1VY
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O4 | C4 | doub | 1.22Å | 1.24Å | |
| C4 | N3 | sing | 1.35Å | 1.36Å | |
| C4 | C4A | sing | 1.47Å | 1.40Å | |
| N5 | C4A | doub | 1.32Å | 1.36Å | |
| N5 | C6 | sing | 1.32Å | 1.35Å | |
| N3 | C2 | sing | 1.34Å | 1.36Å | |
| C4A | C8A | sing | 1.42Å | 1.40Å | |
| C9 | C6 | sing | 1.51Å | 1.42Å | |
| C6 | C7 | doub | 1.39Å | 1.39Å | |
| O4' | C4' | sing | 1.43Å | 1.40Å | |
| C2 | O2 | doub | 1.22Å | 1.23Å | |
| C2 | N1 | sing | 1.33Å | 1.35Å | |
| C8A | N1 | doub | 1.33Å | 1.35Å | |
| C8A | N8 | sing | 1.37Å | 1.37Å | |
| O2' | C2' | sing | 1.43Å | 1.45Å | |
| C7 | N8 | sing | 1.35Å | 1.35Å | |
| C7 | O7 | sing | 1.35Å | 1.37Å | |
| C3' | C4' | sing | 1.53Å | 1.55Å | |
| C3' | O3' | sing | 1.43Å | 1.47Å | |
| C3' | C2' | sing | 1.53Å | 1.53Å | |
| C4' | C5' | sing | 1.53Å | 1.52Å | |
| N8 | C1' | sing | 1.46Å | 1.48Å | |
| C2' | C1' | sing | 1.53Å | 1.52Å | |
| C5' | O5' | sing | 1.43Å | 1.44Å | |
| C9 | H1 | sing | 1.09Å | 1.10Å | |
| C9 | H2 | sing | 1.09Å | 1.10Å | |
| C9 | H3 | sing | 1.09Å | 1.10Å | |
| N3 | H5 | sing | 0.97Å | 1.00Å | |
| C1' | H6 | sing | 1.09Å | 1.10Å | |
| C1' | H7 | sing | 1.09Å | 1.10Å | |
| C2' | H8 | sing | 1.09Å | 1.10Å | |
| O2' | H9 | sing | 0.97Å | 0.95Å | |
| C3' | H10 | sing | 1.09Å | 1.10Å | |
| O3' | H11 | sing | 0.97Å | 0.95Å | |
| C4' | H12 | sing | 1.09Å | 1.10Å | |
| O4' | H13 | sing | 0.97Å | 0.95Å | |
| C5' | H14 | sing | 1.09Å | 1.10Å | |
| C5' | H15 | sing | 1.09Å | 1.10Å | |
| O5' | H16 | sing | 0.97Å | 0.95Å | |
| O7 | H17 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O4 | C4 | N3 | 119.0° | 121.2° |
| O4 | C4 | C4A | 120.6° | 121.3° |
| N3 | C4 | C4A | 119.8° | 117.5° |
| C4 | N3 | C2 | 120.1° | 120.6° |
| C4 | N3 | H5 | 119.9° | 119.7° |
| C4 | C4A | N5 | 120.9° | 121.7° |
| C4 | C4A | C8A | 119.1° | 117.9° |
| C4A | N5 | C6 | 120.8° | 120.5° |
| N5 | C4A | C8A | 119.8° | 120.4° |
| N5 | C6 | C9 | 121.0° | 119.5° |
| N5 | C6 | C7 | 119.0° | 121.0° |
| N3 | C2 | O2 | 121.7° | 118.4° |
| N3 | C2 | N1 | 120.3° | 123.1° |
| C2 | N3 | H5 | 120.0° | 119.8° |
| C4A | C8A | N1 | 118.4° | 119.3° |
| C4A | C8A | N8 | 119.8° | 119.1° |
| C9 | C6 | C7 | 120.0° | 119.5° |
| C6 | C9 | H1 | 109.5° | 109.5° |
| C6 | C9 | H2 | 109.5° | 109.4° |
| C6 | C9 | H3 | 109.4° | 109.5° |
| C6 | C7 | N8 | 121.6° | 120.2° |
| C6 | C7 | O7 | 116.4° | 119.9° |
| O4' | C4' | C3' | 105.5° | 109.5° |
| O4' | C4' | C5' | 105.3° | 109.5° |
| O4' | C4' | H12 | 112.6° | 109.5° |
| C4' | O4' | H13 | 109.5° | 114.1° |
| O2 | C2 | N1 | 118.1° | 118.4° |
| C2 | N1 | C8A | 122.2° | 121.7° |
| N1 | C8A | N8 | 121.8° | 121.6° |
| C8A | N8 | C7 | 119.1° | 118.7° |
| C8A | N8 | C1' | 122.2° | 120.6° |
| O2' | C2' | C3' | 112.6° | 109.5° |
| O2' | C2' | C1' | 110.9° | 109.4° |
| O2' | C2' | H8 | 108.2° | 109.4° |
| C2' | O2' | H9 | 109.5° | 114.0° |
| N8 | C7 | O7 | 121.9° | 119.9° |
| C7 | N8 | C1' | 118.1° | 120.7° |
| C7 | O7 | H17 | 109.5° | 116.9° |
| C4' | C3' | O3' | 112.8° | 109.5° |
| C4' | C3' | C2' | 111.4° | 109.5° |
| C3' | C4' | C5' | 112.3° | 109.4° |
| C4' | C3' | H10 | 106.5° | 109.5° |
| C3' | C4' | H12 | 110.3° | 109.5° |
| O3' | C3' | C2' | 111.5° | 109.4° |
| O3' | C3' | H10 | 107.5° | 109.5° |
| C3' | O3' | H11 | 109.5° | 114.0° |
| C3' | C2' | C1' | 110.3° | 109.5° |
| C3' | C2' | H8 | 107.2° | 109.5° |
| C2' | C3' | H10 | 106.7° | 109.4° |
| C4' | C5' | O5' | 115.4° | 109.5° |
| C5' | C4' | H12 | 110.7° | 109.5° |
| C4' | C5' | H14 | 108.0° | 109.5° |
| C4' | C5' | H15 | 108.0° | 109.5° |
| N8 | C1' | C2' | 119.3° | 109.5° |
| N8 | C1' | H6 | 106.9° | 109.5° |
| N8 | C1' | H7 | 107.0° | 109.5° |
| C2' | C1' | H6 | 107.0° | 109.5° |
| C2' | C1' | H7 | 107.0° | 109.5° |
| C1' | C2' | H8 | 107.4° | 109.5° |
| O5' | C5' | H14 | 108.0° | 109.4° |
| O5' | C5' | H15 | 108.0° | 109.5° |
| C5' | O5' | H16 | 109.5° | 114.0° |
| H1 | C9 | H2 | 109.4° | 109.4° |
| H1 | C9 | H3 | 109.5° | 109.5° |
| H2 | C9 | H3 | 109.5° | 109.5° |
| H6 | C1' | H7 | 109.5° | 109.5° |
| H14 | C5' | H15 | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O4 | C4 | N3 | C4A | 171.2° | 180.0° |
| O4 | C4 | C4A | N5 | 3.2° | 0.0° |
| O4 | C4 | N3 | C2 | 174.9° | 180.0° |
| O4 | C4 | C4A | C8A | 171.7° | 180.0° |
| O4 | C4 | N3 | H5 | 5.1° | 0.0° |
| N3 | C4 | C4A | N5 | 174.2° | 180.0° |
| C4 | N3 | C2 | H5 | 180.0° | 180.0° |
| N3 | C4 | C4A | C8A | 0.7° | 0.0° |
| C4 | N3 | C2 | O2 | 174.3° | 180.0° |
| C4 | N3 | C2 | N1 | 4.3° | 0.0° |
| C4 | C4A | N5 | C8A | 174.9° | 180.0° |
| C4 | C4A | N5 | C6 | 175.2° | 180.0° |
| C4A | C4 | N3 | C2 | 3.7° | 0.0° |
| C4 | C4A | C8A | N1 | 1.8° | 0.0° |
| C4 | C4A | C8A | N8 | 175.7° | 180.0° |
| C4A | C4 | N3 | H5 | 176.3° | 180.0° |
| C4A | N5 | C6 | C9 | 179.1° | 180.0° |
| C4A | N5 | C6 | C7 | 0.6° | 0.1° |
| N5 | C4A | C8A | N1 | 176.7° | 180.0° |
| N5 | C4A | C8A | N8 | 0.7° | 0.0° |
| C6 | N5 | C4A | C8A | 0.3° | 0.0° |
| N5 | C6 | C9 | C7 | 179.7° | 179.9° |
| N5 | C6 | C7 | N8 | 1.3° | 0.1° |
| N5 | C6 | C7 | O7 | 177.6° | 179.7° |
| N5 | C6 | C9 | H1 | 0.0° | 89.9° |
| N5 | C6 | C9 | H2 | 120.0° | 30.1° |
| N5 | C6 | C9 | H3 | 120.0° | 150.0° |
| N3 | C2 | O2 | N1 | 178.7° | 180.0° |
| N3 | C2 | N1 | C8A | 1.9° | 0.0° |
| C4A | C8A | N1 | C2 | 1.2° | 0.0° |
| C4A | C8A | N1 | N8 | 177.4° | 180.0° |
| C4A | C8A | N8 | C7 | 1.4° | 0.0° |
| C4A | C8A | N8 | C1' | 172.1° | 179.6° |
| C9 | C6 | C7 | N8 | 178.4° | 180.0° |
| C9 | C6 | C7 | O7 | 2.1° | 0.3° |
| C6 | C9 | H1 | H2 | 120.0° | 119.9° |
| C6 | C9 | H1 | H3 | 120.0° | 120.0° |
| C6 | C9 | H2 | H3 | 120.0° | 120.0° |
| C6 | C7 | N8 | C8A | 1.7° | 0.0° |
| C6 | C7 | N8 | O7 | 176.1° | 179.7° |
| C6 | C7 | N8 | C1' | 172.8° | 179.7° |
| C7 | C6 | C9 | H1 | 179.7° | 90.0° |
| C7 | C6 | C9 | H2 | 60.3° | 150.0° |
| C7 | C6 | C9 | H3 | 59.7° | 30.1° |
| C6 | C7 | O7 | H17 | 180.0° | 0.2° |
| O4' | C4' | C3' | C5' | 114.2° | 120.0° |
| O4' | C4' | C3' | H12 | 121.8° | 120.1° |
| O4' | C4' | C3' | O3' | 62.5° | 180.0° |
| O4' | C4' | C3' | C2' | 171.2° | 60.0° |
| O4' | C4' | C5' | H12 | 121.9° | 120.1° |
| O4' | C4' | C5' | O5' | 109.2° | 65.1° |
| O4' | C4' | C3' | H10 | 55.2° | 60.0° |
| O4' | C4' | C5' | H14 | 130.0° | 175.0° |
| O4' | C4' | C5' | H15 | 11.7° | 55.0° |
| O2 | C2 | N1 | C8A | 176.8° | 180.0° |
| O2 | C2 | N3 | H5 | 5.7° | 0.0° |
| C2 | N1 | C8A | N8 | 176.2° | 180.0° |
| N1 | C2 | N3 | H5 | 175.6° | 180.0° |
| N1 | C8A | N8 | C7 | 176.0° | 180.0° |
| N1 | C8A | N8 | C1' | 5.2° | 0.3° |
| C8A | N8 | C7 | C1' | 171.1° | 179.7° |
| C8A | N8 | C7 | O7 | 177.8° | 179.7° |
| C8A | N8 | C1' | C2' | 99.7° | 90.3° |
| C8A | N8 | C1' | H6 | 138.9° | 29.7° |
| C8A | N8 | C1' | H7 | 21.7° | 149.7° |
| O2' | C2' | C3' | C4' | 76.5° | 60.0° |
| O2' | C2' | C3' | O3' | 156.4° | 180.0° |
| O2' | C2' | C3' | C1' | 124.5° | 120.0° |
| O2' | C2' | C3' | H8 | 118.9° | 119.9° |
| O2' | C2' | C1' | N8 | 44.4° | 59.9° |
| O2' | C2' | C1' | H8 | 118.0° | 119.9° |
| O2' | C2' | C1' | H6 | 76.9° | 179.9° |
| O2' | C2' | C1' | H7 | 165.8° | 60.1° |
| O2' | C2' | C3' | H10 | 39.3° | 60.0° |
| C7 | N8 | C1' | C2' | 89.5° | 90.0° |
| C7 | N8 | C1' | H6 | 31.9° | 150.0° |
| C7 | N8 | C1' | H7 | 149.1° | 30.0° |
| N8 | C7 | O7 | H17 | 3.7° | 180.0° |
| O7 | C7 | N8 | C1' | 11.1° | 0.0° |
| C4' | C3' | O3' | C2' | 126.3° | 120.0° |
| C4' | C3' | O3' | H10 | 117.1° | 120.1° |
| C4' | C3' | C2' | H10 | 115.9° | 120.0° |
| C3' | C4' | C5' | H12 | 123.8° | 120.0° |
| C4' | C3' | C2' | C1' | 159.0° | 180.0° |
| C3' | C4' | C5' | O5' | 136.5° | 175.0° |
| C4' | C3' | C2' | H8 | 42.4° | 59.9° |
| C4' | C3' | O3' | H11 | 180.0° | 60.0° |
| C3' | C4' | O4' | H13 | 180.0° | 60.0° |
| C3' | C4' | C5' | H14 | 15.7° | 55.0° |
| C3' | C4' | C5' | H15 | 102.6° | 65.0° |
| O3' | C3' | C2' | H10 | 117.1° | 120.0° |
| O3' | C3' | C4' | C5' | 51.7° | 60.0° |
| O3' | C3' | C2' | C1' | 31.9° | 60.0° |
| O3' | C3' | C2' | H8 | 84.7° | 60.1° |
| O3' | C3' | C4' | H12 | 175.7° | 60.0° |
| C2' | C3' | C4' | C5' | 74.6° | 180.0° |
| C3' | C2' | C1' | N8 | 81.0° | 180.0° |
| C3' | C2' | C1' | H8 | 116.5° | 120.1° |
| C3' | C2' | C1' | H6 | 157.6° | 60.0° |
| C3' | C2' | C1' | H7 | 40.4° | 60.0° |
| C3' | C2' | O2' | H9 | 180.0° | 60.0° |
| C2' | C3' | O3' | H11 | 53.7° | 60.0° |
| C2' | C3' | C4' | H12 | 49.4° | 60.0° |
| C4' | C5' | O5' | H14 | 120.8° | 120.0° |
| C4' | C5' | O5' | H15 | 120.9° | 120.0° |
| C5' | C4' | C3' | H10 | 169.4° | 60.0° |
| C5' | C4' | O4' | H13 | 61.0° | 60.0° |
| C4' | C5' | H14 | H15 | 117.3° | 120.0° |
| C4' | C5' | O5' | H16 | 180.0° | 180.0° |
| N8 | C1' | C2' | H6 | 121.4° | 120.0° |
| N8 | C1' | C2' | H7 | 121.4° | 120.0° |
| N8 | C1' | H6 | H7 | 115.5° | 120.0° |
| N8 | C1' | C2' | H8 | 162.5° | 60.0° |
| C2' | C1' | H6 | H7 | 115.6° | 120.0° |
| C1' | C2' | O2' | H9 | 55.8° | 60.1° |
| C1' | C2' | C3' | H10 | 85.1° | 60.0° |
| O5' | C5' | C4' | H12 | 12.8° | 55.0° |
| O5' | C5' | H14 | H15 | 117.3° | 120.0° |
| H1 | C9 | H2 | H3 | 120.0° | 120.1° |
| H6 | C1' | C2' | H8 | 41.1° | 60.0° |
| H7 | C1' | C2' | H8 | 76.2° | 180.0° |
| H8 | C2' | O2' | H9 | 61.7° | 179.9° |
| H8 | C2' | C3' | H10 | 158.2° | 180.0° |
| H10 | C3' | O3' | H11 | 62.9° | 179.9° |
| H10 | C3' | C4' | H12 | 66.6° | 180.0° |
| H12 | C4' | O4' | H13 | 59.7° | 180.0° |
| H12 | C4' | C5' | H14 | 108.1° | 64.9° |
| H12 | C4' | C5' | H15 | 133.6° | 175.0° |
| H14 | C5' | O5' | H16 | 59.2° | 60.0° |
| H15 | C5' | O5' | H16 | 59.1° | 60.0° |
