A chemical table or an .sdf file can be converted to 3D and sampled using the conformational generator with the _confGen script provided with the ICM distribution.

Syntax:

icm _confGen input.sdf output.sdf [options]

Options:

• auto=(0) : number of rotatable bonds to auto switch between systematic and MC. 0:always MC
• effort=(1.) : the relative mc sampling effort. Increase to 3. or 10. for more rigorous sampling
• maxenergy=(10.) : skip conformations with higher than 10. kcal/mole energies from the base
• mnconf=(50) : the maximal number of conformers per compound
• sizelimit=(80) : do not sample bigger molecules than atoms
• vicinity=(30) : [deg] the torsion root-mean-square deviation threshold for cluster size.
• -b : same as -c (see below) but without bond lengths (only angles and torsions)
• -c : improve geometries and energies with Cartesian MMFF minimization
• -d : sample cis/trans for Double bonds (not needed 'as drawn' is OK)
• -e : only evaluate conformational Entropy for compound (no poses)
• -f : Force-overwrite of the output file
• -h : Help
• -q : Quiet (suppress warnings)
• -p : optimize pyramidal molecular geometry (set automatically by -S or -e options)
• -r : sample flexible Ring systems
• -s : use Systematic search instead of MC
• -v : verbose
• -A : use AI-assisted sampling instead of torsion stochastic sampling
• -C : set formal charges according to pKa model. Use if you do not trust the charge defined by the chemical structure as drawn.
• -H : sample polar hydrogens
• -I : force update of the Input data file index
• -S : evaluate Strain of this particular conformation from 3D mol file (implies -keep3D)
• -V : shows script commands
• -fr=.. -to=.. from and to indexes of the database to be screened.
• -hydrogen : keep hydrogens in the result table
• -keep3D : keep conformation from a 3D mol file
• -molcart=connect_string : host,user,pass,database
• -proc= : start n parallel threads

Example:

 icm64 _confGen input.sdf output.sdf effort=5. -A -H -r -C -c -f