The data about interactions enhance the binding properties of potential drugs and helps to identify them. Small molecule-protein docking systems also scan the conformational space of ligands and proteins using different scoring systems and search strategies in order to forecast energetically favourable binding locations ( ). By exposing the fundamental architecture of protein-ligand interactions, small molecule-protein docking helps to generate more selective and successful treatments. This helps advance new therapies for many diseases and accelerates drug discovery ( ). The conformation of a ligand is one of the significant values to evaluate docking results, such as RMSD ( ). RMSD calculates the average distance between the atoms of stacked proteins or ligands and assesses the similarity between the reference structure and the expected docked location. A known experimental structure is often used to determine the accuracy of docking predictions using docked conformation. Once the conformation of ligands approaches the natural structure, the RMSD of small ligands is close to zero.