# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:33:18 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (2,4-dichlorophenoxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1ccc(Cl)cc1Cl
#
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
 CFA  CFA  '(2,4-dichlorophenoxy)acetic acid'  ligand  18  13  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CFA
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
 CFA  C1    C   C      0   0.385   0.4167  -0.0102   3.8266
 CFA  C2    C   CH2    0  -0.338   0.9490  -0.0060   2.3836
 CFA  C1'   C   CR6    0   0.474   0.1531  -0.0147   0.1534
 CFA  C2'   C   CR6    0  -0.169  -0.9359  -0.0275  -0.7288
 CFA  C3'   C   CR16   0  -0.163  -0.7641  -0.0270  -2.0993
 CFA  C4'   C   CR6    0  -0.075   0.5231  -0.0136  -2.6163
 CFA  C5'   C   CR16   0  -0.194   1.6195  -0.0013  -1.7752
 CFA  CL3   CL  CL     0  -0.101  -2.5343  -0.0441  -0.0753
 CFA  C6'   C   CR16   0  -0.398   1.4324  -0.0017  -0.3996
 CFA  O1    O   OC    -1  -0.621   1.3208  -0.0121   4.6843
 CFA  O2    O   O      0  -0.586  -0.8088  -0.0097   4.0028
 CFA  O1'   O   O2     0  -0.436  -0.1244  -0.0159   1.4557
 CFA  CL4   CL  CL     0  -0.129   0.7458  -0.0126  -4.3351
 CFA  H2C1  H   HCH2   0   0.235   1.5754   0.8820   2.2355
 CFA  H2C2  H   HCH2   0   0.235   1.5926  -0.8812   2.2344
 CFA  H3'   H   HCR6   0   0.299  -1.6251  -0.0364  -2.7530
 CFA  H5'   H   HCR6   0   0.286   2.6238   0.0092  -2.1761
 CFA  H6'   H   HCR6   0   0.297   2.3067   0.0079   0.2356

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
 CFA  C1   C2    single    1.538  0.020  1.538
 CFA  C1   O1    deloc     1.246  0.020  1.246
 CFA  C1   O2    deloc     1.238  0.020  1.238
 CFA  C2   O1'   single    1.419  0.020  1.419
 CFA  C2   H2C1  single    0.970  0.020  1.090
 CFA  C2   H2C2  single    0.970  0.020  1.090
 CFA  C1'  C2'   aromatic  1.401  0.020  1.401
 CFA  C1'  C6'   aromatic  1.394  0.020  1.394
 CFA  C1'  O1'   single    1.332  0.020  1.332
 CFA  C2'  C3'   aromatic  1.381  0.020  1.381
 CFA  C2'  CL3   single    1.727  0.020  1.727
 CFA  C3'  C4'   aromatic  1.387  0.020  1.387
 CFA  C3'  H3'   single    0.930  0.020  1.080
 CFA  C4'  C5'   aromatic  1.382  0.020  1.382
 CFA  C4'  CL4   single    1.733  0.020  1.733
 CFA  C5'  C6'   aromatic  1.388  0.020  1.388
 CFA  C5'  H5'   single    0.930  0.020  1.080
 CFA  C6'  H6'   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
 CFA  O2    C1   O1    128.33  3.000
 CFA  O2    C1   C2    118.43  3.000
 CFA  O1    C1   C2    113.24  3.000
 CFA  H2C2  C2   H2C1  107.01  3.000
 CFA  H2C2  C2   O1'   110.46  3.000
 CFA  H2C1  C2   O1'   110.45  3.000
 CFA  H2C2  C2   C1    109.18  3.000
 CFA  H2C1  C2   C1    109.06  3.000
 CFA  O1'   C2   C1    110.59  3.000
 CFA  O1'   C1'  C6'   125.40  3.000
 CFA  O1'   C1'  C2'   116.99  3.000
 CFA  C6'   C1'  C2'   117.61  3.000
 CFA  CL3   C2'  C3'   119.38  3.000
 CFA  CL3   C2'  C1'   118.75  3.000
 CFA  C3'   C2'  C1'   121.87  3.000
 CFA  H3'   C3'  C4'   120.91  3.000
 CFA  H3'   C3'  C2'   120.06  3.000
 CFA  C4'   C3'  C2'   119.03  3.000
 CFA  CL4   C4'  C5'   120.11  3.000
 CFA  CL4   C4'  C3'   119.26  3.000
 CFA  C5'   C4'  C3'   120.63  3.000
 CFA  H5'   C5'  C6'   119.51  3.000
 CFA  H5'   C5'  C4'   120.75  3.000
 CFA  C6'   C5'  C4'   119.75  3.000
 CFA  H6'   C6'  C5'   118.25  3.000
 CFA  H6'   C6'  C1'   120.63  3.000
 CFA  C5'   C6'  C1'   121.12  3.000
 CFA  C1'   O1'  C2    118.82  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
 CFA  CONST_01  C4'   C3'  C2'  C1'    0.00   0.0  0
 CFA  CONST_02  C4'   C5'  C6'  C1'    0.00   0.0  0
 CFA  CONST_03  C5'   C6'  C1'  C2'    0.00   0.0  0
 CFA  CONST_04  C5'   C4'  C3'  C2'    0.00   0.0  0
 CFA  CONST_05  C6'   C1'  C2'  C3'    0.00   0.0  0
 CFA  CONST_06  C6'   C5'  C4'  C3'    0.00   0.0  0
 CFA  CONST_07  CL4   C4'  C3'  C2'  180.00   0.0  0
 CFA  CONST_08  O1'   C1'  C2'  C3'  180.00   0.0  0
 CFA  CONST_09  CL3   C2'  C3'  C4'  180.00   0.0  0
 CFA  CONST_10  O1'   C1'  C6'  C5'  180.00   0.0  0
 CFA  CONST_11  C6'   C1'  C2'  CL3  180.00   0.0  0
 CFA  CONST_12  CL4   C4'  C5'  C6'  180.00   0.0  0
 CFA  CONST_13  H3'   C3'  C2'  C1'  180.00   0.0  0
 CFA  CONST_14  H5'   C5'  C6'  C1'  180.00   0.0  0
 CFA  CONST_15  H6'   C6'  C1'  C2'  180.00   0.0  0
 CFA  Var_01    C2'   C1'  O1'  C2   179.87  30.0  2
 CFA  Var_02    H2C1  C2   O1'  C1'   59.21  30.0  2
 CFA  Var_03    O1'   C2   C1   O1   179.49  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
 CFA  plan-1  C1'  0.020
 CFA  plan-1  C2'  0.020
 CFA  plan-1  C3'  0.020
 CFA  plan-1  C4'  0.020
 CFA  plan-1  C5'  0.020
 CFA  plan-1  CL3  0.020
 CFA  plan-1  C6'  0.020
 CFA  plan-1  O1'  0.020
 CFA  plan-1  CL4  0.020
 CFA  plan-1  H3'  0.020
 CFA  plan-1  H5'  0.020
 CFA  plan-1  H6'  0.020
 CFA  plan-2  C1   0.020
 CFA  plan-2  C2   0.020
 CFA  plan-2  O1   0.020
 CFA  plan-2  O2   0.020

