# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 14:17:49 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-methyl-6-phenyl-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)Nc2ncc(cc12)c3ccccc3
#
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
 0DF  0DF  1-methyl-6-phenyl-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one  ligand  28  17  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0DF
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
 0DF  O1   O  O     0  -0.487  -4.8686  -0.3017   0.0252
 0DF  C3   C  CR5   0   0.648  -3.6828  -0.0460  -0.0342
 0DF  N1   N  NR5   0  -0.588  -2.6351  -0.9262   0.1382
 0DF  C7   C  CH3   0  -0.535  -2.7770  -2.3313   0.4254
 0DF  C2   C  CR56  0   0.299  -1.4411  -0.2627  -0.0065
 0DF  C6   C  CR16  0  -0.266  -0.1279  -0.6523   0.0753
 0DF  C5   C  CR6   0  -0.007   0.8407   0.3457  -0.1253
 0DF  C4   C  CR16  0  -0.132   0.4170   1.6450  -0.3969
 0DF  N3   N  N     0  -0.413  -0.8625   2.0264  -0.4717
 0DF  C1   C  CR56  0   0.449  -1.7418   1.0799  -0.2756
 0DF  N2   N  NR15  0  -0.727  -3.1079   1.1794  -0.2872
 0DF  C8   C  CR6   0   0.083   2.2791   0.0254  -0.0609
 0DF  C13  C  CR16  0  -0.311   2.7647  -1.1770  -0.5785
 0DF  C12  C  CR16  0  -0.240   4.1172  -1.4792  -0.5219
 0DF  C11  C  CR16  0  -0.266   5.0114  -0.5840   0.0506
 0DF  C10  C  CR16  0  -0.239   4.5399   0.6149   0.5691
 0DF  C9   C  CR16  0  -0.311   3.1865   0.9150   0.5176
 0DF  H1   H  HCH3  0   0.271  -3.8296  -2.5619   0.5577
 0DF  H2   H  HCH3  0   0.259  -2.3859  -2.9344  -0.3934
 0DF  H3   H  HCH3  0   0.259  -2.2461  -2.5891   1.3411
 0DF  H4   H  HCR6  0   0.285   0.1537  -1.6719   0.3053
 0DF  H5   H  HCR6  0   0.261   1.1498   2.4214  -0.5826
 0DF  H6   H  HNR5  0   0.424  -3.6391   2.0204  -0.4530
 0DF  H7   H  HCR6  0   0.255   2.0845  -1.8769  -1.0485
 0DF  H8   H  HCR6  0   0.259   4.4740  -2.4143  -0.9336
 0DF  H9   H  HCR6  0   0.258   6.0667  -0.8196   0.0928
 0DF  H10  H  HCR6  0   0.258   5.2258   1.3169   1.0256
 0DF  H11  H  HCR6  0   0.255   2.8326   1.8420   0.9512

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
 0DF  C7   N1   single    1.441  0.020  1.441
 0DF  O1   C3   double    1.215  0.020  1.215
 0DF  N1   C3   single    1.379  0.020  1.379
 0DF  N1   C2   single    1.374  0.020  1.374
 0DF  C3   N2   single    1.377  0.020  1.377
 0DF  C2   C6   aromatic  1.372  0.020  1.372
 0DF  C2   C1   aromatic  1.402  0.020  1.402
 0DF  N2   C1   single    1.370  0.020  1.370
 0DF  C6   C5   aromatic  1.405  0.020  1.405
 0DF  C1   N3   aromatic  1.307  0.020  1.307
 0DF  C13  C12  aromatic  1.387  0.020  1.387
 0DF  C13  C8   aromatic  1.396  0.020  1.396
 0DF  C5   C8   single    1.475  0.020  1.475
 0DF  C5   C4   aromatic  1.393  0.020  1.393
 0DF  N3   C4   aromatic  1.337  0.020  1.337
 0DF  C12  C11  aromatic  1.389  0.020  1.389
 0DF  C8   C9   aromatic  1.396  0.020  1.396
 0DF  C11  C10  aromatic  1.389  0.020  1.389
 0DF  C9   C10  aromatic  1.387  0.020  1.387
 0DF  C7   H1   single    0.970  0.020  1.090
 0DF  C7   H2   single    0.970  0.020  1.090
 0DF  C7   H3   single    0.970  0.020  1.090
 0DF  C6   H4   single    0.930  0.020  1.080
 0DF  C4   H5   single    0.930  0.020  1.080
 0DF  N2   H6   single    0.860  0.020  1.020
 0DF  C13  H7   single    0.930  0.020  1.080
 0DF  C12  H8   single    0.930  0.020  1.080
 0DF  C11  H9   single    0.930  0.020  1.080
 0DF  C10  H10  single    0.930  0.020  1.080
 0DF  C9   H11  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
 0DF  N2   C3   N1   105.89  3.000
 0DF  N2   C3   O1   127.16  3.000
 0DF  N1   C3   O1   126.96  3.000
 0DF  C2   N1   C7   125.28  3.000
 0DF  C2   N1   C3   109.81  3.000
 0DF  C7   N1   C3   124.91  3.000
 0DF  H3   C7   H2   109.00  3.000
 0DF  H3   C7   H1   108.65  3.000
 0DF  H2   C7   H1   108.79  3.000
 0DF  H3   C7   N1   110.51  3.000
 0DF  H2   C7   N1   110.77  3.000
 0DF  H1   C7   N1   109.08  3.000
 0DF  C1   C2   C6   119.25  3.000
 0DF  C1   C2   N1   107.23  3.000
 0DF  C6   C2   N1   133.51  3.000
 0DF  H4   C6   C5   121.33  3.000
 0DF  H4   C6   C2   121.95  3.000
 0DF  C5   C6   C2   116.71  3.000
 0DF  C8   C5   C4   120.50  3.000
 0DF  C4   C5   C6   118.72  3.000
 0DF  C8   C5   C6   120.78  3.000
 0DF  H5   C4   N3   115.66  3.000
 0DF  H5   C4   C5   119.73  3.000
 0DF  N3   C4   C5   124.60  3.000
 0DF  C1   N3   C4   115.39  3.000
 0DF  N2   C1   N3   128.11  3.000
 0DF  N3   C1   C2   125.32  3.000
 0DF  N2   C1   C2   106.57  3.000
 0DF  H6   N2   C1   125.97  3.000
 0DF  H6   N2   C3   123.53  3.000
 0DF  C1   N2   C3   110.50  3.000
 0DF  C9   C8   C13  118.44  3.000
 0DF  C9   C8   C5   120.89  3.000
 0DF  C13  C8   C5   120.67  3.000
 0DF  H7   C13  C12  119.29  3.000
 0DF  H7   C13  C8   119.92  3.000
 0DF  C12  C13  C8   120.78  3.000
 0DF  H8   C12  C11  120.11  3.000
 0DF  H8   C12  C13  119.62  3.000
 0DF  C11  C12  C13  120.28  3.000
 0DF  H9   C11  C10  120.30  3.000
 0DF  H9   C11  C12  120.24  3.000
 0DF  C10  C11  C12  119.46  3.000
 0DF  H10  C10  C9   119.57  3.000
 0DF  H10  C10  C11  120.15  3.000
 0DF  C9   C10  C11  120.27  3.000
 0DF  H11  C9   C10  119.29  3.000
 0DF  H11  C9   C8   119.93  3.000
 0DF  C10  C9   C8   120.77  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
 0DF  CONST_01  C8   C5   C6   C2   180.00   0.0  0
 0DF  CONST_02  C4   C5   C6   C2     0.00   0.0  0
 0DF  CONST_03  C4   N3   C1   C2     0.00   0.0  0
 0DF  CONST_04  N3   C1   C2   C6     0.00   0.0  0
 0DF  CONST_07  N3   C4   C5   C6     0.00   0.0  0
 0DF  CONST_08  C1   C2   C6   C5     0.00   0.0  0
 0DF  CONST_09  C12  C13  C8   C5   180.00   0.0  0
 0DF  CONST_10  C10  C9   C8   C5   180.00   0.0  0
 0DF  CONST_11  C1   N3   C4   C5     0.00   0.0  0
 0DF  CONST_14  C8   C5   C4   N3   180.00   0.0  0
 0DF  CONST_15  C11  C12  C13  C8     0.00   0.0  0
 0DF  CONST_16  C11  C10  C9   C8     0.00   0.0  0
 0DF  CONST_17  C10  C11  C12  C13    0.00   0.0  0
 0DF  CONST_18  C10  C9   C8   C13    0.00   0.0  0
 0DF  CONST_19  C9   C8   C13  C12    0.00   0.0  0
 0DF  CONST_20  C9   C10  C11  C12    0.00   0.0  0
 0DF  CONST_21  C1   C2   N1   C3     0.00   0.0  0
 0DF  CONST_22  C2   C1   N2   C3     0.00   0.0  0
 0DF  CONST_23  C1   N2   C3   N1     0.00   0.0  0
 0DF  CONST_24  N2   C1   C2   N1     0.00   0.0  0
 0DF  CONST_25  N2   C3   N1   C2     0.00   0.0  0
 0DF  CONST_26  C2   N1   C3   O1   180.00   0.0  0
 0DF  CONST_27  C1   N2   C3   O1   180.00   0.0  0
 0DF  CONST_28  N2   C3   N1   C7   180.00   0.0  0
 0DF  CONST_29  C1   C2   N1   C7   180.00   0.0  0
 0DF  CONST_30  H4   C6   C2   N1     0.00   0.0  0
 0DF  CONST_31  H5   C4   C5   C6   180.00   0.0  0
 0DF  CONST_32  H7   C13  C8   C5     0.00   0.0  0
 0DF  CONST_33  H11  C9   C8   C5     0.00   0.0  0
 0DF  CONST_34  H8   C12  C13  C8   180.00   0.0  0
 0DF  CONST_35  H10  C10  C9   C8   180.00   0.0  0
 0DF  CONST_36  H9   C11  C12  C13  180.00   0.0  0
 0DF  CONST_37  H6   N2   C3   N1   180.00   0.0  0
 0DF  CONST_38  C7   N1   C3   O1     0.00   0.0  0
 0DF  Var_01    H1   C7   N1   C3    -4.29  30.0  3

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
 0DF  plan-1  C5   0.020
 0DF  plan-1  C8   0.020
 0DF  plan-1  C13  0.020
 0DF  plan-1  C12  0.020
 0DF  plan-1  C11  0.020
 0DF  plan-1  C10  0.020
 0DF  plan-1  C9   0.020
 0DF  plan-1  H7   0.020
 0DF  plan-1  H8   0.020
 0DF  plan-1  H9   0.020
 0DF  plan-1  H10  0.020
 0DF  plan-1  H11  0.020
 0DF  plan-2  O1   0.020
 0DF  plan-2  C3   0.020
 0DF  plan-2  N1   0.020
 0DF  plan-2  C7   0.020
 0DF  plan-2  C2   0.020
 0DF  plan-2  C6   0.020
 0DF  plan-2  C5   0.020
 0DF  plan-2  C4   0.020
 0DF  plan-2  N3   0.020
 0DF  plan-2  C1   0.020
 0DF  plan-2  N2   0.020
 0DF  plan-2  C8   0.020
 0DF  plan-2  H4   0.020
 0DF  plan-2  H5   0.020
 0DF  plan-2  H6   0.020

