e-LBOW is a ligand building program written in Python and c++ designed to produce a three dimensional optimised geometry from a number of 2D and 3D chemical formats. It is specifically designed for use with structure determination of proteins and is part of the PHENIX project.
e-LBOW can also be used to generate geometries independently.
The general procedure involves interpreting the input data into a Python class. One of the key outputs is a CIF format the allows refinement of the ligand in conjunction with crystallographic data and a protein model. This format requires detailed information of the topological state of the ligand including bonds, angle, dihedrals, chiral centres and planes.
Much of the processing involved is attempting to determine appropriate topological elements. For input formats that lack bonding connections and bond orders this process is further complicated by the ambiguity of atomic positions.
Once the bonding of the ligand is determined, a simple geometry optimisation using a force-field potential energy including bond, angle, dihedral, non-bonded, chirality and planar contributions. The bond lengths for this force-field are calculated using the quantum level of Hartree-Fock with a 6-31G(d,p) basis set.
To increase the chemical accuracy, a geometry optimisation module using the semi-empirical method [AM1] written in c++ is included in the e-LBOW distribution. External quantum packages can also be utilised.
The output of an e-LBOW run includes a PDB file of the final geometry and a CIF file for refinement applications. Information on the computer resources required is given here.