YB9
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O3' | C3' | sing | 1.43Å | 1.39Å | |
| O4' | C4' | sing | 1.43Å | 1.41Å | |
| C2' | C3' | sing | 1.53Å | 1.51Å | |
| C2' | C1' | sing | 1.53Å | 1.54Å | |
| C3' | C4' | sing | 1.53Å | 1.52Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| C5' | O5' | sing | 1.43Å | 1.38Å | |
| OP2 | P | doub | 1.48Å | 1.50Å | |
| C1' | N1 | sing | 1.47Å | 1.47Å | |
| OP1 | P | sing | 1.61Å | 1.50Å | |
| O5' | P | sing | 1.61Å | 1.65Å | |
| N1 | C2 | sing | 1.35Å | 1.44Å | |
| O2 | C2 | doub | 1.22Å | 1.21Å | |
| C2 | N2 | sing | 1.35Å | 1.27Å | |
| P | O1 | sing | 1.61Å | 1.59Å | |
| N1 | H1 | sing | 0.97Å | 1.00Å | |
| N2 | H2 | sing | 0.97Å | 1.00Å | |
| N2 | H3 | sing | 0.97Å | 1.00Å | |
| C1' | H4 | sing | 1.09Å | 1.10Å | |
| C1' | H5 | sing | 1.09Å | 1.10Å | |
| C2' | H6 | sing | 1.09Å | 1.10Å | |
| C2' | H7 | sing | 1.09Å | 1.10Å | |
| C3' | H8 | sing | 1.09Å | 1.10Å | |
| C4' | H9 | sing | 1.09Å | 1.10Å | |
| C5' | H10 | sing | 1.09Å | 1.10Å | |
| C5' | H11 | sing | 1.09Å | 1.10Å | |
| O3' | H12 | sing | 0.97Å | 0.95Å | |
| O4' | H13 | sing | 0.97Å | 0.95Å | |
| OP1 | H14 | sing | 0.97Å | 0.95Å | |
| O1 | H15 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O3' | C3' | C2' | 100.9° | 109.5° |
| O3' | C3' | C4' | 108.5° | 109.5° |
| O3' | C3' | H8 | 115.3° | 109.5° |
| C3' | O3' | H12 | 109.5° | 114.0° |
| O4' | C4' | C3' | 108.5° | 109.4° |
| O4' | C4' | C5' | 109.9° | 109.5° |
| O4' | C4' | H9 | 109.9° | 109.5° |
| C4' | O4' | H13 | 109.5° | 114.0° |
| C3' | C2' | C1' | 112.9° | 109.5° |
| C2' | C3' | C4' | 104.9° | 109.5° |
| C3' | C2' | H6 | 108.6° | 109.5° |
| C3' | C2' | H7 | 108.6° | 109.5° |
| C2' | C3' | H8 | 113.2° | 109.5° |
| C2' | C1' | N1 | 108.8° | 109.5° |
| C2' | C1' | H4 | 109.6° | 109.5° |
| C2' | C1' | H5 | 109.6° | 109.5° |
| C1' | C2' | H6 | 108.6° | 109.5° |
| C1' | C2' | H7 | 108.6° | 109.5° |
| C3' | C4' | C5' | 111.6° | 109.5° |
| C4' | C3' | H8 | 113.0° | 109.4° |
| C3' | C4' | H9 | 108.4° | 109.5° |
| C4' | C5' | O5' | 107.3° | 109.5° |
| C5' | C4' | H9 | 108.6° | 109.5° |
| C4' | C5' | H10 | 110.0° | 109.5° |
| C4' | C5' | H11 | 110.0° | 109.5° |
| C5' | O5' | P | 120.2° | 123.0° |
| O5' | C5' | H10 | 110.0° | 109.5° |
| O5' | C5' | H11 | 110.0° | 109.4° |
| OP2 | P | OP1 | 113.6° | 109.4° |
| OP2 | P | O5' | 111.2° | 109.5° |
| OP2 | P | O1 | 120.9° | 109.4° |
| C1' | N1 | C2 | 118.8° | 120.0° |
| C1' | N1 | H1 | 120.6° | 120.0° |
| N1 | C1' | H4 | 109.6° | 109.5° |
| N1 | C1' | H5 | 109.6° | 109.4° |
| OP1 | P | O5' | 114.1° | 109.5° |
| OP1 | P | O1 | 104.7° | 109.5° |
| P | OP1 | H14 | 109.5° | 114.0° |
| O5' | P | O1 | 90.4° | 109.5° |
| N1 | C2 | O2 | 121.8° | 120.0° |
| N1 | C2 | N2 | 117.4° | 120.0° |
| C2 | N1 | H1 | 120.6° | 120.0° |
| O2 | C2 | N2 | 120.8° | 120.0° |
| C2 | N2 | H2 | 120.0° | 120.0° |
| C2 | N2 | H3 | 120.0° | 120.0° |
| P | O1 | H15 | 109.5° | 114.0° |
| H2 | N2 | H3 | 120.0° | 120.0° |
| H4 | C1' | H5 | 109.5° | 109.5° |
| H6 | C2' | H7 | 109.4° | 109.4° |
| H10 | C5' | H11 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O3' | C3' | C4' | O4' | 65.8° | 65.0° |
| O3' | C3' | C2' | C4' | 112.7° | 120.0° |
| O3' | C3' | C2' | H8 | 123.7° | 120.0° |
| O3' | C3' | C2' | C1' | 151.4° | 65.0° |
| O3' | C3' | C4' | H8 | 129.1° | 120.0° |
| O3' | C3' | C4' | C5' | 55.4° | 54.9° |
| O3' | C3' | C2' | H6 | 30.9° | 175.0° |
| O3' | C3' | C2' | H7 | 88.1° | 55.0° |
| O3' | C3' | C4' | H9 | 174.9° | 175.0° |
| O4' | C4' | C3' | C2' | 41.4° | 55.0° |
| O4' | C4' | C3' | C5' | 121.1° | 120.0° |
| O4' | C4' | C3' | H9 | 119.3° | 120.0° |
| O4' | C4' | C5' | H9 | 120.2° | 120.0° |
| O4' | C4' | C5' | O5' | 123.4° | 65.0° |
| O4' | C4' | C3' | H8 | 165.1° | 175.0° |
| O4' | C4' | C5' | H10 | 3.7° | 55.0° |
| O4' | C4' | C5' | H11 | 117.0° | 175.0° |
| C3' | C2' | C1' | H6 | 120.5° | 120.0° |
| C3' | C2' | C1' | H7 | 120.5° | 120.0° |
| C2' | C3' | C4' | H8 | 123.7° | 120.0° |
| C2' | C3' | C4' | C5' | 162.6° | 175.0° |
| C3' | C2' | C1' | N1 | 124.2° | 180.0° |
| C3' | C2' | C1' | H4 | 4.3° | 60.0° |
| C3' | C2' | C1' | H5 | 116.0° | 60.0° |
| C3' | C2' | H6 | H7 | 118.5° | 120.0° |
| C2' | C3' | C4' | H9 | 77.9° | 65.0° |
| C2' | C3' | O3' | H12 | 180.0° | 59.9° |
| C1' | C2' | C3' | C4' | 95.9° | 175.0° |
| C2' | C1' | N1 | H4 | 119.9° | 120.0° |
| C2' | C1' | N1 | H5 | 119.9° | 120.0° |
| C2' | C1' | N1 | C2 | 127.6° | 180.0° |
| C2' | C1' | N1 | H1 | 52.5° | 0.1° |
| C2' | C1' | H4 | H5 | 120.3° | 120.0° |
| C1' | C2' | H6 | H7 | 118.4° | 120.0° |
| C1' | C2' | C3' | H8 | 27.7° | 55.0° |
| C3' | C4' | C5' | H9 | 119.5° | 120.1° |
| C3' | C4' | C5' | O5' | 116.3° | 175.0° |
| C4' | C3' | C2' | H6 | 143.6° | 55.0° |
| C4' | C3' | C2' | H7 | 24.6° | 65.0° |
| C3' | C4' | C5' | H10 | 124.1° | 65.0° |
| C3' | C4' | C5' | H11 | 3.4° | 55.0° |
| C4' | C3' | O3' | H12 | 70.1° | 60.1° |
| C3' | C4' | O4' | H13 | 180.0° | 60.0° |
| C4' | C5' | O5' | H10 | 119.7° | 120.0° |
| C4' | C5' | O5' | H11 | 119.7° | 120.0° |
| C4' | C5' | O5' | P | 167.8° | 180.0° |
| C5' | C4' | C3' | H8 | 73.7° | 65.0° |
| C4' | C5' | H10 | H11 | 121.0° | 120.0° |
| C5' | C4' | O4' | H13 | 57.8° | 60.0° |
| C5' | O5' | P | OP2 | 55.6° | 55.0° |
| C5' | O5' | P | OP1 | 74.4° | 175.0° |
| C5' | O5' | P | O1 | 179.2° | 65.0° |
| O5' | C5' | C4' | H9 | 3.2° | 54.9° |
| O5' | C5' | H10 | H11 | 121.0° | 120.0° |
| OP2 | P | OP1 | O5' | 128.8° | 120.0° |
| OP2 | P | OP1 | O1 | 134.0° | 119.9° |
| OP2 | P | O5' | O1 | 123.6° | 120.0° |
| OP2 | P | OP1 | H14 | 0.0° | 60.0° |
| OP2 | P | O1 | H15 | 0.0° | 180.0° |
| C1' | N1 | C2 | H1 | 180.0° | 179.9° |
| C1' | N1 | C2 | O2 | 2.3° | 0.3° |
| C1' | N1 | C2 | N2 | 178.7° | 180.0° |
| N1 | C1' | H4 | H5 | 120.3° | 120.0° |
| N1 | C1' | C2' | H6 | 115.3° | 60.0° |
| N1 | C1' | C2' | H7 | 3.7° | 60.0° |
| OP1 | P | O5' | O1 | 106.3° | 120.0° |
| OP1 | P | O1 | H15 | 129.7° | 60.1° |
| P | O5' | C5' | H10 | 48.1° | 60.0° |
| P | O5' | C5' | H11 | 72.6° | 60.0° |
| O5' | P | OP1 | H14 | 128.8° | 180.0° |
| O5' | P | O1 | H15 | 115.2° | 60.0° |
| N1 | C2 | O2 | N2 | 178.9° | 179.7° |
| N1 | C2 | N2 | H2 | 179.0° | 0.1° |
| N1 | C2 | N2 | H3 | 1.0° | 180.0° |
| C2 | N1 | C1' | H4 | 112.6° | 60.0° |
| C2 | N1 | C1' | H5 | 7.7° | 60.0° |
| O2 | C2 | N1 | H1 | 177.7° | 179.8° |
| O2 | C2 | N2 | H2 | 0.0° | 179.8° |
| O2 | C2 | N2 | H3 | 180.0° | 0.3° |
| N2 | C2 | N1 | H1 | 1.3° | 0.1° |
| C2 | N2 | H2 | H3 | 180.0° | 179.9° |
| O1 | P | OP1 | H14 | 134.0° | 59.9° |
| H1 | N1 | C1' | H4 | 67.4° | 119.9° |
| H1 | N1 | C1' | H5 | 172.3° | 120.1° |
| H4 | C1' | C2' | H6 | 124.8° | 180.0° |
| H4 | C1' | C2' | H7 | 116.2° | 60.0° |
| H5 | C1' | C2' | H6 | 4.6° | 60.0° |
| H5 | C1' | C2' | H7 | 123.5° | 180.0° |
| H6 | C2' | C3' | H8 | 92.9° | 65.0° |
| H7 | C2' | C3' | H8 | 148.2° | 175.0° |
| H8 | C3' | C4' | H9 | 45.8° | 55.0° |
| H8 | C3' | O3' | H12 | 57.8° | 180.0° |
| H9 | C4' | C5' | H10 | 116.5° | 175.0° |
| H9 | C4' | C5' | H11 | 122.8° | 65.0° |
| H9 | C4' | O4' | H13 | 61.6° | 179.9° |
