ADL: Can oxygen or other diatomic molecule used for molecular docking?

Van Dam, Hubertus hvandam at
Mon Dec 21 08:39:34 PST 2020

Hi Aziana,

The shape of all diatomic molecules is essentially the same. The charge distribution will differ a bit depending on the electronegativities of the elements involved (basically excluding all homonuclear diatomics as the charges will be zero). However, there are only going to be few diatomics that come into consideration a drug molecules (and some obvious ones are well known to be extremely toxic such as CN and CO). So diatomics are not going to be selective in their binding due to shape, only heteronuclear diatomics will have some electrostatic interactions, and then they might still be toxic or salts or acids (think HF, HCl, etc.). After all that there is not much left. But this is just my guess.

Best wishes,


Hubertus van Dam, 631-344-6020, hvandam at
Brookhaven National Laboratory

On 12/20/20, 09:39, "autodock-bounces at on behalf of Aziana Azral" <autodock-bounces at on behalf of aziana.azral at> wrote:

    Can anyone explain why does molecular docking of oxygen or other diatomic
    atom is not suitable?
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