7.8 Evaluation of the interactions OpenGL

In order to analyze the docking results, VEGA can calculate the interaction energy ligand - biomacromolecule and evaluate the contribute of each residue. This function is available choosing Claculate -> 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 lignad 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 applies the CVFF force field parametrization using the R6-R12 Lennard-Johnes' and the Coulomb's equations. Only the residues in which the energetic contribute is over the Trashold (%), are showed in the table and in the graphic main window.

Evaluation of the interactions

You can modify the visualization choosing the coloring method (Ligand by atom, By molecue and By residue) and which residues to show (Ligand, receptor Residues and Water molecules).

An output example is the following:

Interactions    Red = receptor residues

   Green = ligand

In the console you can find all numerical data:

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

Ligand name..........: DES_9999
Ligand atoms.........: 75
Dielectric constant..: 20.000

Total................:  -51.6411 Kcal/mol
Non-bond.............:  -34.3118 Kcal/mol
Coulombic............:  -17.3293 Kcal/mol


 Res    Num     R6-R12    Coulomb     Total      %
=====================================================
 LYS    110    -5.7706    -1.7536    -7.5243   14.57
 ZN     732    -0.2007    -6.6566    -6.8574   13.28
 HIS    542    -3.0452    -1.0418    -4.0870    7.91
 ARG    585    -0.9352    -2.8797    -3.8150    7.39
 LYS    588    -0.6616    -2.7608    -3.4224    6.63
 HIS    147    -3.0544    -0.0717    -3.1262    6.05
 TYR    655    -3.1364     0.0201    -3.1163    6.03
 TYR    594    -2.7546    -0.0895    -2.8441    5.51