# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:31:30 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R)-2-(4-{[3-chloro-5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(Oc2ncc(cc2Cl)C(F)(F)F)cc1)C(O)=O
#
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
 H1L  H1L  '(2R)-2-(4-{[3-chloro-5-(trifluoromethyl)pyridin-2-yl]oxy}phenoxy)propanoic acid'  ligand  34  24  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H1L
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
 H1L  O1A   O   O      0  -0.591   6.6329  -1.6019  -1.2060
 H1L  C1    C   C      0   0.401   6.5825  -1.2074  -0.0317
 H1L  O1B   O   OC    -1  -0.616   7.3654  -1.4789   0.8994
 H1L  C2    C   CH1    0  -0.123   5.4292  -0.2617   0.3750
 H1L  C2A   C   CH3    0  -0.684   5.9665   1.0776   0.8611
 H1L  O2    O   O2     0  -0.472   4.5693  -0.0878  -0.7466
 H1L  C3    C   CR6    0   0.399   3.3120   0.3495  -0.5832
 H1L  C4    C   CR16   0  -0.384   2.7036   0.6212   0.6430
 H1L  C5    C   CR16   0  -0.290   1.3851   1.0572   0.6885
 H1L  C6    C   CR16   0  -0.359   2.5708   0.5286  -1.7560
 H1L  C7    C   CR16   0  -0.289   1.2582   0.9603  -1.7071
 H1L  C8    C   CR6    0   0.326   0.6716   1.2259  -0.4807
 H1L  O8    O   O2     0  -0.502  -0.6197   1.7273  -0.4400
 H1L  C9    C   C      0   0.596  -1.6352   0.8851  -0.2508
 H1L  N9    N   N      0  -0.438  -1.4196  -0.3994  -0.1237
 H1L  C10   C   C1     0  -0.048  -2.4496  -1.2165   0.0690
 H1L  C11   C   C      0  -0.334  -3.7530  -0.7670   0.1421
 H1L  C12   C   CT     0   1.068  -4.9045  -1.6888   0.3684
 H1L  F1    F   F      0  -0.300  -4.5233  -2.9644   0.4581
 H1L  F2    F   F      0  -0.311  -5.5605  -1.3894   1.4978
 H1L  F3    F   F      0  -0.311  -5.8022  -1.6104  -0.6233
 H1L  C13   C   C1     0  -0.093  -3.9906   0.6016   0.0031
 H1L  C14   C   C      0  -0.187  -2.9234   1.4405  -0.1968
 H1L  CL1   CL  CL     0  -0.081  -3.1395   3.1350  -0.3773
 H1L  H2    H   HCH1   0   0.226   4.8795  -0.7540   1.1872
 H1L  H2A1  H   HCH3   0   0.229   6.5529   1.5675   0.0816
 H1L  H2A2  H   HCH3   0   0.233   5.1693   1.7601   1.1587
 H1L  H2A3  H   HCH3   0   0.237   6.6106   0.9247   1.7243
 H1L  H4    H   HCR6   0   0.282   3.2331   0.5038   1.5777
 H1L  H6    H   HCR6   0   0.266   3.0337   0.3211  -2.7124
 H1L  H5    H   HCR6   0   0.275   0.9277   1.2710   1.6462
 H1L  H7    H   HCR6   0   0.273   0.6989   1.0971  -2.6239
 H1L  H10   H   H      0   0.291  -2.2053  -2.2665   0.1663
 H1L  H13   H   H      0   0.312  -4.9918   1.0107   0.0497

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
 H1L  O1A  C1    deloc     1.240  0.020  1.240
 H1L  C1   O1B   deloc     1.246  0.020  1.246
 H1L  C1   C2    single    1.546  0.020  1.546
 H1L  C2   C2A   single    1.523  0.020  1.523
 H1L  C2   O2    single    1.424  0.020  1.424
 H1L  O2   C3    single    1.341  0.020  1.341
 H1L  C3   C4    aromatic  1.396  0.020  1.396
 H1L  C3   C6    aromatic  1.399  0.020  1.399
 H1L  C4   C5    aromatic  1.389  0.020  1.389
 H1L  C5   C8    aromatic  1.380  0.020  1.380
 H1L  C6   C7    aromatic  1.383  0.020  1.383
 H1L  C7   C8    aromatic  1.385  0.020  1.385
 H1L  C8   O8    single    1.386  0.020  1.386
 H1L  O8   C9    single    1.333  0.020  1.333
 H1L  C9   N9    aromatic  1.309  0.020  1.309
 H1L  C9   C14   aromatic  1.404  0.020  1.404
 H1L  N9   C10   aromatic  1.329  0.020  1.329
 H1L  C10  C11   aromatic  1.381  0.020  1.381
 H1L  C11  C12   single    1.492  0.020  1.492
 H1L  C11  C13   aromatic  1.396  0.020  1.396
 H1L  C12  F1    single    1.334  0.020  1.334
 H1L  C12  F2    single    1.340  0.020  1.340
 H1L  C12  F3    single    1.340  0.020  1.340
 H1L  C13  C14   aromatic  1.372  0.020  1.372
 H1L  C14  CL1   single    1.718  0.020  1.718
 H1L  C2   H2    single    0.970  0.020  1.090
 H1L  C2A  H2A1  single    0.970  0.020  1.090
 H1L  C2A  H2A2  single    0.970  0.020  1.090
 H1L  C2A  H2A3  single    0.970  0.020  1.090
 H1L  C4   H4    single    0.930  0.020  1.080
 H1L  C6   H6    single    0.930  0.020  1.080
 H1L  C5   H5    single    0.930  0.020  1.080
 H1L  C7   H7    single    0.930  0.020  1.080
 H1L  C10  H10   single    0.930  0.020  1.080
 H1L  C13  H13   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
 H1L  C2    C1   O1B   113.91  3.000
 H1L  C2    C1   O1A   118.30  3.000
 H1L  O1B   C1   O1A   127.79  3.000
 H1L  H2    C2   O2    109.59  3.000
 H1L  H2    C2   C2A   109.58  3.000
 H1L  O2    C2   C2A   110.92  3.000
 H1L  H2    C2   C1    107.10  3.000
 H1L  O2    C2   C1    108.54  3.000
 H1L  C2A   C2   C1    111.03  3.000
 H1L  H2A3  C2A  H2A2  107.71  3.000
 H1L  H2A3  C2A  H2A1  108.16  3.000
 H1L  H2A2  C2A  H2A1  107.86  3.000
 H1L  H2A3  C2A  C2    109.79  3.000
 H1L  H2A2  C2A  C2    112.30  3.000
 H1L  H2A1  C2A  C2    110.87  3.000
 H1L  C3    O2   C2    120.66  3.000
 H1L  C6    C3   C4    118.73  3.000
 H1L  C6    C3   O2    115.87  3.000
 H1L  C4    C3   O2    125.40  3.000
 H1L  H4    C4   C5    118.08  3.000
 H1L  H4    C4   C3    121.68  3.000
 H1L  C5    C4   C3    120.24  3.000
 H1L  H5    C5   C8    120.45  3.000
 H1L  H5    C5   C4    119.46  3.000
 H1L  C8    C5   C4    120.08  3.000
 H1L  H6    C6   C7    119.80  3.000
 H1L  H6    C6   C3    119.31  3.000
 H1L  C7    C6   C3    120.89  3.000
 H1L  H7    C7   C8    120.45  3.000
 H1L  H7    C7   C6    120.00  3.000
 H1L  C8    C7   C6    119.55  3.000
 H1L  O8    C8   C7    119.34  3.000
 H1L  O8    C8   C5    120.07  3.000
 H1L  C7    C8   C5    120.51  3.000
 H1L  C9    O8   C8    119.05  3.000
 H1L  C14   C9   N9    122.39  3.000
 H1L  C14   C9   O8    117.04  3.000
 H1L  N9    C9   O8    120.56  3.000
 H1L  C10   N9   C9    119.34  3.000
 H1L  H10   C10  C11   121.61  3.000
 H1L  H10   C10  N9    115.76  3.000
 H1L  C11   C10  N9    122.63  3.000
 H1L  C13   C11  C12   119.30  3.000
 H1L  C13   C11  C10   118.33  3.000
 H1L  C12   C11  C10   122.37  3.000
 H1L  F3    C12  F2    106.42  3.000
 H1L  F3    C12  F1    107.28  3.000
 H1L  F2    C12  F1    107.26  3.000
 H1L  F3    C12  C11   111.63  3.000
 H1L  F2    C12  C11   111.57  3.000
 H1L  F1    C12  C11   112.35  3.000
 H1L  H13   C13  C14   119.64  3.000
 H1L  H13   C13  C11   121.57  3.000
 H1L  C14   C13  C11   118.78  3.000
 H1L  CL1   C14  C13   121.37  3.000
 H1L  CL1   C14  C9    120.11  3.000
 H1L  C13   C14  C9    118.52  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
 H1L  CONST_01  C8   C5   C4   C3     0.00   0.0  0
 H1L  CONST_02  C8   C7   C6   C3     0.00   0.0  0
 H1L  CONST_03  C7   C6   C3   C4     0.00   0.0  0
 H1L  CONST_04  C7   C8   C5   C4     0.00   0.0  0
 H1L  CONST_05  C6   C3   C4   C5     0.00   0.0  0
 H1L  CONST_06  C6   C7   C8   C5     0.00   0.0  0
 H1L  CONST_07  C11  C10  N9   C9     0.00   0.0  0
 H1L  CONST_08  C11  C13  C14  C9     0.00   0.0  0
 H1L  CONST_09  C13  C14  C9   N9     0.00   0.0  0
 H1L  CONST_10  C13  C11  C10  N9     0.00   0.0  0
 H1L  CONST_11  C14  C9   N9   C10    0.00   0.0  0
 H1L  CONST_12  C14  C13  C11  C10    0.00   0.0  0
 H1L  CONST_13  C5   C4   C3   O2   180.00   0.0  0
 H1L  CONST_14  C7   C6   C3   O2   180.00   0.0  0
 H1L  CONST_15  O8   C8   C5   C4   180.00   0.0  0
 H1L  CONST_16  O8   C8   C7   C6   180.00   0.0  0
 H1L  CONST_17  C10  N9   C9   O8   180.00   0.0  0
 H1L  CONST_18  C13  C14  C9   O8   180.00   0.0  0
 H1L  CONST_19  CL1  C14  C9   N9   180.00   0.0  0
 H1L  CONST_20  C12  C11  C10  N9   180.00   0.0  0
 H1L  CONST_21  CL1  C14  C13  C11  180.00   0.0  0
 H1L  CONST_22  C14  C13  C11  C12  180.00   0.0  0
 H1L  CONST_23  H5   C5   C4   C3   180.00   0.0  0
 H1L  CONST_24  H7   C7   C6   C3   180.00   0.0  0
 H1L  CONST_25  H6   C6   C3   C4   180.00   0.0  0
 H1L  CONST_26  H4   C4   C3   C6   180.00   0.0  0
 H1L  CONST_27  H10  C10  N9   C9   180.00   0.0  0
 H1L  CONST_28  H13  C13  C14  C9   180.00   0.0  0
 H1L  Var_01    N9   C9   O8   C8    -0.95  30.0  2
 H1L  Var_02    C4   C3   O2   C2    -2.68  30.0  2
 H1L  Var_03    F1   C12  C11  C10   -1.34  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
 H1L  chir_01  C2  C1  C2A  O2  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
 H1L  plan-1  O2   0.020
 H1L  plan-1  C3   0.020
 H1L  plan-1  C4   0.020
 H1L  plan-1  C5   0.020
 H1L  plan-1  C6   0.020
 H1L  plan-1  C7   0.020
 H1L  plan-1  C8   0.020
 H1L  plan-1  O8   0.020
 H1L  plan-1  H4   0.020
 H1L  plan-1  H6   0.020
 H1L  plan-1  H5   0.020
 H1L  plan-1  H7   0.020
 H1L  plan-2  O8   0.020
 H1L  plan-2  C9   0.020
 H1L  plan-2  N9   0.020
 H1L  plan-2  C10  0.020
 H1L  plan-2  C11  0.020
 H1L  plan-2  C12  0.020
 H1L  plan-2  C13  0.020
 H1L  plan-2  C14  0.020
 H1L  plan-2  CL1  0.020
 H1L  plan-2  H10  0.020
 H1L  plan-2  H13  0.020
 H1L  plan-3  O1A  0.020
 H1L  plan-3  C1   0.020
 H1L  plan-3  O1B  0.020
 H1L  plan-3  C2   0.020

