problems on mapping CoA to produce a chiral CoA product

We want to add a CoASH to a carboxyl group to form a thioester.





I did three tests in Jchem3.2.1 and jchem 3.1.7,





In Jchem3.1.7 all the atoms in CoASH is mapped and the product is right (a chiral CoASH molecule).

Code:

substrate: CCCCCCCC([O-])=O react -v -r ../molecules/bt0094_317.mrv "CCCCCCCC([O-])=O" CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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

But in the jchem3.2.1, there is an exception when I ran the above command line,





Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1





If CoASH is partially mapped as in the attached bt0094_321_1.mrv ,


when given a chiral CoASH molecule,


changing mapping produces a non-chiral CoA adduct, and


partial (automatic) mapping produces a product lacking CoA

Code:

/react -a changing -v -r ../molecules/bt0094_321_1.mrv "CCCCCCCC([O-])=O" CCCCCCCC(=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 react -a partial -v -r ../molecules/bt0094_312_1.mrv "CCCCCCCC([O-])=O" CCCCCCCCO

Also, I made another file, unmapped all the atoms in CoA but only mapped the CoA group, they also produces a non-chiral CoA adduct:

Code:

react -a changing -v -r ../molecules/bt0094_321_2.mrv "CCCCCCCC([O-])=O" CCCCCCCC(=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 react -a partial -v -r ../molecules/bt0094_321_2.mrv "CCCCCCCC([O-])=O" CCCCCCCC(=O)[S:5][CH2:6][CH2:7][NH:8][C:9](=[O:10])[CH2:11][CH2:12][NH:13][C:14](=[O:15])[CH:16]([OH:50])[C:17]([CH3:51])([CH3:52])[CH2:18][O:19][P:20]([OH:49])(=[O:21])[O:22][P:23]([OH:48])(=[O:24])[O:25][CH2:26][CH:27]1[O:28][CH:29]([CH:30]([OH:45])[CH:31]1[O:32][P:33]([OH:46])([OH:47])=[O:34])[n:35]2[cH:36][n:37][c:38]3[c:39]([NH2:44])[n:40][cH:41][n:42][c:43]23

If I want to get the following product,





Wanted products:

Code:

CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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

But not,

Code:

CCCCCCCC(=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

What is the proper way to map it? Thanks in advance!

Hi,





We are working on better contracted abbreviated group support in Reactor.

JeffGao wrote:

What is the proper way to map it? Thanks in advance!

We plan to support both:


- only the abbreviated group is mapped


- all atoms of the abbreviated group are mapped





Regards,


Zsolt