The commercial compounds Afinitor, Ixabipilone, Letrozole, Halaven, Lapatinib, Palbociclib, Raloxifene and Tamoxifen and the natural compounds isolated from Aurora globostellata, Stigmasterol and Oleic acid are considered as the ligands against the target HER-2. The ligand structures are downloaded from Pubchem. The ligands have been segregated into three groups; the first group consisting of the five commercial compounds Afinitor, Ixabipilone, Letrozole, Halaven, Lapatinib; the second group representing the next three potential commercial compounds (Palbociclib, Raloxifene and Tamoxifen) and the last group as the isolated compounds (Stigmasterol and Oleic acid). Ligprep was used for ligand preparation. It generates various structures with ionization states at pH 7.0±2.0 with ionizer. The force field Merck Molecular Force field MMFF94 is used for the optimization, producing low energy conformation of the ligand .