The human angiontensin-converting enzyme I (hACEI) is a zinc metalloproteinase that hydrolytically cleaves a C-terminal dipeptide from a wide range of peptide substrates, and it plays an important role in regulating blood pressure. MD simulations and interaction energy calculations for docking and crystal structures were performed to investigate the correct conformation of the ACE with enalaprilat and nanopepetide. The analysis of root-mean-squrared fluctuation (RMSF), which is usually applied to measure the mobility and flexibility of the proteins, and dynamic correlation of residues show that the fluctuation pattern of the each two structure of the same ligand is almost the same mode. Hydrogen bond analysis shows that the correct crystal conformation is more stable than a wrong docking conformation. In addition, we are demonstrating that calculating interaction energy between protein and its ligands is an accurate and efficient way to select the correct conformation from docking conformations.