Ligand R-group Rotation Panel

Rotate a specified R group by a specified angle in a set of related ligands.

To open this panel: click the Tasks button and browse to Ligand Preparation and Library Design → Ligand R-Group Rotation.

  • Using
  • Features
  • Additional Resources

Using the Ligand R-group Rotation Panel

This panel is primarily intended for preparing a set of ligands with a common core or a common set of R groups for use with FEP+. Ideally the ligands have been generated by R-group enumeration or by core hopping. You can specify whether the ligands have a common core or a common set of R groups. In either case, the R group is rotated with respect to the core. If the core is common, the R group can be different for each ligand; if the R group is common, the core can be different for each ligand.

Rotations at a given angle increment are generated, up to 360°. The resultant structures are written to a Maestro file, which is incorporated into the project when the job finishes.

Ligand R-group Rotation Panel Features

Select ligands 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.
Load button

Load the structures from the Project Table or Workspace into the panel.

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.

Select enumeration options

Select the type of enumeration used for the input structures, from R-group, where the R group is varied on a common core, or Corehop, where the core is varied for a set of common R groups. This option determines the function of the following text box.

If the input did not come from an enumeration, use this option to decide how to define the R group to be rotated as if the input did come from an enumeration.

Fixed common core text box and Load from Selection button

Enter the SMARTS pattern for the fixed common core in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Load from Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace.

If the ligands have a common core, the R group can be different for each ligand.

R-group to rotate text box and Load from Selection button

Enter the SMARTS pattern for the R group to rotate in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Load from Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace.

If the R group is common between the ligands, the core can be different for each ligand.

Pick bond for rotation text box and Pick option

Enter the SMARTS pattern that identifies the bond to rotate in this text box, or check the Pick option and pick the bond in the Workspace. The bond must be connected to the common core or R-group that you specified. If you specify the SMARTS pattern, it must be a copy of the one entered above with the addition of one extra atom. This atom must be bonded to just one other atom in the SMARTS pattern; this atom and the one it is bonded to define the bond to rotate.

Angle of rotation text box

Specify the angle increment by which the R group is rotated, in degrees. One structure is produced for each increment, up to 360°. The default is 180°, which for a ring structure would correspond to a flip.

Job toolbar

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

The Job Settings button opens the Ligand R-group Rotation - 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.

Reset button

Reset the panel to its default settings.

Related Topics