# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:47:45 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 2-[4-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[S](=O)(=O)c1ccc(cc1)c2ccc(C3CCCC3)c(c2)[C@H]4C[C@H]4c5ccccn5
#
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
 9MC  9MC  2-[4-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol  ligand  61  32  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9MC
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
 9MC  C2   C  CH2   0  -0.413  -4.9402  -0.3535  -1.7768
 9MC  C12  C  CR16  0  -0.212   3.3912  -2.1101   0.1709
 9MC  C13  C  CH2   0  -0.137   7.9632  -0.6070  -0.6810
 9MC  C14  C  CH2   0  -0.624   6.4412  -0.5784  -0.6673
 9MC  C15  C  CR6   0  -0.195   4.0543  -1.0213   0.7218
 9MC  C17  C  CR6   0   0.096  -0.1617  -0.8576   0.1797
 9MC  C18  C  CR16  0  -0.367  -0.9887  -0.2391   1.1131
 9MC  C19  C  CH1   0  -0.300  -3.1953   0.4530   2.0222
 9MC  C20  C  CR6   0   0.065  -2.3696  -0.1816   0.9552
 9MC  N1   N  N     0  -0.434  -5.0157   2.8714   0.0258
 9MC  C5   C  CH2   0  -0.455  -6.4228  -0.7267  -1.7420
 9MC  C6   C  CR6   0   0.176  -2.9616  -0.7617  -0.1767
 9MC  C7   C  CR16  0  -0.318  -2.1285  -1.3797  -1.1079
 9MC  C9   C  CR6   0   0.102   1.2984  -0.9113   0.3732
 9MC  O3   O  OS    0  -0.667   6.1915  -2.4911   1.1373
 9MC  O2   O  OS    0  -0.666   6.2097  -0.1030   1.9225
 9MC  O1   O  OH1   0  -0.662   8.3575  -0.1866  -1.9640
 9MC  C16  C  CR16  0  -0.217   3.3632   0.1188   1.1064
 9MC  C10  C  CR16  0  -0.299   1.9906   0.1653   0.9313
 9MC  C11  C  CR16  0  -0.300   2.0208  -2.0469  -0.0022
 9MC  C8   C  CR16  0  -0.304  -0.7566  -1.4324  -0.9416
 9MC  C1   C  CH1   0  -0.377  -4.4501  -0.7614  -0.3854
 9MC  C3   C  CH2   0  -0.420  -5.1170  -2.1323  -0.1965
 9MC  C4   C  CH2   0  -0.446  -6.5130  -1.9686  -0.8235
 9MC  C27  C  CH1   0  -0.317  -3.8950   1.7869   1.8158
 9MC  C21  C  CH2   0  -0.493  -2.7284   1.6654   2.7513
 9MC  C22  C  CR6   0   0.301  -3.8338   2.5046   0.5227
 9MC  C23  C  CR16  0  -0.337  -2.6441   2.7668  -0.1575
 9MC  C24  C  CR16  0  -0.158  -2.6957   3.4102  -1.3813
 9MC  C25  C  CR16  0  -0.325  -3.9281   3.7856  -1.8964
 9MC  C26  C  CR16  0  -0.090  -5.0551   3.4939  -1.1457
 9MC  H1   H  HCH2  0   0.220  -4.4251  -0.9313  -2.5490
 9MC  H2   H  HCH2  0   0.241  -4.7665   0.7028  -1.9872
 9MC  H3   H  HCR6  0   0.286   3.9267  -3.0053  -0.1154
 9MC  H4   H  HCH2  0   0.219   8.3508   0.0542   0.1014
 9MC  H5   H  HCH2  0   0.221   8.3130  -1.6211  -0.4604
 9MC  H6   H  HCH2  0   0.307   6.0595   0.4272  -0.8531
 9MC  H7   H  HCH2  0   0.306   6.0259  -1.2582  -1.4136
 9MC  H8   H  HCR6  0   0.252  -0.5520   0.1847   2.0098
 9MC  H9   H  HCH1  0   0.287  -3.7827  -0.2510   2.6047
 9MC  H10  H  HCH2  0   0.225  -6.9991   0.0980  -1.3172
 9MC  H11  H  HCH2  0   0.229  -6.8256  -0.9134  -2.7382
 9MC  H12  H  HCR6  0   0.249  -2.5556  -1.8285  -1.9961
 9MC  H13  H  HOH1  0   0.462   9.3172  -0.2285  -2.0078
 9MC  H14  H  HCR6  0   0.286   3.8793   0.9678   1.5335
 9MC  H15  H  HCR6  0   0.266   1.4590   1.0631   1.2181
 9MC  H16  H  HCR6  0   0.271   1.5053  -2.9049  -0.4131
 9MC  H17  H  HCR6  0   0.254  -0.1485  -1.9075  -1.7016
 9MC  H18  H  HCH1  0   0.257  -4.9109  -0.0730   0.3263
 9MC  H19  H  HCH2  0   0.223  -4.5441  -2.8938  -0.7327
 9MC  H20  H  HCH2  0   0.236  -5.1529  -2.4382   0.8504
 9MC  H21  H  HCH2  0   0.228  -7.2715  -1.8221  -0.0536
 9MC  H22  H  HCH2  0   0.228  -6.8024  -2.8632  -1.3759
 9MC  H23  H  HCH1  0   0.270  -4.8735   1.8556   2.2755
 9MC  H24  H  HCH2  0   0.271  -2.9311   1.7424   3.8114
 9MC  H25  H  HCH2  0   0.255  -1.7906   2.1197   2.4527
 9MC  H26  H  HCR6  0   0.253  -1.6888   2.4744   0.2548
 9MC  H27  H  HCR6  0   0.270  -1.7827   3.6176  -1.9240
 9MC  H28  H  HCR6  0   0.265  -4.0156   4.2933  -2.8471
 9MC  H29  H  HCR6  0   0.258  -6.0390   3.7743  -1.5060
 9MC  S1   S  S     0   1.199   5.8102  -1.0953   0.9260

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
 9MC  C4   C5   single    1.547  0.020  1.547
 9MC  C4   C3   single    1.539  0.020  1.539
 9MC  C5   C2   single    1.529  0.020  1.529
 9MC  C3   C1   single    1.536  0.020  1.536
 9MC  C7   C8   aromatic  1.383  0.020  1.383
 9MC  C7   C6   aromatic  1.394  0.020  1.394
 9MC  C2   C1   single    1.531  0.020  1.531
 9MC  O1   C13  single    1.407  0.020  1.407
 9MC  C8   C17  aromatic  1.393  0.020  1.393
 9MC  C1   C6   single    1.503  0.020  1.503
 9MC  C13  C14  single    1.522  0.020  1.522
 9MC  C6   C20  aromatic  1.403  0.020  1.403
 9MC  C10  C16  aromatic  1.384  0.020  1.384
 9MC  C10  C9   aromatic  1.396  0.020  1.396
 9MC  C16  C15  aromatic  1.388  0.020  1.388
 9MC  C17  C9   single    1.474  0.020  1.474
 9MC  C17  C18  aromatic  1.392  0.020  1.392
 9MC  C9   C11  aromatic  1.397  0.020  1.397
 9MC  C14  S1   single    1.790  0.020  1.790
 9MC  C20  C18  aromatic  1.391  0.020  1.391
 9MC  C20  C19  single    1.491  0.020  1.491
 9MC  O2   S1   double    1.462  0.020  1.462
 9MC  C15  S1   single    1.769  0.020  1.769
 9MC  C15  C12  aromatic  1.389  0.020  1.389
 9MC  S1   O3   double    1.462  0.020  1.462
 9MC  C11  C12  aromatic  1.383  0.020  1.383
 9MC  C26  N1   aromatic  1.327  0.020  1.327
 9MC  C26  C25  aromatic  1.385  0.020  1.385
 9MC  N1   C22  aromatic  1.334  0.020  1.334
 9MC  C19  C21  single    1.490  0.020  1.490
 9MC  C19  C27  single    1.520  0.020  1.520
 9MC  C21  C27  single    1.500  0.020  1.500
 9MC  C25  C24  aromatic  1.387  0.020  1.387
 9MC  C22  C27  single    1.480  0.020  1.480
 9MC  C22  C23  aromatic  1.395  0.020  1.395
 9MC  C24  C23  aromatic  1.384  0.020  1.384
 9MC  C2   H1   single    0.970  0.020  1.090
 9MC  C2   H2   single    0.970  0.020  1.090
 9MC  C12  H3   single    0.930  0.020  1.080
 9MC  C13  H4   single    0.970  0.020  1.090
 9MC  C13  H5   single    0.970  0.020  1.090
 9MC  C14  H6   single    0.970  0.020  1.090
 9MC  C14  H7   single    0.970  0.020  1.090
 9MC  C18  H8   single    0.930  0.020  1.080
 9MC  C19  H9   single    0.970  0.020  1.090
 9MC  C5   H10  single    0.970  0.020  1.090
 9MC  C5   H11  single    0.970  0.020  1.090
 9MC  C7   H12  single    0.930  0.020  1.080
 9MC  O1   H13  single    0.850  0.020  0.980
 9MC  C16  H14  single    0.930  0.020  1.080
 9MC  C10  H15  single    0.930  0.020  1.080
 9MC  C11  H16  single    0.930  0.020  1.080
 9MC  C8   H17  single    0.930  0.020  1.080
 9MC  C1   H18  single    0.970  0.020  1.090
 9MC  C3   H19  single    0.970  0.020  1.090
 9MC  C3   H20  single    0.970  0.020  1.090
 9MC  C4   H21  single    0.970  0.020  1.090
 9MC  C4   H22  single    0.970  0.020  1.090
 9MC  C27  H23  single    0.970  0.020  1.090
 9MC  C21  H24  single    0.970  0.020  1.090
 9MC  C21  H25  single    0.970  0.020  1.090
 9MC  C23  H26  single    0.930  0.020  1.080
 9MC  C24  H27  single    0.930  0.020  1.080
 9MC  C25  H28  single    0.930  0.020  1.080
 9MC  C26  H29  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
 9MC  H2   C2   H1   107.49  3.000
 9MC  H2   C2   C1   112.48  3.000
 9MC  H1   C2   C1   110.51  3.000
 9MC  H2   C2   C5   113.27  3.000
 9MC  H1   C2   C5   110.11  3.000
 9MC  C1   C2   C5   102.99  3.000
 9MC  H3   C12  C11  119.69  3.000
 9MC  H3   C12  C15  121.16  3.000
 9MC  C11  C12  C15  119.15  3.000
 9MC  H5   C13  H4   107.59  3.000
 9MC  H5   C13  O1   111.78  3.000
 9MC  H4   C13  O1   111.84  3.000
 9MC  H5   C13  C14  109.57  3.000
 9MC  H4   C13  C14  109.64  3.000
 9MC  O1   C13  C14  106.43  3.000
 9MC  H7   C14  H6   108.92  3.000
 9MC  H7   C14  S1   107.13  3.000
 9MC  H6   C14  S1   107.11  3.000
 9MC  H7   C14  C13  111.26  3.000
 9MC  H6   C14  C13  111.44  3.000
 9MC  S1   C14  C13  110.79  3.000
 9MC  C16  C15  S1   119.78  3.000
 9MC  S1   C15  C12  119.13  3.000
 9MC  C16  C15  C12  121.08  3.000
 9MC  C8   C17  C9   120.90  3.000
 9MC  C9   C17  C18  121.11  3.000
 9MC  C8   C17  C18  117.98  3.000
 9MC  H8   C18  C20  118.54  3.000
 9MC  H8   C18  C17  119.29  3.000
 9MC  C20  C18  C17  122.14  3.000
 9MC  H9   C19  C21  115.75  3.000
 9MC  H9   C19  C27  113.11  3.000
 9MC  C21  C19  C27   59.78  3.000
 9MC  H9   C19  C20  114.04  3.000
 9MC  C27  C19  C20  122.08  3.000
 9MC  C21  C19  C20  121.54  3.000
 9MC  C6   C20  C19  121.31  3.000
 9MC  C19  C20  C18  119.08  3.000
 9MC  C6   C20  C18  119.56  3.000
 9MC  C26  N1   C22  118.96  3.000
 9MC  H11  C5   H10  106.84  3.000
 9MC  H11  C5   C4   112.54  3.000
 9MC  H10  C5   C4   110.14  3.000
 9MC  H11  C5   C2   112.28  3.000
 9MC  H10  C5   C2   109.64  3.000
 9MC  C4   C5   C2   105.42  3.000
 9MC  C1   C6   C7   119.95  3.000
 9MC  C1   C6   C20  121.99  3.000
 9MC  C7   C6   C20  118.04  3.000
 9MC  H12  C7   C8   118.30  3.000
 9MC  H12  C7   C6   119.73  3.000
 9MC  C8   C7   C6   121.97  3.000
 9MC  C11  C9   C10  118.54  3.000
 9MC  C11  C9   C17  120.44  3.000
 9MC  C10  C9   C17  121.03  3.000
 9MC  H13  O1   C13  107.95  3.000
 9MC  H14  C16  C10  119.78  3.000
 9MC  H14  C16  C15  121.11  3.000
 9MC  C10  C16  C15  119.10  3.000
 9MC  H15  C10  C16  118.77  3.000
 9MC  H15  C10  C9   120.14  3.000
 9MC  C16  C10  C9   121.07  3.000
 9MC  H16  C11  C9   120.01  3.000
 9MC  H16  C11  C12  118.91  3.000
 9MC  C9   C11  C12  121.06  3.000
 9MC  H17  C8   C7   119.29  3.000
 9MC  H17  C8   C17  120.40  3.000
 9MC  C7   C8   C17  120.30  3.000
 9MC  H18  C1   C3   107.41  3.000
 9MC  H18  C1   C6   109.12  3.000
 9MC  C3   C1   C6   114.37  3.000
 9MC  H18  C1   C2   106.82  3.000
 9MC  C6   C1   C2   116.32  3.000
 9MC  C3   C1   C2   102.16  3.000
 9MC  H20  C3   H19  107.00  3.000
 9MC  H20  C3   C4   113.00  3.000
 9MC  H19  C3   C4   110.46  3.000
 9MC  H20  C3   C1   112.48  3.000
 9MC  H19  C3   C1   109.50  3.000
 9MC  C4   C3   C1   104.41  3.000
 9MC  H22  C4   H21  106.45  3.000
 9MC  H22  C4   C3   111.09  3.000
 9MC  H21  C4   C3   110.95  3.000
 9MC  H22  C4   C5   111.91  3.000
 9MC  H21  C4   C5   110.60  3.000
 9MC  C3   C4   C5   105.92  3.000
 9MC  H23  C27  C22  112.17  3.000
 9MC  H23  C27  C21  116.29  3.000
 9MC  C22  C27  C21  123.50  3.000
 9MC  H23  C27  C19  114.43  3.000
 9MC  C22  C27  C19  121.67  3.000
 9MC  C21  C27  C19   59.10  3.000
 9MC  H25  C21  H24  113.71  3.000
 9MC  H25  C21  C27  117.84  3.000
 9MC  H24  C21  C27  117.35  3.000
 9MC  H25  C21  C19  118.52  3.000
 9MC  H24  C21  C19  118.59  3.000
 9MC  C27  C21  C19   61.12  3.000
 9MC  C23  C22  C27  123.52  3.000
 9MC  C23  C22  N1   121.49  3.000
 9MC  C27  C22  N1   114.98  3.000
 9MC  H26  C23  C24  119.75  3.000
 9MC  H26  C23  C22  121.12  3.000
 9MC  C24  C23  C22  119.13  3.000
 9MC  H27  C24  C25  120.76  3.000
 9MC  H27  C24  C23  120.08  3.000
 9MC  C25  C24  C23  119.17  3.000
 9MC  H28  C25  C26  120.63  3.000
 9MC  H28  C25  C24  121.69  3.000
 9MC  C26  C25  C24  117.68  3.000
 9MC  H29  C26  C25  120.23  3.000
 9MC  H29  C26  N1   116.20  3.000
 9MC  C25  C26  N1   123.57  3.000
 9MC  O2   S1   O3   118.57  3.000
 9MC  O3   S1   C15  108.38  3.000
 9MC  O2   S1   C15  108.75  3.000
 9MC  O3   S1   C14  108.20  3.000
 9MC  C15  S1   C14  103.60  3.000
 9MC  O2   S1   C14  108.32  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
 9MC  CONST_01  C10  C16  C15  C12     0.00   0.0  0
 9MC  CONST_02  C10  C9   C11  C12     0.00   0.0  0
 9MC  CONST_03  C17  C9   C11  C12   180.00   0.0  0
 9MC  CONST_04  C9   C10  C16  C15     0.00   0.0  0
 9MC  CONST_05  C9   C11  C12  C15     0.00   0.0  0
 9MC  CONST_06  C6   C7   C8   C17     0.00   0.0  0
 9MC  CONST_07  C16  C10  C9   C17   180.00   0.0  0
 9MC  CONST_08  C6   C20  C18  C17     0.00   0.0  0
 9MC  CONST_09  C7   C8   C17  C18     0.00   0.0  0
 9MC  CONST_12  C7   C6   C20  C18     0.00   0.0  0
 9MC  CONST_13  C8   C7   C6   C20     0.00   0.0  0
 9MC  CONST_14  C8   C17  C18  C20     0.00   0.0  0
 9MC  CONST_15  C9   C17  C18  C20   180.00   0.0  0
 9MC  CONST_16  C24  C25  C26  N1      0.00   0.0  0
 9MC  CONST_17  C24  C23  C22  N1      0.00   0.0  0
 9MC  CONST_18  C9   C17  C8   C7    180.00   0.0  0
 9MC  CONST_19  C11  C9   C10  C16     0.00   0.0  0
 9MC  CONST_20  C11  C12  C15  C16     0.00   0.0  0
 9MC  CONST_23  C25  C26  N1   C22     0.00   0.0  0
 9MC  CONST_24  C25  C24  C23  C22     0.00   0.0  0
 9MC  CONST_25  C26  N1   C22  C23     0.00   0.0  0
 9MC  CONST_26  C26  C25  C24  C23     0.00   0.0  0
 9MC  CONST_27  C19  C20  C18  C17   180.00   0.0  0
 9MC  CONST_28  C1   C6   C20  C18   180.00   0.0  0
 9MC  CONST_29  C7   C6   C20  C19   180.00   0.0  0
 9MC  CONST_30  C1   C6   C20  C19     0.00   0.0  0
 9MC  CONST_31  C1   C6   C7   C8    180.00   0.0  0
 9MC  CONST_32  C26  N1   C22  C27   180.00   0.0  0
 9MC  CONST_33  C24  C23  C22  C27   180.00   0.0  0
 9MC  CONST_34  C10  C16  C15  S1    180.00   0.0  0
 9MC  CONST_35  C11  C12  C15  S1    180.00   0.0  0
 9MC  CONST_36  H14  C16  C15  C12   180.00   0.0  0
 9MC  CONST_37  H15  C10  C16  C15   180.00   0.0  0
 9MC  CONST_38  H16  C11  C12  C15   180.00   0.0  0
 9MC  CONST_39  H12  C7   C8   C17   180.00   0.0  0
 9MC  CONST_40  H17  C8   C17  C18   180.00   0.0  0
 9MC  CONST_41  H8   C18  C20  C19     0.00   0.0  0
 9MC  CONST_42  H28  C25  C26  N1    180.00   0.0  0
 9MC  CONST_43  H26  C23  C22  N1    180.00   0.0  0
 9MC  CONST_44  H3   C12  C11  C9    180.00   0.0  0
 9MC  CONST_45  H29  C26  N1   C22   180.00   0.0  0
 9MC  CONST_46  H27  C24  C23  C22   180.00   0.0  0
 9MC  Var_01    C3   C4   C5   C2      8.39  30.0  1
 9MC  Var_02    C21  C19  C20  C18    37.96  30.0  2
 9MC  Var_03    C22  C27  C21  C19  -109.73  30.0  1
 9MC  Var_04    N1   C22  C27  C19   128.29  30.0  2
 9MC  Var_05    C27  C21  C19  C20   111.32  30.0  1
 9MC  Var_06    C1   C3   C4   C5     18.59  30.0  1
 9MC  Var_07    C4   C5   C2   C1    -32.22  30.0  1
 9MC  Var_08    C14  S1   C15  C12    85.08  30.0  2
 9MC  Var_09    C15  S1   C14  C13  -178.98  30.0  3
 9MC  Var_10    O1   C13  C14  S1   -179.93  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
 9MC  chir_02  C1   C3   C2   C6   positiv
 9MC  chir_03  C19  C20  C21  C27  both
 9MC  chir_04  C27  C19  C21  C22  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
 9MC  plan-1  C17  0.020
 9MC  plan-1  C18  0.020
 9MC  plan-1  C19  0.020
 9MC  plan-1  C20  0.020
 9MC  plan-1  C6   0.020
 9MC  plan-1  C7   0.020
 9MC  plan-1  C9   0.020
 9MC  plan-1  C8   0.020
 9MC  plan-1  C1   0.020
 9MC  plan-1  H8   0.020
 9MC  plan-1  H12  0.020
 9MC  plan-1  H17  0.020
 9MC  plan-2  C12  0.020
 9MC  plan-2  C15  0.020
 9MC  plan-2  C17  0.020
 9MC  plan-2  C9   0.020
 9MC  plan-2  C16  0.020
 9MC  plan-2  C10  0.020
 9MC  plan-2  C11  0.020
 9MC  plan-2  H3   0.020
 9MC  plan-2  H14  0.020
 9MC  plan-2  H15  0.020
 9MC  plan-2  H16  0.020
 9MC  plan-2  S1   0.020
 9MC  plan-3  N1   0.020
 9MC  plan-3  C27  0.020
 9MC  plan-3  C22  0.020
 9MC  plan-3  C23  0.020
 9MC  plan-3  C24  0.020
 9MC  plan-3  C25  0.020
 9MC  plan-3  C26  0.020
 9MC  plan-3  H26  0.020
 9MC  plan-3  H27  0.020
 9MC  plan-3  H28  0.020
 9MC  plan-3  H29  0.020

