3.8.3. RDF of PPARδ complexes
Hydrogen bond analysis revealed the active residues of the PPARδ (GLN250 and THR256 of Iloprost-PPARδ, Arg248, and Tyr437 of Lifitegrast-PPARδ and ILE327 and THR253 of Lanifibranor-PPARδ) were found as key residues involved in strong intermolecular interactions. An RDF graph was generated for interacting residues with ligands for further investigation. In the Iloprost-PPARδ complex, GLN250:NE2 was making two hydrogen bonds. At the beginning of the simulation, the highest peak for GLN250:NE2 and atom O6 the ligand appeared at 2.7 Å and g(r) value was 2.59, atom O8 of the ligand was also found interacting with GLN250:NE2 value 4.7 Å having the g(r) value 0.40. At time 100 ns, the peak for GLN250:NE2 with O6 and O8 of the ligand appeared at 4.3 Å and 2.8 Å with the value of g (r) 0.30 and 2.0 respectively whereas finally at the end of simulation GLN250:NE2 interacting with ligand, distributed to a maximum value of g(r) value 1.02 for O6 and 1.44 for O8 of the ligand at 2.7 Å. It was observed that the peak was high initially. The other residue THR256:OG interacting with the O4 of the ligand, at the start of the simulation showed a maximum distribution peak at 2.9 Å and the g(r) value was 1.21. At 100 ns the distribution peak was observed for THR256:OG1 and atom O4 of the ligand at 3.6 Å with the g(r) of 0.55. Finally, at the 200 ns time scale, the distribution peak for the same interaction was observed at 3.5 Å having the g (r) value of 0.46. The distribution peak in the graph shows that the peak was narrow in width initially than at the end of the simulation.In the Lifitegrast-PPARδ complex, hydrogen bond analysis showed that ARG248 was forming two hydrogen bonds (