FreeForm - Bound 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


FreeForm - Bound Ligand Configurational Free Energies with SZYBKI evaluates the free energy associated with selecting a particular conformer (or a set of conformers) out of the whole conformational ensemble in solution, as well as the additional energy required to restrain to the particular conformation in the bound state.

The minimal input into FreeForm Restriction Energies is a dataset of molecules in 3D format.

Output from the FreeForm Restriction Energies floe consists of two datasets. The first results dataset mimics that of the FreeForm Conformer Energies containing a conformational ensemble per input molecule, along with the associated free energies, and the probability of states for each conformer. The second dataset provides information regarding the total and global restriction energies associated with each input 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]

None (in_mol_field): Input ensemble conformer field

  • Type: field_parameter::mol

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’]