I want to know how can I determine the significance of the different bonds (such as H-bonding, Pi-alkyl, Pi-anion, Unfavorable acceptor-acceptor) between my ligand and the protein and how they contribute to stabilizing the overall formed structure. I tried a lot of articles but they are not really explaining in depth.
Thanks in advance
First, you have to determine which binding mode you are going to select. In the selection of the binding pose normally, I would prefer to give priority to the binding energy, then binding pose, and also the number of hydrogen bonds formed which makes the complex stable.
Second, save this molecuale as a complex (using the docking software) as a .pdb or pdbqt file.
Third, Open the saved complex file using PyMOL. Use the below link: https://www.youtube.com/watch?v=DWbrDsFo_QQ
Binding free energy, an attribute of ensemble, can be calculated from average interatomic electrostatic and van der Waals interactions (between the ligand and its surrounding environment); the individual interatomic contributions can be grouped to quantify the effects of hydrogen bonds, aromatic stacking, and so on.
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