Custom R-Group Enumeration Panel

Add custom or standard fragment collections to selected positions on a core-containing structure, and enumerate the structures resulting from all possible chemically distinct combinations of fragments at each position.

To open this panel, click Create Enumerated Entries in the 3D Builder panel, after selecting attachment atoms, or click the Tasks button and browse to Enumeration and Ideation → R-Group Enumeration.

  • Using
  • Features
  • Additional Resources

Using the Custom R-Group Enumeration Panel

To use this panel:

  1. Display the desired core-containing molecule in the Workspace.

    You should make sure that there is only one molecule in the Workspace.

  2. Pick the attachment atoms on the core-containing molecule.

    Each of these atoms is substituted when the job is run. If the atom is not a terminal atom, the smallest fragment is considered to be the R group, and is replaced from the fragment collection in the enumeration.

    If you want to change the attachment atoms, you can do so by adding or removing atoms from the Workspace selection, then clicking Update from Selection in this panel. If you remove atoms from the selection, the corresponding R groups are also removed.

  3. Open the panel.

    R groups are assigned to each attachment atom, and labeled in the Workspace.

  4. For each R group, choose a fragment collection from the list in the R-Group Library column.

    If you choose File, a file selector opens, so you can navigate to the desired R-group structure file, which must be a Maestro file ( .mae, .mae.gz, .maegz). You can create fragment collections with the R-Group Creator Panel.

  5. Enter a job name and click Run to run the job, or click the Settings button to make job settings and then run the job.

    The job can take some time, so you might want to distribute it over multiple processors. The result is the set of structures in which all possible combinations of fragments are added, with no chemically identical duplicates.

To perform homo-substitution, i.e. the same R group at each attachment position, you can set the R group for each position to R1. As each fragment is selected from the library, it is added at all attachment positions, by default. You can perform different homo-substitutions in different sets of attachment positions, by setting the R group to R1 for one set, to R2 for the next set, and so on.

If you want to perform homo-substitution at some but not all of the attachment positions in a set, select Allow partial substitution. A column labeled % Positions Substituted is displayed in the table, and you can choose the percentage of positions to substitute from the menu in the table column for the first of the positions in the set. The percentage is copied to the row for the other positions in the set. All combinations of positions within each set are enumerated: so for example if you have 3 positions for R1 and you choose 67% of positions, the substitution is done at positions 1 and 2 to produce one molecule, at positions 1 and 3 to produce another, and at positions 2 and 3 to produce a third.

Custom R-Group Enumeration Panel Features

Define R-groups table

This table lists the positions on the Workspace structure, the R-group to be attached to that position, and the fragment collection for the R group. The table can be used to assign the R groups to positions and to associate fragment collections with R groups. Each row corresponds to an attachment position; the maximum number of positions is 10.

Position The index of the position on the molecule in the Workspace. This is just a numerical index: it does not have to match the R-group number, though the initial R-group number matches the position number.
R-Group The label for the R group. Click the arrow to change the R group assigned to the given position. The fragment collection column is updated when you change the R group to show the collection assigned to the selected R group. You can assign the same R group at more than one position, and the same library is used at each such position, and the same fragment is attached at each such position (homo-substitution).
R-Group Library The name of the R-group library, which is a description if the library is one of the standard libraries, and the file name if the library is a custom library, produced in the R-Group Creator Panel. Click the arrow to assign a collection from a list of available collections. If you click File, a file selector opens, so you can navigate to the desired R-group file, which must be a Maestro file ( .mae, .mae.gz, .maegz) and contain an R-group library.
# Positions Substituted If partial substitution is allowed, this column specifies the number of positions with the same R group that are substituted in the enumeration. The first position with a common R group has an arrow, to indicate that there is a menu from which you can choose the number out of the total. This column is only present if you select Allow partial substitution and choose per R group. A Maestro property is added for each R group recording the percentage corresponding to these numbers, named occupation Rn.
Library Size

The number shown represents the maximum size of the library to be output. The actual number of structures that are generated will depend on whether partial substitution is being used and what kinds of Output Filters have been defined. Redundant conformers are eliminated.

Enantiomers are considered distinct and are maintained in the output list. If you do not want to include both enantimers in the output list, you can choose that in the R-Group Filter Dialog Box.

Note: Enantimers are considered distinct and are maintained in the output list.

Update from Selection button

Update the table from the selected atoms in the Workspace. If you change the atom selection, positions are added to or removed from the table.

The maximum size of the library is shown below the table.

Allow partial substitution option and menu

Allow substitution on less than the total number of positions. The menu allows you to choose how the partial substitution is performed.

  • across all positions—select the number of positions to substitute from the total number of positions. When this option is chosen, the Use M of N text box is displayed, to choose the number of positions M to substitute.

  • per R group—select the number of positions to substitute when multiple positions have the same R group. The substitution is done within each such set of positions. Selecting this option adds a column to the table, labeled # Positions Substituted. In this column you can specify the number of positions with the same R group to substitute in the enumeration. All possible combinations of positions are enumerated. This option is only available when you assign the same R group to more than one position.

Output Filters button

Set options for filtering the generated structures based on properties that are calculated for these structures. Opens the R-Group Filter Dialog Box.

Job toolbar

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

The Job Settings button opens the Custom R-Group Enumeration - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes 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.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Tutorials

Related Topics