OEPotentialTermsΒΆ

This namespace contains constants describing potential terms which might be calculated in different Szybki runs. Entries: OEPotentialTerms.VdW, OEPotentialTerms.Coulomb, OEPotentialTerms.Bond, OEPotentialTerms.Bend, OEPotentialTerms.StretchBend, OEPotentialTerms.Torsion and OEPotentialTerms.ImproperTorsion correspond to the total MMFF94 or Smirnoff potential terms. In the case of partial optimization of the protein, entries with a prefix Ligand refer to the force field terms of the ligand (for example OEPotentialTerms.LigandVdW), while entries with a prefix Protein (for example OEPotentialTerms.ProteinVdW) are for the MMFF94 or Smirnoff terms of the flexible part of the protein. Force field terms describing VdW and Coulomb interactions between the ligand and the flexible part of the protein are defined with the constants OEPotentialTerms.ProteinLigandVdW and OEPotentialTerms.ProteinLigandCoulomb respectively. Term OEPotentialTerms.ProteinLigandInteraction describes complete ligand-protein interaction according to the protein electrostatic model chosen. Values defined by OEPotentialTerms.SheffieldSolvation, OEPotentialTerms.PBSolvation and OEPotentialTerms.CavitySolvation refer to solvation energies used to optimize a ligand in solution, while the term OEPotentialTerms.HarmonicConstraint determines the he value of the imposed harmonic constraint. Entries: OEPotentialTerms.VdWProteinLigand, OEPotentialTerms.CoulombProteinLigand, OEPotentialTerms.ProteinDesolvation, OEPotentialTerms.LigandDesolvation, OEPotentialTerms.SolventScreening, OEPotentialTerms.GridCoulomb and OEPotentialTerms.ExactCoulomb are used to break down the total protein-ligand interaction energy into components. Value of the OEPotentialTerms.ProteinPseudoLigandInteraction represents the interaction of the flexible part of of the optimized protein-ligand system (ligand + flexible part of the protein) with the rest of the protein and as such is not an observable quantity. When Amber force field is applied for protein-ligand interaction, values of OEPotentialTerms.ProteinLigandAmberVdW and OEPotentialTerms.ProteinLigandAmberCoulomb are used for the corresponding vdW and Coulomb protein-ligand energies. Term OEPotentialTerms.TorsionHarmonicConstraint is the value of the constraint torsion harmonic potential. Two terms: OEPotentialTerms.IEFFInteraction and OEPotentialTerms.InterLigandIEFF are IEFF energies, total and interligand respectively. The latter has nonzero value when more than one ligand are present in the active site of the protein.

VdW

Value of vdW energy

Coulomb

Value of Coulomb energy

Bond

Value of bond stretch energy

Bend

Value of angle bend energy

StretchBend

Value of stretch-bend energy. This potential term appears only when MMFF force field is used

Torsion

Value of torsion energy

ImproperTorsion

Value of improper torsion energy

LigandVdW

Value of ligand vdW energy

LigandCoulomb

Value of ligand Coulomb energy

LigandBond

Value of ligand bond energy

LigandBend

Value of ligand angle bend energy

LigandStretchBend

Value of ligand stretch-bend energy. This potential term appears only when MMFF force field is used

LigandTorsion

Value of ligand torsion energy

LigandImproperTorsion

Value of ligand improper torsion energy

ProteinVdW

Value of protein vdW energy

ProteinCoulomb

Value of protein Coulomb energy

ProteinBond

Value of protein bond energy

ProteinBend

Value of protein angle bend energy

ProteinStretchBend

Value of protein stretch-bend energy. This potential term appears only when MMFF force field is used

ProteinTorsion

Value of protein torsion energy

ProteinImproperTorsion

Value of protein improper torsion energy

ProteinLigandVdW

Value of protein-ligand vdW energy

ProteinLigandCoulomb

Value of protein-ligand Coulomb energy

ProteinLigandInteraction

Value of total protein-ligand interaction

SheffieldSolvation

Value of Sheffield solvation energy

HarmonicConstraint

Value of atom harmonic constraint energy

PBSolvation

Value of PB solvation energy

CavitySolvation

Value of cavity solvation energy

VdWProteinLigand

Value of protein-ligand vdW interaction energy

CoulombProteinLigand

Value of protein-ligand Coulomb interaction energy

ProteinDesolvation

Value of protein desolvation energy

LigandDesolvation

Value of ligand desolvation energy

SolventScreening

Value of PB solvent screening energy

GridCoulomb

Value of protein-ligand Coulomb energy on grid

ExactCoulomb

Value of exact protein-ligand Coulomb energy

ProteinPseudoLigandInteraction

Value of ligand and flexible protein (pseudoligand) interaction with the rest of the protein energy

ProteinLigandAmberVdW

Value of Amber protein-ligand vdW energy

ProteinLigandAmberCoulomb

Value of Amber protein-ligand Coulomb energy

TorsionHarmonicConstraint

Value of torsion harmonic constraint energy

IEFFInteraction

Value of total IEFF intermolecular energy

InterLigandIEFF

Value of interligand IEFF energy

Max

Number of potential terms