# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 17:14:23 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-{[6-(4-chloro-3-fluorophenoxy)-1-methyl-1H-benzimidazol-2-yl]methoxy}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(COc2cccc(c2)C(O)=O)nc3ccc(Oc4ccc(Cl)c(F)c4)cc13
#
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
 RTE  RTE  '3-{[6-(4-chloro-3-fluorophenoxy)-1-methyl-1H-benzimidazol-2-yl]methoxy}benzoic acid'  ligand  46  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RTE
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
 RTE  C1   C   CR6   0  -0.259   6.3257  -1.7052  -0.0175
 RTE  C2   C   CR6   0   0.637   5.0417  -1.6068  -0.5204
 RTE  C3   C   CR16  0  -0.501   4.2636  -0.4810  -0.3323
 RTE  C4   C   CR6   0   0.392   4.7985   0.5820   0.3857
 RTE  C5   C   CR16  0  -0.343   6.0904   0.5040   0.9010
 RTE  C6   C   CR16  0  -0.200   6.8450  -0.6362   0.6988
 RTE  O7   O   O2    0  -0.509   4.1202   1.7272   0.6351
 RTE  C8   C   CR6   0   0.287   2.8663   1.9015   0.0935
 RTE  F9   F   F     0  -0.294   4.5329  -2.6310  -1.2066
 RTE  C10  C   CR16  0  -0.373   1.7656   1.6173   0.8767
 RTE  C11  C   CR56  0   0.361   0.5293   1.8689   0.2924
 RTE  C12  C   CR56  0   0.137   0.3893   2.3727  -1.0098
 RTE  C13  C   CR16  0  -0.327   1.5231   2.6415  -1.7754
 RTE  C14  C   CR16  0  -0.314   2.7613   2.3992  -1.2131
 RTE  N15  N   NR5   0  -0.531  -0.7448   1.7242   0.7649
 RTE  C16  C   CR5   0   0.444  -1.5752   2.1321  -0.2363
 RTE  N17  N   N     0  -0.467  -0.9411   2.5225  -1.3072
 RTE  C18  C   CH3   0  -0.543  -1.0886   1.2602   2.0898
 RTE  C19  C   CH2   0  -0.319  -3.0575   2.1202  -0.1106
 RTE  O20  O   O2    0  -0.474  -3.4681   0.7640  -0.0849
 RTE  C21  C   CR6   0   0.419  -4.7854   0.4950   0.0356
 RTE  C22  C   CR16  0  -0.361  -5.1278  -0.8529   0.0915
 RTE  C23  C   CR6   0  -0.069  -6.4578  -1.2328   0.2055
 RTE  C24  C   CR16  0  -0.282  -7.4621  -0.2658   0.2691
 RTE  C25  C   CR16  0  -0.228  -7.1108   1.0710   0.2173
 RTE  C26  C   CR16  0  -0.365  -5.7827   1.4638   0.1004
 RTE  C27  C   C     0   0.539  -6.7562  -2.6880   0.2580
 RTE  O28  O   O     0  -0.436  -5.9098  -3.5489   0.2282
 RTE  O29  O   OH1   0  -0.592  -8.0526  -2.9475   0.3407
 RTE  CL1  CL  CL    0  -0.098   7.2455  -3.1382  -0.2842
 RTE  H1   H   HCR6  0   0.308   3.2624  -0.4583  -0.7429
 RTE  H2   H   HCR6  0   0.285   6.5011   1.3338   1.4603
 RTE  H3   H   HCR6  0   0.294   7.8470  -0.6964   1.1006
 RTE  H4   H   HCR6  0   0.289   1.8741   1.2343   1.8834
 RTE  H5   H   HCR6  0   0.266   1.4375   3.0327  -2.7806
 RTE  H6   H   HCR6  0   0.275   3.6645   2.6011  -1.7745
 RTE  H7   H   HCH3  0   0.265  -0.6814   1.9336   2.8421
 RTE  H8   H   HCH3  0   0.279  -2.1662   1.2205   2.2088
 RTE  H9   H   HCH3  0   0.267  -0.6895   0.2608   2.2544
 RTE  H10  H   HCH2  0   0.263  -3.3756   2.6399   0.7993
 RTE  H11  H   HCH2  0   0.279  -3.4753   2.6508  -0.9701
 RTE  H12  H   HCR6  0   0.275  -4.3455  -1.5994   0.0440
 RTE  H13  H   HCR6  0   0.267  -8.5028  -0.5417   0.3587
 RTE  H14  H   HCR6  0   0.272  -7.8792   1.8306   0.2661
 RTE  H15  H   HCR6  0   0.295  -5.5541   2.5201   0.0587
 RTE  H16  H   HOH1  0   0.489  -8.1964  -3.9053   0.3698

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
 RTE  O28  C27  double    1.208  0.020  1.208
 RTE  C27  O29  single    1.325  0.020  1.325
 RTE  C27  C23  single    1.486  0.020  1.486
 RTE  C24  C23  aromatic  1.396  0.020  1.396
 RTE  C24  C25  aromatic  1.383  0.020  1.383
 RTE  C23  C22  aromatic  1.388  0.020  1.388
 RTE  C25  C26  aromatic  1.390  0.020  1.390
 RTE  C22  C21  aromatic  1.392  0.020  1.392
 RTE  C26  C21  aromatic  1.392  0.020  1.392
 RTE  C21  O20  single    1.350  0.020  1.350
 RTE  O20  C19  single    1.417  0.020  1.417
 RTE  C19  C16  single    1.488  0.020  1.488
 RTE  C16  N17  aromatic  1.304  0.020  1.304
 RTE  C16  N15  aromatic  1.363  0.020  1.363
 RTE  N17  C12  aromatic  1.371  0.020  1.371
 RTE  C18  N15  single    1.445  0.020  1.445
 RTE  N15  C11  aromatic  1.367  0.020  1.367
 RTE  C12  C11  aromatic  1.403  0.020  1.403
 RTE  C12  C13  aromatic  1.394  0.020  1.394
 RTE  C11  C10  aromatic  1.390  0.020  1.390
 RTE  C13  C14  aromatic  1.381  0.020  1.381
 RTE  C10  C8   aromatic  1.380  0.020  1.380
 RTE  C14  C8   aromatic  1.402  0.020  1.402
 RTE  C8   O7   single    1.377  0.020  1.377
 RTE  O7   C4   single    1.354  0.020  1.354
 RTE  C5   C4   aromatic  1.393  0.020  1.393
 RTE  C5   C6   aromatic  1.382  0.020  1.382
 RTE  C4   C3   aromatic  1.390  0.020  1.390
 RTE  C6   C1   aromatic  1.388  0.020  1.388
 RTE  C3   C2   aromatic  1.381  0.020  1.381
 RTE  C1   C2   aromatic  1.382  0.020  1.382
 RTE  C1   CL1  single    1.724  0.020  1.724
 RTE  C2   F9   single    1.334  0.020  1.334
 RTE  C3   H1   single    0.930  0.020  1.080
 RTE  C5   H2   single    0.930  0.020  1.080
 RTE  C6   H3   single    0.930  0.020  1.080
 RTE  C10  H4   single    0.930  0.020  1.080
 RTE  C13  H5   single    0.930  0.020  1.080
 RTE  C14  H6   single    0.930  0.020  1.080
 RTE  C18  H7   single    0.970  0.020  1.090
 RTE  C18  H8   single    0.970  0.020  1.090
 RTE  C18  H9   single    0.970  0.020  1.090
 RTE  C19  H10  single    0.970  0.020  1.090
 RTE  C19  H11  single    0.970  0.020  1.090
 RTE  C22  H12  single    0.930  0.020  1.080
 RTE  C24  H13  single    0.930  0.020  1.080
 RTE  C25  H14  single    0.930  0.020  1.080
 RTE  C26  H15  single    0.930  0.020  1.080
 RTE  O29  H16  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
 RTE  CL1  C1   C6   121.38  3.000
 RTE  CL1  C1   C2   119.91  3.000
 RTE  C6   C1   C2   118.72  3.000
 RTE  F9   C2   C3   118.75  3.000
 RTE  F9   C2   C1   119.13  3.000
 RTE  C3   C2   C1   122.12  3.000
 RTE  H1   C3   C4   122.41  3.000
 RTE  H1   C3   C2   119.11  3.000
 RTE  C4   C3   C2   118.48  3.000
 RTE  O7   C4   C5   116.34  3.000
 RTE  C5   C4   C3   120.35  3.000
 RTE  O7   C4   C3   123.31  3.000
 RTE  H2   C5   C6   120.08  3.000
 RTE  H2   C5   C4   120.03  3.000
 RTE  C6   C5   C4   119.89  3.000
 RTE  H3   C6   C5   119.83  3.000
 RTE  H3   C6   C1   119.72  3.000
 RTE  C5   C6   C1   120.45  3.000
 RTE  C8   O7   C4   119.39  3.000
 RTE  C14  C8   C10  122.82  3.000
 RTE  C14  C8   O7   118.67  3.000
 RTE  C10  C8   O7   118.48  3.000
 RTE  H4   C10  C11  122.95  3.000
 RTE  H4   C10  C8   121.37  3.000
 RTE  C11  C10  C8   115.68  3.000
 RTE  N15  C11  C12  105.42  3.000
 RTE  C12  C11  C10  122.93  3.000
 RTE  N15  C11  C10  131.65  3.000
 RTE  N17  C12  C13  130.44  3.000
 RTE  C13  C12  C11  119.84  3.000
 RTE  N17  C12  C11  109.71  3.000
 RTE  H5   C13  C14  120.83  3.000
 RTE  H5   C13  C12  121.03  3.000
 RTE  C14  C13  C12  118.14  3.000
 RTE  H6   C14  C13  120.27  3.000
 RTE  H6   C14  C8   119.14  3.000
 RTE  C13  C14  C8   120.58  3.000
 RTE  C18  N15  C16  128.64  3.000
 RTE  C18  N15  C11  124.94  3.000
 RTE  C16  N15  C11  106.40  3.000
 RTE  C19  C16  N17  123.79  3.000
 RTE  N17  C16  N15  113.36  3.000
 RTE  C19  C16  N15  122.86  3.000
 RTE  C16  N17  C12  105.12  3.000
 RTE  H9   C18  H8   108.30  3.000
 RTE  H9   C18  H7   109.04  3.000
 RTE  H8   C18  H7   108.56  3.000
 RTE  H9   C18  N15  110.25  3.000
 RTE  H8   C18  N15  110.40  3.000
 RTE  H7   C18  N15  110.23  3.000
 RTE  H11  C19  H10  108.18  3.000
 RTE  H11  C19  O20  111.59  3.000
 RTE  H10  C19  O20  110.79  3.000
 RTE  H11  C19  C16  108.09  3.000
 RTE  H10  C19  C16  110.85  3.000
 RTE  O20  C19  C16  107.33  3.000
 RTE  C21  O20  C19  118.36  3.000
 RTE  C26  C21  C22  119.73  3.000
 RTE  C26  C21  O20  124.38  3.000
 RTE  C22  C21  O20  115.89  3.000
 RTE  H12  C22  C23  120.49  3.000
 RTE  H12  C22  C21  119.24  3.000
 RTE  C23  C22  C21  120.27  3.000
 RTE  C27  C23  C24  122.16  3.000
 RTE  C24  C23  C22  120.25  3.000
 RTE  C27  C23  C22  117.60  3.000
 RTE  H13  C24  C25  119.64  3.000
 RTE  H13  C24  C23  121.33  3.000
 RTE  C25  C24  C23  119.02  3.000
 RTE  H14  C25  C26  118.96  3.000
 RTE  H14  C25  C24  119.78  3.000
 RTE  C26  C25  C24  121.26  3.000
 RTE  H15  C26  C25  118.76  3.000
 RTE  H15  C26  C21  121.77  3.000
 RTE  C25  C26  C21  119.47  3.000
 RTE  O29  C27  O28  123.22  3.000
 RTE  O29  C27  C23  112.98  3.000
 RTE  O28  C27  C23  123.80  3.000
 RTE  H16  O29  C27  109.92  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
 RTE  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 RTE  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 RTE  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 RTE  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 RTE  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 RTE  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 RTE  CONST_07  N15  C11  C10  C8    180.00   0.0  0
 RTE  CONST_08  C12  C11  C10  C8      0.00   0.0  0
 RTE  CONST_09  C12  C13  C14  C8      0.00   0.0  0
 RTE  CONST_10  C16  N15  C11  C10   180.00   0.0  0
 RTE  CONST_11  N17  C12  C11  C10   180.00   0.0  0
 RTE  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 RTE  CONST_13  C13  C14  C8   C10     0.00   0.0  0
 RTE  CONST_14  N17  C16  N15  C11     0.00   0.0  0
 RTE  CONST_15  C16  N17  C12  C11     0.00   0.0  0
 RTE  CONST_16  C14  C13  C12  C11     0.00   0.0  0
 RTE  CONST_17  C14  C8   C10  C11     0.00   0.0  0
 RTE  CONST_18  N15  C16  N17  C12     0.00   0.0  0
 RTE  CONST_19  C16  N15  C11  C12     0.00   0.0  0
 RTE  CONST_20  C16  N17  C12  C13   180.00   0.0  0
 RTE  CONST_21  N15  C11  C12  C13   180.00   0.0  0
 RTE  CONST_22  N17  C12  C13  C14   180.00   0.0  0
 RTE  CONST_23  N17  C12  C11  N15     0.00   0.0  0
 RTE  CONST_24  C24  C23  C22  C21     0.00   0.0  0
 RTE  CONST_25  C24  C25  C26  C21     0.00   0.0  0
 RTE  CONST_26  C25  C24  C23  C22     0.00   0.0  0
 RTE  CONST_27  C25  C26  C21  C22     0.00   0.0  0
 RTE  CONST_28  C26  C25  C24  C23     0.00   0.0  0
 RTE  CONST_29  C26  C21  C22  C23     0.00   0.0  0
 RTE  CONST_30  O7   C4   C3   C2    180.00   0.0  0
 RTE  CONST_31  CL1  C1   C2   C3    180.00   0.0  0
 RTE  CONST_32  F9   C2   C3   C4    180.00   0.0  0
 RTE  CONST_33  CL1  C1   C6   C5    180.00   0.0  0
 RTE  CONST_34  O7   C4   C5   C6    180.00   0.0  0
 RTE  CONST_35  F9   C2   C1   C6    180.00   0.0  0
 RTE  CONST_36  C11  C10  C8   O7    180.00   0.0  0
 RTE  CONST_37  C13  C14  C8   O7    180.00   0.0  0
 RTE  CONST_38  C18  N15  C11  C10     0.00   0.0  0
 RTE  CONST_39  C19  C16  N15  C11   180.00   0.0  0
 RTE  CONST_40  C19  C16  N17  C12   180.00   0.0  0
 RTE  CONST_41  C18  N15  C11  C12   180.00   0.0  0
 RTE  CONST_42  C18  N15  C16  N17   180.00   0.0  0
 RTE  CONST_43  C23  C22  C21  O20   180.00   0.0  0
 RTE  CONST_44  C25  C26  C21  O20   180.00   0.0  0
 RTE  CONST_45  C27  C23  C22  C21   180.00   0.0  0
 RTE  CONST_46  C27  C23  C24  C25   180.00   0.0  0
 RTE  CONST_47  H2   C5   C6   C1    180.00   0.0  0
 RTE  CONST_48  H1   C3   C2   C1    180.00   0.0  0
 RTE  CONST_49  H3   C6   C1   C2    180.00   0.0  0
 RTE  CONST_50  H5   C13  C14  C8    180.00   0.0  0
 RTE  CONST_51  H6   C14  C8   C10   180.00   0.0  0
 RTE  CONST_52  H4   C10  C11  C12   180.00   0.0  0
 RTE  CONST_53  H14  C25  C26  C21   180.00   0.0  0
 RTE  CONST_54  H13  C24  C23  C22   180.00   0.0  0
 RTE  CONST_55  H15  C26  C21  C22   180.00   0.0  0
 RTE  CONST_56  H12  C22  C23  C24   180.00   0.0  0
 RTE  CONST_57  H16  O29  C27  C23   180.00   0.0  0
 RTE  Var_01    C10  C8   O7   C4     97.19  30.0  2
 RTE  Var_02    O20  C19  C16  N15   -69.20  30.0  1
 RTE  Var_03    C22  C21  O20  C19  -178.34  30.0  2
 RTE  Var_04    O28  C27  C23  C22     1.20  30.0  2
 RTE  Var_05    H7   C18  N15  C11    60.96  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
 RTE  plan-1  C1   0.020
 RTE  plan-1  C2   0.020
 RTE  plan-1  C3   0.020
 RTE  plan-1  C4   0.020
 RTE  plan-1  C5   0.020
 RTE  plan-1  C6   0.020
 RTE  plan-1  O7   0.020
 RTE  plan-1  F9   0.020
 RTE  plan-1  CL1  0.020
 RTE  plan-1  H1   0.020
 RTE  plan-1  H2   0.020
 RTE  plan-1  H3   0.020
 RTE  plan-2  O20  0.020
 RTE  plan-2  C21  0.020
 RTE  plan-2  C22  0.020
 RTE  plan-2  C23  0.020
 RTE  plan-2  C24  0.020
 RTE  plan-2  C25  0.020
 RTE  plan-2  C26  0.020
 RTE  plan-2  C27  0.020
 RTE  plan-2  H12  0.020
 RTE  plan-2  H13  0.020
 RTE  plan-2  H14  0.020
 RTE  plan-2  H15  0.020
 RTE  plan-3  O7   0.020
 RTE  plan-3  C8   0.020
 RTE  plan-3  C10  0.020
 RTE  plan-3  C11  0.020
 RTE  plan-3  C12  0.020
 RTE  plan-3  C13  0.020
 RTE  plan-3  C14  0.020
 RTE  plan-3  N15  0.020
 RTE  plan-3  C16  0.020
 RTE  plan-3  N17  0.020
 RTE  plan-3  C18  0.020
 RTE  plan-3  C19  0.020
 RTE  plan-3  H4   0.020
 RTE  plan-3  H5   0.020
 RTE  plan-3  H6   0.020
 RTE  plan-4  C23  0.020
 RTE  plan-4  C27  0.020
 RTE  plan-4  O28  0.020
 RTE  plan-4  O29  0.020
 RTE  plan-4  H16  0.020

