I previously blogged about the fact that we had embedded a 3D optimizer under Jmol so that that 3D molecules could be displayed. There were two problems with the approach we took. 1) It was very time-consuming to wait for real-time 3D optimization for molecules 2) The 3D optimizer would sometimes fail to optimize a structure based on the starting geometry.


We have just finished publishing millions of pre-optimized structures onto the  ChemSpider database. In MOST, but not all, cases the molecules are now pre-optimized. This makes display of the 3D molecule in JMol much faster. Since we were optimizing  millions of molecules we did set a threshold for the time within which the molecule should reach some minimum. As a result some molecules were not optimized and the 3D coordinates are still not available so a real time optimization is attempted using smi23d as discussed previously. If you find any structures which don’t optimize please send us the ChemSpiderID and comment to feedback|at|chemspider|DOT|com.

Stumble it!

2 Responses to “Millions of Pre-optimized 3D Structures now Deposited on ChemSpider”

  1. Rich Apodaca says:

    Antony, nice work. How could I access the raw 3D coordinates (just text file – no viewer) through a ChemSpider URL?

    For example, the CSID for benzene is 236. I can see its compound summary sheet at:


    What would be the URL to view:

    (1) the 2D molfile
    (2) the 3D molfile

    Also – any plans to deposit these 3D coordinates into PubChem (via molfile)?

    Not sure if it’s possible – just asking.

  2. Antony Williams says:

    There’s no way to drop the 3D coordinates at present. They only just got deposited and we just haven’t done the work to expose them.

    No plans to deposit the 3D coordinates into PubChem at present. They’d only need them if they were going to use them and I am not aware of any projects where they want the 3D coordinates. I can check in with them and find out.

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