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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