Ligand Preparation Options Dialog Box

Ligand Preparation Options Dialog Box Features

• Generate possible states at target pH text boxes
• Using options
• Add Epik metal binding states option
• Obtain stereochemical information from options
• Unspecified stereocenters text box

Generate possible states at target pH text boxes

Generate ionization and tautomeric states that have significant probability in the given pH range. Enter the target pH and the range in the text boxes.

Using options

Select the program for generating states. Selecting Ionizer generates ionization states with the ionizer program, and tautomeric states with the tautomerizer program, separately. Selecting Epik generates ionization and tautomeric states with Epik at the same time.

Add Epik metal binding states option

Generate extra states that are suitable for binding to metals in proteins, using Epik. Only available when Epik is selected for state generation.

Obtain stereochemical information from options

These options allow you to specify the source of stereochemical information. If you have 3D structures, select 3D geometry to determine the stereochemistry from the geometry. Otherwise, select Specified 2D stereo properties, to use information from the stereochemical properties in the input file. Any stereochemical center whose chirality is not determined from this information will have its chirality varied.

Unspecified stereocenters text box

Enter the maximum number of stereoisomers to be retained by LigPrep in this text box. LigPrep generates up to 32 stereoisomers, which are then filtered to retain those with the lowest energies. Note that the LigPrep run preserves any existing chirality information in the input file, and selects starting chiralities based on the chemistry of naturally occurring steroids, fused rings and peptides.