I’d like some feedback… what are some good databases that provide 3D coordinates and search capabilities?
In Avo2, there’s support for importing molecules from PQR (the Pitt Quantum Repository). It needs some work. But as part of that work, I’d like to expand the “search a database” to other sources.
PubChem
There’s access for programs like Avogadro through the “PUG” API, which returns results for queries.
This even includes images:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/lipitor/PNG
Crystallographic Open Database
http://crystallography.net/cod/
This doesn’t have an image preview, but has a variety of useful data as a “preview:”
AFLOW Prototypes
The AFLOW project has generalized the older Navy Crystal Prototypes, now offering 1100 common crystal structures for substitution, lattice scaling, etc.
It does offer PNG previews, e.g.
https://aflow.org/prototype-encyclopedia/prototype_index.html
Northwestern MOF Database
International Zeolite Database
Includes previews, e.g. (ABW)
http://www.iza-structure.org/databases/
Is there a way Avogadro could access PubChem’s 3D conformers directly based on the record’s CID number?
This is based on an answer here and the observation that section 1.2 for this entry is a non-flat 3D conformer in NIH’s interactive depiction. The .sdf fetched from this section’s interface however was flat 2D, requiring an Ctrl + Alt + O geometry optimization to obtain a more reasonable conformer.
If one doesn’t mind that the entries live in silico only, COD’s sibling Theoretical Crystallography Open Database may be of interest, too.
Yes, for molecules that have a 3D geometry, one can get the generated conformer.
Not sure what happened for you, but there is definitely a 3D SDF file for that compound.
Affirmative, display and download of the .sdf in section “1.2 3D Conformer” retain the 3D information of the conformer NIH deposit. It is uncertain if I picked a wrong file, back in the day.
