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 parametrization 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).
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 (Ligand, Best residues, Worse residues and Water molecules).
An output example is the following:
![]() |
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.