ADL: Double bonds in pdbqt file?

Diogo Martins diogo.stmart at gmail.com
Mon Jan 22 23:52:07 PST 2018


Yes, you are right about the types for carbon: "A" for aromatic and "C" for
non-aromatic. For other elements, the atom type does not specify whether
the atom is aromatic or not. For example "NA" is nitrogen that is hydrogen
bond acceptor, while "N" is nitrogen that does not accept hydrogen bonds.
Examples:
 - Aromatic "NA": pyridine
 - Aromatic "N": indole
 - Non-aromatic "NA": metylamine
 - Non-aromatic "N": nitromethane

The BRANCH keyword defines rotatable bonds:

BRANCH 7 8

makes the bond between atoms 6 and 7 rotatable. So the bond between 6 and 7
is definitely a single bond because only single bonds can rotate. One of
the two atoms may be sp2/aromatic. For example, in phenol, the C-O bond is
rotatable and the carbon is sp2 and aromatic.

In closed cycles (e.g. sugars, heterocycles) single bonds will not be
rotatable and it may be impossible to know bond orders from the pdbqt file.








On Jan 22, 2018 9:22 PM, "dr. sakura" <lalehan.ozalp at gmail.com> wrote:

Hello again,

What I mean is, according to what you wrote here:

[If two carbons are aromatic (either C-C or C=C depending on the resonance
structure), they would be typed "A" instead of "C", and the bond would not
be rotatable.]  ...  so we can understand whether a C atom is aromatic or
not, right? and the nomenclature for this purpose is A or C.

So, I'm asking, if the C (or N) atom is NOT aromatic, but still not in a
rotatable bond? Is there a way to understand this by only looking at the
.pdbqt file?

Hope I'm clear now.




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