# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:32:54 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3-chlorophenoxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cccc(Cl)c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 JMV  JMV  '(3-chlorophenoxy)acetic acid'  ligand  19  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JMV
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 JMV  C10   C   CR6   0  -0.007   2.2693  -0.1841  -0.0117
 JMV  O01   O   OH1   0  -0.564  -4.0180  -1.4787  -0.0379
 JMV  C02   C   C     0   0.531  -3.3857  -0.3169   0.0109
 JMV  O03   O   O     0  -0.499  -3.9222   0.7545   0.0369
 JMV  C04   C   CH2   0  -0.273  -1.8930  -0.5409   0.0144
 JMV  O05   O   O2    0  -0.510  -1.2736   0.7089   0.0804
 JMV  C06   C   CR6   0   0.309   0.0718   0.7601   0.0498
 JMV  C07   C   CR16  0  -0.266   0.6360   2.0363   0.0606
 JMV  C08   C   CR16  0  -0.220   2.0087   2.1783   0.0336
 JMV  C09   C   CR16  0  -0.300   2.8475   1.0694  -0.0033
 JMV  CL11  CL  CL    0  -0.117   3.2803  -1.5883  -0.0540
 JMV  C12   C   CR16  0  -0.264   0.8918  -0.3627   0.0133
 JMV  H1    H   HOH1  0   0.503  -4.9719  -1.3261  -0.0568
 JMV  H042  H   HCH2  0   0.236  -1.6369  -1.1809   0.8682
 JMV  H041  H   HCH2  0   0.297  -1.6143  -1.0873  -0.8956
 JMV  H071  H   HCR6  0   0.280  -0.0141   2.9001   0.0879
 JMV  H081  H   HCR6  0   0.276   2.4413   3.1699   0.0412
 JMV  H091  H   HCR6  0   0.274   3.9215   1.1834  -0.0239
 JMV  H121  H   HCR6  0   0.312   0.4895  -1.3659   0.0077

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
_chem_comp_bond.value_dist_neutron
 JMV  CL11  C10   single    1.731  0.020  1.731
 JMV  C10   C12   aromatic  1.389  0.020  1.389
 JMV  C10   C09   aromatic  1.380  0.020  1.380
 JMV  C12   C06   aromatic  1.391  0.020  1.391
 JMV  C09   C08   aromatic  1.391  0.020  1.391
 JMV  C06   O05   single    1.347  0.020  1.347
 JMV  C06   C07   aromatic  1.395  0.020  1.395
 JMV  C08   C07   aromatic  1.380  0.020  1.380
 JMV  O05   C04   single    1.396  0.020  1.396
 JMV  C04   C02   single    1.509  0.020  1.509
 JMV  O03   C02   double    1.199  0.020  1.199
 JMV  C02   O01   single    1.324  0.020  1.324
 JMV  O01   H1    single    0.850  0.020  0.980
 JMV  C04   H042  single    0.970  0.020  1.090
 JMV  C04   H041  single    0.970  0.020  1.090
 JMV  C07   H071  single    0.930  0.020  1.080
 JMV  C08   H081  single    0.930  0.020  1.080
 JMV  C09   H091  single    0.930  0.020  1.080
 JMV  C12   H121  single    0.930  0.020  1.080

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
 JMV  C12   C10  CL11  118.37  3.000
 JMV  C12   C10  C09   122.14  3.000
 JMV  CL11  C10  C09   119.49  3.000
 JMV  H1    O01  C02   109.49  3.000
 JMV  C04   C02  O03   125.12  3.000
 JMV  O03   C02  O01   124.86  3.000
 JMV  C04   C02  O01   110.01  3.000
 JMV  H041  C04  H042  107.19  3.000
 JMV  H041  C04  O05   111.85  3.000
 JMV  H042  C04  O05   112.44  3.000
 JMV  H041  C04  C02   108.85  3.000
 JMV  H042  C04  C02   108.62  3.000
 JMV  O05   C04  C02   107.81  3.000
 JMV  C06   O05  C04   118.43  3.000
 JMV  C12   C06  C07   120.01  3.000
 JMV  C07   C06  O05   116.01  3.000
 JMV  C12   C06  O05   123.98  3.000
 JMV  H071  C07  C08   121.07  3.000
 JMV  H071  C07  C06   119.19  3.000
 JMV  C08   C07  C06   119.73  3.000
 JMV  H081  C08  C09   119.32  3.000
 JMV  H081  C08  C07   119.46  3.000
 JMV  C09   C08  C07   121.22  3.000
 JMV  H091  C09  C08   121.07  3.000
 JMV  H091  C09  C10   120.80  3.000
 JMV  C08   C09  C10   118.13  3.000
 JMV  H121  C12  C06   122.00  3.000
 JMV  H121  C12  C10   119.23  3.000
 JMV  C06   C12  C10   118.76  3.000

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
 JMV  CONST_01  C07   C06  C12  C10     0.00   0.0  0
 JMV  CONST_02  C07   C08  C09  C10     0.00   0.0  0
 JMV  CONST_03  C09   C10  C12  C06     0.00   0.0  0
 JMV  CONST_04  C09   C08  C07  C06     0.00   0.0  0
 JMV  CONST_05  C12   C10  C09  C08     0.00   0.0  0
 JMV  CONST_06  C12   C06  C07  C08     0.00   0.0  0
 JMV  CONST_07  O05   C06  C12  C10   180.00   0.0  0
 JMV  CONST_08  C08   C07  C06  O05   180.00   0.0  0
 JMV  CONST_09  CL11  C10  C12  C06   180.00   0.0  0
 JMV  CONST_10  CL11  C10  C09  C08   180.00   0.0  0
 JMV  CONST_11  H081  C08  C09  C10   180.00   0.0  0
 JMV  CONST_12  H121  C12  C06  C07   180.00   0.0  0
 JMV  CONST_13  H091  C09  C08  C07   180.00   0.0  0
 JMV  CONST_14  H071  C07  C08  C09   180.00   0.0  0
 JMV  CONST_15  H1    O01  C02  O03     0.00   0.0  0
 JMV  Var_01    C12   C06  O05  C04    -2.85  30.0  3
 JMV  Var_02    H042  C04  O05  C06    62.52  30.0  3
 JMV  Var_03    O05   C04  C02  O01  -179.40  30.0  2

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
 JMV  plan-1  C10   0.020
 JMV  plan-1  O05   0.020
 JMV  plan-1  C06   0.020
 JMV  plan-1  C07   0.020
 JMV  plan-1  C08   0.020
 JMV  plan-1  C09   0.020
 JMV  plan-1  CL11  0.020
 JMV  plan-1  C12   0.020
 JMV  plan-1  H071  0.020
 JMV  plan-1  H081  0.020
 JMV  plan-1  H091  0.020
 JMV  plan-1  H121  0.020
 JMV  plan-2  O01   0.020
 JMV  plan-2  C02   0.020
 JMV  plan-2  O03   0.020
 JMV  plan-2  C04   0.020
 JMV  plan-2  H1    0.020

