ADL: Nitrogen atom types - NA or N?

Tomek Wlodarski tomek.wlodarski at
Fri Jan 11 11:38:17 PST 2008

Hi Sargis,
Thank you for your help.
But my question was more about when in chemistry we talk about nitrogen
which is hydrogen bond acceptor- because I am not quite sure if AutoDock do
it correctly...

Hi Tomasz,
> 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
> atoms.

Ok I understand that sp1, sp2 and sp3 nitrogen can be hydrogen bond
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 used the following commands after reading ind.pdb and using Ligand ->
> Input ->
> Choose...:
>  >>> 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.
I would be gratefull for help,


> Hope this helps,
> Sargis

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