**2.8 Molecular dynamics simulation and MM-PBSA calculation of protein–ligand complexes**

By employing GROMACS 2018 [31], the chain A of *Lm*TR and the *Lm*TR–ligand complexes were subjected to molecular dynamics simulations. Ligand topologies were generated via PRODRG which were converted to .gro files. Solvation of each of the protein–ligand complexes in a dodecahedron box was followed by neutralization of the output with sodium and chlorine ions. Each complex was minimized using the steepest descent algorithm coupled with the GROMOS43A force field. Equilibration protocol was carried out to restrain and relax protein–ligand positions. The MD production run was carried out for 100 ns. The output file was used in

downstream processes to generate root mean-square deviation (RMSD), root mean-square fluctuation (RMSF) and radius of gyration (Rg) plots with Xmgrace (https://plasma-gate.weizmann.ac.il/Grace/). Molecular mechanics Poisson– Boltzmann surface area (MM-PBSA) was employed in calculating the free energies of the complexes. MM-PBSA was carried out using g\_mmpbsa, which calculates binding energy components and the per-residue energy decomposition [46]. Graphs were generated using R-programming showing energy interactions.
