# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:54:37 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-(2,4-dihydroxyphenyl)-1,3-dihydro-2H-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(N2C(=O)Nc3ccccc23)c(O)c1
#
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
 MEX  MEX  1-(2,4-dihydroxyphenyl)-1,3-dihydro-2H-benzimidazol-2-one  ligand  28  18  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MEX
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
 MEX  C1    C  CR16  0  -0.251  -1.5053  -0.0986   1.4924
 MEX  C2    C  CR6   0   0.174  -0.8522   0.1179   0.2883
 MEX  C3    C  CR6   0   0.364  -1.5465  -0.0540  -0.9111
 MEX  C4    C  CR16  0  -0.522  -2.8827  -0.4389  -0.8857
 MEX  C5    C  CR6   0   0.387  -3.5227  -0.6542   0.3313
 MEX  C6    C  CR16  0  -0.373  -2.8328  -0.4828   1.5314
 MEX  O7    O  OH1   0  -0.628  -4.8103  -1.0298   0.4010
 MEX  O8    O  OH1   0  -0.611  -0.8755   0.1647  -2.0495
 MEX  N9    N  NR5   0  -0.671   0.5078   0.4861   0.2535
 MEX  C10   C  CR56  0   0.322   1.5795  -0.3872   0.1841
 MEX  C11   C  CR56  0   0.326   2.7329   0.3947   0.0791
 MEX  N12   N  NR15  0  -0.747   2.3163   1.7088   0.0746
 MEX  C13   C  CR5   0   0.637   0.9524   1.7920   0.1669
 MEX  C14   C  CR16  0  -0.312   1.6408  -1.7655   0.2094
 MEX  C15   C  CR16  0  -0.276   2.9033  -2.3500   0.1270
 MEX  C16   C  CR16  0  -0.276   4.0534  -1.5729   0.0253
 MEX  C17   C  CR16  0  -0.310   3.9857  -0.1812  -0.0010
 MEX  O18   O  O     0  -0.492   0.2643   2.7936   0.1759
 MEX  H1    H  HCR6  0   0.271  -0.9575   0.0382   2.4161
 MEX  H4    H  HCR6  0   0.289  -3.4225  -0.5740  -1.8178
 MEX  H6    H  HCR6  0   0.267  -3.3322  -0.6517   2.4760
 MEX  HO7   H  HOH1  0   0.478  -5.1830  -1.1416  -0.4809
 MEX  HO8   H  HOH1  0   0.483  -1.4471   0.0251  -2.8136
 MEX  HN12  H  HNR5  0   0.419   2.9132   2.5170   0.0007
 MEX  H14   H  HCR6  0   0.269   0.7473  -2.3707   0.2889
 MEX  H15   H  HCR6  0   0.256   2.9877  -3.4284   0.1428
 MEX  H16   H  HCR6  0   0.256   5.0199  -2.0551  -0.0368
 MEX  H17   H  HCR6  0   0.269   4.8789   0.4239  -0.0833

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
 MEX  C2   C1    aromatic  1.387  0.020  1.387
 MEX  C1   C6    aromatic  1.383  0.020  1.383
 MEX  C1   H1    single    0.930  0.020  1.080
 MEX  N9   C2    single    1.409  0.020  1.409
 MEX  C2   C3    aromatic  1.396  0.020  1.396
 MEX  O8   C3    single    1.339  0.020  1.339
 MEX  C3   C4    aromatic  1.391  0.020  1.391
 MEX  C4   C5    aromatic  1.392  0.020  1.392
 MEX  C4   H4    single    0.930  0.020  1.080
 MEX  C6   C5    aromatic  1.395  0.020  1.395
 MEX  C5   O7    single    1.343  0.020  1.343
 MEX  C6   H6    single    0.930  0.020  1.080
 MEX  O7   HO7   single    0.850  0.020  0.980
 MEX  O8   HO8   single    0.850  0.020  0.980
 MEX  C13  N9    single    1.382  0.020  1.382
 MEX  C10  N9    single    1.384  0.020  1.384
 MEX  C11  C10   aromatic  1.397  0.020  1.397
 MEX  C10  C14   aromatic  1.380  0.020  1.380
 MEX  C17  C11   aromatic  1.381  0.020  1.381
 MEX  N12  C11   single    1.379  0.020  1.379
 MEX  N12  C13   single    1.370  0.020  1.370
 MEX  N12  HN12  single    0.860  0.020  1.020
 MEX  O18  C13   double    1.215  0.020  1.215
 MEX  C15  C14   aromatic  1.394  0.020  1.394
 MEX  C14  H14   single    0.930  0.020  1.080
 MEX  C16  C15   aromatic  1.392  0.020  1.392
 MEX  C15  H15   single    0.930  0.020  1.080
 MEX  C17  C16   aromatic  1.394  0.020  1.394
 MEX  C16  H16   single    0.930  0.020  1.080
 MEX  C17  H17   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
 MEX  H1    C1   C6   119.79  3.000
 MEX  H1    C1   C2   118.87  3.000
 MEX  C6    C1   C2   121.33  3.000
 MEX  N9    C2   C3   119.38  3.000
 MEX  C3    C2   C1   119.50  3.000
 MEX  N9    C2   C1   121.10  3.000
 MEX  O8    C3   C4   122.82  3.000
 MEX  C4    C3   C2   119.73  3.000
 MEX  O8    C3   C2   117.45  3.000
 MEX  H4    C4   C5   120.19  3.000
 MEX  H4    C4   C3   119.77  3.000
 MEX  C5    C4   C3   120.04  3.000
 MEX  O7    C5   C6   117.64  3.000
 MEX  O7    C5   C4   121.97  3.000
 MEX  C6    C5   C4   120.39  3.000
 MEX  H6    C6   C5   120.25  3.000
 MEX  H6    C6   C1   120.75  3.000
 MEX  C5    C6   C1   119.00  3.000
 MEX  HO7   O7   C5   110.83  3.000
 MEX  HO8   O8   C3   110.67  3.000
 MEX  C13   N9   C10  110.12  3.000
 MEX  C10   N9   C2   125.70  3.000
 MEX  C13   N9   C2   123.97  3.000
 MEX  C14   C10  C11  121.58  3.000
 MEX  C14   C10  N9   131.58  3.000
 MEX  C11   C10  N9   106.84  3.000
 MEX  C17   C11  N12  132.18  3.000
 MEX  N12   C11  C10  106.51  3.000
 MEX  C17   C11  C10  121.31  3.000
 MEX  HN12  N12  C13  123.11  3.000
 MEX  HN12  N12  C11  125.87  3.000
 MEX  C13   N12  C11  111.02  3.000
 MEX  O18   C13  N12  127.91  3.000
 MEX  O18   C13  N9   126.60  3.000
 MEX  N12   C13  N9   105.49  3.000
 MEX  H14   C14  C15  121.18  3.000
 MEX  H14   C14  C10  121.56  3.000
 MEX  C15   C14  C10  117.26  3.000
 MEX  H15   C15  C16  119.55  3.000
 MEX  H15   C15  C14  119.20  3.000
 MEX  C16   C15  C14  121.24  3.000
 MEX  H16   C16  C17  119.17  3.000
 MEX  H16   C16  C15  119.57  3.000
 MEX  C17   C16  C15  121.26  3.000
 MEX  H17   C17  C16  121.32  3.000
 MEX  H17   C17  C11  121.33  3.000
 MEX  C16   C17  C11  117.35  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
 MEX  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 MEX  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 MEX  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 MEX  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 MEX  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 MEX  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 MEX  CONST_07  C16   C17  C11  C10    0.00   0.0  0
 MEX  CONST_08  C16   C15  C14  C10    0.00   0.0  0
 MEX  CONST_09  C15   C14  C10  C11    0.00   0.0  0
 MEX  CONST_10  C15   C16  C17  C11    0.00   0.0  0
 MEX  CONST_11  C17   C11  C10  C14    0.00   0.0  0
 MEX  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 MEX  CONST_13  N9    C2   C3   C4   180.00   0.0  0
 MEX  CONST_14  N9    C2   C1   C6   180.00   0.0  0
 MEX  CONST_15  N12   C13  N9   C2   180.00   0.0  0
 MEX  CONST_16  C11   C10  N9   C2   180.00   0.0  0
 MEX  CONST_17  C11   N12  C13  N9     0.00   0.0  0
 MEX  CONST_18  N12   C11  C10  N9     0.00   0.0  0
 MEX  CONST_19  N12   C13  N9   C10    0.00   0.0  0
 MEX  CONST_20  C13   N12  C11  C10    0.00   0.0  0
 MEX  CONST_21  C13   N9   C10  C11    0.00   0.0  0
 MEX  CONST_22  O8    C3   C2   C1   180.00   0.0  0
 MEX  CONST_23  O7    C5   C6   C1   180.00   0.0  0
 MEX  CONST_24  O7    C5   C4   C3   180.00   0.0  0
 MEX  CONST_25  O8    C3   C4   C5   180.00   0.0  0
 MEX  CONST_26  N9    C2   C3   O8     0.00   0.0  0
 MEX  CONST_27  O18   C13  N9   C2     0.00   0.0  0
 MEX  CONST_28  O18   C13  N9   C10  180.00   0.0  0
 MEX  CONST_29  O18   C13  N12  C11  180.00   0.0  0
 MEX  CONST_30  H6    C6   C1   C2   180.00   0.0  0
 MEX  CONST_31  H4    C4   C3   C2   180.00   0.0  0
 MEX  CONST_32  H1    C1   C2   C3   180.00   0.0  0
 MEX  CONST_33  H14   C14  C10  N9     0.00   0.0  0
 MEX  CONST_34  H17   C17  C11  C10  180.00   0.0  0
 MEX  CONST_35  H15   C15  C14  C10  180.00   0.0  0
 MEX  CONST_36  H16   C16  C17  C11  180.00   0.0  0
 MEX  CONST_37  HN12  N12  C13  N9   180.00   0.0  0
 MEX  Var_01    C13   N9   C2   C1   -95.23  30.0  2

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
 MEX  plan-1  C1    0.020
 MEX  plan-1  C2    0.020
 MEX  plan-1  C3    0.020
 MEX  plan-1  C4    0.020
 MEX  plan-1  C5    0.020
 MEX  plan-1  C6    0.020
 MEX  plan-1  O7    0.020
 MEX  plan-1  O8    0.020
 MEX  plan-1  N9    0.020
 MEX  plan-1  H1    0.020
 MEX  plan-1  H4    0.020
 MEX  plan-1  H6    0.020
 MEX  plan-2  C2    0.020
 MEX  plan-2  N9    0.020
 MEX  plan-2  C10   0.020
 MEX  plan-2  C11   0.020
 MEX  plan-2  N12   0.020
 MEX  plan-2  C13   0.020
 MEX  plan-2  C14   0.020
 MEX  plan-2  C15   0.020
 MEX  plan-2  C16   0.020
 MEX  plan-2  C17   0.020
 MEX  plan-2  O18   0.020
 MEX  plan-2  HN12  0.020
 MEX  plan-2  H14   0.020
 MEX  plan-2  H15   0.020
 MEX  plan-2  H16   0.020
 MEX  plan-2  H17   0.020

