FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/SZYBKI

  • Solution-based/Small Molecule Lead-opt/Ligand Entropy

  • Role-based/Computational Chemist

  • Task-based/Ligand Posing & Analysis

Description

FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI is a tool for evaluating the conformer free energy of compounds in solution. The conformer free energy is the free energy required to select a particular conformer out of the whole conformational ensemble in solution.

The minimal input into FreeForm Conformer Energies is a dataset of molecules in 1D (SMILES), 2D (SD, mol2), or 3D format.

Output from the FreeForm Conformer Energies floe is a conformational ensemble per input molecule, along with the associated free energies, and the probability of states for each conformer. The unit of free energy is kcal/mol.

Promoted Parameters

Title in user interface (promoted name)

FreeForm settings

Use input ensemble (use_inp_ens): Flag to use input ensemble conformers. Setting this to true would bypass any new conformer generation.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Include input conformer (include_input): Flag to include the input conformers in ensemble. Setting this to true would add the input conformers to the internally generated conformers.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Force Field (ff_type): Built-in force field model to be used.

  • Type: string

  • Default: sage_openff200

  • Choices: [‘mmff94s’, ‘smirnoff99frost’, ‘parsley_openff100’, ‘parsley_openff111’, ‘parsley_openff121’, ‘parsley_openff131’, ‘sage_openff200’]

Custom FF File (ff): Custom smirnoff force field file. Entry in this field overrides any other force field selections

  • Type: file_in

Ionic state (ionic_state): Ionic state of molecules to be used

  • Type: string

  • Default: ph74

  • Choices: [‘ph74’, ‘uncharged’, ‘input’]