HMF
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N | CA | sing | 1.47Å | 1.53Å | |
| N | H | sing | 1.01Å | 1.00Å | |
| N | H2 | sing | 1.01Å | 1.00Å | |
| CA | C | sing | 1.51Å | 1.50Å | |
| CA | CB | sing | 1.53Å | 1.54Å | |
| CA | HA | sing | 1.09Å | 1.10Å | |
| C | O | doub | 1.21Å | 1.23Å | |
| C | OXT | sing | 1.34Å | 1.30Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å | |
| CB | CG | sing | 1.53Å | 1.47Å | |
| CB | HB2 | sing | 1.09Å | 1.10Å | |
| CB | HB3 | sing | 1.09Å | 1.10Å | |
| CG | C1 | sing | 1.51Å | 1.50Å | |
| CG | HG2 | sing | 1.09Å | 1.10Å | |
| CG | HG3 | sing | 1.09Å | 1.10Å | |
| C1 | C2 | doub | 1.38Å | 1.38Å | Aromatic |
| C1 | C6 | sing | 1.38Å | 1.38Å | Aromatic |
| C2 | C3 | sing | 1.38Å | 1.40Å | Aromatic |
| C2 | HC2 | sing | 1.08Å | 1.08Å | |
| C6 | C5 | doub | 1.38Å | 1.39Å | Aromatic |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C3 | C4 | doub | 1.38Å | 1.34Å | Aromatic |
| C3 | H3 | sing | 1.08Å | 1.08Å | |
| C5 | C4 | sing | 1.38Å | 1.37Å | Aromatic |
| C5 | H5 | sing | 1.08Å | 1.08Å | |
| C4 | H4 | sing | 1.08Å | 1.08Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CA | N | H | 109.5° | 111.0° |
| CA | N | H2 | 109.5° | 111.0° |
| N | CA | C | 105.2° | 109.5° |
| N | CA | CB | 93.6° | 109.5° |
| N | CA | HA | 128.9° | 109.4° |
| H | N | H2 | 109.5° | 111.0° |
| C | CA | CB | 126.6° | 109.5° |
| C | CA | HA | 97.6° | 109.4° |
| CA | C | O | 115.6° | 119.9° |
| CA | C | OXT | 120.7° | 120.0° |
| CB | CA | HA | 108.5° | 109.4° |
| CA | CB | CG | 114.7° | 109.5° |
| CA | CB | HB2 | 107.7° | 109.5° |
| CA | CB | HB3 | 107.8° | 109.4° |
| O | C | OXT | 123.7° | 120.1° |
| C | OXT | HXT | 109.5° | 117.0° |
| CG | CB | HB2 | 107.8° | 109.5° |
| CG | CB | HB3 | 107.7° | 109.5° |
| CB | CG | C1 | 123.9° | 109.5° |
| CB | CG | HG2 | 104.9° | 109.5° |
| CB | CG | HG3 | 104.9° | 109.5° |
| HB2 | CB | HB3 | 111.1° | 109.5° |
| C1 | CG | HG2 | 104.9° | 109.5° |
| C1 | CG | HG3 | 104.9° | 109.5° |
| CG | C1 | C2 | 125.1° | 120.0° |
| CG | C1 | C6 | 120.7° | 120.0° |
| HG2 | CG | HG3 | 113.6° | 109.4° |
| C2 | C1 | C6 | 114.2° | 120.0° |
| C1 | C2 | C3 | 121.1° | 120.0° |
| C1 | C2 | HC2 | 119.5° | 120.0° |
| C1 | C6 | C5 | 125.7° | 120.0° |
| C1 | C6 | H6 | 117.2° | 120.0° |
| C3 | C2 | HC2 | 119.5° | 120.0° |
| C2 | C3 | C4 | 122.3° | 120.0° |
| C2 | C3 | H3 | 118.9° | 120.0° |
| C5 | C6 | H6 | 117.2° | 120.0° |
| C6 | C5 | C4 | 117.1° | 120.0° |
| C6 | C5 | H5 | 121.5° | 120.0° |
| C4 | C3 | H3 | 118.8° | 120.0° |
| C3 | C4 | C5 | 119.6° | 120.0° |
| C3 | C4 | H4 | 120.2° | 120.0° |
| C4 | C5 | H5 | 121.5° | 120.0° |
| C5 | C4 | H4 | 120.2° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CA | N | H | H2 | 120.0° | 123.9° |
| N | CA | C | CB | 106.4° | 120.1° |
| N | CA | C | HA | 133.8° | 120.0° |
| N | CA | CB | HA | 133.1° | 120.0° |
| N | CA | C | O | 71.5° | 20.0° |
| N | CA | C | OXT | 105.5° | 160.0° |
| N | CA | CB | CG | 140.1° | 65.0° |
| N | CA | CB | HB2 | 99.9° | 175.0° |
| N | CA | CB | HB3 | 20.1° | 55.0° |
| H | N | CA | C | 180.0° | 60.0° |
| H | N | CA | CB | 50.5° | 60.1° |
| H | N | CA | HA | 66.8° | 180.0° |
| H2 | N | CA | C | 60.0° | 63.9° |
| H2 | N | CA | CB | 69.5° | 176.0° |
| H2 | N | CA | HA | 173.2° | 56.1° |
| C | CA | CB | HA | 114.9° | 120.0° |
| CA | C | O | OXT | 176.8° | 180.0° |
| CA | C | OXT | HXT | 176.7° | 179.9° |
| C | CA | CB | CG | 108.0° | 175.0° |
| C | CA | CB | HB2 | 12.0° | 55.0° |
| C | CA | CB | HB3 | 132.0° | 65.0° |
| CB | CA | C | O | 34.9° | 100.0° |
| CB | CA | C | OXT | 148.2° | 80.0° |
| CA | CB | CG | HB2 | 120.0° | 120.1° |
| CA | CB | CG | HB3 | 120.0° | 120.0° |
| CA | CB | HB2 | HB3 | 117.9° | 120.0° |
| CA | CB | CG | C1 | 4.8° | 180.0° |
| CA | CB | CG | HG2 | 115.2° | 59.9° |
| CA | CB | CG | HG3 | 124.8° | 60.0° |
| HA | CA | C | O | 154.7° | 140.0° |
| HA | CA | C | OXT | 28.3° | 40.0° |
| HA | CA | CB | CG | 6.9° | 55.0° |
| HA | CA | CB | HB2 | 126.9° | 65.0° |
| HA | CA | CB | HB3 | 113.0° | 175.0° |
| O | C | OXT | HXT | 0.0° | 0.1° |
| CG | CB | HB2 | HB3 | 117.9° | 120.0° |
| CB | CG | C1 | HG2 | 120.0° | 120.0° |
| CB | CG | C1 | HG3 | 120.0° | 120.0° |
| CB | CG | HG2 | HG3 | 114.0° | 120.0° |
| CB | CG | C1 | C2 | 72.2° | 90.0° |
| CB | CG | C1 | C6 | 108.4° | 90.3° |
| HB2 | CB | CG | C1 | 124.8° | 60.0° |
| HB2 | CB | CG | HG2 | 4.8° | 180.0° |
| HB2 | CB | CG | HG3 | 115.2° | 60.0° |
| HB3 | CB | CG | C1 | 115.2° | 60.0° |
| HB3 | CB | CG | HG2 | 124.8° | 60.0° |
| HB3 | CB | CG | HG3 | 4.8° | 180.0° |
| C1 | CG | HG2 | HG3 | 114.0° | 120.0° |
| CG | C1 | C2 | C6 | 179.4° | 179.7° |
| CG | C1 | C2 | C3 | 178.7° | 180.0° |
| CG | C1 | C2 | HC2 | 1.3° | 0.1° |
| CG | C1 | C6 | C5 | 176.6° | 180.0° |
| CG | C1 | C6 | H6 | 3.4° | 0.0° |
| HG2 | CG | C1 | C2 | 167.7° | 30.0° |
| HG2 | CG | C1 | C6 | 11.6° | 149.7° |
| HG3 | CG | C1 | C2 | 47.7° | 150.0° |
| HG3 | CG | C1 | C6 | 131.6° | 29.7° |
| C1 | C2 | C3 | HC2 | 180.0° | 179.9° |
| C2 | C1 | C6 | C5 | 2.8° | 0.3° |
| C2 | C1 | C6 | H6 | 177.2° | 179.7° |
| C1 | C2 | C3 | C4 | 0.9° | 0.0° |
| C1 | C2 | C3 | H3 | 179.1° | 179.9° |
| C6 | C1 | C2 | C3 | 0.7° | 0.3° |
| C6 | C1 | C2 | HC2 | 179.3° | 179.8° |
| C1 | C6 | C5 | H6 | 180.0° | 180.0° |
| C1 | C6 | C5 | C4 | 3.3° | 0.0° |
| C1 | C6 | C5 | H5 | 176.7° | 180.0° |
| C2 | C3 | C4 | H3 | 180.0° | 179.9° |
| C2 | C3 | C4 | C5 | 0.4° | 0.3° |
| C2 | C3 | C4 | H4 | 179.6° | 180.0° |
| HC2 | C2 | C3 | C4 | 179.2° | 179.9° |
| HC2 | C2 | C3 | H3 | 0.8° | 0.0° |
| C6 | C5 | C4 | C3 | 1.5° | 0.3° |
| C6 | C5 | C4 | H5 | 180.0° | 179.9° |
| C6 | C5 | C4 | H4 | 178.5° | 180.0° |
| H6 | C6 | C5 | C4 | 176.8° | 179.9° |
| H6 | C6 | C5 | H5 | 3.2° | 0.0° |
| C3 | C4 | C5 | H4 | 180.0° | 179.7° |
| C3 | C4 | C5 | H5 | 178.5° | 179.7° |
| H3 | C3 | C4 | C5 | 179.6° | 179.8° |
| H3 | C3 | C4 | H4 | 0.4° | 0.1° |
| H5 | C5 | C4 | H4 | 1.5° | 0.1° |
