# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:27:43 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-benzyl-6-[(2,4-difluorophenyl)amino]-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Nc2cnc3N(Cc4ccccc4)C(=O)Nc3c2)c(F)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
 J9G  J9G  3-benzyl-6-[(2,4-difluorophenyl)amino]-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one  ligand  40  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J9G
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
 J9G  C4   C  CR16  0  -0.288   3.1373   0.9989   0.2686
 J9G  C5   C  CR6   0   0.159   3.4642  -0.1513  -0.4481
 J9G  C7   C  CR6   0   0.234   1.1882  -1.0601  -0.5917
 J9G  C8   C  CR16  0  -0.168   0.1981  -1.1260  -1.5694
 J9G  C10  C  CR56  0   0.456  -1.4350  -1.2108  -0.0406
 J9G  C13  C  CR6   0   0.134  -4.4473   0.1106  -0.4845
 J9G  C15  C  CR16  0  -0.243  -5.7960   1.9993   0.1798
 J9G  C17  C  CR16  0  -0.243  -4.4222   2.1437  -1.7860
 J9G  C24  C  CR16  0  -0.257   0.8178  -1.0754   0.7635
 J9G  C14  C  CR16  0  -0.297  -5.3559   0.6991   0.3903
 J9G  C16  C  CR16  0  -0.264  -5.3286   2.7248  -0.9080
 J9G  C18  C  CR16  0  -0.292  -3.9855   0.8431  -1.5753
 J9G  C19  C  CR5   0   0.667  -2.6152  -1.2475   1.8786
 J9G  C2   C  CR6   0   0.517   5.4417   1.5448   0.5437
 J9G  C23  C  CR56  0   0.302  -0.5270  -1.1344   1.0254
 J9G  C25  C  CR6   0   0.493   4.8232  -0.3996  -0.6472
 J9G  C27  C  CR16  0  -0.555   5.8196   0.4267  -0.1765
 J9G  C3   C  CR16  0  -0.415   4.1160   1.8421   0.7770
 J9G  F1   F  F     0  -0.315   6.3976   2.3579   1.0206
 J9G  F26  F  F     0  -0.308   5.1677  -1.4943  -1.3427
 J9G  N11  N  NR5   0  -0.557  -2.6979  -1.2915   0.5033
 J9G  N21  N  NR15  0  -0.757  -1.2746  -1.1633   2.1752
 J9G  N6   N  NH1   0  -0.779   2.5307  -1.0436  -0.9628
 J9G  N9   N  N     0  -0.425  -1.1091  -1.2168  -1.3034
 J9G  O20  O  O     0  -0.489  -3.5418  -1.2814   2.6639
 J9G  H1   H  HCR6  0   0.291   2.0994   1.2521   0.4355
 J9G  H2   H  HCR6  0   0.267   0.4779  -1.1156  -2.6169
 J9G  H3   H  HCR6  0   0.257  -6.5057   2.4456   0.8646
 J9G  H4   H  HCR6  0   0.256  -4.0571   2.7031  -2.6378
 J9G  H5   H  HCR6  0   0.298   1.5552  -1.0519   1.5548
 J9G  H6   H  HCH2  0   0.287  -4.6720  -1.8673   0.3290
 J9G  H7   H  HCH2  0   0.285  -3.7679  -1.8116  -1.1750
 J9G  H8   H  HCR6  0   0.252  -5.7228   0.1368   1.2403
 J9G  H9   H  HCR6  0   0.257  -5.6714   3.7379  -1.0736
 J9G  H10  H  HCR6  0   0.252  -3.2788   0.3923  -2.2616
 J9G  H11  H  HCR6  0   0.304   6.8610   0.1941  -0.3576
 J9G  H12  H  HCR6  0   0.285   3.8378   2.7276   1.3324
 J9G  H13  H  HNR5  0   0.424  -0.9214  -1.1260   3.1186
 J9G  H14  H  HNH1  0   0.399   2.7249  -1.3933  -1.8883
 J9G  C12  C  CH2   0  -0.423  -3.9430  -1.2875  -0.2356

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
 J9G  O20  C19  double    1.215  0.020  1.215
 J9G  C15  C14  aromatic  1.389  0.020  1.389
 J9G  C15  C16  aromatic  1.389  0.020  1.389
 J9G  C19  N21  single    1.376  0.020  1.376
 J9G  C19  N11  single    1.379  0.020  1.379
 J9G  C14  C13  aromatic  1.392  0.020  1.392
 J9G  C16  C17  aromatic  1.389  0.020  1.389
 J9G  N21  C23  single    1.372  0.020  1.372
 J9G  C13  C12  single    1.507  0.020  1.507
 J9G  C13  C18  aromatic  1.393  0.020  1.393
 J9G  C17  C18  aromatic  1.388  0.020  1.388
 J9G  N11  C12  single    1.448  0.020  1.448
 J9G  N11  C10  single    1.377  0.020  1.377
 J9G  C23  C10  aromatic  1.402  0.020  1.402
 J9G  C23  C24  aromatic  1.371  0.020  1.371
 J9G  C10  N9   aromatic  1.304  0.020  1.304
 J9G  C24  C7   aromatic  1.405  0.020  1.405
 J9G  N9   C8   aromatic  1.337  0.020  1.337
 J9G  F26  C25  single    1.342  0.020  1.342
 J9G  C27  C25  aromatic  1.377  0.020  1.377
 J9G  C27  C2   aromatic  1.383  0.020  1.383
 J9G  C7   C8   aromatic  1.393  0.020  1.393
 J9G  C7   N6   single    1.393  0.020  1.393
 J9G  F1   C2   single    1.342  0.020  1.342
 J9G  C25  C5   aromatic  1.396  0.020  1.396
 J9G  C2   C3   aromatic  1.378  0.020  1.378
 J9G  C5   N6   single    1.390  0.020  1.390
 J9G  C5   C4   aromatic  1.394  0.020  1.394
 J9G  C3   C4   aromatic  1.388  0.020  1.388
 J9G  C4   H1   single    0.930  0.020  1.080
 J9G  C8   H2   single    0.930  0.020  1.080
 J9G  C15  H3   single    0.930  0.020  1.080
 J9G  C17  H4   single    0.930  0.020  1.080
 J9G  C24  H5   single    0.930  0.020  1.080
 J9G  C12  H6   single    0.970  0.020  1.090
 J9G  C12  H7   single    0.970  0.020  1.090
 J9G  C14  H8   single    0.930  0.020  1.080
 J9G  C16  H9   single    0.930  0.020  1.080
 J9G  C18  H10  single    0.930  0.020  1.080
 J9G  C27  H11  single    0.930  0.020  1.080
 J9G  C3   H12  single    0.930  0.020  1.080
 J9G  N21  H13  single    0.860  0.020  1.020
 J9G  N6   H14  single    0.890  0.020  1.040

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
 J9G  H1   C4   C3   118.55  3.000
 J9G  H1   C4   C5   119.84  3.000
 J9G  C3   C4   C5   121.61  3.000
 J9G  N6   C5   C25  119.14  3.000
 J9G  N6   C5   C4   124.22  3.000
 J9G  C25  C5   C4   116.64  3.000
 J9G  N6   C7   C24  120.74  3.000
 J9G  N6   C7   C8   119.90  3.000
 J9G  C24  C7   C8   119.28  3.000
 J9G  H2   C8   N9   116.43  3.000
 J9G  H2   C8   C7   119.62  3.000
 J9G  N9   C8   C7   123.95  3.000
 J9G  N9   C10  N11  127.67  3.000
 J9G  N9   C10  C23  125.07  3.000
 J9G  N11  C10  C23  107.25  3.000
 J9G  C18  C13  C14  119.10  3.000
 J9G  C18  C13  C12  120.42  3.000
 J9G  C14  C13  C12  120.46  3.000
 J9G  H3   C15  C16  120.06  3.000
 J9G  H3   C15  C14  119.86  3.000
 J9G  C16  C15  C14  120.08  3.000
 J9G  H4   C17  C18  119.84  3.000
 J9G  H4   C17  C16  120.08  3.000
 J9G  C18  C17  C16  120.08  3.000
 J9G  H5   C24  C23  121.98  3.000
 J9G  H5   C24  C7   121.71  3.000
 J9G  C23  C24  C7   116.31  3.000
 J9G  H8   C14  C15  119.84  3.000
 J9G  H8   C14  C13  119.66  3.000
 J9G  C15  C14  C13  120.50  3.000
 J9G  H9   C16  C17  120.10  3.000
 J9G  H9   C16  C15  120.15  3.000
 J9G  C17  C16  C15  119.75  3.000
 J9G  H10  C18  C17  119.93  3.000
 J9G  H10  C18  C13  119.58  3.000
 J9G  C17  C18  C13  120.49  3.000
 J9G  O20  C19  N21  127.27  3.000
 J9G  N21  C19  N11  105.99  3.000
 J9G  O20  C19  N11  126.74  3.000
 J9G  F1   C2   C3   119.60  3.000
 J9G  C3   C2   C27  121.70  3.000
 J9G  F1   C2   C27  118.70  3.000
 J9G  N21  C23  C24  134.06  3.000
 J9G  C24  C23  C10  119.48  3.000
 J9G  N21  C23  C10  106.45  3.000
 J9G  F26  C25  C27  118.74  3.000
 J9G  C27  C25  C5   123.29  3.000
 J9G  F26  C25  C5   117.97  3.000
 J9G  H11  C27  C25  120.66  3.000
 J9G  H11  C27  C2   121.59  3.000
 J9G  C25  C27  C2   117.74  3.000
 J9G  H12  C3   C2   120.72  3.000
 J9G  H12  C3   C4   120.26  3.000
 J9G  C2   C3   C4   119.01  3.000
 J9G  C19  N11  C12  124.10  3.000
 J9G  C12  N11  C10  125.93  3.000
 J9G  C19  N11  C10  109.70  3.000
 J9G  H13  N21  C23  126.35  3.000
 J9G  H13  N21  C19  123.06  3.000
 J9G  C23  N21  C19  110.59  3.000
 J9G  H14  N6   C7   115.22  3.000
 J9G  H14  N6   C5   115.66  3.000
 J9G  C7   N6   C5   123.79  3.000
 J9G  C10  N9   C8   115.88  3.000
 J9G  H7   C12  H6   107.36  3.000
 J9G  H7   C12  N11  107.48  3.000
 J9G  H6   C12  N11  108.03  3.000
 J9G  H7   C12  C13  110.95  3.000
 J9G  H6   C12  C13  110.82  3.000
 J9G  N11  C12  C13  112.00  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
 J9G  CONST_01  C27  C25  C5   C4     0.00   0.0  0
 J9G  CONST_02  C27  C2   C3   C4     0.00   0.0  0
 J9G  CONST_03  C2   C27  C25  C5     0.00   0.0  0
 J9G  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 J9G  CONST_05  C10  C23  C24  C7     0.00   0.0  0
 J9G  CONST_06  C10  N9   C8   C7     0.00   0.0  0
 J9G  CONST_07  C23  C10  N9   C8     0.00   0.0  0
 J9G  CONST_08  C23  C24  C7   C8     0.00   0.0  0
 J9G  CONST_09  C16  C15  C14  C13    0.00   0.0  0
 J9G  CONST_10  C16  C17  C18  C13    0.00   0.0  0
 J9G  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 J9G  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 J9G  CONST_13  C14  C15  C16  C17    0.00   0.0  0
 J9G  CONST_14  C14  C13  C18  C17    0.00   0.0  0
 J9G  CONST_15  N9   C10  C23  C24    0.00   0.0  0
 J9G  CONST_16  N9   C8   C7   C24    0.00   0.0  0
 J9G  CONST_17  C3   C2   C27  C25    0.00   0.0  0
 J9G  CONST_18  C3   C4   C5   C25    0.00   0.0  0
 J9G  CONST_19  N21  C19  N11  C10    0.00   0.0  0
 J9G  CONST_20  C19  N21  C23  C10    0.00   0.0  0
 J9G  CONST_21  C23  C10  N11  C19    0.00   0.0  0
 J9G  CONST_22  N11  C19  N21  C23    0.00   0.0  0
 J9G  CONST_23  N21  C23  C10  N11    0.00   0.0  0
 J9G  CONST_24  F26  C25  C5   C4   180.00   0.0  0
 J9G  CONST_25  F1   C2   C3   C4   180.00   0.0  0
 J9G  CONST_26  C12  C13  C14  C15  180.00   0.0  0
 J9G  CONST_27  C12  C13  C18  C17  180.00   0.0  0
 J9G  CONST_28  F26  C25  C27  C2   180.00   0.0  0
 J9G  CONST_29  N6   C7   C24  C23  180.00   0.0  0
 J9G  CONST_30  F1   C2   C27  C25  180.00   0.0  0
 J9G  CONST_31  N6   C5   C25  C27  180.00   0.0  0
 J9G  CONST_32  N6   C5   C4   C3   180.00   0.0  0
 J9G  CONST_33  N9   C8   C7   N6   180.00   0.0  0
 J9G  CONST_34  O20  C19  N11  C10  180.00   0.0  0
 J9G  CONST_35  N21  C19  N11  C12  180.00   0.0  0
 J9G  CONST_36  C23  C10  N11  C12  180.00   0.0  0
 J9G  CONST_37  O20  C19  N21  C23  180.00   0.0  0
 J9G  CONST_38  H11  C27  C25  C5   180.00   0.0  0
 J9G  CONST_39  H12  C3   C4   C5   180.00   0.0  0
 J9G  CONST_40  H5   C24  C7   C8   180.00   0.0  0
 J9G  CONST_41  H2   C8   N9   C10  180.00   0.0  0
 J9G  CONST_42  H3   C15  C14  C13  180.00   0.0  0
 J9G  CONST_43  H4   C17  C18  C13  180.00   0.0  0
 J9G  CONST_44  H9   C16  C15  C14  180.00   0.0  0
 J9G  CONST_45  H10  C18  C13  C14  180.00   0.0  0
 J9G  CONST_46  H8   C14  C15  C16  180.00   0.0  0
 J9G  CONST_47  H1   C4   C3   C2   180.00   0.0  0
 J9G  CONST_48  H13  N21  C23  C10  180.00   0.0  0
 J9G  CONST_49  O20  C19  N11  C12    0.00   0.0  0
 J9G  Var_01    C7   N6   C5   C4   -14.26  30.0  2
 J9G  Var_02    C24  C7   N6   C5   -50.17  30.0  1
 J9G  Var_03    C13  C12  N11  C10  -87.52  30.0  3
 J9G  Var_04    N11  C12  C13  C14  -93.73  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
 J9G  plan-1  C13  0.020
 J9G  plan-1  C15  0.020
 J9G  plan-1  C17  0.020
 J9G  plan-1  C14  0.020
 J9G  plan-1  C16  0.020
 J9G  plan-1  C18  0.020
 J9G  plan-1  H3   0.020
 J9G  plan-1  H4   0.020
 J9G  plan-1  H8   0.020
 J9G  plan-1  H9   0.020
 J9G  plan-1  H10  0.020
 J9G  plan-1  C12  0.020
 J9G  plan-2  C4   0.020
 J9G  plan-2  C5   0.020
 J9G  plan-2  C2   0.020
 J9G  plan-2  C25  0.020
 J9G  plan-2  C27  0.020
 J9G  plan-2  C3   0.020
 J9G  plan-2  F1   0.020
 J9G  plan-2  F26  0.020
 J9G  plan-2  N6   0.020
 J9G  plan-2  H1   0.020
 J9G  plan-2  H11  0.020
 J9G  plan-2  H12  0.020
 J9G  plan-3  C7   0.020
 J9G  plan-3  C8   0.020
 J9G  plan-3  C10  0.020
 J9G  plan-3  C24  0.020
 J9G  plan-3  C19  0.020
 J9G  plan-3  C23  0.020
 J9G  plan-3  N11  0.020
 J9G  plan-3  N21  0.020
 J9G  plan-3  N6   0.020
 J9G  plan-3  N9   0.020
 J9G  plan-3  O20  0.020
 J9G  plan-3  H2   0.020
 J9G  plan-3  H5   0.020
 J9G  plan-3  H13  0.020
 J9G  plan-3  C12  0.020

