Does there exist any data repository of chemical compound that gives the structure of the compounds with the help of coordinate geometry. It would be like each atom has a coordinate and the list of bonds it has with other atoms so that the 3D structure of the compound can be created from this very theoretical description?
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$\begingroup$ I'd keep in mind that the 2D line drawings that we draw for molecules are the "theoretical" models; describing a molecule with just atom coordinates is way more grounded in physical reality. $\endgroup$– Curt F.Jul 23, 2015 at 16:37
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1$\begingroup$ @CurtF. Except that an organic molecule may exist in a wide variety of conformations, and the preferred conformation may depend on the solvent, so a huge variety of different datasets may be necessary for a single substance. A 2D line drawing with bond lengths and angles, plus a bit of knowledge of polarity and hydrogen bonding will help to decide if the model is reasonable. For example, one of the first proposed helical models for DNA had the phosphate groups on the inside. It was later realised that in aqueous solution the phosphate groups would have to be on the outside. $\endgroup$– Level River StJul 23, 2015 at 16:58
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$\begingroup$ Very true Steve. I was thinking of atom coordinates derived from things like x-ray crystallography, more or less experimentally measured atom coordinates. But in the case where those measurements aren't available then everything you say is right on the money. $\endgroup$– Curt F.Jul 23, 2015 at 17:08
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2 Answers
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I'm not entirely clear on what you want - I guess a database of a bunch of 3D coordinates for many organic compounds?
By far the largest such database is NIH PubChem with over 30 million compounds - mostly organic. You can search by structure or name or identifier. Most of these have 2D and 3D geometries you can visualize or download and many computed properties.
A similar database is the RSC ChemSpider with over 34 million compounds. Much like PubChem, names, 2D and 3D geometries and other properties are available.
I'll put in a plug for the Pitt Quantum Repository which contains ~64,000 molecules and growing, all with geometries computed using quantum chemical methods. One benefit of PQR is that you can easily access the site using smartphones and tablets and use a QR code or DOI to link to the compound.
answered Jul 23, 2015 at 15:20
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1$\begingroup$ What happened to PQR? Whenever I try to access it, I'm only getting an error, which seems to be caught in a loop. $\endgroup$– Martin - マーチン ♦May 16, 2019 at 8:38
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$\begingroup$ It is
https://pqr.pitt.edu/502/if that helps any, and thank you for taking a look. And it just says 'There was an error, please try again You will be redirected to the home page in 5 seconds'. In chrome I got a warning about unsafe scripts, but I allowed that and nothing changed. I've tried a few OS (win,xubu,and) all with chrome and different networks... all samesies. It's a great resource, it should be used! :D $\endgroup$– Martin - マーチン ♦May 16, 2019 at 14:45
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A pretty good database of experimental data compiled into one place has a geometry section. Check out http://cccbdb.nist.gov/
Go to the experimental data section, then click on summary of geometry data for one molecule. The database is fairly large, but not all molecules have a full geometric data set.
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1$\begingroup$ I think the NIST resource is great, but I've never understood why it's so hard to get the geometries. $\endgroup$ Jul 23, 2015 at 15:21
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$\begingroup$ I agree - I imagine that finding the geometry experimentally gets more and more difficult with increasing molecule size (due to increasing vibrational modes) I forgot to mention that the NIST site also has a calculated data section, which has a ton more geometries as calculated by different models. $\endgroup$ Jul 23, 2015 at 17:53