Noncovalent bimolecular complex generated from SMILES

In the following example we will generate conformers of the isopentane-water complex using CREST

SMILES

CCC(C)C.O

nocov_bimol_chemdraw

nocov_bimol_3D

We start by importing the packages

from pathlib import Path
from aqme.csearch import csearch

Compared with the organic molecule example this time we are going to use the default location for the output file. As a consequence we can now proceed to run the conformer search from the smiles string:

smiles = 'CCC(C)C.O'
csearch(smi=smiles,
        name='isopent-water-complex',
        program='crest',
        nprocs=12,
        crest_keywords='--nci',     # indicate that it is a non-covalent complex
        cregen=True,                # Include CREGEN post-analysis
        cregen_keywords='--ewin 3') # energy window for CREGEN == 3.0 kcal/mol