1YJ
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C7 | N8 | sing | 1.47Å | 1.48Å | |
| C7 | C6 | sing | 1.54Å | 1.54Å | |
| N8 | C8A | sing | 1.39Å | 1.34Å | |
| C6 | N5 | sing | 1.47Å | 1.45Å | |
| C6 | C9 | sing | 1.53Å | 1.54Å | |
| N10 | C9 | sing | 1.47Å | 1.44Å | |
| N10 | C4' | sing | 1.39Å | 1.35Å | |
| C3' | C4' | doub | 1.39Å | 1.40Å | Aromatic |
| C3' | C2' | sing | 1.38Å | 1.39Å | Aromatic |
| C8A | C4A | doub | 1.39Å | 1.40Å | |
| C8A | N1 | sing | 1.34Å | 1.35Å | |
| N5 | C4A | sing | 1.41Å | 1.36Å | |
| C4' | C5' | sing | 1.39Å | 1.40Å | Aromatic |
| C4A | C4 | sing | 1.40Å | 1.40Å | |
| N1 | C2 | doub | 1.32Å | 1.36Å | |
| C2' | C1' | doub | 1.40Å | 1.40Å | Aromatic |
| C2 | N3 | sing | 1.36Å | 1.34Å | |
| C2 | N2 | sing | 1.37Å | 1.35Å | |
| C4 | N3 | sing | 1.35Å | 1.35Å | |
| C4 | O4 | doub | 1.22Å | 1.36Å | |
| C5' | C6' | doub | 1.38Å | 1.40Å | Aromatic |
| C1' | C6' | sing | 1.40Å | 1.40Å | Aromatic |
| C1' | C11 | sing | 1.48Å | 1.49Å | |
| O11 | C11 | doub | 1.22Å | 1.22Å | |
| C11 | N | sing | 1.35Å | 1.34Å | |
| N | CA | sing | 1.46Å | 1.46Å | |
| CA | C | sing | 1.51Å | 1.51Å | |
| CA | CB | sing | 1.53Å | 1.53Å | |
| C | OX1 | doub | 1.21Å | 1.26Å | |
| C | OX2 | sing | 1.34Å | 1.26Å | |
| CG | CB | sing | 1.53Å | 1.52Å | |
| CG | CD | sing | 1.51Å | 1.52Å | |
| OE1 | CD | doub | 1.21Å | 1.26Å | |
| CD | OE2 | sing | 1.34Å | 1.26Å | |
| C7 | H3 | sing | 1.09Å | 1.10Å | |
| C7 | H4 | sing | 1.09Å | 1.10Å | |
| C6 | H5 | sing | 1.09Å | 1.10Å | |
| N5 | H6 | sing | 0.97Å | 1.00Å | |
| C9 | H8 | sing | 1.09Å | 1.10Å | |
| C3' | H9 | sing | 1.08Å | 1.08Å | |
| C2' | H10 | sing | 1.08Å | 1.08Å | |
| C6' | H11 | sing | 1.08Å | 1.08Å | |
| C5' | H12 | sing | 1.08Å | 1.08Å | |
| N | H13 | sing | 0.97Å | 1.00Å | |
| CA | H14 | sing | 1.09Å | 1.10Å | |
| OX2 | H15 | sing | 0.97Å | 0.95Å | |
| CB | H16 | sing | 1.09Å | 1.10Å | |
| CB | H17 | sing | 1.09Å | 1.10Å | |
| CG | H18 | sing | 1.09Å | 1.10Å | |
| CG | H19 | sing | 1.09Å | 1.10Å | |
| OE2 | H20 | sing | 0.97Å | 0.95Å | |
| N2 | H21 | sing | 0.97Å | 1.00Å | |
| N2 | H22 | sing | 0.97Å | 1.00Å | |
| N3 | H23 | sing | 0.97Å | 1.00Å | |
| N8 | H1 | sing | 0.97Å | 1.00Å | |
| C9 | H2 | sing | 1.09Å | 1.10Å | |
| N10 | H7 | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| N8 | C7 | C6 | 115.6° | 108.3° |
| C7 | N8 | C8A | 117.2° | 119.1° |
| N8 | C7 | H3 | 107.9° | 109.7° |
| N8 | C7 | H4 | 107.9° | 109.7° |
| C7 | N8 | H1 | 107.5° | 120.4° |
| C7 | C6 | N5 | 108.2° | 108.2° |
| C7 | C6 | C9 | 121.0° | 109.8° |
| C6 | C7 | H3 | 107.9° | 109.7° |
| C6 | C7 | H4 | 107.9° | 109.7° |
| C7 | C6 | H5 | 107.4° | 109.7° |
| N8 | C8A | C4A | 122.1° | 119.9° |
| N8 | C8A | N1 | 116.7° | 120.5° |
| C8A | N8 | H1 | 107.5° | 120.5° |
| N5 | C6 | C9 | 104.0° | 109.5° |
| C6 | N5 | C4A | 117.3° | 118.6° |
| N5 | C6 | H5 | 108.5° | 109.8° |
| C6 | N5 | H6 | 107.5° | 120.7° |
| C6 | C9 | N10 | 115.3° | 109.5° |
| C9 | C6 | H5 | 107.3° | 109.8° |
| C6 | C9 | H8 | 108.0° | 109.5° |
| C6 | C9 | H2 | 108.0° | 109.5° |
| C9 | N10 | C4' | 125.5° | 120.0° |
| N10 | C9 | H8 | 108.0° | 109.4° |
| N10 | C9 | H2 | 108.0° | 109.4° |
| C9 | N10 | H7 | 105.4° | 120.0° |
| N10 | C4' | C3' | 115.1° | 119.9° |
| N10 | C4' | C5' | 126.5° | 120.0° |
| C4' | N10 | H7 | 105.3° | 120.0° |
| C4' | C3' | C2' | 121.7° | 120.0° |
| C3' | C4' | C5' | 118.1° | 120.1° |
| C4' | C3' | H9 | 119.1° | 119.9° |
| C3' | C2' | C1' | 120.2° | 120.0° |
| C2' | C3' | H9 | 119.1° | 120.0° |
| C3' | C2' | H10 | 119.9° | 120.0° |
| C4A | C8A | N1 | 121.2° | 119.6° |
| C8A | C4A | N5 | 121.9° | 120.1° |
| C8A | C4A | C4 | 118.6° | 119.1° |
| C8A | N1 | C2 | 117.8° | 121.0° |
| N5 | C4A | C4 | 119.4° | 120.8° |
| C4A | N5 | H6 | 107.5° | 120.7° |
| C4' | C5' | C6' | 120.1° | 120.1° |
| C4' | C5' | H12 | 120.0° | 119.9° |
| C4A | C4 | N3 | 118.6° | 118.5° |
| C4A | C4 | O4 | 125.3° | 120.7° |
| N1 | C2 | N3 | 122.8° | 121.7° |
| N1 | C2 | N2 | 119.9° | 119.2° |
| C2' | C1' | C6' | 118.3° | 119.9° |
| C2' | C1' | C11 | 116.7° | 120.1° |
| C1' | C2' | H10 | 119.9° | 120.1° |
| N3 | C2 | N2 | 117.0° | 119.2° |
| C2 | N3 | C4 | 120.7° | 120.2° |
| C2 | N3 | H23 | 119.7° | 119.9° |
| C2 | N2 | H21 | 120.0° | 120.0° |
| C2 | N2 | H22 | 120.0° | 120.0° |
| N3 | C4 | O4 | 115.9° | 120.8° |
| C4 | N3 | H23 | 119.6° | 119.9° |
| C5' | C6' | C1' | 121.5° | 119.9° |
| C5' | C6' | H11 | 119.2° | 120.1° |
| C6' | C5' | H12 | 119.9° | 120.0° |
| C6' | C1' | C11 | 124.9° | 120.1° |
| C1' | C6' | H11 | 119.3° | 120.0° |
| C1' | C11 | O11 | 115.4° | 120.0° |
| C1' | C11 | N | 122.4° | 120.0° |
| O11 | C11 | N | 122.1° | 120.0° |
| C11 | N | CA | 125.7° | 120.0° |
| C11 | N | H13 | 117.1° | 120.0° |
| N | CA | C | 117.2° | 109.5° |
| N | CA | CB | 104.2° | 109.5° |
| CA | N | H13 | 117.2° | 120.0° |
| N | CA | H14 | 110.7° | 109.5° |
| C | CA | CB | 104.4° | 109.5° |
| CA | C | OX1 | 115.5° | 120.0° |
| CA | C | OX2 | 121.0° | 120.0° |
| C | CA | H14 | 110.0° | 109.5° |
| CA | CB | CG | 110.6° | 109.5° |
| CB | CA | H14 | 109.7° | 109.4° |
| CA | CB | H16 | 109.2° | 109.5° |
| CA | CB | H17 | 109.2° | 109.5° |
| OX1 | C | OX2 | 123.4° | 120.0° |
| C | OX2 | H15 | 109.5° | 117.0° |
| CB | CG | CD | 113.2° | 109.5° |
| CG | CB | H16 | 109.2° | 109.4° |
| CG | CB | H17 | 109.2° | 109.5° |
| CB | CG | H18 | 108.5° | 109.5° |
| CB | CG | H19 | 108.5° | 109.5° |
| CG | CD | OE1 | 114.0° | 119.9° |
| CG | CD | OE2 | 121.3° | 120.0° |
| CD | CG | H18 | 108.6° | 109.4° |
| CD | CG | H19 | 108.5° | 109.5° |
| OE1 | CD | OE2 | 124.7° | 120.1° |
| CD | OE2 | H20 | 109.5° | 117.0° |
| H3 | C7 | H4 | 109.5° | 109.7° |
| H8 | C9 | H2 | 109.4° | 109.5° |
| H16 | CB | H17 | 109.5° | 109.5° |
| H18 | CG | H19 | 109.5° | 109.5° |
| H21 | N2 | H22 | 120.0° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| N8 | C7 | C6 | H3 | 120.9° | 119.7° |
| N8 | C7 | C6 | H4 | 120.9° | 119.7° |
| C7 | N8 | C8A | H1 | 121.1° | 179.9° |
| N8 | C7 | C6 | N5 | 45.2° | 56.2° |
| N8 | C7 | C6 | C9 | 74.4° | 63.3° |
| C7 | N8 | C8A | C4A | 0.1° | 17.4° |
| C7 | N8 | C8A | N1 | 177.6° | 162.6° |
| N8 | C7 | H3 | H4 | 117.2° | 120.6° |
| N8 | C7 | C6 | H5 | 162.1° | 175.9° |
| C6 | C7 | N8 | C8A | 24.5° | 45.7° |
| C7 | C6 | N5 | C9 | 129.8° | 119.6° |
| C7 | C6 | N5 | H5 | 116.2° | 119.7° |
| C7 | C6 | C9 | H5 | 123.5° | 120.7° |
| C7 | C6 | C9 | N10 | 37.3° | 175.0° |
| C7 | C6 | N5 | C4A | 44.6° | 43.7° |
| C6 | C7 | H3 | H4 | 117.2° | 120.5° |
| C7 | C6 | N5 | H6 | 76.5° | 135.9° |
| C7 | C6 | C9 | H8 | 83.6° | 65.0° |
| C6 | C7 | N8 | H1 | 96.6° | 134.4° |
| C7 | C6 | C9 | H2 | 158.1° | 55.0° |
| N8 | C8A | C4A | N1 | 177.4° | 179.9° |
| N8 | C8A | C4A | N5 | 1.3° | 0.2° |
| N8 | C8A | C4A | C4 | 178.8° | 179.7° |
| N8 | C8A | N1 | C2 | 178.7° | 179.9° |
| C8A | N8 | C7 | H3 | 96.4° | 74.0° |
| C8A | N8 | C7 | H4 | 145.4° | 165.4° |
| N5 | C6 | C9 | H5 | 114.9° | 120.7° |
| N5 | C6 | C9 | N10 | 158.9° | 56.4° |
| C6 | N5 | C4A | C8A | 23.8° | 15.6° |
| C6 | N5 | C4A | H6 | 121.1° | 179.6° |
| C6 | N5 | C4A | C4 | 153.7° | 164.3° |
| N5 | C6 | C7 | H3 | 75.7° | 63.6° |
| N5 | C6 | C7 | H4 | 166.1° | 175.9° |
| N5 | C6 | C9 | H8 | 38.1° | 176.4° |
| N5 | C6 | C9 | H2 | 80.2° | 63.6° |
| C6 | C9 | N10 | H8 | 120.9° | 120.0° |
| C6 | C9 | N10 | H2 | 120.9° | 120.0° |
| C6 | C9 | N10 | C4' | 160.3° | 180.0° |
| C9 | C6 | N5 | C4A | 85.2° | 75.9° |
| C9 | C6 | C7 | H3 | 164.7° | 177.0° |
| C9 | C6 | C7 | H4 | 46.5° | 56.4° |
| C9 | C6 | N5 | H6 | 153.6° | 104.5° |
| C6 | C9 | H8 | H2 | 117.3° | 120.1° |
| C6 | C9 | N10 | H7 | 77.6° | 0.0° |
| C9 | N10 | C4' | H7 | 122.2° | 180.0° |
| C9 | N10 | C4' | C3' | 154.6° | 0.3° |
| C9 | N10 | C4' | C5' | 19.4° | 180.0° |
| N10 | C9 | C6 | H5 | 86.2° | 64.3° |
| N10 | C9 | H8 | H2 | 117.3° | 119.9° |
| N10 | C4' | C3' | C5' | 174.6° | 179.8° |
| N10 | C4' | C3' | C2' | 177.2° | 180.0° |
| N10 | C4' | C5' | C6' | 176.8° | 179.7° |
| C4' | N10 | C9 | H8 | 39.4° | 60.0° |
| N10 | C4' | C3' | H9 | 2.8° | 0.0° |
| N10 | C4' | C5' | H12 | 3.2° | 0.0° |
| C4' | N10 | C9 | H2 | 78.9° | 60.0° |
| C4' | C3' | C2' | H9 | 180.0° | 180.0° |
| C4' | C3' | C2' | C1' | 1.5° | 0.0° |
| C3' | C4' | C5' | C6' | 2.9° | 0.5° |
| C4' | C3' | C2' | H10 | 178.5° | 180.0° |
| C3' | C4' | C5' | H12 | 177.1° | 179.7° |
| C3' | C4' | N10 | H7 | 83.2° | 179.8° |
| C2' | C3' | C4' | C5' | 2.6° | 0.2° |
| C3' | C2' | C1' | H10 | 180.0° | 180.0° |
| C3' | C2' | C1' | C6' | 0.8° | 0.1° |
| C3' | C2' | C1' | C11 | 176.9° | 180.0° |
| C8A | C4A | N5 | C4 | 177.5° | 179.8° |
| C4A | C8A | N1 | C2 | 1.2° | 0.2° |
| C8A | C4A | C4 | N3 | 2.0° | 0.5° |
| C8A | C4A | C4 | O4 | 177.3° | 179.9° |
| C8A | C4A | N5 | H6 | 97.3° | 164.0° |
| C4A | C8A | N8 | H1 | 121.0° | 162.7° |
| N1 | C8A | C4A | N5 | 176.1° | 179.7° |
| N1 | C8A | C4A | C4 | 1.5° | 0.4° |
| C8A | N1 | C2 | N3 | 2.5° | 0.0° |
| C8A | N1 | C2 | N2 | 176.5° | 180.0° |
| N1 | C8A | N8 | H1 | 56.5° | 17.4° |
| N5 | C4A | C4 | N3 | 179.6° | 179.6° |
| N5 | C4A | C4 | O4 | 5.1° | 0.1° |
| C4A | N5 | C6 | H5 | 160.7° | 163.4° |
| C4' | C5' | C6' | H12 | 180.0° | 179.7° |
| C4' | C5' | C6' | C1' | 2.3° | 0.6° |
| C5' | C4' | C3' | H9 | 177.4° | 179.8° |
| C4' | C5' | C6' | H11 | 177.7° | 179.7° |
| C5' | C4' | N10 | H7 | 102.8° | 0.0° |
| C4A | C4 | N3 | C2 | 5.6° | 0.4° |
| C4A | C4 | N3 | O4 | 175.8° | 179.6° |
| C4 | C4A | N5 | H6 | 85.1° | 16.2° |
| C4A | C4 | N3 | H23 | 174.3° | 179.9° |
| N1 | C2 | N3 | N2 | 174.1° | 179.9° |
| N1 | C2 | N3 | C4 | 6.1° | 0.2° |
| N1 | C2 | N2 | H21 | 0.0° | 180.0° |
| N1 | C2 | N2 | H22 | 180.0° | 0.1° |
| N1 | C2 | N3 | H23 | 173.9° | 179.9° |
| C2' | C1' | C6' | C5' | 1.2° | 0.4° |
| C2' | C1' | C6' | C11 | 177.5° | 179.9° |
| C2' | C1' | C11 | O11 | 1.8° | 0.0° |
| C2' | C1' | C11 | N | 173.3° | 180.0° |
| C1' | C2' | C3' | H9 | 178.5° | 180.0° |
| C2' | C1' | C6' | H11 | 178.9° | 180.0° |
| C2 | N3 | C4 | H23 | 180.0° | 179.7° |
| C2 | N3 | C4 | O4 | 178.6° | 180.0° |
| N3 | C2 | N2 | H21 | 174.3° | 0.1° |
| N3 | C2 | N2 | H22 | 5.8° | 180.0° |
| N2 | C2 | N3 | C4 | 179.8° | 179.9° |
| C2 | N2 | H21 | H22 | 180.0° | 179.9° |
| N2 | C2 | N3 | H23 | 0.2° | 0.2° |
| O4 | C4 | N3 | H23 | 1.5° | 0.3° |
| C5' | C6' | C1' | H11 | 180.0° | 179.7° |
| C5' | C6' | C1' | C11 | 176.3° | 179.7° |
| C6' | C1' | C11 | O11 | 179.4° | 179.9° |
| C6' | C1' | C11 | N | 4.3° | 0.1° |
| C6' | C1' | C2' | H10 | 179.2° | 179.9° |
| C1' | C6' | C5' | H12 | 177.7° | 179.7° |
| C1' | C11 | O11 | N | 175.1° | 180.0° |
| C1' | C11 | N | CA | 177.5° | 180.0° |
| C11 | C1' | C2' | H10 | 3.1° | 0.0° |
| C11 | C1' | C6' | H11 | 3.6° | 0.1° |
| C1' | C11 | N | H13 | 2.5° | 0.1° |
| O11 | C11 | N | CA | 2.7° | 0.0° |
| O11 | C11 | N | H13 | 177.3° | 179.9° |
| C11 | N | CA | H13 | 180.0° | 179.9° |
| C11 | N | CA | C | 119.4° | 85.0° |
| C11 | N | CA | CB | 125.8° | 155.0° |
| C11 | N | CA | H14 | 7.9° | 35.1° |
| N | CA | C | CB | 114.7° | 120.0° |
| N | CA | C | H14 | 127.7° | 120.0° |
| N | CA | CB | H14 | 118.6° | 120.0° |
| N | CA | C | OX1 | 156.2° | 0.0° |
| N | CA | C | OX2 | 24.9° | 180.0° |
| N | CA | CB | CG | 74.4° | 65.0° |
| N | CA | CB | H16 | 45.8° | 55.0° |
| N | CA | CB | H17 | 165.5° | 175.0° |
| C | CA | CB | H14 | 117.8° | 120.0° |
| CA | C | OX1 | OX2 | 178.8° | 180.0° |
| C | CA | CB | CG | 162.1° | 175.0° |
| C | CA | N | H13 | 60.7° | 94.9° |
| CA | C | OX2 | H15 | 178.8° | 180.0° |
| C | CA | CB | H16 | 77.7° | 65.0° |
| C | CA | CB | H17 | 41.9° | 55.0° |
| CB | CA | C | OX1 | 89.1° | 120.0° |
| CB | CA | C | OX2 | 89.8° | 60.0° |
| CA | CB | CG | H16 | 120.2° | 120.0° |
| CA | CB | CG | H17 | 120.1° | 120.0° |
| CA | CB | CG | CD | 179.5° | 180.0° |
| CB | CA | N | H13 | 54.1° | 25.1° |
| CA | CB | H16 | H17 | 119.5° | 120.0° |
| CA | CB | CG | H18 | 58.9° | 60.1° |
| CA | CB | CG | H19 | 60.0° | 60.0° |
| OX1 | C | CA | H14 | 28.6° | 120.0° |
| OX1 | C | OX2 | H15 | 0.0° | 0.0° |
| OX2 | C | CA | H14 | 152.6° | 60.0° |
| CB | CG | CD | H18 | 120.6° | 120.0° |
| CB | CG | CD | H19 | 120.5° | 120.0° |
| CB | CG | CD | OE1 | 169.9° | 0.1° |
| CB | CG | CD | OE2 | 10.2° | 180.0° |
| CG | CB | CA | H14 | 44.3° | 55.0° |
| CG | CB | H16 | H17 | 119.5° | 120.0° |
| CB | CG | H18 | H19 | 118.3° | 120.0° |
| CG | CD | OE1 | OE2 | 179.9° | 179.9° |
| CD | CG | CB | H16 | 60.4° | 60.0° |
| CD | CG | CB | H17 | 59.3° | 60.0° |
| CD | CG | H18 | H19 | 118.3° | 120.0° |
| CG | CD | OE2 | H20 | 179.9° | 180.0° |
| OE1 | CD | CG | H18 | 69.5° | 120.0° |
| OE1 | CD | CG | H19 | 49.4° | 120.0° |
| OE1 | CD | OE2 | H20 | 0.0° | 0.1° |
| OE2 | CD | CG | H18 | 110.4° | 60.1° |
| OE2 | CD | CG | H19 | 130.7° | 59.9° |
| H3 | C7 | C6 | H5 | 41.3° | 56.2° |
| H3 | C7 | N8 | H1 | 142.5° | 106.0° |
| H4 | C7 | C6 | H5 | 77.0° | 64.3° |
| H4 | C7 | N8 | H1 | 24.3° | 14.7° |
| H5 | C6 | N5 | H6 | 39.6° | 16.1° |
| H5 | C6 | C9 | H8 | 153.0° | 55.7° |
| H5 | C6 | C9 | H2 | 34.7° | 175.7° |
| H8 | C9 | N10 | H7 | 161.5° | 120.0° |
| H9 | C3' | C2' | H10 | 1.5° | 0.0° |
| H11 | C6' | C5' | H12 | 2.2° | 0.0° |
| H13 | N | CA | H14 | 172.1° | 145.0° |
| H14 | CA | CB | H16 | 164.4° | 175.0° |
| H14 | CA | CB | H17 | 75.9° | 65.0° |
| H16 | CB | CG | H18 | 179.1° | 180.0° |
| H16 | CB | CG | H19 | 60.2° | 60.0° |
| H17 | CB | CG | H18 | 61.3° | 60.0° |
| H17 | CB | CG | H19 | 179.8° | 180.0° |
| H2 | C9 | N10 | H7 | 43.3° | 120.0° |
