Looks like we have a bad set of SMILES. This is a useful sanity check.
Thanks Paolo.
On Fri, Jul 1, 2016 at 6:40 PM, Paolo Tosco <[email protected]> wrote:
> Dear Richard,
>
> the reason why that SMILES fails to generate 3D conformations is that the
> stereochemistry on the bridged ring system cannot be satisfied, as the
> bridge would have to cross the ring, which is not possible. The
> stereocentres on the bridgehead carbons cannot be both R, as required by
> the SMILES string. Epimerizing either allows the molecule to yield 3D
> conformations without problems:
>
> http://nbviewer.jupyter.org/gist/ptosco/cd175166d2a44e223d4e559a2f310287
>
> Cheers,
> p.
>
>
> On 07/01/16 16:25, Richard Cooper wrote:
>
> Hi RDKitters,
>
> Asking for a friend.
>
> The example below using the given molecule and EmbedMultipleConfs returns
> an empty list without throwing anything or producing any warnings. I've got
> quite a few smiles that fail in the same manner, but can't see any obvious
> pattern. It might be related to chirality.
>
> Cheers, Richard
>
>
>
> from rdkit.Chem import AllChem
> from rdkit import Chem, rdBase
>
> print rdBase.rdkitVersion
>
> m = Chem.MolFromSmiles('CN1C(=O)[C@H]2[C@H](C1=O)[C@@]1(C)CC[C@H]2O1')
> m = AllChem.AddHs(m)
> print Chem.MolToSmiles(m, isomericSmiles=True)
>
> ids = AllChem.EmbedMultipleConfs(m, 5)
> print list(ids)
>
>
> Output:
> 2016.03.1
> [H]C([H])([H])N1C(=O)[C@@]2([H])[C@]([H])(C1=O)[C@]1(C([H])([H])[H])O[C@
> ]2([H])C([H])([H])C1([H])[H]
> []
>
>
>
>
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