Identification of the binding pose of a ligand in a protein pocket is challenging as it is a complex process. Here we introduce an approach using supervised molecular dynamics, coupled with scoring the binding poses using Dynamical Averaging of Quantum Mechanics Fragment Molecular Orbital (DA-QM-FMO). For SARS-COV2 protein PL-pro, this method outperformed the other methods used for docking ligands into the protein pockets.