Hi everyone, I took a random molecule from PDB ligand library: http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=sb3&operation=ccid and - read it in several different input formats, - printed it out, - compared the outputs and the original mmcif -- visually, no detailed diff.
The inputs are PDB ideal & experimental coordinates (available from the download tab of the above URL) files, and the strings copy-pasted from mmCIF: SMILES ACDLabs 10.04 SMILES_CANONICAL CACTVS 3.341 SMILES CACTVS 3.341 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 SMILES "OpenEye OEToolkits" 1.5.0 InChI 1.03 The outputs are different and don't match PDB's mmcif. First discrepancy: mmcif original lists an 'R' carbon and an 'S' carbon. OpenBabel outputs two 'R' carbons in 7 out of 8 cases. In the 8th case: inchi input, there's no chirality. Second discrepancy: input inchi string ends with "/t23-,24+/m0/s1". Inchi generated by OpenBabel (2.3.2, inchi-1.04) from that is identical, so at least it's self-consistent. For other inputs: - both pdb files, acdlabs smiles: ".../t23-,24-/m0/s1/i29+1" - cactus canonical: ".../t23-,24+/m0/s1/i29+1" - cactus and openeye: ".../t23-,24+/m1/s1" - openeye canonical: ".../t23-,24-/m0/s1" Knowing RCSB I wouldn't be too surprised if their ligand file is put together from several processing streams and their atom list doesn't exactly match their inchi. But getting 4 different inchi strings for allegedly the same molecule doesn't sound right to me. Am I missing something? TIA -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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