Molecular Docking Study

To understand the binding interactions of the target compounds with the active site of cytochrome bc ₁ complex, the molecular docking procedures were carried out using AutoDock 4.2.6 software according to the reported paper (Lin et al., 2019; Du et al., 2020). The target protein PDB file for the cytochrome bc ₁ complex (PDB ID 1SQB, 2.69 Å in resolution) was downloaded from the RCSB PDB web (https://www.rcsb.org/). The site of the Azoxystrobin ligand was chosen as the docking domain. Before docking calculations, all of the other small molecules such as some ligands (except for Azoxystrobin ligand) and water molecules in the crystal were removed. The torsional bonds of each docked compound were automatically set by the AUTOTORS module. A grid map with a 60 × 60 × 60 point grid box (X = 69.364, Y = 57.986, Z = 168.988) with 0.375 Å spacing was selected around the site of the azoxystrobin ligand. The grid box was generated by applying default parameters. The docking calculations were performed using the Lamarckian genetic algorithm (GA) and the number of GA runs was set to 20 conformations. The lowest binding energy in the maximum cluster for the docked conformations was chosen as the representative binding energy. The binding energy between the docked compound and the enzyme was calculated using the AutoGrid program with a grid spacing of 0.375 Å and the Lamarckian genetic algorithm as a searching method. When the docking results were generated, the binding energies of all docked compounds were also automatically obtained in this program.