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

Here we have to specify the metalic centers --metal_atoms "['Pd']" as well as their oxidation state --metal_oxi "[2]".

We can also specify the multiplicity --mult 1

We also need to specify which template geometry to use for the complex --complex_type squareplanar

We specify the output directory where the sdf with conformations will be generated --destination Pd_sdf_files and the base name of the file --name Pd_complex

We provide the smiles string of the molecule --smi "I[Pd]([PH3+])(F)Cl"

And we need to specify that we will be using the CSEARCH module with rdkit to generate the conformers --csearch --program rdkit

The full command that we will execute will look as follows:

python -m aqme --csearch --smi "I[Pd]([PH3+])(F)Cl" --destination Pd_sdf_files --name Pd_complex --program rdkit --metal_atoms "['Pd']" --metal_oxi "[2]" --mult 1 --complex_type squareplanar