Re: [Rdkit-discuss] Incorrect gold particle placement

[Jan Halborg Jensen]

One option is to use AllChem.MMFFOptimizeMolecule(mol3D, 
ignoreInterfragInteractions=False), but I am not sure MMFF can handle Au.

Another option is to define the Au-S bond ('C(C1C(C(C(C(O1)S[Au])O)O)O)O’) and 
use AllChem.UFFOptimizeMolecule(mol3D)

Best regards, Jan

On 1 Dec 2020, at 13.36, Anthony Nash 
<anthony.n...@ndcn.ox.ac.uk<mailto:anthony.n...@ndcn.ox.ac.uk>> wrote:


Dear all,

I'm new to RDKit and cheminformatics in general. I'm using the latest RDKit 
libraries. Any suggestions you can offer would be kindly received.

Using the canonical SMILES   C(C1C(C(C(C(O1)[S-])O)O)O)O.[Au+]   of 
Aurothioglucose  (Pubchem CID: 454937) I've generated a 3D structure using the 
python RDKit code:

mol = Chem.MolFromSmiles(self.canonicalSMILES)
mol3D = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol3D)
AllChem.MMFFOptimizeMolecule(mol3D)

Unfortunately, the mol3D representation has Au+ right in the middle of and in 
the plane of the benzene rings, too far from the negatively charged sulfur. I'm 
new at generating structures from SMILES. Are there any steps I'm missing that 
could help correct the placement of Au+?

Thanks
Anthony

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