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 <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 <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 > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> 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 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/
