In the pursuit of effective anti-diabetic treatments, Dean et al. utilized low-affinity biochemical screening and high-throughput co-crystallography to design compounds that selectively modulate all three-peroxisome proliferator-activated receptors (PPARs). The lead molecule, Indeglitazar, PDB-ID: 3ET3, is emerged from a low-affinity smaller fragment (PDB-ID: 3ET0). We apply FMOPhore to analyze the Q-SAR of the Indeglitazar molecule. By analyzing the FMOPhore, (Figure .) calculated on the holo-complex bound structures for the fragment (starting point) and the Indeglitazar, both molecules are found to bind to the Ser-A-289, His-A-323, Phe-A-363, His-A-449, and Tyr-A-473. This critical binding site was named pocket A as per Dean et al, study with another pocket named pocket B which was left unoccupied. The starting point fragment PDB-ID 3ET0,