# $Id: AD4.1_bound.dat,v 1.2.2.1 2009/04/15 22:35:26 rhuey Exp $ # # AutoDock # # Copyright (C) 1989-2007, Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson, # All Rights Reserved. # # AutoDock is a Trade Mark of The Scripps Research Institute. # # This program is free software; you can redistribute it and/or # modify it under the terms of the GNU General Public License # as published by the Free Software Foundation; either version 2 # of the License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # AutoDock Linear Free Energy Model Coefficients and Energetic Parameters # Version 4.1 Bound # $Revision: 1.2.2.1 $ # FE_unbound_model is used to specify how the internal energy of the # ligand should be treated when estimating the free energy of binding, # and can be set to one of the following strings: # unbound_same_as_bound, extended, or compact # unbound_same_as_bound -- this assumes the internal energy of the ligand is the # same before and after binding. # extended -- this assumes the internal energy of the ligand is that of an # extended conformation when unbound. # compact -- this assumes the internal energy of the ligand is that of a # compact conformation when unbound. #FE_unbound_model unbound_same_as_bound # AutoDock 4 free energy coefficients with respect to original (AD2) energetic parameters # This model assumes that the bound and unbound conformations are the same. # See Table 3 in Huey,Morris,Olson&Goodsell (2007) J Comput Chem 28: 1145-1152. # # Free Energy Coefficient # ------ FE_coeff_vdW 0.1662 FE_coeff_hbond 0.1209 FE_coeff_estat 0.1406 FE_coeff_desolv 0.1322 FE_coeff_tors 0.2983 # AutoDock 4 Energy Parameters # - Atomic solvation volumes and parameters # - Unweighted vdW and Unweighted H-bond Well Depths # # - Atom Types # - Rii = sum of vdW radii of two like atoms (in Angstrom) # - epsii = vdW well depth (in Kcal/mol) # - vol = atomic solvation volume (in Angstrom^3) # - solpar = atomic solvation parameter # - Rij_hb = H-bond radius of the heteroatom in contact with a hydrogen (in Angstrom) # - epsij_hb = well depth of H-bond (in Kcal/mol) # - hbond = integer indicating type of H-bonding atom (0=no H-bond) # - rec_index = initialised to -1, but later on holds count of how many of this atom type are in receptor # - map_index = initialised to -1, but later on holds the index of the AutoGrid map # - bond_index = used in AutoDock to detect bonds; see "mdist.h", enum {C,N,O,H,XX,P,S} # # - To obtain the Rij value for non H-bonding atoms, calculate the # arithmetic mean of the Rii values for the two atom types. # Rij = (Rii + Rjj) / 2 # # - To obtain the epsij value for non H-bonding atoms, calculate the # geometric mean of the epsii values for the two atom types. # epsij = sqrt( epsii * epsjj ) # # - Note that the Rij_hb value is non-zero for heteroatoms only, and zero for H atoms; # to obtain the length of an H-bond, look up Rij_hb for the heteroatom only; # this is combined with the Rii value for H in the receptor, in AutoGrid. # For example, the Rij_hb for OA-HD H-bonds will be (1.9 + 1.0) Angstrom, # and the weighted epsij_hb will be 5.0 kcal/mol * FE_coeff_hbond. # # Atom Rii Rij_hb rec_index # Type epsii solpar epsij_hb map_index # vol hbond bond_index # -- ---- ----- ------- -------- --- --- - -- -- -- atom_par H 2.00 0.020 0.0000 0.00051 0.0 0.0 0 -1 -1 3 # Non H-bonding Hydrogen atom_par HD 2.00 0.020 0.0000 0.00051 0.0 0.0 2 -1 -1 3 # Donor 1 H-bond Hydrogen atom_par HS 2.00 0.020 0.0000 0.00051 0.0 0.0 1 -1 -1 3 # Donor S Spherical Hydrogen atom_par C 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Non H-bonding Aliphatic Carbon atom_par A 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0 # Non H-bonding Aromatic Carbon atom_par N 3.50 0.160 22.4493 -0.00162 0.0 0.0 0 -1 -1 1 # Non H-bonding Nitrogen atom_par NA 3.50 0.160 22.4493 -0.00162 1.9 5.0 4 -1 -1 1 # Acceptor 1 H-bond Nitrogen atom_par NS 3.50 0.160 22.4493 -0.00162 1.9 5.0 3 -1 -1 1 # Acceptor S Spherical Nitrogen atom_par OA 3.20 0.200 17.1573 -0.00251 1.9 5.0 5 -1 -1 2 # Acceptor 2 H-bonds Oxygen atom_par OS 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor S Spherical Oxygen atom_par F 3.09 0.080 15.4480 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Fluorine atom_par Mg 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Magnesium atom_par MG 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Magnesium atom_par P 4.20 0.200 38.7924 -0.00110 0.0 0.0 0 -1 -1 5 # Non H-bonding Phosphorus atom_par SA 4.00 0.200 33.5103 -0.00214 2.5 1.0 5 -1 -1 6 # Acceptor 2 H-bonds Sulphur atom_par S 4.00 0.200 33.5103 -0.00214 0.0 0.0 0 -1 -1 6 # Non H-bonding Sulphur atom_par Cl 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Chlorine atom_par CL 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Chlorine atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Calcium atom_par Mn 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Manganese atom_par MN 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Manganese atom_par Fe 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Iron atom_par FE 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Iron atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Zinc atom_par ZN 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Zinc atom_par Br 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Bromine atom_par BR 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Bromine atom_par I 4.72 0.550 55.0585 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding Iodine atom_par Z 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Non H-bonding covalent map atom_par G 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aliphatic Carbon # SF atom_par GA 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aromatic Carbon # SF atom_par J 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aliphatic Carbon # SF atom_par Q 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Ring closure Glue Aliphatic Carbon # SF