Using crystal structure as template for 3D coordinates for new molecules


I am working on the enumeration of spiracetals and I would like to use them in “in silico” screening.
My issue is that, I have a crystal structure of my spiroacetal core molecule and it is clear that the compound is in its double anomeric form. However, the 3D conformers that I can get with the RDKit Optimize Geometry node are not always in the double anomeric form.
So my question is whether it is possible to import my crystal structure and use it as a template during conformer optimisation?
Or do you have any advice how can I possibly overcome this issue?

Thank you very much.
Best wishes,

Welcome to the forum @Trabirider .

My first instinct here is to use some other software to extract the molecule in the binding conformation (PyMOL, Discovery Studio, VMD, Avogadro, etc) and save it as a mol or sd file. I’d then try using this as a template in the Templated Conformer Generation (RDKit) node for aligning the generated conformations see what results.

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Thank you very much for the answer.
That node was quite useful. I still have to understand it a bit more, so I can fit my compounds on it more strictly, but it was a good start.

Thanks :slight_smile:

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