ADL: Nitrogen atom types - NA or N?

Tomek Wlodarski tomek.wlodarski at
Sat Jan 12 09:28:20 PST 2008

Hi Sargis!
Thanks for your fast reply!

> > 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 will be also very happy to discuss chemistry of nitrogen as a hydrogen
bond acceptor. :)
I am not a chemistry expert so I am not sure if I am right...
That is true that first condition looks good for me and this is also true
that I think that something is missing in the second condition- but frankly
I do not know how should the second condition look like...
I am only curious why "Nam", "Npl" and "Ng+" are acceptors of hydrogen bond
only if they are bonded to 2 atoms - do you know any chemical explanation?

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

I am talking about N1 and N3 because they are for me te same atoms type, I
do not see any differences between them... I do not understand why they have
different atom type... Especially why one of them is "N3+" ?
*"N3+"=sp*3-hybridized nitrogen with formal positive charge, so why Autodock
thinks that N3 has formal positive charge...??
I think that AutoDock make mistakes in choosing atom types, which is
especially important in nitrogen case - because some hydrogen bonds which
could be created are not created because of wrong nitrogen atom type...
Unfortunately I can not tell you if you should add N3+ or not, because this
was my question :) - "Which nitrogens can be a hydrogen bond acceptors" :)
and after searching I still do not know...
I would be very grateful for any help!


Thank you,
> Sargis
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