RYJ
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C4 | S | sing | 1.76Å | 1.69Å | |
| O2S | S | doub | 1.42Å | 1.58Å | |
| N3S | S | sing | 1.66Å | 1.48Å | |
| S | O1S | doub | 1.42Å | 1.45Å | |
| C1' | N' | sing | 1.46Å | 1.47Å | |
| N' | C7 | sing | 1.35Å | 1.32Å | |
| N' | HN' | sing | 0.97Å | 1.00Å | |
| O' | C7 | doub | 1.22Å | 1.26Å | |
| C7 | C1 | sing | 1.48Å | 1.50Å | |
| C1 | C5 | doub | 1.40Å | 1.38Å | Aromatic |
| C1 | C3 | sing | 1.40Å | 1.35Å | Aromatic |
| C3 | C2 | doub | 1.38Å | 1.43Å | Aromatic |
| C2 | C4 | sing | 1.38Å | 1.43Å | Aromatic |
| C2 | H2 | sing | 1.08Å | 1.08Å | |
| C3 | H3 | sing | 1.08Å | 1.08Å | |
| C6 | C4 | doub | 1.38Å | 1.40Å | Aromatic |
| C5 | C6 | sing | 1.38Å | 1.39Å | Aromatic |
| C5 | H5 | sing | 1.08Å | 1.08Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C2' | F2'1 | sing | 1.40Å | 1.35Å | |
| C2' | F2'2 | sing | 1.40Å | 1.31Å | |
| F2'3 | C2' | sing | 1.40Å | 1.33Å | |
| C1' | C2' | sing | 1.53Å | 1.53Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| C1' | H1'A | sing | 1.09Å | 1.10Å | |
| N3S | HN3S | sing | 0.97Å | 1.00Å | |
| N3S | HN3A | sing | 0.97Å | 1.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C4 | S | O2S | 108.5° | 106.4° |
| C4 | S | N3S | 103.6° | 107.2° |
| C4 | S | O1S | 107.1° | 106.4° |
| S | C4 | C2 | 120.9° | 119.9° |
| S | C4 | C6 | 123.0° | 119.8° |
| O2S | S | N3S | 110.6° | 106.4° |
| O2S | S | O1S | 110.0° | 123.2° |
| N3S | S | O1S | 116.5° | 106.4° |
| S | N3S | HN3S | 109.5° | 120.0° |
| S | N3S | HN3A | 109.5° | 119.9° |
| C1' | N' | C7 | 120.7° | 120.0° |
| C1' | N' | HN' | 119.6° | 120.1° |
| N' | C1' | C2' | 108.4° | 109.5° |
| N' | C1' | H1' | 109.9° | 109.5° |
| N' | C1' | H1'A | 109.8° | 109.4° |
| C7 | N' | HN' | 119.7° | 120.0° |
| N' | C7 | O' | 120.1° | 120.0° |
| N' | C7 | C1 | 120.8° | 120.0° |
| O' | C7 | C1 | 119.0° | 120.0° |
| C7 | C1 | C5 | 120.9° | 120.2° |
| C7 | C1 | C3 | 118.9° | 120.1° |
| C5 | C1 | C3 | 120.2° | 119.7° |
| C1 | C5 | C6 | 123.2° | 119.9° |
| C1 | C5 | H5 | 118.4° | 120.0° |
| C1 | C3 | C2 | 118.0° | 119.8° |
| C1 | C3 | H3 | 121.0° | 120.0° |
| C3 | C2 | C4 | 122.6° | 120.2° |
| C3 | C2 | H2 | 118.7° | 119.9° |
| C2 | C3 | H3 | 121.0° | 120.1° |
| C4 | C2 | H2 | 118.7° | 119.9° |
| C2 | C4 | C6 | 115.9° | 120.3° |
| C4 | C6 | C5 | 119.8° | 120.1° |
| C4 | C6 | H6 | 120.1° | 119.9° |
| C6 | C5 | H5 | 118.4° | 120.0° |
| C5 | C6 | H6 | 120.1° | 120.0° |
| F2'1 | C2' | F2'2 | 99.7° | 109.5° |
| F2'1 | C2' | F2'3 | 108.8° | 109.4° |
| F2'1 | C2' | C1' | 113.8° | 109.5° |
| F2'2 | C2' | F2'3 | 110.5° | 109.5° |
| F2'2 | C2' | C1' | 115.6° | 109.5° |
| F2'3 | C2' | C1' | 108.1° | 109.4° |
| C2' | C1' | H1' | 109.8° | 109.5° |
| C2' | C1' | H1'A | 109.8° | 109.5° |
| H1' | C1' | H1'A | 109.1° | 109.5° |
| HN3S | N3S | HN3A | 109.5° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C4 | S | O2S | N3S | 113.0° | 114.1° |
| C4 | S | O2S | O1S | 116.9° | 123.0° |
| C4 | S | N3S | O1S | 117.3° | 113.5° |
| S | C4 | C2 | C3 | 177.6° | 179.9° |
| S | C4 | C2 | C6 | 175.4° | 180.0° |
| S | C4 | C2 | H2 | 2.4° | 0.0° |
| S | C4 | C6 | C5 | 179.0° | 180.0° |
| S | C4 | C6 | H6 | 1.0° | 0.0° |
| C4 | S | N3S | HN3S | 180.0° | 90.0° |
| C4 | S | N3S | HN3A | 60.0° | 90.0° |
| O2S | S | N3S | O1S | 126.6° | 132.9° |
| O2S | S | C4 | C2 | 53.8° | 23.5° |
| O2S | S | C4 | C6 | 131.1° | 156.4° |
| O2S | S | N3S | HN3S | 63.9° | 23.5° |
| O2S | S | N3S | HN3A | 176.1° | 156.5° |
| N3S | S | C4 | C2 | 171.5° | 90.0° |
| N3S | S | C4 | C6 | 13.5° | 90.1° |
| S | N3S | HN3S | HN3A | 120.0° | 180.0° |
| O1S | S | C4 | C2 | 64.9° | 156.5° |
| O1S | S | C4 | C6 | 110.2° | 23.5° |
| O1S | S | N3S | HN3S | 62.7° | 156.5° |
| O1S | S | N3S | HN3A | 57.3° | 23.5° |
| C1' | N' | C7 | HN' | 180.0° | 179.9° |
| C1' | N' | C7 | O' | 6.3° | 0.1° |
| C1' | N' | C7 | C1 | 176.6° | 180.0° |
| N' | C1' | C2' | F2'1 | 60.0° | 59.9° |
| N' | C1' | C2' | F2'2 | 54.5° | 179.9° |
| N' | C1' | C2' | F2'3 | 178.9° | 60.0° |
| N' | C1' | C2' | H1' | 120.0° | 120.0° |
| N' | C1' | C2' | H1'A | 120.0° | 120.0° |
| N' | C1' | H1' | H1'A | 120.5° | 120.0° |
| N' | C7 | O' | C1 | 177.2° | 179.9° |
| N' | C7 | C1 | C5 | 178.5° | 179.9° |
| N' | C7 | C1 | C3 | 1.1° | 0.2° |
| C7 | N' | C1' | C2' | 97.2° | 180.0° |
| C7 | N' | C1' | H1' | 142.7° | 59.9° |
| C7 | N' | C1' | H1'A | 22.8° | 60.1° |
| HN' | N' | C7 | O' | 173.7° | 180.0° |
| HN' | N' | C7 | C1 | 3.4° | 0.1° |
| HN' | N' | C1' | C2' | 82.8° | 0.1° |
| HN' | N' | C1' | H1' | 37.3° | 120.0° |
| HN' | N' | C1' | H1'A | 157.3° | 120.0° |
| O' | C7 | C1 | C5 | 4.3° | 0.0° |
| O' | C7 | C1 | C3 | 178.3° | 179.7° |
| C7 | C1 | C5 | C3 | 177.4° | 179.7° |
| C7 | C1 | C3 | C2 | 179.2° | 179.7° |
| C7 | C1 | C3 | H3 | 0.8° | 0.3° |
| C7 | C1 | C5 | C6 | 177.7° | 179.8° |
| C7 | C1 | C5 | H5 | 2.3° | 0.3° |
| C5 | C1 | C3 | C2 | 3.4° | 0.0° |
| C5 | C1 | C3 | H3 | 176.6° | 180.0° |
| C1 | C5 | C6 | C4 | 0.5° | 0.1° |
| C1 | C5 | C6 | H5 | 180.0° | 179.9° |
| C1 | C5 | C6 | H6 | 179.5° | 179.9° |
| C1 | C3 | C2 | H3 | 180.0° | 179.9° |
| C1 | C3 | C2 | C4 | 6.9° | 0.1° |
| C1 | C3 | C2 | H2 | 173.1° | 180.0° |
| C3 | C1 | C5 | C6 | 0.3° | 0.1° |
| C3 | C1 | C5 | H5 | 179.7° | 180.0° |
| C3 | C2 | C4 | H2 | 180.0° | 179.9° |
| C3 | C2 | C4 | C6 | 7.0° | 0.0° |
| C4 | C2 | C3 | H3 | 173.1° | 180.0° |
| C2 | C4 | C6 | C5 | 3.7° | 0.0° |
| C2 | C4 | C6 | H6 | 176.3° | 180.0° |
| H2 | C2 | C3 | H3 | 6.9° | 0.1° |
| H2 | C2 | C4 | C6 | 173.0° | 179.9° |
| C4 | C6 | C5 | H6 | 180.0° | 180.0° |
| C4 | C6 | C5 | H5 | 179.5° | 180.0° |
| H5 | C5 | C6 | H6 | 0.5° | 0.0° |
| F2'1 | C2' | F2'2 | F2'3 | 114.4° | 120.0° |
| F2'1 | C2' | F2'2 | C1' | 122.4° | 120.0° |
| F2'1 | C2' | F2'3 | C1' | 124.0° | 120.0° |
| F2'1 | C2' | C1' | H1' | 60.0° | 180.0° |
| F2'1 | C2' | C1' | H1'A | 180.0° | 60.0° |
| F2'2 | C2' | F2'3 | C1' | 127.4° | 120.0° |
| F2'2 | C2' | C1' | H1' | 174.6° | 60.0° |
| F2'2 | C2' | C1' | H1'A | 65.5° | 60.0° |
| F2'3 | C2' | C1' | H1' | 61.0° | 60.0° |
| F2'3 | C2' | C1' | H1'A | 58.9° | 180.0° |
| C2' | C1' | H1' | H1'A | 120.4° | 120.0° |
