Problems with superatoms in reactions

When writing reactions involving a CoA superatom, we are experiencing problems with Jchem 3.2.1 producing the correct products. We have a number of reactions where the substrate contains CoA, and a CoA molecule is being added producing two CoA containing products. We have mapped only the sulfur atoms in the CoA molecule, similarly to our other CoA reactions, which work fine.

Code:

react -a changing  -v -r ../molecules/CoArule.mrv "CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCSC(=O)CC(=O)CCCC([O-])=O" CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23 [O-]C(=O)CCCC(S)=O

In the above example (also attached as .mrv), the substrate is: CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCSC(=O)CC(=O)CCCC([O-])=O


The predicted products are:


CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23


[O-]C(=O)CCCC(S)=O


The first product is correct, but the second should be:


CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCSC(=O)CCCC([O-])=O


The second CoA molecule is not being predicted in the product.


Please let us know if this is a mapping error that we can fix or another problem.

Hi,





You have to map the CoA of the second product. According to the definition of the changing mapping style the CoA group of the second product is an "orphan atom" and have to be mapped.





Reaction results the expected products using the correctly mapped reaction:

Code:

$ react -a changing -r CoArule2.mrv "CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCSC(=O)CC(=O)CCCC([O-])=O" CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23 CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)n2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCSC(=O)CCCC([O-])=O

I have attached the correctly mapped reaction molecule (CoArule2.mrv).





Best regards,


Zsolt

Your example works perfectly! Unfortunately, we cannot map superatoms using our version of Marvin Sketch 3.4. When I copy your mrv file and open it in Marvin Sketch, I have the ability to map the CoA superatom, but can only map the specific CoA that you have mapped as 6. For instance, when I right click on the CoA that you mapped, I get the options "Map, Expand, Ungroup, Remove", but when I right click on any of the unmapped CoAs, I only get the options "Expand, Ungroup, Remove." Technically I can keep coping your CoA and use it over and over to fix our reactions, but this is round about and we would prefer not to do this. Thank you for your help!

Hi,

Rlong wrote:

Your example works perfectly! Unfortunately, we cannot map superatoms using our version of Marvin Sketch 3.4.

JChem 3.2.1 includes Marvin 4.1.3. Why don't you use this version of Marvin?





Best regards,


Zsolt