Wrong charges when importing a mol2 file

Hi,

I imported into Marvin Sketch some mol2 files generated by some other programs (MOE, pymol). In some of the cases (like the attached one) I can see what I think are wrong charge assignments. For instance in the carbon of the carbonyl group, carbon gets a + charge and oxygen a - charge, etc.

Is it ok? I guess probably there is some threshold in the program to determine when depending on the charge value, the atom gets an entire positive or negative charge or not, if it is like that, can it be changed? I just need a "clean" 2D representation of the molecule for cases like this.

 

Thanks in advance

 

Horacio

Hi,

being interested in this field, I immediately downloaded the example and tried to analyse the problem.

As can be seen in the text-presentation (attached image left side) the charges at the heteroatoms are very high. So there are questions:

Are these pi-charges or sigma-charges or total charges ?  What is the calculation-method of these charges ?

N9 has the charge -0.4210 and gets no minus, N10 has the charge -0.5490 and it has a minus sign.

So the threshold seems to be near  0.5000.

What are these calculated charges for molecules with formal charges near plus/minus one ?

Can you please post the same calculation result for the betain of alanine ( C[C@H]([NH3+])C([O-])=O ), also as mol2-file. ?

Regards, Hans-Ulrich

Dear Horacio, Dear Hans-Ulrich,

 

Currently when charge data found during mol2 import it is rounded (to the nearest integral value) and used as formal charge. This is the cause of the reported "false" charges.

Mol2 export uses charge plugin if available (licensed) to calculate partial charges. If charge plugin is not available formal charges will be used.

 

Regards,

Gabor