Marvin Sketch 5.3.8 Not Rendering Nitro Groups Correctly

If I create a compound with nitro groups in Marvin Sketch and save it as a mol2 file, when the file is reopened, the nitro groups are no longer shown correctly (i.e., with a double bond to one O atom, a single bond to the other O atom, a negative charge on one O atom and a positive charge on the N atom). Instead, the nitro group now has the single-bonded O atom with a hydrogen attached, HO-N=O. Is this a bug? If not, is there a way to correct this behavior? Thank you.

Dear Rudy,

 

Thanks for the bug report and sorry for the late answer. The calculated partial charges are saved to the mol2 file instead of the specified formal charge.  As a workaround you can edit the mol file by writing "1.0000" and "-1.0000" to the appropriate atoms charge field. See attached example.

We will discuss our possibilities about this problem and get back to you soon.

 

Regards,

Gabor

Dear Rudy !

 

The bug is already corrected. Nitro compounds saved as a .mol2 format are rendered correctly. 

I made a test with Marvin 5.10 and 5.11.

 

Daniel

Dear Daniel,

Thank you for your reply. I find if I draw 1,3-dinitrobenzene and save it as a mol2 file, when I reopen the file in MarvinSketch 5.11.3 (on Mac 10.8.2), the nitro groups are still not rendered correctly. However, if I save the structure as an sdf file, when I reopen the file the structure is rendered correctly. This procedure is working sufficiently well for me that I would consider the issue solved.