Re: [Rdkit-discuss] Incorrect gold particle placement
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
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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Re: [Rdkit-discuss] Incorrect gold particle placement
Dear Anthony, >From MMFF or UFF you shouldn’t expect reasonable structures of metal-containing compounds. If you need a quick and qualitatively OK method, I recommend xtb. Best wishes, Michal Krompiec, Merck KGaA On Tue, Dec 1, 2020 at 1:09 PM Anthony Nash 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 > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Incorrect gold particle placement
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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
