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Table S1 Root Mean Square Difference (RMSD) between the conformations of the simulated complexes and the crystal structure of the human C3c:W4A9 complex (all values in ?).

Table S2A Intermolecular hydrogen bond occupancies (%) of the 1st-generation complexes.

Table S2B Intermolecular hydrogen bond occupancies (%) of the 2nd-generation complexes.

Table S2C Intermolecular hydrogen bond occupancies (%) of the 3rd-generation complexes.

Table S2D Intermolecular hydrogen bond occupancies (%) of the 4th-generation complexes.

Table S3 Association free energies for complexes not included in table 3 of main text.

Figure S1 Alignment of human, rat and mouse C3 sequences, prepared with CLUSTALW v. 2.0.123.

Figure S2 Residue secondary structure probability (%) profiles for selected analogs.

Figure S3 Residue intermolecular interaction energies for compstatin analogs (left panel) and C3 (right panel).

Figure S4Probability density maps (%) of side chain contacts for selected protein-ligand side chain pairs.

Figure S5 Simulation structures of the compstatin binding site for the complexes S-1S0:H (A, B) and S-1S0:M (C, D) at the end of runs S-1S0:H1 and S-1S0:M, respectively.

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