# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:55:08 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  50  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.373   -7.5283   0.6143  -0.2170
 B9Z  C5   C  CR16   0  -0.328   -7.1256  -0.6008   0.3416
 B9Z  C6   C  CR16   0  -0.295   -5.7895  -0.8442   0.5905
 B9Z  C8   C  CR16   0  -0.306   -2.9857  -0.8972   1.6824
 B9Z  C10  C  CR6    0  -0.163   -0.6633  -0.6924   1.0655
 B9Z  C20  C  CR16   0  -0.321    3.3257  -1.5904  -1.8042
 B9Z  C21  C  CR6    0   0.157    2.8832  -1.0764  -0.5829
 B9Z  C22  C  CH1    0  -0.428    3.7308  -0.1039   0.1962
 B9Z  C1   C  CR6    0   0.066   -4.8061   0.1054   0.2947
 B9Z  C12  C  CR16   0  -0.303   -2.3825   0.3069  -0.2942
 B9Z  C19  C  CR16   0  -0.245    2.5955  -2.5301  -2.5138
 B9Z  C23  C  C      0   0.437    4.5005  -0.9631   1.2405
 B9Z  C3   C  CR16   0  -0.369   -6.5641   1.5728  -0.5189
 B9Z  C2   C  CR16   0  -0.297   -5.2249   1.3104  -0.2632
 B9Z  C11  C  CR16   0  -0.202   -1.0447   0.0597  -0.0440
 B9Z  C16  C  CR6    0  -0.198    1.6644  -1.5575  -0.0844
 B9Z  C17  C  CR16   0  -0.201    0.9365  -2.5159  -0.7885
 B9Z  C18  C  CR16   0  -0.274    1.3914  -2.9972  -2.0040
 B9Z  C26  C  CH2    0  -0.393    4.6165   0.7885  -0.6675
 B9Z  C27  C  CH2    0  -0.590    5.2391   1.9238   0.1292
 B9Z  C28  C  C      0   0.408    6.1200   2.9013  -0.6676
 B9Z  C7   C  CR6    0   0.087   -3.3814  -0.1634   0.5646
 B9Z  C9   C  CR16   0  -0.247   -1.6471  -1.1678   1.9259
 B9Z  O14  O  O2     0  -0.469   -8.8485   0.7694  -0.4251
 B9Z  O24  O  OC    -1  -0.593    3.8000  -1.4484   2.1515
 B9Z  O25  O  O      0  -0.590    5.7198  -1.1369   1.0680
 B9Z  O29  O  OC    -1  -0.636    6.7734   3.7243   0.0100
 B9Z  O30  O  O      0  -0.611    6.1150   2.8164  -1.9120
 B9Z  H1   H  HCR6   0   0.263   -7.8683  -1.3550   0.5709
 B9Z  H2   H  HCR6   0   0.255   -5.5055  -1.8031   1.0053
 B9Z  H3   H  HCR6   0   0.254   -3.7278  -1.2634   2.3812
 B9Z  H4   H  HCR6   0   0.248    4.2630  -1.2414  -2.2170
 B9Z  H5   H  HCH1   0   0.231    3.0462   0.5433   0.7577
 B9Z  H6   H  HCR6   0   0.254   -2.6536   0.8672  -1.1805
 B9Z  H7   H  HCR6   0   0.251    2.9679  -2.8998  -3.4604
 B9Z  H8   H  HCR6   0   0.280   -6.8346   2.5294  -0.9445
 B9Z  H9   H  HCR6   0   0.257   -4.4998   2.0824  -0.4896
 B9Z  H10  H  HCR6   0   0.263   -0.2939   0.4400  -0.7253
 B9Z  H11  H  HCH3   0   0.229   -9.0623   2.8424  -0.3535
 B9Z  H12  H  HCH3   0   0.229   -8.8950   2.1543  -1.9841
 B9Z  H13  H  HCH3   0   0.260  -10.3873   1.9020  -1.0612
 B9Z  H14  H  HCR6   0   0.260    0.0020  -2.8841  -0.3841
 B9Z  H15  H  HCR6   0   0.253    0.8133  -3.7369  -2.5423
 B9Z  H16  H  HCH2   0   0.201    5.4076   0.2005  -1.1369
 B9Z  H17  H  HCH2   0   0.203    4.0186   1.2058  -1.4823
 B9Z  H18  H  HCH2   0   0.214    4.4461   2.5090   0.6131
 B9Z  H19  H  HCH2   0   0.219    5.8336   1.5158   0.9506
 B9Z  H20  H  HCR6   0   0.264   -1.3708  -1.7542   2.7935
 B9Z  C15  C  CH3    0  -0.437   -9.3060   1.9843  -0.9853
 B9Z  S13  S  S2     0   0.081    1.0371  -0.9833   1.4782

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  deloc     1.247  0.020  1.247
 B9Z  O25  C23  deloc     1.244  0.020  1.244
 B9Z  O24  C23  deloc     1.247  0.020  1.247
 B9Z  C28  O29  deloc     1.250  0.020  1.250
 B9Z  C28  C27  single    1.538  0.020  1.538
 B9Z  C26  C27  single    1.520  0.020  1.520
 B9Z  C26  C22  single    1.525  0.020  1.525
 B9Z  C23  C22  single    1.556  0.020  1.556
 B9Z  C22  C21  single    1.507  0.020  1.507
 B9Z  C21  C20  aromatic  1.397  0.020  1.397
 B9Z  C21  C16  aromatic  1.402  0.020  1.402
 B9Z  C3   C2   aromatic  1.388  0.020  1.388
 B9Z  C3   C4   aromatic  1.393  0.020  1.393
 B9Z  C20  C19  aromatic  1.386  0.020  1.386
 B9Z  C2   C1   aromatic  1.392  0.020  1.392
 B9Z  O14  C4   single    1.345  0.020  1.345
 B9Z  O14  C15  single    1.414  0.020  1.414
 B9Z  C12  C11  aromatic  1.383  0.020  1.383
 B9Z  C12  C7   aromatic  1.399  0.020  1.399
 B9Z  C11  C10  aromatic  1.394  0.020  1.394
 B9Z  C4   C5   aromatic  1.397  0.020  1.397
 B9Z  C1   C7   single    1.475  0.020  1.475
 B9Z  C1   C6   aromatic  1.399  0.020  1.399
 B9Z  C7   C8   aromatic  1.394  0.020  1.394
 B9Z  C10  S13  single    1.774  0.020  1.774
 B9Z  C10  C9   aromatic  1.391  0.020  1.391
 B9Z  C5   C6   aromatic  1.381  0.020  1.381
 B9Z  C19  C18  aromatic  1.389  0.020  1.389
 B9Z  C16  S13  single    1.779  0.020  1.779
 B9Z  C16  C17  aromatic  1.394  0.020  1.394
 B9Z  C8   C9   aromatic  1.387  0.020  1.387
 B9Z  C17  C18  aromatic  1.384  0.020  1.384
 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

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   124.51  3.000
 B9Z  O14  C4   C5   116.43  3.000
 B9Z  C3   C4   C5   119.07  3.000
 B9Z  H1   C5   C6   120.18  3.000
 B9Z  H1   C5   C4   119.52  3.000
 B9Z  C6   C5   C4   120.30  3.000
 B9Z  H2   C6   C1   119.86  3.000
 B9Z  H2   C6   C5   118.62  3.000
 B9Z  C1   C6   C5   121.51  3.000
 B9Z  H3   C8   C9   118.81  3.000
 B9Z  H3   C8   C7   120.05  3.000
 B9Z  C9   C8   C7   121.14  3.000
 B9Z  S13  C10  C9   118.56  3.000
 B9Z  C9   C10  C11  118.91  3.000
 B9Z  S13  C10  C11  122.42  3.000
 B9Z  H4   C20  C19  118.68  3.000
 B9Z  H4   C20  C21  119.29  3.000
 B9Z  C19  C20  C21  122.03  3.000
 B9Z  C16  C21  C22  121.77  3.000
 B9Z  C16  C21  C20  117.39  3.000
 B9Z  C22  C21  C20  120.75  3.000
 B9Z  H5   C22  C26  107.89  3.000
 B9Z  H5   C22  C23  106.92  3.000
 B9Z  C26  C22  C23  114.57  3.000
 B9Z  H5   C22  C21  107.12  3.000
 B9Z  C23  C22  C21  105.59  3.000
 B9Z  C26  C22  C21  114.29  3.000
 B9Z  C7   C1   C2   121.45  3.000
 B9Z  C7   C1   C6   121.11  3.000
 B9Z  C2   C1   C6   117.44  3.000
 B9Z  H6   C12  C7   119.85  3.000
 B9Z  H6   C12  C11  118.85  3.000
 B9Z  C7   C12  C11  121.30  3.000
 B9Z  H7   C19  C18  120.30  3.000
 B9Z  H7   C19  C20  119.88  3.000
 B9Z  C18  C19  C20  119.81  3.000
 B9Z  O25  C23  O24  126.69  3.000
 B9Z  O24  C23  C22  115.29  3.000
 B9Z  O25  C23  C22  117.97  3.000
 B9Z  H8   C3   C2   118.75  3.000
 B9Z  H8   C3   C4   121.39  3.000
 B9Z  C2   C3   C4   119.85  3.000
 B9Z  H9   C2   C3   118.20  3.000
 B9Z  H9   C2   C1   119.95  3.000
 B9Z  C3   C2   C1   121.84  3.000
 B9Z  H10  C11  C12  119.60  3.000
 B9Z  H10  C11  C10  120.05  3.000
 B9Z  C12  C11  C10  120.34  3.000
 B9Z  S13  C16  C17  118.77  3.000
 B9Z  C17  C16  C21  120.67  3.000
 B9Z  S13  C16  C21  120.54  3.000
 B9Z  H14  C17  C18  119.56  3.000
 B9Z  H14  C17  C16  119.72  3.000
 B9Z  C18  C17  C16  120.72  3.000
 B9Z  H15  C18  C17  119.93  3.000
 B9Z  H15  C18  C19  120.70  3.000
 B9Z  C17  C18  C19  119.37  3.000
 B9Z  H17  C26  H16  106.34  3.000
 B9Z  H17  C26  C27  109.23  3.000
 B9Z  H16  C26  C27  109.31  3.000
 B9Z  H17  C26  C22  109.13  3.000
 B9Z  H16  C26  C22  110.44  3.000
 B9Z  C27  C26  C22  112.21  3.000
 B9Z  H19  C27  H18  105.10  3.000
 B9Z  H19  C27  C28  108.36  3.000
 B9Z  H18  C27  C28  107.65  3.000
 B9Z  H19  C27  C26  109.74  3.000
 B9Z  H18  C27  C26  109.46  3.000
 B9Z  C28  C27  C26  115.95  3.000
 B9Z  O30  C28  O29  125.98  3.000
 B9Z  O29  C28  C27  115.90  3.000
 B9Z  O30  C28  C27  118.11  3.000
 B9Z  C12  C7   C1   121.08  3.000
 B9Z  C1   C7   C8   121.11  3.000
 B9Z  C12  C7   C8   117.81  3.000
 B9Z  H20  C9   C10  120.02  3.000
 B9Z  H20  C9   C8   119.50  3.000
 B9Z  C10  C9   C8   120.49  3.000
 B9Z  C15  O14  C4   118.54  3.000
 B9Z  H13  C15  H12  108.78  3.000
 B9Z  H13  C15  H11  108.76  3.000
 B9Z  H12  C15  H11  108.79  3.000
 B9Z  H13  C15  O14  106.52  3.000
 B9Z  H12  C15  O14  111.96  3.000
 B9Z  H11  C15  O14  111.92  3.000
 B9Z  C16  S13  C10  100.76  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  Var_01    C21  C16  S13  C10   135.12  30.0  1
 B9Z  Var_02    C9   C10  S13  C16   133.44  30.0  2
 B9Z  Var_03    H11  C15  O14  C4    -60.92  30.0  3
 B9Z  Var_04    C28  C27  C26  C22  -178.38  30.0  3
 B9Z  Var_05    O30  C28  C27  C26     9.81  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
 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-5  C27  0.020
 B9Z  plan-5  C28  0.020
 B9Z  plan-5  O29  0.020
 B9Z  plan-5  O30  0.020

