# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:38:20 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-{3-[(4-methyl-1-benzothiophen-3-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2scc(CN3C(=O)N(CCCC(O)=O)c4ccccc34)c12
#
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
 0BB  0BB  '4-{3-[(4-methyl-1-benzothiophen-3-yl)methyl]-2-oxo-2,3-dihydro-1H-benzimidazol-1-yl}butanoic acid'  ligand  46  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0BB
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
 0BB  C1    C  CH2    0  -0.308   3.3782   0.5968   1.2511
 0BB  O1    O  O      0  -0.502   0.8360  -0.2942   2.3959
 0BB  C3    C  CR16   0  -0.312  -0.3572   2.7628  -1.0510
 0BB  C4    C  CR16   0  -0.277   0.4226   3.5174  -1.9257
 0BB  C5    C  CR16   0  -0.274   1.8121   3.4603  -1.8835
 0BB  C6    C  CR16   0  -0.318   2.4761   2.6472  -0.9669
 0BB  C7    C  CR56   0   0.333   1.7009   1.9008  -0.0995
 0BB  C8    C  CR56   0   0.324   0.3047   1.9618  -0.1419
 0BB  N9    N  NR5    0  -0.604  -0.1601   1.1137   0.8435
 0BB  C10   C  CR5    0   0.680   0.9011   0.5161   1.4892
 0BB  N11   N  NR5    0  -0.594   2.0379   1.0231   0.9105
 0BB  C12   C  CH2    0  -0.423   3.9101  -0.4874   0.3224
 0BB  C13   C  CH2    0  -0.590   5.3192  -0.8989   0.7124
 0BB  C17   C  CH2    0  -0.373  -1.5399   0.8545   1.1478
 0BB  C18   C  CR5    0   0.128  -2.1790  -0.1223   0.1973
 0BB  C19   C  CR5    0   0.203  -3.5855  -0.4718   0.1810
 0BB  C20   C  CR5    0  -0.226  -3.8553  -1.4366  -0.8097
 0BB  S21   S  S2     0   0.220  -2.4295  -1.8797  -1.6840
 0BB  C22   C  CR15   0  -0.537  -1.4760  -0.7989  -0.7396
 0BB  C23   C  C      0   0.045  -4.6558  -0.0059   0.9771
 0BB  C24   C  C1     0  -0.315  -5.9153  -0.5316   0.7416
 0BB  C25   C  C1     0  -0.257  -6.1573  -1.4910  -0.2465
 0BB  C26   C  C1     0  -0.294  -5.1280  -1.9539  -1.0362
 0BB  C34   C  CH3    0  -0.765  -4.4910   1.0328   2.0497
 0BB  C39   C  C      0   0.416   5.9549  -2.0027  -0.1529
 0BB  O40   O  O      0  -0.606   5.2696  -2.4860  -1.0747
 0BB  O41   O  OC    -1  -0.631   7.1225  -2.3253   0.1505
 0BB  H1    H  HCH2   0   0.253   4.0271   1.4753   1.2333
 0BB  H1A   H  HCH2   0   0.260   3.3609   0.2432   2.2821
 0BB  H3    H  HCR6   0   0.267  -1.4377   2.8052  -1.0930
 0BB  H4    H  HCR6   0   0.257  -0.0655   4.1529  -2.6525
 0BB  H5    H  HCR6   0   0.257   2.3930   4.0534  -2.5771
 0BB  H6    H  HCR6   0   0.270   3.5573   2.6067  -0.9433
 0BB  H12   H  HCH2   0   0.223   3.2383  -1.3482   0.3581
 0BB  H12A  H  HCH2   0   0.222   3.8954  -0.1259  -0.7092
 0BB  H13   H  HCH2   0   0.225   5.9797  -0.0246   0.6890
 0BB  H13A  H  HCH2   0   0.226   5.3303  -1.2344   1.7560
 0BB  H17   H  HCH2   0   0.289  -1.5914   0.4788   2.1707
 0BB  H17A  H  HCH2   0   0.274  -2.0749   1.8052   1.1441
 0BB  H22   H  HCR5   0   0.292  -0.4180  -0.7276  -0.9425
 0BB  H24   H  H      0   0.251  -6.7440  -0.1851   1.3473
 0BB  H25   H  H      0   0.260  -7.1604  -1.8712  -0.3886
 0BB  H26   H  H      0   0.268  -5.2987  -2.6951  -1.8059
 0BB  H34   H  HCH3   0   0.249  -4.1922   1.9986   1.6389
 0BB  H34A  H  HCH3   0   0.265  -5.4327   1.1852   2.5746
 0BB  H34B  H  HCH3   0   0.249  -3.7473   0.7498   2.7945

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
 0BB  N11  C1    single    1.447  0.020  1.447
 0BB  C1   C12   single    1.523  0.020  1.523
 0BB  C1   H1    single    0.970  0.020  1.090
 0BB  C1   H1A   single    0.970  0.020  1.090
 0BB  O1   C10   double    1.218  0.020  1.218
 0BB  C8   C3    aromatic  1.381  0.020  1.381
 0BB  C3   C4    aromatic  1.394  0.020  1.394
 0BB  C3   H3    single    0.930  0.020  1.080
 0BB  C4   C5    aromatic  1.391  0.020  1.391
 0BB  C4   H4    single    0.930  0.020  1.080
 0BB  C6   C5    aromatic  1.394  0.020  1.394
 0BB  C5   H5    single    0.930  0.020  1.080
 0BB  C7   C6    aromatic  1.382  0.020  1.382
 0BB  C6   H6    single    0.930  0.020  1.080
 0BB  C8   C7    aromatic  1.398  0.020  1.398
 0BB  N11  C7    single    1.380  0.020  1.380
 0BB  N9   C8    single    1.381  0.020  1.381
 0BB  C17  N9    single    1.437  0.020  1.437
 0BB  N9   C10   single    1.378  0.020  1.378
 0BB  C10  N11   single    1.373  0.020  1.373
 0BB  C13  C12   single    1.519  0.020  1.519
 0BB  C12  H12   single    0.970  0.020  1.090
 0BB  C12  H12A  single    0.970  0.020  1.090
 0BB  C13  C39   single    1.540  0.020  1.540
 0BB  C13  H13   single    0.970  0.020  1.090
 0BB  C13  H13A  single    0.970  0.020  1.090
 0BB  C18  C17   single    1.505  0.020  1.505
 0BB  C17  H17   single    0.970  0.020  1.090
 0BB  C17  H17A  single    0.970  0.020  1.090
 0BB  C19  C18   aromatic  1.449  0.020  1.449
 0BB  C18  C22   aromatic  1.353  0.020  1.353
 0BB  C23  C19   aromatic  1.413  0.020  1.413
 0BB  C20  C19   aromatic  1.409  0.020  1.409
 0BB  C26  C20   aromatic  1.392  0.020  1.392
 0BB  C20  S21   aromatic  1.730  0.020  1.730
 0BB  S21  C22   aromatic  1.723  0.020  1.723
 0BB  C22  H22   single    0.930  0.020  1.080
 0BB  C24  C23   aromatic  1.385  0.020  1.385
 0BB  C34  C23   single    1.502  0.020  1.502
 0BB  C25  C24   aromatic  1.398  0.020  1.398
 0BB  C24  H24   single    0.930  0.020  1.080
 0BB  C25  C26   aromatic  1.377  0.020  1.377
 0BB  C25  H25   single    0.930  0.020  1.080
 0BB  C26  H26   single    0.930  0.020  1.080
 0BB  C34  H34   single    0.970  0.020  1.090
 0BB  C34  H34A  single    0.970  0.020  1.090
 0BB  C34  H34B  single    0.970  0.020  1.090
 0BB  O40  C39   deloc     1.246  0.020  1.246
 0BB  C39  O41   deloc     1.249  0.020  1.249

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
 0BB  H1A   C1   H1    106.60  3.000
 0BB  H1A   C1   C12   110.57  3.000
 0BB  H1    C1   C12   110.79  3.000
 0BB  H1A   C1   N11   107.67  3.000
 0BB  H1    C1   N11   108.03  3.000
 0BB  C12   C1   N11   112.92  3.000
 0BB  H3    C3   C8    121.80  3.000
 0BB  H3    C3   C4    120.87  3.000
 0BB  C8    C3   C4    117.33  3.000
 0BB  H4    C4   C5    119.68  3.000
 0BB  H4    C4   C3    119.15  3.000
 0BB  C5    C4   C3    121.16  3.000
 0BB  H5    C5   C6    119.06  3.000
 0BB  H5    C5   C4    119.62  3.000
 0BB  C6    C5   C4    121.31  3.000
 0BB  H6    C6   C7    121.76  3.000
 0BB  H6    C6   C5    120.81  3.000
 0BB  C7    C6   C5    117.43  3.000
 0BB  N11   C7   C8    107.08  3.000
 0BB  N11   C7   C6    131.75  3.000
 0BB  C8    C7   C6    121.17  3.000
 0BB  N9    C8   C7    106.72  3.000
 0BB  N9    C8   C3    131.68  3.000
 0BB  C7    C8   C3    121.60  3.000
 0BB  C17   N9   C10   124.20  3.000
 0BB  C10   N9   C8    109.97  3.000
 0BB  C17   N9   C8    125.82  3.000
 0BB  N11   C10  N9    106.26  3.000
 0BB  N11   C10  O1    127.15  3.000
 0BB  N9    C10  O1    126.59  3.000
 0BB  C10   N11  C7    109.96  3.000
 0BB  C10   N11  C1    123.99  3.000
 0BB  C7    N11  C1    125.86  3.000
 0BB  H12A  C12  H12   106.45  3.000
 0BB  H12A  C12  C13   110.14  3.000
 0BB  H12   C12  C13   110.40  3.000
 0BB  H12A  C12  C1    109.59  3.000
 0BB  H12   C12  C1    109.03  3.000
 0BB  C13   C12  C1    111.11  3.000
 0BB  H13A  C13  H13   104.97  3.000
 0BB  H13A  C13  C39   108.14  3.000
 0BB  H13   C13  C39   108.12  3.000
 0BB  H13A  C13  C12   109.68  3.000
 0BB  H13   C13  C12   109.73  3.000
 0BB  C39   C13  C12   115.65  3.000
 0BB  H17A  C17  H17   106.27  3.000
 0BB  H17A  C17  C18   110.80  3.000
 0BB  H17   C17  C18   110.39  3.000
 0BB  H17A  C17  N9    108.25  3.000
 0BB  H17   C17  N9    107.82  3.000
 0BB  C18   C17  N9    113.02  3.000
 0BB  C22   C18  C19   112.08  3.000
 0BB  C22   C18  C17   122.77  3.000
 0BB  C19   C18  C17   125.14  3.000
 0BB  C23   C19  C20   118.49  3.000
 0BB  C20   C19  C18   111.03  3.000
 0BB  C23   C19  C18   130.48  3.000
 0BB  C26   C20  S21   125.16  3.000
 0BB  S21   C20  C19   111.89  3.000
 0BB  C26   C20  C19   122.95  3.000
 0BB  C22   S21  C20    91.06  3.000
 0BB  H22   C22  S21   118.74  3.000
 0BB  H22   C22  C18   127.33  3.000
 0BB  S21   C22  C18   113.94  3.000
 0BB  C34   C23  C24   118.92  3.000
 0BB  C34   C23  C19   123.18  3.000
 0BB  C24   C23  C19   117.90  3.000
 0BB  H24   C24  C25   118.82  3.000
 0BB  H24   C24  C23   118.63  3.000
 0BB  C25   C24  C23   122.54  3.000
 0BB  H25   C25  C26   119.95  3.000
 0BB  H25   C25  C24   119.62  3.000
 0BB  C26   C25  C24   120.42  3.000
 0BB  H26   C26  C25   121.34  3.000
 0BB  H26   C26  C20   120.96  3.000
 0BB  C25   C26  C20   117.70  3.000
 0BB  H34B  C34  H34A  107.28  3.000
 0BB  H34B  C34  H34   107.46  3.000
 0BB  H34A  C34  H34   107.12  3.000
 0BB  H34B  C34  C23   112.54  3.000
 0BB  H34A  C34  C23   110.25  3.000
 0BB  H34   C34  C23   111.92  3.000
 0BB  O41   C39  O40   126.42  3.000
 0BB  O41   C39  C13   115.76  3.000
 0BB  O40   C39  C13   117.82  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
 0BB  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 0BB  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 0BB  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 0BB  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 0BB  CONST_05  C8   C3   C4   C5      0.00   0.0  0
 0BB  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 0BB  CONST_07  C24  C23  C19  C18   180.00   0.0  0
 0BB  CONST_08  C26  C20  C19  C18   180.00   0.0  0
 0BB  CONST_09  S21  C20  C19  C18     0.00   0.0  0
 0BB  CONST_10  C20  S21  C22  C18     0.00   0.0  0
 0BB  CONST_11  S21  C22  C18  C19     0.00   0.0  0
 0BB  CONST_12  C25  C24  C23  C19     0.00   0.0  0
 0BB  CONST_13  C25  C26  C20  C19     0.00   0.0  0
 0BB  CONST_14  C22  S21  C20  C19     0.00   0.0  0
 0BB  CONST_15  C22  C18  C19  C20     0.00   0.0  0
 0BB  CONST_16  C24  C23  C19  C20     0.00   0.0  0
 0BB  CONST_17  C24  C25  C26  C20     0.00   0.0  0
 0BB  CONST_18  C23  C19  C20  S21   180.00   0.0  0
 0BB  CONST_19  C25  C26  C20  S21   180.00   0.0  0
 0BB  CONST_20  C23  C19  C18  C22   180.00   0.0  0
 0BB  CONST_21  C26  C20  S21  C22   180.00   0.0  0
 0BB  CONST_22  C26  C20  C19  C23     0.00   0.0  0
 0BB  CONST_23  C26  C25  C24  C23     0.00   0.0  0
 0BB  CONST_24  C10  N9   C8   C7      0.00   0.0  0
 0BB  CONST_25  N9   C10  N11  C7      0.00   0.0  0
 0BB  CONST_26  C10  N11  C7   C8      0.00   0.0  0
 0BB  CONST_27  N11  C10  N9   C8      0.00   0.0  0
 0BB  CONST_28  N11  C7   C8   N9      0.00   0.0  0
 0BB  CONST_29  C23  C19  C18  C17     0.00   0.0  0
 0BB  CONST_30  C20  C19  C18  C17   180.00   0.0  0
 0BB  CONST_31  S21  C22  C18  C17   180.00   0.0  0
 0BB  CONST_32  C34  C23  C19  C18     0.00   0.0  0
 0BB  CONST_33  C34  C23  C19  C20   180.00   0.0  0
 0BB  CONST_34  C34  C23  C24  C25   180.00   0.0  0
 0BB  CONST_35  C8   C7   N11  C1    180.00   0.0  0
 0BB  CONST_36  N9   C10  N11  C1    180.00   0.0  0
 0BB  CONST_37  C8   N9   C10  O1    180.00   0.0  0
 0BB  CONST_38  C7   N11  C10  O1    180.00   0.0  0
 0BB  CONST_39  C17  N9   C8   C7    180.00   0.0  0
 0BB  CONST_40  C17  N9   C10  N11   180.00   0.0  0
 0BB  CONST_41  H5   C5   C4   C3    180.00   0.0  0
 0BB  CONST_42  H6   C6   C5   C4    180.00   0.0  0
 0BB  CONST_43  H3   C3   C4   C5    180.00   0.0  0
 0BB  CONST_44  H4   C4   C5   C6    180.00   0.0  0
 0BB  CONST_45  H22  C22  C18  C19   180.00   0.0  0
 0BB  CONST_46  H24  C24  C23  C19   180.00   0.0  0
 0BB  CONST_47  H26  C26  C20  C19   180.00   0.0  0
 0BB  CONST_48  H25  C25  C26  C20   180.00   0.0  0
 0BB  CONST_49  O1   C10  N11  C1      0.00   0.0  0
 0BB  CONST_50  C17  N9   C10  O1      0.00   0.0  0
 0BB  Var_01    C18  C17  N9   C8     79.34  30.0  2
 0BB  Var_02    C19  C18  C17  N9   -173.73  30.0  2
 0BB  Var_03    C12  C1   N11  C7    -79.47  30.0  3
 0BB  Var_04    H34  C34  C23  C19    64.69  30.0  2
 0BB  Var_05    C13  C12  C1   N11   179.74  30.0  3
 0BB  Var_06    C39  C13  C12  C1    179.44  30.0  2
 0BB  Var_07    O40  C39  C13  C12    -1.36  30.0  3

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
 0BB  plan-1  C1   0.020
 0BB  plan-1  O1   0.020
 0BB  plan-1  C3   0.020
 0BB  plan-1  C4   0.020
 0BB  plan-1  C5   0.020
 0BB  plan-1  C6   0.020
 0BB  plan-1  C7   0.020
 0BB  plan-1  C8   0.020
 0BB  plan-1  N9   0.020
 0BB  plan-1  C10  0.020
 0BB  plan-1  N11  0.020
 0BB  plan-1  C17  0.020
 0BB  plan-1  H3   0.020
 0BB  plan-1  H4   0.020
 0BB  plan-1  H5   0.020
 0BB  plan-1  H6   0.020
 0BB  plan-2  C17  0.020
 0BB  plan-2  C18  0.020
 0BB  plan-2  C19  0.020
 0BB  plan-2  C20  0.020
 0BB  plan-2  S21  0.020
 0BB  plan-2  C22  0.020
 0BB  plan-2  C23  0.020
 0BB  plan-2  C24  0.020
 0BB  plan-2  C25  0.020
 0BB  plan-2  C26  0.020
 0BB  plan-2  C34  0.020
 0BB  plan-2  H22  0.020
 0BB  plan-2  H24  0.020
 0BB  plan-2  H25  0.020
 0BB  plan-2  H26  0.020
 0BB  plan-3  C13  0.020
 0BB  plan-3  C39  0.020
 0BB  plan-3  O40  0.020
 0BB  plan-3  O41  0.020

