Maybe more information on that here: https://developer.rsc.org/? I'm not an expert and only used it interactively... Julie
On Tue, 6 Dec 2022 at 12:19, Harry Powell <[email protected]> wrote: > Hi Julie > > Ta. > > Do you know if there’s an API (pref. Python 3.9 or later) for downloading > the 3D coordinates from ChemSpider? > > Harry > > > On 6 Dec 2022, at 12:04, Julie Tucker < > [email protected]> wrote: > > > > Chemspider can also provide you with a .mol file amongst other things. > > > http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194 > > Best wishes > > Julie > > > > On Tue, 6 Dec 2022 at 11:55, Oliver Smart <[email protected]> > wrote: > > Hi Harry, > > > > The SDF found at ChEBI is a 2D SDF with the coordinates used for the > diagram. I do not think that ChEBI has > > 3D coordinates. Why not use PubChem instead as this does provide 3D sdf > files? > > > > For your caffeine example: > > > > https://pubchem.ncbi.nlm.nih.gov/compound/64119 > > > > There > > > > > https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519 > > > > Provides a SDF file. > > > > Hope this helps > > > > Oliver > > > > p.s. I you are stuck with ChEBI identifiers it would be possible to > programatically find the equivalent PubChem CID. > > > > > > > > > >> On 6 Dec 2022, at 11:31, Harry Powell < > [email protected]> wrote: > >> > >> Hi folks > >> > >> Can anyone help with this? > >> > >> I must have missed something in the documentation, because I don’t > understand why the .mol and .sdf files downloaded from > >> > >> https://www.ebi.ac.uk/chebi > >> > >> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few > decades now since I solved any small molecule structures, but something > around 1.395Å rings a faint bell). > >> > >> I need to have ligands that have realistic sizes, and while I’m > perfectly at ease scaling the models to what I think are sensible sizes, I > can’t help but think that this isn’t necessary and I’ve missed something > somewhere. > >> > >> Here’s an example of a molecule that I used this morning - > >> > >> > https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0 > >> > >> contents of downloaded file - > >>> > >>> Marvin 01140911122D > >>> > >>> 15 15 0 0 0 0 999 V2000 > >>> -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> -0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 0.0000 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 1.4992 0.6674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 1.4992 -0.6675 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 1.9841 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> -1.4289 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 0.0001 1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 0.0001 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 1.7541 1.4520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> -1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 2.0809 -1.5365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 > >>> 10 1 2 0 0 0 0 > >>> 1 2 1 0 0 0 0 > >>> 14 2 1 0 0 0 0 > >>> 8 3 1 0 0 0 0 > >>> 4 3 2 0 0 0 0 > >>> 7 4 1 0 0 0 0 > >>> 1 5 1 0 0 0 0 > >>> 5 3 1 0 0 0 0 > >>> 12 5 1 0 0 0 0 > >>> 6 2 1 0 0 0 0 > >>> 6 4 1 0 0 0 0 > >>> 11 6 2 0 0 0 0 > >>> 9 7 1 0 0 0 0 > >>> 13 7 1 0 0 0 0 > >>> 9 8 2 0 0 0 0 > >>> M END > >>> > >> > >> Harry > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >> > >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > -- > > Julie Tucker > > York Biomedical Research Institute > > Department of Biology and HYMS > > University of York > > > > My normal working days are Monday-Tuesday and Thursday-Friday. Please be > patient if you do not hear from me promptly. I choose to work flexibly; > please only respond to this message when convenient for you to do so. > > > > Email disclaimer > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > -- Julie Tucker York Biomedical Research Institute Department of Biology and HYMS University of York *My normal working days are Monday-Tuesday and Thursday-Friday. Please be patient if you do not hear from me promptly. I choose to work flexibly; please only respond to this message when convenient for you to do so.* Email disclaimer <https://www.york.ac.uk/about/legal-statements/email-disclaimer/> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
