There are two levels of geometry optimisation in e-LBOW. The first is the quickest and uses a simple force field with equilibrium bond lengths taken from quantum chemical calculations (HF/6-31G).
To run elbow with a SMILES string (Getting a SMILES for your ligand):
elbow.builder --smiles "FOO"
or with an input file:
elbow.builder --file chemical_input_format_file.ext
The second optimisation takes more time but is chemically more accurate. A semi-empirical energy known as AM1 is used to optmise the molecular geometry.
To run elbow with [AM1]:
elbow.builder --smiles "FOO" --opt
Upon conclusion, there will be an elbow.LIG.pdb and elbow.LIG.cif file in the current directory.
For a more details to running e-LBOW and output files.
For a complete list of builder options (expert options here).