8Y9
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O3' | C3' | sing | 1.43Å | 1.45Å | |
| C3' | C4' | sing | 1.55Å | 1.50Å | |
| C3' | C2' | sing | 1.55Å | 1.52Å | |
| OP1 | P | doub | 1.48Å | 1.50Å | |
| C4' | O4' | sing | 1.45Å | 1.43Å | |
| C4' | C5' | sing | 1.53Å | 1.53Å | |
| OP2 | P | sing | 1.61Å | 1.51Å | |
| O5' | P | sing | 1.61Å | 1.64Å | |
| O5' | C5' | sing | 1.43Å | 1.41Å | |
| O4' | C1' | sing | 1.44Å | 1.43Å | |
| C2' | C1' | sing | 1.54Å | 1.51Å | |
| C1' | N9 | sing | 1.47Å | 1.47Å | |
| O8 | C8 | doub | 1.22Å | 1.30Å | |
| N9 | C8 | sing | 1.34Å | 1.34Å | |
| N9 | C4 | sing | 1.47Å | 1.44Å | |
| C8 | N7 | sing | 1.34Å | 1.35Å | |
| C4 | N3 | sing | 1.46Å | 1.43Å | |
| C4 | C5 | sing | 1.52Å | 1.46Å | |
| N7 | C5 | sing | 1.35Å | 1.35Å | |
| N3 | C2 | sing | 1.37Å | 1.34Å | |
| C5 | O5 | doub | 1.21Å | 1.29Å | |
| C2 | N12 | doub | 1.30Å | 1.27Å | |
| C2 | N11 | sing | 1.38Å | 1.35Å | |
| P | O1 | sing | 1.61Å | 1.61Å | |
| N3 | H1 | sing | 0.97Å | 1.00Å | |
| C4 | H2 | sing | 1.09Å | 1.10Å | |
| N7 | H3 | sing | 0.97Å | 1.00Å | |
| C1' | H4 | sing | 1.09Å | 1.10Å | |
| N11 | H5 | sing | 0.97Å | 1.00Å | |
| N11 | H6 | sing | 0.97Å | 1.00Å | |
| N12 | H7 | sing | 0.97Å | 1.00Å | |
| C2' | H8 | sing | 1.09Å | 1.10Å | |
| C2' | H9 | sing | 1.09Å | 1.10Å | |
| C3' | H10 | sing | 1.09Å | 1.10Å | |
| O3' | H11 | sing | 0.97Å | 0.95Å | |
| C4' | H12 | sing | 1.09Å | 1.10Å | |
| C5' | H13 | sing | 1.09Å | 1.10Å | |
| C5' | H14 | sing | 1.09Å | 1.10Å | |
| OP2 | H15 | sing | 0.97Å | 0.95Å | |
| O1 | H16 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O3' | C3' | C4' | 109.9° | 110.9° |
| O3' | C3' | C2' | 109.7° | 111.0° |
| O3' | C3' | H10 | 112.0° | 110.9° |
| C3' | O3' | H11 | 109.5° | 114.0° |
| C4' | C3' | C2' | 102.5° | 102.1° |
| C3' | C4' | O4' | 103.2° | 103.6° |
| C3' | C4' | C5' | 113.9° | 110.6° |
| C4' | C3' | H10 | 111.3° | 110.9° |
| C3' | C4' | H12 | 109.7° | 110.6° |
| C3' | C2' | C1' | 98.1° | 104.2° |
| C3' | C2' | H8 | 112.2° | 110.5° |
| C3' | C2' | H9 | 112.3° | 110.6° |
| C2' | C3' | H10 | 111.0° | 110.8° |
| OP1 | P | OP2 | 116.6° | 109.5° |
| OP1 | P | O5' | 110.0° | 109.4° |
| OP1 | P | O1 | 107.9° | 109.4° |
| O4' | C4' | C5' | 109.6° | 110.6° |
| C4' | O4' | C1' | 109.8° | 106.9° |
| O4' | C4' | H12 | 110.9° | 110.5° |
| C4' | C5' | O5' | 108.7° | 109.5° |
| C5' | C4' | H12 | 109.4° | 110.7° |
| C4' | C5' | H13 | 109.6° | 109.4° |
| C4' | C5' | H14 | 109.7° | 109.5° |
| OP2 | P | O5' | 107.8° | 109.5° |
| OP2 | P | O1 | 109.3° | 109.5° |
| P | OP2 | H15 | 109.5° | 114.0° |
| P | O5' | C5' | 119.9° | 123.0° |
| O5' | P | O1 | 104.7° | 109.5° |
| O5' | C5' | H13 | 109.7° | 109.5° |
| O5' | C5' | H14 | 109.7° | 109.5° |
| O4' | C1' | C2' | 106.5° | 107.4° |
| O4' | C1' | N9 | 105.3° | 109.9° |
| O4' | C1' | H4 | 108.5° | 109.8° |
| C2' | C1' | N9 | 120.6° | 109.9° |
| C2' | C1' | H4 | 107.4° | 109.9° |
| C1' | C2' | H8 | 112.2° | 110.5° |
| C1' | C2' | H9 | 112.2° | 110.5° |
| C1' | N9 | C8 | 127.1° | 126.7° |
| C1' | N9 | C4 | 118.0° | 126.7° |
| N9 | C1' | H4 | 108.0° | 109.9° |
| O8 | C8 | N9 | 122.6° | 123.8° |
| O8 | C8 | N7 | 125.1° | 123.7° |
| C8 | N9 | C4 | 114.9° | 106.7° |
| N9 | C8 | N7 | 112.3° | 112.4° |
| N9 | C4 | N3 | 118.7° | 110.6° |
| N9 | C4 | C5 | 91.1° | 103.6° |
| N9 | C4 | H2 | 113.1° | 110.7° |
| C8 | N7 | C5 | 99.1° | 111.6° |
| C8 | N7 | H3 | 130.5° | 124.2° |
| N3 | C4 | C5 | 105.3° | 110.6° |
| C4 | N3 | C2 | 123.4° | 120.0° |
| C4 | N3 | H1 | 118.3° | 120.0° |
| N3 | C4 | H2 | 113.3° | 110.5° |
| C4 | C5 | N7 | 122.5° | 105.7° |
| C4 | C5 | O5 | 117.5° | 127.2° |
| C5 | C4 | H2 | 112.8° | 110.7° |
| N7 | C5 | O5 | 120.0° | 127.2° |
| C5 | N7 | H3 | 130.4° | 124.2° |
| N3 | C2 | N12 | 116.3° | 120.0° |
| N3 | C2 | N11 | 123.4° | 120.0° |
| C2 | N3 | H1 | 118.3° | 120.0° |
| N12 | C2 | N11 | 120.3° | 120.0° |
| C2 | N12 | H7 | 112.0° | 120.0° |
| C2 | N11 | H5 | 120.0° | 120.0° |
| C2 | N11 | H6 | 120.0° | 120.0° |
| P | O1 | H16 | 109.5° | 114.0° |
| H5 | N11 | H6 | 120.0° | 120.0° |
| H8 | C2' | H9 | 109.5° | 110.4° |
| H13 | C5' | H14 | 109.4° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O3' | C3' | C4' | C2' | 116.6° | 118.3° |
| O3' | C3' | C4' | H10 | 124.8° | 123.6° |
| O3' | C3' | C2' | H10 | 124.4° | 123.6° |
| O3' | C3' | C4' | O4' | 78.2° | 155.2° |
| O3' | C3' | C4' | C5' | 163.1° | 86.2° |
| O3' | C3' | C2' | C1' | 73.4° | 139.1° |
| O3' | C3' | C2' | H8 | 168.5° | 20.4° |
| O3' | C3' | C2' | H9 | 44.7° | 102.2° |
| O3' | C3' | C4' | H12 | 40.0° | 36.8° |
| C4' | C3' | C2' | H10 | 118.9° | 118.2° |
| C3' | C4' | O4' | C5' | 121.7° | 118.6° |
| C3' | C4' | O4' | H12 | 117.4° | 118.5° |
| C3' | C4' | C5' | H12 | 123.2° | 123.0° |
| C3' | C4' | C5' | O5' | 72.8° | 175.0° |
| C3' | C4' | O4' | C1' | 17.0° | 39.9° |
| C4' | C3' | C2' | C1' | 43.4° | 20.9° |
| C4' | C3' | C2' | H8 | 74.7° | 97.8° |
| C4' | C3' | C2' | H9 | 161.5° | 139.6° |
| C4' | C3' | O3' | H11 | 180.0° | 180.0° |
| C3' | C4' | C5' | H13 | 47.1° | 55.0° |
| C3' | C4' | C5' | H14 | 167.3° | 65.0° |
| C2' | C3' | C4' | O4' | 38.4° | 36.9° |
| C2' | C3' | C4' | C5' | 80.3° | 155.5° |
| C3' | C2' | C1' | O4' | 33.8° | 2.0° |
| C3' | C2' | C1' | H8 | 118.1° | 118.7° |
| C3' | C2' | C1' | H9 | 118.1° | 118.9° |
| C3' | C2' | C1' | N9 | 153.6° | 121.4° |
| C3' | C2' | C1' | H4 | 82.3° | 117.5° |
| C3' | C2' | H8 | H9 | 125.3° | 122.7° |
| C2' | C3' | O3' | H11 | 68.0° | 67.3° |
| C2' | C3' | C4' | H12 | 156.6° | 81.5° |
| OP1 | P | OP2 | O5' | 124.2° | 120.0° |
| OP1 | P | OP2 | O1 | 122.6° | 120.0° |
| OP1 | P | O5' | O1 | 115.6° | 119.9° |
| OP1 | P | O5' | C5' | 60.9° | 55.0° |
| OP1 | P | OP2 | H15 | 0.0° | 60.0° |
| OP1 | P | O1 | H16 | 0.0° | 179.9° |
| O4' | C4' | C5' | H12 | 121.8° | 122.8° |
| O4' | C4' | C5' | O5' | 172.2° | 70.8° |
| C4' | O4' | C1' | C2' | 11.3° | 26.3° |
| C4' | O4' | C1' | N9 | 140.5° | 145.8° |
| C4' | O4' | C1' | H4 | 104.1° | 93.2° |
| O4' | C4' | C3' | H10 | 157.0° | 81.2° |
| O4' | C4' | C5' | H13 | 67.9° | 169.2° |
| O4' | C4' | C5' | H14 | 52.3° | 49.2° |
| C4' | C5' | O5' | P | 127.3° | 180.0° |
| C4' | C5' | O5' | H13 | 119.9° | 120.0° |
| C4' | C5' | O5' | H14 | 119.9° | 120.0° |
| C5' | C4' | O4' | C1' | 104.7° | 158.4° |
| C5' | C4' | C3' | H10 | 38.3° | 37.4° |
| C4' | C5' | H13 | H14 | 120.3° | 120.0° |
| OP2 | P | O5' | O1 | 116.3° | 120.0° |
| OP2 | P | O5' | C5' | 171.0° | 175.0° |
| OP2 | P | O1 | H16 | 127.7° | 60.0° |
| P | O5' | C5' | H13 | 112.8° | 60.0° |
| P | O5' | C5' | H14 | 7.4° | 60.0° |
| O5' | P | OP2 | H15 | 124.2° | 180.0° |
| O5' | P | O1 | H16 | 117.1° | 60.0° |
| C5' | O5' | P | O1 | 54.7° | 65.0° |
| O5' | C5' | C4' | H12 | 50.4° | 52.0° |
| O5' | C5' | H13 | H14 | 120.4° | 120.0° |
| O4' | C1' | C2' | N9 | 119.7° | 119.5° |
| O4' | C1' | C2' | H4 | 116.1° | 119.5° |
| O4' | C1' | N9 | H4 | 115.8° | 121.0° |
| O4' | C1' | N9 | C8 | 90.1° | 53.3° |
| O4' | C1' | N9 | C4 | 90.4° | 126.7° |
| O4' | C1' | C2' | H8 | 84.3° | 120.6° |
| O4' | C1' | C2' | H9 | 152.0° | 116.9° |
| C1' | O4' | C4' | H12 | 134.4° | 78.7° |
| C2' | C1' | N9 | H4 | 123.9° | 121.1° |
| C2' | C1' | N9 | C8 | 149.6° | 64.7° |
| C2' | C1' | N9 | C4 | 29.9° | 115.4° |
| C1' | C2' | H8 | H9 | 125.3° | 122.5° |
| C1' | C2' | C3' | H10 | 162.3° | 97.3° |
| C1' | N9 | C8 | O8 | 1.2° | 0.0° |
| C1' | N9 | C8 | C4 | 179.5° | 180.0° |
| C1' | N9 | C8 | N7 | 179.5° | 180.0° |
| C1' | N9 | C4 | N3 | 71.4° | 61.5° |
| C1' | N9 | C4 | C5 | 179.6° | 180.0° |
| C1' | N9 | C4 | H2 | 65.0° | 61.3° |
| N9 | C1' | C2' | H8 | 35.5° | 119.9° |
| N9 | C1' | C2' | H9 | 88.3° | 2.6° |
| O8 | C8 | N9 | N7 | 179.4° | 180.0° |
| O8 | C8 | N9 | C4 | 178.3° | 180.0° |
| O8 | C8 | N7 | C5 | 178.8° | 180.0° |
| O8 | C8 | N7 | H3 | 1.2° | 0.1° |
| C8 | N9 | C4 | N3 | 109.1° | 118.5° |
| C8 | N9 | C4 | C5 | 0.9° | 0.0° |
| N9 | C8 | N7 | C5 | 0.6° | 0.0° |
| C8 | N9 | C4 | H2 | 114.5° | 118.6° |
| N9 | C8 | N7 | H3 | 179.4° | 179.9° |
| C8 | N9 | C1' | H4 | 25.7° | 174.3° |
| C4 | N9 | C8 | N7 | 1.1° | 0.0° |
| N9 | C4 | N3 | C5 | 100.0° | 114.1° |
| N9 | C4 | N3 | H2 | 136.3° | 123.0° |
| N9 | C4 | C5 | H2 | 115.7° | 118.7° |
| N9 | C4 | C5 | N7 | 0.6° | 0.1° |
| N9 | C4 | N3 | C2 | 158.8° | 110.6° |
| N9 | C4 | C5 | O5 | 178.8° | 179.9° |
| N9 | C4 | N3 | H1 | 21.2° | 69.5° |
| C4 | N9 | C1' | H4 | 153.8° | 5.7° |
| C8 | N7 | C5 | C4 | 0.1° | 0.1° |
| C8 | N7 | C5 | H3 | 180.0° | 179.9° |
| C8 | N7 | C5 | O5 | 179.3° | 179.9° |
| N3 | C4 | C5 | H2 | 124.0° | 122.8° |
| N3 | C4 | C5 | N7 | 120.9° | 118.5° |
| C4 | N3 | C2 | H1 | 180.0° | 179.9° |
| N3 | C4 | C5 | O5 | 58.5° | 61.6° |
| C4 | N3 | C2 | N12 | 178.2° | 5.0° |
| C4 | N3 | C2 | N11 | 3.9° | 174.9° |
| C4 | C5 | N7 | O5 | 179.4° | 179.9° |
| C5 | C4 | N3 | C2 | 101.2° | 135.3° |
| C5 | C4 | N3 | H1 | 78.7° | 44.6° |
| C4 | C5 | N7 | H3 | 179.9° | 180.0° |
| N7 | C5 | C4 | H2 | 115.1° | 118.7° |
| N3 | C2 | N12 | N11 | 177.9° | 179.9° |
| C2 | N3 | C4 | H2 | 22.5° | 12.4° |
| N3 | C2 | N11 | H5 | 177.8° | 175.0° |
| N3 | C2 | N11 | H6 | 2.3° | 5.1° |
| N3 | C2 | N12 | H7 | 177.9° | 180.0° |
| O5 | C5 | C4 | H2 | 65.5° | 61.2° |
| O5 | C5 | N7 | H3 | 0.7° | 0.2° |
| N12 | C2 | N3 | H1 | 1.8° | 174.9° |
| N12 | C2 | N11 | H5 | 0.0° | 4.9° |
| N12 | C2 | N11 | H6 | 180.0° | 175.0° |
| N11 | C2 | N3 | H1 | 176.1° | 5.2° |
| C2 | N11 | H5 | H6 | 180.0° | 179.9° |
| N11 | C2 | N12 | H7 | 0.0° | 0.0° |
| O1 | P | OP2 | H15 | 122.6° | 59.9° |
| H1 | N3 | C4 | H2 | 157.5° | 167.5° |
| H4 | C1' | C2' | H8 | 159.6° | 1.2° |
| H4 | C1' | C2' | H9 | 35.9° | 123.7° |
| H8 | C2' | C3' | H10 | 44.2° | 144.0° |
| H9 | C2' | C3' | H10 | 79.6° | 21.5° |
| H10 | C3' | O3' | H11 | 55.7° | 56.4° |
| H10 | C3' | C4' | H12 | 84.7° | 160.4° |
| H12 | C4' | C5' | H13 | 170.3° | 68.0° |
| H12 | C4' | C5' | H14 | 69.5° | 172.0° |
