2.4.2. AutoDock Vina

The compounds were docked by AutoDock Vina (version 1.1.2, Scripps Research, San Deigo, California Jupitar, Florida, USA) using PyRx—Virtual Screening Tool (https://pyrx.sourceforge.io/ (accessed on 18 February 2021)). AutoDock Vina requires the receptor and the ligand files in PDBQT (protein data bank, partial charge (Q) and atom type (T)) file format. The PDB files of receptors and the mol2 files of ligands were converted to PQBQT format by PyRx. For VS, docking search space was defined around 3 Å of co-crystallized ligand with a grid box size of 70 Å × 70 Å × 70 Å points and grid spacing of 0.375 Å. The numbers of binding modes and exhaustiveness of search were set to 30 and 8, respectively. The Lamarckian genetic algorithm and empirical energy function were used for docking. By default, ten docked conformations were generated for each docked ligand.