MD_simulation input folder has SHP2 and SHP1 in complex with SHP099 and C8 input files and the job file (run.sh) to run the classical MD simaultion. MD_simulation output folder has files needed to run MMGBSA calculations and the analyses of the output files (RMSD, RMSF and hydrogen bond analysis) of the system and the job file (Analyses.sh). It also has the parmtop files for solvated and unsolvated complex, protein and the ligand. Clustering_input_files It has the input files to run Clustering metrics and analyses.It has the script to submit all the files for the different clusters It has the job file (COVID-19.sh) and the python scripts to plot the metrics for DBI (get_cluster_metrics.py) and SSR(get_SSR_SST.py). CpHMD input folder has the input files for CpHMD simulation for pH5.5, 7.5 and 12 for protonated and unprotonated SHP099. It also has the parmtop file of the complex (4LYT.parm7). And the job script contains the MD simulation commands (run.sh) and the output analysis (RMSD and RMSF). CphMD output file has the MMGBSA job script (Analyses_run.sh) for the different systems. It also has the parmtop files for solvated and unsolvated complex, protein and the ligand.