# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:04:10 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfonylphenyl]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2ccc(cc2)[S](=O)(=O)c3ccccc3[C@H](CCC(O)=O)C(O)=O
#
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
 B9N  B9N  '(2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfonylphenyl]pentanedioic acid'  ligand  52  32  .  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_B9N
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
 B9N  O32  O  OS     0  -0.660  -2.3454   1.2229  -2.4738
 B9N  S13  S  S      0   1.194  -1.6774   2.1078  -1.5199
 B9N  O31  O  OS     0  -0.662  -1.4648   3.4971  -1.9291
 B9N  C14  C  CR6    0  -0.280  -2.5883   2.1355   0.0128
 B9N  C19  C  CR6    0   0.284  -2.8475   0.9728   0.7513
 B9N  C20  C  CH1    0  -0.475  -2.3108  -0.3899   0.4082
 B9N  C25  C  C      0   0.453  -1.1006  -0.7603   1.3198
 B9N  O27  O  OC    -1  -0.577  -0.1719  -1.3797   0.7773
 B9N  O26  O  O      0  -0.602  -1.1947  -0.4472   2.5232
 B9N  C21  C  CH2    0  -0.402  -3.4015  -1.4730   0.5206
 B9N  C22  C  CH2    0  -0.587  -2.9830  -2.8091  -0.0729
 B9N  C23  C  C      0   0.408  -4.0571  -3.9094  -0.0402
 B9N  O30  O  O      0  -0.611  -5.0839  -3.7078   0.6389
 B9N  O29  O  OC    -1  -0.635  -3.8017  -4.9423  -0.6962
 B9N  C18  C  CR16   0  -0.296  -3.6271   1.1372   1.8994
 B9N  C17  C  CR16   0  -0.230  -4.1254   2.3703   2.2831
 B9N  C16  C  CR16   0  -0.268  -3.8453   3.5051   1.5348
 B9N  C15  C  CR16   0  -0.248  -3.0720   3.3853   0.3953
 B9N  C3   C  CR6    0  -0.184  -0.0941   1.4318  -1.1212
 B9N  C2   C  CR16   0  -0.210   0.4222   0.4004  -1.8861
 B9N  C4   C  CR16   0  -0.189   0.6425   2.0048  -0.0940
 B9N  C5   C  CR16   0  -0.303   1.9052   1.5163   0.1799
 B9N  C6   C  CR6    0   0.126   2.4511   0.4733  -0.5729
 B9N  C1   C  CR16   0  -0.294   1.6934  -0.0678  -1.6105
 B9N  C7   C  CR6    0   0.055   3.7987  -0.0451  -0.2818
 B9N  C12  C  CR16   0  -0.289   4.0841  -1.4094  -0.3970
 B9N  C11  C  CR16   0  -0.328   5.3457  -1.9045  -0.1365
 B9N  C10  C  CR6    0   0.376   6.3759  -1.0423   0.2476
 B9N  O28  O  O2     0  -0.468   7.5741  -1.6079   0.4750
 B9N  C29  C  CH3    0  -0.437   8.6494  -0.7782   0.8693
 B9N  C9   C  CR16   0  -0.369   6.1097   0.3197   0.3702
 B9N  C8   C  CR16   0  -0.293   4.8333   0.7998   0.1094
 B9N  H1   H  HCH1   0   0.230  -1.9680  -0.4110  -0.6243
 B9N  H3   H  HCH2   0   0.210  -3.6854  -1.6169   1.5645
 B9N  H4   H  HCH2   0   0.214  -4.3000  -1.1169   0.0079
 B9N  H5   H  HCH2   0   0.209  -2.6606  -2.6704  -1.1106
 B9N  H6   H  HCH2   0   0.231  -2.0966  -3.1875   0.4455
 B9N  H8   H  HCR6   0   0.252  -3.8591   0.2736   2.5048
 B9N  H9   H  HCR6   0   0.261  -4.7317   2.4465   3.1766
 B9N  H10  H  HCR6   0   0.262  -4.2248   4.4735   1.8312
 B9N  H11  H  HCR6   0   0.277  -2.8484   4.2633  -0.1935
 B9N  H12  H  HCR6   0   0.275  -0.1548  -0.0401  -2.6876
 B9N  H13  H  HCR6   0   0.277   0.2347   2.8097   0.5047
 B9N  H14  H  HCR6   0   0.261   2.4659   1.9393   1.0033
 B9N  H15  H  HCR6   0   0.258   2.1033  -0.8605  -2.2229
 B9N  H16  H  HCR6   0   0.258   3.2997  -2.1029  -0.6744
 B9N  H17  H  HCR6   0   0.265   5.5422  -2.9660  -0.2218
 B9N  H18  H  HCH3   0   0.260   9.5105  -1.4291   0.9984
 B9N  H19  H  HCH3   0   0.230   8.8866  -0.0289   0.1097
 B9N  H20  H  HCH3   0   0.230   8.4468  -0.2701   1.8155
 B9N  H21  H  HCR6   0   0.281   6.8803   1.0228   0.6562
 B9N  H22  H  HCR6   0   0.259   4.6604   1.8657   0.1930

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
 B9N  C17  C16  aromatic  1.388  0.020  1.388
 B9N  C17  C18  aromatic  1.384  0.020  1.384
 B9N  C16  C15  aromatic  1.382  0.020  1.382
 B9N  C18  C19  aromatic  1.397  0.020  1.397
 B9N  O30  C23  deloc     1.247  0.020  1.247
 B9N  C15  C14  aromatic  1.394  0.020  1.394
 B9N  C23  O29  deloc     1.250  0.020  1.250
 B9N  C23  C22  single    1.538  0.020  1.538
 B9N  C19  C14  aromatic  1.402  0.020  1.402
 B9N  C19  C20  single    1.504  0.020  1.504
 B9N  C14  S13  single    1.783  0.020  1.783
 B9N  C22  C21  single    1.521  0.020  1.521
 B9N  C21  C20  single    1.541  0.020  1.541
 B9N  O32  S13  double    1.463  0.020  1.463
 B9N  O26  C25  deloc     1.247  0.020  1.247
 B9N  C20  C25  single    1.560  0.020  1.560
 B9N  S13  O31  double    1.464  0.020  1.464
 B9N  S13  C3   single    1.767  0.020  1.767
 B9N  C25  O27  deloc     1.241  0.020  1.241
 B9N  C4   C3   aromatic  1.388  0.020  1.388
 B9N  C4   C5   aromatic  1.381  0.020  1.381
 B9N  C3   C2   aromatic  1.384  0.020  1.384
 B9N  C5   C6   aromatic  1.397  0.020  1.397
 B9N  C2   C1   aromatic  1.382  0.020  1.382
 B9N  C6   C1   aromatic  1.394  0.020  1.394
 B9N  C6   C7   single    1.473  0.020  1.473
 B9N  C8   C7   aromatic  1.392  0.020  1.392
 B9N  C8   C9   aromatic  1.388  0.020  1.388
 B9N  C7   C12  aromatic  1.399  0.020  1.399
 B9N  C9   C10  aromatic  1.393  0.020  1.393
 B9N  C12  C11  aromatic  1.380  0.020  1.380
 B9N  C10  C11  aromatic  1.397  0.020  1.397
 B9N  C10  O28  single    1.344  0.020  1.344
 B9N  C29  O28  single    1.414  0.020  1.414
 B9N  C20  H1   single    0.970  0.020  1.090
 B9N  C21  H3   single    0.970  0.020  1.090
 B9N  C21  H4   single    0.970  0.020  1.090
 B9N  C22  H5   single    0.970  0.020  1.090
 B9N  C22  H6   single    0.970  0.020  1.090
 B9N  C18  H8   single    0.930  0.020  1.080
 B9N  C17  H9   single    0.930  0.020  1.080
 B9N  C16  H10  single    0.930  0.020  1.080
 B9N  C15  H11  single    0.930  0.020  1.080
 B9N  C2   H12  single    0.930  0.020  1.080
 B9N  C4   H13  single    0.930  0.020  1.080
 B9N  C5   H14  single    0.930  0.020  1.080
 B9N  C1   H15  single    0.930  0.020  1.080
 B9N  C12  H16  single    0.930  0.020  1.080
 B9N  C11  H17  single    0.930  0.020  1.080
 B9N  C29  H18  single    0.970  0.020  1.090
 B9N  C29  H19  single    0.970  0.020  1.090
 B9N  C29  H20  single    0.970  0.020  1.090
 B9N  C9   H21  single    0.930  0.020  1.080
 B9N  C8   H22  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
 B9N  C3   S13  C14  105.65  3.000
 B9N  C3   S13  O31  107.22  3.000
 B9N  C14  S13  O31  107.44  3.000
 B9N  C3   S13  O32  108.96  3.000
 B9N  O31  S13  O32  117.27  3.000
 B9N  C14  S13  O32  109.67  3.000
 B9N  C15  C14  C19  122.35  3.000
 B9N  C19  C14  S13  122.31  3.000
 B9N  C15  C14  S13  115.29  3.000
 B9N  C18  C19  C20  119.54  3.000
 B9N  C20  C19  C14  124.42  3.000
 B9N  C18  C19  C14  116.01  3.000
 B9N  H1   C20  C21  106.17  3.000
 B9N  H1   C20  C25  107.79  3.000
 B9N  C21  C20  C25  109.85  3.000
 B9N  H1   C20  C19  110.27  3.000
 B9N  C25  C20  C19  111.02  3.000
 B9N  C21  C20  C19  111.56  3.000
 B9N  O26  C25  O27  127.12  3.000
 B9N  O27  C25  C20  116.34  3.000
 B9N  O26  C25  C20  116.48  3.000
 B9N  H4   C21  H3   106.11  3.000
 B9N  H4   C21  C22  109.21  3.000
 B9N  H3   C21  C22  109.21  3.000
 B9N  H4   C21  C20  108.56  3.000
 B9N  H3   C21  C20  110.27  3.000
 B9N  C22  C21  C20  113.22  3.000
 B9N  H6   C22  H5   104.73  3.000
 B9N  H6   C22  C23  107.95  3.000
 B9N  H5   C22  C23  108.44  3.000
 B9N  H6   C22  C21  109.99  3.000
 B9N  H5   C22  C21  109.84  3.000
 B9N  C23  C22  C21  115.35  3.000
 B9N  O29  C23  O30  125.97  3.000
 B9N  O29  C23  C22  115.93  3.000
 B9N  O30  C23  C22  118.09  3.000
 B9N  H8   C18  C17  118.66  3.000
 B9N  H8   C18  C19  119.10  3.000
 B9N  C17  C18  C19  122.23  3.000
 B9N  H9   C17  C16  120.03  3.000
 B9N  H9   C17  C18  119.55  3.000
 B9N  C16  C17  C18  120.42  3.000
 B9N  H10  C16  C15  119.99  3.000
 B9N  H10  C16  C17  120.90  3.000
 B9N  C15  C16  C17  119.11  3.000
 B9N  H11  C15  C16  119.64  3.000
 B9N  H11  C15  C14  120.48  3.000
 B9N  C16  C15  C14  119.88  3.000
 B9N  C4   C3   C2   121.25  3.000
 B9N  C2   C3   S13  119.65  3.000
 B9N  C4   C3   S13  118.98  3.000
 B9N  H12  C2   C1   120.03  3.000
 B9N  H12  C2   C3   120.94  3.000
 B9N  C1   C2   C3   119.03  3.000
 B9N  H13  C4   C5   119.84  3.000
 B9N  H13  C4   C3   121.08  3.000
 B9N  C5   C4   C3   119.07  3.000
 B9N  H14  C5   C6   119.95  3.000
 B9N  H14  C5   C4   119.09  3.000
 B9N  C6   C5   C4   120.95  3.000
 B9N  C7   C6   C1   120.52  3.000
 B9N  C7   C6   C5   120.90  3.000
 B9N  C1   C6   C5   118.58  3.000
 B9N  H15  C1   C6   119.97  3.000
 B9N  H15  C1   C2   118.91  3.000
 B9N  C6   C1   C2   121.11  3.000
 B9N  C8   C7   C12  117.62  3.000
 B9N  C12  C7   C6   120.91  3.000
 B9N  C8   C7   C6   121.47  3.000
 B9N  H16  C12  C11  118.73  3.000
 B9N  H16  C12  C7   119.86  3.000
 B9N  C11  C12  C7   121.40  3.000
 B9N  H17  C11  C10  119.52  3.000
 B9N  H17  C11  C12  120.18  3.000
 B9N  C10  C11  C12  120.30  3.000
 B9N  C9   C10  O28  124.52  3.000
 B9N  O28  C10  C11  116.36  3.000
 B9N  C9   C10  C11  119.12  3.000
 B9N  C29  O28  C10  118.56  3.000
 B9N  H20  C29  H19  108.86  3.000
 B9N  H20  C29  H18  108.80  3.000
 B9N  H19  C29  H18  108.73  3.000
 B9N  H20  C29  O28  111.91  3.000
 B9N  H19  C29  O28  111.93  3.000
 B9N  H18  C29  O28  106.51  3.000
 B9N  H21  C9   C8   118.68  3.000
 B9N  H21  C9   C10  121.51  3.000
 B9N  C8   C9   C10  119.82  3.000
 B9N  H22  C8   C9   118.20  3.000
 B9N  H22  C8   C7   120.03  3.000
 B9N  C9   C8   C7   121.75  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
 B9N  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 B9N  CONST_02  C17  C18  C19  C14     0.00   0.0  0
 B9N  CONST_03  C16  C17  C18  C19     0.00   0.0  0
 B9N  CONST_04  C16  C15  C14  C19     0.00   0.0  0
 B9N  CONST_05  C15  C16  C17  C18     0.00   0.0  0
 B9N  CONST_06  C15  C14  C19  C18     0.00   0.0  0
 B9N  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 B9N  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 B9N  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 B9N  CONST_10  C5   C6   C1   C2      0.00   0.0  0
 B9N  CONST_11  C7   C6   C1   C2    180.00   0.0  0
 B9N  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 B9N  CONST_13  C1   C6   C5   C4      0.00   0.0  0
 B9N  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 B9N  CONST_17  C9   C8   C7   C6    180.00   0.0  0
 B9N  CONST_18  C11  C12  C7   C6    180.00   0.0  0
 B9N  CONST_21  C10  C9   C8   C7      0.00   0.0  0
 B9N  CONST_22  C10  C11  C12  C7      0.00   0.0  0
 B9N  CONST_23  C9   C8   C7   C12     0.00   0.0  0
 B9N  CONST_24  C9   C10  C11  C12     0.00   0.0  0
 B9N  CONST_25  C8   C7   C12  C11     0.00   0.0  0
 B9N  CONST_26  C8   C9   C10  C11     0.00   0.0  0
 B9N  CONST_27  C16  C15  C14  S13   180.00   0.0  0
 B9N  CONST_28  C18  C19  C14  S13   180.00   0.0  0
 B9N  CONST_29  C5   C4   C3   S13   180.00   0.0  0
 B9N  CONST_30  C1   C2   C3   S13   180.00   0.0  0
 B9N  CONST_31  C17  C18  C19  C20   180.00   0.0  0
 B9N  CONST_32  C15  C14  C19  C20   180.00   0.0  0
 B9N  CONST_33  O28  C10  C11  C12   180.00   0.0  0
 B9N  CONST_34  C8   C9   C10  O28   180.00   0.0  0
 B9N  CONST_35  H10  C16  C15  C14   180.00   0.0  0
 B9N  CONST_36  H8   C18  C19  C14   180.00   0.0  0
 B9N  CONST_37  H9   C17  C18  C19   180.00   0.0  0
 B9N  CONST_38  H11  C15  C14  C19   180.00   0.0  0
 B9N  CONST_39  H14  C5   C4   C3    180.00   0.0  0
 B9N  CONST_40  H15  C1   C2   C3    180.00   0.0  0
 B9N  CONST_41  H13  C4   C3   C2    180.00   0.0  0
 B9N  CONST_42  H12  C2   C3   C4    180.00   0.0  0
 B9N  CONST_43  H22  C8   C7   C6      0.00   0.0  0
 B9N  CONST_44  H16  C12  C7   C6      0.00   0.0  0
 B9N  CONST_45  H21  C9   C8   C7    180.00   0.0  0
 B9N  CONST_46  H17  C11  C12  C7    180.00   0.0  0
 B9N  Var_01    C4   C3   S13  C14   -53.40  30.0  2
 B9N  Var_02    C3   S13  C14  C19   -59.37  30.0  2
 B9N  Var_03    C9   C10  O28  C29     0.13  30.0  2
 B9N  Var_04    H18  C29  O28  C10   179.98  30.0  3
 B9N  Var_05    C23  C22  C21  C20  -177.54  30.0  3
 B9N  Var_06    O30  C23  C22  C21   -11.06  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
 B9N  chir_01  C20  C19  C21  C25  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
 B9N  plan-1  S13  0.020
 B9N  plan-1  C14  0.020
 B9N  plan-1  C19  0.020
 B9N  plan-1  C20  0.020
 B9N  plan-1  C18  0.020
 B9N  plan-1  C17  0.020
 B9N  plan-1  C16  0.020
 B9N  plan-1  C15  0.020
 B9N  plan-1  H8   0.020
 B9N  plan-1  H9   0.020
 B9N  plan-1  H10  0.020
 B9N  plan-1  H11  0.020
 B9N  plan-2  S13  0.020
 B9N  plan-2  C3   0.020
 B9N  plan-2  C2   0.020
 B9N  plan-2  C4   0.020
 B9N  plan-2  C5   0.020
 B9N  plan-2  C6   0.020
 B9N  plan-2  C1   0.020
 B9N  plan-2  C7   0.020
 B9N  plan-2  H12  0.020
 B9N  plan-2  H13  0.020
 B9N  plan-2  H14  0.020
 B9N  plan-2  H15  0.020
 B9N  plan-3  C6   0.020
 B9N  plan-3  C7   0.020
 B9N  plan-3  C12  0.020
 B9N  plan-3  C11  0.020
 B9N  plan-3  C10  0.020
 B9N  plan-3  O28  0.020
 B9N  plan-3  C9   0.020
 B9N  plan-3  C8   0.020
 B9N  plan-3  H16  0.020
 B9N  plan-3  H17  0.020
 B9N  plan-3  H21  0.020
 B9N  plan-3  H22  0.020
 B9N  plan-4  C20  0.020
 B9N  plan-4  C25  0.020
 B9N  plan-4  O27  0.020
 B9N  plan-4  O26  0.020
 B9N  plan-5  C22  0.020
 B9N  plan-5  C23  0.020
 B9N  plan-5  O30  0.020
 B9N  plan-5  O29  0.020

