YCO
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | OP2 | sing | 1.61Å | 1.84Å | |
| P | OP3 | sing | 1.61Å | 1.72Å | |
| N1 | C1' | sing | 1.46Å | 1.50Å | |
| N1 | C6 | sing | 1.38Å | 1.42Å | |
| C2 | N1 | sing | 1.34Å | 1.41Å | |
| O2 | C2 | doub | 1.22Å | 1.35Å | |
| N3 | C2 | sing | 1.35Å | 1.35Å | |
| N3 | C4 | sing | 1.38Å | 1.35Å | |
| N3 | HN3 | sing | 0.97Å | 1.00Å | |
| C4 | C5 | sing | 1.47Å | 1.49Å | |
| C5 | C6 | doub | 1.35Å | 1.39Å | |
| C5 | O14 | sing | 1.36Å | 1.37Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| N7 | C4 | doub | 1.31Å | 1.35Å | |
| N7 | C8 | sing | 1.37Å | 1.36Å | |
| C8 | C13 | sing | 1.40Å | 1.41Å | Aromatic |
| C9 | C8 | doub | 1.40Å | 1.40Å | Aromatic |
| C9 | C10 | sing | 1.38Å | 1.40Å | Aromatic |
| C9 | H9 | sing | 1.08Å | 1.08Å | |
| C1' | C2' | sing | 1.54Å | 1.52Å | |
| C1' | O4' | sing | 1.44Å | 1.44Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C10 | C11 | doub | 1.38Å | 1.40Å | Aromatic |
| C10 | H10 | sing | 1.08Å | 1.08Å | |
| C11 | C12 | sing | 1.38Å | 1.40Å | Aromatic |
| C11 | H11 | sing | 1.08Å | 1.08Å | |
| C12 | H12 | sing | 1.08Å | 1.08Å | |
| C13 | C12 | doub | 1.38Å | 1.40Å | Aromatic |
| C13 | O14 | sing | 1.36Å | 1.38Å | |
| C2' | C3' | sing | 1.55Å | 1.51Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C2' | H2'A | sing | 1.09Å | 1.10Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C3' | C4' | sing | 1.55Å | 1.51Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C4' | C5' | sing | 1.53Å | 1.51Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C4' | sing | 1.44Å | 1.43Å | |
| C5' | O5' | sing | 1.43Å | 1.41Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'A | sing | 1.09Å | 1.10Å | |
| O5' | P | sing | 1.61Å | 1.71Å | |
| OP1 | P | doub | 1.48Å | 1.80Å | |
| 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) |
| OP2 | P | OP3 | 92.2° | 109.4° |
| OP2 | P | O5' | 119.3° | 109.5° |
| OP2 | P | OP1 | 120.0° | 109.5° |
| P | OP2 | HOP2 | 109.5° | 114.0° |
| OP3 | P | O5' | 97.6° | 109.5° |
| OP3 | P | OP1 | 95.2° | 109.5° |
| P | OP3 | HOP3 | 109.5° | 114.0° |
| C1' | N1 | C6 | 120.4° | 119.2° |
| C1' | N1 | C2 | 118.1° | 119.2° |
| N1 | C1' | C2' | 113.9° | 109.9° |
| N1 | C1' | O4' | 109.2° | 109.9° |
| N1 | C1' | H1' | 106.3° | 109.9° |
| C6 | N1 | C2 | 118.1° | 121.7° |
| N1 | C6 | C5 | 119.4° | 119.5° |
| N1 | C6 | H6 | 120.3° | 120.2° |
| N1 | C2 | O2 | 118.5° | 119.1° |
| N1 | C2 | N3 | 122.3° | 121.8° |
| O2 | C2 | N3 | 118.7° | 119.1° |
| C2 | N3 | C4 | 121.1° | 119.5° |
| C2 | N3 | HN3 | 119.4° | 120.3° |
| C4 | N3 | HN3 | 119.4° | 120.3° |
| N3 | C4 | C5 | 119.3° | 118.7° |
| N3 | C4 | N7 | 121.2° | 121.5° |
| C4 | C5 | C6 | 118.8° | 118.8° |
| C4 | C5 | O14 | 118.7° | 119.5° |
| C5 | C4 | N7 | 119.5° | 119.8° |
| C6 | C5 | O14 | 122.5° | 121.7° |
| C5 | C6 | H6 | 120.3° | 120.3° |
| C5 | O14 | C13 | 119.5° | 119.2° |
| C4 | N7 | C8 | 120.7° | 120.3° |
| N7 | C8 | C13 | 120.8° | 120.8° |
| N7 | C8 | C9 | 119.3° | 119.7° |
| C13 | C8 | C9 | 119.9° | 119.6° |
| C8 | C13 | C12 | 119.7° | 119.8° |
| C8 | C13 | O14 | 120.7° | 120.4° |
| C8 | C9 | C10 | 120.2° | 119.9° |
| C8 | C9 | H9 | 119.9° | 120.0° |
| C10 | C9 | H9 | 119.9° | 120.1° |
| C9 | C10 | C11 | 120.1° | 120.3° |
| C9 | C10 | H10 | 120.0° | 119.8° |
| C2' | C1' | O4' | 108.4° | 107.3° |
| C2' | C1' | H1' | 107.1° | 109.9° |
| C1' | C2' | C3' | 102.0° | 104.2° |
| C1' | C2' | H2' | 112.1° | 110.5° |
| C1' | C2' | H2'A | 112.1° | 110.5° |
| O4' | C1' | H1' | 112.0° | 110.0° |
| C1' | O4' | C4' | 108.8° | 107.0° |
| C11 | C10 | H10 | 120.0° | 119.9° |
| C10 | C11 | C12 | 119.9° | 120.3° |
| C10 | C11 | H11 | 120.0° | 119.9° |
| C12 | C11 | H11 | 120.0° | 119.8° |
| C11 | C12 | H12 | 119.9° | 120.0° |
| C11 | C12 | C13 | 120.3° | 120.1° |
| H12 | C12 | C13 | 119.9° | 119.9° |
| C12 | C13 | O14 | 119.6° | 119.7° |
| C3' | C2' | H2' | 112.0° | 110.5° |
| C3' | C2' | H2'A | 112.0° | 110.5° |
| C2' | C3' | O3' | 112.0° | 110.9° |
| C2' | C3' | C4' | 104.2° | 102.1° |
| C2' | C3' | H3' | 111.7° | 110.9° |
| H2' | C2' | H2'A | 106.8° | 110.5° |
| O3' | C3' | C4' | 110.6° | 110.9° |
| O3' | C3' | H3' | 105.4° | 110.8° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| C4' | C3' | H3' | 113.1° | 111.0° |
| C3' | C4' | C5' | 108.0° | 110.6° |
| C3' | C4' | H4' | 113.3° | 110.6° |
| C3' | C4' | O4' | 105.7° | 103.5° |
| C5' | C4' | H4' | 108.4° | 110.5° |
| C5' | C4' | O4' | 110.8° | 110.7° |
| C4' | C5' | O5' | 108.4° | 109.4° |
| C4' | C5' | H5' | 109.9° | 109.5° |
| C4' | C5' | H5'A | 109.9° | 109.4° |
| H4' | C4' | O4' | 110.6° | 110.8° |
| O5' | C5' | H5' | 109.8° | 109.5° |
| O5' | C5' | H5'A | 109.8° | 109.4° |
| C5' | O5' | P | 119.3° | 123.0° |
| H5' | C5' | H5'A | 109.1° | 109.5° |
| O5' | P | OP1 | 118.4° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP2 | P | OP3 | O5' | 120.0° | 120.0° |
| OP2 | P | OP3 | OP1 | 120.4° | 120.0° |
| OP2 | P | O5' | C5' | 1.2° | 175.1° |
| OP2 | P | O5' | OP1 | 162.9° | 120.0° |
| OP2 | P | OP3 | HOP3 | 120.4° | 60.0° |
| OP3 | P | O5' | C5' | 98.1° | 65.0° |
| OP3 | P | O5' | OP1 | 100.2° | 120.0° |
| OP3 | P | OP2 | HOP2 | 180.0° | 60.0° |
| C1' | N1 | C6 | C2 | 158.9° | 179.8° |
| C1' | N1 | C2 | O2 | 17.5° | 0.0° |
| C1' | N1 | C2 | N3 | 170.5° | 180.0° |
| C1' | N1 | C6 | C5 | 169.5° | 179.7° |
| C1' | N1 | C6 | H6 | 10.5° | 0.0° |
| N1 | C1' | C2' | O4' | 121.8° | 119.5° |
| N1 | C1' | C2' | H1' | 117.2° | 121.0° |
| N1 | C1' | O4' | H1' | 117.5° | 121.1° |
| N1 | C1' | C2' | C3' | 101.2° | 121.4° |
| N1 | C1' | C2' | H2' | 138.9° | 119.9° |
| N1 | C1' | C2' | H2'A | 18.8° | 2.8° |
| N1 | C1' | O4' | C4' | 123.7° | 145.9° |
| C6 | N1 | C2 | O2 | 176.9° | 179.8° |
| C6 | N1 | C2 | N3 | 11.1° | 0.2° |
| N1 | C6 | C5 | C4 | 5.6° | 0.4° |
| N1 | C6 | C5 | H6 | 180.0° | 179.8° |
| N1 | C6 | C5 | O14 | 175.2° | 179.8° |
| C6 | N1 | C1' | C2' | 96.1° | 115.1° |
| C6 | N1 | C1' | O4' | 25.3° | 127.1° |
| C6 | N1 | C1' | H1' | 146.3° | 6.0° |
| N1 | C2 | O2 | N3 | 172.2° | 180.0° |
| N1 | C2 | N3 | C4 | 6.4° | 0.1° |
| N1 | C2 | N3 | HN3 | 173.7° | 180.0° |
| C2 | N1 | C6 | C5 | 10.6° | 0.5° |
| C2 | N1 | C6 | H6 | 169.4° | 179.7° |
| C2 | N1 | C1' | C2' | 62.9° | 64.7° |
| C2 | N1 | C1' | O4' | 175.8° | 53.1° |
| C2 | N1 | C1' | H1' | 54.8° | 174.2° |
| O2 | C2 | N3 | C4 | 178.3° | 180.0° |
| O2 | C2 | N3 | HN3 | 1.8° | 0.0° |
| C2 | N3 | C4 | HN3 | 180.0° | 179.9° |
| C2 | N3 | C4 | C5 | 1.0° | 0.1° |
| C2 | N3 | C4 | N7 | 178.3° | 180.0° |
| N3 | C4 | C5 | N7 | 179.3° | 179.9° |
| N3 | C4 | C5 | C6 | 0.7° | 0.2° |
| N3 | C4 | C5 | O14 | 179.9° | 180.0° |
| N3 | C4 | N7 | C8 | 179.6° | 180.0° |
| HN3 | N3 | C4 | C5 | 179.1° | 180.0° |
| HN3 | N3 | C4 | N7 | 1.7° | 0.1° |
| C4 | C5 | C6 | O14 | 179.1° | 179.8° |
| C4 | C5 | C6 | H6 | 174.3° | 179.8° |
| C5 | C4 | N7 | C8 | 1.2° | 0.1° |
| C4 | C5 | O14 | C13 | 0.2° | 0.1° |
| C6 | C5 | C4 | N7 | 178.6° | 179.7° |
| C6 | C5 | O14 | C13 | 179.3° | 179.7° |
| O14 | C5 | C6 | H6 | 4.8° | 0.0° |
| O14 | C5 | C4 | N7 | 0.6° | 0.1° |
| C5 | O14 | C13 | C8 | 0.4° | 0.1° |
| C5 | O14 | C13 | C12 | 179.7° | 179.9° |
| C4 | N7 | C8 | C13 | 1.0° | 0.1° |
| C4 | N7 | C8 | C9 | 179.3° | 180.0° |
| N7 | C8 | C13 | C9 | 179.8° | 180.0° |
| N7 | C8 | C9 | C10 | 179.5° | 179.9° |
| N7 | C8 | C9 | H9 | 0.5° | 0.1° |
| N7 | C8 | C13 | C12 | 179.8° | 179.9° |
| N7 | C8 | C13 | O14 | 0.1° | 0.1° |
| C13 | C8 | C9 | C10 | 0.3° | 0.0° |
| C13 | C8 | C9 | H9 | 179.7° | 180.0° |
| C8 | C13 | C12 | C11 | 0.1° | 0.0° |
| C8 | C13 | C12 | H12 | 179.8° | 180.0° |
| C8 | C13 | C12 | O14 | 179.9° | 180.0° |
| C8 | C9 | C10 | H9 | 180.0° | 180.0° |
| C8 | C9 | C10 | C11 | 0.5° | 0.0° |
| C8 | C9 | C10 | H10 | 179.5° | 180.0° |
| C9 | C8 | C13 | C12 | 0.1° | 0.0° |
| C9 | C8 | C13 | O14 | 179.9° | 180.0° |
| C9 | C10 | C11 | H10 | 180.0° | 179.9° |
| C9 | C10 | C11 | C12 | 0.4° | 0.0° |
| C9 | C10 | C11 | H11 | 179.5° | 180.0° |
| H9 | C9 | C10 | C11 | 179.5° | 180.0° |
| H9 | C9 | C10 | H10 | 0.5° | 0.0° |
| C2' | C1' | O4' | H1' | 117.9° | 119.5° |
| C1' | C2' | C3' | H2' | 120.0° | 118.7° |
| C1' | C2' | C3' | H2'A | 120.0° | 118.7° |
| C1' | C2' | H2' | H2'A | 123.1° | 122.6° |
| C1' | C2' | C3' | O3' | 151.0° | 139.1° |
| C1' | C2' | C3' | C4' | 31.4° | 20.9° |
| C1' | C2' | C3' | H3' | 91.0° | 97.4° |
| C2' | C1' | O4' | C4' | 1.0° | 26.5° |
| O4' | C1' | C2' | C3' | 20.6° | 2.0° |
| O4' | C1' | C2' | H2' | 99.4° | 120.7° |
| O4' | C1' | C2' | H2'A | 140.6° | 116.7° |
| C1' | O4' | C4' | C3' | 19.4° | 40.0° |
| C1' | O4' | C4' | C5' | 136.1° | 158.5° |
| C1' | O4' | C4' | H4' | 103.6° | 78.5° |
| H1' | C1' | C2' | C3' | 141.6° | 117.5° |
| H1' | C1' | C2' | H2' | 21.6° | 1.2° |
| H1' | C1' | C2' | H2'A | 98.4° | 123.8° |
| H1' | C1' | O4' | C4' | 118.9° | 93.0° |
| C10 | C11 | C12 | H11 | 180.0° | 180.0° |
| C10 | C11 | C12 | H12 | 179.9° | 180.0° |
| C10 | C11 | C12 | C13 | 0.1° | 0.0° |
| H10 | C10 | C11 | C12 | 179.6° | 180.0° |
| H10 | C10 | C11 | H11 | 0.4° | 0.1° |
| C11 | C12 | H12 | C13 | 180.0° | 180.0° |
| C11 | C12 | C13 | O14 | 179.8° | 180.0° |
| H11 | C11 | C12 | H12 | 0.1° | 0.1° |
| H11 | C11 | C12 | C13 | 179.9° | 180.0° |
| H12 | C12 | C13 | O14 | 0.2° | 0.0° |
| C3' | C2' | H2' | H2'A | 123.0° | 122.6° |
| C2' | C3' | O3' | C4' | 115.7° | 112.7° |
| C2' | C3' | O3' | H3' | 121.7° | 123.7° |
| C2' | C3' | C4' | H3' | 121.5° | 118.2° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.5° |
| C2' | C3' | C4' | C5' | 150.7° | 155.6° |
| C2' | C3' | C4' | H4' | 89.1° | 81.7° |
| C2' | C3' | C4' | O4' | 32.2° | 37.0° |
| H2' | C2' | C3' | O3' | 31.0° | 20.3° |
| H2' | C2' | C3' | C4' | 88.6° | 97.8° |
| H2' | C2' | C3' | H3' | 149.0° | 143.9° |
| H2'A | C2' | C3' | O3' | 89.0° | 102.3° |
| H2'A | C2' | C3' | C4' | 151.4° | 139.6° |
| H2'A | C2' | C3' | H3' | 29.0° | 21.3° |
| O3' | C3' | C4' | H3' | 118.0° | 123.6° |
| O3' | C3' | C4' | C5' | 88.7° | 86.2° |
| O3' | C3' | C4' | H4' | 31.4° | 36.5° |
| O3' | C3' | C4' | O4' | 152.7° | 155.2° |
| C4' | C3' | O3' | HO3' | 64.3° | 174.1° |
| C3' | C4' | C5' | H4' | 123.2° | 122.8° |
| C3' | C4' | C5' | O4' | 115.3° | 114.1° |
| C3' | C4' | H4' | O4' | 118.4° | 114.2° |
| C3' | C4' | C5' | O5' | 163.8° | 175.0° |
| C3' | C4' | C5' | H5' | 76.3° | 55.0° |
| C3' | C4' | C5' | H5'A | 43.8° | 65.1° |
| H3' | C3' | O3' | HO3' | 58.3° | 62.2° |
| H3' | C3' | C4' | C5' | 29.2° | 37.3° |
| H3' | C3' | C4' | H4' | 149.4° | 160.1° |
| H3' | C3' | C4' | O4' | 89.3° | 81.2° |
| C5' | C4' | H4' | O4' | 121.7° | 123.0° |
| C4' | C5' | O5' | H5' | 120.0° | 120.1° |
| C4' | C5' | O5' | H5'A | 120.0° | 119.9° |
| C4' | C5' | H5' | H5'A | 120.5° | 120.0° |
| C4' | C5' | O5' | P | 121.9° | 180.0° |
| H4' | C4' | C5' | O5' | 73.1° | 52.2° |
| H4' | C4' | C5' | H5' | 46.9° | 67.8° |
| H4' | C4' | C5' | H5'A | 166.9° | 172.1° |
| O4' | C4' | C5' | O5' | 48.5° | 70.9° |
| O4' | C4' | C5' | H5' | 168.5° | 169.1° |
| O4' | C4' | C5' | H5'A | 71.5° | 49.0° |
| O5' | C5' | H5' | H5'A | 120.4° | 120.0° |
| C5' | O5' | P | OP1 | 161.7° | 55.1° |
| H5' | C5' | O5' | P | 1.9° | 60.0° |
| H5'A | C5' | O5' | P | 118.1° | 60.1° |
| O5' | P | OP2 | HOP2 | 80.0° | 180.0° |
| O5' | P | OP3 | HOP3 | 119.6° | 60.0° |
| OP1 | P | OP2 | HOP2 | 82.7° | 60.0° |
| OP1 | P | OP3 | HOP3 | 0.0° | 180.0° |
