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note
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3 were modified to form the desired inhibitor. Ideal ionization states for Asp25A and Asp25B were decided after examining different permutations. An interacting water molecule (present in both PDB 1MSM and 1HPX) was added. Inhibitor and PR residues with hydrogen bond interactions to inhibitor were made flexible. Energy minimization (force field MMFF94x) was performed after each step.
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