# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 00:54:11 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (1S)-4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-1-methylcyclohex-3-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CCC(=CC1)c2nn(C(=O)c3c(Cl)cccc3C(F)(F)F)c4cccc(F)c24)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
 4Y6  4Y6  '(1S)-4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-1-methylcyclohex-3-ene-1-carboxylic acid'  ligand  50  33  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4Y6
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
 4Y6  F3   F   F     0  -0.293   2.5657   3.6050  -0.1234
 4Y6  C    C   CR6   0   0.504   1.2430   3.6013  -0.3054
 4Y6  C5   C   CR56  0  -0.386   0.5385   2.4006  -0.2934
 4Y6  C6   C   CR5   0   0.348   0.8418   0.9983  -0.1060
 4Y6  C15  C   C     0   0.045   2.1178   0.3032   0.0796
 4Y6  C20  C   C1    0  -0.274   3.2247   0.6846  -0.5614
 4Y6  C19  C   CH2   0  -0.449   4.5387  -0.0235  -0.4730
 4Y6  C18  C   CT    0  -0.253   4.4126  -1.4459   0.0994
 4Y6  C22  C   CH3   0  -0.651   3.8652  -2.4039  -0.9697
 4Y6  C21  C   C     0   0.591   5.7840  -1.9443   0.5201
 4Y6  O2   O   O     0  -0.435   6.0606  -2.3818   1.6096
 4Y6  O1   O   OH1   0  -0.594   6.6741  -1.8606  -0.4629
 4Y6  C17  C   CH2   0  -0.420   3.4857  -1.4058   1.3159
 4Y6  C16  C   CH2   0  -0.499   2.0897  -0.9180   0.9556
 4Y6  N    N   N     0  -0.242  -0.2571   0.3059  -0.0986
 4Y6  N1   N   NR5   0  -0.450  -1.2873   1.1570  -0.3022
 4Y6  C4   C   CR56  0   0.486  -0.8556   2.4631  -0.4277
 4Y6  C3   C   CR16  0  -0.298  -1.5527   3.6530  -0.6150
 4Y6  C2   C   CR16  0  -0.244  -0.7982   4.8099  -0.6488
 4Y6  C1   C   CR16  0  -0.422   0.5913   4.7969  -0.4886
 4Y6  C7   C   C     0   0.448  -2.5714   0.6704  -0.3497
 4Y6  O    O   O     0  -0.377  -3.5306   1.3847  -0.4953
 4Y6  C8   C   CR6   0   0.086  -2.6882  -0.8217  -0.2373
 4Y6  C13  C   CR6   0  -0.232  -3.1201  -1.4468   0.9310
 4Y6  C14  C   CT    0   1.069  -3.4127  -0.6350   2.1600
 4Y6  F2   F   F     0  -0.312  -2.5314   0.3619   2.3183
 4Y6  F1   F   F     0  -0.308  -4.6271  -0.0762   2.1046
 4Y6  F    F   F     0  -0.296  -3.3715  -1.3728   3.2697
 4Y6  C12  C   CR16  0  -0.275  -3.3006  -2.8222   0.9622
 4Y6  C11  C   CR16  0  -0.251  -3.0562  -3.5791  -0.1729
 4Y6  C10  C   CR16  0  -0.194  -2.6294  -2.9731  -1.3414
 4Y6  C9   C   CR6   0  -0.045  -2.4497  -1.6003  -1.3606
 4Y6  CL   CL  CL    0  -0.095  -1.9122  -0.8388  -2.8146
 4Y6  H1   H   H     0   0.250   3.2035   1.5462  -1.2161
 4Y6  H2   H   HCH2  0   0.260   4.9939  -0.0488  -1.4658
 4Y6  H3   H   HCH2  0   0.266   5.2128   0.5828   0.1445
 4Y6  H4   H   HCH3  0   0.246   4.5351  -2.4799  -1.8254
 4Y6  H5   H   HCH3  0   0.242   3.7181  -3.4055  -0.5619
 4Y6  H6   H   HCH3  0   0.247   2.9026  -2.0555  -1.3442
 4Y6  H7   H   HOH1  0   0.481   7.5321  -2.1959  -0.1617
 4Y6  H8   H   HCH2  0   0.245   3.4125  -2.3951   1.7714
 4Y6  H9   H   HCH2  0   0.241   3.9122  -0.7423   2.0732
 4Y6  H10  H   HCH2  0   0.258   1.5426  -0.6947   1.8747
 4Y6  H11  H   HCH2  0   0.251   1.5123  -1.7066   0.4634
 4Y6  H12  H   HCR6  0   0.289  -2.6246   3.6869  -0.7202
 4Y6  H13  H   HCR6  0   0.282  -1.2951   5.7595  -0.7930
 4Y6  H14  H   HCR6  0   0.290   1.1538   5.7210  -0.4982
 4Y6  H15  H   HCR6  0   0.285  -3.6292  -3.3169   1.8650
 4Y6  H16  H   HCR6  0   0.287  -3.1970  -4.6505  -0.1462
 4Y6  H17  H   HCR6  0   0.297  -2.4351  -3.5605  -2.2281

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
 4Y6  C2   C3   aromatic  1.382  0.020  1.382
 4Y6  C2   C1   aromatic  1.399  0.020  1.399
 4Y6  C3   C4   aromatic  1.392  0.020  1.392
 4Y6  C1   C    aromatic  1.374  0.020  1.374
 4Y6  O    C7   double    1.205  0.020  1.205
 4Y6  C4   N1   aromatic  1.381  0.020  1.381
 4Y6  C4   C5   aromatic  1.402  0.020  1.402
 4Y6  C7   N1   single    1.374  0.020  1.374
 4Y6  C7   C8   single    1.501  0.020  1.501
 4Y6  C    C5   aromatic  1.392  0.020  1.392
 4Y6  C    F3   single    1.335  0.020  1.335
 4Y6  CL   C9   single    1.727  0.020  1.727
 4Y6  N1   N    aromatic  1.352  0.020  1.352
 4Y6  C5   C6   aromatic  1.447  0.020  1.447
 4Y6  F1   C14  single    1.338  0.020  1.338
 4Y6  C8   C9   aromatic  1.387  0.020  1.387
 4Y6  C8   C13  aromatic  1.394  0.020  1.394
 4Y6  C9   C10  aromatic  1.385  0.020  1.385
 4Y6  N    C6   aromatic  1.299  0.020  1.299
 4Y6  C10  C11  aromatic  1.384  0.020  1.384
 4Y6  C13  C14  single    1.502  0.020  1.502
 4Y6  C13  C12  aromatic  1.388  0.020  1.388
 4Y6  C6   C15  single    1.465  0.020  1.465
 4Y6  C14  F    single    1.333  0.020  1.333
 4Y6  C14  F2   single    1.340  0.020  1.340
 4Y6  C11  C12  aromatic  1.386  0.020  1.386
 4Y6  C15  C20  double    1.335  0.020  1.335
 4Y6  C15  C16  single    1.503  0.020  1.503
 4Y6  C20  C19  single    1.495  0.020  1.495
 4Y6  C16  C17  single    1.522  0.020  1.522
 4Y6  C19  C18  single    1.538  0.020  1.538
 4Y6  C17  C18  single    1.530  0.020  1.530
 4Y6  C18  C22  single    1.536  0.020  1.536
 4Y6  C18  C21  single    1.519  0.020  1.519
 4Y6  C21  O2   double    1.206  0.020  1.206
 4Y6  C21  O1   single    1.329  0.020  1.329
 4Y6  C20  H1   single    0.930  0.020  1.080
 4Y6  C19  H2   single    0.970  0.020  1.090
 4Y6  C19  H3   single    0.970  0.020  1.090
 4Y6  C22  H4   single    0.970  0.020  1.090
 4Y6  C22  H5   single    0.970  0.020  1.090
 4Y6  C22  H6   single    0.970  0.020  1.090
 4Y6  O1   H7   single    0.850  0.020  0.980
 4Y6  C17  H8   single    0.970  0.020  1.090
 4Y6  C17  H9   single    0.970  0.020  1.090
 4Y6  C16  H10  single    0.970  0.020  1.090
 4Y6  C16  H11  single    0.970  0.020  1.090
 4Y6  C3   H12  single    0.930  0.020  1.080
 4Y6  C2   H13  single    0.930  0.020  1.080
 4Y6  C1   H14  single    0.930  0.020  1.080
 4Y6  C12  H15  single    0.930  0.020  1.080
 4Y6  C11  H16  single    0.930  0.020  1.080
 4Y6  C10  H17  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
 4Y6  C1   C    C5   120.77  3.000
 4Y6  C5   C    F3   120.17  3.000
 4Y6  C1   C    F3   119.06  3.000
 4Y6  C4   C5   C6   105.31  3.000
 4Y6  C6   C5   C    136.97  3.000
 4Y6  C4   C5   C    117.64  3.000
 4Y6  N    C6   C15  118.90  3.000
 4Y6  C15  C6   C5   131.21  3.000
 4Y6  N    C6   C5   109.88  3.000
 4Y6  C16  C15  C20  121.84  3.000
 4Y6  C16  C15  C6   116.30  3.000
 4Y6  C20  C15  C6   121.73  3.000
 4Y6  H1   C20  C19  115.47  3.000
 4Y6  H1   C20  C15  120.11  3.000
 4Y6  C19  C20  C15  124.40  3.000
 4Y6  H3   C19  H2   105.56  3.000
 4Y6  H3   C19  C18  110.61  3.000
 4Y6  H2   C19  C18  110.54  3.000
 4Y6  H3   C19  C20  108.15  3.000
 4Y6  H2   C19  C20  108.87  3.000
 4Y6  C18  C19  C20  112.82  3.000
 4Y6  C17  C18  C21  109.60  3.000
 4Y6  C21  C18  C22  108.05  3.000
 4Y6  C17  C18  C22  110.72  3.000
 4Y6  C21  C18  C19  109.42  3.000
 4Y6  C22  C18  C19  110.29  3.000
 4Y6  C17  C18  C19  108.74  3.000
 4Y6  H6   C22  H5   107.62  3.000
 4Y6  H6   C22  H4   107.18  3.000
 4Y6  H5   C22  H4   108.20  3.000
 4Y6  H6   C22  C18  110.76  3.000
 4Y6  H5   C22  C18  111.12  3.000
 4Y6  H4   C22  C18  111.78  3.000
 4Y6  O1   C21  O2   122.50  3.000
 4Y6  O1   C21  C18  112.30  3.000
 4Y6  O2   C21  C18  125.20  3.000
 4Y6  H7   O1   C21  109.97  3.000
 4Y6  H9   C17  H8   106.69  3.000
 4Y6  H9   C17  C16  109.10  3.000
 4Y6  H8   C17  C16  109.13  3.000
 4Y6  H9   C17  C18  109.29  3.000
 4Y6  H8   C17  C18  110.41  3.000
 4Y6  C16  C17  C18  112.08  3.000
 4Y6  H11  C16  H10  105.16  3.000
 4Y6  H11  C16  C17  111.06  3.000
 4Y6  H10  C16  C17  109.00  3.000
 4Y6  H11  C16  C15  109.46  3.000
 4Y6  H10  C16  C15  109.49  3.000
 4Y6  C17  C16  C15  112.40  3.000
 4Y6  N1   N    C6   107.96  3.000
 4Y6  C7   N1   C4   128.60  3.000
 4Y6  C7   N1   N    119.64  3.000
 4Y6  C4   N1   N    111.76  3.000
 4Y6  C3   C4   N1   131.61  3.000
 4Y6  N1   C4   C5   105.07  3.000
 4Y6  C3   C4   C5   123.31  3.000
 4Y6  H12  C3   C2   120.96  3.000
 4Y6  H12  C3   C4   122.57  3.000
 4Y6  C2   C3   C4   116.47  3.000
 4Y6  H13  C2   C1   118.67  3.000
 4Y6  H13  C2   C3   119.19  3.000
 4Y6  C1   C2   C3   122.14  3.000
 4Y6  H14  C1   C2   120.50  3.000
 4Y6  H14  C1   C    119.85  3.000
 4Y6  C2   C1   C    119.64  3.000
 4Y6  C8   C7   O    122.45  3.000
 4Y6  C8   C7   N1   114.98  3.000
 4Y6  O    C7   N1   122.56  3.000
 4Y6  C9   C8   C13  118.71  3.000
 4Y6  C13  C8   C7   122.19  3.000
 4Y6  C9   C8   C7   118.94  3.000
 4Y6  C12  C13  C14  119.48  3.000
 4Y6  C12  C13  C8   120.24  3.000
 4Y6  C14  C13  C8   120.27  3.000
 4Y6  F    C14  F1   107.08  3.000
 4Y6  F    C14  F2   107.04  3.000
 4Y6  F1   C14  F2   106.93  3.000
 4Y6  F2   C14  C13  111.76  3.000
 4Y6  F    C14  C13  112.09  3.000
 4Y6  F1   C14  C13  111.64  3.000
 4Y6  H15  C12  C11  119.20  3.000
 4Y6  H15  C12  C13  120.80  3.000
 4Y6  C11  C12  C13  120.00  3.000
 4Y6  H16  C11  C10  119.68  3.000
 4Y6  H16  C11  C12  119.87  3.000
 4Y6  C10  C11  C12  120.45  3.000
 4Y6  H17  C10  C9   120.27  3.000
 4Y6  H17  C10  C11  120.66  3.000
 4Y6  C9   C10  C11  119.07  3.000
 4Y6  CL   C9   C10  119.29  3.000
 4Y6  C10  C9   C8   121.53  3.000
 4Y6  CL   C9   C8   119.19  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
 4Y6  CONST_01  C3   C2   C1   C       0.00   0.0  0
 4Y6  CONST_02  C3   C4   C5   C       0.00   0.0  0
 4Y6  CONST_03  N1   C4   C5   C     180.00   0.0  0
 4Y6  CONST_04  N    C6   C5   C     180.00   0.0  0
 4Y6  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 4Y6  CONST_06  N    N1   C4   C5      0.00   0.0  0
 4Y6  CONST_07  C2   C1   C    C5      0.00   0.0  0
 4Y6  CONST_08  N1   N    C6   C5      0.00   0.0  0
 4Y6  CONST_09  C3   C4   C5   C6    180.00   0.0  0
 4Y6  CONST_10  N1   C4   C5   C6      0.00   0.0  0
 4Y6  CONST_11  C1   C    C5   C6    180.00   0.0  0
 4Y6  CONST_12  C4   N1   N    C6      0.00   0.0  0
 4Y6  CONST_13  C3   C4   N1   N     180.00   0.0  0
 4Y6  CONST_14  C4   C5   C6   N       0.00   0.0  0
 4Y6  CONST_15  C2   C3   C4   N1    180.00   0.0  0
 4Y6  CONST_16  C1   C2   C3   C4      0.00   0.0  0
 4Y6  CONST_17  C1   C    C5   C4      0.00   0.0  0
 4Y6  CONST_18  C11  C10  C9   C8      0.00   0.0  0
 4Y6  CONST_19  C11  C12  C13  C8      0.00   0.0  0
 4Y6  CONST_20  C10  C9   C8   C13     0.00   0.0  0
 4Y6  CONST_21  C10  C11  C12  C13     0.00   0.0  0
 4Y6  CONST_22  C9   C8   C13  C12     0.00   0.0  0
 4Y6  CONST_23  C9   C10  C11  C12     0.00   0.0  0
 4Y6  CONST_24  C15  C6   C5   C       0.00   0.0  0
 4Y6  CONST_25  C4   C5   C6   C15   180.00   0.0  0
 4Y6  CONST_26  N1   N    C6   C15   180.00   0.0  0
 4Y6  CONST_27  C2   C1   C    F3    180.00   0.0  0
 4Y6  CONST_28  C4   C5   C    F3    180.00   0.0  0
 4Y6  CONST_29  C6   C5   C    F3      0.00   0.0  0
 4Y6  CONST_30  C7   N1   C4   C5    180.00   0.0  0
 4Y6  CONST_31  C7   N1   N    C6    180.00   0.0  0
 4Y6  CONST_32  C7   N1   C4   C3      0.00   0.0  0
 4Y6  CONST_33  C10  C9   C8   C7    180.00   0.0  0
 4Y6  CONST_34  C12  C13  C8   C7    180.00   0.0  0
 4Y6  CONST_35  CL   C9   C8   C13   180.00   0.0  0
 4Y6  CONST_36  C9   C8   C13  C14   180.00   0.0  0
 4Y6  CONST_37  C11  C12  C13  C14   180.00   0.0  0
 4Y6  CONST_38  CL   C9   C10  C11   180.00   0.0  0
 4Y6  CONST_39  C8   C7   N1   N       0.00   0.0  0
 4Y6  CONST_40  C8   C7   N1   C4    180.00   0.0  0
 4Y6  CONST_41  H13  C2   C1   C     180.00   0.0  0
 4Y6  CONST_42  H12  C3   C4   C5    180.00   0.0  0
 4Y6  CONST_43  H14  C1   C    C5    180.00   0.0  0
 4Y6  CONST_44  H17  C10  C9   C8    180.00   0.0  0
 4Y6  CONST_45  H15  C12  C13  C8    180.00   0.0  0
 4Y6  CONST_46  H16  C11  C12  C13   180.00   0.0  0
 4Y6  CONST_47  O    C7   N1   N     180.00   0.0  0
 4Y6  CONST_48  O    C7   N1   C4      0.00   0.0  0
 4Y6  CONST_49  H7   O1   C21  C18   180.00   0.0  0
 4Y6  Var_01    C20  C15  C6   C5    -36.87  30.0  2
 4Y6  Var_02    C19  C20  C15  C6   -176.61  30.0  1
 4Y6  Var_03    C17  C16  C15  C6   -168.49  30.0  1
 4Y6  Var_04    C18  C19  C20  C15    16.28  30.0  1
 4Y6  Var_05    C18  C17  C16  C15   -45.85  30.0  1
 4Y6  Var_06    C9   C8   C7   N1    -79.97  30.0  2
 4Y6  Var_07    F1   C14  C13  C8     80.93  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
 4Y6  chir_01  C18  C17  C19  C21  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
 4Y6  plan-1  C7   0.020
 4Y6  plan-1  C8   0.020
 4Y6  plan-1  C13  0.020
 4Y6  plan-1  C14  0.020
 4Y6  plan-1  C12  0.020
 4Y6  plan-1  C11  0.020
 4Y6  plan-1  C10  0.020
 4Y6  plan-1  C9   0.020
 4Y6  plan-1  CL   0.020
 4Y6  plan-1  H15  0.020
 4Y6  plan-1  H16  0.020
 4Y6  plan-1  H17  0.020
 4Y6  plan-2  F3   0.020
 4Y6  plan-2  C    0.020
 4Y6  plan-2  C5   0.020
 4Y6  plan-2  C6   0.020
 4Y6  plan-2  C15  0.020
 4Y6  plan-2  N    0.020
 4Y6  plan-2  N1   0.020
 4Y6  plan-2  C4   0.020
 4Y6  plan-2  C3   0.020
 4Y6  plan-2  C2   0.020
 4Y6  plan-2  C1   0.020
 4Y6  plan-2  C7   0.020
 4Y6  plan-2  O    0.020
 4Y6  plan-2  C8   0.020
 4Y6  plan-2  H12  0.020
 4Y6  plan-2  H13  0.020
 4Y6  plan-2  H14  0.020
 4Y6  plan-3  C18  0.020
 4Y6  plan-3  C21  0.020
 4Y6  plan-3  O2   0.020
 4Y6  plan-3  O1   0.020
 4Y6  plan-3  H7   0.020

