# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:10:33 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: N-(pyridin-3-yl)-2-(thiophen-3-yl)-3H-imidazo[4,5-b]pyridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cccnc1)c2ccnc3[nH]c(nc23)c4cscc4
#
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
 0KD  0KD  N-(pyridin-3-yl)-2-(thiophen-3-yl)-3H-imidazo[4,5-b]pyridine-7-carboxamide  ligand  34  23  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0KD
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
 0KD  C1   C  CR15  0  -0.191  -3.5673   1.8987   0.2364
 0KD  C2   C  CR15  0  -0.465  -4.7569   2.5142   0.4527
 0KD  S3   S  S2    0   0.263  -6.0280   1.3813   0.6602
 0KD  C4   C  CR15  0  -0.548  -4.9700   0.0616   0.4563
 0KD  C5   C  CR5   0   0.086  -3.6835   0.4755   0.2363
 0KD  C6   C  CR5   0   0.504  -2.5455  -0.3971   0.0261
 0KD  N7   N  NR15  0  -0.716  -2.6452  -1.7530  -0.0503
 0KD  C8   C  CR56  0   0.458  -1.3863  -2.2375  -0.2498
 0KD  C9   C  CR56  0   0.109  -0.5627  -1.0944  -0.2882
 0KD  N10  N  N     0  -0.461  -1.3136   0.0303  -0.1111
 0KD  N11  N  N     0  -0.412  -1.0147  -3.4930  -0.3761
 0KD  C12  C  CR16  0  -0.084   0.2913  -3.6633  -0.5486
 0KD  C13  C  CR16  0  -0.370   1.2187  -2.6207  -0.5867
 0KD  C14  C  CR6   0  -0.057   0.8055  -1.2987  -0.4545
 0KD  C15  C  C     0   0.520   1.7528  -0.1481  -0.5351
 0KD  N16  N  NH1   0  -0.746   2.9266  -0.3588   0.1123
 0KD  C17  C  CR6   0   0.290   4.0344   0.4823   0.1994
 0KD  C18  C  CR16  0  -0.210   4.1788   1.7039  -0.4546
 0KD  C19  C  CR16  0  -0.312   5.3551   2.4126  -0.2624
 0KD  C20  C  CR16  0  -0.082   6.3411   1.8968   0.5611
 0KD  N21  N  N     0  -0.388   6.2078   0.7314   1.1855
 0KD  C22  C  CR16  0  -0.144   5.0908   0.0511   1.0083
 0KD  O23  O  O     0  -0.440   1.4673   0.8691  -1.1352
 0KD  H1   H  HCR5  0   0.271  -2.6374   2.4239   0.0769
 0KD  H2   H  HCR5  0   0.304  -4.9566   3.5732   0.4990
 0KD  H3   H  HCR5  0   0.300  -5.3531  -0.9460   0.5166
 0KD  H4   H  HNR5  0   0.427  -3.4828  -2.3108   0.0182
 0KD  H6   H  HCR6  0   0.271   0.6339  -4.6839  -0.6657
 0KD  H7   H  HCR6  0   0.282   2.2601  -2.8645  -0.7495
 0KD  H8   H  HNH1  0   0.427   2.9992  -1.2150   0.6432
 0KD  H9   H  HCR6  0   0.296   3.4087   2.1014  -1.0944
 0KD  H10  H  HCR6  0   0.276   5.5003   3.3647  -0.7538
 0KD  H11  H  HCR6  0   0.266   7.2663   2.4372   0.7238
 0KD  H12  H  HCR6  0   0.275   5.0101  -0.8980   1.5316

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
 0KD  C2   S3   aromatic  1.715  0.020  1.715
 0KD  C2   C1   aromatic  1.357  0.020  1.357
 0KD  S3   C4   aromatic  1.704  0.020  1.704
 0KD  C1   C5   aromatic  1.428  0.020  1.428
 0KD  C4   C5   aromatic  1.369  0.020  1.369
 0KD  C5   C6   single    1.449  0.020  1.449
 0KD  C6   N7   aromatic  1.362  0.020  1.362
 0KD  C6   N10  aromatic  1.311  0.020  1.311
 0KD  N7   C8   aromatic  1.364  0.020  1.364
 0KD  N10  C9   aromatic  1.364  0.020  1.364
 0KD  C8   N11  aromatic  1.315  0.020  1.315
 0KD  C8   C9   aromatic  1.409  0.020  1.409
 0KD  N11  C12  aromatic  1.328  0.020  1.328
 0KD  C9   C14  aromatic  1.393  0.020  1.393
 0KD  C12  C13  aromatic  1.396  0.020  1.396
 0KD  C14  C13  aromatic  1.391  0.020  1.391
 0KD  C14  C15  single    1.493  0.020  1.493
 0KD  C18  C19  aromatic  1.387  0.020  1.387
 0KD  C18  C17  aromatic  1.393  0.020  1.393
 0KD  N16  C15  single    1.357  0.020  1.357
 0KD  N16  C17  single    1.394  0.020  1.394
 0KD  C15  O23  double    1.215  0.020  1.215
 0KD  C19  C20  aromatic  1.384  0.020  1.384
 0KD  C17  C22  aromatic  1.399  0.020  1.399
 0KD  C20  N21  aromatic  1.329  0.020  1.329
 0KD  C22  N21  aromatic  1.320  0.020  1.320
 0KD  C1   H1   single    0.930  0.020  1.080
 0KD  C2   H2   single    0.930  0.020  1.080
 0KD  C4   H3   single    0.930  0.020  1.080
 0KD  N7   H4   single    0.860  0.020  1.020
 0KD  C12  H6   single    0.930  0.020  1.080
 0KD  C13  H7   single    0.930  0.020  1.080
 0KD  N16  H8   single    0.860  0.020  1.020
 0KD  C18  H9   single    0.930  0.020  1.080
 0KD  C19  H10  single    0.930  0.020  1.080
 0KD  C20  H11  single    0.930  0.020  1.080
 0KD  C22  H12  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
 0KD  H1   C1   C5   123.70  3.000
 0KD  H1   C1   C2   123.92  3.000
 0KD  C5   C1   C2   112.38  3.000
 0KD  H2   C2   S3   120.41  3.000
 0KD  H2   C2   C1   127.91  3.000
 0KD  S3   C2   C1   111.68  3.000
 0KD  C4   S3   C2    92.12  3.000
 0KD  H3   C4   C5   128.64  3.000
 0KD  H3   C4   S3   119.73  3.000
 0KD  C5   C4   S3   111.63  3.000
 0KD  C6   C5   C4   125.39  3.000
 0KD  C6   C5   C1   122.42  3.000
 0KD  C4   C5   C1   112.19  3.000
 0KD  N10  C6   N7   112.80  3.000
 0KD  N10  C6   C5   123.82  3.000
 0KD  N7   C6   C5   123.38  3.000
 0KD  H4   N7   C8   125.46  3.000
 0KD  H4   N7   C6   127.42  3.000
 0KD  C8   N7   C6   107.12  3.000
 0KD  N11  C8   C9   127.33  3.000
 0KD  C9   C8   N7   104.79  3.000
 0KD  N11  C8   N7   127.88  3.000
 0KD  C14  C9   N10  132.61  3.000
 0KD  C14  C9   C8   117.27  3.000
 0KD  N10  C9   C8   110.09  3.000
 0KD  C9   N10  C6   105.19  3.000
 0KD  C12  N11  C8   114.37  3.000
 0KD  H6   C12  C13  119.39  3.000
 0KD  H6   C12  N11  116.48  3.000
 0KD  C13  C12  N11  124.12  3.000
 0KD  H7   C13  C14  120.95  3.000
 0KD  H7   C13  C12  118.38  3.000
 0KD  C14  C13  C12  120.65  3.000
 0KD  C15  C14  C13  122.60  3.000
 0KD  C15  C14  C9   121.11  3.000
 0KD  C13  C14  C9   116.25  3.000
 0KD  O23  C15  N16  124.67  3.000
 0KD  O23  C15  C14  121.53  3.000
 0KD  N16  C15  C14  113.80  3.000
 0KD  H8   N16  C17  114.94  3.000
 0KD  H8   N16  C15  116.40  3.000
 0KD  C17  N16  C15  128.59  3.000
 0KD  C22  C17  C18  117.61  3.000
 0KD  C22  C17  N16  116.77  3.000
 0KD  C18  C17  N16  125.61  3.000
 0KD  H9   C18  C19  120.02  3.000
 0KD  H9   C18  C17  121.88  3.000
 0KD  C19  C18  C17  118.10  3.000
 0KD  H10  C19  C20  120.18  3.000
 0KD  H10  C19  C18  120.06  3.000
 0KD  C20  C19  C18  119.75  3.000
 0KD  H11  C20  N21  116.90  3.000
 0KD  H11  C20  C19  120.77  3.000
 0KD  N21  C20  C19  122.33  3.000
 0KD  C22  N21  C20  118.28  3.000
 0KD  H12  C22  N21  116.64  3.000
 0KD  H12  C22  C17  119.44  3.000
 0KD  N21  C22  C17  123.92  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
 0KD  CONST_01  C4   S3   C2   C1     0.00   0.0  0
 0KD  CONST_02  S3   C4   C5   C1     0.00   0.0  0
 0KD  CONST_03  N7   C6   C5   C1   180.00   0.0  0
 0KD  CONST_04  N10  C6   C5   C1     0.00   0.0  0
 0KD  CONST_05  C5   C4   S3   C2     0.00   0.0  0
 0KD  CONST_06  C4   C5   C1   C2     0.00   0.0  0
 0KD  CONST_07  C6   C5   C1   C2   180.00   0.0  0
 0KD  CONST_08  C5   C1   C2   S3     0.00   0.0  0
 0KD  CONST_09  C6   C5   C4   S3   180.00   0.0  0
 0KD  CONST_10  N7   C6   C5   C4     0.00   0.0  0
 0KD  CONST_11  N10  C6   C5   C4   180.00   0.0  0
 0KD  CONST_12  C8   N7   C6   C5   180.00   0.0  0
 0KD  CONST_13  C9   N10  C6   C5   180.00   0.0  0
 0KD  CONST_14  N11  C8   N7   C6   180.00   0.0  0
 0KD  CONST_15  C9   C8   N7   C6     0.00   0.0  0
 0KD  CONST_16  C8   C9   N10  C6     0.00   0.0  0
 0KD  CONST_17  C14  C9   N10  C6   180.00   0.0  0
 0KD  CONST_18  C9   N10  C6   N7     0.00   0.0  0
 0KD  CONST_19  C12  N11  C8   N7   180.00   0.0  0
 0KD  CONST_20  N10  C9   C8   N7     0.00   0.0  0
 0KD  CONST_21  C14  C9   C8   N7   180.00   0.0  0
 0KD  CONST_22  N10  C6   N7   C8     0.00   0.0  0
 0KD  CONST_23  C13  C12  N11  C8     0.00   0.0  0
 0KD  CONST_24  C13  C14  C9   C8     0.00   0.0  0
 0KD  CONST_25  C12  N11  C8   C9     0.00   0.0  0
 0KD  CONST_26  C12  C13  C14  C9     0.00   0.0  0
 0KD  CONST_27  N11  C8   C9   N10  180.00   0.0  0
 0KD  CONST_28  C13  C14  C9   N10  180.00   0.0  0
 0KD  CONST_29  C14  C9   C8   N11    0.00   0.0  0
 0KD  CONST_30  C14  C13  C12  N11    0.00   0.0  0
 0KD  CONST_31  C20  C19  C18  C17    0.00   0.0  0
 0KD  CONST_32  C20  N21  C22  C17    0.00   0.0  0
 0KD  CONST_33  N21  C20  C19  C18    0.00   0.0  0
 0KD  CONST_34  N21  C22  C17  C18    0.00   0.0  0
 0KD  CONST_35  C22  C17  C18  C19    0.00   0.0  0
 0KD  CONST_36  C22  N21  C20  C19    0.00   0.0  0
 0KD  CONST_37  C15  C14  C9   C8   180.00   0.0  0
 0KD  CONST_38  C15  C14  C9   N10    0.00   0.0  0
 0KD  CONST_39  C15  C14  C13  C12  180.00   0.0  0
 0KD  CONST_40  C19  C18  C17  N16  180.00   0.0  0
 0KD  CONST_41  N21  C22  C17  N16  180.00   0.0  0
 0KD  CONST_42  H3   C4   C5   C1   180.00   0.0  0
 0KD  CONST_43  H1   C1   C2   S3   180.00   0.0  0
 0KD  CONST_44  H2   C2   S3   C4   180.00   0.0  0
 0KD  CONST_45  H4   N7   C6   C5     0.00   0.0  0
 0KD  CONST_46  H6   C12  N11  C8   180.00   0.0  0
 0KD  CONST_47  H7   C13  C14  C9   180.00   0.0  0
 0KD  CONST_48  H10  C19  C18  C17  180.00   0.0  0
 0KD  CONST_49  H11  C20  C19  C18  180.00   0.0  0
 0KD  CONST_50  H12  C22  C17  C18  180.00   0.0  0
 0KD  CONST_51  H9   C18  C19  C20  180.00   0.0  0
 0KD  CONST_52  C17  N16  C15  C14  180.00   0.0  0
 0KD  CONST_53  C18  C17  N16  C15    0.00   0.0  0
 0KD  CONST_54  C22  C17  N16  C15  180.00   0.0  0
 0KD  CONST_55  H8   N16  C17  C18  180.00   0.0  0
 0KD  CONST_56  O23  C15  N16  C17    0.00   0.0  0
 0KD  Var_01    N16  C15  C14  C9   140.76  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
 0KD  plan-1  C1   0.020
 0KD  plan-1  C2   0.020
 0KD  plan-1  S3   0.020
 0KD  plan-1  C4   0.020
 0KD  plan-1  C5   0.020
 0KD  plan-1  C6   0.020
 0KD  plan-1  H1   0.020
 0KD  plan-1  H2   0.020
 0KD  plan-1  H3   0.020
 0KD  plan-2  N16  0.020
 0KD  plan-2  C17  0.020
 0KD  plan-2  C18  0.020
 0KD  plan-2  C19  0.020
 0KD  plan-2  C20  0.020
 0KD  plan-2  N21  0.020
 0KD  plan-2  C22  0.020
 0KD  plan-2  H9   0.020
 0KD  plan-2  H10  0.020
 0KD  plan-2  H11  0.020
 0KD  plan-2  H12  0.020
 0KD  plan-3  C5   0.020
 0KD  plan-3  C6   0.020
 0KD  plan-3  N7   0.020
 0KD  plan-3  C8   0.020
 0KD  plan-3  C9   0.020
 0KD  plan-3  N10  0.020
 0KD  plan-3  N11  0.020
 0KD  plan-3  C12  0.020
 0KD  plan-3  C13  0.020
 0KD  plan-3  C14  0.020
 0KD  plan-3  C15  0.020
 0KD  plan-3  H4   0.020
 0KD  plan-3  H6   0.020
 0KD  plan-3  H7   0.020
 0KD  plan-4  C14  0.020
 0KD  plan-4  C15  0.020
 0KD  plan-4  N16  0.020
 0KD  plan-4  C17  0.020
 0KD  plan-4  O23  0.020
 0KD  plan-4  H8   0.020

