Phosphatic compounds are perform a wide variety of specific functions associated with life processes. They are involved in stabilizing the structure of folded proteins.Phosphatic compounds play a key role in the biosynthesis and metabolism of a number of bioactive peptides and are very useful for catabolism of many biosynthetic activities. Regardless of the phoshphatic compounds and its precise pattern of ligation to the protein, there is a common qualitative feature to the binding site: the Phosphatic Compounds are ligated by a shell of hydrophilic atomic groups (containing oxygen, nitrogen, Phosphorous, sulfur atoms) and this hydrophilic shell is embedded within a larger shell of hydrophobic atomic groups (containing carbon atoms). In this study, we design a on-line tool that analyze the activity of these ligand molecules with protein complexes. This tool calculate the RMSD value of ligand and protein residue under a defined chain with defined ligand molecule.