I want to create conformations of molecules using restraints but many of
the resulting conformers have wrong geometries (distorted aromatic, rings,
out-of-plane hydrogens, etc.). I would like to define some rules of thump
to recognize such wrong geometries. One possible way is to look at the
total energy of the molecules as given by
AllChem.UFFGetMoleculeForceField.CalcEnergy(). However, the energy
threshold is different for every molecule. Therefore I thought to define an
arbitrary threshold dependent on the total number of heavy atoms, like N*20
kcal/mol. When all the generated conformers exceed that energy thresholds,
then more conformers are generated until I get at least one with valid
energy. I would like to know your opinion on this matter. What would be a
reasonable multiplier (in my example I used 20 kcal/mol)? Would you
recommend adding other factors (e.g. number of rotatable bonds) in my
empirical rule to exclude wrong geometries?

Another way could be to apply bond and dihedral angle constrains to the
aromatic atoms based on their configuration in the starting conformation
(which has always correct geometry). But that would be more tedious than
the energy threshold approach. Do you think that this is the right way to

Thanks in advance.



Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic


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