# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:33:53 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 4-bromo-3-(carboxymethoxy)-5-{3-[(3,3,5,5-tetramethylcyclohexyl)amino]phenyl}thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CC(CC(C)(C)C1)Nc2cccc(c2)c3sc(C(O)=O)c(OCC(O)=O)c3Br
#
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
 4B3  4B3  '4-bromo-3-(carboxymethoxy)-5-{3-[(3,3,5,5-tetramethylcyclohexyl)amino]phenyl}thiophene-2-carboxylic acid'  ligand  59  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4B3
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
 4B3  S1    S   S2    0   0.320  -2.4284   2.4473  -0.2278
 4B3  C2    C   CR5   0  -0.431  -3.8922   1.5564  -0.3692
 4B3  C3    C   CR5   0   0.484  -3.7224   0.2613   0.0511
 4B3  C4    C   CR5   0  -0.132  -2.3922   0.0063   0.4796
 4B3  C5    C   CR5   0  -0.195  -1.5698   1.0975   0.3950
 4B3  C6    C   C     0   0.550  -5.1227   2.1813  -0.8498
 4B3  O7    O   O     0  -0.425  -6.1700   1.6021  -1.0030
 4B3  O8    O   OH1   0  -0.601  -4.9380   3.4721  -1.0954
 4B3  C9    C   CR6   0   0.103  -0.1573   1.2549   0.7509
 4B3  C10   C   CR16  0  -0.406   0.7805   0.3370   0.2979
 4B3  C11   C   CR6   0   0.414   2.1405   0.4667   0.6189
 4B3  C12   C   CR16  0  -0.344   2.5299   1.5729   1.3898
 4B3  C13   C   CR16  0  -0.232   1.5872   2.4885   1.8292
 4B3  C14   C   CR16  0  -0.341   0.2431   2.3480   1.5230
 4B3  BR1   BR  BR    0   0.011  -1.9181  -1.6557   1.1786
 4B3  O20   O   O2    0  -0.455  -4.6812  -0.6736   0.1176
 4B3  C21   C   CH2   0  -0.271  -4.8939  -1.4000  -1.0766
 4B3  C22   C   C     0   0.505  -5.7999  -2.5606  -0.7515
 4B3  O25   O   OH1   0  -0.590  -6.0351  -3.2731  -1.8423
 4B3  O26   O   O     0  -0.423  -6.2430  -2.8025   0.3373
 4B3  N27   N   NH1   0  -0.699   3.0190  -0.4969   0.2024
 4B3  C28   C   CH1   0  -0.092   4.4566  -0.3107   0.1607
 4B3  C30   C   CH2   0  -0.402   5.1243  -1.6683  -0.0204
 4B3  C31   C   CT    0  -0.101   6.6567  -1.5913  -0.0459
 4B3  C32   C   CH2   0  -0.359   7.1004  -0.5278  -1.0662
 4B3  C33   C   CT    0  -0.098   6.4103   0.8476  -1.0222
 4B3  C34   C   CH2   0  -0.394   4.8914   0.6435  -0.9528
 4B3  C42   C   CH3   0  -0.640   7.2047  -2.9453  -0.5050
 4B3  C46   C   CH3   0  -0.649   7.2025  -1.3288   1.3618
 4B3  C50   C   CH3   0  -0.639   6.7492   1.5826  -2.3217
 4B3  C54   C   CH3   0  -0.652   6.8928   1.7243   0.1385
 4B3  HO8   H   HOH1  0   0.495  -5.7578   3.8781  -1.4155
 4B3  H10   H   HCR6  0   0.259   0.4694  -0.4901  -0.3295
 4B3  H12   H   HCR6  0   0.262   3.5673   1.7258   1.6540
 4B3  H13   H   HCR6  0   0.259   1.9132   3.3310   2.4256
 4B3  H14   H   HCR6  0   0.254  -0.4829   3.0600   1.8932
 4B3  H211  H   HCH2  0   0.283  -5.3633  -0.7764  -1.8436
 4B3  H212  H   HCH2  0   0.279  -3.9548  -1.7843  -1.4897
 4B3  HO25  H   HOH1  0   0.490  -6.6148  -4.0228  -1.6392
 4B3  HN27  H   HNH1  0   0.374   2.6585  -1.1167  -0.5074
 4B3  H28   H   HCH1  0   0.228   4.7568   0.0949   1.1311
 4B3  H301  H   HCH2  0   0.234   4.8007  -2.3502   0.7721
 4B3  H302  H   HCH2  0   0.218   4.7742  -2.1005  -0.9673
 4B3  H321  H   HCH2  0   0.219   8.1856  -0.3895  -0.9986
 4B3  H322  H   HCH2  0   0.212   6.9113  -0.9430  -2.0633
 4B3  H341  H   HCH2  0   0.216   4.5440   0.2242  -1.9052
 4B3  H342  H   HCH2  0   0.230   4.3919   1.6117  -0.8402
 4B3  H421  H   HCH3  0   0.221   6.8505  -3.1972  -1.5066
 4B3  H422  H   HCH3  0   0.223   8.2969  -2.9419  -0.5293
 4B3  H423  H   HCH3  0   0.222   6.8924  -3.7442   0.1719
 4B3  H461  H   HCH3  0   0.224   7.0093  -2.1872   2.0092
 4B3  H462  H   HCH3  0   0.223   8.2830  -1.1718   1.3378
 4B3  H463  H   HCH3  0   0.227   6.7615  -0.4590   1.8459
 4B3  H501  H   HCH3  0   0.221   6.4046   1.0234  -3.1944
 4B3  H502  H   HCH3  0   0.222   6.2799   2.5685  -2.3486
 4B3  H503  H   HCH3  0   0.222   7.8275   1.7273  -2.4239
 4B3  H541  H   HCH3  0   0.224   7.9837   1.7617   0.1720
 4B3  H542  H   HCH3  0   0.224   6.5332   2.7480   0.0125
 4B3  H543  H   HCH3  0   0.226   6.5503   1.3865   1.1150

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
 4B3  S1   C2    aromatic  1.719  0.020  1.719
 4B3  S1   C5    aromatic  1.717  0.020  1.717
 4B3  C2   C3    aromatic  1.372  0.020  1.372
 4B3  C2   C6    single    1.461  0.020  1.461
 4B3  C3   C4    aromatic  1.421  0.020  1.421
 4B3  C3   O20   single    1.341  0.020  1.341
 4B3  C4   C5    aromatic  1.369  0.020  1.369
 4B3  C4   BR1   single    1.864  0.020  1.864
 4B3  C5   C9    single    1.465  0.020  1.465
 4B3  C6   O7    double    1.207  0.020  1.207
 4B3  C6   O8    single    1.327  0.020  1.327
 4B3  O8   HO8   single    0.850  0.020  0.980
 4B3  C9   C10   aromatic  1.388  0.020  1.388
 4B3  C9   C14   aromatic  1.397  0.020  1.397
 4B3  C10  C11   aromatic  1.403  0.020  1.403
 4B3  C10  H10   single    0.930  0.020  1.080
 4B3  C11  C12   aromatic  1.403  0.020  1.403
 4B3  C11  N27   single    1.369  0.020  1.369
 4B3  C12  C13   aromatic  1.386  0.020  1.386
 4B3  C12  H12   single    0.930  0.020  1.080
 4B3  C13  C14   aromatic  1.386  0.020  1.386
 4B3  C13  H13   single    0.930  0.020  1.080
 4B3  C14  H14   single    0.930  0.020  1.080
 4B3  O20  C21   single    1.414  0.020  1.414
 4B3  C21  C22   single    1.508  0.020  1.508
 4B3  C21  H211  single    0.970  0.020  1.090
 4B3  C21  H212  single    0.970  0.020  1.090
 4B3  C22  O25   single    1.324  0.020  1.324
 4B3  C22  O26   double    1.200  0.020  1.200
 4B3  O25  HO25  single    0.850  0.020  0.980
 4B3  N27  C28   single    1.450  0.020  1.450
 4B3  N27  HN27  single    0.890  0.020  1.040
 4B3  C28  C30   single    1.524  0.020  1.524
 4B3  C28  C34   single    1.529  0.020  1.529
 4B3  C28  H28   single    0.970  0.020  1.090
 4B3  C30  C31   single    1.535  0.020  1.535
 4B3  C30  H301  single    0.970  0.020  1.090
 4B3  C30  H302  single    0.970  0.020  1.090
 4B3  C31  C32   single    1.539  0.020  1.539
 4B3  C31  C42   single    1.531  0.020  1.531
 4B3  C31  C46   single    1.532  0.020  1.532
 4B3  C32  C33   single    1.539  0.020  1.539
 4B3  C32  H321  single    0.970  0.020  1.090
 4B3  C32  H322  single    0.970  0.020  1.090
 4B3  C33  C34   single    1.534  0.020  1.534
 4B3  C33  C50   single    1.531  0.020  1.531
 4B3  C33  C54   single    1.533  0.020  1.533
 4B3  C34  H341  single    0.970  0.020  1.090
 4B3  C34  H342  single    0.970  0.020  1.090
 4B3  C42  H421  single    0.970  0.020  1.090
 4B3  C42  H422  single    0.970  0.020  1.090
 4B3  C42  H423  single    0.970  0.020  1.090
 4B3  C46  H461  single    0.970  0.020  1.090
 4B3  C46  H462  single    0.970  0.020  1.090
 4B3  C46  H463  single    0.970  0.020  1.090
 4B3  C50  H501  single    0.970  0.020  1.090
 4B3  C50  H502  single    0.970  0.020  1.090
 4B3  C50  H503  single    0.970  0.020  1.090
 4B3  C54  H541  single    0.970  0.020  1.090
 4B3  C54  H542  single    0.970  0.020  1.090
 4B3  C54  H543  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
 4B3  C5    S1   C2     92.77  3.000
 4B3  C6    C2   C3    127.48  3.000
 4B3  C6    C2   S1    121.49  3.000
 4B3  C3    C2   S1    111.01  3.000
 4B3  O20   C3   C4    121.97  3.000
 4B3  O20   C3   C2    125.79  3.000
 4B3  C4    C3   C2    112.19  3.000
 4B3  BR1   C4   C5    125.52  3.000
 4B3  BR1   C4   C3    120.74  3.000
 4B3  C5    C4   C3    113.63  3.000
 4B3  C9    C5   C4    130.52  3.000
 4B3  C9    C5   S1    119.07  3.000
 4B3  C4    C5   S1    110.40  3.000
 4B3  O8    C6   O7    124.35  3.000
 4B3  O8    C6   C2    111.08  3.000
 4B3  O7    C6   C2    124.57  3.000
 4B3  HO8   O8   C6    110.54  3.000
 4B3  C14   C9   C10   120.27  3.000
 4B3  C14   C9   C5    119.65  3.000
 4B3  C10   C9   C5    120.07  3.000
 4B3  H10   C10  C11   118.76  3.000
 4B3  H10   C10  C9    119.98  3.000
 4B3  C11   C10  C9    121.26  3.000
 4B3  N27   C11  C12   122.95  3.000
 4B3  N27   C11  C10   119.17  3.000
 4B3  C12   C11  C10   117.87  3.000
 4B3  H12   C12  C13   118.80  3.000
 4B3  H12   C12  C11   120.79  3.000
 4B3  C13   C12  C11   120.41  3.000
 4B3  H13   C13  C14   119.53  3.000
 4B3  H13   C13  C12   118.95  3.000
 4B3  C14   C13  C12   121.52  3.000
 4B3  H14   C14  C13   120.56  3.000
 4B3  H14   C14  C9    120.77  3.000
 4B3  C13   C14  C9    118.65  3.000
 4B3  C21   O20  C3    115.09  3.000
 4B3  H212  C21  H211  107.65  3.000
 4B3  H212  C21  C22   109.05  3.000
 4B3  H211  C21  C22   109.39  3.000
 4B3  H212  C21  O20   111.70  3.000
 4B3  H211  C21  O20   111.33  3.000
 4B3  C22   C21  O20   107.68  3.000
 4B3  O26   C22  O25   124.99  3.000
 4B3  O26   C22  C21   124.93  3.000
 4B3  O25   C22  C21   110.08  3.000
 4B3  HO25  O25  C22   110.48  3.000
 4B3  HN27  N27  C28   114.38  3.000
 4B3  HN27  N27  C11   114.65  3.000
 4B3  C28   N27  C11   123.69  3.000
 4B3  H28   C28  C34   109.66  3.000
 4B3  H28   C28  C30   108.40  3.000
 4B3  C34   C28  C30   110.17  3.000
 4B3  H28   C28  N27   107.11  3.000
 4B3  C34   C28  N27   112.51  3.000
 4B3  C30   C28  N27   108.87  3.000
 4B3  H302  C30  H301  106.55  3.000
 4B3  H302  C30  C31   108.89  3.000
 4B3  H301  C30  C31   109.78  3.000
 4B3  H302  C30  C28   108.27  3.000
 4B3  H301  C30  C28   109.85  3.000
 4B3  C31   C30  C28   113.26  3.000
 4B3  C46   C31  C42   107.42  3.000
 4B3  C46   C31  C32   112.82  3.000
 4B3  C42   C31  C32   108.01  3.000
 4B3  C46   C31  C30   110.43  3.000
 4B3  C42   C31  C30   108.55  3.000
 4B3  C32   C31  C30   109.48  3.000
 4B3  H322  C32  H321  105.94  3.000
 4B3  H322  C32  C33   106.68  3.000
 4B3  H321  C32  C33   109.23  3.000
 4B3  H322  C32  C31   106.94  3.000
 4B3  H321  C32  C31   109.37  3.000
 4B3  C33   C32  C31   117.98  3.000
 4B3  C54   C33  C50   107.37  3.000
 4B3  C54   C33  C34   110.70  3.000
 4B3  C50   C33  C34   108.75  3.000
 4B3  C54   C33  C32   113.06  3.000
 4B3  C50   C33  C32   107.79  3.000
 4B3  C34   C33  C32   109.04  3.000
 4B3  H342  C34  H341  106.42  3.000
 4B3  H342  C34  C33   109.79  3.000
 4B3  H341  C34  C33   108.97  3.000
 4B3  H342  C34  C28   110.31  3.000
 4B3  H341  C34  C28   107.67  3.000
 4B3  C33   C34  C28   113.41  3.000
 4B3  H423  C42  H422  107.57  3.000
 4B3  H423  C42  H421  107.87  3.000
 4B3  H422  C42  H421  107.73  3.000
 4B3  H423  C42  C31   111.01  3.000
 4B3  H422  C42  C31   111.21  3.000
 4B3  H421  C42  C31   111.28  3.000
 4B3  H463  C46  H462  107.19  3.000
 4B3  H463  C46  H461  107.01  3.000
 4B3  H462  C46  H461  107.52  3.000
 4B3  H463  C46  C31   113.65  3.000
 4B3  H462  C46  C31   110.91  3.000
 4B3  H461  C46  C31   110.29  3.000
 4B3  H503  C50  H502  107.58  3.000
 4B3  H503  C50  H501  107.73  3.000
 4B3  H502  C50  H501  107.88  3.000
 4B3  H503  C50  C33   111.18  3.000
 4B3  H502  C50  C33   111.05  3.000
 4B3  H501  C50  C33   111.26  3.000
 4B3  H543  C54  H542  106.90  3.000
 4B3  H543  C54  H541  107.30  3.000
 4B3  H542  C54  H541  107.48  3.000
 4B3  H543  C54  C33   113.75  3.000
 4B3  H542  C54  C33   110.19  3.000
 4B3  H541  C54  C33   110.93  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
 4B3  CONST_01  C4    C3   C2   S1     0.00   0.0  0
 4B3  CONST_02  C3    C4   C5   S1     0.00   0.0  0
 4B3  CONST_05  C4    C5   S1   C2     0.00   0.0  0
 4B3  CONST_06  C9    C5   S1   C2   180.00   0.0  0
 4B3  CONST_07  C5    C4   C3   C2     0.00   0.0  0
 4B3  CONST_08  C5    S1   C2   C3     0.00   0.0  0
 4B3  CONST_09  C9    C5   C4   C3   180.00   0.0  0
 4B3  CONST_12  C11   C10  C9   C5   180.00   0.0  0
 4B3  CONST_13  C13   C14  C9   C5   180.00   0.0  0
 4B3  CONST_14  C12   C11  C10  C9     0.00   0.0  0
 4B3  CONST_15  C12   C13  C14  C9     0.00   0.0  0
 4B3  CONST_16  C13   C14  C9   C10    0.00   0.0  0
 4B3  CONST_17  C13   C12  C11  C10    0.00   0.0  0
 4B3  CONST_18  C14   C9   C10  C11    0.00   0.0  0
 4B3  CONST_19  C14   C13  C12  C11    0.00   0.0  0
 4B3  CONST_20  O20   C3   C2   S1   180.00   0.0  0
 4B3  CONST_21  BR1   C4   C5   S1   180.00   0.0  0
 4B3  CONST_22  BR1   C4   C3   C2   180.00   0.0  0
 4B3  CONST_23  C6    C2   C3   C4   180.00   0.0  0
 4B3  CONST_24  C6    C2   S1   C5   180.00   0.0  0
 4B3  CONST_25  O20   C3   C4   C5   180.00   0.0  0
 4B3  CONST_26  BR1   C4   C5   C9     0.00   0.0  0
 4B3  CONST_27  N27   C11  C10  C9   180.00   0.0  0
 4B3  CONST_28  N27   C11  C12  C13  180.00   0.0  0
 4B3  CONST_31  H10   C10  C9   C5     0.00   0.0  0
 4B3  CONST_32  H14   C14  C9   C5     0.00   0.0  0
 4B3  CONST_33  H13   C13  C14  C9   180.00   0.0  0
 4B3  CONST_34  H12   C12  C11  C10  180.00   0.0  0
 4B3  CONST_35  HN27  N27  C11  C10    0.00   0.0  0
 4B3  CONST_36  HO8   O8   C6   C2   180.00   0.0  0
 4B3  CONST_37  HO25  O25  C22  C21  180.00   0.0  0
 4B3  Var_01    C32   C31  C30  C28  -51.24  30.0  1
 4B3  Var_02    C32   C33  C34  C28   51.60  30.0  1
 4B3  Var_03    C33   C32  C31  C30   47.75  30.0  1
 4B3  Var_04    C34   C33  C32  C31  -47.83  30.0  1
 4B3  Var_05    O7    C6   C2   S1   178.01  30.0  2
 4B3  Var_06    H421  C42  C31  C30   60.45  30.0  3
 4B3  Var_07    H461  C46  C31  C30   66.76  30.0  3
 4B3  Var_08    H501  C50  C33  C32   59.56  30.0  3
 4B3  Var_09    H541  C54  C33  C32   49.66  30.0  3
 4B3  Var_10    C22   C21  O20  C3   169.45  30.0  3
 4B3  Var_11    O25   C22  C21  O20  179.78  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
 4B3  chir_01  C28  N27  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
 4B3  plan-1  S1    0.020
 4B3  plan-1  C2    0.020
 4B3  plan-1  C3    0.020
 4B3  plan-1  C4    0.020
 4B3  plan-1  C5    0.020
 4B3  plan-1  C6    0.020
 4B3  plan-1  C9    0.020
 4B3  plan-1  BR1   0.020
 4B3  plan-1  O20   0.020
 4B3  plan-2  C5    0.020
 4B3  plan-2  C9    0.020
 4B3  plan-2  C10   0.020
 4B3  plan-2  C11   0.020
 4B3  plan-2  C12   0.020
 4B3  plan-2  C13   0.020
 4B3  plan-2  C14   0.020
 4B3  plan-2  N27   0.020
 4B3  plan-2  H10   0.020
 4B3  plan-2  H12   0.020
 4B3  plan-2  H13   0.020
 4B3  plan-2  H14   0.020
 4B3  plan-3  C11   0.020
 4B3  plan-3  N27   0.020
 4B3  plan-3  C28   0.020
 4B3  plan-3  HN27  0.020
 4B3  plan-4  C2    0.020
 4B3  plan-4  C6    0.020
 4B3  plan-4  O7    0.020
 4B3  plan-4  O8    0.020
 4B3  plan-4  HO8   0.020
 4B3  plan-5  C21   0.020
 4B3  plan-5  C22   0.020
 4B3  plan-5  O25   0.020
 4B3  plan-5  O26   0.020
 4B3  plan-5  HO25  0.020

