[Dock-fans] negatively charged sulfonamides

[Eric Pettersen]

Hi John,
	I guess I didn't mention that the sulfonamide NH2 -> NH- is just a  
special case of a general rule that Chimera will be using, namely:  
remove a proton from metal-coordinating nitrogens, which I think  
covers the cases you mentioned.  My question then more generally is  
whether Chimera needs to allow the user to prevent the removal if it  
results in NH-, simply for docking considerations.

--Eric

On Mar 24, 2009, at 12:22 PM, John J. Irwin wrote:

> Hi Eric
>
> Thanks for looking at this issue.
>
> Eric Pettersen wrote:
>>
>> Hi all,
>>  The issue was raised recently about problems with Chimera's  
>> treatment of metal-coordinating sulfonamides.  It's been decided to  
>> treat such an amide as NH-.  It's been proposed that this may be  
>> hard to deal with in some docking scoring methods because of the  
>> ionization energy.  The question is how much of an issue is it?  If  
>> it was a big deal then I could provide an option to treat the amide  
>> as NH2 instead.  Of course, I don't want to write the code to  
>> handle the option unless I really need to!
> I think there needs to be an amidate atom type, for both primary and  
> secondary sulfonamides.  R'(R'')NH -> R'(R"")[N-] and R'NH2 ->  
> R'[NH-].  What I don't know is to what extent this can be handled by  
> existing code/options/atom types.
>
> I can drop by to chat if that would help.
>
> John
>
>