Table I.

The four energy levels used in the design process and the terms from which they are comprised. For the proteins, van der Waals parameters, atomic radii and torsional parameters were taken from the CHARMM22 force field.²⁷ For the small molecules, van der Waals parameters, atomic radii and torsional parameters were taken from the CHARMm22 force field.³⁸ For all electrostatic calculations, the proteins were assigned PARSE charges³⁴ and the heme group and all small molecules were assigned partial charges using a RESP fit.³²,³³ All energy minimization was performed using CHARMM.²⁷ The surface area term is calculated as a constant value of 0.005 kcal/mol multiplied by the change in surface area upon binding in Å2. The internal deformation on binding comprises electrostatic, van der Waals, and torsional contributions.

Calculation	van der Waals	Continuum Electrostatic Interaction	Continuum Electrostatic Ligand Desolvation	Continuum Electrostatic Protein Desolvation	Surface Area Term	Internal Deformation On Binding
Low Resolution	Grid Based	Grid Based	Grid Based	Constant	No	None
Medium Resolution	Explicit	Grid Based	Delphi Calculation	Constant	No	None
High Resolution	Explicit	Delphi Calculation	Delphi Calculation	Delphi Calculation	Yes	None
Energy Minimization	Explicit	Delphi Calculation	Delphi Calculation	Delphi Calculation	Yes	Bound - Unbound