D3Y
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| O4' | C4' | sing | 1.44Å | 1.47Å | |
| O4' | C1' | sing | 1.45Å | 1.46Å | |
| C5' | C4' | sing | 1.53Å | 1.54Å | |
| C5' | O5' | sing | 1.43Å | 1.43Å | |
| C4' | C3' | sing | 1.54Å | 1.53Å | |
| OH | CZ | sing | 1.36Å | 1.36Å | |
| O2' | C2' | sing | 1.43Å | 1.44Å | |
| C1' | C2' | sing | 1.54Å | 1.53Å | |
| C1' | N9 | sing | 1.46Å | 1.50Å | |
| N | CA | sing | 1.47Å | 1.48Å | |
| CZ | CE2 | doub | 1.39Å | 1.40Å | Aromatic |
| CZ | CE1 | sing | 1.39Å | 1.39Å | Aromatic |
| CE2 | CD2 | sing | 1.38Å | 1.40Å | Aromatic |
| C2' | C3' | sing | 1.55Å | 1.52Å | |
| C3' | N8 | sing | 1.47Å | 1.46Å | |
| N8 | C | sing | 1.35Å | 1.33Å | |
| C8 | N9 | sing | 1.36Å | 1.34Å | Aromatic |
| C8 | N7 | doub | 1.30Å | 1.33Å | Aromatic |
| CE1 | CD1 | doub | 1.38Å | 1.39Å | Aromatic |
| N9 | C4 | sing | 1.37Å | 1.34Å | Aromatic |
| CD2 | CG | doub | 1.38Å | 1.39Å | Aromatic |
| CD1 | CG | sing | 1.38Å | 1.40Å | Aromatic |
| CG | CB | sing | 1.51Å | 1.53Å | |
| CA | C | sing | 1.51Å | 1.54Å | |
| CA | CB | sing | 1.53Å | 1.53Å | |
| N7 | C5 | sing | 1.36Å | 1.34Å | Aromatic |
| C | O | doub | 1.21Å | 1.24Å | |
| C4 | C5 | doub | 1.40Å | 1.39Å | Aromatic |
| C4 | N3 | sing | 1.33Å | 1.35Å | Aromatic |
| C5 | C6 | sing | 1.41Å | 1.39Å | Aromatic |
| N3 | C2 | doub | 1.32Å | 1.33Å | Aromatic |
| C6 | N6 | sing | 1.38Å | 1.33Å | |
| C6 | N1 | doub | 1.33Å | 1.36Å | Aromatic |
| C2 | N1 | sing | 1.32Å | 1.33Å | Aromatic |
| CD1 | H1 | sing | 1.08Å | 1.08Å | |
| CE1 | H2 | sing | 1.08Å | 1.08Å | |
| OH | H3 | sing | 0.97Å | 0.95Å | |
| CE2 | H4 | sing | 1.08Å | 1.08Å | |
| CD2 | H5 | sing | 1.08Å | 1.08Å | |
| CB | H6 | sing | 1.09Å | 1.10Å | |
| CB | H7 | sing | 1.09Å | 1.10Å | |
| CA | H8 | sing | 1.09Å | 1.10Å | |
| N | H9 | sing | 1.01Å | 1.00Å | |
| N | H10 | sing | 1.01Å | 1.00Å | |
| N8 | H12 | sing | 0.97Å | 1.00Å | |
| C3' | H13 | sing | 1.09Å | 1.10Å | |
| C2' | H14 | sing | 1.09Å | 1.10Å | |
| O2' | H15 | sing | 0.97Å | 0.95Å | |
| C4' | H16 | sing | 1.09Å | 1.10Å | |
| C5' | H17 | sing | 1.09Å | 1.10Å | |
| C5' | H18 | sing | 1.09Å | 1.10Å | |
| O5' | H19 | sing | 0.97Å | 0.95Å | |
| C1' | H20 | sing | 1.09Å | 1.10Å | |
| C8 | H21 | sing | 1.08Å | 1.08Å | |
| C2 | H22 | sing | 1.08Å | 1.08Å | |
| N6 | H23 | sing | 0.97Å | 1.00Å | |
| N6 | H24 | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C4' | O4' | C1' | 108.2° | 105.3° |
| O4' | C4' | C5' | 110.8° | 110.5° |
| O4' | C4' | C3' | 105.0° | 104.8° |
| O4' | C4' | H16 | 109.7° | 110.3° |
| O4' | C1' | C2' | 106.9° | 104.8° |
| O4' | C1' | N9 | 106.1° | 110.4° |
| O4' | C1' | H20 | 109.5° | 110.4° |
| C4' | C5' | O5' | 109.8° | 109.4° |
| C5' | C4' | C3' | 113.8° | 110.4° |
| C5' | C4' | H16 | 108.7° | 110.3° |
| C4' | C5' | H17 | 109.4° | 109.5° |
| C4' | C5' | H18 | 109.4° | 109.5° |
| O5' | C5' | H17 | 109.4° | 109.5° |
| O5' | C5' | H18 | 109.4° | 109.4° |
| C5' | O5' | H19 | 109.5° | 113.9° |
| C4' | C3' | C2' | 102.6° | 104.2° |
| C4' | C3' | N8 | 108.4° | 110.4° |
| C4' | C3' | H13 | 111.2° | 110.5° |
| C3' | C4' | H16 | 108.8° | 110.4° |
| OH | CZ | CE2 | 120.4° | 120.1° |
| OH | CZ | CE1 | 119.7° | 120.0° |
| CZ | OH | H3 | 109.5° | 114.0° |
| O2' | C2' | C1' | 108.3° | 110.6° |
| O2' | C2' | C3' | 111.6° | 110.5° |
| O2' | C2' | H14 | 112.8° | 110.4° |
| C2' | O2' | H15 | 109.5° | 114.0° |
| C2' | C1' | N9 | 116.6° | 110.5° |
| C1' | C2' | C3' | 100.8° | 104.1° |
| C1' | C2' | H14 | 111.3° | 110.5° |
| C2' | C1' | H20 | 108.6° | 110.3° |
| C1' | N9 | C8 | 124.1° | 126.3° |
| C1' | N9 | C4 | 127.4° | 126.3° |
| N9 | C1' | H20 | 109.0° | 110.4° |
| N | CA | C | 110.8° | 109.5° |
| N | CA | CB | 110.3° | 109.5° |
| N | CA | H8 | 109.0° | 109.5° |
| CA | N | H9 | 109.5° | 111.0° |
| CA | N | H10 | 109.4° | 111.0° |
| CE2 | CZ | CE1 | 119.9° | 119.9° |
| CZ | CE2 | CD2 | 120.2° | 119.9° |
| CZ | CE2 | H4 | 119.9° | 120.0° |
| CZ | CE1 | CD1 | 119.9° | 119.9° |
| CZ | CE1 | H2 | 120.1° | 120.1° |
| CE2 | CD2 | CG | 120.0° | 120.1° |
| CD2 | CE2 | H4 | 119.9° | 120.0° |
| CE2 | CD2 | H5 | 120.0° | 120.0° |
| C2' | C3' | N8 | 110.7° | 110.5° |
| C2' | C3' | H13 | 111.3° | 110.5° |
| C3' | C2' | H14 | 111.4° | 110.5° |
| C3' | N8 | C | 122.6° | 120.0° |
| C3' | N8 | H12 | 118.7° | 120.0° |
| N8 | C3' | H13 | 112.2° | 110.5° |
| N8 | C | CA | 113.5° | 120.0° |
| N8 | C | O | 124.2° | 120.0° |
| C | N8 | H12 | 118.7° | 120.0° |
| N9 | C8 | N7 | 109.6° | 110.0° |
| C8 | N9 | C4 | 108.4° | 107.4° |
| N9 | C8 | H21 | 125.2° | 125.0° |
| C8 | N7 | C5 | 107.6° | 109.4° |
| N7 | C8 | H21 | 125.2° | 125.0° |
| CE1 | CD1 | CG | 120.4° | 120.1° |
| CE1 | CD1 | H1 | 119.8° | 120.0° |
| CD1 | CE1 | H2 | 120.1° | 120.0° |
| N9 | C4 | C5 | 106.5° | 106.0° |
| N9 | C4 | N3 | 134.0° | 134.9° |
| CD2 | CG | CD1 | 119.6° | 120.1° |
| CD2 | CG | CB | 119.3° | 120.0° |
| CG | CD2 | H5 | 120.0° | 120.0° |
| CD1 | CG | CB | 121.0° | 120.0° |
| CG | CD1 | H1 | 119.8° | 119.9° |
| CG | CB | CA | 116.6° | 109.4° |
| CG | CB | H6 | 107.7° | 109.5° |
| CG | CB | H7 | 107.7° | 109.5° |
| C | CA | CB | 110.1° | 109.5° |
| CA | C | O | 122.2° | 120.0° |
| C | CA | H8 | 108.3° | 109.4° |
| CA | CB | H6 | 107.7° | 109.4° |
| CA | CB | H7 | 107.7° | 109.4° |
| CB | CA | H8 | 108.3° | 109.5° |
| N7 | C5 | C4 | 107.8° | 107.2° |
| N7 | C5 | C6 | 133.6° | 134.6° |
| C5 | C4 | N3 | 119.5° | 119.1° |
| C4 | C5 | C6 | 118.6° | 118.2° |
| C4 | N3 | C2 | 120.5° | 120.6° |
| C5 | C6 | N6 | 119.9° | 120.8° |
| C5 | C6 | N1 | 119.0° | 118.4° |
| N3 | C2 | N1 | 121.3° | 122.5° |
| N3 | C2 | H22 | 119.3° | 118.8° |
| N6 | C6 | N1 | 121.1° | 120.7° |
| C6 | N6 | H23 | 109.5° | 119.9° |
| C6 | N6 | H24 | 109.4° | 120.0° |
| C6 | N1 | C2 | 121.1° | 121.2° |
| N1 | C2 | H22 | 119.4° | 118.8° |
| H6 | CB | H7 | 109.5° | 109.5° |
| H9 | N | H10 | 109.4° | 111.0° |
| H17 | C5' | H18 | 109.5° | 109.5° |
| H23 | N6 | H24 | 109.5° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O4' | C4' | C5' | C3' | 118.1° | 115.4° |
| O4' | C4' | C5' | H16 | 120.6° | 122.3° |
| O4' | C4' | C5' | O5' | 51.4° | 69.5° |
| O4' | C4' | C3' | H16 | 117.4° | 118.8° |
| C4' | O4' | C1' | C2' | 10.6° | 40.4° |
| C4' | O4' | C1' | N9 | 114.5° | 159.4° |
| O4' | C4' | C3' | C2' | 34.7° | 23.9° |
| O4' | C4' | C3' | N8 | 151.8° | 142.6° |
| O4' | C4' | C3' | H13 | 84.4° | 94.8° |
| O4' | C4' | C5' | H17 | 68.7° | 170.5° |
| O4' | C4' | C5' | H18 | 171.4° | 50.4° |
| C4' | O4' | C1' | H20 | 128.0° | 78.3° |
| C1' | O4' | C4' | C5' | 138.3° | 159.2° |
| C1' | O4' | C4' | C3' | 15.0° | 40.4° |
| O4' | C1' | C2' | O2' | 85.6° | 142.6° |
| O4' | C1' | C2' | N9 | 118.5° | 118.9° |
| O4' | C1' | C2' | H20 | 118.0° | 118.8° |
| O4' | C1' | N9 | H20 | 117.8° | 122.3° |
| O4' | C1' | C2' | C3' | 31.6° | 23.9° |
| O4' | C1' | N9 | C8 | 14.3° | 23.9° |
| O4' | C1' | N9 | C4 | 167.6° | 156.5° |
| O4' | C1' | C2' | H14 | 149.8° | 94.8° |
| C1' | O4' | C4' | H16 | 101.8° | 78.5° |
| C4' | C5' | O5' | H17 | 120.1° | 120.0° |
| C4' | C5' | O5' | H18 | 120.1° | 119.9° |
| C5' | C4' | C3' | H16 | 121.3° | 122.3° |
| C5' | C4' | C3' | C2' | 156.1° | 142.8° |
| C5' | C4' | C3' | N8 | 86.8° | 98.5° |
| C5' | C4' | C3' | H13 | 37.0° | 24.1° |
| C4' | C5' | H17 | H18 | 119.8° | 120.0° |
| C4' | C5' | O5' | H19 | 180.0° | 180.0° |
| O5' | C5' | C4' | C3' | 66.7° | 175.1° |
| O5' | C5' | C4' | H16 | 171.9° | 52.7° |
| O5' | C5' | H17 | H18 | 119.8° | 120.0° |
| C4' | C3' | C2' | O2' | 75.1° | 118.8° |
| C4' | C3' | C2' | C1' | 39.8° | 0.0° |
| C4' | C3' | C2' | N8 | 115.4° | 118.6° |
| C4' | C3' | C2' | H13 | 119.0° | 118.7° |
| C4' | C3' | N8 | H13 | 123.2° | 122.6° |
| C4' | C3' | N8 | C | 154.0° | 88.4° |
| C4' | C3' | N8 | H12 | 26.0° | 91.7° |
| C4' | C3' | C2' | H14 | 157.9° | 118.6° |
| C3' | C4' | C5' | H17 | 173.2° | 55.1° |
| C3' | C4' | C5' | H18 | 53.4° | 65.0° |
| OH | CZ | CE2 | CE1 | 179.8° | 180.0° |
| OH | CZ | CE2 | CD2 | 180.0° | 180.0° |
| OH | CZ | CE1 | CD1 | 179.8° | 180.0° |
| OH | CZ | CE1 | H2 | 0.2° | 0.0° |
| OH | CZ | CE2 | H4 | 0.1° | 0.0° |
| O2' | C2' | C1' | C3' | 117.2° | 118.7° |
| O2' | C2' | C1' | H14 | 124.5° | 122.6° |
| O2' | C2' | C1' | N9 | 155.9° | 98.5° |
| O2' | C2' | C3' | H14 | 127.0° | 122.5° |
| O2' | C2' | C3' | N8 | 40.4° | 0.2° |
| O2' | C2' | C3' | H13 | 165.9° | 122.4° |
| O2' | C2' | C1' | H20 | 32.4° | 23.9° |
| C2' | C1' | N9 | H20 | 123.3° | 122.3° |
| C1' | C2' | C3' | H14 | 118.2° | 118.7° |
| C1' | C2' | C3' | N8 | 155.2° | 118.6° |
| C2' | C1' | N9 | C8 | 133.2° | 91.5° |
| C2' | C1' | N9 | C4 | 48.7° | 88.1° |
| C1' | C2' | C3' | H13 | 79.3° | 118.7° |
| C1' | C2' | O2' | H15 | 180.0° | 65.3° |
| N9 | C1' | C2' | C3' | 86.9° | 142.8° |
| C1' | N9 | C8 | C4 | 178.4° | 179.7° |
| C1' | N9 | C8 | N7 | 178.8° | 180.0° |
| C1' | N9 | C4 | C5 | 178.7° | 179.9° |
| C1' | N9 | C4 | N3 | 2.1° | 0.0° |
| N9 | C1' | C2' | H14 | 31.3° | 24.1° |
| C1' | N9 | C8 | H21 | 1.3° | 0.1° |
| N | CA | C | N8 | 1.3° | 160.0° |
| N | CA | CB | CG | 51.7° | 65.0° |
| N | CA | C | CB | 122.3° | 120.0° |
| N | CA | C | H8 | 119.5° | 120.0° |
| N | CA | CB | H8 | 119.2° | 120.0° |
| N | CA | C | O | 177.3° | 20.0° |
| N | CA | CB | H6 | 172.7° | 55.0° |
| N | CA | CB | H7 | 69.3° | 175.0° |
| CA | N | H9 | H10 | 120.0° | 124.0° |
| CZ | CE2 | CD2 | H4 | 180.0° | 180.0° |
| CE2 | CZ | CE1 | CD1 | 0.0° | 0.0° |
| CZ | CE2 | CD2 | CG | 0.2° | 0.1° |
| CE2 | CZ | CE1 | H2 | 180.0° | 180.0° |
| CE2 | CZ | OH | H3 | 180.0° | 90.0° |
| CZ | CE2 | CD2 | H5 | 179.8° | 180.0° |
| CE1 | CZ | CE2 | CD2 | 0.2° | 0.1° |
| CZ | CE1 | CD1 | H2 | 180.0° | 180.0° |
| CZ | CE1 | CD1 | CG | 0.5° | 0.0° |
| CZ | CE1 | CD1 | H1 | 179.5° | 179.7° |
| CE1 | CZ | OH | H3 | 0.2° | 90.0° |
| CE1 | CZ | CE2 | H4 | 179.8° | 180.0° |
| CE2 | CD2 | CG | H5 | 180.0° | 179.9° |
| CE2 | CD2 | CG | CD1 | 0.7° | 0.1° |
| CE2 | CD2 | CG | CB | 179.2° | 179.7° |
| C2' | C3' | N8 | H13 | 125.0° | 122.7° |
| C2' | C3' | N8 | C | 94.2° | 156.9° |
| C2' | C3' | N8 | H12 | 85.8° | 23.0° |
| C3' | C2' | O2' | H15 | 69.9° | 180.0° |
| C2' | C3' | C4' | H16 | 82.6° | 94.9° |
| C3' | C2' | C1' | H20 | 149.6° | 94.8° |
| C3' | N8 | C | H12 | 180.0° | 179.9° |
| C3' | N8 | C | CA | 178.4° | 180.0° |
| C3' | N8 | C | O | 0.2° | 0.1° |
| N8 | C3' | C2' | H14 | 86.6° | 122.7° |
| N8 | C3' | C4' | H16 | 34.5° | 23.8° |
| N8 | C | CA | O | 178.6° | 179.9° |
| N8 | C | CA | CB | 123.6° | 80.0° |
| N8 | C | CA | H8 | 118.2° | 39.9° |
| C | N8 | C3' | H13 | 30.8° | 34.2° |
| N9 | C8 | N7 | H21 | 180.0° | 180.0° |
| N9 | C8 | N7 | C5 | 0.2° | 0.1° |
| C8 | N9 | C4 | C5 | 0.3° | 0.4° |
| C8 | N9 | C4 | N3 | 179.5° | 179.7° |
| C8 | N9 | C1' | H20 | 103.5° | 146.2° |
| N7 | C8 | N9 | C4 | 0.3° | 0.3° |
| C8 | N7 | C5 | C4 | 0.1° | 0.2° |
| C8 | N7 | C5 | C6 | 179.5° | 180.0° |
| CE1 | CD1 | CG | CD2 | 0.9° | 0.0° |
| CE1 | CD1 | CG | H1 | 180.0° | 179.7° |
| CE1 | CD1 | CG | CB | 179.3° | 179.7° |
| N9 | C4 | C5 | N7 | 0.2° | 0.4° |
| N9 | C4 | C5 | N3 | 179.3° | 179.9° |
| N9 | C4 | C5 | C6 | 179.4° | 179.8° |
| N9 | C4 | N3 | C2 | 179.1° | 180.0° |
| C4 | N9 | C1' | H20 | 74.6° | 34.2° |
| C4 | N9 | C8 | H21 | 179.7° | 179.7° |
| CD2 | CG | CD1 | CB | 178.4° | 179.6° |
| CD2 | CG | CB | CA | 117.4° | 90.3° |
| CD2 | CG | CD1 | H1 | 179.1° | 179.6° |
| CG | CD2 | CE2 | H4 | 179.8° | 179.9° |
| CD2 | CG | CB | H6 | 121.6° | 29.6° |
| CD2 | CG | CB | H7 | 3.7° | 149.7° |
| CD1 | CG | CB | CA | 64.3° | 90.1° |
| CG | CD1 | CE1 | H2 | 179.5° | 180.0° |
| CD1 | CG | CD2 | H5 | 179.2° | 180.0° |
| CD1 | CG | CB | H6 | 56.8° | 150.0° |
| CD1 | CG | CB | H7 | 174.7° | 29.9° |
| CG | CB | CA | C | 70.9° | 175.0° |
| CG | CB | CA | H6 | 121.0° | 120.0° |
| CG | CB | CA | H7 | 121.0° | 120.0° |
| CB | CG | CD1 | H1 | 0.7° | 0.0° |
| CB | CG | CD2 | H5 | 0.8° | 0.4° |
| CG | CB | H6 | H7 | 116.8° | 120.1° |
| CG | CB | CA | H8 | 170.9° | 55.0° |
| C | CA | CB | H8 | 118.2° | 120.0° |
| C | CA | CB | H6 | 50.2° | 65.0° |
| C | CA | CB | H7 | 168.1° | 55.0° |
| C | CA | N | H9 | 180.0° | 176.0° |
| C | CA | N | H10 | 60.0° | 60.0° |
| CA | C | N8 | H12 | 1.6° | 0.1° |
| CB | CA | C | O | 55.0° | 100.0° |
| CA | CB | H6 | H7 | 116.8° | 119.9° |
| CB | CA | N | H9 | 57.8° | 63.9° |
| CB | CA | N | H10 | 62.2° | 60.0° |
| N7 | C5 | C4 | C6 | 179.6° | 179.9° |
| N7 | C5 | C4 | N3 | 179.6° | 179.7° |
| N7 | C5 | C6 | N6 | 0.2° | 0.1° |
| N7 | C5 | C6 | N1 | 179.2° | 179.3° |
| C5 | N7 | C8 | H21 | 179.9° | 180.0° |
| O | C | CA | H8 | 63.2° | 140.0° |
| O | C | N8 | H12 | 179.8° | 180.0° |
| C5 | C4 | N3 | C2 | 0.0° | 0.1° |
| C4 | C5 | C6 | N6 | 179.7° | 179.7° |
| C4 | C5 | C6 | N1 | 0.3° | 0.5° |
| N3 | C4 | C5 | C6 | 0.0° | 0.1° |
| C4 | N3 | C2 | N1 | 0.3° | 0.0° |
| C4 | N3 | C2 | H22 | 179.7° | 180.0° |
| C5 | C6 | N6 | N1 | 179.4° | 179.2° |
| C5 | C6 | N1 | C2 | 0.6° | 0.6° |
| C5 | C6 | N6 | H23 | 179.3° | 0.1° |
| C5 | C6 | N6 | H24 | 60.6° | 180.0° |
| N3 | C2 | N1 | C6 | 0.6° | 0.4° |
| N3 | C2 | N1 | H22 | 180.0° | 179.9° |
| N6 | C6 | N1 | C2 | 180.0° | 179.9° |
| C6 | N6 | H23 | H24 | 120.0° | 180.0° |
| C6 | N1 | C2 | H22 | 179.4° | 179.6° |
| N1 | C6 | N6 | H23 | 0.0° | 179.3° |
| N1 | C6 | N6 | H24 | 120.0° | 0.7° |
| H1 | CD1 | CE1 | H2 | 0.5° | 0.3° |
| H4 | CE2 | CD2 | H5 | 0.3° | 0.0° |
| H6 | CB | CA | H8 | 68.1° | 175.0° |
| H7 | CB | CA | H8 | 49.9° | 65.0° |
| H8 | CA | N | H9 | 61.0° | 56.0° |
| H8 | CA | N | H10 | 179.1° | 180.0° |
| H12 | N8 | C3' | H13 | 149.2° | 145.7° |
| H13 | C3' | C2' | H14 | 38.9° | 0.1° |
| H13 | C3' | C4' | H16 | 158.2° | 146.4° |
| H14 | C2' | O2' | H15 | 56.4° | 57.4° |
| H14 | C2' | C1' | H20 | 92.2° | 146.5° |
| H16 | C4' | C5' | H17 | 51.9° | 67.3° |
| H16 | C4' | C5' | H18 | 68.0° | 172.7° |
| H17 | C5' | O5' | H19 | 60.0° | 60.0° |
| H18 | C5' | O5' | H19 | 59.9° | 60.1° |
