The Set Charges option calculates quantum-derived atomic partial charges and assigns them to the molecule in ICM. It uses the existing molecular conformation without minimizing or changing its geometry.

Charges are calculated using the RESP (Restrained Electrostatic Potential) method, which fits atomic partial charges to the quantum-mechanical electrostatic potential. The default calculation level is HF/6-31G*, the conventional level used for RESP charge calculations.

To assign charges:

1. Read a chemical structure into ICM and convert it to a 3D ICM object.
2. Check that hydrogen atoms are present and the atomic formal charges are correct.
3. Select MolMechanics/Quantum Mechanics/Set Charges.

The fitted values are assigned as the molecule's atomic partial charges. Chemically equivalent atoms, such as the three hydrogen atoms of a methyl group, are constrained to receive identical charges.

Further information: set charge quantum and PsiRESP documentation.