# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 06:15:29 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-[(~{S})-methoxy-(4-propan-2-ylphenyl)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)C(C)C
#
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
 UJ5  UJ5  "2-[(~{S})-methoxy-(4-propan-2-ylphenyl)methyl]-3~{H}-benzimidazole-5-carboxylic acid"  ligand  43  24  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UJ5
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
 UJ5  C4   C  CR5    0   0.416  5.0271   8.5314  -10.6409
 UJ5  C6   C  CR56   0   0.125  6.5936   7.1040  -10.8202
 UJ5  C7   C  CR56   0   0.361  5.4188   6.3692  -10.5948
 UJ5  C10  C  CR6    0  -0.125  6.6055   4.3139  -10.6709
 UJ5  C13  C  C      0   0.398  6.6462   2.7894  -10.5955
 UJ5  C17  C  CR16   0  -0.269  4.7163  10.6636  -12.9502
 UJ5  C20  C  CR16   0  -0.317  2.0954  10.2683  -13.7360
 UJ5  C21  C  CR16   0  -0.290  2.4874   9.9579  -12.4390
 UJ5  C24  C  CH3    0  -0.644  3.3394  10.3544  -17.1084
 UJ5  O2   O  O2     0  -0.467  4.9564  10.8745  -10.1030
 UJ5  C3   C  CH1    0  -0.084  4.2237   9.8061  -10.6259
 UJ5  N5   N  N      0  -0.461  6.3129   8.4502  -10.8450
 UJ5  C12  C  CR16   0  -0.325  7.8024   6.4248  -10.9742
 UJ5  C11  C  CR16   0  -0.301  7.7870   5.0449  -10.8996
 UJ5  N8   N  NR15   0  -0.697  4.4367   7.3209  -10.4836
 UJ5  C9   C  CR16   0  -0.365  5.4000   4.9839  -10.5139
 UJ5  O14  O  OC    -1  -0.589  5.5668   2.2142  -10.3547
 UJ5  O15  O  O      0  -0.588  7.7547   2.2514  -10.7822
 UJ5  C16  C  CR6    0   0.078  3.7989  10.1542  -12.0327
 UJ5  C18  C  CR16   0  -0.295  4.3179  10.9798  -14.2377
 UJ5  C19  C  CR6    0   0.163  2.9992  10.7881  -14.6550
 UJ5  C23  C  CH3    0  -0.642  2.6813  12.6493  -16.3050
 UJ5  H34  H  HCR6   0   0.247  5.7487  10.8148  -12.6616
 UJ5  H36  H  HCR6   0   0.246  1.0648  10.1097  -14.0321
 UJ5  H37  H  HCR6   0   0.249  1.7592   9.5654  -11.7387
 UJ5  H38  H  HCH1   0   0.239  1.5069  10.8737  -16.1476
 UJ5  H42  H  HCH3   0   0.230  3.2363   9.2796  -16.9553
 UJ5  H44  H  HCH3   0   0.229  2.9724  10.5874  -18.1091
 UJ5  H43  H  HCH3   0   0.221  4.4035  10.5961  -17.0837
 UJ5  H26  H  HCH3   0   0.241  5.7269  11.6831   -8.4181
 UJ5  H25  H  HCH3   0   0.211  4.2784  10.6996   -8.1433
 UJ5  H27  H  HCH3   0   0.214  5.8390   9.9180   -8.4669
 UJ5  H28  H  HCH1   0   0.255  3.3175   9.6214  -10.0269
 UJ5  H32  H  HCR6   0   0.242  8.7242   6.9660  -11.1478
 UJ5  H31  H  HCR6   0   0.236  8.7126   4.4980  -11.0182
 UJ5  H29  H  HNR5   0   0.417  3.4574   7.1568  -10.3054
 UJ5  H30  H  HCR6   0   0.249  4.4838   4.4371  -10.3346
 UJ5  H35  H  HCR6   0   0.248  5.0502  11.3812  -14.9287
 UJ5  H40  H  HCH3   0   0.230  2.1048  13.2198  -15.5760
 UJ5  H39  H  HCH3   0   0.220  3.7196  12.9807  -16.2441
 UJ5  H41  H  HCH3   0   0.229  2.3111  12.9042  -17.2993
 UJ5  C1   C  CH3    0  -0.410  5.2074  10.7750   -8.7194
 UJ5  C22  C  CH1    0  -0.325  2.5631  11.1454  -16.0563

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
 UJ5  C24  C22  single    1.528  0.020  1.528
 UJ5  C23  C22  single    1.529  0.020  1.529
 UJ5  C22  C19  single    1.510  0.020  1.510
 UJ5  C19  C18  aromatic  1.396  0.020  1.396
 UJ5  C19  C20  aromatic  1.390  0.020  1.390
 UJ5  C18  C17  aromatic  1.384  0.020  1.384
 UJ5  C20  C21  aromatic  1.390  0.020  1.390
 UJ5  C17  C16  aromatic  1.394  0.020  1.394
 UJ5  C21  C16  aromatic  1.387  0.020  1.387
 UJ5  C16  C3   single    1.510  0.020  1.510
 UJ5  O14  C13  deloc     1.246  0.020  1.246
 UJ5  C12  C11  aromatic  1.382  0.020  1.382
 UJ5  C12  C6   aromatic  1.395  0.020  1.395
 UJ5  C11  C10  aromatic  1.408  0.020  1.408
 UJ5  N5   C6   aromatic  1.375  0.020  1.375
 UJ5  N5   C4   aromatic  1.304  0.020  1.304
 UJ5  C6   C7   aromatic  1.404  0.020  1.404
 UJ5  C10  C13  single    1.527  0.020  1.527
 UJ5  C10  C9   aromatic  1.388  0.020  1.388
 UJ5  C13  O15  deloc     1.246  0.020  1.246
 UJ5  C4   C3   single    1.507  0.020  1.507
 UJ5  C4   N8   aromatic  1.356  0.020  1.356
 UJ5  C7   C9   aromatic  1.388  0.020  1.388
 UJ5  C7   N8   aromatic  1.372  0.020  1.372
 UJ5  C3   O2   single    1.397  0.020  1.397
 UJ5  O2   C1   single    1.410  0.020  1.410
 UJ5  C17  H34  single    0.930  0.020  1.080
 UJ5  C20  H36  single    0.930  0.020  1.080
 UJ5  C21  H37  single    0.930  0.020  1.080
 UJ5  C22  H38  single    0.970  0.020  1.090
 UJ5  C24  H42  single    0.970  0.020  1.090
 UJ5  C24  H44  single    0.970  0.020  1.090
 UJ5  C24  H43  single    0.970  0.020  1.090
 UJ5  C1   H26  single    0.970  0.020  1.090
 UJ5  C1   H25  single    0.970  0.020  1.090
 UJ5  C1   H27  single    0.970  0.020  1.090
 UJ5  C3   H28  single    0.970  0.020  1.090
 UJ5  C12  H32  single    0.930  0.020  1.080
 UJ5  C11  H31  single    0.930  0.020  1.080
 UJ5  N8   H29  single    0.860  0.020  1.020
 UJ5  C9   H30  single    0.930  0.020  1.080
 UJ5  C18  H35  single    0.930  0.020  1.080
 UJ5  C23  H40  single    0.970  0.020  1.090
 UJ5  C23  H39  single    0.970  0.020  1.090
 UJ5  C23  H41  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
 UJ5  N8   C4   N5   113.06  3.000
 UJ5  N8   C4   C3   121.46  3.000
 UJ5  N5   C4   C3   125.43  3.000
 UJ5  C12  C6   N5   130.64  3.000
 UJ5  N5   C6   C7   110.15  3.000
 UJ5  C12  C6   C7   119.21  3.000
 UJ5  C9   C7   N8   132.69  3.000
 UJ5  N8   C7   C6   104.41  3.000
 UJ5  C9   C7   C6   122.90  3.000
 UJ5  C9   C10  C11  119.77  3.000
 UJ5  C9   C10  C13  119.97  3.000
 UJ5  C11  C10  C13  120.27  3.000
 UJ5  O15  C13  O14  126.87  3.000
 UJ5  O15  C13  C10  116.57  3.000
 UJ5  O14  C13  C10  116.56  3.000
 UJ5  H34  C17  C18  119.37  3.000
 UJ5  H34  C17  C16  120.21  3.000
 UJ5  C18  C17  C16  120.42  3.000
 UJ5  H36  C20  C19  119.50  3.000
 UJ5  H36  C20  C21  119.36  3.000
 UJ5  C19  C20  C21  121.14  3.000
 UJ5  H37  C21  C16  119.82  3.000
 UJ5  H37  C21  C20  119.62  3.000
 UJ5  C16  C21  C20  120.55  3.000
 UJ5  H43  C24  H44  107.54  3.000
 UJ5  H43  C24  H42  107.89  3.000
 UJ5  H44  C24  H42  107.91  3.000
 UJ5  H43  C24  C22  111.41  3.000
 UJ5  H44  C24  C22  110.49  3.000
 UJ5  H42  C24  C22  111.44  3.000
 UJ5  C3   O2   C1   114.00  3.000
 UJ5  H28  C3   C16  108.28  3.000
 UJ5  H28  C3   O2   110.86  3.000
 UJ5  C16  C3   O2   108.66  3.000
 UJ5  H28  C3   C4   107.58  3.000
 UJ5  O2   C3   C4   111.78  3.000
 UJ5  C16  C3   C4   109.61  3.000
 UJ5  C6   N5   C4   105.03  3.000
 UJ5  H32  C12  C11  121.14  3.000
 UJ5  H32  C12  C6   120.79  3.000
 UJ5  C11  C12  C6   118.07  3.000
 UJ5  H31  C11  C12  119.30  3.000
 UJ5  H31  C11  C10  118.25  3.000
 UJ5  C12  C11  C10  122.44  3.000
 UJ5  H29  N8   C7   126.60  3.000
 UJ5  H29  N8   C4   126.04  3.000
 UJ5  C7   N8   C4   107.35  3.000
 UJ5  H30  C9   C10  120.68  3.000
 UJ5  H30  C9   C7   121.71  3.000
 UJ5  C10  C9   C7   117.61  3.000
 UJ5  C3   C16  C21  120.41  3.000
 UJ5  C3   C16  C17  120.82  3.000
 UJ5  C21  C16  C17  118.77  3.000
 UJ5  H35  C18  C19  119.89  3.000
 UJ5  H35  C18  C17  118.89  3.000
 UJ5  C19  C18  C17  121.22  3.000
 UJ5  C18  C19  C22  121.16  3.000
 UJ5  C18  C19  C20  117.90  3.000
 UJ5  C22  C19  C20  120.94  3.000
 UJ5  H41  C23  H39  107.62  3.000
 UJ5  H41  C23  H40  107.91  3.000
 UJ5  H39  C23  H40  107.86  3.000
 UJ5  H41  C23  C22  110.60  3.000
 UJ5  H39  C23  C22  111.29  3.000
 UJ5  H40  C23  C22  111.41  3.000
 UJ5  H27  C1   H25  108.31  3.000
 UJ5  H27  C1   H26  108.30  3.000
 UJ5  H25  C1   H26  108.45  3.000
 UJ5  H27  C1   O2   112.62  3.000
 UJ5  H25  C1   O2   111.72  3.000
 UJ5  H26  C1   O2   107.32  3.000
 UJ5  H38  C22  C23  107.78  3.000
 UJ5  H38  C22  C19  107.30  3.000
 UJ5  C23  C22  C19  111.18  3.000
 UJ5  H38  C22  C24  107.71  3.000
 UJ5  C19  C22  C24  111.69  3.000
 UJ5  C23  C22  C24  110.97  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
 UJ5  CONST_01  C12  C6   N5   C4    180.00   0.0  0
 UJ5  CONST_02  C7   C6   N5   C4      0.00   0.0  0
 UJ5  CONST_03  C6   C7   N8   C4      0.00   0.0  0
 UJ5  CONST_04  C9   C7   N8   C4    180.00   0.0  0
 UJ5  CONST_05  C10  C11  C12  C6      0.00   0.0  0
 UJ5  CONST_06  N8   C4   N5   C6      0.00   0.0  0
 UJ5  CONST_07  C10  C9   C7   C6      0.00   0.0  0
 UJ5  CONST_08  C11  C12  C6   C7      0.00   0.0  0
 UJ5  CONST_09  C11  C10  C9   C7      0.00   0.0  0
 UJ5  CONST_10  N5   C4   N8   C7      0.00   0.0  0
 UJ5  CONST_11  N8   C7   C9   C10   180.00   0.0  0
 UJ5  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 UJ5  CONST_13  C20  C21  C16  C17     0.00   0.0  0
 UJ5  CONST_14  C18  C19  C20  C21     0.00   0.0  0
 UJ5  CONST_15  C18  C17  C16  C21     0.00   0.0  0
 UJ5  CONST_16  C11  C12  C6   N5    180.00   0.0  0
 UJ5  CONST_17  C9   C7   C6   N5    180.00   0.0  0
 UJ5  CONST_18  N8   C7   C6   N5      0.00   0.0  0
 UJ5  CONST_19  C9   C10  C11  C12     0.00   0.0  0
 UJ5  CONST_20  C9   C7   C6   C12     0.00   0.0  0
 UJ5  CONST_21  N8   C7   C6   C12   180.00   0.0  0
 UJ5  CONST_22  C19  C18  C17  C16     0.00   0.0  0
 UJ5  CONST_23  C19  C20  C21  C16     0.00   0.0  0
 UJ5  CONST_24  C3   C4   N5   C6    180.00   0.0  0
 UJ5  CONST_25  C13  C10  C9   C7    180.00   0.0  0
 UJ5  CONST_26  C3   C4   N8   C7    180.00   0.0  0
 UJ5  CONST_27  C12  C11  C10  C13   180.00   0.0  0
 UJ5  CONST_28  C22  C19  C18  C17   180.00   0.0  0
 UJ5  CONST_29  C3   C16  C21  C20   180.00   0.0  0
 UJ5  CONST_30  C22  C19  C20  C21   180.00   0.0  0
 UJ5  CONST_31  C18  C17  C16  C3    180.00   0.0  0
 UJ5  CONST_32  H31  C11  C12  C6    180.00   0.0  0
 UJ5  CONST_33  H30  C9   C7   C6    180.00   0.0  0
 UJ5  CONST_34  H29  N8   C7   C6    180.00   0.0  0
 UJ5  CONST_35  H32  C12  C6   C7    180.00   0.0  0
 UJ5  CONST_36  H32  C12  C11  C10   180.00   0.0  0
 UJ5  CONST_37  H37  C21  C16  C17   180.00   0.0  0
 UJ5  CONST_38  H35  C18  C19  C20   180.00   0.0  0
 UJ5  CONST_39  H34  C17  C16  C21   180.00   0.0  0
 UJ5  CONST_40  H32  C12  C6   N5      0.00   0.0  0
 UJ5  CONST_41  H29  N8   C4   N5    180.00   0.0  0
 UJ5  CONST_42  H30  C9   C10  C11   180.00   0.0  0
 UJ5  CONST_43  H30  C9   C7   N8      0.00   0.0  0
 UJ5  CONST_44  H31  C11  C10  C9    180.00   0.0  0
 UJ5  CONST_45  H29  N8   C7   C9      0.00   0.0  0
 UJ5  CONST_46  H35  C18  C17  C16   180.00   0.0  0
 UJ5  CONST_47  H36  C20  C21  C16   180.00   0.0  0
 UJ5  CONST_48  H36  C20  C19  C18   180.00   0.0  0
 UJ5  CONST_49  H34  C17  C18  C19   180.00   0.0  0
 UJ5  CONST_50  H37  C21  C20  C19   180.00   0.0  0
 UJ5  Var_01    C24  C22  C19  C20  -120.29  30.0  2
 UJ5  Var_02    C23  C22  C19  C20   115.16  30.0  2
 UJ5  Var_03    C18  C19  C22  C24    60.28  30.0  2
 UJ5  Var_04    O14  C13  C10  C11   178.13  30.0  2
 UJ5  Var_05    O15  C13  C10  C11    -1.92  30.0  2
 UJ5  Var_06    O14  C13  C10  C9     -1.88  30.0  2
 UJ5  Var_07    O15  C13  C10  C9    178.07  30.0  2
 UJ5  Var_08    C23  C22  C19  C18   -64.27  30.0  2
 UJ5  Var_09    H38  C22  C19  C20    -2.46  30.0  2
 UJ5  Var_10    H38  C22  C19  C18   178.11  30.0  2
 UJ5  Var_11    H42  C24  C22  C19    56.99  30.0  3
 UJ5  Var_12    H44  C24  C22  C19   176.95  30.0  3
 UJ5  Var_13    H43  C24  C22  C19   -63.57  30.0  3
 UJ5  Var_14    H40  C23  C22  C19   -56.78  30.0  3
 UJ5  Var_15    H39  C23  C22  C19    63.64  30.0  3
 UJ5  Var_16    H41  C23  C22  C19  -176.79  30.0  3
 UJ5  Var_17    H40  C23  C22  C24   178.26  30.0  3
 UJ5  Var_18    H39  C23  C22  C24   -61.32  30.0  3
 UJ5  Var_19    H41  C23  C22  C24    58.25  30.0  3
 UJ5  Var_20    H26  C1   O2   C3   -176.65  30.0  3
 UJ5  Var_21    H25  C1   O2   C3    -57.90  30.0  3
 UJ5  Var_22    H27  C1   O2   C3     64.26  30.0  3
 UJ5  Var_23    H42  C24  C22  C23  -178.34  30.0  3
 UJ5  Var_24    H44  C24  C22  C23   -58.38  30.0  3
 UJ5  Var_25    H43  C24  C22  C23    61.10  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
 UJ5  chir_01  C3  C16  C4  O2  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
 UJ5  plan-1  C17  0.020
 UJ5  plan-1  C20  0.020
 UJ5  plan-1  C21  0.020
 UJ5  plan-1  C3   0.020
 UJ5  plan-1  C16  0.020
 UJ5  plan-1  C18  0.020
 UJ5  plan-1  C19  0.020
 UJ5  plan-1  H34  0.020
 UJ5  plan-1  H36  0.020
 UJ5  plan-1  H37  0.020
 UJ5  plan-1  H35  0.020
 UJ5  plan-1  C22  0.020
 UJ5  plan-2  C4   0.020
 UJ5  plan-2  C6   0.020
 UJ5  plan-2  C7   0.020
 UJ5  plan-2  C10  0.020
 UJ5  plan-2  C13  0.020
 UJ5  plan-2  C3   0.020
 UJ5  plan-2  N5   0.020
 UJ5  plan-2  C12  0.020
 UJ5  plan-2  C11  0.020
 UJ5  plan-2  N8   0.020
 UJ5  plan-2  C9   0.020
 UJ5  plan-2  H32  0.020
 UJ5  plan-2  H31  0.020
 UJ5  plan-2  H29  0.020
 UJ5  plan-2  H30  0.020
 UJ5  plan-3  C10  0.020
 UJ5  plan-3  C13  0.020
 UJ5  plan-3  O14  0.020
 UJ5  plan-3  O15  0.020

