# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:00:25 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-{2-[(1R)-1-[3-(cyclopropyloxy)-4-(difluoromethoxy)phenyl]-2-(1-oxidopyridin-3-yl)ethyl]-1,3-thiazol-5-yl}-1,1,1,3,3,3-hexafluoropropan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(c1sc(nc1)[C@H](Cc2ccc[n+]([O-])c2)c3ccc(OC(F)F)c(OC4CC4)c3)(C(F)(F)F)C(F)(F)F
#
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
 M99  M99  2-{2-[(1R)-1-[3-(cyclopropyloxy)-4-(difluoromethoxy)phenyl]-2-(1-oxidopyridin-3-yl)ethyl]-1,3-thiazol-5-yl}-1,1,1,3,3,3-hexafluoropropan-2-ol  ligand  56  38  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M99
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
 M99  F1    F  F      0  -0.311  -2.1459  -0.1847   3.5186
 M99  F2    F  F      0  -0.333  -2.4301  -0.5307   1.4074
 M99  C1    C  CH1    0   0.638  -1.5593  -0.7130   2.4320
 M99  O1    O  O2     0  -0.476  -0.4251  -0.0005   2.2168
 M99  C12   C  CH2    0  -0.517   3.2559   2.3043   4.1295
 M99  C13   C  CH2    0  -0.527   3.8679   2.0466   2.7788
 M99  C8    C  CH1    0  -0.011   3.2150   0.9422   3.5425
 M99  O2    O  O2     0  -0.460   1.9566   0.4899   3.1329
 M99  C2    C  CR6    0   0.247   0.6196  -0.6115   1.5709
 M99  C3    C  CR6    0   0.348   1.9005  -0.3296   2.0663
 M99  C4    C  CR16   0  -0.405   3.0016  -0.8993   1.4471
 M99  C5    C  CR6    0   0.186   2.8456  -1.7233   0.3332
 M99  C6    C  CR16   0  -0.336   1.5755  -1.9856  -0.1472
 M99  C7    C  CR16   0  -0.312   0.4602  -1.4288   0.4703
 M99  C9    C  CH1    0  -0.422   4.0570  -2.3028  -0.3666
 M99  C10   C  CR5    0   0.106   4.7275  -3.3082   0.5233
 M99  C11   C  CR15   0   0.019   5.9871  -4.1156   2.1299
 M99  N1    N  N      0  -0.389   5.6050  -3.0134   1.4293
 M99  S1    S  S2     0   0.314   4.3062  -4.9732   0.4558
 M99  C14   C  CR5    0  -0.284   5.3929  -5.2795   1.7517
 M99  C15   C  CT     0  -0.202   5.5383  -6.6789   2.2776
 M99  O3    O  OH1    0  -0.646   4.7375  -7.4872   1.4837
 M99  C16   C  CT     0   1.019   5.0257  -6.7230   3.7389
 M99  F5    F  F      0  -0.286   3.7688  -6.2925   3.7790
 M99  F6    F  F      0  -0.287   5.7481  -5.9575   4.5530
 M99  F7    F  F      0  -0.295   5.0410  -7.9650   4.2273
 M99  C17   C  CT     0   1.021   7.0134  -7.1313   2.1449
 M99  F8    F  F      0  -0.288   7.8417  -6.3895   2.8767
 M99  F9    F  F      0  -0.286   7.3936  -7.0389   0.8749
 M99  F10   F  F      0  -0.295   7.1701  -8.4026   2.5199
 M99  C18   C  CH2    0  -0.506   5.0656  -1.2242  -0.8079
 M99  C19   C  CR6    0   0.018   4.3856  -0.1119  -1.5481
 M99  C20   C  CR16   0  -0.186   3.8849  -0.2734  -2.8348
 M99  C21   C  CR16   0  -0.347   3.2131   0.7877  -3.4182
 M99  C22   C  CR16   0  -0.035   4.2033   1.0986  -0.9113
 M99  C23   C  CR16   0  -0.023   3.0440   1.9711  -2.7339
 M99  N2    N  NR6    1  -0.022   3.5361   2.1261  -1.4835
 M99  H11   H  HCH1   0   0.206  -1.3938  -1.7840   2.5702
 M99  H122  H  HCH2   0   0.265   2.3324   2.8690   4.1570
 M99  H131  H  HCH2   0   0.266   3.3490   2.4435   1.9141
 M99  H132  H  HCH2   0   0.262   4.9468   2.0299   2.6900
 M99  H88   H  HCH1   0   0.265   3.8456   0.1746   3.9837
 M99  H44   H  HCR6   0   0.282   3.9952  -0.7034   1.8294
 M99  H66   H  HCR6   0   0.260   1.4393  -2.6138  -1.0179
 M99  H77   H  HCR6   0   0.286  -0.5225  -1.6239   0.0620
 M99  H99   H  HCH1   0   0.299   3.7028  -2.8205  -1.2625
 M99  H111  H  HCR5   0   0.288   6.7175  -4.0036   2.9175
 M99  H181  H  HCH2   0   0.288   5.8205  -1.6942  -1.4408
 M99  H182  H  HCH2   0   0.269   5.5868  -0.8286   0.0643
 M99  H220  H  HCR6   0   0.275   4.0149  -1.2050  -3.3695
 M99  H221  H  HCR6   0   0.291   2.8067   0.7101  -4.4166
 M99  H222  H  HCR6   0   0.303   4.5730   1.2942   0.0843
 M99  H223  H  HCR6   0   0.311   2.5235   2.8247  -3.1405
 M99  HO1   H  HOH1   0   0.484   4.7565  -8.4139   1.7585
 M99  O4    O  O     -1  -0.584   3.3733   3.2185  -0.8500
 M99  H121  H  HCH2   0   0.263   3.9099   2.4656   4.9762

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
 M99  F1   C1    single    1.343  0.020  1.343
 M99  F2   C1    single    1.357  0.020  1.357
 M99  C1   O1    single    1.357  0.020  1.357
 M99  C1   H11   single    0.970  0.020  1.090
 M99  O1   C2    single    1.372  0.020  1.372
 M99  C12  C13   single    1.505  0.020  1.505
 M99  C12  C8    single    1.484  0.020  1.484
 M99  C12  H121  single    0.970  0.020  1.090
 M99  C12  H122  single    0.970  0.020  1.090
 M99  C13  C8    single    1.493  0.020  1.493
 M99  C13  H131  single    0.970  0.020  1.090
 M99  C13  H132  single    0.970  0.020  1.090
 M99  C8   O2    single    1.399  0.020  1.399
 M99  C8   H88   single    0.970  0.020  1.090
 M99  O2   C3    single    1.346  0.020  1.346
 M99  C2   C3    aromatic  1.402  0.020  1.402
 M99  C2   C7    aromatic  1.380  0.020  1.380
 M99  C3   C4    aromatic  1.386  0.020  1.386
 M99  C4   C5    aromatic  1.394  0.020  1.394
 M99  C4   H44   single    0.930  0.020  1.080
 M99  C5   C6    aromatic  1.383  0.020  1.383
 M99  C5   C9    single    1.514  0.020  1.514
 M99  C6   C7    aromatic  1.391  0.020  1.391
 M99  C6   H66   single    0.930  0.020  1.080
 M99  C7   H77   single    0.930  0.020  1.080
 M99  C9   C10   single    1.501  0.020  1.501
 M99  C9   C18   single    1.541  0.020  1.541
 M99  C9   H99   single    0.970  0.020  1.090
 M99  C10  N1    aromatic  1.295  0.020  1.295
 M99  C10  S1    aromatic  1.719  0.020  1.719
 M99  C11  N1    aromatic  1.361  0.020  1.361
 M99  C11  C14   aromatic  1.360  0.020  1.360
 M99  C11  H111  single    0.930  0.020  1.080
 M99  S1   C14   aromatic  1.719  0.020  1.719
 M99  C14  C15   single    1.502  0.020  1.502
 M99  C15  O3    single    1.387  0.020  1.387
 M99  C15  C16   single    1.549  0.020  1.549
 M99  C15  C17   single    1.549  0.020  1.549
 M99  C16  F5    single    1.329  0.020  1.329
 M99  C16  F6    single    1.331  0.020  1.331
 M99  C16  F7    single    1.335  0.020  1.335
 M99  C17  F8    single    1.331  0.020  1.331
 M99  C17  F9    single    1.329  0.020  1.329
 M99  C17  F10   single    1.335  0.020  1.335
 M99  C18  C19   single    1.499  0.020  1.499
 M99  C18  H181  single    0.970  0.020  1.090
 M99  C18  H182  single    0.970  0.020  1.090
 M99  C19  C20   aromatic  1.390  0.020  1.390
 M99  C19  C22   aromatic  1.380  0.020  1.380
 M99  C20  C21   aromatic  1.385  0.020  1.385
 M99  C20  H220  single    0.930  0.020  1.080
 M99  C21  C23   aromatic  1.377  0.020  1.377
 M99  C21  H221  single    0.930  0.020  1.080
 M99  C22  N2    aromatic  1.352  0.020  1.352
 M99  C22  H222  single    0.930  0.020  1.080
 M99  C23  N2    aromatic  1.353  0.020  1.353
 M99  C23  H223  single    0.930  0.020  1.080
 M99  O4   N2    single    1.273  0.020  1.273
 M99  HO1  O3    single    0.850  0.020  0.980

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
 M99  H11   C1   O1    114.10  3.000
 M99  H11   C1   F2    108.93  3.000
 M99  O1    C1   F2    110.25  3.000
 M99  H11   C1   F1    110.46  3.000
 M99  O1    C1   F1    106.67  3.000
 M99  F2    C1   F1    106.13  3.000
 M99  C2    O1   C1    118.52  3.000
 M99  H122  C12  H121  114.71  3.000
 M99  H122  C12  C8    117.73  3.000
 M99  H121  C12  C8    117.59  3.000
 M99  H122  C12  C13   117.31  3.000
 M99  H121  C12  C13   118.81  3.000
 M99  C8    C12  C13    59.93  3.000
 M99  H132  C13  H131  114.66  3.000
 M99  H132  C13  C8    117.79  3.000
 M99  H131  C13  C8    118.01  3.000
 M99  H132  C13  C12   118.79  3.000
 M99  H131  C13  C12   117.30  3.000
 M99  C8    C13  C12    59.32  3.000
 M99  H88   C8   O2    114.36  3.000
 M99  H88   C8   C13   118.44  3.000
 M99  O2    C8   C13   118.88  3.000
 M99  H88   C8   C12   118.15  3.000
 M99  O2    C8   C12   115.95  3.000
 M99  C13   C8   C12    60.74  3.000
 M99  C3    O2   C8    117.80  3.000
 M99  C7    C2   C3    120.42  3.000
 M99  C7    C2   O1    123.46  3.000
 M99  C3    C2   O1    116.10  3.000
 M99  C4    C3   C2    119.04  3.000
 M99  C4    C3   O2    124.83  3.000
 M99  C2    C3   O2    116.13  3.000
 M99  H44   C4   C5    119.46  3.000
 M99  H44   C4   C3    119.81  3.000
 M99  C5    C4   C3    120.73  3.000
 M99  C9    C5   C6    120.11  3.000
 M99  C9    C5   C4    120.38  3.000
 M99  C6    C5   C4    119.49  3.000
 M99  H66   C6   C7    119.24  3.000
 M99  H66   C6   C5    120.34  3.000
 M99  C7    C6   C5    120.41  3.000
 M99  H77   C7   C6    119.24  3.000
 M99  H77   C7   C2    120.84  3.000
 M99  C6    C7   C2    119.90  3.000
 M99  H99   C9   C18   107.98  3.000
 M99  H99   C9   C10   108.26  3.000
 M99  C18   C9   C10   110.26  3.000
 M99  H99   C9   C5    107.49  3.000
 M99  C18   C9   C5    112.83  3.000
 M99  C10   C9   C5    109.86  3.000
 M99  S1    C10  N1    114.46  3.000
 M99  S1    C10  C9    121.07  3.000
 M99  N1    C10  C9    124.40  3.000
 M99  H111  C11  C14   125.94  3.000
 M99  H111  C11  N1    118.78  3.000
 M99  C14   C11  N1    115.28  3.000
 M99  C11   N1   C10   111.47  3.000
 M99  C14   S1   C10    89.31  3.000
 M99  C15   C14  S1    119.42  3.000
 M99  C15   C14  C11   131.10  3.000
 M99  S1    C14  C11   109.47  3.000
 M99  C17   C15  C16   112.81  3.000
 M99  C17   C15  O3    109.30  3.000
 M99  C16   C15  O3    109.40  3.000
 M99  C17   C15  C14   109.54  3.000
 M99  C16   C15  C14   108.95  3.000
 M99  O3    C15  C14   106.65  3.000
 M99  HO1   O3   C15   112.61  3.000
 M99  F7    C16  F6    107.77  3.000
 M99  F7    C16  F5    107.53  3.000
 M99  F6    C16  F5    107.97  3.000
 M99  F7    C16  C15   111.58  3.000
 M99  F6    C16  C15   112.40  3.000
 M99  F5    C16  C15   109.40  3.000
 M99  F10   C17  F9    107.53  3.000
 M99  F10   C17  F8    107.66  3.000
 M99  F9    C17  F8    107.97  3.000
 M99  F10   C17  C15   111.47  3.000
 M99  F9    C17  C15   109.52  3.000
 M99  F8    C17  C15   112.51  3.000
 M99  H182  C18  H181  106.83  3.000
 M99  H182  C18  C19   110.04  3.000
 M99  H181  C18  C19   110.30  3.000
 M99  H182  C18  C9    109.74  3.000
 M99  H181  C18  C9    108.49  3.000
 M99  C19   C18  C9    111.33  3.000
 M99  C22   C19  C20   118.79  3.000
 M99  C22   C19  C18   118.87  3.000
 M99  C20   C19  C18   122.29  3.000
 M99  H220  C20  C21   120.65  3.000
 M99  H220  C20  C19   120.95  3.000
 M99  C21   C20  C19   118.40  3.000
 M99  H221  C21  C23   118.32  3.000
 M99  H221  C21  C20   121.11  3.000
 M99  C23   C21  C20   120.57  3.000
 M99  H222  C22  N2    114.93  3.000
 M99  H222  C22  C19   122.63  3.000
 M99  N2    C22  C19   122.44  3.000
 M99  H223  C23  N2    115.66  3.000
 M99  H223  C23  C21   123.47  3.000
 M99  N2    C23  C21   120.86  3.000
 M99  O4    N2   C23   120.78  3.000
 M99  O4    N2   C22   120.29  3.000
 M99  C23   N2   C22   118.92  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
 M99  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 M99  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 M99  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 M99  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 M99  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 M99  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 M99  CONST_07  C14   C11  N1   C10     0.00   0.0  0
 M99  CONST_08  C11   C14  S1   C10     0.00   0.0  0
 M99  CONST_09  S1    C10  N1   C11     0.00   0.0  0
 M99  CONST_10  C14   S1   C10  N1      0.00   0.0  0
 M99  CONST_11  S1    C14  C11  N1      0.00   0.0  0
 M99  CONST_12  C23   C21  C20  C19     0.00   0.0  0
 M99  CONST_13  C23   N2   C22  C19     0.00   0.0  0
 M99  CONST_14  N2    C22  C19  C20     0.00   0.0  0
 M99  CONST_15  N2    C23  C21  C20     0.00   0.0  0
 M99  CONST_16  C22   C19  C20  C21     0.00   0.0  0
 M99  CONST_17  C22   N2   C23  C21     0.00   0.0  0
 M99  CONST_18  C4    C3   C2   O1    180.00   0.0  0
 M99  CONST_19  C6    C7   C2   O1    180.00   0.0  0
 M99  CONST_20  C7    C2   C3   O2    180.00   0.0  0
 M99  CONST_21  C5    C4   C3   O2    180.00   0.0  0
 M99  CONST_22  C9    C5   C4   C3    180.00   0.0  0
 M99  CONST_23  C9    C5   C6   C7    180.00   0.0  0
 M99  CONST_24  C11   N1   C10  C9    180.00   0.0  0
 M99  CONST_25  C14   S1   C10  C9    180.00   0.0  0
 M99  CONST_26  C15   C14  S1   C10   180.00   0.0  0
 M99  CONST_27  C15   C14  C11  N1    180.00   0.0  0
 M99  CONST_28  C21   C20  C19  C18   180.00   0.0  0
 M99  CONST_29  N2    C22  C19  C18   180.00   0.0  0
 M99  CONST_30  O4    N2   C22  C19   180.00   0.0  0
 M99  CONST_31  O4    N2   C23  C21   180.00   0.0  0
 M99  CONST_32  H44   C4   C3   C2    180.00   0.0  0
 M99  CONST_33  H66   C6   C7   C2    180.00   0.0  0
 M99  CONST_34  H77   C7   C2   C3    180.00   0.0  0
 M99  CONST_35  H111  C11  N1   C10   180.00   0.0  0
 M99  CONST_36  H221  C21  C20  C19   180.00   0.0  0
 M99  CONST_37  H222  C22  C19  C20   180.00   0.0  0
 M99  CONST_38  H223  C23  C21  C20   180.00   0.0  0
 M99  CONST_39  H220  C20  C19  C22   180.00   0.0  0
 M99  Var_01    O2    C8   C13  C12   105.30  30.0  1
 M99  Var_02    C2    C3   O2   C8   -171.37  30.0  2
 M99  Var_03    C3    C2   O1   C1   -139.87  30.0  2
 M99  Var_04    C20   C19  C18  C9    -71.77  30.0  2
 M99  Var_05    O3    C15  C14  C11  -177.52  30.0  2
 M99  Var_06    F5    C16  C15  C14    56.63  30.0  3
 M99  Var_07    F8    C17  C15  C14    63.06  30.0  3
 M99  Var_08    H11   C1   O1   C2     31.02  30.0  3

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
 M99  chir_02  C9  C5   C10  C18  positiv
 M99  chir_03  C8  C12  C13  O2   both

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
 M99  plan-1  C9    0.020
 M99  plan-1  C10   0.020
 M99  plan-1  C11   0.020
 M99  plan-1  N1    0.020
 M99  plan-1  S1    0.020
 M99  plan-1  C14   0.020
 M99  plan-1  C15   0.020
 M99  plan-1  H111  0.020
 M99  plan-2  O1    0.020
 M99  plan-2  O2    0.020
 M99  plan-2  C2    0.020
 M99  plan-2  C3    0.020
 M99  plan-2  C4    0.020
 M99  plan-2  C5    0.020
 M99  plan-2  C6    0.020
 M99  plan-2  C7    0.020
 M99  plan-2  C9    0.020
 M99  plan-2  H44   0.020
 M99  plan-2  H66   0.020
 M99  plan-2  H77   0.020
 M99  plan-3  C18   0.020
 M99  plan-3  C19   0.020
 M99  plan-3  C20   0.020
 M99  plan-3  C21   0.020
 M99  plan-3  C22   0.020
 M99  plan-3  C23   0.020
 M99  plan-3  N2    0.020
 M99  plan-3  H220  0.020
 M99  plan-3  H221  0.020
 M99  plan-3  H222  0.020
 M99  plan-3  H223  0.020
 M99  plan-3  O4    0.020

