# This file defines two covalent links between PPACK and His57/Ser195 of a # trypsin-like serine protease. # Two link files produced with JLigand 1.0.35 were manually merged. # # Author: Wolfgang Skala # Date: 20120522 # # LINK records for pdb file: # LINK C2 0G6 A 301 OG SER A 195 0G6-SER # LINK C3 0G6 A 301 NE2 HIS A 57 0G6-HIS global_ _lib_name mon_lib _lib_version 5.28 _lib_update 10/04/2011 # ----------------------- 1 LISTS --------------------------------------------- # ----------------------- 1.1 COMPOUND LIST ----------------------------------- data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.number_atoms_all _chem_comp.number_atoms_nh 0G6 0G6 'PPACK' 65 31 # ----------------------- 1.2 MODIFICATIONS LIST ------------------------------ data_mod_list loop_ _chem_mod.id _chem_mod.name _chem_mod.comp_id 0G6mod1 'PPACK for bonds to His57/Ser195' 0G6 SERmod1 'Ser195 for bond to PPACK' SER HISmod1 'His57 for bond to PPACK' HIS # ----------------------- 1.3 LINK LIST --------------------------------------- data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.name 0G6-SER 0G6 0G6mod1 SER SERmod1 0G6-SER 0G6-HIS 0G6 0G6mod1 HIS HISmod1 0G6-HIS # ----------------------- 2 PPACK DATA ---------------------------------------- data_comp_0G6 # ----------------------- 2.1 ATOMS ------------------------------------------- loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z 0G6 CL Cl CL 0.000 -9.809 6.706 4.583 0G6 C3 C CH2 0.000 -8.555 5.737 3.752 0G6 H11 H H 0.000 -7.580 5.958 4.187 0G6 H21 H H 0.000 -8.756 4.675 3.900 0G6 C2 C CH1 0.000 -8.569 6.055 2.257 0G6 H33 H H 0.000 -9.560 5.776 1.876 0G6 O2 O OH1 0.000 -8.395 7.467 2.067 0G6 H34 H H 0.000 -9.118 7.942 2.497 0G6 CA2 C CH1 0.000 -7.508 5.257 1.483 0G6 HA2 H H 0.000 -7.296 4.333 2.039 0G6 CB2 C CH2 0.000 -6.182 5.997 1.274 0G6 HB22 H H 0.000 -6.353 6.892 0.673 0G6 HB32 H H 0.000 -5.510 5.351 0.704 0G6 CG2 C CH2 0.000 -5.489 6.389 2.577 0G6 HG21 H H 0.000 -5.430 5.521 3.236 0G6 HG31 H H 0.000 -6.072 7.159 3.085 0G6 CD3 C CH2 0.000 -4.088 6.935 2.324 0G6 HD22 H H 0.000 -4.127 7.655 1.505 0G6 HD31 H H 0.000 -3.429 6.118 2.022 0G6 NE N NH1 0.000 -3.548 7.579 3.511 0G6 HE H H 0.000 -4.114 7.555 4.347 0G6 CZ1 C C 0.000 -2.363 8.196 3.549 0G6 NH2 N NH2 1.000 -1.561 8.266 2.482 0G6 HH21 H H 0.000 -1.827 7.847 1.603 0G6 NH1 N NH2 0.000 -1.969 8.765 4.690 0G6 HH12 H H 0.000 -1.078 9.238 4.740 0G6 HH11 H H 0.000 -2.560 8.725 5.508 0G6 N2 N NH1 0.000 -8.038 4.900 0.175 0G6 H1 H H 0.000 -7.707 5.420 -0.626 0G6 C1 C C 0.000 -8.939 3.929 -0.004 0G6 O1 O O 0.000 -9.390 3.257 0.912 0G6 CA1 C CH1 0.000 -9.396 3.702 -1.420 0G6 HA1 H H 0.000 -8.559 3.835 -2.113 0G6 CB1 C CH2 0.000 -10.437 4.752 -1.800 0G6 HB21 H H 0.000 -10.862 5.219 -0.908 0G6 HB31 H H 0.000 -9.986 5.527 -2.422 0G6 CG1 C CH2 0.000 -11.517 4.020 -2.568 0G6 HG2 H H 0.000 -12.498 4.455 -2.365 0G6 HG3 H H 0.000 -11.321 4.060 -3.641 0G6 CD C CH2 0.000 -11.449 2.591 -2.063 0G6 HD21 H H 0.000 -12.133 2.446 -1.225 0G6 HD3 H H 0.000 -11.704 1.890 -2.860 0G6 N1 N N 0.000 -10.061 2.405 -1.637 0G6 C C C 0.000 -9.503 1.193 -1.470 0G6 O O O 0.000 -10.215 0.280 -1.080 0G6 CA C CH1 0.000 -8.046 0.855 -1.734 0G6 HA H H 0.000 -7.602 0.626 -0.757 0G6 N N NH2 0.000 -7.262 1.904 -2.368 0G6 H2 H H 0.000 -6.902 1.775 -3.304 0G6 H H H 0.000 -7.014 2.734 -1.854 0G6 CB C CH2 0.000 -7.960 -0.409 -2.602 0G6 HB2 H H 0.000 -8.389 -0.192 -3.582 0G6 HB3 H H 0.000 -8.565 -1.198 -2.151 0G6 CG C CR6 0.000 -6.549 -0.945 -2.793 0G6 CD2 C CR16 0.000 -5.499 -0.672 -1.908 0G6 HD2 H H 0.000 -5.652 -0.045 -1.040 0G6 CE2 C CR16 0.000 -4.231 -1.201 -2.137 0G6 HE2 H H 0.000 -3.423 -0.981 -1.450 0G6 CZ C CR16 0.000 -3.999 -2.012 -3.244 0G6 HZ H H 0.000 -3.013 -2.422 -3.420 0G6 CE1 C CR16 0.000 -5.040 -2.292 -4.124 0G6 HE1 H H 0.000 -4.864 -2.923 -4.987 0G6 CD1 C CR16 0.000 -6.309 -1.765 -3.895 0G6 HD1 H H 0.000 -7.114 -1.986 -4.585 0G6 HNH2 H H 0.000 -0.673 8.743 2.552 # ----------------------- 2.2 BONDS ------------------------------------------- loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd 0G6 CL C3 single 1.790 0.020 0G6 C3 H21 single 1.092 0.020 0G6 C3 H11 single 1.092 0.020 0G6 C3 C2 single 1.524 0.020 0G6 C2 H33 single 1.099 0.020 0G6 C2 O2 single 1.432 0.020 0G6 C2 CA2 single 1.524 0.020 0G6 O2 H34 single 0.967 0.020 0G6 CA2 HA2 single 1.099 0.020 0G6 CA2 CB2 single 1.524 0.020 0G6 CA2 N2 single 1.450 0.020 0G6 CB2 HB22 single 1.092 0.020 0G6 CB2 HB32 single 1.092 0.020 0G6 CB2 CG2 single 1.524 0.020 0G6 CG2 HG21 single 1.092 0.020 0G6 CG2 HG31 single 1.092 0.020 0G6 CG2 CD3 single 1.524 0.020 0G6 CD3 HD22 single 1.092 0.020 0G6 CD3 HD31 single 1.092 0.020 0G6 CD3 NE single 1.450 0.020 0G6 NE HE single 1.010 0.020 0G6 NE CZ1 single 1.330 0.020 0G6 CZ1 NH2 double 1.332 0.020 0G6 CZ1 NH1 single 1.332 0.020 0G6 NH1 HH12 single 1.010 0.020 0G6 NH1 HH11 single 1.010 0.020 0G6 N2 H1 single 1.010 0.020 0G6 N2 C1 single 1.330 0.020 0G6 C1 O1 double 1.220 0.020 0G6 C1 CA1 single 1.500 0.020 0G6 CA1 HA1 single 1.099 0.020 0G6 CA1 CB1 single 1.524 0.020 0G6 CA1 N1 single 1.455 0.020 0G6 CB1 HB31 single 1.092 0.020 0G6 CB1 HB21 single 1.092 0.020 0G6 CB1 CG1 single 1.524 0.020 0G6 CG1 HG2 single 1.092 0.020 0G6 CG1 HG3 single 1.092 0.020 0G6 CG1 CD single 1.524 0.020 0G6 CD HD21 single 1.092 0.020 0G6 CD HD3 single 1.092 0.020 0G6 CD N1 single 1.455 0.020 0G6 N1 C single 1.330 0.020 0G6 C O double 1.220 0.020 0G6 C CA single 1.500 0.020 0G6 CA HA single 1.099 0.020 0G6 CA N single 1.450 0.020 0G6 CA CB single 1.524 0.020 0G6 N H2 single 1.010 0.020 0G6 N H single 1.010 0.020 0G6 CB HB2 single 1.092 0.020 0G6 CB HB3 single 1.092 0.020 0G6 CB CG single 1.511 0.020 0G6 CG CD2 single 1.390 0.020 0G6 CG CD1 double 1.390 0.020 0G6 CD2 HD2 single 1.083 0.020 0G6 CD2 CE2 double 1.390 0.020 0G6 CE2 HE2 single 1.083 0.020 0G6 CE2 CZ single 1.390 0.020 0G6 CZ HZ single 1.083 0.020 0G6 CZ CE1 double 1.390 0.020 0G6 CE1 HE1 single 1.083 0.020 0G6 CE1 CD1 single 1.390 0.020 0G6 CD1 HD1 single 1.083 0.020 0G6 NH2 HNH2 single 1.010 0.020 0G6 NH2 HH21 single 1.010 0.020 # ----------------------- 2.3 ANGLES ------------------------------------------ loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd 0G6 O C CA 120.500 3.000 0G6 N1 C O 123.000 3.000 0G6 N1 C CA 116.500 3.000 0G6 C CA HA 108.810 3.000 0G6 C CA CB 109.470 3.000 0G6 C CA N 109.470 3.000 0G6 HA CA CB 108.340 3.000 0G6 HA CA N 109.470 3.000 0G6 N CA CB 109.470 3.000 0G6 CA CB HB2 109.470 3.000 0G6 CA CB HB3 109.470 3.000 0G6 CA CB CG 109.470 3.000 0G6 HB2 CB HB3 107.900 3.000 0G6 HB2 CB CG 109.470 3.000 0G6 HB3 CB CG 109.470 3.000 0G6 CB CG CD1 120.000 3.000 0G6 CB CG CD2 120.000 3.000 0G6 CD2 CG CD1 120.000 3.000 0G6 CG CD1 HD1 120.000 3.000 0G6 CG CD1 CE1 120.000 3.000 0G6 CE1 CD1 HD1 120.000 3.000 0G6 HE1 CE1 CD1 120.000 3.000 0G6 CZ CE1 CD1 120.000 3.000 0G6 CZ CE1 HE1 120.000 3.000 0G6 HZ CZ CE1 120.000 3.000 0G6 CE2 CZ CE1 120.000 3.000 0G6 CE2 CZ HZ 120.000 3.000 0G6 HE2 CE2 CZ 120.000 3.000 0G6 CD2 CE2 CZ 120.000 3.000 0G6 CD2 CE2 HE2 120.000 3.000 0G6 HD2 CD2 CE2 120.000 3.000 0G6 CG CD2 CE2 120.000 3.000 0G6 CG CD2 HD2 120.000 3.000 0G6 CA N H 120.000 3.000 0G6 CA N H2 120.000 3.000 0G6 H2 N H 120.000 3.000 0G6 CD N1 C 127.000 3.000 0G6 CA1 N1 C 121.000 3.000 0G6 CA1 N1 CD 112.000 3.000 0G6 HD21 CD N1 109.470 3.000 0G6 HD3 CD N1 109.470 3.000 0G6 CG1 CD N1 105.000 3.000 0G6 HD21 CD HD3 107.900 3.000 0G6 CG1 CD HD21 109.470 3.000 0G6 CG1 CD HD3 109.470 3.000 0G6 HG2 CG1 CD 109.470 3.000 0G6 HG3 CG1 CD 109.470 3.000 0G6 CB1 CG1 CD 111.000 3.000 0G6 HG2 CG1 HG3 107.900 3.000 0G6 CB1 CG1 HG2 109.470 3.000 0G6 CB1 CG1 HG3 109.470 3.000 0G6 HB21 CB1 CG1 109.470 3.000 0G6 HB31 CB1 CG1 109.470 3.000 0G6 CA1 CB1 CG1 111.000 3.000 0G6 HB21 CB1 HB31 107.900 3.000 0G6 CA1 CB1 HB21 109.470 3.000 0G6 CA1 CB1 HB31 109.470 3.000 0G6 HA1 CA1 N1 109.470 3.000 0G6 C1 CA1 N1 111.600 3.000 0G6 CB1 CA1 N1 105.000 3.000 0G6 C1 CA1 HA1 108.810 3.000 0G6 HA1 CA1 CB1 108.340 3.000 0G6 C1 CA1 CB1 109.470 3.000 0G6 O1 C1 CA1 120.500 3.000 0G6 N2 C1 CA1 116.500 3.000 0G6 N2 C1 O1 123.000 3.000 0G6 H1 N2 C1 120.000 3.000 0G6 CA2 N2 C1 121.500 3.000 0G6 CA2 N2 H1 118.500 3.000 0G6 HA2 CA2 N2 108.550 3.000 0G6 C2 CA2 N2 110.000 3.000 0G6 CB2 CA2 N2 110.000 3.000 0G6 C2 CA2 HA2 108.340 3.000 0G6 HA2 CA2 CB2 108.340 3.000 0G6 C2 CA2 CB2 111.000 3.000 0G6 H33 C2 CA2 108.340 3.000 0G6 O2 C2 CA2 109.470 3.000 0G6 C3 C2 CA2 111.000 3.000 0G6 H33 C2 O2 109.470 3.000 0G6 C3 C2 H33 108.340 3.000 0G6 C3 C2 O2 109.470 3.000 0G6 C2 O2 H34 109.470 3.000 0G6 H11 C3 C2 109.470 3.000 0G6 H21 C3 C2 109.470 3.000 0G6 CL C3 C2 109.500 3.000 0G6 H11 C3 H21 107.900 3.000 0G6 CL C3 H11 109.500 3.000 0G6 CL C3 H21 109.500 3.000 0G6 CA2 CB2 HB22 109.470 3.000 0G6 CA2 CB2 HB32 109.470 3.000 0G6 CA2 CB2 CG2 111.000 3.000 0G6 HB22 CB2 HB32 107.900 3.000 0G6 HB22 CB2 CG2 109.470 3.000 0G6 HB32 CB2 CG2 109.470 3.000 0G6 CB2 CG2 HG21 109.470 3.000 0G6 CB2 CG2 HG31 109.470 3.000 0G6 CB2 CG2 CD3 111.000 3.000 0G6 HG21 CG2 HG31 107.900 3.000 0G6 HG21 CG2 CD3 109.470 3.000 0G6 HG31 CG2 CD3 109.470 3.000 0G6 CG2 CD3 HD22 109.470 3.000 0G6 CG2 CD3 HD31 109.470 3.000 0G6 CG2 CD3 NE 112.000 3.000 0G6 HD22 CD3 HD31 107.900 3.000 0G6 HD22 CD3 NE 109.470 3.000 0G6 HD31 CD3 NE 109.470 3.000 0G6 CD3 NE HE 118.500 3.000 0G6 CD3 NE CZ1 121.500 3.000 0G6 HE NE CZ1 120.000 3.000 0G6 NE CZ1 NH2 120.000 3.000 0G6 NE CZ1 NH1 120.000 3.000 0G6 NH2 CZ1 NH1 120.000 3.000 0G6 CZ1 NH2 HH21 120.000 3.000 0G6 CZ1 NH2 HNH2 120.000 3.000 0G6 HH21 NH2 HNH2 120.000 3.000 0G6 CZ1 NH1 HH11 120.000 3.000 0G6 CZ1 NH1 HH12 120.000 3.000 0G6 HH12 NH1 HH11 120.000 3.000 # ----------------------- 2.4 TORSIONS ---------------------------------------- loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period 0G6 var_1 O C CA N 175.000 20.000 3 0G6 var_2 C CA CB CG 175.000 20.000 3 0G6 var_3 CA CB CG CD1 175.000 20.000 2 0G6 CONST_1 CB CG CD2 CE2 180.000 0.000 0 0G6 CONST_2 CB CG CD1 CE1 180.000 0.000 0 0G6 CONST_3 CG CD1 CE1 CZ 0.000 0.000 0 0G6 CONST_4 CE2 CZ CE1 CD1 0.000 0.000 0 0G6 CONST_5 CD2 CE2 CZ CE1 0.000 0.000 0 0G6 CONST_6 CG CD2 CE2 CZ 0.000 0.000 0 0G6 var_4 C CA N H2 175.000 20.000 1 0G6 CONST_7 CA1 N1 C O 180.000 0.000 0 0G6 var_5 CG1 CD N1 C -120.000 20.000 1 0G6 var_6 CB1 CG1 CD N1 -60.000 20.000 3 0G6 var_7 CA1 CB1 CG1 CD 30.000 20.000 3 0G6 var_8 C1 CA1 N1 C -90.000 20.000 3 0G6 var_9 CG1 CB1 CA1 N1 0.000 20.000 3 0G6 var_10 N2 C1 CA1 N1 175.000 20.000 3 0G6 CONST_8 CA2 N2 C1 CA1 180.000 0.000 0 0G6 var_11 CB2 CA2 N2 C1 175.000 20.000 3 0G6 var_12 C3 C2 CA2 N2 175.000 20.000 3 0G6 var_13 H34 O2 C2 CA2 175.000 20.000 1 0G6 var_14 CL C3 C2 CA2 175.000 20.000 3 0G6 var_15 CG2 CB2 CA2 N2 175.000 20.000 3 0G6 var_16 CA2 CB2 CG2 CD3 175.000 20.000 3 0G6 var_17 CB2 CG2 CD3 NE 175.000 20.000 3 0G6 var_18 CG2 CD3 NE CZ1 175.000 20.000 3 0G6 CONST_9 CD3 NE CZ1 NH1 180.000 0.000 0 0G6 CONST_10 NE CZ1 NH2 HNH2 180.000 0.000 0 0G6 CONST_11 NE CZ1 NH1 HH12 180.000 0.000 0 # ----------------------- 2.5 CHIRALITIES ------------------------------------- loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign 0G6 chir_01 C2 C3 CA2 O2 positiv 0G6 chir_02 CA2 C2 CB2 N2 positiv 0G6 chir_03 CA1 C1 CB1 N1 positiv 0G6 chir_04 CA C CB N negativ # ----------------------- 2.6 PLANES ------------------------------------------ loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd 0G6 plan-1 CD3 0.020 0G6 plan-1 NE 0.020 0G6 plan-1 HE 0.020 0G6 plan-1 CZ1 0.020 0G6 plan-2 NE 0.020 0G6 plan-2 HE 0.020 0G6 plan-2 CZ1 0.020 0G6 plan-2 NH2 0.020 0G6 plan-2 HH21 0.020 0G6 plan-2 NH1 0.020 0G6 plan-2 HH12 0.020 0G6 plan-2 HH11 0.020 0G6 plan-2 HNH2 0.020 0G6 plan-3 CZ1 0.020 0G6 plan-3 NH1 0.020 0G6 plan-3 HH12 0.020 0G6 plan-3 HH11 0.020 0G6 plan-4 CA2 0.020 0G6 plan-4 N2 0.020 0G6 plan-4 H1 0.020 0G6 plan-4 C1 0.020 0G6 plan-5 N2 0.020 0G6 plan-5 H1 0.020 0G6 plan-5 C1 0.020 0G6 plan-5 O1 0.020 0G6 plan-5 CA1 0.020 0G6 plan-6 CA1 0.020 0G6 plan-6 CD 0.020 0G6 plan-6 N1 0.020 0G6 plan-6 C 0.020 0G6 plan-7 N1 0.020 0G6 plan-7 C 0.020 0G6 plan-7 O 0.020 0G6 plan-7 CA 0.020 0G6 plan-8 CA 0.020 0G6 plan-8 N 0.020 0G6 plan-8 H2 0.020 0G6 plan-8 H 0.020 0G6 plan-9 CB 0.020 0G6 plan-9 CG 0.020 0G6 plan-9 CD2 0.020 0G6 plan-9 HD2 0.020 0G6 plan-9 CE2 0.020 0G6 plan-9 HE2 0.020 0G6 plan-9 CZ 0.020 0G6 plan-9 HZ 0.020 0G6 plan-9 CE1 0.020 0G6 plan-9 HE1 0.020 0G6 plan-9 CD1 0.020 0G6 plan-9 HD1 0.020 # ----------------------- 3 PPACK MODIFICATIONS ------------------------------- # delete atoms H33, H34 and CL, # bonds C2-H33, O2-H34 and CL-C3, # angles H33-C2-CA2/O2/C3, H34-O2-C2, and CL-C3-C2/H11/H21, and # the chiral center at C2 (chir_01) # change atom type of C2 from CH1 ("connected to 1 hydrogen") # to CT ("without hydrogen") # change atom type of O2 from OH1 ("oxygen of alcohol groups") # to OC ("with a NET charge") data_mod_0G6mod1 loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge 0G6mod1 change C2 . . CT . 0G6mod1 change O2 . . OC -1.000 0G6mod1 delete H33 . . . . 0G6mod1 delete H34 . . . . 0G6mod1 delete CL . . . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd 0G6mod1 delete C2 H33 single . . 0G6mod1 delete O2 H34 single . . 0G6mod1 delete CL C3 single . . loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd 0G6mod1 delete H33 C2 CA2 . . 0G6mod1 delete H33 C2 O2 . . 0G6mod1 delete C3 C2 H33 . . 0G6mod1 delete C2 O2 H34 . . 0G6mod1 delete CL C3 C2 . . 0G6mod1 delete CL C3 H11 . . 0G6mod1 delete CL C3 H21 . . loop_ _chem_mod_chir.mod_id _chem_mod_chir.function _chem_mod_chir.id _chem_mod_chir.atom_id_centre _chem_mod_chir.atom_id_1 _chem_mod_chir.atom_id_2 _chem_mod_chir.atom_id_3 _chem_mod_chir.new_volume_sign 0G6mod1 delete chir_01 C2 C3 CA2 O2 positiv 0G6mod1 add chir_01 C2 C3 O2 CA2 both # ----------------------- 4 SERINE MODIFICATIONS ------------------------------ # delete atom HG, # the OG-HG single bond, and # the CB-OG-HG angle # change atom type of OG from OH1 ("oxygen of alcohol groups") # to O2 ("connected to 2 atoms") data_mod_SERmod1 loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge SERmod1 change OG . . O2 . SERmod1 delete HG . . . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd SERmod1 delete OG HG single . . loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd SERmod1 delete CB OG HG . . # ----------------------- 5 HISTIDINE MODIFICATIONS --------------------------- # delete atom HE2, # the bond NE2-HE2, # the angles HE2-NE2-CD2/CE1, and # plan-1 (plane of the imidazole ring) # change atom type of NE2 from NR15 ("connected to 1 hyd. in 5 atoms ring") # to NR5 ("connected to 3 atoms in 5 atoms ring") # change angle CE1-NE2-CE2 from 108° +- 3° to 126° +- 3° data_mod_HISmod1 loop_ _chem_mod_atom.mod_id _chem_mod_atom.function _chem_mod_atom.atom_id _chem_mod_atom.new_atom_id _chem_mod_atom.new_type_symbol _chem_mod_atom.new_type_energy _chem_mod_atom.new_partial_charge HISmod1 change NE2 . . NR5 . HISmod1 delete HE2 . . . . loop_ _chem_mod_bond.mod_id _chem_mod_bond.function _chem_mod_bond.atom_id_1 _chem_mod_bond.atom_id_2 _chem_mod_bond.new_type _chem_mod_bond.new_value_dist _chem_mod_bond.new_value_dist_esd HISmod1 delete NE2 HE2 single . . loop_ _chem_mod_angle.mod_id _chem_mod_angle.function _chem_mod_angle.atom_id_1 _chem_mod_angle.atom_id_2 _chem_mod_angle.atom_id_3 _chem_mod_angle.new_value_angle _chem_mod_angle.new_value_angle_esd HISmod1 delete HE2 NE2 CD2 . . HISmod1 change CE1 NE2 CD2 126.000 3.000 HISmod1 delete CE1 NE2 HE2 . . loop_ _chem_mod_plane_atom.mod_id _chem_mod_plane_atom.function _chem_mod_plane_atom.plane_id _chem_mod_plane_atom.atom_id _chem_mod_plane_atom.new_dist_esd HISmod1 delete plan-1 CB . HISmod1 delete plan-1 CG . HISmod1 delete plan-1 ND1 . HISmod1 delete plan-1 HD1 . HISmod1 delete plan-1 CE1 . HISmod1 delete plan-1 NE2 . HISmod1 delete plan-1 HE2 . HISmod1 delete plan-1 CD2 . HISmod1 delete plan-1 HD2 . # ----------------------- 6 PPACK-SER LINK ------------------------------------ # create a single bond between PPACK_C2 and SER_OG, and # angles P_C2-S_OG-S_CB, S_OG-P_C2-P_O2/CA2/C3 data_link_0G6-SER loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd 0G6-SER 1 C2 2 OG single 1.426 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd 0G6-SER 1 C2 2 OG 2 CB 111.800 3.000 0G6-SER 1 O2 1 C2 2 OG 109.500 3.000 0G6-SER 1 C3 1 C2 2 OG 109.470 3.000 0G6-SER 1 CA2 1 C2 2 OG 109.470 3.000 # ----------------------- 7 PPACK-HIS LINK ------------------------------------ # create a single bond between PPACK_C3 and HIS_NE2, and # angles H_NE2-P_C3-P_H11/H21/C2 and P_C3-H_NE2-H_CE1/CD2, and # a new plane (imidazole ring, basically the same plane # that was deleted under § 5 with P_C3 instead of H_HE2) data_link_0G6-HIS loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd 0G6-HIS 1 C3 2 NE2 single 1.462 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd 0G6-HIS 1 C3 2 NE2 2 CD2 126.000 3.000 0G6-HIS 1 C3 2 NE2 2 CE1 108.000 3.000 0G6-HIS 1 H21 1 C3 2 NE2 109.500 3.000 0G6-HIS 1 H11 1 C3 2 NE2 109.500 3.000 0G6-HIS 1 C2 1 C3 2 NE2 109.500 3.000 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd 0G6-HIS plan-10 1 C3 0.020 0G6-HIS plan-10 2 CB 0.020 0G6-HIS plan-10 2 CG 0.020 0G6-HIS plan-10 2 ND1 0.020 0G6-HIS plan-10 2 HD1 0.020 0G6-HIS plan-10 2 CE1 0.020 0G6-HIS plan-10 2 NE2 0.020 0G6-HIS plan-10 2 CD2 0.020 0G6-HIS plan-10 2 HD2 0.020