# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:30:24 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-(2,4-dichlorophenyl)-4-hydroxy-N-(2-{4-[(methylsulfonyl)amino]phenyl}ethyl)-1H-benzimidazole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Nc1ccc(CCNC(=O)c2ccc(O)c3nc([nH]c23)c4ccc(Cl)cc4Cl)cc1
#
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
 HBM  HBM  2-(2,4-dichlorophenyl)-4-hydroxy-N-(2-{4-[(methylsulfonyl)amino]phenyl}ethyl)-1H-benzimidazole-7-carboxamide  ligand  54  34  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HBM
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
 HBM  C2    C   CR16  0  -0.306   0.9445   0.4401   2.5051
 HBM  C4    C   CR6   0   0.306   2.6973  -1.2349   2.4395
 HBM  C6    C   CR56  0   0.366   0.3875  -1.7769   1.9359
 HBM  C10   C   CR6   0   0.087   0.2390  -5.3167   1.3400
 HBM  C11   C   CR16  0  -0.300  -0.4945  -5.5783   0.1843
 HBM  C1    C   CR6   0  -0.080  -0.0484  -0.4682   2.1634
 HBM  C3    C   CR16  0  -0.357   2.2902   0.0789   2.6266
 HBM  C5    C   CR56  0   0.011   1.7167  -2.1742   2.1022
 HBM  N7    N   NR15  0  -0.694  -0.2680  -2.9284   1.6216
 HBM  C8    C   CR5   0   0.442   0.6428  -3.9401   1.6367
 HBM  N9    N   N     0  -0.447   1.8479  -3.5248   1.9112
 HBM  C12   C   CR16  0  -0.169  -0.9121  -6.8584  -0.1348
 HBM  C13   C   CR6   0  -0.056  -0.5870  -7.8963   0.7233
 HBM  C14   C   CR16  0  -0.113   0.1258  -7.6728   1.8892
 HBM  C15   C   CR6   0  -0.086   0.5293  -6.3828   2.1894
 HBM  CL16  CL  CL    0  -0.103  -1.0881  -9.5055   0.3441
 HBM  CL17  CL  CL    0  -0.092   1.3468  -6.1220   3.6830
 HBM  C18   C   C     0   0.539  -1.4990  -0.1833   2.0747
 HBM  N19   N   NH1   0  -0.629  -1.9682   0.8000   2.8679
 HBM  C20   C   CH2   0  -0.286  -3.3758   0.9392   3.1673
 HBM  C21   C   CH2   0  -0.509  -3.7721   0.1381   4.4169
 HBM  C22   C   CR6   0   0.137  -3.3926  -1.3110   4.3030
 HBM  C23   C   CR16  0  -0.257  -4.2184  -2.2171   3.6440
 HBM  C24   C   CR16  0  -0.249  -3.8383  -3.5381   3.4716
 HBM  C25   C   CR6   0   0.237  -2.6011  -3.9747   3.9362
 HBM  C26   C   CR16  0  -0.213  -1.7589  -3.0795   4.5841
 HBM  C27   C   CR16  0  -0.295  -2.1642  -1.7673   4.7755
 HBM  N28   N   NC1   0  -0.803  -2.1836  -5.3159   3.7328
 HBM  S29   S   S     0   1.317  -2.1810  -6.3728   5.0179
 HBM  C30   C   CH3   0  -0.777  -3.8826  -6.5495   5.5068
 HBM  O31   O   OS    0  -0.627  -1.7192  -7.6464   4.4949
 HBM  O32   O   OS    0  -0.619  -1.4673  -5.7339   6.1095
 HBM  O33   O   O     0  -0.461  -2.2160  -0.8506   1.3369
 HBM  O34   O   OH1   0  -0.600   3.9830  -1.5751   2.5894
 HBM  H2    H   HCR6  0   0.233   0.6877   1.4785   2.6756
 HBM  H11   H   HCR6  0   0.257  -0.7320  -4.7663  -0.4909
 HBM  H3    H   HCR6  0   0.250   3.0241   0.8330   2.8802
 HBM  HN7   H   HNR5  0   0.411  -1.2631  -3.0070   1.4752
 HBM  H12   H   HCR6  0   0.265  -1.4739  -7.0411  -1.0398
 HBM  H14   H   HCR6  0   0.287   0.3517  -8.4861   2.5633
 HBM  HN19  H   HNH1  0   0.373  -1.3341   1.1972   3.5432
 HBM  H201  H   HCH2  0   0.258  -3.9515   0.6088   2.3051
 HBM  H202  H   HCH2  0   0.249  -3.6008   1.9943   3.3257
 HBM  H211  H   HCH2  0   0.235  -3.2887   0.5828   5.2903
 HBM  H212  H   HCH2  0   0.248  -4.8494   0.2466   4.5624
 HBM  H23   H   HCR6  0   0.229  -5.1761  -1.8890   3.2576
 HBM  H24   H   HCR6  0   0.229  -4.5014  -4.2289   2.9642
 HBM  H26   H   HCR6  0   0.263  -0.7829  -3.4024   4.9182
 HBM  H27   H   HCR6  0   0.227  -1.4998  -1.0846   5.2915
 HBM  HN28  H   HNC1  0   0.384  -2.5472  -5.7553   2.8935
 HBM  H301  H   HCH3  0   0.259  -4.4523  -6.9637   4.6783
 HBM  H302  H   HCH3  0   0.292  -3.9163  -7.2277   6.3579
 HBM  H303  H   HCH3  0   0.279  -4.2836  -5.5799   5.7936
 HBM  HO34  H   HOH1  0   0.457   4.0930  -2.5221   2.4329

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
 HBM  C2   C1    aromatic  1.388  0.020  1.388
 HBM  C2   C3    aromatic  1.399  0.020  1.399
 HBM  C2   H2    single    0.930  0.020  1.080
 HBM  C4   C5    aromatic  1.399  0.020  1.399
 HBM  C4   O34   single    1.338  0.020  1.338
 HBM  C4   C3    aromatic  1.388  0.020  1.388
 HBM  C6   N7    aromatic  1.362  0.020  1.362
 HBM  C6   C5    aromatic  1.397  0.020  1.397
 HBM  C6   C1    aromatic  1.398  0.020  1.398
 HBM  C10  C11   aromatic  1.394  0.020  1.394
 HBM  C10  C15   aromatic  1.394  0.020  1.394
 HBM  C10  C8    single    1.465  0.020  1.465
 HBM  C11  C12   aromatic  1.384  0.020  1.384
 HBM  C11  H11   single    0.930  0.020  1.080
 HBM  C1   C18   single    1.481  0.020  1.481
 HBM  C3   H3    single    0.930  0.020  1.080
 HBM  C5   N9    aromatic  1.370  0.020  1.370
 HBM  N7   C8    aromatic  1.361  0.020  1.361
 HBM  N7   HN7   single    0.860  0.020  1.020
 HBM  C8   N9    aromatic  1.304  0.020  1.304
 HBM  C12  C13   aromatic  1.385  0.020  1.385
 HBM  C12  H12   single    0.930  0.020  1.080
 HBM  C13  CL16  single    1.728  0.020  1.728
 HBM  C13  C14   aromatic  1.385  0.020  1.385
 HBM  C14  C15   aromatic  1.385  0.020  1.385
 HBM  C14  H14   single    0.930  0.020  1.080
 HBM  C15  CL17  single    1.723  0.020  1.723
 HBM  C18  N19   single    1.348  0.020  1.348
 HBM  C18  O33   double    1.226  0.020  1.226
 HBM  N19  C20   single    1.446  0.020  1.446
 HBM  N19  HN19  single    0.890  0.020  1.040
 HBM  C20  C21   single    1.536  0.020  1.536
 HBM  C20  H201  single    0.970  0.020  1.090
 HBM  C20  H202  single    0.970  0.020  1.090
 HBM  C21  C22   single    1.502  0.020  1.502
 HBM  C21  H211  single    0.970  0.020  1.090
 HBM  C21  H212  single    0.970  0.020  1.090
 HBM  C22  C23   aromatic  1.392  0.020  1.392
 HBM  C22  C27   aromatic  1.393  0.020  1.393
 HBM  C23  C24   aromatic  1.385  0.020  1.385
 HBM  C23  H23   single    0.930  0.020  1.080
 HBM  C24  C25   aromatic  1.392  0.020  1.392
 HBM  C24  H24   single    0.930  0.020  1.080
 HBM  C25  N28   single    1.419  0.020  1.419
 HBM  C25  C26   aromatic  1.389  0.020  1.389
 HBM  C26  C27   aromatic  1.387  0.020  1.387
 HBM  C26  H26   single    0.930  0.020  1.080
 HBM  C27  H27   single    0.930  0.020  1.080
 HBM  N28  S29   single    1.664  0.020  1.664
 HBM  N28  HN28  single    0.890  0.020  1.040
 HBM  S29  O31   double    1.452  0.020  1.452
 HBM  S29  C30   single    1.779  0.020  1.779
 HBM  S29  O32   double    1.452  0.020  1.452
 HBM  C30  H301  single    0.970  0.020  1.090
 HBM  C30  H302  single    0.970  0.020  1.090
 HBM  C30  H303  single    0.970  0.020  1.090
 HBM  O34  HO34  single    0.850  0.020  0.980

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
 HBM  H2    C2   C3    117.52  3.000
 HBM  H2    C2   C1    119.75  3.000
 HBM  C3    C2   C1    122.72  3.000
 HBM  O34   C4   C5    121.98  3.000
 HBM  O34   C4   C3    120.48  3.000
 HBM  C5    C4   C3    117.54  3.000
 HBM  N7    C6   C5    104.19  3.000
 HBM  C5    C6   C1    122.92  3.000
 HBM  N7    C6   C1    132.76  3.000
 HBM  C15   C10  C8    122.54  3.000
 HBM  C8    C10  C11   119.30  3.000
 HBM  C15   C10  C11   118.13  3.000
 HBM  H11   C11  C12   118.94  3.000
 HBM  H11   C11  C10   119.47  3.000
 HBM  C12   C11  C10   121.58  3.000
 HBM  C18   C1   C6    118.41  3.000
 HBM  C18   C1   C2    126.11  3.000
 HBM  C6    C1   C2    115.43  3.000
 HBM  H3    C3   C4    119.48  3.000
 HBM  H3    C3   C2    119.52  3.000
 HBM  C4    C3   C2    120.99  3.000
 HBM  N9    C5   C6    110.77  3.000
 HBM  N9    C5   C4    128.92  3.000
 HBM  C6    C5   C4    120.30  3.000
 HBM  HN7   N7   C8    127.13  3.000
 HBM  HN7   N7   C6    125.05  3.000
 HBM  C8    N7   C6    107.68  3.000
 HBM  N9    C8   N7    112.58  3.000
 HBM  N9    C8   C10   126.63  3.000
 HBM  N7    C8   C10   120.78  3.000
 HBM  C8    N9   C5    104.76  3.000
 HBM  H12   C12  C13   120.93  3.000
 HBM  H12   C12  C11   120.42  3.000
 HBM  C13   C12  C11   118.64  3.000
 HBM  CL16  C13  C14   118.98  3.000
 HBM  C14   C13  C12   121.43  3.000
 HBM  CL16  C13  C12   119.59  3.000
 HBM  H14   C14  C15   120.35  3.000
 HBM  H14   C14  C13   120.77  3.000
 HBM  C15   C14  C13   118.87  3.000
 HBM  CL17  C15  C14   117.86  3.000
 HBM  CL17  C15  C10   120.77  3.000
 HBM  C14   C15  C10   121.32  3.000
 HBM  O33   C18  N19   123.20  3.000
 HBM  O33   C18  C1    120.27  3.000
 HBM  N19   C18  C1    116.50  3.000
 HBM  HN19  N19  C20   115.84  3.000
 HBM  HN19  N19  C18   117.57  3.000
 HBM  C20   N19  C18   122.08  3.000
 HBM  H202  C20  H201  107.44  3.000
 HBM  H202  C20  C21   109.46  3.000
 HBM  H201  C20  C21   110.47  3.000
 HBM  H202  C20  N19   108.91  3.000
 HBM  H201  C20  N19   108.77  3.000
 HBM  C21   C20  N19   111.68  3.000
 HBM  H212  C21  H211  106.82  3.000
 HBM  H212  C21  C22   110.79  3.000
 HBM  H211  C21  C22   109.96  3.000
 HBM  H212  C21  C20   108.11  3.000
 HBM  H211  C21  C20   108.89  3.000
 HBM  C22   C21  C20   112.09  3.000
 HBM  C27   C22  C23   118.07  3.000
 HBM  C27   C22  C21   120.87  3.000
 HBM  C23   C22  C21   120.93  3.000
 HBM  H23   C23  C24   119.13  3.000
 HBM  H23   C23  C22   119.75  3.000
 HBM  C24   C23  C22   121.12  3.000
 HBM  H24   C24  C25   120.01  3.000
 HBM  H24   C24  C23   119.88  3.000
 HBM  C25   C24  C23   120.10  3.000
 HBM  N28   C25  C26   119.82  3.000
 HBM  C26   C25  C24   119.49  3.000
 HBM  N28   C25  C24   120.67  3.000
 HBM  H26   C26  C27   120.26  3.000
 HBM  H26   C26  C25   119.93  3.000
 HBM  C27   C26  C25   119.79  3.000
 HBM  H27   C27  C26   118.87  3.000
 HBM  H27   C27  C22   119.73  3.000
 HBM  C26   C27  C22   121.40  3.000
 HBM  HN28  N28  S29   111.36  3.000
 HBM  HN28  N28  C25   114.98  3.000
 HBM  S29   N28  C25   119.34  3.000
 HBM  O32   S29  O31   120.02  3.000
 HBM  O32   S29  C30   107.89  3.000
 HBM  O31   S29  C30   108.43  3.000
 HBM  O32   S29  N28   107.57  3.000
 HBM  C30   S29  N28   105.89  3.000
 HBM  O31   S29  N28   106.22  3.000
 HBM  H303  C30  H302  109.74  3.000
 HBM  H303  C30  H301  110.32  3.000
 HBM  H302  C30  H301  110.00  3.000
 HBM  H303  C30  S29   109.67  3.000
 HBM  H302  C30  S29   107.84  3.000
 HBM  H301  C30  S29   109.24  3.000
 HBM  HO34  O34  C4    109.90  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
 HBM  CONST_01  N7    C6   C1   C2   180.00   0.0  0
 HBM  CONST_02  C5    C6   C1   C2     0.00   0.0  0
 HBM  CONST_03  C5    C4   C3   C2     0.00   0.0  0
 HBM  CONST_04  N7    C6   C5   C4   180.00   0.0  0
 HBM  CONST_05  C1    C6   C5   C4     0.00   0.0  0
 HBM  CONST_06  C8    N9   C5   C4   180.00   0.0  0
 HBM  CONST_07  C1    C2   C3   C4     0.00   0.0  0
 HBM  CONST_08  C10   C8   N7   C6   180.00   0.0  0
 HBM  CONST_09  N9    C8   N7   C6     0.00   0.0  0
 HBM  CONST_10  C3    C4   C5   C6     0.00   0.0  0
 HBM  CONST_11  C8    N9   C5   C6     0.00   0.0  0
 HBM  CONST_12  C3    C2   C1   C6     0.00   0.0  0
 HBM  CONST_13  C13   C12  C11  C10    0.00   0.0  0
 HBM  CONST_14  C13   C14  C15  C10    0.00   0.0  0
 HBM  CONST_15  C5    N9   C8   C10  180.00   0.0  0
 HBM  CONST_16  C14   C15  C10  C11    0.00   0.0  0
 HBM  CONST_19  C14   C13  C12  C11    0.00   0.0  0
 HBM  CONST_20  C8    N7   C6   C1   180.00   0.0  0
 HBM  CONST_21  N9    C5   C6   C1   180.00   0.0  0
 HBM  CONST_22  N9    C5   C4   C3   180.00   0.0  0
 HBM  CONST_23  C8    N7   C6   C5     0.00   0.0  0
 HBM  CONST_24  N7    C8   N9   C5     0.00   0.0  0
 HBM  CONST_25  N9    C5   C6   N7     0.00   0.0  0
 HBM  CONST_27  C12   C11  C10  C8   180.00   0.0  0
 HBM  CONST_28  C14   C15  C10  C8   180.00   0.0  0
 HBM  CONST_30  C15   C10  C11  C12    0.00   0.0  0
 HBM  CONST_31  C15   C14  C13  C12    0.00   0.0  0
 HBM  CONST_32  C25   C24  C23  C22    0.00   0.0  0
 HBM  CONST_33  C25   C26  C27  C22    0.00   0.0  0
 HBM  CONST_34  C26   C27  C22  C23    0.00   0.0  0
 HBM  CONST_35  C26   C25  C24  C23    0.00   0.0  0
 HBM  CONST_36  C27   C22  C23  C24    0.00   0.0  0
 HBM  CONST_37  C27   C26  C25  C24    0.00   0.0  0
 HBM  CONST_38  O34   C4   C3   C2   180.00   0.0  0
 HBM  CONST_39  O34   C4   C5   C6   180.00   0.0  0
 HBM  CONST_40  CL17  C15  C10  C11  180.00   0.0  0
 HBM  CONST_41  CL16  C13  C12  C11  180.00   0.0  0
 HBM  CONST_42  C18   C1   C2   C3   180.00   0.0  0
 HBM  CONST_43  C18   C1   C6   C5   180.00   0.0  0
 HBM  CONST_44  C18   C1   C6   N7     0.00   0.0  0
 HBM  CONST_45  CL17  C15  C10  C8     0.00   0.0  0
 HBM  CONST_46  O34   C4   C5   N9     0.00   0.0  0
 HBM  CONST_47  CL17  C15  C14  C13  180.00   0.0  0
 HBM  CONST_48  CL16  C13  C14  C15  180.00   0.0  0
 HBM  CONST_49  C24   C23  C22  C21  180.00   0.0  0
 HBM  CONST_50  C26   C27  C22  C21  180.00   0.0  0
 HBM  CONST_51  N28   C25  C24  C23  180.00   0.0  0
 HBM  CONST_52  N28   C25  C26  C27  180.00   0.0  0
 HBM  CONST_53  H2    C2   C3   C4   180.00   0.0  0
 HBM  CONST_54  H12   C12  C11  C10  180.00   0.0  0
 HBM  CONST_55  H14   C14  C15  C10  180.00   0.0  0
 HBM  CONST_56  HN7   N7   C8   C10    0.00   0.0  0
 HBM  CONST_57  H3    C3   C2   C1   180.00   0.0  0
 HBM  CONST_58  H11   C11  C10  C8     0.00   0.0  0
 HBM  CONST_59  H24   C24  C23  C22  180.00   0.0  0
 HBM  CONST_60  H26   C26  C27  C22  180.00   0.0  0
 HBM  CONST_61  H27   C27  C22  C23  180.00   0.0  0
 HBM  CONST_62  H23   C23  C24  C25  180.00   0.0  0
 HBM  CONST_67  HN19  N19  C18  C1     0.00   0.0  0
 HBM  Var_01    N19   C18  C1   C2   -28.38  30.0  2
 HBM  Var_02    C23   C22  C21  C20  -83.79  30.0  2
 HBM  Var_03    C22   C21  C20  N19  -55.04  30.0  3
 HBM  Var_04    O31   S29  N28  C25  179.65  30.0  3
 HBM  Var_05    C21   C20  N19  C18   89.42  30.0  3
 HBM  Var_06    H301  C30  S29  N28   61.20  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
 HBM  plan-1  C10   0.020
 HBM  plan-1  C11   0.020
 HBM  plan-1  C8    0.020
 HBM  plan-1  C12   0.020
 HBM  plan-1  C13   0.020
 HBM  plan-1  C14   0.020
 HBM  plan-1  C15   0.020
 HBM  plan-1  CL16  0.020
 HBM  plan-1  CL17  0.020
 HBM  plan-1  H11   0.020
 HBM  plan-1  H12   0.020
 HBM  plan-1  H14   0.020
 HBM  plan-2  C21   0.020
 HBM  plan-2  C22   0.020
 HBM  plan-2  C23   0.020
 HBM  plan-2  C24   0.020
 HBM  plan-2  C25   0.020
 HBM  plan-2  C26   0.020
 HBM  plan-2  C27   0.020
 HBM  plan-2  N28   0.020
 HBM  plan-2  H23   0.020
 HBM  plan-2  H24   0.020
 HBM  plan-2  H26   0.020
 HBM  plan-2  H27   0.020
 HBM  plan-3  C2    0.020
 HBM  plan-3  C4    0.020
 HBM  plan-3  C6    0.020
 HBM  plan-3  C10   0.020
 HBM  plan-3  C1    0.020
 HBM  plan-3  C3    0.020
 HBM  plan-3  C5    0.020
 HBM  plan-3  N7    0.020
 HBM  plan-3  C8    0.020
 HBM  plan-3  N9    0.020
 HBM  plan-3  C18   0.020
 HBM  plan-3  O34   0.020
 HBM  plan-3  H2    0.020
 HBM  plan-3  H3    0.020
 HBM  plan-3  HN7   0.020
 HBM  plan-4  C1    0.020
 HBM  plan-4  C18   0.020
 HBM  plan-4  N19   0.020
 HBM  plan-4  C20   0.020
 HBM  plan-4  O33   0.020
 HBM  plan-4  HN19  0.020
 HBM  plan-5  C25   0.020
 HBM  plan-5  N28   0.020
 HBM  plan-5  S29   0.020
 HBM  plan-5  HN28  0.020

