# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:28:58 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S)-(4-chlorophenyl)[3-(trifluoromethyl)phenoxy]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Oc1cccc(c1)C(F)(F)F)c2ccc(Cl)cc2
#
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
 MSZ  MSZ  '(2S)-(4-chlorophenyl)[3-(trifluoromethyl)phenoxy]ethanoic acid'  ligand  31  22  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MSZ
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
 MSZ  C16  C   CR16   0  -0.360  -1.7182   1.6382   1.0352
 MSZ  C13  C   CR6    0   0.439  -1.3171   0.4242   0.4765
 MSZ  C14  C   CR16   0  -0.391  -2.2843  -0.4832   0.0510
 MSZ  C15  C   CR6    0  -0.175  -3.6317  -0.1797   0.1818
 MSZ  C18  C   CR16   0  -0.315  -4.0393   1.0289   0.7316
 MSZ  C17  C   CR16   0  -0.233  -3.0690   1.9245   1.1557
 MSZ  C19  C   CT     0   1.048  -4.6274  -1.1816  -0.3130
 MSZ  F22  F   F      0  -0.302  -5.8891  -0.8338  -0.0454
 MSZ  F21  F   F      0  -0.316  -4.5421  -1.3483  -1.6421
 MSZ  O12  O   O2     0  -0.480  -0.0431   0.0246   0.3515
 MSZ  C8   C   CH1    0  -0.154   0.9936   0.9683   0.5377
 MSZ  C9   C   C      0   0.394   0.9443   2.1371  -0.4916
 MSZ  O10  O   OC    -1  -0.590   1.6015   3.1374  -0.1589
 MSZ  O11  O   O      0  -0.573   0.3043   1.9350  -1.5319
 MSZ  C2   C   CR6    0  -0.055   4.7545  -0.9736  -0.0839
 MSZ  C4   C   CR16   0  -0.199   4.6266  -0.0343   0.9263
 MSZ  C3   C   CR16   0  -0.313   3.3951   0.5707   1.1303
 MSZ  C7   C   CR6    0   0.101   2.2957   0.2462   0.3435
 MSZ  C6   C   CR16   0  -0.297   2.4522  -0.6930  -0.6726
 MSZ  C5   C   CR16   0  -0.198   3.6758  -1.3092  -0.8876
 MSZ  H1   H   HCR6   0   0.284  -0.9978   2.3676   1.3801
 MSZ  H2   H   HCR6   0   0.276  -1.9597  -1.4242  -0.3769
 MSZ  H3   H   HCR6   0   0.266  -5.0845   1.2806   0.8379
 MSZ  H4   H   HCR6   0   0.269  -3.3701   2.8682   1.5904
 MSZ  H5   H   HCH1   0   0.251   0.9606   1.3753   1.5555
 MSZ  H7   H   HCR6   0   0.278   5.4720   0.2243   1.5495
 MSZ  H8   H   HCR6   0   0.259   3.2926   1.2988   1.9249
 MSZ  H9   H   HCR6   0   0.260   1.6187  -0.9529  -1.3115
 MSZ  H10  H   HCR6   0   0.277   3.7843  -2.0416  -1.6760
 MSZ  F20  F   F      0  -0.315  -4.4317  -2.3912   0.2323
 MSZ  CL   CL  CL     0  -0.135   6.2872  -1.7434  -0.3472

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
 MSZ  O11  C9   deloc     1.238  0.020  1.238
 MSZ  C17  C16  aromatic  1.386  0.020  1.386
 MSZ  C17  C18  aromatic  1.387  0.020  1.387
 MSZ  C16  C13  aromatic  1.395  0.020  1.395
 MSZ  C9   O10  deloc     1.242  0.020  1.242
 MSZ  C9   C8   single    1.558  0.020  1.558
 MSZ  C18  C15  aromatic  1.389  0.020  1.389
 MSZ  O12  C13  single    1.341  0.020  1.341
 MSZ  O12  C8   single    1.414  0.020  1.414
 MSZ  C13  C14  aromatic  1.393  0.020  1.393
 MSZ  C8   C7   single    1.502  0.020  1.502
 MSZ  C15  C14  aromatic  1.387  0.020  1.387
 MSZ  C15  C19  single    1.497  0.020  1.497
 MSZ  C3   C7   aromatic  1.390  0.020  1.390
 MSZ  C3   C4   aromatic  1.387  0.020  1.387
 MSZ  F21  C19  single    1.342  0.020  1.342
 MSZ  C7   C6   aromatic  1.393  0.020  1.393
 MSZ  C4   C2   aromatic  1.385  0.020  1.385
 MSZ  C19  F20  single    1.341  0.020  1.341
 MSZ  C19  F22  single    1.336  0.020  1.336
 MSZ  C6   C5   aromatic  1.387  0.020  1.387
 MSZ  C2   C5   aromatic  1.386  0.020  1.386
 MSZ  C2   CL   single    1.735  0.020  1.735
 MSZ  C16  H1   single    0.930  0.020  1.080
 MSZ  C14  H2   single    0.930  0.020  1.080
 MSZ  C18  H3   single    0.930  0.020  1.080
 MSZ  C17  H4   single    0.930  0.020  1.080
 MSZ  C8   H5   single    0.970  0.020  1.090
 MSZ  C4   H7   single    0.930  0.020  1.080
 MSZ  C3   H8   single    0.930  0.020  1.080
 MSZ  C6   H9   single    0.930  0.020  1.080
 MSZ  C5   H10  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
 MSZ  H1   C16  C17  118.82  3.000
 MSZ  H1   C16  C13  121.54  3.000
 MSZ  C17  C16  C13  119.64  3.000
 MSZ  O12  C13  C14  115.93  3.000
 MSZ  C14  C13  C16  119.31  3.000
 MSZ  O12  C13  C16  124.72  3.000
 MSZ  H2   C14  C15  121.21  3.000
 MSZ  H2   C14  C13  118.58  3.000
 MSZ  C15  C14  C13  120.21  3.000
 MSZ  C19  C15  C18  121.20  3.000
 MSZ  C19  C15  C14  117.94  3.000
 MSZ  C18  C15  C14  120.85  3.000
 MSZ  H3   C18  C17  119.76  3.000
 MSZ  H3   C18  C15  121.71  3.000
 MSZ  C17  C18  C15  118.53  3.000
 MSZ  H4   C17  C18  119.44  3.000
 MSZ  H4   C17  C16  119.10  3.000
 MSZ  C18  C17  C16  121.46  3.000
 MSZ  F21  C19  F22  106.90  3.000
 MSZ  F22  C19  F20  106.93  3.000
 MSZ  F21  C19  F20  106.34  3.000
 MSZ  F22  C19  C15  112.82  3.000
 MSZ  F20  C19  C15  111.85  3.000
 MSZ  F21  C19  C15  111.61  3.000
 MSZ  C8   O12  C13  119.04  3.000
 MSZ  H5   C8   C7   108.94  3.000
 MSZ  H5   C8   C9   109.50  3.000
 MSZ  C7   C8   C9   107.63  3.000
 MSZ  H5   C8   O12  110.35  3.000
 MSZ  C7   C8   O12  107.32  3.000
 MSZ  C9   C8   O12  112.98  3.000
 MSZ  O11  C9   O10  129.05  3.000
 MSZ  O10  C9   C8   114.22  3.000
 MSZ  O11  C9   C8   116.68  3.000
 MSZ  CL   C2   C5   119.46  3.000
 MSZ  CL   C2   C4   119.54  3.000
 MSZ  C5   C2   C4   121.00  3.000
 MSZ  H7   C4   C3   120.32  3.000
 MSZ  H7   C4   C2   120.67  3.000
 MSZ  C3   C4   C2   119.01  3.000
 MSZ  H8   C3   C7   119.84  3.000
 MSZ  H8   C3   C4   119.03  3.000
 MSZ  C7   C3   C4   121.13  3.000
 MSZ  C6   C7   C3   118.78  3.000
 MSZ  C6   C7   C8   121.08  3.000
 MSZ  C3   C7   C8   120.02  3.000
 MSZ  H9   C6   C5   118.78  3.000
 MSZ  H9   C6   C7   120.42  3.000
 MSZ  C5   C6   C7   120.79  3.000
 MSZ  H10  C5   C6   120.16  3.000
 MSZ  H10  C5   C2   120.56  3.000
 MSZ  C6   C5   C2   119.28  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
 MSZ  CONST_01  C15  C18  C17  C16    0.00   0.0  0
 MSZ  CONST_02  C15  C14  C13  C16    0.00   0.0  0
 MSZ  CONST_03  C18  C17  C16  C13    0.00   0.0  0
 MSZ  CONST_04  C18  C15  C14  C13    0.00   0.0  0
 MSZ  CONST_05  C17  C16  C13  C14    0.00   0.0  0
 MSZ  CONST_06  C17  C18  C15  C14    0.00   0.0  0
 MSZ  CONST_07  C7   C3   C4   C2     0.00   0.0  0
 MSZ  CONST_08  C7   C6   C5   C2     0.00   0.0  0
 MSZ  CONST_09  C6   C7   C3   C4     0.00   0.0  0
 MSZ  CONST_10  C6   C5   C2   C4     0.00   0.0  0
 MSZ  CONST_11  C5   C6   C7   C3     0.00   0.0  0
 MSZ  CONST_12  C5   C2   C4   C3     0.00   0.0  0
 MSZ  CONST_13  C19  C15  C14  C13  180.00   0.0  0
 MSZ  CONST_14  O12  C13  C14  C15  180.00   0.0  0
 MSZ  CONST_15  O12  C13  C16  C17  180.00   0.0  0
 MSZ  CONST_16  C19  C15  C18  C17  180.00   0.0  0
 MSZ  CONST_17  C4   C3   C7   C8   180.00   0.0  0
 MSZ  CONST_18  C5   C6   C7   C8   180.00   0.0  0
 MSZ  CONST_19  CL   C2   C4   C3   180.00   0.0  0
 MSZ  CONST_20  CL   C2   C5   C6   180.00   0.0  0
 MSZ  CONST_21  H3   C18  C17  C16  180.00   0.0  0
 MSZ  CONST_22  H2   C14  C13  C16  180.00   0.0  0
 MSZ  CONST_23  H4   C17  C16  C13  180.00   0.0  0
 MSZ  CONST_24  H1   C16  C13  C14  180.00   0.0  0
 MSZ  CONST_25  H8   C3   C4   C2   180.00   0.0  0
 MSZ  CONST_26  H9   C6   C5   C2   180.00   0.0  0
 MSZ  CONST_27  H10  C5   C2   C4   180.00   0.0  0
 MSZ  CONST_28  H7   C4   C3   C7   180.00   0.0  0
 MSZ  Var_01    F21  C19  C15  C14  -64.41  30.0  2

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
 MSZ  chir_01  C8  C9  O12  C7  negativ

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
 MSZ  plan-1  C16  0.020
 MSZ  plan-1  C13  0.020
 MSZ  plan-1  C14  0.020
 MSZ  plan-1  C15  0.020
 MSZ  plan-1  C18  0.020
 MSZ  plan-1  C17  0.020
 MSZ  plan-1  C19  0.020
 MSZ  plan-1  O12  0.020
 MSZ  plan-1  H1   0.020
 MSZ  plan-1  H2   0.020
 MSZ  plan-1  H3   0.020
 MSZ  plan-1  H4   0.020
 MSZ  plan-2  C8   0.020
 MSZ  plan-2  C2   0.020
 MSZ  plan-2  C4   0.020
 MSZ  plan-2  C3   0.020
 MSZ  plan-2  C7   0.020
 MSZ  plan-2  C6   0.020
 MSZ  plan-2  C5   0.020
 MSZ  plan-2  H7   0.020
 MSZ  plan-2  H8   0.020
 MSZ  plan-2  H9   0.020
 MSZ  plan-2  H10  0.020
 MSZ  plan-2  CL   0.020
 MSZ  plan-3  C8   0.020
 MSZ  plan-3  C9   0.020
 MSZ  plan-3  O10  0.020
 MSZ  plan-3  O11  0.020

