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 <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/
