# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 06:36:24 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-[(~{S})-methoxy-(4-phenylphenyl)methyl]-3~{H}-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H](c1[nH]c2cc(ccc2n1)C(O)=O)c3ccc(cc3)c4ccccc4
#
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
 UJ2  UJ2  "2-[(~{S})-methoxy-(4-phenylphenyl)methyl]-3~{H}-benzimidazole-5-carboxylic acid"  ligand  44  27  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UJ2
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
 UJ2  C4   C  CR6    0  -0.125  -1.1801  -2.3099   -3.9537
 UJ2  C5   C  CR16   0  -0.302  -2.0212  -2.9485   -3.0221
 UJ2  C6   C  CR16   0  -0.325  -2.4463  -4.2544   -3.1808
 UJ2  C8   C  CR5    0   0.410  -1.6649  -6.3579   -5.8692
 UJ2  C10  C  CH1    0  -0.113  -1.6031  -7.6118   -6.7045
 UJ2  C13  C  CR16   0  -0.297  -1.1262  -7.8631  -10.4599
 UJ2  C15  C  CR16   0  -0.296  -2.7464  -6.1519  -10.0405
 UJ2  C17  C  CR6    0   0.089  -2.1235  -6.6545  -12.4078
 UJ2  C20  C  CR16   0  -0.263  -2.3465  -6.1915  -15.1621
 UJ2  C21  C  CR16   0  -0.237  -2.3833  -5.1290  -14.2690
 UJ2  C22  C  CR16   0  -0.309  -2.2733  -5.3585  -12.9055
 UJ2  C1   C  CR56   0   0.124  -2.0242  -4.9479   -4.3149
 UJ2  N7   N  N      0  -0.466  -2.3004  -6.2281   -4.7386
 UJ2  N9   N  NR15   0  -0.696  -0.9719  -5.2425   -6.2169
 UJ2  C11  C  CR6    0   0.055  -1.7399  -7.3250   -8.1858
 UJ2  C12  C  CR16   0  -0.290  -1.0013  -8.0738   -9.0962
 UJ2  C16  C  CR16   0  -0.251  -2.6179  -6.3625   -8.6775
 UJ2  C14  C  CR6    0   0.080  -2.0005  -6.8952  -10.9561
 UJ2  C18  C  CR16   0  -0.307  -2.0882  -7.7143  -13.3159
 UJ2  C19  C  CR16   0  -0.239  -2.1992  -7.4853  -14.6794
 UJ2  O23  O  O2     0  -0.460  -2.4839  -8.5945   -6.2346
 UJ2  C2   C  CR56   0   0.364  -1.1836  -4.3067   -5.2369
 UJ2  C3   C  CR16   0  -0.366  -0.7479  -2.9992   -5.0785
 UJ2  C25  C  C      0   0.398  -0.7484  -0.8614   -3.7377
 UJ2  O26  O  O      0  -0.589   0.0485  -0.3884   -4.5716
 UJ2  O27  O  OC    -1  -0.588  -1.2340  -0.2767   -2.7500
 UJ2  H29  H  HCR6   0   0.236  -2.3422  -2.3902   -2.1532
 UJ2  H30  H  HCR6   0   0.242  -3.0907  -4.7267   -2.4498
 UJ2  H32  H  HCH1   0   0.288  -0.6046  -8.0377   -6.5466
 UJ2  H34  H  HCR6   0   0.256  -0.5164  -8.4412  -11.1423
 UJ2  H35  H  HCR6   0   0.256  -3.4493  -5.4080  -10.3935
 UJ2  H39  H  HCR6   0   0.256  -2.4317  -6.0131  -16.2261
 UJ2  H40  H  HCR6   0   0.256  -2.4907  -4.1160  -14.6349
 UJ2  H41  H  HCR6   0   0.254  -2.2813  -4.5159  -12.2245
 UJ2  H42  H  HCH3   0   0.241  -4.3886  -9.1946   -5.9763
 UJ2  H44  H  HCH3   0   0.213  -4.2290  -7.4423   -6.1448
 UJ2  H43  H  HCH3   0   0.215  -4.0872  -8.4903   -7.5697
 UJ2  H31  H  HNR5   0   0.417  -0.4178  -5.1172   -7.0500
 UJ2  H33  H  HCR6   0   0.259  -0.3052  -8.8214   -8.7347
 UJ2  H36  H  HCR6   0   0.266  -3.2151  -5.7652   -7.9988
 UJ2  H37  H  HCR6   0   0.254  -1.9921  -8.7307  -12.9547
 UJ2  H38  H  HCR6   0   0.256  -2.1765  -8.3217  -15.3660
 UJ2  H28  H  HCR6   0   0.249  -0.1002  -2.5241   -5.8032
 UJ2  C24  C  CH3    0  -0.414  -3.8562  -8.4046   -6.5041

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
 UJ2  C20  C19  aromatic  1.389  0.020  1.389
 UJ2  C20  C21  aromatic  1.388  0.020  1.388
 UJ2  C19  C18  aromatic  1.387  0.020  1.387
 UJ2  C21  C22  aromatic  1.387  0.020  1.387
 UJ2  C18  C17  aromatic  1.396  0.020  1.396
 UJ2  C22  C17  aromatic  1.396  0.020  1.396
 UJ2  C17  C14  single    1.477  0.020  1.477
 UJ2  C14  C13  aromatic  1.395  0.020  1.395
 UJ2  C14  C15  aromatic  1.396  0.020  1.396
 UJ2  C13  C12  aromatic  1.386  0.020  1.386
 UJ2  C15  C16  aromatic  1.385  0.020  1.385
 UJ2  C12  C11  aromatic  1.391  0.020  1.391
 UJ2  C16  C11  aromatic  1.392  0.020  1.392
 UJ2  C11  C10  single    1.515  0.020  1.515
 UJ2  C24  O23  single    1.411  0.020  1.411
 UJ2  C10  O23  single    1.401  0.020  1.401
 UJ2  C10  C8   single    1.508  0.020  1.508
 UJ2  N9   C8   aromatic  1.358  0.020  1.358
 UJ2  N9   C2   aromatic  1.371  0.020  1.371
 UJ2  C8   N7   aromatic  1.303  0.020  1.303
 UJ2  N7   C1   aromatic  1.377  0.020  1.377
 UJ2  C2   C3   aromatic  1.387  0.020  1.387
 UJ2  C2   C1   aromatic  1.403  0.020  1.403
 UJ2  C3   C4   aromatic  1.388  0.020  1.388
 UJ2  C1   C6   aromatic  1.395  0.020  1.395
 UJ2  O26  C25  deloc     1.247  0.020  1.247
 UJ2  C4   C25  single    1.527  0.020  1.527
 UJ2  C4   C5   aromatic  1.408  0.020  1.408
 UJ2  C6   C5   aromatic  1.382  0.020  1.382
 UJ2  C25  O27  deloc     1.246  0.020  1.246
 UJ2  C5   H29  single    0.930  0.020  1.080
 UJ2  C6   H30  single    0.930  0.020  1.080
 UJ2  C10  H32  single    0.970  0.020  1.090
 UJ2  C13  H34  single    0.930  0.020  1.080
 UJ2  C15  H35  single    0.930  0.020  1.080
 UJ2  C20  H39  single    0.930  0.020  1.080
 UJ2  C21  H40  single    0.930  0.020  1.080
 UJ2  C22  H41  single    0.930  0.020  1.080
 UJ2  C24  H42  single    0.970  0.020  1.090
 UJ2  C24  H44  single    0.970  0.020  1.090
 UJ2  C24  H43  single    0.970  0.020  1.090
 UJ2  N9   H31  single    0.860  0.020  1.020
 UJ2  C12  H33  single    0.930  0.020  1.080
 UJ2  C16  H36  single    0.930  0.020  1.080
 UJ2  C18  H37  single    0.930  0.020  1.080
 UJ2  C19  H38  single    0.930  0.020  1.080
 UJ2  C3   H28  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
 UJ2  C25  C4   C3   119.85  3.000
 UJ2  C25  C4   C5   120.36  3.000
 UJ2  C3   C4   C5   119.79  3.000
 UJ2  H29  C5   C6   119.24  3.000
 UJ2  H29  C5   C4   118.34  3.000
 UJ2  C6   C5   C4   122.42  3.000
 UJ2  H30  C6   C1   120.80  3.000
 UJ2  H30  C6   C5   121.17  3.000
 UJ2  C1   C6   C5   118.03  3.000
 UJ2  N9   C8   N7   112.89  3.000
 UJ2  N7   C8   C10  125.68  3.000
 UJ2  N9   C8   C10  121.34  3.000
 UJ2  H32  C10  O23  104.58  3.000
 UJ2  H32  C10  C11  107.24  3.000
 UJ2  O23  C10  C11  113.83  3.000
 UJ2  H32  C10  C8   106.29  3.000
 UJ2  O23  C10  C8   111.83  3.000
 UJ2  C11  C10  C8   112.36  3.000
 UJ2  H34  C13  C14  119.94  3.000
 UJ2  H34  C13  C12  119.24  3.000
 UJ2  C14  C13  C12  120.79  3.000
 UJ2  H35  C15  C14  119.94  3.000
 UJ2  H35  C15  C16  119.06  3.000
 UJ2  C14  C15  C16  121.00  3.000
 UJ2  C18  C17  C14  120.90  3.000
 UJ2  C14  C17  C22  120.71  3.000
 UJ2  C18  C17  C22  118.38  3.000
 UJ2  H39  C20  C19  120.24  3.000
 UJ2  H39  C20  C21  120.27  3.000
 UJ2  C19  C20  C21  119.48  3.000
 UJ2  H40  C21  C22  119.67  3.000
 UJ2  H40  C21  C20  120.09  3.000
 UJ2  C22  C21  C20  120.24  3.000
 UJ2  H41  C22  C21  119.25  3.000
 UJ2  H41  C22  C17  119.90  3.000
 UJ2  C21  C22  C17  120.83  3.000
 UJ2  C2   C1   N7   110.06  3.000
 UJ2  C2   C1   C6   119.25  3.000
 UJ2  N7   C1   C6   130.69  3.000
 UJ2  C1   N7   C8   105.17  3.000
 UJ2  H31  N9   C2   126.18  3.000
 UJ2  H31  N9   C8   126.43  3.000
 UJ2  C2   N9   C8   107.38  3.000
 UJ2  C16  C11  C12  118.41  3.000
 UJ2  C16  C11  C10  122.21  3.000
 UJ2  C12  C11  C10  119.34  3.000
 UJ2  H33  C12  C11  119.62  3.000
 UJ2  H33  C12  C13  119.42  3.000
 UJ2  C11  C12  C13  120.96  3.000
 UJ2  H36  C16  C11  120.49  3.000
 UJ2  H36  C16  C15  118.77  3.000
 UJ2  C11  C16  C15  120.74  3.000
 UJ2  C17  C14  C15  120.90  3.000
 UJ2  C15  C14  C13  118.10  3.000
 UJ2  C17  C14  C13  120.99  3.000
 UJ2  H37  C18  C19  119.33  3.000
 UJ2  H37  C18  C17  119.85  3.000
 UJ2  C19  C18  C17  120.81  3.000
 UJ2  H38  C19  C18  119.63  3.000
 UJ2  H38  C19  C20  120.11  3.000
 UJ2  C18  C19  C20  120.26  3.000
 UJ2  C24  O23  C10  116.93  3.000
 UJ2  C3   C2   N9   132.55  3.000
 UJ2  C3   C2   C1   122.95  3.000
 UJ2  N9   C2   C1   104.49  3.000
 UJ2  H28  C3   C2   121.69  3.000
 UJ2  H28  C3   C4   120.74  3.000
 UJ2  C2   C3   C4   117.56  3.000
 UJ2  O27  C25  O26  126.96  3.000
 UJ2  O27  C25  C4   116.55  3.000
 UJ2  O26  C25  C4   116.49  3.000
 UJ2  H43  C24  H44  108.50  3.000
 UJ2  H43  C24  H42  108.19  3.000
 UJ2  H44  C24  H42  108.22  3.000
 UJ2  H43  C24  O23  112.39  3.000
 UJ2  H44  C24  O23  112.79  3.000
 UJ2  H42  C24  O23  106.57  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
 UJ2  CONST_01  N9   C2   C3   C4    180.00   0.0  0
 UJ2  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 UJ2  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 UJ2  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 UJ2  CONST_05  N7   C1   C6   C5    180.00   0.0  0
 UJ2  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 UJ2  CONST_07  C8   N7   C1   C6    180.00   0.0  0
 UJ2  CONST_08  N9   C2   C1   C6    180.00   0.0  0
 UJ2  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 UJ2  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 UJ2  CONST_11  C3   C2   N9   C8    180.00   0.0  0
 UJ2  CONST_12  C1   C2   N9   C8      0.00   0.0  0
 UJ2  CONST_13  C2   C1   N7   C8      0.00   0.0  0
 UJ2  CONST_16  C16  C15  C14  C13     0.00   0.0  0
 UJ2  CONST_17  C16  C11  C12  C13     0.00   0.0  0
 UJ2  CONST_20  C12  C13  C14  C15     0.00   0.0  0
 UJ2  CONST_21  C12  C11  C16  C15     0.00   0.0  0
 UJ2  CONST_22  C20  C19  C18  C17     0.00   0.0  0
 UJ2  CONST_23  C20  C21  C22  C17     0.00   0.0  0
 UJ2  CONST_24  C12  C13  C14  C17   180.00   0.0  0
 UJ2  CONST_25  C16  C15  C14  C17   180.00   0.0  0
 UJ2  CONST_26  C18  C19  C20  C21     0.00   0.0  0
 UJ2  CONST_27  C18  C17  C22  C21     0.00   0.0  0
 UJ2  CONST_28  C14  C17  C22  C21   180.00   0.0  0
 UJ2  CONST_29  C19  C20  C21  C22     0.00   0.0  0
 UJ2  CONST_30  C19  C18  C17  C22     0.00   0.0  0
 UJ2  CONST_31  N9   C8   N7   C1      0.00   0.0  0
 UJ2  CONST_32  C2   N9   C8   N7      0.00   0.0  0
 UJ2  CONST_33  N9   C2   C1   N7      0.00   0.0  0
 UJ2  CONST_34  C3   C2   C1   N7    180.00   0.0  0
 UJ2  CONST_35  C14  C13  C12  C11     0.00   0.0  0
 UJ2  CONST_36  C14  C15  C16  C11     0.00   0.0  0
 UJ2  CONST_37  C19  C18  C17  C14   180.00   0.0  0
 UJ2  CONST_38  C25  C4   C5   C6    180.00   0.0  0
 UJ2  CONST_39  C13  C12  C11  C10   180.00   0.0  0
 UJ2  CONST_40  C15  C16  C11  C10   180.00   0.0  0
 UJ2  CONST_41  C2   N9   C8   C10   180.00   0.0  0
 UJ2  CONST_42  C1   N7   C8   C10   180.00   0.0  0
 UJ2  CONST_43  C25  C4   C3   C2    180.00   0.0  0
 UJ2  CONST_44  H30  C6   C5   C4    180.00   0.0  0
 UJ2  CONST_45  H28  C3   C4   C5    180.00   0.0  0
 UJ2  CONST_46  H35  C15  C14  C13   180.00   0.0  0
 UJ2  CONST_47  H34  C13  C14  C15   180.00   0.0  0
 UJ2  CONST_48  H38  C19  C18  C17   180.00   0.0  0
 UJ2  CONST_49  H40  C21  C22  C17   180.00   0.0  0
 UJ2  CONST_50  H34  C13  C14  C17     0.00   0.0  0
 UJ2  CONST_51  H35  C15  C14  C17     0.00   0.0  0
 UJ2  CONST_52  H37  C18  C19  C20   180.00   0.0  0
 UJ2  CONST_53  H41  C22  C21  C20   180.00   0.0  0
 UJ2  CONST_54  H38  C19  C20  C21   180.00   0.0  0
 UJ2  CONST_55  H39  C20  C21  C22   180.00   0.0  0
 UJ2  CONST_56  H37  C18  C17  C22   180.00   0.0  0
 UJ2  CONST_57  H31  N9   C2   C1    180.00   0.0  0
 UJ2  CONST_58  H28  C3   C2   C1    180.00   0.0  0
 UJ2  CONST_59  H29  C5   C6   C1    180.00   0.0  0
 UJ2  CONST_60  H31  N9   C8   N7    180.00   0.0  0
 UJ2  CONST_61  H30  C6   C1   N7      0.00   0.0  0
 UJ2  CONST_62  H28  C3   C2   N9      0.00   0.0  0
 UJ2  CONST_63  H34  C13  C12  C11   180.00   0.0  0
 UJ2  CONST_64  H35  C15  C16  C11   180.00   0.0  0
 UJ2  CONST_65  H36  C16  C11  C12   180.00   0.0  0
 UJ2  CONST_66  H33  C12  C11  C16   180.00   0.0  0
 UJ2  CONST_67  H37  C18  C17  C14     0.00   0.0  0
 UJ2  CONST_68  H41  C22  C17  C14     0.00   0.0  0
 UJ2  CONST_69  H33  C12  C13  C14   180.00   0.0  0
 UJ2  CONST_70  H36  C16  C15  C14   180.00   0.0  0
 UJ2  CONST_71  H39  C20  C19  C18   180.00   0.0  0
 UJ2  CONST_72  H41  C22  C17  C18   180.00   0.0  0
 UJ2  CONST_73  H40  C21  C20  C19   180.00   0.0  0
 UJ2  CONST_74  H30  C6   C1   C2    180.00   0.0  0
 UJ2  CONST_75  H31  N9   C2   C3      0.00   0.0  0
 UJ2  CONST_76  H29  C5   C4   C3    180.00   0.0  0
 UJ2  Var_01    O26  C25  C4   C5    176.59  30.0  2
 UJ2  Var_02    O27  C25  C4   C5     -3.68  30.0  2
 UJ2  Var_03    O26  C25  C4   C3     -3.79  30.0  2
 UJ2  Var_04    O27  C25  C4   C3    175.94  30.0  2
 UJ2  Var_05    H42  C24  O23  C10  -173.86  30.0  3
 UJ2  Var_06    H44  C24  O23  C10   -55.25  30.0  3
 UJ2  Var_07    H43  C24  O23  C10    67.80  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
 UJ2  chir_01  C10  C11  O23  C8  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
 UJ2  plan-1  C17  0.020
 UJ2  plan-1  C20  0.020
 UJ2  plan-1  C21  0.020
 UJ2  plan-1  C22  0.020
 UJ2  plan-1  C14  0.020
 UJ2  plan-1  C18  0.020
 UJ2  plan-1  C19  0.020
 UJ2  plan-1  H39  0.020
 UJ2  plan-1  H40  0.020
 UJ2  plan-1  H41  0.020
 UJ2  plan-1  H37  0.020
 UJ2  plan-1  H38  0.020
 UJ2  plan-2  C10  0.020
 UJ2  plan-2  C13  0.020
 UJ2  plan-2  C15  0.020
 UJ2  plan-2  C17  0.020
 UJ2  plan-2  C11  0.020
 UJ2  plan-2  C12  0.020
 UJ2  plan-2  C16  0.020
 UJ2  plan-2  C14  0.020
 UJ2  plan-2  H34  0.020
 UJ2  plan-2  H35  0.020
 UJ2  plan-2  H33  0.020
 UJ2  plan-2  H36  0.020
 UJ2  plan-3  C4   0.020
 UJ2  plan-3  C5   0.020
 UJ2  plan-3  C6   0.020
 UJ2  plan-3  C8   0.020
 UJ2  plan-3  C10  0.020
 UJ2  plan-3  C1   0.020
 UJ2  plan-3  N7   0.020
 UJ2  plan-3  N9   0.020
 UJ2  plan-3  C2   0.020
 UJ2  plan-3  C3   0.020
 UJ2  plan-3  C25  0.020
 UJ2  plan-3  H29  0.020
 UJ2  plan-3  H30  0.020
 UJ2  plan-3  H31  0.020
 UJ2  plan-3  H28  0.020
 UJ2  plan-4  C4   0.020
 UJ2  plan-4  C25  0.020
 UJ2  plan-4  O26  0.020
 UJ2  plan-4  O27  0.020

