5DB
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O3' | C3' | sing | 1.43Å | 1.43Å | |
| C3' | C2' | sing | 1.55Å | 1.51Å | |
| C3' | C4' | sing | 1.55Å | 1.52Å | |
| C2' | C1' | sing | 1.54Å | 1.52Å | |
| C4' | C5' | sing | 1.53Å | 1.52Å | |
| C4' | O4' | sing | 1.44Å | 1.42Å | |
| C5' | O5' | sing | 1.43Å | 1.43Å | |
| C1' | O4' | sing | 1.44Å | 1.43Å | |
| C1' | N1 | sing | 1.47Å | 1.45Å | |
| OP2 | P | doub | 1.48Å | 1.51Å | |
| O5' | P | sing | 1.61Å | 1.61Å | |
| O2 | C2 | doub | 1.22Å | 1.26Å | |
| P | OP1 | sing | 1.61Å | 1.51Å | |
| N1 | C2 | sing | 1.35Å | 1.41Å | |
| N1 | C6 | sing | 1.36Å | 1.34Å | |
| C2 | N3 | sing | 1.33Å | 1.36Å | |
| C6 | C5 | doub | 1.36Å | 1.39Å | |
| N3 | C4 | doub | 1.32Å | 1.35Å | |
| C5 | C4 | sing | 1.41Å | 1.49Å | |
| C5 | C7 | sing | 1.51Å | 1.51Å | |
| C4 | O4 | sing | 1.35Å | 1.37Å | |
| O4 | C1 | sing | 1.43Å | 1.43Å | |
| OP1 | H1 | sing | 0.97Å | 0.95Å | |
| C5' | H2 | sing | 1.09Å | 1.10Å | |
| C5' | H3 | sing | 1.09Å | 1.10Å | |
| C4' | H4 | sing | 1.09Å | 1.10Å | |
| C3' | H5 | sing | 1.09Å | 1.10Å | |
| O3' | H6 | sing | 0.97Å | 0.95Å | |
| C2' | H7 | sing | 1.09Å | 1.10Å | |
| C2' | H8 | sing | 1.09Å | 1.10Å | |
| C1' | H9 | sing | 1.09Å | 1.10Å | |
| C6 | H10 | sing | 1.08Å | 1.08Å | |
| C7 | H11 | sing | 1.09Å | 1.10Å | |
| C7 | H12 | sing | 1.09Å | 1.10Å | |
| C7 | H13 | sing | 1.09Å | 1.10Å | |
| C1 | H15 | sing | 1.09Å | 1.10Å | |
| C1 | H16 | sing | 1.09Å | 1.10Å | |
| C1 | H17 | sing | 1.09Å | 1.10Å | |
| P | OP3 | sing | 1.61Å | 68.59Å | |
| OP3 | H19 | sing | 0.97Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O3' | C3' | C2' | 108.8° | 110.9° |
| O3' | C3' | C4' | 106.9° | 110.9° |
| O3' | C3' | H5 | 112.4° | 110.8° |
| C3' | O3' | H6 | 109.5° | 114.0° |
| C2' | C3' | C4' | 106.6° | 102.1° |
| C3' | C2' | C1' | 100.0° | 104.2° |
| C2' | C3' | H5 | 111.0° | 110.9° |
| C3' | C2' | H7 | 111.8° | 110.5° |
| C3' | C2' | H8 | 111.8° | 110.5° |
| C3' | C4' | C5' | 113.2° | 110.6° |
| C3' | C4' | O4' | 105.1° | 103.5° |
| C3' | C4' | H4 | 110.1° | 110.7° |
| C4' | C3' | H5 | 110.9° | 110.9° |
| C2' | C1' | O4' | 107.3° | 107.2° |
| C2' | C1' | N1 | 113.3° | 109.9° |
| C1' | C2' | H7 | 111.8° | 110.5° |
| C1' | C2' | H8 | 111.8° | 110.5° |
| C2' | C1' | H9 | 109.2° | 109.9° |
| C5' | C4' | O4' | 106.5° | 110.6° |
| C4' | C5' | O5' | 107.8° | 109.5° |
| C4' | C5' | H2 | 109.9° | 109.5° |
| C4' | C5' | H3 | 109.9° | 109.4° |
| C5' | C4' | H4 | 110.2° | 110.6° |
| C4' | O4' | C1' | 110.4° | 107.0° |
| O4' | C4' | H4 | 111.6° | 110.7° |
| C5' | O5' | P | 121.9° | 123.0° |
| O5' | C5' | H2 | 109.9° | 109.5° |
| O5' | C5' | H3 | 109.9° | 109.5° |
| O4' | C1' | N1 | 106.6° | 109.9° |
| O4' | C1' | H9 | 110.4° | 109.9° |
| C1' | N1 | C2 | 117.2° | 119.9° |
| C1' | N1 | C6 | 120.7° | 119.8° |
| N1 | C1' | H9 | 110.0° | 110.0° |
| OP2 | P | O5' | 110.2° | 109.4° |
| OP2 | P | OP1 | 112.4° | 109.4° |
| OP2 | P | OP3 | 111.6° | 109.5° |
| O5' | P | OP1 | 109.4° | 109.5° |
| O5' | P | OP3 | 49.2° | 109.5° |
| O2 | C2 | N1 | 118.4° | 119.5° |
| O2 | C2 | N3 | 121.2° | 119.5° |
| P | OP1 | H1 | 109.5° | 114.0° |
| OP1 | P | OP3 | 63.7° | 109.5° |
| C2 | N1 | C6 | 122.2° | 120.3° |
| N1 | C2 | N3 | 120.3° | 121.0° |
| N1 | C6 | C5 | 119.6° | 119.2° |
| N1 | C6 | H10 | 120.2° | 120.4° |
| C2 | N3 | C4 | 120.4° | 120.7° |
| C6 | C5 | C4 | 117.9° | 119.0° |
| C6 | C5 | C7 | 120.7° | 120.5° |
| C5 | C6 | H10 | 120.2° | 120.4° |
| N3 | C4 | C5 | 119.6° | 119.7° |
| N3 | C4 | O4 | 119.6° | 120.2° |
| C4 | C5 | C7 | 121.4° | 120.5° |
| C5 | C4 | O4 | 120.8° | 120.2° |
| C5 | C7 | H11 | 109.5° | 109.5° |
| C5 | C7 | H12 | 109.5° | 109.5° |
| C5 | C7 | H13 | 109.5° | 109.5° |
| C4 | O4 | C1 | 120.5° | 117.0° |
| O4 | C1 | H15 | 109.5° | 109.4° |
| O4 | C1 | H16 | 109.4° | 109.5° |
| O4 | C1 | H17 | 109.5° | 109.4° |
| H2 | C5' | H3 | 109.5° | 109.5° |
| H7 | C2' | H8 | 109.5° | 110.6° |
| H11 | C7 | H12 | 109.5° | 109.4° |
| H11 | C7 | H13 | 109.4° | 109.5° |
| H12 | C7 | H13 | 109.5° | 109.5° |
| H15 | C1 | H16 | 109.5° | 109.5° |
| H15 | C1 | H17 | 109.5° | 109.4° |
| H16 | C1 | H17 | 109.4° | 109.5° |
| P | OP3 | H19 | 90.0° | 114.1° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O3' | C3' | C2' | C4' | 114.9° | 118.2° |
| O3' | C3' | C2' | H5 | 124.2° | 123.6° |
| O3' | C3' | C4' | H5 | 122.8° | 123.6° |
| O3' | C3' | C2' | C1' | 85.0° | 139.1° |
| O3' | C3' | C4' | C5' | 146.3° | 86.3° |
| O3' | C3' | C4' | O4' | 97.9° | 155.3° |
| O3' | C3' | C4' | H4 | 22.5° | 36.7° |
| O3' | C3' | C2' | H7 | 156.5° | 102.2° |
| O3' | C3' | C2' | H8 | 33.4° | 20.4° |
| C2' | C3' | C4' | H5 | 120.9° | 118.2° |
| C3' | C2' | C1' | H7 | 118.4° | 118.7° |
| C3' | C2' | C1' | H8 | 118.4° | 118.7° |
| C2' | C3' | C4' | C5' | 97.5° | 155.5° |
| C2' | C3' | C4' | O4' | 18.3° | 37.0° |
| C3' | C2' | C1' | O4' | 31.6° | 2.1° |
| C3' | C2' | C1' | N1 | 149.0° | 121.5° |
| C2' | C3' | C4' | H4 | 138.7° | 81.6° |
| C2' | C3' | O3' | H6 | 180.0° | 61.4° |
| C3' | C2' | H7 | H8 | 124.4° | 122.6° |
| C3' | C2' | C1' | H9 | 88.1° | 117.4° |
| C4' | C3' | C2' | C1' | 29.9° | 20.9° |
| C3' | C4' | C5' | O4' | 115.0° | 114.0° |
| C3' | C4' | C5' | H4 | 123.8° | 123.0° |
| C3' | C4' | O4' | H4 | 119.3° | 118.6° |
| C3' | C4' | C5' | O5' | 71.9° | 179.4° |
| C3' | C4' | O4' | C1' | 2.3° | 40.1° |
| C3' | C4' | C5' | H2 | 168.3° | 60.5° |
| C3' | C4' | C5' | H3 | 47.8° | 59.5° |
| C4' | C3' | O3' | H6 | 65.2° | 174.2° |
| C4' | C3' | C2' | H7 | 88.6° | 139.5° |
| C4' | C3' | C2' | H8 | 148.3° | 97.8° |
| C2' | C1' | O4' | C4' | 22.1° | 26.6° |
| C2' | C1' | O4' | N1 | 121.6° | 119.4° |
| C2' | C1' | O4' | H9 | 118.9° | 119.5° |
| C2' | C1' | N1 | H9 | 122.5° | 121.1° |
| C2' | C1' | N1 | C2 | 128.9° | 65.0° |
| C2' | C1' | N1 | C6 | 52.5° | 115.3° |
| C1' | C2' | C3' | H5 | 150.7° | 97.3° |
| C1' | C2' | H7 | H8 | 124.4° | 122.6° |
| C5' | C4' | O4' | H4 | 120.3° | 122.9° |
| C4' | C5' | O5' | H2 | 119.7° | 120.0° |
| C4' | C5' | O5' | H3 | 119.8° | 120.0° |
| C5' | C4' | O4' | C1' | 122.6° | 158.6° |
| C4' | C5' | O5' | P | 164.0° | 180.0° |
| C4' | C5' | H2 | H3 | 120.8° | 119.9° |
| C5' | C4' | C3' | H5 | 23.5° | 37.3° |
| O4' | C4' | C5' | O5' | 43.0° | 66.5° |
| C4' | O4' | C1' | N1 | 143.8° | 146.0° |
| O4' | C4' | C5' | H2 | 76.7° | 53.6° |
| O4' | C4' | C5' | H3 | 162.8° | 173.5° |
| O4' | C4' | C3' | H5 | 139.3° | 81.2° |
| C4' | O4' | C1' | H9 | 96.7° | 92.9° |
| C5' | O5' | P | OP2 | 36.8° | 55.0° |
| C5' | O5' | P | OP1 | 160.8° | 64.9° |
| O5' | C5' | H2 | H3 | 120.8° | 120.0° |
| O5' | C5' | C4' | H4 | 164.2° | 56.4° |
| C5' | O5' | P | OP3 | 138.4° | 175.0° |
| O4' | C1' | N1 | H9 | 119.7° | 121.1° |
| O4' | C1' | N1 | C2 | 113.3° | 52.8° |
| O4' | C1' | N1 | C6 | 65.2° | 127.0° |
| C1' | O4' | C4' | H4 | 117.1° | 78.6° |
| O4' | C1' | C2' | H7 | 86.8° | 116.6° |
| O4' | C1' | C2' | H8 | 150.0° | 120.7° |
| C1' | N1 | C2 | O2 | 0.8° | 0.0° |
| C1' | N1 | C2 | C6 | 178.5° | 179.8° |
| C1' | N1 | C2 | N3 | 179.2° | 179.7° |
| C1' | N1 | C6 | C5 | 179.5° | 180.0° |
| N1 | C1' | C2' | H7 | 30.5° | 2.7° |
| N1 | C1' | C2' | H8 | 92.6° | 119.9° |
| C1' | N1 | C6 | H10 | 0.5° | 0.0° |
| OP2 | P | O5' | OP1 | 124.0° | 120.0° |
| OP2 | P | O5' | OP3 | 101.7° | 120.0° |
| OP2 | P | OP1 | OP3 | 104.0° | 120.0° |
| OP2 | P | OP1 | H1 | 0.0° | 179.9° |
| OP2 | P | OP3 | H19 | 90.0° | 60.0° |
| O5' | P | OP1 | OP3 | 18.8° | 120.1° |
| O5' | P | OP1 | H1 | 122.7° | 60.0° |
| P | O5' | C5' | H2 | 76.3° | 60.0° |
| P | O5' | C5' | H3 | 44.3° | 60.0° |
| O5' | P | OP3 | H19 | 90.0° | 180.0° |
| O2 | C2 | N1 | N3 | 180.0° | 179.7° |
| O2 | C2 | N1 | C6 | 179.4° | 179.7° |
| O2 | C2 | N3 | C4 | 179.9° | 179.7° |
| OP1 | P | OP3 | H19 | 90.0° | 59.9° |
| C2 | N1 | C6 | C5 | 1.0° | 0.2° |
| N1 | C2 | N3 | C4 | 0.2° | 0.6° |
| C2 | N1 | C1' | H9 | 6.4° | 173.9° |
| C2 | N1 | C6 | H10 | 179.0° | 179.7° |
| C6 | N1 | C2 | N3 | 0.7° | 0.5° |
| N1 | C6 | C5 | H10 | 180.0° | 180.0° |
| N1 | C6 | C5 | C4 | 0.9° | 0.0° |
| N1 | C6 | C5 | C7 | 179.4° | 180.0° |
| C6 | N1 | C1' | H9 | 175.0° | 5.9° |
| C2 | N3 | C4 | C5 | 0.1° | 0.3° |
| C2 | N3 | C4 | O4 | 179.6° | 179.8° |
| C6 | C5 | C4 | N3 | 0.4° | 0.0° |
| C6 | C5 | C4 | C7 | 179.7° | 180.0° |
| C6 | C5 | C4 | O4 | 179.9° | 180.0° |
| C6 | C5 | C7 | H11 | 180.0° | 90.0° |
| C6 | C5 | C7 | H12 | 60.0° | 150.0° |
| C6 | C5 | C7 | H13 | 60.0° | 30.0° |
| N3 | C4 | C5 | O4 | 179.5° | 179.9° |
| N3 | C4 | C5 | C7 | 179.9° | 180.0° |
| N3 | C4 | O4 | C1 | 25.0° | 0.0° |
| C5 | C4 | O4 | C1 | 155.5° | 180.0° |
| C4 | C5 | C6 | H10 | 179.1° | 180.0° |
| C4 | C5 | C7 | H11 | 0.3° | 89.9° |
| C4 | C5 | C7 | H12 | 119.7° | 30.0° |
| C4 | C5 | C7 | H13 | 120.3° | 150.0° |
| C7 | C5 | C4 | O4 | 0.3° | 0.1° |
| C7 | C5 | C6 | H10 | 0.6° | 0.0° |
| C5 | C7 | H11 | H12 | 120.0° | 120.0° |
| C5 | C7 | H11 | H13 | 120.0° | 120.0° |
| C5 | C7 | H12 | H13 | 120.0° | 120.0° |
| C4 | O4 | C1 | H15 | 180.0° | 60.0° |
| C4 | O4 | C1 | H16 | 60.0° | 60.0° |
| C4 | O4 | C1 | H17 | 60.0° | 180.0° |
| O4 | C1 | H15 | H16 | 120.0° | 120.0° |
| O4 | C1 | H15 | H17 | 120.0° | 119.9° |
| O4 | C1 | H16 | H17 | 120.0° | 120.0° |
| H1 | OP1 | P | OP3 | 104.0° | 60.1° |
| H2 | C5' | C4' | H4 | 44.5° | 176.5° |
| H3 | C5' | C4' | H4 | 76.0° | 63.6° |
| H4 | C4' | C3' | H5 | 100.4° | 160.2° |
| H5 | C3' | O3' | H6 | 56.7° | 62.2° |
| H5 | C3' | C2' | H7 | 32.3° | 21.3° |
| H5 | C3' | C2' | H8 | 90.8° | 144.0° |
| H7 | C2' | C1' | H9 | 153.5° | 123.9° |
| H8 | C2' | C1' | H9 | 30.4° | 1.3° |
| H11 | C7 | H12 | H13 | 120.0° | 120.0° |
| H15 | C1 | H16 | H17 | 120.0° | 120.0° |
