# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:04:14 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-[[6-(2,6-dimethylpyridin-3-yl)oxy-7-fluoranyl-1-methyl-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(C)nc4C)c(F)c13
#
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
 B1O  B1O  '3-[[6-(2,6-dimethylpyridin-3-yl)oxy-7-fluoranyl-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid'  ligand  51  31  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B1O
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
 B1O  O1   O  O2    0  -0.507  -4.5164   0.9760  -0.0835
 B1O  C2   C  CR6   0   0.138  -3.2756   1.3155   0.3803
 B1O  C3   C  CR6   0   0.488  -2.1753   1.0809  -0.4193
 B1O  C4   C  CR16  0  -0.336  -1.9056   2.3250   2.1023
 B1O  C5   C  CR16  0  -0.328  -3.1403   1.9281   1.6329
 B1O  C6   C  CR56  0   0.137  -0.7910   2.0919   1.2964
 B1O  C7   C  CR56  0   0.191  -0.9278   1.4756   0.0415
 B1O  N8   N  NR5   0  -0.528   0.3341   1.4075  -0.4811
 B1O  C9   C  CR5   0   0.453   1.1577   1.9559   0.4569
 B1O  N10  N  N     0  -0.465   0.5305   2.3731   1.5205
 B1O  C11  C  CH2   0  -0.321   2.6308   2.0636   0.2754
 B1O  O12  O  O2    0  -0.474   3.1506   0.7474   0.2281
 B1O  C13  C  CH3   0  -0.537   0.7008   0.8644  -1.7737
 B1O  C14  C  CR6   0   0.420   4.4713   0.5864  -0.0036
 B1O  C15  C  CR16  0  -0.364   5.3843   1.6319  -0.1038
 B1O  C16  C  CR16  0  -0.227   6.7243   1.3484  -0.3400
 B1O  C17  C  CR16  0  -0.282   7.1687   0.0458  -0.4769
 B1O  C18  C  CR6   0  -0.069   6.2485  -0.9987  -0.3754
 B1O  C19  C  CR16  0  -0.361   4.9077  -0.7279  -0.1414
 B1O  C20  C  C     0   0.539   6.6495  -2.4233  -0.5138
 B1O  O21  O  O     0  -0.436   5.8818  -3.3502  -0.4172
 B1O  O22  O  OH1   0  -0.592   7.9428  -2.5741  -0.7574
 B1O  C23  C  CR6   0   0.276  -4.9434  -0.3115   0.0591
 B1O  C24  C  CR16  0  -0.235  -4.2814  -1.2791   0.7892
 B1O  C25  C  CR16  0  -0.333  -4.8427  -2.5469   0.8647
 B1O  C26  C  CR6   0   0.159  -6.1493  -0.6350  -0.5750
 B1O  N27  N  N     0  -0.434  -6.6615  -1.8520  -0.4852
 B1O  C28  C  CR6   0   0.217  -6.0386  -2.8028   0.2129
 B1O  C29  C  CH3   0  -0.715  -6.6927  -4.1498   0.2544
 B1O  F30  F  F     0  -0.293  -2.3239   0.4755  -1.6014
 B1O  C31  C  CH3   0  -0.726  -6.8912   0.3888  -1.3777
 B1O  H1   H  HCR6  0   0.269  -1.8029   2.8002   3.0683
 B1O  H2   H  HCR6  0   0.282  -4.0306   2.0849   2.2273
 B1O  H3   H  HCH2  0   0.264   2.8714   2.6139  -0.6418
 B1O  H4   H  HCH2  0   0.282   3.0331   2.6260   1.1218
 B1O  H5   H  HCH3  0   0.269   0.1044   1.3239  -2.5573
 B1O  H6   H  HCH3  0   0.275   1.7443   1.0760  -1.9787
 B1O  H7   H  HCH3  0   0.268   0.5582  -0.2142  -1.7938
 B1O  H8   H  HCR6  0   0.295   5.0804   2.6644   0.0029
 B1O  H9   H  HCR6  0   0.272   7.4277   2.1664  -0.4155
 B1O  H10  H  HCR6  0   0.268   8.2167  -0.1440  -0.6573
 B1O  H11  H  HCR6  0   0.275   4.1893  -1.5339  -0.0659
 B1O  H12  H  HOH1  0   0.489   8.1560  -3.5155  -0.8376
 B1O  H13  H  HCR6  0   0.287  -3.3495  -1.0695   1.2988
 B1O  H14  H  HCR6  0   0.266  -4.3480  -3.3234   1.4326
 B1O  H15  H  HCH3  0   0.247  -7.7100  -4.0766   0.6411
 B1O  H16  H  HCH3  0   0.248  -6.7598  -4.5820  -0.7455
 B1O  H17  H  HCH3  0   0.242  -6.1409  -4.8449   0.8848
 B1O  H18  H  HCH3  0   0.251  -6.3071   0.7209  -2.2380
 B1O  H19  H  HCH3  0   0.249  -7.8241  -0.0348  -1.7424
 B1O  H20  H  HCH3  0   0.249  -7.1241   1.2777  -0.7894

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
 B1O  C17  C16  aromatic  1.383  0.020  1.383
 B1O  C17  C18  aromatic  1.396  0.020  1.396
 B1O  C16  C15  aromatic  1.390  0.020  1.390
 B1O  O21  C20  double    1.207  0.020  1.207
 B1O  C20  C18  single    1.486  0.020  1.486
 B1O  C20  O22  single    1.325  0.020  1.325
 B1O  C18  C19  aromatic  1.388  0.020  1.388
 B1O  C15  C14  aromatic  1.392  0.020  1.392
 B1O  C19  C14  aromatic  1.392  0.020  1.392
 B1O  C14  O12  single    1.351  0.020  1.351
 B1O  O12  C11  single    1.416  0.020  1.416
 B1O  C11  C9   single    1.488  0.020  1.488
 B1O  C9   N10  aromatic  1.303  0.020  1.303
 B1O  C9   N8   aromatic  1.363  0.020  1.363
 B1O  N10  C6   aromatic  1.370  0.020  1.370
 B1O  N8   C13  single    1.449  0.020  1.449
 B1O  N8   C7   aromatic  1.368  0.020  1.368
 B1O  C6   C7   aromatic  1.405  0.020  1.405
 B1O  C6   C4   aromatic  1.395  0.020  1.395
 B1O  C7   C3   aromatic  1.387  0.020  1.387
 B1O  C4   C5   aromatic  1.379  0.020  1.379
 B1O  C3   F30  single    1.336  0.020  1.336
 B1O  C3   C2   aromatic  1.380  0.020  1.380
 B1O  C5   C2   aromatic  1.401  0.020  1.401
 B1O  C2   O1   single    1.367  0.020  1.367
 B1O  O1   C23  single    1.364  0.020  1.364
 B1O  C24  C23  aromatic  1.381  0.020  1.381
 B1O  C24  C25  aromatic  1.389  0.020  1.389
 B1O  C23  C26  aromatic  1.400  0.020  1.400
 B1O  C25  C28  aromatic  1.386  0.020  1.386
 B1O  C26  C31  single    1.498  0.020  1.498
 B1O  C26  N27  aromatic  1.323  0.020  1.323
 B1O  C28  N27  aromatic  1.334  0.020  1.334
 B1O  C28  C29  single    1.498  0.020  1.498
 B1O  C4   H1   single    0.930  0.020  1.080
 B1O  C5   H2   single    0.930  0.020  1.080
 B1O  C11  H3   single    0.970  0.020  1.090
 B1O  C11  H4   single    0.970  0.020  1.090
 B1O  C13  H5   single    0.970  0.020  1.090
 B1O  C13  H6   single    0.970  0.020  1.090
 B1O  C13  H7   single    0.970  0.020  1.090
 B1O  C15  H8   single    0.930  0.020  1.080
 B1O  C16  H9   single    0.930  0.020  1.080
 B1O  C17  H10  single    0.930  0.020  1.080
 B1O  C19  H11  single    0.930  0.020  1.080
 B1O  O22  H12  single    0.850  0.020  0.980
 B1O  C24  H13  single    0.930  0.020  1.080
 B1O  C25  H14  single    0.930  0.020  1.080
 B1O  C29  H15  single    0.970  0.020  1.090
 B1O  C29  H16  single    0.970  0.020  1.090
 B1O  C29  H17  single    0.970  0.020  1.090
 B1O  C31  H18  single    0.970  0.020  1.090
 B1O  C31  H19  single    0.970  0.020  1.090
 B1O  C31  H20  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
 B1O  C23  O1   C2   118.88  3.000
 B1O  C5   C2   C3   121.01  3.000
 B1O  C5   C2   O1   119.96  3.000
 B1O  C3   C2   O1   119.00  3.000
 B1O  F30  C3   C7   121.51  3.000
 B1O  F30  C3   C2   120.05  3.000
 B1O  C7   C3   C2   118.44  3.000
 B1O  H1   C4   C6   120.91  3.000
 B1O  H1   C4   C5   121.03  3.000
 B1O  C6   C4   C5   118.07  3.000
 B1O  H2   C5   C4   120.53  3.000
 B1O  H2   C5   C2   118.37  3.000
 B1O  C4   C5   C2   121.10  3.000
 B1O  N10  C6   C7   109.28  3.000
 B1O  C7   C6   C4   120.77  3.000
 B1O  N10  C6   C4   129.95  3.000
 B1O  N8   C7   C6   105.86  3.000
 B1O  C6   C7   C3   120.61  3.000
 B1O  N8   C7   C3   133.53  3.000
 B1O  C13  N8   C9   127.70  3.000
 B1O  C13  N8   C7   126.37  3.000
 B1O  C9   N8   C7   105.93  3.000
 B1O  C11  C9   N10  123.55  3.000
 B1O  N10  C9   N8   113.54  3.000
 B1O  C11  C9   N8   122.90  3.000
 B1O  C9   N10  C6   105.37  3.000
 B1O  H4   C11  H3   107.99  3.000
 B1O  H4   C11  O12  111.66  3.000
 B1O  H3   C11  O12  110.98  3.000
 B1O  H4   C11  C9   107.89  3.000
 B1O  H3   C11  C9   110.83  3.000
 B1O  O12  C11  C9   107.47  3.000
 B1O  C14  O12  C11  118.40  3.000
 B1O  H7   C13  H6   108.43  3.000
 B1O  H7   C13  H5   109.50  3.000
 B1O  H6   C13  H5   108.02  3.000
 B1O  H7   C13  N8   110.78  3.000
 B1O  H6   C13  N8   109.82  3.000
 B1O  H5   C13  N8   110.23  3.000
 B1O  C19  C14  C15  119.78  3.000
 B1O  C19  C14  O12  115.87  3.000
 B1O  C15  C14  O12  124.36  3.000
 B1O  H8   C15  C16  118.84  3.000
 B1O  H8   C15  C14  121.72  3.000
 B1O  C16  C15  C14  119.44  3.000
 B1O  H9   C16  C17  119.77  3.000
 B1O  H9   C16  C15  118.99  3.000
 B1O  C17  C16  C15  121.24  3.000
 B1O  H10  C17  C18  121.35  3.000
 B1O  H10  C17  C16  119.59  3.000
 B1O  C18  C17  C16  119.07  3.000
 B1O  C20  C18  C19  117.61  3.000
 B1O  C19  C18  C17  120.21  3.000
 B1O  C20  C18  C17  122.18  3.000
 B1O  H11  C19  C18  120.51  3.000
 B1O  H11  C19  C14  119.23  3.000
 B1O  C18  C19  C14  120.26  3.000
 B1O  O22  C20  O21  123.24  3.000
 B1O  O22  C20  C18  112.93  3.000
 B1O  O21  C20  C18  123.83  3.000
 B1O  H12  O22  C20  109.92  3.000
 B1O  C26  C23  C24  119.37  3.000
 B1O  C26  C23  O1   116.12  3.000
 B1O  C24  C23  O1   124.51  3.000
 B1O  H13  C24  C25  119.94  3.000
 B1O  H13  C24  C23  121.72  3.000
 B1O  C25  C24  C23  118.33  3.000
 B1O  H14  C25  C28  120.60  3.000
 B1O  H14  C25  C24  119.94  3.000
 B1O  C28  C25  C24  119.46  3.000
 B1O  C31  C26  N27  118.24  3.000
 B1O  N27  C26  C23  121.00  3.000
 B1O  C31  C26  C23  120.76  3.000
 B1O  C28  N27  C26  120.68  3.000
 B1O  C29  C28  N27  116.85  3.000
 B1O  C29  C28  C25  121.99  3.000
 B1O  N27  C28  C25  121.16  3.000
 B1O  H17  C29  H16  107.99  3.000
 B1O  H17  C29  H15  108.08  3.000
 B1O  H16  C29  H15  107.10  3.000
 B1O  H17  C29  C28  111.65  3.000
 B1O  H16  C29  C28  110.95  3.000
 B1O  H15  C29  C28  110.89  3.000
 B1O  H20  C31  H19  108.36  3.000
 B1O  H20  C31  H18  106.93  3.000
 B1O  H19  C31  H18  108.25  3.000
 B1O  H20  C31  C26  111.95  3.000
 B1O  H19  C31  C26  109.78  3.000
 B1O  H18  C31  C26  111.43  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
 B1O  CONST_01  N8   C7   C3   C2   180.00   0.0  0
 B1O  CONST_02  C6   C7   C3   C2     0.00   0.0  0
 B1O  CONST_03  C6   C4   C5   C2     0.00   0.0  0
 B1O  CONST_04  C9   N8   C7   C3   180.00   0.0  0
 B1O  CONST_05  N10  C6   C7   C3   180.00   0.0  0
 B1O  CONST_06  C4   C6   C7   C3     0.00   0.0  0
 B1O  CONST_07  C4   C5   C2   C3     0.00   0.0  0
 B1O  CONST_08  C9   N10  C6   C4   180.00   0.0  0
 B1O  CONST_09  N8   C7   C6   C4   180.00   0.0  0
 B1O  CONST_10  N10  C6   C4   C5   180.00   0.0  0
 B1O  CONST_11  C7   C6   C4   C5     0.00   0.0  0
 B1O  CONST_12  C7   C3   C2   C5     0.00   0.0  0
 B1O  CONST_13  N8   C9   N10  C6     0.00   0.0  0
 B1O  CONST_14  C9   N8   C7   C6     0.00   0.0  0
 B1O  CONST_15  N10  C9   N8   C7     0.00   0.0  0
 B1O  CONST_16  C9   N10  C6   C7     0.00   0.0  0
 B1O  CONST_17  N10  C6   C7   N8     0.00   0.0  0
 B1O  CONST_18  C17  C16  C15  C14    0.00   0.0  0
 B1O  CONST_19  C17  C18  C19  C14    0.00   0.0  0
 B1O  CONST_20  C18  C17  C16  C15    0.00   0.0  0
 B1O  CONST_21  C18  C19  C14  C15    0.00   0.0  0
 B1O  CONST_22  C19  C18  C17  C16    0.00   0.0  0
 B1O  CONST_23  C19  C14  C15  C16    0.00   0.0  0
 B1O  CONST_24  C28  C25  C24  C23    0.00   0.0  0
 B1O  CONST_25  C28  N27  C26  C23    0.00   0.0  0
 B1O  CONST_26  N27  C26  C23  C24    0.00   0.0  0
 B1O  CONST_27  N27  C28  C25  C24    0.00   0.0  0
 B1O  CONST_28  C26  C23  C24  C25    0.00   0.0  0
 B1O  CONST_29  C26  N27  C28  C25    0.00   0.0  0
 B1O  CONST_30  C7   C3   C2   O1   180.00   0.0  0
 B1O  CONST_31  C4   C5   C2   O1   180.00   0.0  0
 B1O  CONST_32  C25  C24  C23  O1   180.00   0.0  0
 B1O  CONST_33  N27  C26  C23  O1   180.00   0.0  0
 B1O  CONST_34  C13  N8   C7   C3     0.00   0.0  0
 B1O  CONST_35  F30  C3   C2   C5   180.00   0.0  0
 B1O  CONST_36  C11  C9   N10  C6   180.00   0.0  0
 B1O  CONST_37  C13  N8   C7   C6   180.00   0.0  0
 B1O  CONST_38  F30  C3   C7   C6   180.00   0.0  0
 B1O  CONST_39  C11  C9   N8   C7   180.00   0.0  0
 B1O  CONST_40  F30  C3   C7   N8     0.00   0.0  0
 B1O  CONST_41  C13  N8   C9   N10  180.00   0.0  0
 B1O  CONST_42  C16  C15  C14  O12  180.00   0.0  0
 B1O  CONST_43  C18  C19  C14  O12  180.00   0.0  0
 B1O  CONST_44  C20  C18  C19  C14  180.00   0.0  0
 B1O  CONST_45  C20  C18  C17  C16  180.00   0.0  0
 B1O  CONST_46  C31  C26  C23  C24  180.00   0.0  0
 B1O  CONST_47  C29  C28  C25  C24  180.00   0.0  0
 B1O  CONST_48  C29  C28  N27  C26  180.00   0.0  0
 B1O  CONST_49  C31  C26  N27  C28  180.00   0.0  0
 B1O  CONST_50  H1   C4   C5   C2   180.00   0.0  0
 B1O  CONST_51  H2   C5   C2   C3   180.00   0.0  0
 B1O  CONST_52  H9   C16  C15  C14  180.00   0.0  0
 B1O  CONST_53  H10  C17  C16  C15  180.00   0.0  0
 B1O  CONST_54  H11  C19  C14  C15  180.00   0.0  0
 B1O  CONST_55  H8   C15  C16  C17  180.00   0.0  0
 B1O  CONST_56  H14  C25  C24  C23  180.00   0.0  0
 B1O  CONST_57  H13  C24  C23  C26  180.00   0.0  0
 B1O  CONST_58  H12  O22  C20  C18  180.00   0.0  0
 B1O  Var_01    C24  C23  O1   C2     8.37  30.0  2
 B1O  Var_02    O12  C11  C9   N8   -65.03  30.0  2
 B1O  Var_03    C15  C14  O12  C11    4.94  30.0  2
 B1O  Var_04    O21  C20  C18  C17  179.17  30.0  3
 B1O  Var_05    H5   C13  N8   C7    52.78  30.0  2
 B1O  Var_06    H18  C31  C26  C23   63.17  30.0  2
 B1O  Var_07    H15  C29  C28  C25  123.45  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
 B1O  plan-1  O12  0.020
 B1O  plan-1  C14  0.020
 B1O  plan-1  C15  0.020
 B1O  plan-1  C16  0.020
 B1O  plan-1  C17  0.020
 B1O  plan-1  C18  0.020
 B1O  plan-1  C19  0.020
 B1O  plan-1  C20  0.020
 B1O  plan-1  H8   0.020
 B1O  plan-1  H9   0.020
 B1O  plan-1  H10  0.020
 B1O  plan-1  H11  0.020
 B1O  plan-2  O1   0.020
 B1O  plan-2  C23  0.020
 B1O  plan-2  C24  0.020
 B1O  plan-2  C25  0.020
 B1O  plan-2  C26  0.020
 B1O  plan-2  N27  0.020
 B1O  plan-2  C28  0.020
 B1O  plan-2  C29  0.020
 B1O  plan-2  C31  0.020
 B1O  plan-2  H13  0.020
 B1O  plan-2  H14  0.020
 B1O  plan-3  O1   0.020
 B1O  plan-3  C2   0.020
 B1O  plan-3  C3   0.020
 B1O  plan-3  C4   0.020
 B1O  plan-3  C5   0.020
 B1O  plan-3  C6   0.020
 B1O  plan-3  C7   0.020
 B1O  plan-3  N8   0.020
 B1O  plan-3  C9   0.020
 B1O  plan-3  N10  0.020
 B1O  plan-3  C11  0.020
 B1O  plan-3  C13  0.020
 B1O  plan-3  F30  0.020
 B1O  plan-3  H1   0.020
 B1O  plan-3  H2   0.020
 B1O  plan-4  C18  0.020
 B1O  plan-4  C20  0.020
 B1O  plan-4  O21  0.020
 B1O  plan-4  O22  0.020
 B1O  plan-4  H12  0.020

