========================================================================== = Amino Acids Alphas med* Damping Parameters = = (6-31G** HF/LCAO Basis Set) = = = = Supplementary Material for: " = = "A GENERAL METHODOLOGY TO OPTIMIZE DAMPING FUNCTIONS TO = = ACCOUNT FOR CHARGE PENETRATION EFFECTS IN ELECTROSTATIC = = CALCULATIONS USING MULTICENTERED MULTIPOLAR EXPANSIONS" = = Araken S. Werneck, Tarcísio M.R. Filho and Laurent E. Dardenne = = July 2007 = ========================================================================== Modified alpha-med* damping parameters for the twenty amino acids (see results Table VI). This modified amino acid damping parameter set was constructed from the original damping parameters derived for the small fragments and the original amino acid damping parameters shown in the supplementary material A. In this study not only the amino acid side chain were considered but also their peptide junctions. In this way each amino acid has the structure COH-NH-CR-CO-NH2, where R is the respective amino acid side chain, which is the molecular fragment used in the protein OME reassociation method. Original crystallographic coordinates were used for the calculations without modification, only the lacking hydrogens were added with standard geometries. Damping Parameters: bm - bond midpoint Alphas-med parameter set: obtained using the molecular surfaces constructed using the atomic vdW scaled by a factor ranging from 0.5 to 2.0. ================================================================== GLY and PEPTIDE BOND for all amino acids Alphas-med-uniform CA 4.007 HA 3.413 C 5.017 O 3.835 N 3.361 H 4.660 bm(CA-HA) 2.792 bm(C-O) 3.337 bm(CA-N) 3.187 bm(CA-C) 6.330 bm(N-H) 4.603 bm(N-C) 3.180 bm(C-N) 2.994 C 4.134 O 3.872 H 3.399 bm(C-O) 3.138 bm(C-H) 2.883 N 2.994 H 5.062 bm(N-H) 3.919 ================================================================== ALA LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 HA 3.413 HB 3.454 bm(CA-CB) 11.607 bm(CA-HA) 2.792 bm(CB-HB) 2.356 ==================================================================== ARG LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 11.074 CD 11.074 NE 3.361 CZ 6.933 NH 3.301 HA 3.413 HB 3.454 HG 3.454 HD 3.454 HE 4.660 HH 5.581 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD) 11.607 bm(CD-NE) 3.187 bm(NE-CZ) 4.489 bm(CZ-NH) 3.501 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG-HG) 2.356 bm(CD-HD) 2.356 bm(NE-HE) 4.603 bm(NH-HH) 4.613 ==================================================================== ASN LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 5.017 OD1 3.835 ND2 3.182 HA 3.413 HB 3.454 HD2 5.062 bm(CA-CB) 11.607 bm(CB-CG) 2.994 bm(CG-OD1) 3.337 bm(CG-ND2) 2.994 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(ND2-HD2) 3.919 ==================================================================== ASP LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 3.411 CG 4.794 OD 3.752 HA 3.413 HB 3.435 bm(CA-CB) 11.607 bm(CB-CG) 2.373 bm(CG-OD) 3.408 bm(CA-HA) 2.792 bm(CB-HB) 3.029 ==================================================================== CYS LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 10.664 SG 3.053 HA 3.413 HB 3.394 HG 3.715 bm(CA-CB) 11.607 bm(CB-SG) 2.853 bm(CA-HA) 2.792 bm(CB-HB) 2.627 bm(SG-HG) ==================================================================== GLN LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 11.074 CD 5.017 OE1 3.835 NE2 3.182 HA 3.413 HB 3.454 HG 3.454 HE1 5.062 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD) 2.994 bm(CD-OE1) 3.337 bm(CD-NE2) 2.994 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG-HG) 2.356 bm(NE2-HE) 3.919 ==================================================================== GLU LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 3.411 CD 4.794 OE 3.752 HA 3.413 HB 3.454 HG 3.435 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD) 2.373 bm(CD-OE) 3.408 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG-HG) 3.029 ==================================================================== HIS LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 3.627 ND1 3.500 CD2 3.334 NE2 3.749 CE1 3.746 HA 3.413 HB 3.454 HND1 5.787 HCD2 3.863 HCE1 3.863 HNE2 5.787 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-ND1) 5.261 bm(CG-CD2) 2.277 bm(ND1-CE1) 3.290 bm(CD2-NE2) 3.863 bm(CE1-NE2) 4.090 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(ND1-HND1) 3.157 bm(CD2-HCD2) 2.651 bm(CE1-HCE1) 2.651 bm(NE2-HNE2) 3.157 ==================================================================== ILE LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG1 11.074 CG2 11.074 CD1 11.074 HA 3.413 HB 3.454 HG1 3.454 HG2 3.454 HD1 3.454 bm(CA-CB) 11.607 bm(CB-CG1) 11.607 bm(CB-CG2) 11.607 bm(CG1-CD1) 11.607 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG1-HG1) 2.356 bm(CG2-HG2) 2.356 bm(CD1-HD1) 2.356 ==================================================================== LEU LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 11.074 CD1 11.074 CD2 11.074 HA 3.413 HB 3.454 HG 3.454 HD1 3.454 HD2 3.454 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD1) 11.607 bm(CG-CD2) 11.607 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG-HG) 2.356 bm(CD1-HD1) 2.356 bm(CD2-HD2) 2.356 ==================================================================== LYS LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 11.074 CD 11.074 CE 10.748 NZ 3.982 HA 3.413 HB 3.454 HG 3.454 HD 3.454 HE 3.494 HZ 4.417 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD) 11.607 bm(CD-CE) 11.607 bm(CE-NZ) 15.575 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG-HG) 2.356 bm(CD-HD) 2.356 bm(CE-HE) 2.527 bm(NZ-HZ) 3.099 ==================================================================== MET LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 11.074 SD 3.044 CE 11.074 HA 3.413 HB 3.454 HG 3.454 HE 3.454 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-SD) 3.951 bm(SD-CE) 3.951 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG-HG) 2.356 bm(CE-HE) 2.356 ==================================================================== PHE LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 3.284 CD1 3.261 CD2 3.261 CE1 3.261 CE2 3.261 CZ 3.261 HA 3.413 HB 3.454 HD1 3.472 HD2 3.472 HE1 3.472 HE2 3.472 HZ 3.472 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD1) 2.990 bm(CG-CD2) 2.990 bm(CD1-CE1) 2.990 bm(CD2-CE2) 2.990 bm(CE1-CZ) 2.990 bm(CE2-CZ) 2.990 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CD1-HD1) 4.179 bm(CD2-HD2) 4.179 bm(CE1-HE1) 4.179 bm(CE2-HE2) 4.179 bm(CZ-HZ) 4.179 ==================================================================== PRO LATERAL CHAIN Alphas-med-uniform N 3.464 CA 9.284 CB 9.125 CG 9.125 CD 4.373 HA 3.413 HB 3.464 HG 3.464 HD 3.464 bm(CA-N) 2.592 bm(N-CD) 4.000 bm(CA-CB) 9.886 bm(CB-CG) 9.886 bm(CG-CD) 9.866 bm(CA-HA) 2.792 bm(CB-HB) 2.428 bm(CG-HD) 2.428 bm(CD-HD) 2.428 ==================================================================== SER LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 3.836 OG 3.866 HA 3.413 HB 3.291 HG 4.666 bm(CA-CB) 11.607 bm(CB-OG) 19.456 bm(CA-HA) 2.792 bm(CB-HB) 3.160 bm(OG-HG) 6.319 ==================================================================== THR LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 3.836 OG1 3.866 CG2 11.074 HA 3.413 HB 3.291 HG1 4.666 HG2 3.454 bm(CA-CB) 11.607 bm(CB-OG1) 19.456 bm(CB-CG2) 11.607 bm(CA-HA) 2.792 bm(CB-HB) 3.160 bm(OG1-HG1) 6.319 bm(CG2-HG2) 2.356 ==================================================================== TRP LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 3.356 CD1 3.412 CD2 3.357 NE1 3.546 CE2 3.259 CE3 3.727 CZ2 3.259 CZ3 3.259 CH2 3.259 HA 3.413 HB 3.454 HD1 3.928 HNE1 4.644 HCE2 3.599 HCZ2 3.599 HCZ3 3.599 HCH2 3.599 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD1) 2.570 bm(CG-CD2) 2.949 bm(CD1-NE1) 3.182 bm(NE1-CE3) 4.079 bm(CD2-CE3) 2.917 bm(CD2-CE2) 2.324 bm(CE2-CZ2) 3.299 bm(CE3-CZ3) 2.324 bm(CZ2-CH2) 3.299 bm(CZ3-CH2) 3.299 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CD1-HD1) 2.685 bm(NE1-HNE1) 3.148 bm(CE2-HCE2) 3.173 bm(CZ2-HCZ2) 3.173 bm(CH2_HCH2) 3.173 bm(CZ3-HCZ3) 3.173 ==================================================================== TYR LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG 3.284 CD1 3.261 CD2 3.261 CE1 3.261 CE2 3.261 CZ 3.809 OH 3.866 HA 3.413 HB 3.454 HD1 3.472 HD2 3.472 HE1 3.472 HE2 3.472 HH 4.666 bm(CA-CB) 11.607 bm(CB-CG) 11.607 bm(CG-CD1) 2.990 bm(CG-CD2) 2.990 bm(CD1-CE1) 2.990 bm(CD2-CE2) 2.990 bm(CE1-CZ) 2.990 bm(CE2-CZ) 2.990 bm(CZ-OH) 19.456 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CD1-HD1) 4.179 bm(CD2-HD2) 4.179 bm(CE1-HE1) 4.179 bm(CE2-HE2) 4.179 bm(OH-HH) 6.319 ==================================================================== VAL LATERAL CHAIN Alphas-med-uniform CA 4.007 CB 11.074 CG1 11.074 CG2 11.074 HA 3.413 HB 3.454 HG1 3.454 HG2 3.454 bm(CA-CB) 11.607 bm(CB-CG1) 11.607 bm(CB-CG2) 11.607 bm(CA-HA) 2.792 bm(CB-HB) 2.356 bm(CG1-HG1) 2.356 bm(CG2-HG2) 2.356