å | Aromatic |
| C29 | H29 | sing | 1.08Å | 1.08Å | |
| O3' | C3' | sing | 1.43Å | 1.43Å | |
| C3' | C4' | sing | 1.54Å | 1.52Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C31 | C30 | sing | 1.38Å | 1.40Å | Aromatic |
| C30 | H30 | sing | 1.08Å | 1.08Å | |
| C31 | H31 | sing | 1.08Å | 1.08Å | |
| C4' | O4' | sing | 1.44Å | 1.44Å | |
| C4' | C5' | sing | 1.53Å | 1.53Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| C5' | O5' | sing | 1.43Å | 1.43Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'A | sing | 1.09Å | 1.10Å | |
| OP2 | HOP2 | sing | 0.97Å | 0.95Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | O5' | 109.5° | 109.5° |
| OP1 | P | OP3 | 107.5° | 109.5° |
| OP1 | P | OP2 | 118.1° | 109.5° |
| O5' | P | OP3 | 104.1° | 109.5° |
| O5' | P | OP2 | 109.6° | 109.5° |
| P | O5' | C5' | 122.0° | 123.0° |
| OP3 | P | OP2 | 107.1° | 109.4° |
| P | OP3 | HOP3 | 109.5° | 114.0° |
| P | OP2 | HOP2 | 109.5° | 114.0° |
| C1' | N1 | C2 | 121.7° | 119.3° |
| C1' | N1 | C6 | 118.9° | 119.3° |
| N1 | C1' | C2' | 113.8° | 110.4° |
| N1 | C1' | O4' | 110.5° | 110.4° |
| N1 | C1' | H1' | 109.1° | 110.3° |
| C2 | N1 | C6 | 119.5° | 121.5° |
| N1 | C2 | O2 | 119.9° | 118.9° |
| N1 | C2 | N3 | 122.1° | 122.2° |
| N1 | C6 | C5 | 120.8° | 119.4° |
| N1 | C6 | H6 | 119.6° | 120.3° |
| O2 | C2 | N3 | 118.1° | 118.9° |
| C2 | N3 | C4 | 121.0° | 120.4° |
| C2 | N3 | HN3 | 119.5° | 119.8° |
| C4 | N3 | HN3 | 119.5° | 119.8° |
| N3 | C4 | O4 | 119.3° | 120.7° |
| N3 | C4 | C5 | 118.5° | 118.5° |
| O4 | C4 | C5 | 122.1° | 120.7° |
| C4 | C5 | C6 | 118.1° | 118.1° |
| C4 | C5 | C21 | 124.4° | 121.0° |
| C6 | C5 | C21 | 117.5° | 121.0° |
| C5 | C6 | H6 | 119.6° | 120.4° |
| C5 | C21 | O22 | 117.0° | 120.0° |
| C5 | C21 | N23 | 122.4° | 120.0° |
| C2' | C1' | O4' | 105.2° | 104.8° |
| C2' | C1' | H1' | 108.4° | 110.5° |
| C1' | C2' | C3' | 104.3° | 104.1° |
| C1' | C2' | H2' | 110.7° | 110.5° |
| C1' | C2' | H2'A | 110.7° | 110.5° |
| O4' | C1' | H1' | 109.7° | 110.4° |
| C1' | O4' | C4' | 110.1° | 105.3° |
| C3' | C2' | H2' | 110.8° | 110.5° |
| C3' | C2' | H2'A | 110.7° | 110.5° |
| C2' | C3' | O3' | 107.8° | 110.5° |
| C2' | C3' | C4' | 105.6° | 104.1° |
| C2' | C3' | H3' | 111.6° | 110.5° |
| H2' | C2' | H2'A | 109.5° | 110.6° |
| O22 | C21 | N23 | 120.5° | 120.0° |
| C21 | N23 | C24 | 120.2° | 120.0° |
| C21 | N23 | HN23 | 119.9° | 119.9° |
| C24 | N23 | HN23 | 119.9° | 120.0° |
| N23 | C24 | C25 | 108.4° | 109.5° |
| N23 | C24 | H24 | 109.7° | 109.5° |
| N23 | C24 | H24A | 109.7° | 109.5° |
| C25 | C24 | H24 | 109.7° | 109.4° |
| C25 | C24 | H24A | 109.7° | 109.5° |
| C24 | C25 | C26 | 114.5° | 109.5° |
| C24 | C25 | H25 | 108.2° | 109.4° |
| C24 | C25 | H25A | 108.2° | 109.5° |
| H24 | C24 | H24A | 109.5° | 109.5° |
| C26 | C25 | H25 | 108.2° | 109.5° |
| C26 | C25 | H25A | 108.2° | 109.5° |
| C25 | C26 | C31 | 121.6° | 120.0° |
| C25 | C26 | C27 | 117.6° | 120.0° |
| H25 | C25 | H25A | 109.5° | 109.5° |
| C31 | C26 | C27 | 120.8° | 120.0° |
| C26 | C31 | C30 | 118.5° | 120.0° |
| C26 | C31 | H31 | 120.7° | 120.0° |
| C26 | C27 | C28 | 120.5° | 120.0° |
| C26 | C27 | H27 | 119.7° | 120.0° |
| C28 | C27 | H27 | 119.7° | 120.0° |
| C27 | C28 | C29 | 118.9° | 120.0° |
| C27 | C28 | H28 | 120.6° | 120.0° |
| C29 | C28 | H28 | 120.5° | 120.0° |
| C28 | C29 | C30 | 120.2° | 120.0° |
| C28 | C29 | H29 | 119.9° | 120.0° |
| C30 | C29 | H29 | 119.9° | 120.0° |
| C29 | C30 | C31 | 121.0° | 120.0° |
| C29 | C30 | H30 | 119.5° | 120.0° |
| O3' | C3' | C4' | 107.1° | 110.5° |
| O3' | C3' | H3' | 112.9° | 110.5° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| C4' | C3' | H3' | 111.5° | 110.6° |
| C3' | C4' | O4' | 106.8° | 104.8° |
| C3' | C4' | C5' | 112.8° | 110.4° |
| C3' | C4' | H4' | 107.8° | 110.4° |
| C31 | C30 | H30 | 119.5° | 120.0° |
| C30 | C31 | H31 | 120.7° | 119.9° |
| O4' | C4' | C5' | 112.7° | 110.3° |
| O4' | C4' | H4' | 108.9° | 110.4° |
| C5' | C4' | H4' | 107.7° | 110.4° |
| C4' | C5' | O5' | 110.2° | 109.5° |
| C4' | C5' | H5' | 109.3° | 109.4° |
| C4' | C5' | H5'A | 109.3° | 109.4° |
| O5' | C5' | H5' | 109.3° | 109.5° |
| O5' | C5' | H5'A | 109.3° | 109.5° |
| H5' | C5' | H5'A | 109.5° | 109.4° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | O5' | OP3 | 114.7° | 120.0° |
| OP1 | P | O5' | OP2 | 131.0° | 120.0° |
| OP1 | P | OP3 | OP2 | 127.8° | 120.0° |
| OP1 | P | O5' | C5' | 3.8° | 55.0° |
| OP1 | P | OP2 | HOP2 | 0.0° | 180.0° |
| OP1 | P | OP3 | HOP3 | 0.0° | 60.0° |
| O5' | P | OP3 | OP2 | 116.1° | 120.0° |
| P | O5' | C5' | C4' | 90.3° | 180.0° |
| P | O5' | C5' | H5' | 29.8° | 60.0° |
| P | O5' | C5' | H5'A | 149.6° | 60.0° |
| O5' | P | OP2 | HOP2 | 126.3° | 60.0° |
| O5' | P | OP3 | HOP3 | 116.1° | 180.0° |
| OP3 | P | O5' | C5' | 110.8° | 175.0° |
| OP3 | P | OP2 | HOP2 | 121.4° | 60.0° |
| OP2 | P | O5' | C5' | 134.8° | 65.0° |
| OP2 | P | OP3 | HOP3 | 127.8° | 60.0° |
| C1' | N1 | C2 | C6 | 179.2° | 179.7° |
| C1' | N1 | C2 | O2 | 0.9° | 0.3° |
| C1' | N1 | C2 | N3 | 179.4° | 179.8° |
| C1' | N1 | C6 | C5 | 179.3° | 179.7° |
| C1' | N1 | C6 | H6 | 0.7° | 0.2° |
| N1 | C1' | C2' | O4' | 121.1° | 118.8° |
| N1 | C1' | C2' | H1' | 121.6° | 122.3° |
| N1 | C1' | O4' | H1' | 120.4° | 122.3° |
| N1 | C1' | C2' | C3' | 149.1° | 142.8° |
| N1 | C1' | C2' | H2' | 91.7° | 98.5° |
| N1 | C1' | C2' | H2'A | 29.9° | 24.1° |
| N1 | C1' | O4' | C4' | 150.1° | 159.4° |
| N1 | C2 | O2 | N3 | 179.7° | 180.0° |
| N1 | C2 | N3 | C4 | 0.0° | 0.1° |
| N1 | C2 | N3 | HN3 | 180.0° | 180.0° |
| C2 | N1 | C6 | C5 | 0.1° | 0.0° |
| C2 | N1 | C6 | H6 | 179.9° | 180.0° |
| C2 | N1 | C1' | C2' | 74.2° | 61.5° |
| C2 | N1 | C1' | O4' | 167.7° | 53.8° |
| C2 | N1 | C1' | H1' | 47.0° | 176.1° |
| C6 | N1 | C2 | O2 | 179.9° | 180.0° |
| C6 | N1 | C2 | N3 | 0.2° | 0.0° |
| N1 | C6 | C5 | C4 | 0.2° | 0.0° |
| N1 | C6 | C5 | H6 | 180.0° | 180.0° |
| N1 | C6 | C5 | C21 | 179.2° | 180.0° |
| C6 | N1 | C1' | C2' | 106.5° | 118.2° |
| C6 | N1 | C1' | O4' | 11.5° | 126.5° |
| C6 | N1 | C1' | H1' | 132.2° | 4.2° |
| O2 | C2 | N3 | C4 | 179.7° | 180.0° |
| O2 | C2 | N3 | HN3 | 0.3° | 0.0° |
| C2 | N3 | C4 | HN3 | 180.0° | 180.0° |
| C2 | N3 | C4 | O4 | 179.8° | 180.0° |
| C2 | N3 | C4 | C5 | 0.3° | 0.0° |
| N3 | C4 | O4 | C5 | 179.5° | 180.0° |
| N3 | C4 | C5 | C6 | 0.4° | 0.0° |
| N3 | C4 | C5 | C21 | 179.0° | 180.0° |
| HN3 | N3 | C4 | O4 | 0.2° | 0.0° |
| HN3 | N3 | C4 | C5 | 179.7° | 180.0° |
| O4 | C4 | C5 | C6 | 179.9° | 180.0° |
| O4 | C4 | C5 | C21 | 0.5° | 0.0° |
| C4 | C5 | C6 | C21 | 179.4° | 180.0° |
| C4 | C5 | C6 | H6 | 179.8° | 180.0° |
| C4 | C5 | C21 | O22 | 177.9° | 174.3° |
| C4 | C5 | C21 | N23 | 3.6° | 5.7° |
| C6 | C5 | C21 | O22 | 2.7° | 5.7° |
| C6 | C5 | C21 | N23 | 175.8° | 174.3° |
| C21 | C5 | C6 | H6 | 0.8° | 0.0° |
| C5 | C21 | O22 | N23 | 178.5° | 180.0° |
| C5 | C21 | N23 | C24 | 179.2° | 174.9° |
| C5 | C21 | N23 | HN23 | 0.8° | 5.1° |
| C2' | C1' | O4' | H1' | 116.5° | 118.9° |
| C1' | C2' | C3' | H2' | 119.2° | 118.6° |
| C1' | C2' | C3' | H2'A | 119.2° | 118.7° |
| C1' | C2' | H2' | H2'A | 122.3° | 122.7° |
| C1' | C2' | C3' | O3' | 95.1° | 118.7° |
| C1' | C2' | C3' | C4' | 19.1° | 0.0° |
| C1' | C2' | C3' | H3' | 140.4° | 118.7° |
| C2' | C1' | O4' | C4' | 27.0° | 40.5° |
| O4' | C1' | C2' | C3' | 28.1° | 24.0° |
| O4' | C1' | C2' | H2' | 147.2° | 142.6° |
| O4' | C1' | C2' | H2'A | 91.1° | 94.7° |
| C1' | O4' | C4' | C3' | 14.7° | 40.6° |
| C1' | O4' | C4' | C5' | 139.1° | 159.4° |
| C1' | O4' | C4' | H4' | 101.4° | 78.3° |
| H1' | C1' | C2' | C3' | 89.3° | 94.9° |
| H1' | C1' | C2' | H2' | 29.9° | 23.7° |
| H1' | C1' | C2' | H2'A | 151.5° | 146.4° |
| H1' | C1' | O4' | C4' | 89.5° | 78.4° |
| C3' | C2' | H2' | H2'A | 122.4° | 122.7° |
| C2' | C3' | O3' | C4' | 113.2° | 114.6° |
| C2' | C3' | O3' | H3' | 123.7° | 122.7° |
| C2' | C3' | C4' | H3' | 121.4° | 118.7° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.4° |
| C2' | C3' | C4' | O4' | 3.7° | 24.0° |
| C2' | C3' | C4' | C5' | 120.7° | 142.8° |
| C2' | C3' | C4' | H4' | 120.5° | 94.9° |
| H2' | C2' | C3' | O3' | 24.1° | 0.1° |
| H2' | C2' | C3' | C4' | 138.3° | 118.6° |
| H2' | C2' | C3' | H3' | 100.4° | 122.7° |
| H2'A | C2' | C3' | O3' | 145.8° | 122.7° |
| H2'A | C2' | C3' | C4' | 100.0° | 118.7° |
| H2'A | C2' | C3' | H3' | 21.3° | 0.0° |
| O22 | C21 | N23 | C24 | 0.8° | 5.1° |
| O22 | C21 | N23 | HN23 | 179.2° | 174.9° |
| C21 | N23 | C24 | HN23 | 180.0° | 180.0° |
| C21 | N23 | C24 | C25 | 153.9° | 180.0° |
| C21 | N23 | C24 | H24 | 86.3° | 60.0° |
| C21 | N23 | C24 | H24A | 34.0° | 60.0° |
| N23 | C24 | C25 | H24 | 119.8° | 120.0° |
| N23 | C24 | C25 | H24A | 119.8° | 120.0° |
| N23 | C24 | H24 | H24A | 120.5° | 120.0° |
| N23 | C24 | C25 | C26 | 79.9° | 180.0° |
| N23 | C24 | C25 | H25 | 40.8° | 60.0° |
| N23 | C24 | C25 | H25A | 159.4° | 60.0° |
| HN23 | N23 | C24 | C25 | 26.1° | 0.0° |
| HN23 | N23 | C24 | H24 | 93.7° | 120.0° |
| HN23 | N23 | C24 | H24A | 146.0° | 120.0° |
| C25 | C24 | H24 | H24A | 120.5° | 120.0° |
| C24 | C25 | C26 | H25 | 120.7° | 120.0° |
| C24 | C25 | C26 | H25A | 120.7° | 120.0° |
| C24 | C25 | H25 | H25A | 117.7° | 120.0° |
| C24 | C25 | C26 | C31 | 12.9° | 90.3° |
| C24 | C25 | C26 | C27 | 166.6° | 89.9° |
| H24 | C24 | C25 | C26 | 160.3° | 60.0° |
| H24 | C24 | C25 | H25 | 79.0° | NaN° |
| H24 | C24 | C25 | H25A | 39.6° | 60.0° |
| H24A | C24 | C25 | C26 | 39.9° | 60.0° |
| H24A | C24 | C25 | H25 | 160.6° | 60.0° |
| H24A | C24 | C25 | H25A | 80.8° | 180.0° |
| C26 | C25 | H25 | H25A | 117.7° | 120.0° |
| C25 | C26 | C31 | C27 | 179.4° | 179.8° |
| C25 | C26 | C27 | C28 | 179.3° | 180.0° |
| C25 | C26 | C27 | H27 | 0.7° | 0.0° |
| C25 | C26 | C31 | C30 | 179.0° | 179.7° |
| C25 | C26 | C31 | H31 | 1.0° | 0.0° |
| H25 | C25 | C26 | C31 | 133.6° | 149.8° |
| H25 | C25 | C26 | C27 | 45.9° | 30.0° |
| H25A | C25 | C26 | C31 | 107.9° | 29.7° |
| H25A | C25 | C26 | C27 | 72.7° | 150.0° |
| C31 | C26 | C27 | C28 | 0.1° | 0.2° |
| C31 | C26 | C27 | H27 | 179.9° | 179.7° |
| C26 | C31 | C30 | C29 | 0.9° | 0.6° |
| C26 | C31 | C30 | H31 | 180.0° | 179.7° |
| C26 | C31 | C30 | H30 | 179.1° | 179.7° |
| C26 | C27 | C28 | H27 | 180.0° | 180.0° |
| C26 | C27 | C28 | C29 | 0.3° | 0.0° |
| C26 | C27 | C28 | H28 | 179.7° | 180.0° |
| C27 | C26 | C31 | C30 | 0.4° | 0.5° |
| C27 | C26 | C31 | H31 | 179.6° | 179.7° |
| C27 | C28 | C29 | H28 | 180.0° | 180.0° |
| C27 | C28 | C29 | C30 | 0.7° | 0.0° |
| C27 | C28 | C29 | H29 | 179.3° | 179.9° |
| H27 | C27 | C28 | C29 | 179.7° | 180.0° |
| H27 | C27 | C28 | H28 | 0.3° | 0.0° |
| C28 | C29 | C30 | H29 | 180.0° | 179.9° |
| C28 | C29 | C30 | C31 | 1.0° | 0.3° |
| C28 | C29 | C30 | H30 | 179.0° | 179.9° |
| H28 | C28 | C29 | C30 | 179.3° | 180.0° |
| H28 | C28 | C29 | H29 | 0.7° | 0.1° |
| C29 | C30 | C31 | H30 | 180.0° | 179.8° |
| C29 | C30 | C31 | H31 | 179.1° | 179.7° |
| H29 | C29 | C30 | C31 | 179.0° | 179.8° |
| H29 | C29 | C30 | H30 | 1.0° | 0.0° |
| O3' | C3' | C4' | H3' | 123.9° | 122.7° |
| O3' | C3' | C4' | O4' | 111.0° | 142.7° |
| O3' | C3' | C4' | C5' | 124.6° | 98.6° |
| O3' | C3' | C4' | H4' | 5.8° | 23.8° |
| C4' | C3' | O3' | HO3' | 66.8° | 176.1° |
| C3' | C4' | O4' | C5' | 124.4° | 118.8° |
| C3' | C4' | O4' | H4' | 116.2° | 118.9° |
| C3' | C4' | C5' | H4' | 118.9° | 122.3° |
| C3' | C4' | C5' | O5' | 158.7° | 175.0° |
| C3' | C4' | C5' | H5' | 81.2° | 55.0° |
| C3' | C4' | C5' | H5'A | 38.5° | 64.9° |
| H3' | C3' | O3' | HO3' | 56.2° | 61.2° |
| H3' | C3' | C4' | O4' | 125.0° | 94.7° |
| H3' | C3' | C4' | C5' | 0.7° | 24.1° |
| H3' | C3' | C4' | H4' | 118.1° | 146.5° |
| H30 | C30 | C31 | H31 | 0.8° | 0.1° |
| O4' | C4' | C5' | H4' | 120.1° | 122.3° |
| O4' | C4' | C5' | O5' | 37.6° | 69.6° |
| O4' | C4' | C5' | H5' | 157.7° | 170.3° |
| O4' | C4' | C5' | H5'A | 82.5° | 50.4° |
| C4' | C5' | O5' | H5' | 120.1° | 120.0° |
| C4' | C5' | O5' | H5'A | 120.1° | 120.0° |
| C4' | C5' | H5' | H5'A | 119.7° | 119.9° |
| H4' | C4' | C5' | O5' | 82.5° | 52.7° |
| H4' | C4' | C5' | H5' | 37.6° | 67.4° |
| H4' | C4' | C5' | H5'A | 157.4° | 172.7° |
| O5' | C5' | H5' | H5'A | 119.7° | 120.0° |
