# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:14:46 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2ccc(Sc3ccccc3[C@H](CCC(O)=O)C(O)=O)cc2
#
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
 B9Z  B9Z  '(2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid'  ligand  52  30  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B9Z
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
 B9Z  C4   C  CR6   0   0.376   -7.7889   0.1518  -0.0828
 B9Z  C5   C  CR16  0  -0.327   -7.1167  -1.0495   0.1559
 B9Z  C6   C  CR16  0  -0.291   -5.7446  -1.0619   0.3070
 B9Z  C8   C  CR16  0  -0.309   -2.9157  -0.7651   1.3016
 B9Z  C10  C  CR6   0  -0.190   -0.7427   0.0594   0.6861
 B9Z  C20  C  CR16  0  -0.326    3.4552  -1.6342  -1.7928
 B9Z  C21  C  CR6   0   0.194    2.9759  -0.8595  -0.7423
 B9Z  C22  C  CH1   0  -0.485    3.8997  -0.0329   0.1232
 B9Z  C1   C  CR6   0   0.063   -4.9933   0.1146   0.2281
 B9Z  C12  C  CR16  0  -0.307   -2.7145   0.9482  -0.3627
 B9Z  C19  C  CR16  0  -0.249    2.6019  -2.3697  -2.6025
 B9Z  C23  C  C     0   0.562    4.1180  -0.7434   1.4487
 B9Z  C3   C  CR16  0  -0.368   -7.0573   1.3344  -0.1633
 B9Z  C2   C  CR16  0  -0.293   -5.6783   1.3032  -0.0079
 B9Z  C11  C  CR16  0  -0.193   -1.3389   0.9378  -0.2136
 B9Z  C16  C  CR6   0  -0.149    1.5976  -0.8802  -0.4791
 B9Z  C17  C  CR16  0  -0.224    0.7432  -1.6444  -1.2674
 B9Z  C18  C  CR16  0  -0.258    1.2419  -2.3714  -2.3374
 B9Z  C26  C  CH2   0  -0.444    5.2591   0.2731  -0.5282
 B9Z  C27  C  CH2   0  -0.584    6.0262   1.3669   0.1979
 B9Z  C28  C  C     0   0.555    7.3904   1.6089  -0.3876
 B9Z  C7   C  CR6   0   0.100   -3.5283   0.0990   0.3926
 B9Z  C9   C  CR16  0  -0.203   -1.5373  -0.7923   1.4449
 B9Z  O14  O  O2    0  -0.468   -9.1244   0.0731  -0.2153
 B9Z  O24  O  OH1   0  -0.584    4.1192   0.0889   2.4808
 B9Z  O25  O  O     0  -0.425    4.3044  -1.9292   1.5484
 B9Z  O29  O  OH1   0  -0.596    8.0156   2.6069   0.2280
 B9Z  O30  O  O     0  -0.442    7.8781   0.9881  -1.2987
 B9Z  H1   H  HCR6  0   0.265   -7.6803  -1.9719   0.2201
 B9Z  H2   H  HCR6  0   0.257   -5.2507  -2.0098   0.4808
 B9Z  H3   H  HCR6  0   0.261   -3.5195  -1.4208   1.9159
 B9Z  H4   H  HCR6  0   0.261    4.5152  -1.6507  -2.0075
 B9Z  H5   H  HCH1  0   0.289    3.4142   0.9297   0.3185
 B9Z  H6   H  HCR6  0   0.261   -3.1595   1.6219  -1.0842
 B9Z  H7   H  HCR6  0   0.259    3.0024  -2.9450  -3.4265
 B9Z  H8   H  HCR6  0   0.281   -7.5385   2.2864  -0.3407
 B9Z  H9   H  HCR6  0   0.260   -5.1358   2.2394  -0.0551
 B9Z  H10  H  HCR6  0   0.275   -0.7256   1.6065  -0.8037
 B9Z  H11  H  HCH3  0   0.230   -9.7471   1.9722   0.3772
 B9Z  H12  H  HCH3  0   0.230   -9.5484   1.7547  -1.3753
 B9Z  H13  H  HCH3  0   0.261  -10.8974   0.9744  -0.5319
 B9Z  H14  H  HCR6  0   0.265   -0.3166  -1.6739  -1.0549
 B9Z  H15  H  HCR6  0   0.261    0.5643  -2.9563  -2.9454
 B9Z  H16  H  HCH2  0   0.255    5.8615  -0.6340  -0.6004
 B9Z  H17  H  HCH2  0   0.267    5.0621   0.5971  -1.5521
 B9Z  H18  H  HCH2  0   0.287    5.4688   2.3076   0.1622
 B9Z  H19  H  HCH2  0   0.288    6.1573   1.1432   1.2598
 B9Z  H20  H  HCR6  0   0.274   -1.0807  -1.4722   2.1524
 B9Z  H21  H  HOH1  0   0.483    4.2957  -0.3973   3.3013
 B9Z  H22  H  HOH1  0   0.480    8.8928   2.7401  -0.1613
 B9Z  S13  S  S2    0   0.055    1.0108   0.0620   0.9080
 B9Z  C15  C  CH3   0  -0.438   -9.8529   1.2632  -0.4477

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
 B9Z  O30  C28  double    1.206  0.020  1.206
 B9Z  O25  C23  double    1.204  0.020  1.204
 B9Z  O24  C23  single    1.326  0.020  1.326
 B9Z  C28  O29  single    1.329  0.020  1.329
 B9Z  C28  C27  single    1.504  0.020  1.504
 B9Z  C26  C27  single    1.521  0.020  1.521
 B9Z  C26  C22  single    1.538  0.020  1.538
 B9Z  C23  C22  single    1.520  0.020  1.520
 B9Z  C22  C21  single    1.512  0.020  1.512
 B9Z  C21  C20  aromatic  1.390  0.020  1.390
 B9Z  C21  C16  aromatic  1.403  0.020  1.403
 B9Z  C3   C2   aromatic  1.388  0.020  1.388
 B9Z  C3   C4   aromatic  1.393  0.020  1.393
 B9Z  C20  C19  aromatic  1.387  0.020  1.387
 B9Z  C2   C1   aromatic  1.392  0.020  1.392
 B9Z  O14  C4   single    1.344  0.020  1.344
 B9Z  O14  C15  single    1.415  0.020  1.415
 B9Z  C12  C11  aromatic  1.384  0.020  1.384
 B9Z  C12  C7   aromatic  1.398  0.020  1.398
 B9Z  C11  C10  aromatic  1.392  0.020  1.392
 B9Z  C4   C5   aromatic  1.397  0.020  1.397
 B9Z  C1   C7   single    1.474  0.020  1.474
 B9Z  C1   C6   aromatic  1.398  0.020  1.398
 B9Z  C7   C8   aromatic  1.396  0.020  1.396
 B9Z  C10  S13  single    1.768  0.020  1.768
 B9Z  C10  C9   aromatic  1.390  0.020  1.390
 B9Z  C5   C6   aromatic  1.380  0.020  1.380
 B9Z  C19  C18  aromatic  1.386  0.020  1.386
 B9Z  C16  S13  single    1.777  0.020  1.777
 B9Z  C16  C17  aromatic  1.391  0.020  1.391
 B9Z  C8   C9   aromatic  1.386  0.020  1.386
 B9Z  C17  C18  aromatic  1.386  0.020  1.386
 B9Z  C5   H1   single    0.930  0.020  1.080
 B9Z  C6   H2   single    0.930  0.020  1.080
 B9Z  C8   H3   single    0.930  0.020  1.080
 B9Z  C20  H4   single    0.930  0.020  1.080
 B9Z  C22  H5   single    0.970  0.020  1.090
 B9Z  C12  H6   single    0.930  0.020  1.080
 B9Z  C19  H7   single    0.930  0.020  1.080
 B9Z  C3   H8   single    0.930  0.020  1.080
 B9Z  C2   H9   single    0.930  0.020  1.080
 B9Z  C11  H10  single    0.930  0.020  1.080
 B9Z  C15  H11  single    0.970  0.020  1.090
 B9Z  C15  H12  single    0.970  0.020  1.090
 B9Z  C15  H13  single    0.970  0.020  1.090
 B9Z  C17  H14  single    0.930  0.020  1.080
 B9Z  C18  H15  single    0.930  0.020  1.080
 B9Z  C26  H16  single    0.970  0.020  1.090
 B9Z  C26  H17  single    0.970  0.020  1.090
 B9Z  C27  H18  single    0.970  0.020  1.090
 B9Z  C27  H19  single    0.970  0.020  1.090
 B9Z  C9   H20  single    0.930  0.020  1.080
 B9Z  O24  H21  single    0.850  0.020  0.980
 B9Z  O29  H22  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
 B9Z  O14  C4   C3   124.46  3.000
 B9Z  O14  C4   C5   116.39  3.000
 B9Z  C3   C4   C5   119.15  3.000
 B9Z  H1   C5   C6   120.21  3.000
 B9Z  H1   C5   C4   119.48  3.000
 B9Z  C6   C5   C4   120.31  3.000
 B9Z  H2   C6   C1   120.03  3.000
 B9Z  H2   C6   C5   118.61  3.000
 B9Z  C1   C6   C5   121.36  3.000
 B9Z  H3   C8   C9   118.96  3.000
 B9Z  H3   C8   C7   119.98  3.000
 B9Z  C9   C8   C7   121.06  3.000
 B9Z  S13  C10  C9   119.96  3.000
 B9Z  C9   C10  C11  119.66  3.000
 B9Z  S13  C10  C11  120.35  3.000
 B9Z  H4   C20  C19  118.60  3.000
 B9Z  H4   C20  C21  119.76  3.000
 B9Z  C19  C20  C21  121.62  3.000
 B9Z  C16  C21  C22  120.05  3.000
 B9Z  C16  C21  C20  118.16  3.000
 B9Z  C22  C21  C20  121.77  3.000
 B9Z  H5   C22  C26  106.99  3.000
 B9Z  H5   C22  C23  108.60  3.000
 B9Z  C26  C22  C23  109.60  3.000
 B9Z  H5   C22  C21  108.16  3.000
 B9Z  C23  C22  C21  109.36  3.000
 B9Z  C26  C22  C21  113.98  3.000
 B9Z  C7   C1   C2   121.13  3.000
 B9Z  C7   C1   C6   121.25  3.000
 B9Z  C2   C1   C6   117.62  3.000
 B9Z  H6   C12  C7   119.92  3.000
 B9Z  H6   C12  C11  119.02  3.000
 B9Z  C7   C12  C11  121.06  3.000
 B9Z  H7   C19  C18  120.56  3.000
 B9Z  H7   C19  C20  119.92  3.000
 B9Z  C18  C19  C20  119.51  3.000
 B9Z  O25  C23  O24  123.60  3.000
 B9Z  O24  C23  C22  112.68  3.000
 B9Z  O25  C23  C22  123.69  3.000
 B9Z  H8   C3   C2   118.70  3.000
 B9Z  H8   C3   C4   121.55  3.000
 B9Z  C2   C3   C4   119.75  3.000
 B9Z  H9   C2   C3   118.25  3.000
 B9Z  H9   C2   C1   119.93  3.000
 B9Z  C3   C2   C1   121.81  3.000
 B9Z  H10  C11  C12  119.99  3.000
 B9Z  H10  C11  C10  119.98  3.000
 B9Z  C12  C11  C10  120.02  3.000
 B9Z  S13  C16  C17  122.07  3.000
 B9Z  C17  C16  C21  120.33  3.000
 B9Z  S13  C16  C21  117.58  3.000
 B9Z  H14  C17  C18  119.34  3.000
 B9Z  H14  C17  C16  120.36  3.000
 B9Z  C18  C17  C16  120.30  3.000
 B9Z  H15  C18  C17  119.46  3.000
 B9Z  H15  C18  C19  120.51  3.000
 B9Z  C17  C18  C19  120.01  3.000
 B9Z  H17  C26  H16  106.52  3.000
 B9Z  H17  C26  C27  108.99  3.000
 B9Z  H16  C26  C27  110.55  3.000
 B9Z  H17  C26  C22  107.26  3.000
 B9Z  H16  C26  C22  110.52  3.000
 B9Z  C27  C26  C22  112.75  3.000
 B9Z  H19  C27  H18  105.59  3.000
 B9Z  H19  C27  C28  107.60  3.000
 B9Z  H18  C27  C28  108.13  3.000
 B9Z  H19  C27  C26  112.16  3.000
 B9Z  H18  C27  C26  110.24  3.000
 B9Z  C28  C27  C26  112.80  3.000
 B9Z  O30  C28  O29  123.13  3.000
 B9Z  O29  C28  C27  111.54  3.000
 B9Z  O30  C28  C27  125.32  3.000
 B9Z  C12  C7   C1   120.78  3.000
 B9Z  C1   C7   C8   121.02  3.000
 B9Z  C12  C7   C8   118.19  3.000
 B9Z  H20  C9   C10  120.04  3.000
 B9Z  H20  C9   C8   119.96  3.000
 B9Z  C10  C9   C8   119.99  3.000
 B9Z  C15  O14  C4   118.59  3.000
 B9Z  H21  O24  C23  110.12  3.000
 B9Z  H22  O29  C28  110.06  3.000
 B9Z  C16  S13  C10  103.23  3.000
 B9Z  H13  C15  H12  108.75  3.000
 B9Z  H13  C15  H11  108.90  3.000
 B9Z  H12  C15  H11  108.78  3.000
 B9Z  H13  C15  O14  106.50  3.000
 B9Z  H12  C15  O14  111.98  3.000
 B9Z  H11  C15  O14  111.84  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
 B9Z  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 B9Z  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 B9Z  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 B9Z  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 B9Z  CONST_05  C7   C1   C6   C5   180.00   0.0  0
 B9Z  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 B9Z  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 B9Z  CONST_10  C11  C12  C7   C8     0.00   0.0  0
 B9Z  CONST_12  C11  C10  C9   C8     0.00   0.0  0
 B9Z  CONST_13  C7   C12  C11  C10    0.00   0.0  0
 B9Z  CONST_14  C7   C8   C9   C10    0.00   0.0  0
 B9Z  CONST_15  C17  C16  C21  C20    0.00   0.0  0
 B9Z  CONST_16  C17  C18  C19  C20    0.00   0.0  0
 B9Z  CONST_17  C18  C19  C20  C21    0.00   0.0  0
 B9Z  CONST_18  C18  C17  C16  C21    0.00   0.0  0
 B9Z  CONST_19  C11  C12  C7   C1   180.00   0.0  0
 B9Z  CONST_20  C9   C8   C7   C1   180.00   0.0  0
 B9Z  CONST_21  C9   C10  C11  C12    0.00   0.0  0
 B9Z  CONST_23  C9   C8   C7   C12    0.00   0.0  0
 B9Z  CONST_24  C16  C21  C20  C19    0.00   0.0  0
 B9Z  CONST_25  C16  C17  C18  C19    0.00   0.0  0
 B9Z  CONST_26  C7   C1   C2   C3   180.00   0.0  0
 B9Z  CONST_27  O14  C4   C5   C6   180.00   0.0  0
 B9Z  CONST_28  S13  C10  C9   C8   180.00   0.0  0
 B9Z  CONST_29  S13  C16  C21  C20  180.00   0.0  0
 B9Z  CONST_30  C19  C20  C21  C22  180.00   0.0  0
 B9Z  CONST_31  C17  C16  C21  C22  180.00   0.0  0
 B9Z  CONST_32  S13  C10  C11  C12  180.00   0.0  0
 B9Z  CONST_33  O14  C4   C3   C2   180.00   0.0  0
 B9Z  CONST_34  S13  C16  C17  C18  180.00   0.0  0
 B9Z  CONST_35  H9   C2   C3   C4   180.00   0.0  0
 B9Z  CONST_36  H2   C6   C5   C4   180.00   0.0  0
 B9Z  CONST_37  H8   C3   C4   C5   180.00   0.0  0
 B9Z  CONST_38  H6   C12  C7   C8   180.00   0.0  0
 B9Z  CONST_39  H3   C8   C9   C10  180.00   0.0  0
 B9Z  CONST_40  H15  C18  C19  C20  180.00   0.0  0
 B9Z  CONST_41  H7   C19  C20  C21  180.00   0.0  0
 B9Z  CONST_42  H14  C17  C16  C21  180.00   0.0  0
 B9Z  CONST_43  H1   C5   C6   C1   180.00   0.0  0
 B9Z  CONST_44  H20  C9   C10  C11  180.00   0.0  0
 B9Z  CONST_45  H4   C20  C21  C16  180.00   0.0  0
 B9Z  CONST_46  H10  C11  C12  C7   180.00   0.0  0
 B9Z  CONST_47  H21  O24  C23  C22  180.00   0.0  0
 B9Z  CONST_48  H22  O29  C28  C27  180.00   0.0  0
 B9Z  Var_01    C21  C16  S13  C10  168.29  30.0  2
 B9Z  Var_02    C9   C10  S13  C16  102.03  30.0  1
 B9Z  Var_03    H11  C15  O14  C4   -61.69  30.0  3
 B9Z  Var_04    C28  C27  C26  C22  176.51  30.0  3
 B9Z  Var_05    O30  C28  C27  C26   -2.80  30.0  1

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
 B9Z  chir_01  C22  C26  C23  C21  positiv

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
 B9Z  plan-1  C20  0.020
 B9Z  plan-1  C21  0.020
 B9Z  plan-1  C22  0.020
 B9Z  plan-1  C19  0.020
 B9Z  plan-1  C16  0.020
 B9Z  plan-1  C17  0.020
 B9Z  plan-1  C18  0.020
 B9Z  plan-1  H4   0.020
 B9Z  plan-1  H7   0.020
 B9Z  plan-1  H14  0.020
 B9Z  plan-1  H15  0.020
 B9Z  plan-1  S13  0.020
 B9Z  plan-2  C8   0.020
 B9Z  plan-2  C10  0.020
 B9Z  plan-2  C1   0.020
 B9Z  plan-2  C12  0.020
 B9Z  plan-2  C11  0.020
 B9Z  plan-2  C7   0.020
 B9Z  plan-2  C9   0.020
 B9Z  plan-2  H3   0.020
 B9Z  plan-2  H6   0.020
 B9Z  plan-2  H10  0.020
 B9Z  plan-2  H20  0.020
 B9Z  plan-2  S13  0.020
 B9Z  plan-3  C4   0.020
 B9Z  plan-3  C5   0.020
 B9Z  plan-3  C6   0.020
 B9Z  plan-3  C1   0.020
 B9Z  plan-3  C3   0.020
 B9Z  plan-3  C2   0.020
 B9Z  plan-3  C7   0.020
 B9Z  plan-3  O14  0.020
 B9Z  plan-3  H1   0.020
 B9Z  plan-3  H2   0.020
 B9Z  plan-3  H8   0.020
 B9Z  plan-3  H9   0.020
 B9Z  plan-4  C22  0.020
 B9Z  plan-4  C23  0.020
 B9Z  plan-4  O24  0.020
 B9Z  plan-4  O25  0.020
 B9Z  plan-4  H21  0.020
 B9Z  plan-5  C27  0.020
 B9Z  plan-5  C28  0.020
 B9Z  plan-5  O29  0.020
 B9Z  plan-5  O30  0.020
 B9Z  plan-5  H22  0.020

