# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:13:59 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 6-{[1-(benzylsulfonyl)piperidin-4-yl]amino}-3-(carboxymethoxy)thieno[3,2-b][1]benzothiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1c(sc2c1sc3cc(NC4CCN(CC4)[S](=O)(=O)Cc5ccccc5)ccc23)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
 598  598  '6-{[1-(benzylsulfonyl)piperidin-4-yl]amino}-3-(carboxymethoxy)thieno[3,2-b][1]benzothiophene-2-carboxylic acid'  ligand  61  37  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_598
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
 598  S1    S  S2    0   0.275  44.1968  13.9638   0.6562
 598  C2    C  CR5   0  -0.454  44.4713  15.2816   1.7533
 598  C3    C  CR5   0   0.443  45.4627  14.9994   2.6674
 598  C4    C  CR55  0  -0.203  46.0093  13.7177   2.4543
 598  C5    C  CR55  0  -0.150  45.4252  13.0391   1.4080
 598  C6    C  C     0   0.546  43.6428  16.4634   1.5685
 598  O7    O  OH1   0  -0.586  43.9246  17.4495   2.4059
 598  O8    O  O     0  -0.453  42.7850  16.5213   0.7151
 598  O9    O  O2    0  -0.464  45.8514  15.8109   3.6663
 598  C10   C  CH2   0  -0.266  46.9867  16.6062   3.3823
 598  C11   C  C     0   0.508  47.3441  17.4643   4.5693
 598  O14   O  OH1   0  -0.573  46.6009  17.2386   5.6331
 598  O15   O  O     0  -0.445  48.2411  18.2662   4.5135
 598  S18   S  S2    0   0.237  47.2467  12.7911   3.2446
 598  C19   C  CR56  0  -0.226  46.9808  11.4661   2.1300
 598  C20   C  CR56  0   0.212  45.9631  11.7374   1.1969
 598  C21   C  CR16  0  -0.386  47.6749  10.2656   2.1474
 598  C22   C  CR6   0   0.407  47.3555   9.2914   1.1947
 598  C23   C  CR16  0  -0.347  46.3207   9.5583   0.2618
 598  C24   C  CR16  0  -0.316  45.6429  10.7493   0.2590
 598  N28   N  NH1   0  -0.700  48.0182   8.1076   1.1012
 598  C29   C  CH1   0  -0.090  48.9699   7.6064   2.0637
 598  C30   C  CH2   0  -0.437  48.3099   7.0839   3.3402
 598  C31   C  CH2   0  -0.296  49.3234   6.4587   4.2862
 598  N32   N  N     0  -0.598  50.0889   5.4342   3.5846
 598  C33   C  CH2   0  -0.286  50.7843   5.8893   2.3866
 598  C34   C  CH2   0  -0.443  49.7945   6.5041   1.4124
 598  S44   S  S     0   1.376  50.5823   4.1013   4.4015
 598  C45   C  CH2   0  -0.702  49.2240   2.9332   4.2008
 598  C46   C  CR6   0   0.122  48.9618   2.6314   2.7615
 598  C49   C  CR16  0  -0.292  47.9515   3.2996   2.0759
 598  C50   C  CR16  0  -0.241  47.7172   3.0393   0.7330
 598  C51   C  CR16  0  -0.263  48.4946   2.1057   0.0616
 598  C52   C  CR16  0  -0.242  49.5005   1.4292   0.7406
 598  C53   C  CR16  0  -0.271  49.7343   1.6923   2.0821
 598  O59   O  OS    0  -0.664  50.6724   4.3983   5.8269
 598  O60   O  OS    0  -0.656  51.7512   3.5553   3.7257
 598  HO7   H  HOH1  0   0.489  43.3480  18.2065   2.2216
 598  H101  H  HCH2  0   0.282  46.8094  17.2665   2.5279
 598  H102  H  HCH2  0   0.278  47.8605  15.9894   3.1417
 598  H14   H  HOH1  0   0.489  46.8793  17.8168   6.3604
 598  H21   H  HCR6  0   0.280  48.4461  10.0988   2.8870
 598  H23   H  HCR6  0   0.269  46.0692   8.7991  -0.4686
 598  H24   H  HCR6  0   0.260  44.8608  10.9191  -0.4702
 598  H28   H  HNH1  0   0.383  47.6035   7.4176   0.4943
 598  H29   H  HCH1  0   0.244  49.6541   8.4220   2.3255
 598  H301  H  HCH2  0   0.234  47.5553   6.3382   3.0761
 598  H302  H  HCH2  0   0.256  47.7942   7.8896   3.8671
 598  H311  H  HCH2  0   0.269  48.7976   6.0218   5.1338
 598  H312  H  HCH2  0   0.247  49.9970   7.2243   4.6883
 598  H331  H  HCH2  0   0.275  51.2871   5.0531   1.9086
 598  H332  H  HCH2  0   0.239  51.5522   6.6248   2.6532
 598  H341  H  HCH2  0   0.261  50.3466   6.9076   0.5612
 598  H342  H  HCH2  0   0.237  49.1332   5.7200   1.0309
 598  H451  H  HCH2  0   0.314  48.3567   3.3747   4.6946
 598  H452  H  HCH2  0   0.324  49.5234   2.0474   4.7653
 598  H49   H  HCR6  0   0.259  47.3352   4.0224   2.5972
 598  H50   H  HCR6  0   0.259  46.9269   3.5648   0.2129
 598  H51   H  HCR6  0   0.260  48.3131   1.8996  -0.9852
 598  H52   H  HCR6  0   0.259  50.1035   0.6947   0.2228
 598  H53   H  HCR6  0   0.256  50.5156   1.1564   2.6061

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
 598  S1   C2    aromatic  1.736  0.020  1.736
 598  S1   C5    aromatic  1.711  0.020  1.711
 598  C2   C3    aromatic  1.378  0.020  1.378
 598  C2   C6    single    1.455  0.020  1.455
 598  C3   C4    aromatic  1.410  0.020  1.410
 598  C3   O9    single    1.344  0.020  1.344
 598  C4   C5    aromatic  1.377  0.020  1.377
 598  C4   S18   aromatic  1.736  0.020  1.736
 598  C5   C20   aromatic  1.424  0.020  1.424
 598  C6   O7    single    1.324  0.020  1.324
 598  C6   O8    double    1.211  0.020  1.211
 598  O7   HO7   single    0.850  0.020  0.980
 598  O9   C10   single    1.415  0.020  1.415
 598  C10  C11   single    1.508  0.020  1.508
 598  C10  H101  single    0.970  0.020  1.090
 598  C10  H102  single    0.970  0.020  1.090
 598  C11  O14   single    1.317  0.020  1.317
 598  C11  O15   double    1.204  0.020  1.204
 598  O14  H14   single    0.850  0.020  0.980
 598  S18  C19   aromatic  1.752  0.020  1.752
 598  C19  C20   aromatic  1.407  0.020  1.407
 598  C19  C21   aromatic  1.387  0.020  1.387
 598  C20  C24   aromatic  1.400  0.020  1.400
 598  C21  C22   aromatic  1.400  0.020  1.400
 598  C21  H21   single    0.930  0.020  1.080
 598  C22  C23   aromatic  1.419  0.020  1.419
 598  C22  N28   single    1.360  0.020  1.360
 598  C23  C24   aromatic  1.370  0.020  1.370
 598  C23  H23   single    0.930  0.020  1.080
 598  C24  H24   single    0.930  0.020  1.080
 598  N28  C29   single    1.443  0.020  1.443
 598  N28  H28   single    0.890  0.020  1.040
 598  C29  C30   single    1.529  0.020  1.529
 598  C29  C34   single    1.523  0.020  1.523
 598  C29  H29   single    0.970  0.020  1.090
 598  C30  C31   single    1.521  0.020  1.521
 598  C30  H301  single    0.970  0.020  1.090
 598  C30  H302  single    0.970  0.020  1.090
 598  C31  N32   single    1.459  0.020  1.459
 598  C31  H311  single    0.970  0.020  1.090
 598  C31  H312  single    0.970  0.020  1.090
 598  N32  C33   single    1.458  0.020  1.458
 598  N32  S44   single    1.639  0.020  1.639
 598  C33  C34   single    1.519  0.020  1.519
 598  C33  H331  single    0.970  0.020  1.090
 598  C33  H332  single    0.970  0.020  1.090
 598  C34  H341  single    0.970  0.020  1.090
 598  C34  H342  single    0.970  0.020  1.090
 598  S44  C45   single    1.803  0.020  1.803
 598  S44  O59   double    1.459  0.020  1.459
 598  S44  O60   double    1.456  0.020  1.456
 598  C45  C46   single    1.494  0.020  1.494
 598  C45  H451  single    0.970  0.020  1.090
 598  C45  H452  single    0.970  0.020  1.090
 598  C46  C49   aromatic  1.392  0.020  1.392
 598  C46  C53   aromatic  1.393  0.020  1.393
 598  C49  C50   aromatic  1.388  0.020  1.388
 598  C49  H49   single    0.930  0.020  1.080
 598  C50  C51   aromatic  1.388  0.020  1.388
 598  C50  H50   single    0.930  0.020  1.080
 598  C51  C52   aromatic  1.389  0.020  1.389
 598  C51  H51   single    0.930  0.020  1.080
 598  C52  C53   aromatic  1.387  0.020  1.387
 598  C52  H52   single    0.930  0.020  1.080
 598  C53  H53   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
 598  C5    S1   C2     91.09  3.000
 598  C6    C2   C3    131.32  3.000
 598  C6    C2   S1    116.50  3.000
 598  C3    C2   S1    112.18  3.000
 598  O9    C3   C4    123.30  3.000
 598  O9    C3   C2    125.27  3.000
 598  C4    C3   C2    111.41  3.000
 598  S18   C4   C5    112.65  3.000
 598  S18   C4   C3    133.86  3.000
 598  C5    C4   C3    113.48  3.000
 598  C20   C5   C4    113.75  3.000
 598  C20   C5   S1    134.41  3.000
 598  C4    C5   S1    111.84  3.000
 598  O8    C6   O7    124.10  3.000
 598  O8    C6   C2    122.10  3.000
 598  O7    C6   C2    113.79  3.000
 598  HO7   O7   C6    109.56  3.000
 598  C10   O9   C3    114.97  3.000
 598  H102  C10  H101  107.29  3.000
 598  H102  C10  C11   107.70  3.000
 598  H101  C10  C11   108.04  3.000
 598  H102  C10  O9    111.55  3.000
 598  H101  C10  O9    111.47  3.000
 598  C11   C10  O9    110.62  3.000
 598  O15   C11  O14   124.87  3.000
 598  O15   C11  C10   121.26  3.000
 598  O14   C11  C10   113.86  3.000
 598  H14   O14  C11   109.97  3.000
 598  C19   S18  C4     90.34  3.000
 598  C21   C19  C20   122.49  3.000
 598  C21   C19  S18   124.81  3.000
 598  C20   C19  S18   112.70  3.000
 598  C24   C20  C19   118.28  3.000
 598  C24   C20  C5    131.17  3.000
 598  C19   C20  C5    110.55  3.000
 598  H21   C21  C22   121.39  3.000
 598  H21   C21  C19   119.93  3.000
 598  C22   C21  C19   118.67  3.000
 598  N28   C22  C23   118.30  3.000
 598  N28   C22  C21   122.79  3.000
 598  C23   C22  C21   118.89  3.000
 598  H23   C23  C24   119.54  3.000
 598  H23   C23  C22   118.75  3.000
 598  C24   C23  C22   121.72  3.000
 598  H24   C24  C23   119.67  3.000
 598  H24   C24  C20   120.39  3.000
 598  C23   C24  C20   119.94  3.000
 598  H28   N28  C29   115.79  3.000
 598  H28   N28  C22   115.89  3.000
 598  C29   N28  C22   125.29  3.000
 598  H29   C29  C34   107.62  3.000
 598  H29   C29  C30   108.92  3.000
 598  C34   C29  C30   110.09  3.000
 598  H29   C29  N28   108.21  3.000
 598  C34   C29  N28   108.85  3.000
 598  C30   C29  N28   113.00  3.000
 598  H302  C30  H301  107.09  3.000
 598  H302  C30  C31   108.54  3.000
 598  H301  C30  C31   109.25  3.000
 598  H302  C30  C29   110.76  3.000
 598  H301  C30  C29   109.23  3.000
 598  C31   C30  C29   111.84  3.000
 598  H312  C31  H311  106.94  3.000
 598  H312  C31  N32   110.15  3.000
 598  H311  C31  N32   110.25  3.000
 598  H312  C31  C30   110.52  3.000
 598  H311  C31  C30   109.11  3.000
 598  N32   C31  C30   109.83  3.000
 598  S44   N32  C33   121.31  3.000
 598  S44   N32  C31   119.29  3.000
 598  C33   N32  C31   115.23  3.000
 598  H332  C33  H331  107.41  3.000
 598  H332  C33  C34   109.93  3.000
 598  H331  C33  C34   109.32  3.000
 598  H332  C33  N32   110.11  3.000
 598  H331  C33  N32   110.00  3.000
 598  C34   C33  N32   110.03  3.000
 598  H342  C34  H341  107.38  3.000
 598  H342  C34  C33   109.11  3.000
 598  H341  C34  C33   108.67  3.000
 598  H342  C34  C29   109.90  3.000
 598  H341  C34  C29   109.86  3.000
 598  C33   C34  C29   111.81  3.000
 598  O60   S44  O59   118.69  3.000
 598  O60   S44  C45   108.07  3.000
 598  O59   S44  C45   106.69  3.000
 598  O60   S44  N32   108.37  3.000
 598  O59   S44  N32   109.87  3.000
 598  C45   S44  N32   104.16  3.000
 598  H452  C45  H451  108.18  3.000
 598  H452  C45  C46   112.47  3.000
 598  H451  C45  C46   112.23  3.000
 598  H452  C45  S44   105.15  3.000
 598  H451  C45  S44   106.64  3.000
 598  C46   C45  S44   111.74  3.000
 598  C53   C46  C49   119.08  3.000
 598  C53   C46  C45   120.59  3.000
 598  C49   C46  C45   120.33  3.000
 598  H49   C49  C50   119.64  3.000
 598  H49   C49  C46   119.74  3.000
 598  C50   C49  C46   120.61  3.000
 598  H50   C50  C51   120.20  3.000
 598  H50   C50  C49   119.82  3.000
 598  C51   C50  C49   119.97  3.000
 598  H51   C51  C52   120.09  3.000
 598  H51   C51  C50   120.14  3.000
 598  C52   C51  C50   119.77  3.000
 598  H52   C52  C53   119.84  3.000
 598  H52   C52  C51   120.00  3.000
 598  C53   C52  C51   120.16  3.000
 598  H53   C53  C52   119.73  3.000
 598  H53   C53  C46   119.85  3.000
 598  C52   C53  C46   120.41  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
 598  CONST_01  C4   C3   C2   S1      0.00   0.0  0
 598  CONST_02  C3   C4   C5   S1      0.00   0.0  0
 598  CONST_03  S18  C4   C5   S1    180.00   0.0  0
 598  CONST_04  C19  C20  C5   S1    180.00   0.0  0
 598  CONST_05  C24  C20  C5   S1      0.00   0.0  0
 598  CONST_06  C4   C5   S1   C2      0.00   0.0  0
 598  CONST_07  C20  C5   S1   C2    180.00   0.0  0
 598  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 598  CONST_09  S18  C4   C3   C2    180.00   0.0  0
 598  CONST_10  C5   S1   C2   C3      0.00   0.0  0
 598  CONST_11  C20  C5   C4   C3    180.00   0.0  0
 598  CONST_12  C19  S18  C4   C3    180.00   0.0  0
 598  CONST_13  C19  C20  C5   C4      0.00   0.0  0
 598  CONST_14  C24  C20  C5   C4    180.00   0.0  0
 598  CONST_15  C20  C19  S18  C4      0.00   0.0  0
 598  CONST_16  C21  C19  S18  C4    180.00   0.0  0
 598  CONST_17  C19  S18  C4   C5      0.00   0.0  0
 598  CONST_18  S18  C19  C20  C5      0.00   0.0  0
 598  CONST_19  C21  C19  C20  C5    180.00   0.0  0
 598  CONST_20  C23  C24  C20  C5    180.00   0.0  0
 598  CONST_21  C20  C5   C4   S18     0.00   0.0  0
 598  CONST_22  C24  C20  C19  S18   180.00   0.0  0
 598  CONST_23  C22  C21  C19  S18   180.00   0.0  0
 598  CONST_24  C23  C24  C20  C19     0.00   0.0  0
 598  CONST_25  C23  C22  C21  C19     0.00   0.0  0
 598  CONST_26  C22  C21  C19  C20     0.00   0.0  0
 598  CONST_27  C22  C23  C24  C20     0.00   0.0  0
 598  CONST_28  C24  C20  C19  C21     0.00   0.0  0
 598  CONST_29  C24  C23  C22  C21     0.00   0.0  0
 598  CONST_30  C51  C50  C49  C46     0.00   0.0  0
 598  CONST_31  C51  C52  C53  C46     0.00   0.0  0
 598  CONST_32  C52  C53  C46  C49     0.00   0.0  0
 598  CONST_33  C52  C51  C50  C49     0.00   0.0  0
 598  CONST_34  C53  C46  C49  C50     0.00   0.0  0
 598  CONST_35  C53  C52  C51  C50     0.00   0.0  0
 598  CONST_36  O9   C3   C2   S1    180.00   0.0  0
 598  CONST_37  C6   C2   C3   C4    180.00   0.0  0
 598  CONST_38  C6   C2   S1   C5    180.00   0.0  0
 598  CONST_39  O9   C3   C4   C5    180.00   0.0  0
 598  CONST_40  S18  C4   C3   O9      0.00   0.0  0
 598  CONST_41  N28  C22  C21  C19   180.00   0.0  0
 598  CONST_42  N28  C22  C23  C24   180.00   0.0  0
 598  CONST_43  C50  C49  C46  C45   180.00   0.0  0
 598  CONST_44  C52  C53  C46  C45   180.00   0.0  0
 598  CONST_45  C29  N28  C22  C21     0.00   0.0  0
 598  CONST_46  C29  N28  C22  C23   180.00   0.0  0
 598  CONST_47  H24  C24  C20  C5      0.00   0.0  0
 598  CONST_48  H21  C21  C19  S18     0.00   0.0  0
 598  CONST_49  H23  C23  C24  C20   180.00   0.0  0
 598  CONST_50  H50  C50  C49  C46   180.00   0.0  0
 598  CONST_51  H52  C52  C53  C46   180.00   0.0  0
 598  CONST_52  H53  C53  C46  C49   180.00   0.0  0
 598  CONST_53  H51  C51  C50  C49   180.00   0.0  0
 598  CONST_54  H49  C49  C50  C51   180.00   0.0  0
 598  CONST_55  H28  N28  C22  C21   180.00   0.0  0
 598  CONST_56  HO7  O7   C6   C2    180.00   0.0  0
 598  CONST_57  H14  O14  C11  C10   180.00   0.0  0
 598  Var_01    N32  C31  C30  C29   -53.91  30.0  1
 598  Var_02    N32  C33  C34  C29    54.14  30.0  1
 598  Var_03    C33  N32  C31  C30    56.78  30.0  1
 598  Var_04    C34  C33  N32  C31   -56.93  30.0  1
 598  Var_05    O7   C6   C2   S1   -178.03  30.0  2
 598  Var_06    C45  S44  N32  C31    89.56  30.0  3
 598  Var_07    C46  C45  S44  N32    59.34  30.0  3
 598  Var_08    C49  C46  C45  S44   -97.42  30.0  2
 598  Var_09    C11  C10  O9   C3   -179.41  30.0  3
 598  Var_10    O14  C11  C10  O9      4.25  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
 598  chir_01  C29  N28  C30  C34  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
 598  plan-1  C45  0.020
 598  plan-1  C46  0.020
 598  plan-1  C49  0.020
 598  plan-1  C50  0.020
 598  plan-1  C51  0.020
 598  plan-1  C52  0.020
 598  plan-1  C53  0.020
 598  plan-1  H49  0.020
 598  plan-1  H50  0.020
 598  plan-1  H51  0.020
 598  plan-1  H52  0.020
 598  plan-1  H53  0.020
 598  plan-2  S1   0.020
 598  plan-2  C2   0.020
 598  plan-2  C3   0.020
 598  plan-2  C4   0.020
 598  plan-2  C5   0.020
 598  plan-2  C6   0.020
 598  plan-2  O9   0.020
 598  plan-2  S18  0.020
 598  plan-2  C19  0.020
 598  plan-2  C20  0.020
 598  plan-2  C21  0.020
 598  plan-2  C22  0.020
 598  plan-2  C23  0.020
 598  plan-2  C24  0.020
 598  plan-2  N28  0.020
 598  plan-2  H21  0.020
 598  plan-2  H23  0.020
 598  plan-2  H24  0.020
 598  plan-3  C22  0.020
 598  plan-3  N28  0.020
 598  plan-3  C29  0.020
 598  plan-3  H28  0.020
 598  plan-4  C2   0.020
 598  plan-4  C6   0.020
 598  plan-4  O7   0.020
 598  plan-4  O8   0.020
 598  plan-4  HO7  0.020
 598  plan-5  C10  0.020
 598  plan-5  C11  0.020
 598  plan-5  O14  0.020
 598  plan-5  O15  0.020
 598  plan-5  H14  0.020

