2.9.2. Root Mean Square Distance (RMSD)

The interaction of a ligand with a protein can result in considerable conformational change in the structure. The RMSD was measured as a function of time with respect to the initial conformation and is illustrated in Figure 9a. The RMSD average value for *Rv1636* was 0.71379 nm and for the Rv1636\_*β*-amyrin complex it was 0.61481 nm. The RMSD plot evidently implied that the Rv1636 and Rv1636\_*β*-amyrin complexes were stable during the simulation time frame till 45 ns, but after 45 ns there was some hindrance showing fluctuation in the Rv1636\_*β*-amyrin complex, as compared to Rv1636.

**Figure 9.** Structural dynamics of universal stress protein (Rv1636) upon *β*-amyrin binding as a function of time. (**a**) RMSD plot of Rv1636 in complex with *β*-amyrin. (**b**) RMSF plot of Rv1636 in complex with *β*-amyrin. (**c**) Structural compactness and folding Rv1636 upon *β*-amyrin. (**d**) SASA plot of Rv1636 as a function of time before and after *β*-amyrin binding. (**e**) The time evolution of projections of trajectories on both EVs. The free energy landscapes of free Rv1636 protein (**f**) The free energy landscapes of free Rv1636 with *β*-amyrin.
