Question about V3000 mol

I saved one structure to a V2000 mol file and a V3000 mol file.


And converted them by standardizer.





I found the results were different.


Both of the two mol files could be opened in ISIS/Draw


and display a same structure





Do you know why I get the different results?





I pasted the two mol file and config file.


My standardizer is 3.1





Thanks

The input compounds in the V2000.mol and V3000.mol files are different. This can lead to different results.

Hello Gyuri





Thank you for your reply.





(1)The two mol files displayed the same structure in ISIS/Draw.


(2)There is no +1 charge at N in the v3000.mol.


The following is Atom block of V3000.mol


-------------------------------------------------------


M V30 1 N 0.810933 -2.21277 0 0 CFG=3


M V30 2 C 2.21093 -2.53007 0 0 CFG=3


M V30 3 C 0.686733 -0.798966 0 0 CFG=3


M V30 4 O -0.271867 -3.14387 0 0


M V30 5 C 2.93503 -1.31967 0 0 CFG=3


M V30 6 C 1.74193 -3.89557 0 0


M V30 7 C 3.49713 -3.14387 0 0


M V30 8 C 2.00403 -0.230067 0 0


M V30 9 C -0.730467 -1.06797 0 0


M V30 10 C 0.269533 0.587233 0 0


M V30 11 C 4.37303 -1.18867 0 0


M V30 12 O 5.19363 -2.35077 0 0


M V30 13 O 4.97993 0.107934 0 0


------------------------------------------------------


Don't you think it a problem of Marvin?





Thanks

You might be right. Thank you for the report, we are investigating the problem and will get back soon.

The molecule has an invalid valence. In this case, some chemical drawing programs automatically display a positive charge on that nitrogen, others do not.


You are right, Marvin is currently not consistent, because no charge is displayed for the molecule coming from the V2000 format, but a charge is displayed in case of V3000 format.





The source of the problem is, that the V2000 file always contain charge explicitly for all atoms (a 0 at least), but the charge is often not specified in V3000.





We will modify the V3000 import to consider non specified charge as 0.