I am using autodock vina.
After docking, when i analyzed the result ligand have a binding energy of -8.3 kcal/mol.
But when i gone through the interaction, i couldn't find any hydrogen bond.
All interactions observed were Aromatic Interactions/pi-staking.
Can i consider this result of docking ?
The result is perhaps uncommon, but the actual answer may depend on many variables:
- does the ligand have any hydrigen bond donors/acceptors?; how many?
- does the binding site has any residues able to form hydrogen bonds? how many? do you have any experimental data suggesting the binding site, or did you choose it based on something else?
There are some known ligand-protein pairs that have few hydrogen bonds (and not that obvious) and yet show very strong binding; see e.g. http://www.rcsb.org/pdb/explore.do?structureId=3ODU In this respect:
- does the ligand have large hydrophobic and/or aromatic regions that can form strong hydrophobic / pi-cation interactions? Are such interactions present in your docked pose?
- in the above example the hydrogen bonds are not your common hydrogen bonds (-OH groups to N atoms in aromatic systems). Is it possible that autodock visualizer (or any other visualizer) can't recognize them as hydrogen bonds? Or perhaps is not able to accurately evaluate their strenght?
I would better suggest you to evaluate your docked complexes in LigPlot program. It is able to identify even very sensitive pairs of hydrogen bonds that are not displayed in some autoDock interfaces...
I think you could try having a look at the interaction using some other software - say LigPlot+ or Maestro.
Ligplot is a good software to identify both Hydrogen and hydrophobic interactions between ligand protein with hydrogen bond lengths too represented.
Ligplot plus and biovia discovery visualisation studio are free and good softwares to know the different interactions that takes place between ligand and protein.
For ligplot you have to create ligand-protein complex file and in discovery studio you can directly add protein and output file (docking result) to obtain the different interactions. Both can generate interaction diagram in 2D.