This dataset contains the results from virtual screening of SPECS library after predicting the selectivity of molecules against HDAC6 over using a Deep Belief Network model that was trained and tested by the authors. The docking poses of 10 molecules with best docking scores were given along with their MMGBSA scores. The MD trajectory files along with the analysis were also provided for the selected three molecules as well as the reference molecule (co-crystalized ligand).