3.7.3. Hydrogen bond analysis of PPARδ complexes
For more than 80% of the simulation time, hydrogen bonding was detected in PPARδ complexes. PPARδ in complex with crystal ligand, Hydrogen bonds formed at the docking, Cys249, and Thr437 were diminished during the simulation while Thr253 was forming strong bond alternately with O6 and O8 of the ligand, throughout the simulation duration. New hydrogen bonds formed between Gln250, Thr256, His287 His413, and ligand atoms. Bonds between time duration of 100 ns to 160 ns were not observed for Gln250 and Thr256, due to change in orientation of the ligand. The formation and breaking of the hydrogen bonds at various time was noted. Hydrogen bonds in PPARδ and Lifitegrast complex involved, Arg248, Gln250, His413, and Tyr437 reside with the ligand. Gln250 forming a hydrogen bond with the O4 of the ligand was not observed after 160 ns (