# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:24:20 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: {2-[(2R)-4-[4-(hydroxymethyl)-3-(methylsulfonyl)phenyl]-2-(propan-2-yl)piperazin-1-yl]-4-(trifluoromethyl)pyrimidin-5-yl}methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1CN(CCN1c2ncc(CO)c(n2)C(F)(F)F)c3ccc(CO)c(c3)[S](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
 67S  67S  {2-[(2R)-4-[4-(hydroxymethyl)-3-(methylsulfonyl)phenyl]-2-(propan-2-yl)piperazin-1-yl]-4-(trifluoromethyl)pyrimidin-5-yl}methanol  ligand  60  33  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_67S
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
 67S  O4   O  OS    0  -0.665   6.9465  -1.2283  -0.9227
 67S  S    S  S     0   1.205   5.6748  -1.6613  -0.3459
 67S  O3   O  OS    0  -0.664   4.8316  -2.5465  -1.1488
 67S  C19  C  CH3   0  -0.792   5.9900  -2.4797   1.2010
 67S  C18  C  CR6   0  -0.242   4.7174  -0.2230   0.1040
 67S  C20  C  CR16  0  -0.317   3.3550  -0.3231  -0.1177
 67S  C16  C  CR6   0   0.057   5.3163   0.9312   0.6265
 67S  C17  C  CH2   0  -0.192   6.7999   1.0956   0.8603
 67S  O2   O  OH1   0  -0.663   7.0151   2.1967   1.7054
 67S  C15  C  CR16  0  -0.281   4.4480   1.9775   0.9129
 67S  C14  C  CR16  0  -0.329   3.0787   1.8911   0.7117
 67S  C13  C  CR6   0   0.401   2.4934   0.7383   0.1842
 67S  N4   N  NT    0  -0.526   1.1369   0.6286  -0.0826
 67S  C21  C  CH2   0  -0.303   0.3003   1.8045   0.0205
 67S  C4   C  CH1   0  -0.095  -0.9628   1.6429  -0.8257
 67S  C2   C  CH1   0  -0.240  -0.6864   1.6380  -2.3419
 67S  C3   C  CH3   0  -0.659  -1.9463   1.3020  -3.1344
 67S  C1   C  CH3   0  -0.662  -0.1455   2.9924  -2.7949
 67S  C12  C  CH2   0  -0.304   0.4403  -0.5729   0.3506
 67S  C11  C  CH2   0  -0.321  -0.8379  -0.7677  -0.4419
 67S  N1   N  NT    0  -0.512  -1.6480   0.4321  -0.3950
 67S  C5   C  CR6   0   0.658  -2.9312   0.4297   0.0217
 67S  N2   N  N     0  -0.491  -3.4646  -0.7333   0.4083
 67S  C6   C  CR6   0   0.005  -4.7155  -0.7288   0.8127
 67S  C7   C  CT    0   1.046  -5.2425  -2.0869   1.2279
 67S  F2   F  F     0  -0.312  -5.8362  -2.0307   2.4267
 67S  F1   F  F     0  -0.313  -6.1544  -2.5341   0.3538
 67S  F3   F  F     0  -0.290  -4.2845  -3.0008   1.3026
 67S  N3   N  N     0  -0.459  -3.6028   1.5874   0.0293
 67S  C10  C  CR16  0  -0.013  -4.8541   1.5587   0.4375
 67S  C8   C  CR6   0  -0.082  -5.5177   0.4053   0.8572
 67S  C9   C  CH2   0  -0.202  -6.9465   0.4555   1.3303
 67S  O1   O  OH1   0  -0.666  -7.5560   1.6023   0.7912
 67S  H1   H  HCH3  0   0.313   6.5922  -3.3606   0.9798
 67S  H2   H  HCH3  0   0.292   6.5327  -1.8211   1.8746
 67S  H3   H  HCH3  0   0.299   5.0420  -2.7752   1.6439
 67S  H4   H  HCR6  0   0.290   2.9574  -1.2293  -0.5523
 67S  H5   H  HCH2  0   0.205   7.2248   0.1855   1.2983
 67S  H6   H  HCH2  0   0.235   7.2981   1.2341  -0.1052
 67S  H7   H  HOH1  0   0.465   7.9492   2.4200   1.6651
 67S  H8   H  HCR6  0   0.268   4.8411   2.8960   1.3237
 67S  H9   H  HCR6  0   0.279   2.4738   2.7441   0.9870
 67S  H10  H  HCH2  0   0.237   0.0084   2.0068   1.0617
 67S  H11  H  HCH2  0   0.260   0.8455   2.6777  -0.3314
 67S  H12  H  HCH1  0   0.273  -1.6133   2.4886  -0.6042
 67S  H13  H  HCH1  0   0.228   0.0744   0.8813  -2.5581
 67S  H14  H  HCH3  0   0.217  -2.7281   2.0448  -2.9601
 67S  H15  H  HCH3  0   0.232  -1.7299   1.2988  -4.2038
 67S  H16  H  HCH3  0   0.231  -2.3544   0.3225  -2.8828
 67S  H17  H  HCH3  0   0.231   0.8093   3.2451  -2.3345
 67S  H18  H  HCH3  0   0.235   0.0101   2.9963  -3.8743
 67S  H19  H  HCH3  0   0.219  -0.8528   3.7917  -2.5600
 67S  H20  H  HCH2  0   0.265   1.0665  -1.4518   0.2107
 67S  H21  H  HCH2  0   0.229   0.1999  -0.5092   1.4217
 67S  H22  H  HCH2  0   0.246  -0.5947  -1.0099  -1.4809
 67S  H23  H  HCH2  0   0.283  -1.3941  -1.6040  -0.0296
 67S  H24  H  HCR6  0   0.278  -5.3723   2.5100   0.4332
 67S  H25  H  HCH2  0   0.215  -7.4833  -0.4490   1.0248
 67S  H26  H  HCH2  0   0.231  -6.9640   0.4773   2.4269
 67S  H27  H  HOH1  0   0.465  -8.4116   1.7085   1.2169

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
 67S  O1   C9   single    1.406  0.020  1.406
 67S  C9   C8   single    1.506  0.020  1.506
 67S  F1   C7   single    1.340  0.020  1.340
 67S  F2   C7   single    1.339  0.020  1.339
 67S  C8   C10  aromatic  1.395  0.020  1.395
 67S  C8   C6   aromatic  1.390  0.020  1.390
 67S  C10  N3   aromatic  1.316  0.020  1.316
 67S  C7   C6   single    1.515  0.020  1.515
 67S  C7   F3   single    1.326  0.020  1.326
 67S  C6   N2   aromatic  1.315  0.020  1.315
 67S  N3   C5   aromatic  1.338  0.020  1.338
 67S  N2   C5   aromatic  1.337  0.020  1.337
 67S  C5   N1   single    1.349  0.020  1.349
 67S  N1   C4   single    1.456  0.020  1.456
 67S  N1   C11  single    1.448  0.020  1.448
 67S  C4   C21  single    1.529  0.020  1.529
 67S  C4   C2   single    1.541  0.020  1.541
 67S  C1   C2   single    1.527  0.020  1.527
 67S  C21  N4   single    1.447  0.020  1.447
 67S  C11  C12  single    1.516  0.020  1.516
 67S  C2   C3   single    1.526  0.020  1.526
 67S  C12  N4   single    1.455  0.020  1.455
 67S  N4   C13  single    1.387  0.020  1.387
 67S  C13  C14  aromatic  1.396  0.020  1.396
 67S  C13  C20  aromatic  1.400  0.020  1.400
 67S  C14  C15  aromatic  1.387  0.020  1.387
 67S  C20  C18  aromatic  1.384  0.020  1.384
 67S  C15  C16  aromatic  1.389  0.020  1.389
 67S  C18  C16  aromatic  1.401  0.020  1.401
 67S  C18  S    single    1.785  0.020  1.785
 67S  C16  C17  single    1.511  0.020  1.511
 67S  C19  S    single    1.778  0.020  1.778
 67S  S    O3   double    1.463  0.020  1.463
 67S  S    O4   double    1.462  0.020  1.462
 67S  C17  O2   single    1.405  0.020  1.405
 67S  C19  H1   single    0.970  0.020  1.090
 67S  C19  H2   single    0.970  0.020  1.090
 67S  C19  H3   single    0.970  0.020  1.090
 67S  C20  H4   single    0.930  0.020  1.080
 67S  C17  H5   single    0.970  0.020  1.090
 67S  C17  H6   single    0.970  0.020  1.090
 67S  O2   H7   single    0.850  0.020  0.980
 67S  C15  H8   single    0.930  0.020  1.080
 67S  C14  H9   single    0.930  0.020  1.080
 67S  C21  H10  single    0.970  0.020  1.090
 67S  C21  H11  single    0.970  0.020  1.090
 67S  C4   H12  single    0.970  0.020  1.090
 67S  C2   H13  single    0.970  0.020  1.090
 67S  C3   H14  single    0.970  0.020  1.090
 67S  C3   H15  single    0.970  0.020  1.090
 67S  C3   H16  single    0.970  0.020  1.090
 67S  C1   H17  single    0.970  0.020  1.090
 67S  C1   H18  single    0.970  0.020  1.090
 67S  C1   H19  single    0.970  0.020  1.090
 67S  C12  H20  single    0.970  0.020  1.090
 67S  C12  H21  single    0.970  0.020  1.090
 67S  C11  H22  single    0.970  0.020  1.090
 67S  C11  H23  single    0.970  0.020  1.090
 67S  C10  H24  single    0.930  0.020  1.080
 67S  C9   H25  single    0.970  0.020  1.090
 67S  C9   H26  single    0.970  0.020  1.090
 67S  O1   H27  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
 67S  C18  S    C19  104.27  3.000
 67S  C19  S    O3   107.53  3.000
 67S  C18  S    O3   108.47  3.000
 67S  O3   S    O4   117.66  3.000
 67S  C19  S    O4   108.99  3.000
 67S  C18  S    O4   109.10  3.000
 67S  H3   C19  H2   110.33  3.000
 67S  H3   C19  H1   110.17  3.000
 67S  H2   C19  H1   109.85  3.000
 67S  H3   C19  S    108.96  3.000
 67S  H2   C19  S    110.41  3.000
 67S  H1   C19  S    107.06  3.000
 67S  C16  C18  C20  122.69  3.000
 67S  C16  C18  S    121.89  3.000
 67S  C20  C18  S    115.42  3.000
 67S  H4   C20  C13  119.73  3.000
 67S  H4   C20  C18  119.16  3.000
 67S  C13  C20  C18  121.09  3.000
 67S  C15  C16  C17  119.99  3.000
 67S  C17  C16  C18  124.54  3.000
 67S  C15  C16  C18  115.46  3.000
 67S  H6   C17  H5   106.32  3.000
 67S  H6   C17  O2   111.20  3.000
 67S  H5   C17  O2   110.56  3.000
 67S  H6   C17  C16  108.91  3.000
 67S  H5   C17  C16  110.62  3.000
 67S  O2   C17  C16  109.20  3.000
 67S  H7   O2   C17  107.80  3.000
 67S  H8   C15  C14  117.87  3.000
 67S  H8   C15  C16  119.42  3.000
 67S  C14  C15  C16  122.70  3.000
 67S  H9   C14  C13  120.86  3.000
 67S  H9   C14  C15  117.80  3.000
 67S  C13  C14  C15  121.34  3.000
 67S  N4   C13  C14  123.23  3.000
 67S  C14  C13  C20  116.71  3.000
 67S  N4   C13  C20  120.03  3.000
 67S  C12  N4   C21  111.91  3.000
 67S  C12  N4   C13  118.45  3.000
 67S  C21  N4   C13  119.18  3.000
 67S  H11  C21  H10  106.95  3.000
 67S  H11  C21  C4   108.65  3.000
 67S  H10  C21  C4   108.91  3.000
 67S  H11  C21  N4   109.85  3.000
 67S  H10  C21  N4   111.73  3.000
 67S  C4   C21  N4   110.63  3.000
 67S  H12  C4   N1   107.72  3.000
 67S  H12  C4   C2   108.03  3.000
 67S  N1   C4   C2   111.88  3.000
 67S  H12  C4   C21  107.37  3.000
 67S  C2   C4   C21  113.37  3.000
 67S  N1   C4   C21  108.23  3.000
 67S  H13  C2   C1   107.96  3.000
 67S  H13  C2   C3   108.61  3.000
 67S  C1   C2   C3   109.49  3.000
 67S  H13  C2   C4   108.73  3.000
 67S  C3   C2   C4   111.32  3.000
 67S  C1   C2   C4   110.64  3.000
 67S  H16  C3   H15  107.32  3.000
 67S  H16  C3   H14  107.82  3.000
 67S  H15  C3   H14  107.47  3.000
 67S  H16  C3   C2   112.77  3.000
 67S  H15  C3   C2   110.24  3.000
 67S  H14  C3   C2   111.00  3.000
 67S  H19  C1   H18  107.60  3.000
 67S  H19  C1   H17  107.86  3.000
 67S  H18  C1   H17  107.00  3.000
 67S  H19  C1   C2   110.83  3.000
 67S  H18  C1   C2   110.32  3.000
 67S  H17  C1   C2   113.00  3.000
 67S  H21  C12  H20  107.33  3.000
 67S  H21  C12  C11  109.40  3.000
 67S  H20  C12  C11  108.31  3.000
 67S  H21  C12  N4   110.29  3.000
 67S  H20  C12  N4   110.68  3.000
 67S  C11  C12  N4   110.74  3.000
 67S  H23  C11  H22  107.69  3.000
 67S  H23  C11  N1   109.83  3.000
 67S  H22  C11  N1   109.78  3.000
 67S  H23  C11  C12  109.41  3.000
 67S  H22  C11  C12  109.71  3.000
 67S  N1   C11  C12  110.37  3.000
 67S  C5   N1   C11  122.72  3.000
 67S  C11  N1   C4   114.58  3.000
 67S  C5   N1   C4   122.70  3.000
 67S  N3   C5   N2   123.41  3.000
 67S  N2   C5   N1   118.06  3.000
 67S  N3   C5   N1   118.52  3.000
 67S  C6   N2   C5   117.76  3.000
 67S  C8   C6   C7   121.47  3.000
 67S  C7   C6   N2   114.35  3.000
 67S  C8   C6   N2   124.18  3.000
 67S  F3   C7   F1   107.36  3.000
 67S  F3   C7   F2   107.38  3.000
 67S  F1   C7   F2   107.24  3.000
 67S  F3   C7   C6   112.46  3.000
 67S  F2   C7   C6   111.22  3.000
 67S  F1   C7   C6   110.93  3.000
 67S  C10  N3   C5   117.38  3.000
 67S  H24  C10  C8   119.97  3.000
 67S  H24  C10  N3   115.74  3.000
 67S  C8   C10  N3   124.29  3.000
 67S  C9   C8   C10  121.21  3.000
 67S  C10  C8   C6   112.98  3.000
 67S  C9   C8   C6   125.79  3.000
 67S  H26  C9   H25  106.70  3.000
 67S  H26  C9   O1   111.11  3.000
 67S  H25  C9   O1   110.75  3.000
 67S  H26  C9   C8   109.26  3.000
 67S  H25  C9   C8   110.48  3.000
 67S  O1   C9   C8   108.54  3.000
 67S  H27  O1   C9   107.82  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
 67S  CONST_01  C14  C13  C20  C18     0.00   0.0  0
 67S  CONST_02  C14  C15  C16  C18     0.00   0.0  0
 67S  CONST_03  C15  C14  C13  C20     0.00   0.0  0
 67S  CONST_04  C15  C16  C18  C20     0.00   0.0  0
 67S  CONST_05  C13  C14  C15  C16     0.00   0.0  0
 67S  CONST_06  C13  C20  C18  C16     0.00   0.0  0
 67S  CONST_07  C8   C10  N3   C5      0.00   0.0  0
 67S  CONST_08  C8   C6   N2   C5      0.00   0.0  0
 67S  CONST_09  C10  C8   C6   N2      0.00   0.0  0
 67S  CONST_10  C10  N3   C5   N2      0.00   0.0  0
 67S  CONST_11  N3   C10  C8   C6      0.00   0.0  0
 67S  CONST_12  N3   C5   N2   C6      0.00   0.0  0
 67S  CONST_13  N4   C13  C20  C18   180.00   0.0  0
 67S  CONST_14  N4   C13  C14  C15   180.00   0.0  0
 67S  CONST_15  C10  N3   C5   N1    180.00   0.0  0
 67S  CONST_16  C6   N2   C5   N1    180.00   0.0  0
 67S  CONST_17  C13  C20  C18  S     180.00   0.0  0
 67S  CONST_18  C15  C16  C18  S     180.00   0.0  0
 67S  CONST_19  C17  C16  C18  C20   180.00   0.0  0
 67S  CONST_20  C14  C15  C16  C17   180.00   0.0  0
 67S  CONST_21  C7   C6   N2   C5    180.00   0.0  0
 67S  CONST_22  C9   C8   C6   N2    180.00   0.0  0
 67S  CONST_23  C10  C8   C6   C7    180.00   0.0  0
 67S  CONST_24  C9   C8   C10  N3    180.00   0.0  0
 67S  CONST_25  H8   C15  C16  C18   180.00   0.0  0
 67S  CONST_26  H9   C14  C13  C20   180.00   0.0  0
 67S  CONST_27  H4   C20  C18  C16   180.00   0.0  0
 67S  CONST_28  H24  C10  N3   C5    180.00   0.0  0
 67S  Var_01    C21  N4   C13  C20  -169.57  30.0  2
 67S  Var_02    C4   C21  N4   C13   156.81  30.0  1
 67S  Var_03    C11  C12  N4   C13  -158.76  30.0  1
 67S  Var_04    N1   C11  C12  N4    -52.81  30.0  1
 67S  Var_05    N3   C5   N1   C4      0.50  30.0  2
 67S  Var_06    C12  C11  N1   C4     54.62  30.0  1
 67S  Var_07    C20  C18  S    O4    142.17  30.0  2
 67S  Var_08    O2   C17  C16  C18  -164.33  30.0  2
 67S  Var_09    F1   C7   C6   N2   -110.53  30.0  3
 67S  Var_10    O1   C9   C8   C6   -158.89  30.0  3
 67S  Var_11    H1   C19  S    C18  -178.94  30.0  3
 67S  Var_12    H17  C1   C2   C4     62.56  30.0  3
 67S  Var_13    H14  C3   C2   C4     61.29  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
 67S  chir_01  C4  N1  C21  C2  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
 67S  plan-1  S    0.020
 67S  plan-1  C18  0.020
 67S  plan-1  C20  0.020
 67S  plan-1  C16  0.020
 67S  plan-1  C17  0.020
 67S  plan-1  C15  0.020
 67S  plan-1  C14  0.020
 67S  plan-1  C13  0.020
 67S  plan-1  N4   0.020
 67S  plan-1  H4   0.020
 67S  plan-1  H8   0.020
 67S  plan-1  H9   0.020
 67S  plan-2  N1   0.020
 67S  plan-2  C5   0.020
 67S  plan-2  N2   0.020
 67S  plan-2  C6   0.020
 67S  plan-2  C7   0.020
 67S  plan-2  N3   0.020
 67S  plan-2  C10  0.020
 67S  plan-2  C8   0.020
 67S  plan-2  C9   0.020
 67S  plan-2  H24  0.020

