Metal complex from SMILES input

In the following example we will generate various conformers of a Pd complex using RDKit using a template for square planar complexes.

SMILES

I[Pd]([PH3+])(F)Cl

metal_comp_chemdraw

metal_comp_3D

As with the other examples, we start by importing the necesary packages

from pathlib import Path
from aqme.csearch import csearch

Next we specify the output directory where the sdf with conformations will be generated

w_dir_main = Path.cwd()
sdf_path = w_dir_main/'Pd_sdf_files'

Finally we proceed to the conformational search using the smiles string of the molecule.

smiles = 'I[Pd]([PH3+])(F)Cl'
csearch(destination=sdf_path,
        smi=smiles,
        name='Pd_complex',
        program='rdkit',
        metal_atoms=['Pd',],         # Symbol of transition metal atoms included
        metal_oxi=[2,],              # Oxidation number per metal_atom
        mult=1,                      # multiplicity
        complex_type='squareplanar') # Template geometry to use