# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 04:29:43 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (~{S})-1~{H}-benzimidazol-2-yl-(4-propan-2-ylphenyl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1ccc(cc1)[C@H](O)c2[nH]c3ccccc3n2
#
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
 UJ8  UJ8  "(~{S})-1~{H}-benzimidazol-2-yl-(4-propan-2-ylphenyl)methanol"
  ligand  38  20  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UJ8
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
 UJ8  C4   C  CR6   0   0.162  -5.8151   -8.5190   -8.1571
 UJ8  C5   C  CR16  0  -0.316  -4.4287   -8.5695   -8.0663
 UJ8  C6   C  CR16  0  -0.287  -3.7678   -8.1442   -6.9206
 UJ8  C7   C  CR6   0   0.089  -4.4788   -7.6510   -5.8363
 UJ8  C8   C  CR16  0  -0.274  -5.8682   -7.5875   -5.9201
 UJ8  C10  C  CH1   0  -0.106  -3.7452   -7.1579   -4.6111
 UJ8  C15  C  CR16  0  -0.338  -2.6041   -2.4661   -5.5839
 UJ8  C17  C  CR16  0  -0.277  -4.2631   -1.2204   -4.3181
 UJ8  C2   C  CH1   0  -0.324  -6.5307   -9.0132   -9.3923
 UJ8  C1   C  CH3   0  -0.642  -7.3885  -10.2385   -9.0754
 UJ8  C3   C  CH3   0  -0.644  -7.3659   -7.9136  -10.0459
 UJ8  C9   C  CR16  0  -0.295  -6.5223   -8.0181   -7.0627
 UJ8  O11  O  OH1   0  -0.646  -4.4044   -7.6266   -3.4645
 UJ8  C12  C  CR5   0   0.395  -3.6899   -5.6545   -4.6404
 UJ8  N13  N  N     0  -0.462  -2.8311   -4.9556   -5.3284
 UJ8  C14  C  CR56  0   0.142  -3.1787   -3.6434   -5.1062
 UJ8  C16  C  CR16  0  -0.269  -3.1575   -1.2638   -5.1805
 UJ8  C18  C  CR16  0  -0.306  -4.8484   -2.3774   -3.8328
 UJ8  C19  C  CR56  0   0.334  -4.2875   -3.5803   -4.2445
 UJ8  N20  N  NR15  0  -0.684  -4.5881   -4.8889   -3.9729
 UJ8  H28  H  HCR6  0   0.247  -3.8526   -8.9544   -8.8998
 UJ8  H29  H  HCR6  0   0.250  -2.6867   -8.2038   -6.8742
 UJ8  H30  H  HCR6  0   0.251  -6.4514   -7.2026   -5.0925
 UJ8  H32  H  HCH1  0   0.263  -2.7086   -7.5131   -4.6653
 UJ8  H36  H  HCR6  0   0.252  -4.6676   -0.2602   -4.0260
 UJ8  H24  H  HCH1  0   0.239  -5.7642   -9.3197  -10.1106
 UJ8  H23  H  HCH3  0   0.230  -6.7915  -11.0402   -8.6389
 UJ8  H22  H  HCH3  0   0.220  -8.1851   -9.9932   -8.3707
 UJ8  H21  H  HCH3  0   0.229  -7.8572  -10.6244   -9.9822
 UJ8  H26  H  HCH3  0   0.230  -6.7522   -7.0534  -10.3161
 UJ8  H25  H  HCH3  0   0.229  -7.8404   -8.2833  -10.9564
 UJ8  H27  H  HCH3  0   0.220  -8.1588   -7.5629   -9.3826
 UJ8  H31  H  HCR6  0   0.248  -7.6041   -7.9621   -7.0979
 UJ8  H33  H  HOH1  0   0.462  -3.8536   -7.4486   -2.6939
 UJ8  H35  H  HCR6  0   0.250  -2.7310   -0.3348   -5.5357
 UJ8  H37  H  HCR6  0   0.263  -5.7005   -2.3425   -3.1666
 UJ8  H38  H  HNR5  0   0.417  -5.3173   -5.2284   -3.3647
 UJ8  H34  H  HCR6  0   0.251  -1.7500   -2.4958   -6.2485

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
 UJ8  C3   C2   single    1.528  0.020  1.528
 UJ8  C2   C1   single    1.529  0.020  1.529
 UJ8  C2   C4   single    1.511  0.020  1.511
 UJ8  C5   C4   aromatic  1.390  0.020  1.390
 UJ8  C5   C6   aromatic  1.389  0.020  1.389
 UJ8  C4   C9   aromatic  1.396  0.020  1.396
 UJ8  C6   C7   aromatic  1.387  0.020  1.387
 UJ8  C9   C8   aromatic  1.385  0.020  1.385
 UJ8  C7   C8   aromatic  1.393  0.020  1.393
 UJ8  C7   C10  single    1.511  0.020  1.511
 UJ8  C15  C16  aromatic  1.384  0.020  1.384
 UJ8  C15  C14  aromatic  1.394  0.020  1.394
 UJ8  C16  C17  aromatic  1.403  0.020  1.403
 UJ8  N13  C14  aromatic  1.376  0.020  1.376
 UJ8  N13  C12  aromatic  1.304  0.020  1.304
 UJ8  C14  C19  aromatic  1.406  0.020  1.406
 UJ8  C12  C10  single    1.505  0.020  1.505
 UJ8  C12  N20  aromatic  1.356  0.020  1.356
 UJ8  C17  C18  aromatic  1.384  0.020  1.384
 UJ8  C10  O11  single    1.403  0.020  1.403
 UJ8  C19  C18  aromatic  1.390  0.020  1.390
 UJ8  C19  N20  aromatic  1.370  0.020  1.370
 UJ8  C5   H28  single    0.930  0.020  1.080
 UJ8  C6   H29  single    0.930  0.020  1.080
 UJ8  C8   H30  single    0.930  0.020  1.080
 UJ8  C10  H32  single    0.970  0.020  1.090
 UJ8  C15  H34  single    0.930  0.020  1.080
 UJ8  C17  H36  single    0.930  0.020  1.080
 UJ8  C2   H24  single    0.970  0.020  1.090
 UJ8  C1   H23  single    0.970  0.020  1.090
 UJ8  C1   H22  single    0.970  0.020  1.090
 UJ8  C1   H21  single    0.970  0.020  1.090
 UJ8  C3   H26  single    0.970  0.020  1.090
 UJ8  C3   H25  single    0.970  0.020  1.090
 UJ8  C3   H27  single    0.970  0.020  1.090
 UJ8  C9   H31  single    0.930  0.020  1.080
 UJ8  O11  H33  single    0.850  0.020  0.980
 UJ8  C16  H35  single    0.930  0.020  1.080
 UJ8  C18  H37  single    0.930  0.020  1.080
 UJ8  N20  H38  single    0.860  0.020  1.020

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
 UJ8  C9   C4   C2   121.23  3.000
 UJ8  C9   C4   C5   117.84  3.000
 UJ8  C2   C4   C5   120.92  3.000
 UJ8  H28  C5   C6   119.34  3.000
 UJ8  H28  C5   C4   119.52  3.000
 UJ8  C6   C5   C4   121.14  3.000
 UJ8  H29  C6   C7   119.82  3.000
 UJ8  H29  C6   C5   119.54  3.000
 UJ8  C7   C6   C5   120.63  3.000
 UJ8  C10  C7   C8   121.21  3.000
 UJ8  C10  C7   C6   120.07  3.000
 UJ8  C8   C7   C6   118.70  3.000
 UJ8  H30  C8   C9   119.11  3.000
 UJ8  H30  C8   C7   120.47  3.000
 UJ8  C9   C8   C7   120.42  3.000
 UJ8  H32  C10  C12  106.73  3.000
 UJ8  H32  C10  O11  112.09  3.000
 UJ8  C12  C10  O11  111.52  3.000
 UJ8  H32  C10  C7   108.25  3.000
 UJ8  O11  C10  C7   108.99  3.000
 UJ8  C12  C10  C7   109.16  3.000
 UJ8  H34  C15  C16  121.22  3.000
 UJ8  H34  C15  C14  120.81  3.000
 UJ8  C16  C15  C14  117.96  3.000
 UJ8  H36  C17  C18  119.27  3.000
 UJ8  H36  C17  C16  119.20  3.000
 UJ8  C18  C17  C16  121.52  3.000
 UJ8  H24  C2   C3   107.68  3.000
 UJ8  H24  C2   C1   107.73  3.000
 UJ8  C3   C2   C1   111.02  3.000
 UJ8  H24  C2   C4   107.25  3.000
 UJ8  C1   C2   C4   111.01  3.000
 UJ8  C3   C2   C4   111.92  3.000
 UJ8  H21  C1   H22  107.61  3.000
 UJ8  H21  C1   H23  107.92  3.000
 UJ8  H22  C1   H23  107.84  3.000
 UJ8  H21  C1   C2   110.63  3.000
 UJ8  H22  C1   C2   111.29  3.000
 UJ8  H23  C1   C2   111.40  3.000
 UJ8  H27  C3   H25  107.46  3.000
 UJ8  H27  C3   H26  107.80  3.000
 UJ8  H25  C3   H26  107.77  3.000
 UJ8  H27  C3   C2   111.61  3.000
 UJ8  H25  C3   C2   110.54  3.000
 UJ8  H26  C3   C2   111.47  3.000
 UJ8  H31  C9   C8   118.82  3.000
 UJ8  H31  C9   C4   119.92  3.000
 UJ8  C8   C9   C4   121.27  3.000
 UJ8  H33  O11  C10  108.86  3.000
 UJ8  N20  C12  N13  113.17  3.000
 UJ8  N20  C12  C10  122.02  3.000
 UJ8  N13  C12  C10  124.76  3.000
 UJ8  C14  N13  C12  105.05  3.000
 UJ8  C19  C14  N13  109.95  3.000
 UJ8  C19  C14  C15  119.81  3.000
 UJ8  N13  C14  C15  130.24  3.000
 UJ8  H35  C16  C17  119.07  3.000
 UJ8  H35  C16  C15  119.51  3.000
 UJ8  C17  C16  C15  121.42  3.000
 UJ8  H37  C18  C19  121.88  3.000
 UJ8  H37  C18  C17  121.45  3.000
 UJ8  C19  C18  C17  116.67  3.000
 UJ8  N20  C19  C18  132.81  3.000
 UJ8  N20  C19  C14  104.58  3.000
 UJ8  C18  C19  C14  122.61  3.000
 UJ8  H38  N20  C19  126.85  3.000
 UJ8  H38  N20  C12  125.87  3.000
 UJ8  C19  N20  C12  107.25  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
 UJ8  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 UJ8  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 UJ8  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 UJ8  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 UJ8  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 UJ8  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 UJ8  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 UJ8  CONST_08  C12  N13  C14  C15   180.00   0.0  0
 UJ8  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 UJ8  CONST_10  N20  C19  C14  C15   180.00   0.0  0
 UJ8  CONST_11  C14  C15  C16  C17     0.00   0.0  0
 UJ8  CONST_12  C14  C19  C18  C17     0.00   0.0  0
 UJ8  CONST_13  N20  C19  C18  C17   180.00   0.0  0
 UJ8  CONST_14  C19  C14  N13  C12     0.00   0.0  0
 UJ8  CONST_15  C14  C19  N20  C12     0.00   0.0  0
 UJ8  CONST_16  C18  C19  N20  C12   180.00   0.0  0
 UJ8  CONST_17  C16  C15  C14  N13   180.00   0.0  0
 UJ8  CONST_18  C18  C19  C14  N13   180.00   0.0  0
 UJ8  CONST_19  N20  C19  C14  N13     0.00   0.0  0
 UJ8  CONST_20  C19  N20  C12  N13     0.00   0.0  0
 UJ8  CONST_21  N20  C12  N13  C14     0.00   0.0  0
 UJ8  CONST_22  C19  C14  C15  C16     0.00   0.0  0
 UJ8  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 UJ8  CONST_24  C10  C7   C6   C5    180.00   0.0  0
 UJ8  CONST_25  C2   C4   C5   C6    180.00   0.0  0
 UJ8  CONST_26  C2   C4   C9   C8    180.00   0.0  0
 UJ8  CONST_27  C9   C8   C7   C10   180.00   0.0  0
 UJ8  CONST_28  C14  N13  C12  C10   180.00   0.0  0
 UJ8  CONST_29  C19  N20  C12  C10   180.00   0.0  0
 UJ8  CONST_30  H29  C6   C5   C4    180.00   0.0  0
 UJ8  CONST_31  H30  C8   C9   C4    180.00   0.0  0
 UJ8  CONST_32  H31  C9   C4   C5    180.00   0.0  0
 UJ8  CONST_33  H30  C8   C7   C6    180.00   0.0  0
 UJ8  CONST_34  H28  C5   C6   C7    180.00   0.0  0
 UJ8  CONST_35  H31  C9   C8   C7    180.00   0.0  0
 UJ8  CONST_36  H29  C6   C7   C8    180.00   0.0  0
 UJ8  CONST_37  H36  C17  C16  C15   180.00   0.0  0
 UJ8  CONST_38  H34  C15  C16  C17   180.00   0.0  0
 UJ8  CONST_39  H28  C5   C4   C9    180.00   0.0  0
 UJ8  CONST_40  H34  C15  C14  N13     0.00   0.0  0
 UJ8  CONST_41  H38  N20  C12  N13   180.00   0.0  0
 UJ8  CONST_42  H35  C16  C15  C14   180.00   0.0  0
 UJ8  CONST_43  H37  C18  C19  C14   180.00   0.0  0
 UJ8  CONST_44  H38  N20  C19  C14   180.00   0.0  0
 UJ8  CONST_45  H37  C18  C17  C16   180.00   0.0  0
 UJ8  CONST_46  H35  C16  C17  C18   180.00   0.0  0
 UJ8  CONST_47  H38  N20  C19  C18     0.00   0.0  0
 UJ8  CONST_48  H34  C15  C14  C19   180.00   0.0  0
 UJ8  CONST_49  H36  C17  C18  C19   180.00   0.0  0
 UJ8  CONST_50  H37  C18  C19  N20     0.00   0.0  0
 UJ8  Var_01    C3   C2   C4   C5   -120.79  30.0  2
 UJ8  Var_02    C1   C2   C4   C5    114.54  30.0  2
 UJ8  Var_03    C9   C4   C2   C1    -64.39  30.0  2
 UJ8  Var_04    C9   C4   C2   C3     60.28  30.0  2
 UJ8  Var_05    H24  C2   C4   C5     -2.91  30.0  2
 UJ8  Var_06    H24  C2   C4   C9    178.16  30.0  2
 UJ8  Var_07    H26  C3   C2   C4     57.90  30.0  3
 UJ8  Var_08    H25  C3   C2   C4    177.74  30.0  3
 UJ8  Var_09    H27  C3   C2   C4    -62.71  30.0  3
 UJ8  Var_10    H23  C1   C2   C4    -56.73  30.0  3
 UJ8  Var_11    H22  C1   C2   C4     63.66  30.0  3
 UJ8  Var_12    H21  C1   C2   C4   -176.76  30.0  3
 UJ8  Var_13    H26  C3   C2   C1   -177.43  30.0  3
 UJ8  Var_14    H25  C3   C2   C1    -57.59  30.0  3
 UJ8  Var_15    H27  C3   C2   C1     61.95  30.0  3
 UJ8  Var_16    H23  C1   C2   C3    178.10  30.0  3
 UJ8  Var_17    H22  C1   C2   C3    -61.51  30.0  3
 UJ8  Var_18    H21  C1   C2   C3     58.06  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
 UJ8  chir_01  C10  C7  C12  O11  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
 UJ8  plan-1  C4   0.020
 UJ8  plan-1  C5   0.020
 UJ8  plan-1  C6   0.020
 UJ8  plan-1  C7   0.020
 UJ8  plan-1  C8   0.020
 UJ8  plan-1  C10  0.020
 UJ8  plan-1  C2   0.020
 UJ8  plan-1  C9   0.020
 UJ8  plan-1  H28  0.020
 UJ8  plan-1  H29  0.020
 UJ8  plan-1  H30  0.020
 UJ8  plan-1  H31  0.020
 UJ8  plan-2  C10  0.020
 UJ8  plan-2  C15  0.020
 UJ8  plan-2  C17  0.020
 UJ8  plan-2  C12  0.020
 UJ8  plan-2  N13  0.020
 UJ8  plan-2  C14  0.020
 UJ8  plan-2  C16  0.020
 UJ8  plan-2  C18  0.020
 UJ8  plan-2  C19  0.020
 UJ8  plan-2  N20  0.020
 UJ8  plan-2  H36  0.020
 UJ8  plan-2  H35  0.020
 UJ8  plan-2  H37  0.020
 UJ8  plan-2  H38  0.020
 UJ8  plan-2  H34  0.020

