# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:21:35 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 3-[2-(trans-4-methylcyclohexyl)phenyl]-5-phenylthiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC[C@@H](CC1)c2ccccc2c3cc(sc3C(O)=O)c4ccccc4
#
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
 HJZ  HJZ  '3-[2-(trans-4-methylcyclohexyl)phenyl]-5-phenylthiophene-2-carboxylic acid'  ligand  50  27  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJZ
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
 HJZ  S1    S  S2     0   0.216  -1.9402  -0.9863   1.4290
 HJZ  C2    C  CR5    0  -0.202  -2.3564  -0.4965  -0.1705
 HJZ  C3    C  CR15   0  -0.272  -1.2482  -0.5208  -0.9758
 HJZ  C4    C  CR5    0   0.152  -0.0641  -0.9380  -0.3091
 HJZ  C5    C  CR5    0  -0.426  -0.2908  -1.2324   1.0090
 HJZ  C6    C  CR6    0   0.145  -3.7230  -0.1260  -0.5346
 HJZ  C7    C  C      0   0.389   0.6176  -1.7335   2.0978
 HJZ  C8    C  CR6    0   0.050   1.2284  -1.0412  -1.0233
 HJZ  O9    O  O      0  -0.564   1.7967  -1.9695   1.7919
 HJZ  O10   O  OC    -1  -0.602   0.0683  -1.8665   3.2110
 HJZ  C11   C  CR6    0   0.194   2.2222  -0.0623  -0.9084
 HJZ  C12   C  CR16   0  -0.252   3.5661  -1.2849  -2.5241
 HJZ  C13   C  CR16   0  -0.268   2.5728  -2.2474  -2.6387
 HJZ  C14   C  CR16   0  -0.323   3.3818  -0.2081  -1.6700
 HJZ  C15   C  CR16   0  -0.293   1.4122  -2.1155  -1.8926
 HJZ  C16   C  CR16   0  -0.326  -4.8198  -0.5600   0.2152
 HJZ  C17   C  CR16   0  -0.270  -6.3359   0.5818  -1.2656
 HJZ  C18   C  CR16   0  -0.234  -5.2539   1.0169  -2.0210
 HJZ  C19   C  CR16   0  -0.237  -6.1112  -0.2053  -0.1440
 HJZ  C20   C  CR16   0  -0.329  -3.9620   0.6722  -1.6576
 HJZ  C21   C  CH1    0  -0.353   2.0642   1.1459  -0.0186
 HJZ  C22   C  CH2    0  -0.418   3.1501   1.2112   1.0599
 HJZ  C23   C  CH2    0  -0.416   2.9896   2.4429   1.9433
 HJZ  C24   C  CH1    0  -0.223   2.9719   3.7353   1.1293
 HJZ  C25   C  CH2    0  -0.415   1.8821   3.6652   0.0624
 HJZ  C26   C  CH2    0  -0.410   2.0327   2.4430  -0.8359
 HJZ  C27   C  CH3    0  -0.654   2.8012   4.9567   2.0220
 HJZ  H3    H  HCR5   0   0.254  -1.2675  -0.2630  -2.0267
 HJZ  H12   H  HCR6   0   0.247   4.4786  -1.3673  -3.1009
 HJZ  H13   H  HCR6   0   0.248   2.6983  -3.0918  -3.3043
 HJZ  H14   H  HCR6   0   0.240   4.1618   0.5410  -1.5986
 HJZ  H15   H  HCR6   0   0.239   0.6319  -2.8620  -1.9801
 HJZ  H16   H  HCR6   0   0.252  -4.6702  -1.1948   1.0805
 HJZ  H17   H  HCR6   0   0.258  -7.3442   0.8535  -1.5486
 HJZ  H18   H  HCR6   0   0.259  -5.4152   1.6351  -2.8946
 HJZ  H19   H  HCR6   0   0.260  -6.9450  -0.5528   0.4523
 HJZ  H20   H  HCR6   0   0.253  -3.1299   1.0371  -2.2464
 HJZ  H21   H  HCH1   0   0.234   1.1034   1.0703   0.5002
 HJZ  H22   H  HCH2   0   0.243   3.1064   0.3009   1.6603
 HJZ  H22A  H  HCH2   0   0.205   4.1400   1.2348   0.5903
 HJZ  H23   H  HCH2   0   0.203   2.0559   2.3682   2.5154
 HJZ  H23A  H  HCH2   0   0.222   3.7973   2.4790   2.6804
 HJZ  H24   H  HCH1   0   0.205   3.9384   3.8158   0.6136
 HJZ  H25   H  HCH2   0   0.204   0.9023   3.6351   0.5553
 HJZ  H25A  H  HCH2   0   0.223   1.8937   4.5759  -0.5436
 HJZ  H26   H  HCH2   0   0.210   2.9529   2.5319  -1.4242
 HJZ  H26A  H  HCH2   0   0.227   1.2110   2.4018  -1.5563
 HJZ  H27   H  HCH3   0   0.222   3.5981   5.0230   2.7655
 HJZ  H27A  H  HCH3   0   0.222   2.8107   5.8815   1.4417
 HJZ  H27B  H  HCH3   0   0.211   1.8505   4.9164   2.5599

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
 HJZ  S1   C2    aromatic  1.724  0.020  1.724
 HJZ  S1   C5    aromatic  1.720  0.020  1.720
 HJZ  C6   C2    single    1.462  0.020  1.462
 HJZ  C2   C3    aromatic  1.370  0.020  1.370
 HJZ  C3   C4    aromatic  1.421  0.020  1.421
 HJZ  C3   H3    single    0.930  0.020  1.080
 HJZ  C5   C4    aromatic  1.369  0.020  1.369
 HJZ  C4   C8    single    1.480  0.020  1.480
 HJZ  C7   C5    single    1.504  0.020  1.504
 HJZ  C20  C6    aromatic  1.398  0.020  1.398
 HJZ  C6   C16   aromatic  1.398  0.020  1.398
 HJZ  O9   C7    deloc     1.241  0.020  1.241
 HJZ  C7   O10   deloc     1.248  0.020  1.248
 HJZ  C8   C11   aromatic  1.400  0.020  1.400
 HJZ  C8   C15   aromatic  1.394  0.020  1.394
 HJZ  C21  C11   single    1.509  0.020  1.509
 HJZ  C11  C14   aromatic  1.395  0.020  1.395
 HJZ  C14  C12   aromatic  1.387  0.020  1.387
 HJZ  C13  C12   aromatic  1.388  0.020  1.388
 HJZ  C12  H12   single    0.930  0.020  1.080
 HJZ  C15  C13   aromatic  1.386  0.020  1.386
 HJZ  C13  H13   single    0.930  0.020  1.080
 HJZ  C14  H14   single    0.930  0.020  1.080
 HJZ  C15  H15   single    0.930  0.020  1.080
 HJZ  C19  C16   aromatic  1.387  0.020  1.387
 HJZ  C16  H16   single    0.930  0.020  1.080
 HJZ  C18  C17   aromatic  1.389  0.020  1.389
 HJZ  C17  C19   aromatic  1.389  0.020  1.389
 HJZ  C17  H17   single    0.930  0.020  1.080
 HJZ  C18  C20   aromatic  1.386  0.020  1.386
 HJZ  C18  H18   single    0.930  0.020  1.080
 HJZ  C19  H19   single    0.930  0.020  1.080
 HJZ  C20  H20   single    0.930  0.020  1.080
 HJZ  C22  C21   single    1.532  0.020  1.532
 HJZ  C21  C26   single    1.533  0.020  1.533
 HJZ  C21  H21   single    0.970  0.020  1.090
 HJZ  C23  C22   single    1.524  0.020  1.524
 HJZ  C22  H22   single    0.970  0.020  1.090
 HJZ  C22  H22A  single    0.970  0.020  1.090
 HJZ  C23  C24   single    1.527  0.020  1.527
 HJZ  C23  H23   single    0.970  0.020  1.090
 HJZ  C23  H23A  single    0.970  0.020  1.090
 HJZ  C27  C24   single    1.522  0.020  1.522
 HJZ  C24  C25   single    1.527  0.020  1.527
 HJZ  C24  H24   single    0.970  0.020  1.090
 HJZ  C25  C26   single    1.524  0.020  1.524
 HJZ  C25  H25   single    0.970  0.020  1.090
 HJZ  C25  H25A  single    0.970  0.020  1.090
 HJZ  C26  H26   single    0.970  0.020  1.090
 HJZ  C26  H26A  single    0.970  0.020  1.090
 HJZ  C27  H27   single    0.970  0.020  1.090
 HJZ  C27  H27A  single    0.970  0.020  1.090
 HJZ  C27  H27B  single    0.970  0.020  1.090

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
 HJZ  C5    S1   C2     92.61  3.000
 HJZ  C6    C2   C3    127.89  3.000
 HJZ  C3    C2   S1    110.18  3.000
 HJZ  C6    C2   S1    121.92  3.000
 HJZ  H3    C3   C4    122.69  3.000
 HJZ  H3    C3   C2    123.51  3.000
 HJZ  C4    C3   C2    113.79  3.000
 HJZ  C8    C4   C5    126.43  3.000
 HJZ  C8    C4   C3    121.43  3.000
 HJZ  C5    C4   C3    112.13  3.000
 HJZ  C7    C5   C4    131.95  3.000
 HJZ  C7    C5   S1    116.75  3.000
 HJZ  C4    C5   S1    111.29  3.000
 HJZ  C20   C6   C16   118.29  3.000
 HJZ  C16   C6   C2    121.41  3.000
 HJZ  C20   C6   C2    120.29  3.000
 HJZ  O10   C7   O9    128.14  3.000
 HJZ  O10   C7   C5    114.54  3.000
 HJZ  O9    C7   C5    117.31  3.000
 HJZ  C15   C8   C11   119.78  3.000
 HJZ  C15   C8   C4    118.01  3.000
 HJZ  C11   C8   C4    122.11  3.000
 HJZ  C21   C11  C14   119.52  3.000
 HJZ  C14   C11  C8    118.18  3.000
 HJZ  C21   C11  C8    122.29  3.000
 HJZ  H12   C12  C14   119.95  3.000
 HJZ  H12   C12  C13   120.42  3.000
 HJZ  C14   C12  C13   119.63  3.000
 HJZ  H13   C13  C15   120.15  3.000
 HJZ  H13   C13  C12   120.59  3.000
 HJZ  C15   C13  C12   119.26  3.000
 HJZ  H14   C14  C12   118.79  3.000
 HJZ  H14   C14  C11   119.34  3.000
 HJZ  C12   C14  C11   121.86  3.000
 HJZ  H15   C15  C13   119.61  3.000
 HJZ  H15   C15  C8    119.10  3.000
 HJZ  C13   C15  C8    121.29  3.000
 HJZ  H16   C16  C19   119.03  3.000
 HJZ  H16   C16  C6    120.13  3.000
 HJZ  C19   C16  C6    120.83  3.000
 HJZ  H17   C17  C19   120.29  3.000
 HJZ  H17   C17  C18   120.32  3.000
 HJZ  C19   C17  C18   119.39  3.000
 HJZ  H18   C18  C20   119.52  3.000
 HJZ  H18   C18  C17   120.11  3.000
 HJZ  C20   C18  C17   120.37  3.000
 HJZ  H19   C19  C17   120.16  3.000
 HJZ  H19   C19  C16   119.51  3.000
 HJZ  C17   C19  C16   120.33  3.000
 HJZ  H20   C20  C18   119.34  3.000
 HJZ  H20   C20  C6    119.86  3.000
 HJZ  C18   C20  C6    120.79  3.000
 HJZ  H21   C21  C26   107.04  3.000
 HJZ  H21   C21  C22   106.95  3.000
 HJZ  C26   C21  C22   110.72  3.000
 HJZ  H21   C21  C11   108.43  3.000
 HJZ  C26   C21  C11   111.42  3.000
 HJZ  C22   C21  C11   112.03  3.000
 HJZ  H22A  C22  H22   106.85  3.000
 HJZ  H22A  C22  C23   109.03  3.000
 HJZ  H22   C22  C23   110.54  3.000
 HJZ  H22A  C22  C21   109.85  3.000
 HJZ  H22   C22  C21   108.87  3.000
 HJZ  C23   C22  C21   111.58  3.000
 HJZ  H23A  C23  H23   106.21  3.000
 HJZ  H23A  C23  C24   109.85  3.000
 HJZ  H23   C23  C24   109.00  3.000
 HJZ  H23A  C23  C22   109.84  3.000
 HJZ  H23   C23  C22   109.68  3.000
 HJZ  C24   C23  C22   112.09  3.000
 HJZ  H24   C24  C27   108.37  3.000
 HJZ  H24   C24  C25   107.66  3.000
 HJZ  C27   C24  C25   111.50  3.000
 HJZ  H24   C24  C23   107.58  3.000
 HJZ  C25   C24  C23   109.99  3.000
 HJZ  C27   C24  C23   111.57  3.000
 HJZ  H25A  C25  H25   106.33  3.000
 HJZ  H25A  C25  C26   109.88  3.000
 HJZ  H25   C25  C26   109.33  3.000
 HJZ  H25A  C25  C24   109.96  3.000
 HJZ  H25   C25  C24   108.95  3.000
 HJZ  C26   C25  C24   112.21  3.000
 HJZ  H26A  C26  H26   106.28  3.000
 HJZ  H26A  C26  C25   110.13  3.000
 HJZ  H26   C26  C25   109.53  3.000
 HJZ  H26A  C26  C21   109.55  3.000
 HJZ  H26   C26  C21   109.73  3.000
 HJZ  C25   C26  C21   111.48  3.000
 HJZ  H27B  C27  H27A  107.48  3.000
 HJZ  H27B  C27  H27   107.57  3.000
 HJZ  H27A  C27  H27   107.70  3.000
 HJZ  H27B  C27  C24   110.89  3.000
 HJZ  H27A  C27  C24   111.52  3.000
 HJZ  H27   C27  C24   111.48  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
 HJZ  CONST_03  C4   C3   C2   S1     0.00   0.0  0
 HJZ  CONST_04  C3   C4   C5   S1     0.00   0.0  0
 HJZ  CONST_05  C8   C4   C5   S1   180.00   0.0  0
 HJZ  CONST_06  C4   C5   S1   C2     0.00   0.0  0
 HJZ  CONST_07  C18  C20  C6   C2   180.00   0.0  0
 HJZ  CONST_08  C19  C16  C6   C2   180.00   0.0  0
 HJZ  CONST_09  C5   C4   C3   C2     0.00   0.0  0
 HJZ  CONST_10  C8   C4   C3   C2   180.00   0.0  0
 HJZ  CONST_11  C5   S1   C2   C3     0.00   0.0  0
 HJZ  CONST_16  C6   C2   C3   C4   180.00   0.0  0
 HJZ  CONST_17  C14  C11  C8   C4   180.00   0.0  0
 HJZ  CONST_18  C13  C15  C8   C4   180.00   0.0  0
 HJZ  CONST_19  C6   C2   S1   C5   180.00   0.0  0
 HJZ  CONST_22  C17  C18  C20  C6     0.00   0.0  0
 HJZ  CONST_23  C17  C19  C16  C6     0.00   0.0  0
 HJZ  CONST_24  C12  C14  C11  C8     0.00   0.0  0
 HJZ  CONST_25  C12  C13  C15  C8     0.00   0.0  0
 HJZ  CONST_26  C13  C15  C8   C11    0.00   0.0  0
 HJZ  CONST_27  C13  C12  C14  C11    0.00   0.0  0
 HJZ  CONST_28  C15  C8   C11  C14    0.00   0.0  0
 HJZ  CONST_29  C15  C13  C12  C14    0.00   0.0  0
 HJZ  CONST_30  C18  C20  C6   C16    0.00   0.0  0
 HJZ  CONST_31  C18  C17  C19  C16    0.00   0.0  0
 HJZ  CONST_32  C20  C6   C16  C19    0.00   0.0  0
 HJZ  CONST_33  C20  C18  C17  C19    0.00   0.0  0
 HJZ  CONST_34  C21  C11  C8   C4     0.00   0.0  0
 HJZ  CONST_35  C21  C11  C14  C12  180.00   0.0  0
 HJZ  CONST_36  C21  C11  C8   C15  180.00   0.0  0
 HJZ  CONST_37  C7   C5   S1   C2   180.00   0.0  0
 HJZ  CONST_38  C7   C5   C4   C3   180.00   0.0  0
 HJZ  CONST_39  C8   C4   C5   C7     0.00   0.0  0
 HJZ  CONST_40  H3   C3   C2   S1   180.00   0.0  0
 HJZ  CONST_41  H20  C20  C6   C2     0.00   0.0  0
 HJZ  CONST_42  H16  C16  C6   C2     0.00   0.0  0
 HJZ  CONST_43  H15  C15  C8   C4     0.00   0.0  0
 HJZ  CONST_44  H18  C18  C20  C6   180.00   0.0  0
 HJZ  CONST_45  H19  C19  C16  C6   180.00   0.0  0
 HJZ  CONST_46  H14  C14  C11  C8   180.00   0.0  0
 HJZ  CONST_47  H13  C13  C15  C8   180.00   0.0  0
 HJZ  CONST_48  H12  C12  C14  C11  180.00   0.0  0
 HJZ  CONST_49  H17  C17  C19  C16  180.00   0.0  0
 HJZ  Var_01    C24  C23  C22  C21  -55.69  30.0  1
 HJZ  Var_02    C24  C25  C26  C21   55.60  30.0  1
 HJZ  Var_03    O9   C7   C5   S1   176.98  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
 HJZ  chir_01  C21  C11  C22  C26  negativ
 HJZ  chir_02  C24  C25  C27  C23  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
 HJZ  plan-1  S1   0.020
 HJZ  plan-1  C2   0.020
 HJZ  plan-1  C3   0.020
 HJZ  plan-1  C4   0.020
 HJZ  plan-1  C5   0.020
 HJZ  plan-1  C6   0.020
 HJZ  plan-1  C7   0.020
 HJZ  plan-1  C8   0.020
 HJZ  plan-1  H3   0.020
 HJZ  plan-2  C4   0.020
 HJZ  plan-2  C8   0.020
 HJZ  plan-2  C11  0.020
 HJZ  plan-2  C12  0.020
 HJZ  plan-2  C13  0.020
 HJZ  plan-2  C14  0.020
 HJZ  plan-2  C15  0.020
 HJZ  plan-2  C21  0.020
 HJZ  plan-2  H12  0.020
 HJZ  plan-2  H13  0.020
 HJZ  plan-2  H14  0.020
 HJZ  plan-2  H15  0.020
 HJZ  plan-3  C2   0.020
 HJZ  plan-3  C6   0.020
 HJZ  plan-3  C16  0.020
 HJZ  plan-3  C17  0.020
 HJZ  plan-3  C18  0.020
 HJZ  plan-3  C19  0.020
 HJZ  plan-3  C20  0.020
 HJZ  plan-3  H16  0.020
 HJZ  plan-3  H17  0.020
 HJZ  plan-3  H18  0.020
 HJZ  plan-3  H19  0.020
 HJZ  plan-3  H20  0.020
 HJZ  plan-4  C5   0.020
 HJZ  plan-4  C7   0.020
 HJZ  plan-4  O9   0.020
 HJZ  plan-4  O10  0.020

