Scoring Alignments

1. Alignment RMS: This is the root mean squared distance (in Angstroms) between features in the aligned conformation and those in the reference pharmacophore. Lower RMS values correspond to better alignments.
2. Conformation energy: This is the difference (in kcal/mol) between the computed UFF energies of the aligned conformation and a baseline conformation of the probe molecule. The baseline energy is calculated by generating a number of 3D structures of the free probe molecule (not subject to pharmacophore constraints) and taking the lowest energy. Lower conformation energies correspond to more stable alignments. Negative conformation energies do not indicate special stabilization by the pharmacophore, they just indicate a less-than-perfect value for the baseline energy. :-)
3. Shape score: this is the Tanimoto similarity between the shape of the aligned conformation  and that of the reference molecule. The shapes are generated on a Cartesian grid using the van der Waals radii of the atoms. Higher shape scores indicate better shape matches.