CoA removal problem

Dear Chemaxon,





I wrote a reaction string to remove the CoA part from a compound.


E.g., R-C(=O)SCoA -> R-C(=O)[O-]





The configuration file for the standardizer was written as,





<Transformation ID="CoA1" Structure="CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n1cnc2c(N)ncnc12)C(O)C(=O)NCCC(=O)NCCS>>[O-]"/>





When I input the following SMILES string,





CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)c4ccccc4N





I got the following output,





[OH-].Nc1ccccc1C=O





The output contains two compounds. I got them unexpectedly. The expected compound I want to have listed bellow,


Nc1ccccc1C([O-])=O





Could you tell what is wrong in my config file? Thanks much!





Best regards,


Jeff Gao

Transforms are processed on the basis of a mapped transformation scheme. But your transform should be mapped, otherwise maps are placed internally and automatically. Since your reaction scheme contains many oxigen atoms on the left side an a single oxigen on the right, it is very unlikely, that automapping can be correct. You should mark atoms having changing bonds with the same map numbers on both sides of the reaction arrow, and additionally, you should map orphan atoms (atoms or appearing disappearing during the reaction) with unique map numbers.

Quote:

Transforms are processed on the basis of a mapped transformation scheme. But your transform should be mapped, otherwise maps are placed internally and automatically. Since your reaction scheme contains many oxigen atoms on the left side an a single oxigen on the right, it is very unlikely, that automapping can be correct. You should mark atoms having changing bonds with the same map numbers on both sides of the reaction arrow, and additionally, you should map orphan atoms (atoms or appearing disappearing during the reaction) with unique map numbers.