# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 17:42:01 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3-(1-methyl-2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-6-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)Nc2ncc(cc12)c3cccc(c3)C(N)=O
#
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
 0DJ  0DJ  3-(1-methyl-2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-6-yl)benzamide  ligand  32  20  .  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_0DJ
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
 0DJ  C1   C  CR16  0  -0.130  -0.3258   1.2889  -0.6460
 0DJ  C2   C  CR6   0  -0.008  -0.0992  -0.0285  -0.2541
 0DJ  C3   C  CR16  0  -0.264  -1.1999  -0.8350   0.0801
 0DJ  C4   C  CR56  0   0.300  -2.4385  -0.2499   0.0028
 0DJ  C5   C  CR56  0   0.451  -2.5380   1.0905  -0.3979
 0DJ  N6   N  N     0  -0.413  -1.5322   1.8598  -0.7208
 0DJ  N7   N  NR5   0  -0.590  -3.7135  -0.6933   0.2571
 0DJ  C8   C  CR5   0   0.650  -4.6176   0.3201   0.0168
 0DJ  N9   N  NR15  0  -0.726  -3.8698   1.4065  -0.3794
 0DJ  C10  C  CH3   0  -0.535  -4.0669  -2.0283   0.6699
 0DJ  O11  O  O     0  -0.486  -5.8251   0.2638   0.1333
 0DJ  C12  C  CR6   0   0.104   1.2732  -0.5659  -0.2073
 0DJ  C13  C  CR16  0  -0.308   1.5448  -1.8692  -0.6275
 0DJ  C14  C  CR16  0  -0.225   2.8371  -2.3676  -0.5901
 0DJ  C15  C  CR16  0  -0.296   3.8834  -1.5714  -0.1484
 0DJ  C16  C  CR6   0  -0.017   3.6316  -0.2676   0.2722
 0DJ  C17  C  CR16  0  -0.340   2.3278   0.2164   0.2567
 0DJ  C18  C  C     0   0.490   4.7068   0.6389   0.7878
 0DJ  O19  O  O     0  -0.480   4.4410   1.5692   1.5363
 0DJ  N20  N  NH2   0  -0.812   5.9560   0.3657   0.3828
 0DJ  H1   H  HCR6  0   0.262   0.5089   1.9167  -0.9358
 0DJ  H2   H  HCR6  0   0.286  -1.0685  -1.8605   0.4005
 0DJ  H3   H  HNR5  0   0.424  -4.2689   2.3007  -0.6204
 0DJ  H4   H  HCH3  0   0.260  -3.4780  -2.3225   1.5373
 0DJ  H5   H  HCH3  0   0.271  -5.1177  -2.0501   0.9425
 0DJ  H6   H  HCH3  0   0.259  -3.8978  -2.7437  -0.1345
 0DJ  H7   H  HCR6  0   0.263   0.7441  -2.4962  -1.0002
 0DJ  H8   H  HCR6  0   0.267   3.0329  -3.3816  -0.9120
 0DJ  H9   H  HCR6  0   0.263   4.8819  -1.9878  -0.1154
 0DJ  H10  H  HCR6  0   0.261   2.1332   1.2165   0.6221
 0DJ  H11  H  HNH2  0   0.413   6.1534  -0.2919  -0.3511
 0DJ  H12  H  HNH2  0   0.406   6.7108   0.9704   0.6643

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
 0DJ  O19  C18  double    1.223  0.020  1.223
 0DJ  N20  C18  single    1.341  0.020  1.341
 0DJ  C18  C16  single    1.498  0.020  1.498
 0DJ  C16  C15  aromatic  1.393  0.020  1.393
 0DJ  C16  C17  aromatic  1.391  0.020  1.391
 0DJ  C15  C14  aromatic  1.387  0.020  1.387
 0DJ  C17  C12  aromatic  1.393  0.020  1.393
 0DJ  C14  C13  aromatic  1.386  0.020  1.386
 0DJ  C12  C13  aromatic  1.396  0.020  1.396
 0DJ  C12  C2   single    1.475  0.020  1.475
 0DJ  C2   C3   aromatic  1.405  0.020  1.405
 0DJ  C2   C1   aromatic  1.393  0.020  1.393
 0DJ  C3   C4   aromatic  1.372  0.020  1.372
 0DJ  C1   N6   aromatic  1.337  0.020  1.337
 0DJ  N6   C5   aromatic  1.307  0.020  1.307
 0DJ  C4   C5   aromatic  1.403  0.020  1.403
 0DJ  C4   N7   single    1.374  0.020  1.374
 0DJ  C5   N9   single    1.369  0.020  1.369
 0DJ  N7   C10  single    1.441  0.020  1.441
 0DJ  N7   C8   single    1.379  0.020  1.379
 0DJ  N9   C8   single    1.377  0.020  1.377
 0DJ  C8   O11  double    1.214  0.020  1.214
 0DJ  C1   H1   single    0.930  0.020  1.080
 0DJ  C3   H2   single    0.930  0.020  1.080
 0DJ  N9   H3   single    0.860  0.020  1.020
 0DJ  C10  H4   single    0.970  0.020  1.090
 0DJ  C10  H5   single    0.970  0.020  1.090
 0DJ  C10  H6   single    0.970  0.020  1.090
 0DJ  C13  H7   single    0.930  0.020  1.080
 0DJ  C14  H8   single    0.930  0.020  1.080
 0DJ  C15  H9   single    0.930  0.020  1.080
 0DJ  C17  H10  single    0.930  0.020  1.080
 0DJ  N20  H11  single    0.860  0.020  1.020
 0DJ  N20  H12  single    0.860  0.020  1.020

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
 0DJ  H1   C1   N6   115.64  3.000
 0DJ  H1   C1   C2   119.85  3.000
 0DJ  N6   C1   C2   124.50  3.000
 0DJ  C12  C2   C3   120.82  3.000
 0DJ  C3   C2   C1   118.84  3.000
 0DJ  C12  C2   C1   120.33  3.000
 0DJ  H2   C3   C4   122.03  3.000
 0DJ  H2   C3   C2   121.28  3.000
 0DJ  C4   C3   C2   116.69  3.000
 0DJ  N7   C4   C5   107.19  3.000
 0DJ  N7   C4   C3   133.62  3.000
 0DJ  C5   C4   C3   119.18  3.000
 0DJ  N9   C5   N6   128.04  3.000
 0DJ  N9   C5   C4   106.60  3.000
 0DJ  N6   C5   C4   125.36  3.000
 0DJ  C5   N6   C1   115.43  3.000
 0DJ  C10  N7   C8   124.73  3.000
 0DJ  C8   N7   C4   109.82  3.000
 0DJ  C10  N7   C4   125.42  3.000
 0DJ  O11  C8   N9   127.17  3.000
 0DJ  O11  C8   N7   126.94  3.000
 0DJ  N9   C8   N7   105.89  3.000
 0DJ  H3   N9   C8   123.60  3.000
 0DJ  H3   N9   C5   125.91  3.000
 0DJ  C8   N9   C5   110.50  3.000
 0DJ  H6   C10  H5   108.81  3.000
 0DJ  H6   C10  H4   109.06  3.000
 0DJ  H5   C10  H4   108.54  3.000
 0DJ  H6   C10  N7   111.01  3.000
 0DJ  H5   C10  N7   109.14  3.000
 0DJ  H4   C10  N7   110.23  3.000
 0DJ  C17  C12  C13  118.51  3.000
 0DJ  C13  C12  C2   120.78  3.000
 0DJ  C17  C12  C2   120.71  3.000
 0DJ  H7   C13  C14  119.38  3.000
 0DJ  H7   C13  C12  120.01  3.000
 0DJ  C14  C13  C12  120.61  3.000
 0DJ  H8   C14  C15  119.76  3.000
 0DJ  H8   C14  C13  119.86  3.000
 0DJ  C15  C14  C13  120.38  3.000
 0DJ  H9   C15  C16  121.17  3.000
 0DJ  H9   C15  C14  119.00  3.000
 0DJ  C16  C15  C14  119.81  3.000
 0DJ  C18  C16  C17  117.78  3.000
 0DJ  C17  C16  C15  119.46  3.000
 0DJ  C18  C16  C15  122.73  3.000
 0DJ  H10  C17  C16  119.10  3.000
 0DJ  H10  C17  C12  119.69  3.000
 0DJ  C16  C17  C12  121.21  3.000
 0DJ  N20  C18  O19  122.82  3.000
 0DJ  N20  C18  C16  116.19  3.000
 0DJ  O19  C18  C16  120.99  3.000
 0DJ  H12  N20  H11  116.72  3.000
 0DJ  H12  N20  C18  119.42  3.000
 0DJ  H11  N20  C18  122.46  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
 0DJ  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 0DJ  CONST_04  C4   C5   N6   C1      0.00   0.0  0
 0DJ  CONST_05  C16  C17  C12  C2    180.00   0.0  0
 0DJ  CONST_06  C14  C13  C12  C2    180.00   0.0  0
 0DJ  CONST_07  C5   C4   C3   C2      0.00   0.0  0
 0DJ  CONST_08  C5   N6   C1   C2      0.00   0.0  0
 0DJ  CONST_11  N6   C1   C2   C3      0.00   0.0  0
 0DJ  CONST_12  N6   C5   C4   C3      0.00   0.0  0
 0DJ  CONST_13  C12  C2   C3   C4    180.00   0.0  0
 0DJ  CONST_14  C12  C2   C1   N6    180.00   0.0  0
 0DJ  CONST_15  C15  C16  C17  C12     0.00   0.0  0
 0DJ  CONST_16  C15  C14  C13  C12     0.00   0.0  0
 0DJ  CONST_17  C16  C15  C14  C13     0.00   0.0  0
 0DJ  CONST_18  C16  C17  C12  C13     0.00   0.0  0
 0DJ  CONST_19  C17  C16  C15  C14     0.00   0.0  0
 0DJ  CONST_20  C17  C12  C13  C14     0.00   0.0  0
 0DJ  CONST_21  C8   N9   C5   C4      0.00   0.0  0
 0DJ  CONST_22  N9   C8   N7   C4      0.00   0.0  0
 0DJ  CONST_23  C8   N7   C4   C5      0.00   0.0  0
 0DJ  CONST_24  N7   C8   N9   C5      0.00   0.0  0
 0DJ  CONST_25  N9   C5   C4   N7      0.00   0.0  0
 0DJ  CONST_26  C18  C16  C17  C12   180.00   0.0  0
 0DJ  CONST_27  C18  C16  C15  C14   180.00   0.0  0
 0DJ  CONST_28  O11  C8   N7   C4    180.00   0.0  0
 0DJ  CONST_29  C10  N7   C4   C5    180.00   0.0  0
 0DJ  CONST_30  O11  C8   N9   C5    180.00   0.0  0
 0DJ  CONST_31  C10  N7   C8   N9    180.00   0.0  0
 0DJ  CONST_32  H2   C3   C2   C1    180.00   0.0  0
 0DJ  CONST_33  H10  C17  C12  C2      0.00   0.0  0
 0DJ  CONST_34  H7   C13  C12  C2      0.00   0.0  0
 0DJ  CONST_35  H1   C1   C2   C3    180.00   0.0  0
 0DJ  CONST_36  H8   C14  C13  C12   180.00   0.0  0
 0DJ  CONST_37  H9   C15  C14  C13   180.00   0.0  0
 0DJ  CONST_38  H3   N9   C5   C4    180.00   0.0  0
 0DJ  CONST_39  O11  C8   N7   C10     0.00   0.0  0
 0DJ  CONST_40  H11  N20  C18  C16     0.00   0.0  0
 0DJ  CONST_41  H12  N20  C18  C16   180.00   0.0  0
 0DJ  Var_01    O19  C18  C16  C15  -155.75  30.0  2
 0DJ  Var_02    H4   C10  N7   C4     52.28  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
 0DJ  plan-1  C2   0.020
 0DJ  plan-1  C12  0.020
 0DJ  plan-1  C13  0.020
 0DJ  plan-1  C14  0.020
 0DJ  plan-1  C15  0.020
 0DJ  plan-1  C16  0.020
 0DJ  plan-1  C17  0.020
 0DJ  plan-1  C18  0.020
 0DJ  plan-1  H7   0.020
 0DJ  plan-1  H8   0.020
 0DJ  plan-1  H9   0.020
 0DJ  plan-1  H10  0.020
 0DJ  plan-2  C1   0.020
 0DJ  plan-2  C2   0.020
 0DJ  plan-2  C3   0.020
 0DJ  plan-2  C4   0.020
 0DJ  plan-2  C5   0.020
 0DJ  plan-2  N6   0.020
 0DJ  plan-2  N7   0.020
 0DJ  plan-2  C8   0.020
 0DJ  plan-2  N9   0.020
 0DJ  plan-2  C10  0.020
 0DJ  plan-2  O11  0.020
 0DJ  plan-2  C12  0.020
 0DJ  plan-2  H1   0.020
 0DJ  plan-2  H2   0.020
 0DJ  plan-2  H3   0.020
 0DJ  plan-3  C16  0.020
 0DJ  plan-3  C18  0.020
 0DJ  plan-3  O19  0.020
 0DJ  plan-3  N20  0.020
 0DJ  plan-3  H11  0.020
 0DJ  plan-3  H12  0.020

