DOI: 10.5061/dryad.5hqbzkhc6
title: Data from: Compromise docking power evaluation of liganded crystal structures of Mpro SARS-CoV-2

description: A set of 406 liganded SARS-CoV-2 Mpro crystal structures originally
 downloaded from RCSB PBD database is provided. Ligand and protein files
 are processed and corrected for various types of structural errors and are
 provided in pdbqt and mol2 formats for immediate use in molecular docking
 programs AutoDock, AutoDock Vina, and PLANTS. Data are utilized in
 calculations of newly defined compromise docking power to monitor the
 performance of above-mentioned software. The provided dataset can also be
 used for benchmarking of other software and molecular docking protocols on
 liganded SARS-CoV-2 Mpro systems.
description: Provided data set is comprised of 406 SARS-CoV-2
 M<sup>pro</sup> crystal structures (169 noncovalent and 247
 covalent in pdbqt and mol2 formats) ready to use in molecular docking
 programs AutoDock, AutoDock Vina, and PLANTS. The
 initial dataset containing 671 SARS-CoV-2 M<sup>pro</sup>
 crystal structures was downloaded (10<sup>th</sup> of February
 2022) from RCSB PDB database. 161 unliganded structures and two structures
 containing unparametrized atoms in the ligand structure (Se, Zn) were
 discarded from further processing. The remaining 508 crystal structures
 were then stripped of disordered atoms, crystal waters, ions, and
 cosolvents and aligned to a reference structure (PDB ID: 6wqf). Crystal
 structures were then split into separate files for each monomer present,
 and the first chain containing a ligand-protein pair was selected for
 further processing. The integrity of the ligand structure was validated by
 expressing its InChIKey, using OpenBabel 2.3.2, and comparing it with its
 RCSB entry. Discrepancies were recorded and addressed manually by
 transforming the ligand pdb structure from the respective monomer unit to
 the mol2 format using OpenBabel and editing the individual atoms/bond
 orders to produce the desired ligand structure. Ligands with a missing
 fragment (102 in total), i.e., more than hydrogen atoms were omitted.
 OpenBabel was then used to produce the desired file format of both ligand
 and protein structures, pdbqt for AutoDock and AutoDock Vina with only
 polar hydrogens present, and mol2 for PLANTS, with added Gasteiger
 charges.
description: # Data from: Compromise docking power evaluation of liganded crystal
 structures of Mpro SARS-CoV-2
 A set of 406 liganded
 SARS-CoV-2 M<sup>pro</sup> crystal structures originally
 downloaded from RCSB PBD database is provided. Ligand and protein files
 are processed and corrected for various types of structural errors and are
 provided in pdbqt and mol2 formats for immediate use in molecular docking
 programs AutoDock, AutoDock Vina, and PLANTS. Data are utilized in
 calculations of newly defined compromise docking power to monitor the
 performance of above-mentioned software. The provided dataset can also be
 used for benchmarking of other software and molecular docking protocols on
 liganded SARS-CoV-2 M<sup>pro</sup> systems.  ## Description
 of the data and file structure Data are provided as one archive file
 (zip), which contains covalent and noncovalent directories. Each of these
 directories contains additional directories (247 in the covalent and 169
 in the noncovalent directory) denoted by the 4 symbol code, corresponding
 to PDB code on the RCSB database. Every such directory contains protein
 and ligand structures in pdbqt and/or mol2 formats, ready for use in
 AutoDock and AutoDock Vina, and PLANTS, respectively.