OEPotentialTermsΒΆ

This namespace contains constants describing potential terms which might be calculated in different Szybki runs. Entries: OEPotentialTerms.MMFFVdW, OEPotentialTerms.MMFFCoulomb, OEPotentialTerms.MMFFBond, OEPotentialTerms.MMFFBend, OEPotentialTerms.MMFFStretchBend, OEPotentialTerms.MMFFTorsion and OEPotentialTerms.MMFFImproperTorsion correspond to the total MMFF94 potential terms. In the case of partial optimization of the protein, entries with a prefix Ligand refer to the MMFF terms of the ligand (for example OEPotentialTerms.LigandMMFFVdW), while entries with a prefix Protein (for example OEPotentialTerms.ProteinMMFFVdW) are for the MMFF94 terms of the flexible part of the protein. MMFF94 terms describing VdW and Coulomb interactions between the ligand and the flexible part of the protein are defined with the constants OEPotentialTerms.ProteinLigandMMFFVdW and OEPotentialTerms.ProteinLigandMMFFCoulomb 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.

MMFFVdW

Value of MMFF vdW energy

MMFFCoulomb

Value of MMFF Coulomb energy

MMFFBond

Value of MMFF bond stretch energy

MMFFBend

Value of MMFF angle bend energy

MMFFStretchBend

Value of MMFF stretch-bend energy

MMFFTorsion

Value of MMFF torsion energy

MMFFImproperTorsion

Value of MMFF improper torsion energy

LigandMMFFVdW

Value of MMFF ligand vdW energy

LigandMMFFCoulomb

Value of MMFF ligand Coulomb energy

LigandMMFFBond

Value of MMFF ligand bond energy

LigandMMFFBend

Value of MMFF ligand angle bend energy

LigandMMFFStretchBend

Value of MMFF ligand stretch-bend energy

LigandMMFFTorsion

Value of MMFF ligand torsion energy

LigandMMFFImproperTorsion

Value of MMFF ligand improper torsion energy

ProteinMMFFVdW

Value of MMFF protein vdW energy

ProteinMMFFCoulomb

Value of MMFF protein Coulomb energy

ProteinMMFFBond

Value of MMFF protein bond energy

ProteinMMFFBend

Value of MMFF protein angle bend energy

ProteinMMFFStretchBend

Value of MMFF protein stretch-bend energy

ProteinMMFFTorsion

Value of MMFF protein torsion energy

ProteinMMFFImproperTorsion

Value of MMFF protein improper torsion energy

ProteinLigandMMFFVdW

Value of MMFF protein-ligand vdW energy

ProteinLigandMMFFCoulomb

Value of MMFF 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