ADL: Nitrogen atom types - NA or N?

Tomek Wlodarski tomek.wlodarski at gmail.com
Mon Jan 14 03:20:01 PST 2008


Hi !
I have found information and I think answer for my question - maybe it will
be useful for somebody:
In publication: 'Three-dimensional hydrogen-bond geometry and probability
information from a crystal survey' J. E. J. Mills at al. (1996) I have found
information that "only nitrogen atoms belonging to amide groups and attached
to aromatic rings(with the exception of the aniline NH2 group) are not
considered as hydrogen-bond acceptors because their lone pairs are know to
conjugate with the carbonyl group and aromatic ring, respectively"
I will use this information to change atom types in my ligands.
In this article are also present probability values for acceptor groups.
I think information in this article could be helpful to assess nitrogen atom
types added by AutoDock.
Best,

Tomek


On Jan 12, 2008 6:28 PM, Tomek Wlodarski <tomek.wlodarski at gmail.com> wrote:

> 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?
>
>
> > >> http://en.wikipedia.org/wiki/Indinavir
> > >
> > >
> > > 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']
> > >> >>> mv.selection.name
> > >>['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!
> Best,
>
> Tomek
>
> Thank you,
> > Sargis
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
>
>


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