E-sol Calculations (Beta) Panel

Calculate the energy of solvation (E-sol) of one or more molecules with a quantum-mechanical workflow.

To open this panel, do one of the following:

  • Click the Tasks button and browse to ADME and Molecular Properties → E-sol (Beta)
  • Click the Tasks button and browse to Lead Optimization → ADME/Tox → E-sol (Beta)
  • Using
  • Features
  • Additional Resources

Using the E-sol Calculations (Beta) Panel

The E-sol Calculations panel runs a quantum-mechanical workflow that calculates the energy of solvation (E-sol) for one or more molecules. The workflow performs a conformational search, optimizes the conformer geometries, and computes single point energies, then derives the E-sol value from the hydration energy and a state penalty. For a description of the stages and the underlying method, see esol.py: Compute solvation energies with the E-sol Workflow.

To run a calculation:

  1. In the Input tab, choose the source of the molecules from the Use structures from option menu, then select the structures. The selected structures are listed in the table, each with a quality status.
  2. Structures flagged as poor quality by the data quality check are excluded from the job unless you select Allow poor quality inputs. To set the property thresholds used for the quality check, click the Define quality button.
  3. In the Configure tab, choose a combination of methods for the workflow stages from the Presets option menu, or choose Custom to set the stage options individually.

When the job finishes, the results are incorporated into the Project Table. To display a correlation plot of the predicted E-sol values against the experimental data, open the E-sol Viewer Panel, or use the Workflow Action Menu for the results entry group in the Project Table.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see esol.py Command Help. See also esol.py: Compute solvation energies with the E-sol Workflow.

E-sol Calculations (Beta) Panel Features

Input tab

Select the structures for the calculation and control data quality filtering.

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select the entries for the structure source.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Structures table

Lists the structures selected for the calculation. The columns are ID (the entry ID), In (Workspace inclusion), Entry Title, and Quality (the quality status from the data quality check). Click a column heading to sort the table by that column.

Allow poor quality inputs option

Select this option to include structures flagged as poor quality by the data quality check. When this option is not selected, flagged structures are excluded from the job.

Define quality button

Click to open the E-sol Data Quality dialog box, where you set thresholds on structure properties (Solubility, Recovery, and Brain/Plasma Tissue Binding) that are used to flag poor quality input structures. Click Analyze in the dialog box to evaluate the structures against the thresholds and update the Quality column.

Configure tab

Set the methods and parameters for the stages of the E-sol workflow. Choose a combination of predefined stage settings from the Presets option menu, or choose Custom to set the options individually. The fields on this tab are read-only and display the values of the selected preset unless Custom is selected for Presets.

When Custom is selected, not all combinations of theory, basis set, and solvent model are valid. The combination is checked when you run the job, and an error is reported if it is not compatible.

Presets option menu

Choose a predefined group of stage settings:

  • MLFF Optimization—machine-learned force field for the geometry optimization stage and DFT for the single point energy stage (the default).
  • Full MLFF—machine-learned force field for both the geometry optimization and single point energy stages.
  • Full DFT—DFT for both the geometry optimization and single point energy stages.
  • Custom—makes the fields below editable so that you can set each option individually.
Gas Phase Conformational Search section

Settings for the conformational search stage.

Method option menu

Choose the program used for the conformational search.

MLFF filter option

Select this option to filter conformers with a machine-learned force field before the QM stages. Selecting it enables the Filter factor text box.

Solution phase also option

Select this option to perform the conformational search in solution phase in addition to gas phase.

Num kept conformers text box

Specify the number of conformers to keep from the conformational search.

Filter factor text box

Specify the factor by which the conformer energy window is scaled before the MLFF filter is applied. A larger value keeps more conformers for filtering. The default is 1.67. Only available when MLFF filter is selected.

Geometry Optimization section

Settings for the QM geometry optimization stage.

Theory text box and button

Click the button to select the level of theory. A small pane opens with controls for selecting the level of theory. The pane consists of a search text box, a filter button, and a list of available theoretical models. Typing in the text box narrows the list to items that contain the text. Clicking the filter button allows you to set options to restrict the list to certain models, e.g. range-corrected DFT. When you choose an item from the list, the pane closes and the text box (which is noneditable) shows the level of theory you chose.

See DFT Keywords in the Jaguar Input File for information on the density functionals.

Solvent model text box and button

Click the button to select the solvation model applied during the geometry optimization. The available models depend on the selected theory.

Basis set text box and button

Click the button to select the basis set. A small pane opens with controls for selecting the basis set. The pane consists of a search text box, a filter button, and a list of basis sets. Typing in the text box narrows the list to basis set names that contain the text. Clicking the filter button allows you to set options to restrict the list to basis sets with certain features: ECP, diffuse functions, pseudospectral, relativistic, RI-MP2 compatible. When you choose a basis set from the list, the pane closes and the text box (which is noneditable) shows the basis set you chose.

The Basis set controls are not available for approaches that do not use a basis set, such as MLFF, xTB, and 3c methods.

See Basis Sets for information on the basis sets available.

Num kept conformers text box

Specify the number of optimized conformers to use in the single point energy stage.

Single Point Energy section

Settings for the QM single point energy stage.

Theory text box and button

Click the button to select the level of theory. A small pane opens with controls for selecting the level of theory. The pane consists of a search text box, a filter button, and a list of available theoretical models. Typing in the text box narrows the list to items that contain the text. Clicking the filter button allows you to set options to restrict the list to certain models, e.g. range-corrected DFT. When you choose an item from the list, the pane closes and the text box (which is noneditable) shows the level of theory you chose.

See DFT Keywords in the Jaguar Input File for information on the density functionals.

Solvent model text box and button

Click the button to select the solvation model applied during the single point energy calculation. The available models depend on the selected theory.

Basis set text box and button

Click the button to select the basis set. A small pane opens with controls for selecting the basis set. The pane consists of a search text box, a filter button, and a list of basis sets. Typing in the text box narrows the list to basis set names that contain the text. Clicking the filter button allows you to set options to restrict the list to basis sets with certain features: ECP, diffuse functions, pseudospectral, relativistic, RI-MP2 compatible. When you choose a basis set from the list, the pane closes and the text box (which is noneditable) shows the basis set you chose.

The Basis set controls are not available for approaches that do not use a basis set, such as MLFF, xTB, and 3c methods.

See Basis Sets for information on the basis sets available.

Extra keywords text box

Specify additional E-sol keywords as key=value pairs, separated by spaces. The keywords are validated when you run the job. For the available keywords, see esol.py: Compute solvation energies with the E-sol Workflow. Only present when Custom is selected for Presets.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the E-sol Calculations - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Tutorials

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