# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:59:41 2021
#   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  35  24  .  2021-08-11  2022-11-17
;
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  -0.435  46.2118  -41.5036  65.0169
 H1L  C1    C   C     0   0.515  47.0983  -41.0836  64.3179
 H1L  O1B   O   OH1   0  -0.573  48.1536  -41.7821  63.9433
 H1L  C2    C   CH1   0  -0.107  47.1347  -39.6432  63.8268
 H1L  C2A   C   CH3   0  -0.677  47.6796  -38.7517  64.9326
 H1L  O2    O   O2    0  -0.474  47.9653  -39.4751  62.7024
 H1L  C3    C   CR6   0   0.399  47.5775  -39.9661  61.5041
 H1L  C4    C   CR16  0  -0.374  46.3839  -40.6430  61.2716
 H1L  C5    C   CR16  0  -0.291  46.0834  -41.0956  59.9922
 H1L  C6    C   CR16  0  -0.348  48.4626  -39.7512  60.4474
 H1L  C7    C   CR16  0  -0.288  48.1587  -40.2005  59.1759
 H1L  C8    C   CR6   0   0.333  46.9674  -40.8734  58.9565
 H1L  O8    O   O2    0  -0.502  46.6888  -41.3776  57.6981
 H1L  C9    C   CR6   0   0.597  45.9909  -40.6251  56.8454
 H1L  N9    N   N     0  -0.438  45.5983  -39.4248  57.1889
 H1L  C10   C   CR16  0  -0.046  44.8995  -38.6967  56.3253
 H1L  C11   C   CR6   0  -0.333  44.5659  -39.1534  55.0651
 H1L  C12   C   CT    0   1.068  43.7475  -38.3382  54.1199
 H1L  F1    F   F     0  -0.301  43.6707  -37.0588  54.4931
 H1L  F2    F   F     0  -0.309  44.2508  -38.3639  52.8800
 H1L  F3    F   F     0  -0.311  42.4916  -38.7991  54.0319
 H1L  C13   C   CR16  0  -0.094  44.9829  -40.4317  54.6925
 H1L  C14   C   CR6   0  -0.186  45.7056  -41.1791  55.5887
 H1L  CL1   CL  CL    0  -0.080  46.2552  -42.7583  55.1973
 H1L  H1B   H   HOH1  0   0.488  48.1038  -42.6805  64.3048
 H1L  H2    H   HCH1  0   0.280  46.1048  -39.3415  63.6060
 H1L  H2A1  H   HCH3  0   0.263  47.6931  -37.7158  64.5966
 H1L  H2A2  H   HCH3  0   0.253  47.0401  -38.8114  65.8114
 H1L  H2A3  H   HCH3  0   0.249  48.6908  -39.0416  65.2181
 H1L  H4    H   HCR6  0   0.284  45.6626  -40.8315  62.0550
 H1L  H6    H   HCR6  0   0.275  49.3912  -39.2250  60.6283
 H1L  H5    H   HCR6  0   0.280  45.1560  -41.6258  59.8175
 H1L  H7    H   HCR6  0   0.278  48.8516  -40.0305  58.3619
 H1L  H10   H   HCR6  0   0.292  44.6036  -37.7140  56.6694
 H1L  H13   H   HCR6  0   0.312  44.7506  -40.8427  53.7185

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    double    1.205  0.020  1.205
 H1L  C1   O1B   single    1.320  0.020  1.320
 H1L  C1   C2    single    1.522  0.020  1.522
 H1L  C2   C2A   single    1.521  0.020  1.521
 H1L  C2   O2    single    1.408  0.020  1.408
 H1L  O2   C3    single    1.352  0.020  1.352
 H1L  C3   C4    aromatic  1.392  0.020  1.392
 H1L  C3   C6    aromatic  1.395  0.020  1.395
 H1L  C4   C5    aromatic  1.390  0.020  1.390
 H1L  C5   C8    aromatic  1.380  0.020  1.380
 H1L  C6   C7    aromatic  1.382  0.020  1.382
 H1L  C7   C8    aromatic  1.386  0.020  1.386
 H1L  C8   O8    single    1.384  0.020  1.384
 H1L  O8   C9    single    1.334  0.020  1.334
 H1L  C9   N9    aromatic  1.309  0.020  1.309
 H1L  C9   C14   aromatic  1.403  0.020  1.403
 H1L  N9   C10   aromatic  1.328  0.020  1.328
 H1L  C10  C11   aromatic  1.381  0.020  1.381
 H1L  C11  C12   single    1.493  0.020  1.493
 H1L  C11  C13   aromatic  1.395  0.020  1.395
 H1L  C12  F1    single    1.335  0.020  1.335
 H1L  C12  F2    single    1.338  0.020  1.338
 H1L  C12  F3    single    1.341  0.020  1.341
 H1L  C13  C14   aromatic  1.373  0.020  1.373
 H1L  C14  CL1   single    1.717  0.020  1.717
 H1L  O1B  H1B   single    0.850  0.020  0.980
 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   112.96  3.000
 H1L  C2    C1   O1A   122.32  3.000
 H1L  O1B   C1   O1A   124.66  3.000
 H1L  H1B   O1B  C1    110.08  3.000
 H1L  H2    C2   O2    111.15  3.000
 H1L  H2    C2   C2A   108.77  3.000
 H1L  O2    C2   C2A   107.41  3.000
 H1L  H2    C2   C1    107.65  3.000
 H1L  O2    C2   C1    112.63  3.000
 H1L  C2A   C2   C1    109.18  3.000
 H1L  H2A3  C2A  H2A2  108.60  3.000
 H1L  H2A3  C2A  H2A1  108.81  3.000
 H1L  H2A2  C2A  H2A1  107.97  3.000
 H1L  H2A3  C2A  C2    111.52  3.000
 H1L  H2A2  C2A  C2    110.13  3.000
 H1L  H2A1  C2A  C2    109.73  3.000
 H1L  C3    O2   C2    119.69  3.000
 H1L  C6    C3   C4    119.51  3.000
 H1L  C6    C3   O2    115.69  3.000
 H1L  C4    C3   O2    124.80  3.000
 H1L  H4    C4   C5    117.76  3.000
 H1L  H4    C4   C3    122.40  3.000
 H1L  C5    C4   C3    119.84  3.000
 H1L  H5    C5   C8    120.44  3.000
 H1L  H5    C5   C4    119.56  3.000
 H1L  C8    C5   C4    120.00  3.000
 H1L  H6    C6   C7    120.02  3.000
 H1L  H6    C6   C3    119.51  3.000
 H1L  C7    C6   C3    120.47  3.000
 H1L  H7    C7   C8    120.50  3.000
 H1L  H7    C7   C6    119.99  3.000
 H1L  C8    C7   C6    119.51  3.000
 H1L  O8    C8   C7    119.60  3.000
 H1L  O8    C8   C5    119.66  3.000
 H1L  C7    C8   C5    120.68  3.000
 H1L  C9    O8   C8    118.74  3.000
 H1L  C14   C9   N9    122.44  3.000
 H1L  C14   C9   O8    117.14  3.000
 H1L  N9    C9   O8    120.42  3.000
 H1L  C10   N9   C9    119.33  3.000
 H1L  H10   C10  C11   121.62  3.000
 H1L  H10   C10  N9    115.76  3.000
 H1L  C11   C10  N9    122.62  3.000
 H1L  C13   C11  C12   119.68  3.000
 H1L  C13   C11  C10   118.32  3.000
 H1L  C12   C11  C10   121.98  3.000
 H1L  F3    C12  F2    106.55  3.000
 H1L  F3    C12  F1    107.10  3.000
 H1L  F2    C12  F1    107.40  3.000
 H1L  F3    C12  C11   111.55  3.000
 H1L  F2    C12  C11   111.72  3.000
 H1L  F1    C12  C11   112.21  3.000
 H1L  H13   C13  C14   119.59  3.000
 H1L  H13   C13  C11   121.61  3.000
 H1L  C14   C13  C11   118.81  3.000
 H1L  CL1   C14  C13   121.36  3.000
 H1L  CL1   C14  C9    120.16  3.000
 H1L  C13   C14  C9    118.49  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  CONST_29  H1B  O1B  C1   O1A    0.00   0.0  0
 H1L  Var_01    N9   C9   O8   C8     1.12  30.0  2
 H1L  Var_02    C4   C3   O2   C2     0.31  30.0  2
 H1L  Var_03    F1   C12  C11  C10   15.10  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
 H1L  plan-3  H1B  0.020

