- These are not bonds. At a cut-off of 5.0 Å, you are simply looking at pairs of atoms that are so close to each other that water cannot squeeze in between (solvent-excluding contacts) between two structures that have no hydrogen atoms.

- if you want to know how many carbon atoms in alphaCD are within this range, you can specify:

select sele, (alphaCD and elem C) within 5.0 of (carvacrol_out_ligand_01 and elem C)

and get the answer: selection "sele" defined with 35 atoms

Most of these distances are too large to qualify as good Van-der-Waals contacts.

Thank you Annemarie Honegger.

You’re correct, those are not bonds. Your suggested command lines relay helpful to understand number of carbon atoms in receptor falls within 5.0 Å distance from ligand carbons.

Thanks again for your support.

"Hydrophobic interactions", which are the driving force for this type of complexes, are essentially governed by the decrease in entropy of water molecules forced to arrange on a hydrophobic interface without breaking too many hydrogen bonds to other molecules, which would be energetically very unfavourable.

A proxy measurement for the hydrophobic effect is the reduction in solvent accessible surface upon complex formation. You can calculate this as the difference between to sum of the solvent accessible surfaces of the isolated components and the solvent accessible surface of the complex. You can get a rough calculation of these surfaces using the "get_area" command in PyMOL (https://pymolwiki.org/index.php/Get_Area), for more precise calculations you can use Naccess http://www.bioinf.manchester.ac.uk/naccess/

Thank you Annemarie Honegger.

Your suggestions are well taken.

Annemarie Honegger

Dear Dr. Annemarie Honegger,

As you have suggested, first, I have calculated SASA values of individual ligand and receptor and sum it. Then calculated the SASA value of ligand receptor complex and compared these values. As expected, complex SASA values are lower than the sum of individual ligand and receptor values. However, when I look for various non-bonded interactions through discovery studio of these ligand protein complex, I have found many receptor ligand complex did not show any interactions (Though the default distant values for hydrogen bonding was 5 Å, Charge-Charge interaction 5.6 Å, Cation-Pi 5 Å, Pi-Pi interaction 6Å).

Under this circumstances may I know is there any computational method to for Hydrophobic interactions for ligand receptor complex ?

Note: Here receptors are not proteins.

What did you expect? There are no charges in either the ligand nor in the cyclodextrin, therefore you will find no charge-charge interaction, and definitely no Cation-Pi interactions. There are no aromatic rings in either molecule, therefore you will find no Pi-Pi interactions. The only atom in your ligand that could form hydrogen bonds in your ligand is the single oxygen, and while that one would be within the (very large ) cut-off distance for a hydrogen bond, the angles definitely not right. As I explained earlier, the energetics of "hydrophobic interaction" is not dependent on ligand-receptor interactions, but on the effect of solvent exclusion on the arrangement of the surrounding water molecules.

Annemarie Honegger

Thank you. The last sentence of your reply explains the reason for the lack of charge based hydrophobic interaction between ligands and receptors.

Thanks again for your valuable time

Charged groups are hydrophilic - There is no such thing as "charge-based hydrophobic interactions". Charge interactions are electrostatic in nature. Please read https://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html

to better understand how molecular interactions work.

Annemarie Honegger

Thank you for helping me to understand about Molecular Interactions.

PyMOL can be used to count the number of bonds selected number of atoms. The following link contains the instructions PyMOL:

https://fitzkee.chemistry.msstate.edu/sites/default/files/gradbpc/pymol-tutorial.pdf