# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:57:02 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-(benzyloxy)-4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)[S](=O)(=O)C2(CCCC2)c3ccc(OCc4ccccc4)cc3
#
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
 Z7D  Z7D  1-(benzyloxy)-4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}benzene  ligand  52  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z7D
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
 Z7D  C1    C  CR16  0  -0.333   -7.8636  23.4298  16.7330
 Z7D  C2    C  CR6   0   0.391   -8.7372  22.5777  16.0625
 Z7D  C3    C  CR16  0  -0.338   -8.5150  22.3066  14.7158
 Z7D  C4    C  CR16  0  -0.261   -7.4492  22.9029  14.0591
 Z7D  C5    C  CR6   0   0.139   -6.5828  23.7804  14.7051
 Z7D  C6    C  CR16  0  -0.270   -6.8119  24.0210  16.0603
 Z7D  O7    O  O2    0  -0.482   -9.7465  22.0611  16.7932
 Z7D  C8    C  CT    0  -0.386   -5.5088  24.5139  13.9335
 Z7D  S9    S  S     0   1.242   -6.3347  25.8394  12.9768
 Z7D  C10   C  CR6   0  -0.177   -7.3150  26.7029  14.1737
 Z7D  C11   C  CR16  0  -0.215   -6.7506  27.7601  14.8745
 Z7D  C12   C  CR16  0  -0.405   -7.4965  28.4144  15.8411
 Z7D  C13   C  CR6   0   0.554   -8.7910  27.9898  16.0762
 Z7D  C14   C  CR16  0  -0.398   -9.3696  26.9426  15.3819
 Z7D  C15   C  CR16  0  -0.188   -8.6201  26.2920  14.4180
 Z7D  O16   O  OS    0  -0.660   -7.2421  25.2188  12.0110
 Z7D  O17   O  OS    0  -0.664   -5.3195  26.7632  12.4655
 Z7D  F18   F  F     0  -0.302   -9.5119  28.6165  17.0103
 Z7D  C19   C  CH2   0  -0.450   -4.3741  25.0787  14.7918
 Z7D  C20   C  CH2   0  -0.438   -3.5346  23.8352  15.1035
 Z7D  C21   C  CH2   0  -0.441   -3.7391  22.8933  13.8960
 Z7D  C22   C  CH2   0  -0.425   -4.7266  23.6117  12.9642
 Z7D  C23   C  CH2   0  -0.251  -10.8327  21.4460  16.1248
 Z7D  C24   C  CR6   0   0.040  -11.6090  22.4057  15.2602
 Z7D  C25   C  CR16  0  -0.297  -12.1175  21.9876  14.0358
 Z7D  C26   C  CR16  0  -0.241  -12.8592  22.8543  13.2431
 Z7D  C27   C  CR16  0  -0.263  -13.0915  24.1550  13.6664
 Z7D  C28   C  CR16  0  -0.245  -12.5837  24.5806  14.8881
 Z7D  C29   C  CR16  0  -0.271  -11.8499  23.7113  15.6820
 Z7D  H1    H  HCR6  0   0.263   -8.0239  23.6437  17.7823
 Z7D  H3    H  HCR6  0   0.276   -9.1596  21.6465  14.1531
 Z7D  H4    H  HCR6  0   0.258   -7.3212  22.6769  13.0099
 Z7D  H6    H  HCR6  0   0.255   -6.1774  24.6928  16.6214
 Z7D  H11   H  HCR6  0   0.293   -5.7379  28.0843  14.6768
 Z7D  H12   H  HCR6  0   0.295   -7.0785  29.2427  16.3968
 Z7D  H14   H  HCR6  0   0.287  -10.3861  26.6388  15.5929
 Z7D  H15   H  HCR6  0   0.287   -9.0556  25.4673  13.8708
 Z7D  H191  H  HCH2  0   0.267   -3.7882  25.7757  14.1917
 Z7D  H192  H  HCH2  0   0.263   -4.6978  25.6210  15.6789
 Z7D  H202  H  HCH2  0   0.239   -3.8767  23.3615  16.0244
 Z7D  H201  H  HCH2  0   0.246   -2.4885  24.1005  15.2535
 Z7D  H212  H  HCH2  0   0.241   -4.1532  21.9378  14.2186
 Z7D  H211  H  HCH2  0   0.246   -2.8049  22.6769  13.3786
 Z7D  H221  H  HCH2  0   0.266   -5.3544  22.9276  12.3979
 Z7D  H222  H  HCH2  0   0.256   -4.1848  24.2295  12.2442
 Z7D  H232  H  HCH2  0   0.276  -11.4660  21.0602  16.9251
 Z7D  H231  H  HCH2  0   0.242  -10.5025  20.5812  15.5391
 Z7D  H25   H  HCR6  0   0.254  -11.9291  20.9765  13.6924
 Z7D  H26   H  HCR6  0   0.257  -13.2478  22.5145  12.2919
 Z7D  H27   H  HCR6  0   0.257  -13.6645  24.8348  13.0493
 Z7D  H28   H  HCR6  0   0.256  -12.7680  25.5927  15.2259
 Z7D  H29   H  HCR6  0   0.254  -11.4624  24.0561  16.6328

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
 Z7D  O16  S9    double    1.463  0.020  1.463
 Z7D  O17  S9    double    1.465  0.020  1.465
 Z7D  S9   C8    single    1.832  0.020  1.832
 Z7D  S9   C10   single    1.772  0.020  1.772
 Z7D  C22  C8    single    1.538  0.020  1.538
 Z7D  C22  C21   single    1.536  0.020  1.536
 Z7D  C26  C27   aromatic  1.387  0.020  1.387
 Z7D  C26  C25   aromatic  1.389  0.020  1.389
 Z7D  C27  C28   aromatic  1.390  0.020  1.390
 Z7D  C8   C5    single    1.512  0.020  1.512
 Z7D  C8   C19   single    1.531  0.020  1.531
 Z7D  C21  C20   single    1.545  0.020  1.545
 Z7D  C4   C5    aromatic  1.392  0.020  1.392
 Z7D  C4   C3    aromatic  1.387  0.020  1.387
 Z7D  C25  C24   aromatic  1.390  0.020  1.390
 Z7D  C10  C15   aromatic  1.390  0.020  1.390
 Z7D  C10  C11   aromatic  1.388  0.020  1.388
 Z7D  C15  C14   aromatic  1.384  0.020  1.384
 Z7D  C5   C6    aromatic  1.395  0.020  1.395
 Z7D  C3   C2    aromatic  1.392  0.020  1.392
 Z7D  C19  C20   single    1.532  0.020  1.532
 Z7D  C28  C29   aromatic  1.387  0.020  1.387
 Z7D  C11  C12   aromatic  1.385  0.020  1.385
 Z7D  C14  C13   aromatic  1.383  0.020  1.383
 Z7D  C24  C29   aromatic  1.393  0.020  1.393
 Z7D  C24  C23   single    1.507  0.020  1.507
 Z7D  C12  C13   aromatic  1.383  0.020  1.383
 Z7D  C13  F18   single    1.336  0.020  1.336
 Z7D  C2   O7    single    1.349  0.020  1.349
 Z7D  C2   C1    aromatic  1.392  0.020  1.392
 Z7D  C6   C1    aromatic  1.381  0.020  1.381
 Z7D  C23  O7    single    1.416  0.020  1.416
 Z7D  C1   H1    single    0.930  0.020  1.080
 Z7D  C3   H3    single    0.930  0.020  1.080
 Z7D  C4   H4    single    0.930  0.020  1.080
 Z7D  C6   H6    single    0.930  0.020  1.080
 Z7D  C11  H11   single    0.930  0.020  1.080
 Z7D  C12  H12   single    0.930  0.020  1.080
 Z7D  C14  H14   single    0.930  0.020  1.080
 Z7D  C15  H15   single    0.930  0.020  1.080
 Z7D  C19  H191  single    0.970  0.020  1.090
 Z7D  C19  H192  single    0.970  0.020  1.090
 Z7D  C20  H202  single    0.970  0.020  1.090
 Z7D  C20  H201  single    0.970  0.020  1.090
 Z7D  C21  H212  single    0.970  0.020  1.090
 Z7D  C21  H211  single    0.970  0.020  1.090
 Z7D  C22  H221  single    0.970  0.020  1.090
 Z7D  C22  H222  single    0.970  0.020  1.090
 Z7D  C23  H232  single    0.970  0.020  1.090
 Z7D  C23  H231  single    0.970  0.020  1.090
 Z7D  C25  H25   single    0.930  0.020  1.080
 Z7D  C26  H26   single    0.930  0.020  1.080
 Z7D  C27  H27   single    0.930  0.020  1.080
 Z7D  C28  H28   single    0.930  0.020  1.080
 Z7D  C29  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
 Z7D  H1    C1   C6    120.01  3.000
 Z7D  H1    C1   C2    119.64  3.000
 Z7D  C6    C1   C2    120.34  3.000
 Z7D  O7    C2   C3    124.69  3.000
 Z7D  O7    C2   C1    116.30  3.000
 Z7D  C3    C2   C1    119.01  3.000
 Z7D  H3    C3   C4    118.33  3.000
 Z7D  H3    C3   C2    121.84  3.000
 Z7D  C4    C3   C2    119.82  3.000
 Z7D  H4    C4   C5    120.57  3.000
 Z7D  H4    C4   C3    117.44  3.000
 Z7D  C5    C4   C3    121.98  3.000
 Z7D  C8    C5   C6    121.91  3.000
 Z7D  C6    C5   C4    117.21  3.000
 Z7D  C8    C5   C4    120.73  3.000
 Z7D  H6    C6   C5    120.99  3.000
 Z7D  H6    C6   C1    117.39  3.000
 Z7D  C5    C6   C1    121.62  3.000
 Z7D  C23   O7   C2    118.99  3.000
 Z7D  C22   C8   C19   101.12  3.000
 Z7D  C19   C8   S9    111.11  3.000
 Z7D  C22   C8   S9    108.95  3.000
 Z7D  C19   C8   C5    114.79  3.000
 Z7D  C22   C8   C5    113.47  3.000
 Z7D  S9    C8   C5    107.29  3.000
 Z7D  O17   S9   O16   117.84  3.000
 Z7D  O17   S9   C10   108.17  3.000
 Z7D  O16   S9   C10   108.02  3.000
 Z7D  C10   S9   C8    104.44  3.000
 Z7D  O17   S9   C8    109.04  3.000
 Z7D  O16   S9   C8    108.51  3.000
 Z7D  C15   C10  C11   121.21  3.000
 Z7D  C11   C10  S9    119.16  3.000
 Z7D  C15   C10  S9    119.62  3.000
 Z7D  H11   C11  C12   119.35  3.000
 Z7D  H11   C11  C10   121.11  3.000
 Z7D  C12   C11  C10   119.54  3.000
 Z7D  H12   C12  C13   120.65  3.000
 Z7D  H12   C12  C11   120.81  3.000
 Z7D  C13   C12  C11   118.54  3.000
 Z7D  F18   C13  C14   118.71  3.000
 Z7D  F18   C13  C12   118.69  3.000
 Z7D  C14   C13  C12   122.60  3.000
 Z7D  H14   C14  C15   120.86  3.000
 Z7D  H14   C14  C13   120.51  3.000
 Z7D  C15   C14  C13   118.63  3.000
 Z7D  H15   C15  C14   119.54  3.000
 Z7D  H15   C15  C10   120.98  3.000
 Z7D  C14   C15  C10   119.48  3.000
 Z7D  H192  C19  H191  106.84  3.000
 Z7D  H192  C19  C20   113.66  3.000
 Z7D  H191  C19  C20   109.65  3.000
 Z7D  H192  C19  C8    114.85  3.000
 Z7D  H191  C19  C8    109.00  3.000
 Z7D  C20   C19  C8    102.75  3.000
 Z7D  H201  C20  H202  106.90  3.000
 Z7D  H201  C20  C21   112.53  3.000
 Z7D  H202  C20  C21   110.71  3.000
 Z7D  H201  C20  C19   110.88  3.000
 Z7D  H202  C20  C19   110.63  3.000
 Z7D  C21   C20  C19   105.26  3.000
 Z7D  H211  C21  H212  106.98  3.000
 Z7D  H211  C21  C22   110.86  3.000
 Z7D  H212  C21  C22   110.19  3.000
 Z7D  H211  C21  C20   112.25  3.000
 Z7D  H212  C21  C20   110.69  3.000
 Z7D  C22   C21  C20   105.91  3.000
 Z7D  H222  C22  H221  107.38  3.000
 Z7D  H222  C22  C21   110.21  3.000
 Z7D  H221  C22  C21   113.14  3.000
 Z7D  H222  C22  C8    109.62  3.000
 Z7D  H221  C22  C8    113.80  3.000
 Z7D  C21   C22  C8    102.65  3.000
 Z7D  H231  C23  H232  106.73  3.000
 Z7D  H231  C23  C24   110.57  3.000
 Z7D  H232  C23  C24   110.31  3.000
 Z7D  H231  C23  O7    111.35  3.000
 Z7D  H232  C23  O7    104.63  3.000
 Z7D  C24   C23  O7    112.91  3.000
 Z7D  C29   C24  C25   119.03  3.000
 Z7D  C29   C24  C23   120.81  3.000
 Z7D  C25   C24  C23   120.14  3.000
 Z7D  H25   C25  C26   119.59  3.000
 Z7D  H25   C25  C24   119.73  3.000
 Z7D  C26   C25  C24   120.68  3.000
 Z7D  H26   C26  C27   120.16  3.000
 Z7D  H26   C26  C25   119.82  3.000
 Z7D  C27   C26  C25   120.02  3.000
 Z7D  H27   C27  C28   120.15  3.000
 Z7D  H27   C27  C26   120.24  3.000
 Z7D  C28   C27  C26   119.61  3.000
 Z7D  H28   C28  C29   119.81  3.000
 Z7D  H28   C28  C27   119.89  3.000
 Z7D  C29   C28  C27   120.29  3.000
 Z7D  H29   C29  C28   119.48  3.000
 Z7D  H29   C29  C24   120.15  3.000
 Z7D  C28   C29  C24   120.36  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
 Z7D  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 Z7D  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 Z7D  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 Z7D  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 Z7D  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 Z7D  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 Z7D  CONST_07  C13  C14  C15  C10    0.00   0.0  0
 Z7D  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 Z7D  CONST_09  C14  C15  C10  C11    0.00   0.0  0
 Z7D  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 Z7D  CONST_11  C15  C10  C11  C12    0.00   0.0  0
 Z7D  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 Z7D  CONST_13  C27  C26  C25  C24    0.00   0.0  0
 Z7D  CONST_14  C27  C28  C29  C24    0.00   0.0  0
 Z7D  CONST_15  C28  C27  C26  C25    0.00   0.0  0
 Z7D  CONST_16  C28  C29  C24  C25    0.00   0.0  0
 Z7D  CONST_17  C29  C28  C27  C26    0.00   0.0  0
 Z7D  CONST_18  C29  C24  C25  C26    0.00   0.0  0
 Z7D  CONST_19  C8   C5   C6   C1   180.00   0.0  0
 Z7D  CONST_20  C8   C5   C4   C3   180.00   0.0  0
 Z7D  CONST_21  O7   C2   C3   C4   180.00   0.0  0
 Z7D  CONST_22  O7   C2   C1   C6   180.00   0.0  0
 Z7D  CONST_23  C14  C15  C10  S9   180.00   0.0  0
 Z7D  CONST_24  C12  C11  C10  S9   180.00   0.0  0
 Z7D  CONST_25  F18  C13  C12  C11  180.00   0.0  0
 Z7D  CONST_26  F18  C13  C14  C15  180.00   0.0  0
 Z7D  CONST_27  C26  C25  C24  C23  180.00   0.0  0
 Z7D  CONST_28  C28  C29  C24  C23  180.00   0.0  0
 Z7D  CONST_29  H3   C3   C2   C1   180.00   0.0  0
 Z7D  CONST_30  H4   C4   C3   C2   180.00   0.0  0
 Z7D  CONST_31  H6   C6   C1   C2   180.00   0.0  0
 Z7D  CONST_32  H1   C1   C2   C3   180.00   0.0  0
 Z7D  CONST_33  H14  C14  C15  C10  180.00   0.0  0
 Z7D  CONST_34  H12  C12  C11  C10  180.00   0.0  0
 Z7D  CONST_35  H15  C15  C10  C11  180.00   0.0  0
 Z7D  CONST_36  H11  C11  C12  C13  180.00   0.0  0
 Z7D  CONST_37  H26  C26  C25  C24  180.00   0.0  0
 Z7D  CONST_38  H28  C28  C29  C24  180.00   0.0  0
 Z7D  CONST_39  H27  C27  C26  C25  180.00   0.0  0
 Z7D  CONST_40  H29  C29  C24  C25  180.00   0.0  0
 Z7D  CONST_41  H25  C25  C26  C27  180.00   0.0  0
 Z7D  Var_01    C20  C21  C22  C8   -26.07  30.0  1
 Z7D  Var_02    C21  C20  C19  C8    29.44  30.0  1
 Z7D  Var_03    C22  C21  C20  C19   -1.98  30.0  1
 Z7D  Var_04    C15  C10  S9   C8   -89.62  30.0  2
 Z7D  Var_05    C24  C23  O7   C2   -63.62  30.0  1
 Z7D  Var_06    C25  C24  C23  O7   142.45  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
 Z7D  chir_01  C8  C22  C5  C19  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
 Z7D  plan-1  C1   0.020
 Z7D  plan-1  C2   0.020
 Z7D  plan-1  C3   0.020
 Z7D  plan-1  C4   0.020
 Z7D  plan-1  C5   0.020
 Z7D  plan-1  C6   0.020
 Z7D  plan-1  O7   0.020
 Z7D  plan-1  C8   0.020
 Z7D  plan-1  H1   0.020
 Z7D  plan-1  H3   0.020
 Z7D  plan-1  H4   0.020
 Z7D  plan-1  H6   0.020
 Z7D  plan-2  S9   0.020
 Z7D  plan-2  C10  0.020
 Z7D  plan-2  C11  0.020
 Z7D  plan-2  C12  0.020
 Z7D  plan-2  C13  0.020
 Z7D  plan-2  C14  0.020
 Z7D  plan-2  C15  0.020
 Z7D  plan-2  F18  0.020
 Z7D  plan-2  H11  0.020
 Z7D  plan-2  H12  0.020
 Z7D  plan-2  H14  0.020
 Z7D  plan-2  H15  0.020
 Z7D  plan-3  C23  0.020
 Z7D  plan-3  C24  0.020
 Z7D  plan-3  C25  0.020
 Z7D  plan-3  C26  0.020
 Z7D  plan-3  C27  0.020
 Z7D  plan-3  C28  0.020
 Z7D  plan-3  C29  0.020
 Z7D  plan-3  H25  0.020
 Z7D  plan-3  H26  0.020
 Z7D  plan-3  H27  0.020
 Z7D  plan-3  H28  0.020
 Z7D  plan-3  H29  0.020

