In this study, we docked 500 ligands with 2 proteins, to identify highest binding affinity and also visualized their different chemical bonds with amino acids by Biovia study. All ligands, we compared with Lipinski rule of five, where 356 ligands follow Lipinski rule of five and docked with these two proteins by Autodock Vina, PyRx. From all these ligands, ligand 243 showed highest binding affinity between these protein-ligand complexes. The dUTpase protein and ligand 243 complex binding affinity is 18.2 Kcal/mole, where 6-PGL protein with ligand 243 complex binding affinity is -17.5 Kcal/mole. These protein-ligand complexes also showed different amino acid and their chemical bond such as conventional hydrogen bond, Pi-donor bond, carbon bond, water hydrogen bond etc.