# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:49:22 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  18  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 PERFECT
;

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  -0.019   2.2607  -0.1698   0.0112
 JMV  O01   O   OC    -1  -0.620  -4.0636  -1.4186   0.0980
 JMV  C02   C   C      0   0.386  -3.4461  -0.3383   0.0349
 JMV  O03   O   O      0  -0.591  -3.9105   0.8097  -0.0025
 JMV  C04   C   CH2    0  -0.338  -1.9187  -0.5108   0.0010
 JMV  O05   O   O2     0  -0.458  -1.2728   0.7494  -0.0352
 JMV  C06   C   CR6    0   0.393   0.0652   0.7914  -0.0156
 JMV  C07   C   CR16   0  -0.345   0.6501   2.0622   0.0026
 JMV  C08   C   CR16   0  -0.244   2.0251   2.1927   0.0259
 JMV  C09   C   CR16   0  -0.256   2.8566   1.0767   0.0312
 JMV  CL11  CL  CL     0  -0.131   3.2617  -1.5886   0.0156
 JMV  C12   C   CR16   0  -0.342   0.8825  -0.3389  -0.0122
 JMV  H042  H   HCH2   0   0.231  -1.6036  -1.0754   0.8866
 JMV  H041  H   HCH2   0   0.232  -1.6441  -1.1089  -0.8764
 JMV  H071  H   HCR6   0   0.266   0.0144   2.9383   0.0004
 JMV  H081  H   HCR6   0   0.267   2.4648   3.1813   0.0418
 JMV  H091  H   HCR6   0   0.274   3.9320   1.1824   0.0498
 JMV  H121  H   HCR6   0   0.296   0.4703  -1.3379  -0.0284

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    1.736  0.020  1.736
 JMV  C10   C12   aromatic  1.389  0.020  1.389
 JMV  C10   C09   aromatic  1.382  0.020  1.382
 JMV  C12   C06   aromatic  1.395  0.020  1.395
 JMV  C09   C08   aromatic  1.392  0.020  1.392
 JMV  C06   O05   single    1.339  0.020  1.339
 JMV  C06   C07   aromatic  1.399  0.020  1.399
 JMV  C08   C07   aromatic  1.381  0.020  1.381
 JMV  O05   C04   single    1.417  0.020  1.417
 JMV  C04   C02   single    1.538  0.020  1.538
 JMV  O03   C02   deloc     1.239  0.020  1.239
 JMV  C02   O01   deloc     1.246  0.020  1.246
 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  118.21  3.000
 JMV  C12   C10  C09   122.56  3.000
 JMV  CL11  C10  C09   119.24  3.000
 JMV  C04   C02  O03   118.40  3.000
 JMV  O03   C02  O01   128.26  3.000
 JMV  C04   C02  O01   113.34  3.000
 JMV  H041  C04  H042  107.06  3.000
 JMV  H041  C04  O05   110.52  3.000
 JMV  H042  C04  O05   110.35  3.000
 JMV  H041  C04  C02   109.12  3.000
 JMV  H042  C04  C02   108.99  3.000
 JMV  O05   C04  C02   110.71  3.000
 JMV  C06   O05  C04   118.90  3.000
 JMV  C12   C06  C07   119.41  3.000
 JMV  C07   C06  O05   116.52  3.000
 JMV  C12   C06  O05   124.07  3.000
 JMV  H071  C07  C08   120.55  3.000
 JMV  H071  C07  C06   119.31  3.000
 JMV  C08   C07  C06   120.14  3.000
 JMV  H081  C08  C09   119.32  3.000
 JMV  H081  C08  C07   119.41  3.000
 JMV  C09   C08  C07   121.27  3.000
 JMV  H091  C09  C08   121.08  3.000
 JMV  H091  C09  C10   121.17  3.000
 JMV  C08   C09  C10   117.75  3.000
 JMV  H121  C12  C06   121.70  3.000
 JMV  H121  C12  C10   119.43  3.000
 JMV  C06   C12  C10   118.87  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  Var_01    C12   C06  O05  C04     2.54  30.0  2
 JMV  Var_02    H042  C04  O05  C06    56.68  30.0  3
 JMV  Var_03    O05   C04  C02  O01  -178.47  30.0  3

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

