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.