ADL: Nitrogen atom types - NA or N?

Sargis Dallakyan sargis at
Fri Jan 11 16:16:59 PST 2008

>>The following condition in AutoDockTools/ makes nitrogens
>>hydrogen bond acceptor('N' + 'A')
>>                if item.babel_type in ['N3','N2','N1']:
>>                    item.autodock_element = item.element + 'A'
>>                elif item.babel_type in ['Nam', 'Npl', 'Ng+']:
>>                    if len(item.bonds)==2:
>>                        item.autodock_element = item.element + 'A'
>>Translated to English this means, nitrogen is acceptor if:
>>it is sp1, sp2 or sp3 nitrogen, or
>>it is nitrogen amide, trigonal planar or Ng+ (sp3 plus H+?), and its
>>bonded to 2
> Ok I understand that sp1, sp2 and sp3 nitrogen can be hydrogen bond
> acceptor.
> What about nitrogen in amides ? You have written that they are acceptors if
> they are bond to only 2 atoms... after consideration I believe they are very
> poor acceptors because in amides there is conjugate system ??
> And why  "Npl", and "Ng+" are acceptors only when they are bonded to 2 atoms
> ?

I'll be happy to discuss chemistry of nitrogen as a hydrogen bond acceptor and 
make corrections to the code, if necessary. Are there any specific case which we 
are missing or should include in the code? It seems that you agree with the 
first if condition and that we are missing some cases by allowing "Npl" and 
"Ng+" only when they are bonded to 2 atoms. Is this true?

> I used the following commands after reading ind.pdb and using Ligand ->
>>Input ->
>> >>> mv.selectFromString(atoms='N*')
>> >>> mv.selection.autodock_element
>>['N', 'N', 'N', 'N', 'NA']
>> >>> mv.selection.babel_type
>>['N3+', 'Nam', 'Npl', 'Nam', 'Npl']
>> >>>
>>['N1', 'N2', 'N3', 'N4', 'N5']
>>N5 in Indinavir is acceptor because its in the ring and bonded to 2 atoms.
>  Ok but this N atoms in heterocyclic ring - we can say that this nitrogen is
> tertiary amine - so why they cannot be acceptor of hydrogen bond? For sure
> this ring is not planar.

Are we talking about N3? Should I add include 'N3+' in ['Nam', 'Npl', 'Ng+'] 
list and why?

Thank you,

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