Single point energies were computed with the B3LYP functional and the Stuttgart Dresden effective core potential basis set (SDD) [31, 32] augmented by polarization functions for all atoms except Mo, W and H (ζ = 0.600, 1.154, 0.864, and 0.421 for C, O, N, and S, respectively) [30].
Third, a residue's RD is calculated as the average atom depth for all atoms except the hydrogen atoms in this residue.
For example, the alkane compound class should NOT contain any other atom except carbon and hydrogen.
Partial charges from the united-atom AMBER force field were used for all receptor atoms except for Ser5.42, Ser5.43, and Ser5.46, for which the dipole moment was increased as previously described to boost electrostatic scores for poses in polar contact with these important residues.
The structure was refined with anisotropic temperature factors for non-hydrogen atoms, except for regions of increased mobility where the temperature factors were refined isotropically.
X stands for any halogenated atom.
Not surprisingly, Glycine has the largest prediction error (75°/67° for phi/psi angles), which is mainly due to the fact that Glycine has no side-chain atom except for a proton.
The 6-31G baset set was used for all QM region atoms except the iron, the atoms immediately ligated to it, and bound azide, hydroxide, or water, for which TZVP was used.
To provide insight why one iteration of ITKrM acts as contraction, assume again that we know all generating supports I n and that our current estimate for the dictionary consists of all generating atoms except for the first one, ψ k =ϕ k for k≥2.
A cutoff of 10 Å was used for the calculation of nonbonded interactions between all atoms except for those in the EVB region, for which all of the interactions were explicitly calculated up to 99 Å from each atom (i.e., no cutoff was applied).
