If you have a new substrate that never been crystalized before, how would you create a corresponding cif file to refine it? One way was to use eLBOW from Phenix package by using the SMILES string but I'm concerned that the output file is not 100% identical to the molecule and I'm not sure whether it has all the necessary restraints or not. What is your way of generating the cif file for substrate bound structure refinement?
Thank you in advance for your help!