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I am currently working with a molecular docking project, examining potential affinities of a solvent on a protein in an assay to evaluate potential error margin. The solvent is cyclohexanol (referred to as 'ligand'), and I am trying hard to wrap my head around the solution. I have a rotatable bond at the OH group, and this is quite easy to resolve by just rotating it around and trying to fit (most software does it for you, but it can be even calculated by hand, corresponds to left and middle pic). However, cyclohexanol can (theoretically) find itself in two conformations ('chair', 'boat', with latter being much less stable) within its structure (pic at the bottom for those unfamiliar). While one of them is higher energy and therefore not found as commonly in a regular situation, for all what we know, it may have much higher affinity and stability when confronted with aminoacids in the binding site, and therefore it would maybe be unreasonable to consider only the 'easiest' state should I wish to characterise potential energies of whole ligand-protein system. I did not manage to find as of now a way to model such transitions in the context of molecular docking, and I am wondering: should I just fit twice to 'protein 1', considering cyclohexanol-chair as 'ligand 1' and cyclohexanol-boat' as 'ligand 2', or is there a method used in computational chemistry I haven't thought of/managed to find? Or should I just discard the option of a much less energetically favourable 'boat' (third in the picture) ?

Three different energy binding states; two covered by rotatable bond, third not covered

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    $\begingroup$ It sounds like you'd like to see "the smoking gun", that is, see a conformational change under the influence of the interaction with the protein. But this is quite unnecessary. Just run docking with the two different conformers and compare the energies you obtain to those of the "ligands" in the absence of protein. $\endgroup$ – Buck Thorn May 11 at 21:27
  • $\begingroup$ It depends on how much higher in energy the 'unfavorable' conformer is (e.g., 30 kcal/mol can safely be discarded) .. or you can run some dynamics with multiple conformers. As @BuckThorn mentions, it's generally considered okay to dock with multiple conformers - often 'geometrically diverse' to examine a range of possibilities. $\endgroup$ – Geoff Hutchison May 12 at 12:51

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