8.9 Evaluation of the interactions

In order to analyze the docking results, VEGA ZZ can calculate the interaction energy ligand - biomacromolecule and evaluate the contribute of each residue. This function is available choosing Calculate -> Interactions from the main menu.
For the calculation, you must indicate the ligand typing the residue name and the residue number in the Ligand/residue field (format : Residue_Name:Residue_Number). It's possible to put also the lone residue number or to click on the ligand structure in the main windows to select the ligand.
The Dielectric (dielectric constant) and the Cutoff  (cutoff distance) parameters are strictly related to the evaluation of the non-bond interaction energy. VEGA ZZ applies the CVFF force field parameterization using the R6-R12 Lennard-Johnes' and the Coulomb's equations. The residues having a partial interaction energy greater than Threshold (%) of the total energy are shown in the table and in the graphic main window. Checking Worse residues, the residues with the worse energy contribution are shown (click here to change the default values).

Evaluation of the interactions

You can modify the visualization choosing the colouring method (Ligand by atom, By molecule, By residue and By residue energy) and which residues to show (LigandBest residues, Worse residues and Water molecules).

An output example is the following:

Interactions   Cyan = best residues
  Red = worst residues
  Green = ligand

In the console you can find all numerical data:


*********************************************
**** CVFF interaction energy calculation ****
*********************************************

Ligand name..........: FCB:1
Ligand atoms.........: 64
Dielectric constant..: 20.000

Total................:  -46.9799 Kcal/mol
Non-bond.............:  -37.6195 Kcal/mol
Coulombic............:   -9.3604 Kcal/mol


 Res    Num     R6-R12    Coulomb     Total
============================================
 LYS    110    -6.9241    -1.6769    -8.6010
 ZN     732    -0.3585    -6.0425    -6.4010
 TYR    655    -3.4999    -0.0764    -3.5763
 CYS    389    -2.7550    -0.6831    -3.4381
 ASN    111    -3.8072     0.3976    -3.4096
 GLN    108    -2.6736    -0.6580    -3.3316
 LYS    650    -0.8385    -1.9708    -2.8093

 ASP    591    -0.6871     2.7756     2.0885
 ASP    653    -0.4679     2.5735     2.1056

At the end of this output, you can find the worse residues (ASP-591 and ASP-653) in which the energy contribution is positive.

 

WARNING:
To do the evaluation of the interaction energy, you must follow these rules: