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I'm doing docking studies. Upon preparing my ligands, I've conducted conformational analysis to them using RDKit and plot their respective potential energies. I'm just confuse why my thesis advisers told me to pick the high energy conformer to dock to my protein. It has nothing to do with my molecular systems, etc. They said that high potential energy conformer is the most stable conformer.

This is the energy diagram and the structure of the conformer with the highest potential energy. enter image description here Highest Potential Energy Conformer

I've read and read a lot of related literatures and clearly they are stating that the low potential energy conformer is more stable. Why does my adviser told me that "High energy conformer is the most stable"

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    $\begingroup$ I can think of reasons you might want to look into high energy conformations, but that does not answer your question, "Is there any theories or concepts i don't know?" which is impossible to answer, and the more particular question of what your advisors might be thinking, not knowing who they are or a fly in the room in which discussions were held. Maybe you misunderstood? What keeps you from asking them this question? $\endgroup$
    – Buck Thorn ♦
    Commented May 22 at 11:10
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    $\begingroup$ Caryophyllene seems to have been studied extensively. I recommend looking at existing publications of docking studies or simulations. Without some edits this seems otherwise more of a question for academia SE and not for this website. Please see the help pages on what makes a question appropriate for this site. $\endgroup$
    – Buck Thorn ♦
    Commented May 22 at 11:10
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    $\begingroup$ @BuckThorn I keep asking them this question, but they just stating that that is the standard procedure. I know and read some reasons for high energy conformations, but that just doesn't justify what my adviser told me that "high energy conformer is more stable" $\endgroup$
    – Carbon Nanotubes
    Commented May 22 at 11:56
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    $\begingroup$ Well a possible explanation is that the lowest E conformation when docked is not the one you obtain for the free molecule. Still, I recommend you rewrite your question. . $\endgroup$
    – Buck Thorn ♦
    Commented May 22 at 14:15
  • $\begingroup$ In addition to Buck Thorn's comment (lowest energy conformer of an isolated ligand needn't be the one found docking to the host), docking usually leads to a minimum of the sum of the energies of ligand and host. $\endgroup$
    – Buttonwood
    Commented May 22 at 14:29

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