PubChem is unable to generate the conformers of Z-6-Heneicosen-11-one? The website says that the molecule is too flexible

What does flexibility of a molecule mean in this context? I understand that it is a long chain compound, but I assumed that the bonds are rigid and do not flex? In layman’s terms, how does one quantify flexibility? Is it flexible like a skipping rope or like something else?

  • 1
    $\begingroup$ The bonds are rigid, but the torsion angles aren't. $\endgroup$ Jan 14, 2020 at 5:20
  • $\begingroup$ Related: chemistry.stackexchange.com/q/125574/5017 $\endgroup$ Jan 14, 2020 at 5:32
  • $\begingroup$ Rather than to flexible it want to say too much atoms /bonds $\endgroup$
    – Alchimista
    Jan 14, 2020 at 7:58
  • $\begingroup$ @Alchimista - it's not that it has too many atoms or bonds. A rigid molecule with the same number of atoms will appear (e.g, cholesterol is okay). $\endgroup$ Jan 14, 2020 at 14:19

1 Answer 1


PubChem 3D has limits on the number of 'rotatable bonds'

I recently answered a related question about PubChem 3D:

Beyond the limits of MMFF94 and MMFF94s themselves, PubChem3D had several limits indicated in the accompanying manuscript: Bolton et. al. "PubChem3D: a new resource for scientists" J Cheminf. (2011) v. 3, art. 32)

  • Not too large (with ≤ 50 non-hydrogen atoms).
  • Not too flexible (with ≤ 15 rotatable bonds).
  • Consists of only supported elements (H, C, N, O, F, Si, P, S, Cl, Br, and I).
  • Has only a single covalent unit (i.e., not a salt or a mixture).
  • Contains only atom types recognized by the MMFF94s force field.
  • Has fewer than six undefined atom or bond stereo centers.

Your molecule falls into the "more than 15 rotatable bonds" category. I count about 18 $\ce{sp^3}-\ce{sp^3}$ single bonds.

Basically, the problem is that the search space for conformers with that many rotatable bonds is too big. In principal, it's $\approx3^n$ where $n$ is the number of rotatable bonds.


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