# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:23:02 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-[4-(2-methoxy-3H-imidazo[4,5-b]pyridin-3-yl)phenyl]-5-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc2cccnc2n1c3ccc(Nc4ccc(C)cn4)cc3
#
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
 2KR  2KR  N-[4-(2-methoxy-3H-imidazo[4,5-b]pyridin-3-yl)phenyl]-5-methylpyridin-2-amine  ligand  42  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2KR
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
 2KR  C01  C  CH3   0  -0.420   4.0048  -3.1666  -1.3969
 2KR  O02  O  O2    0  -0.448   3.0457  -2.2378  -0.8892
 2KR  C03  C  CR5   0   0.686   3.5003  -1.0666  -0.5189
 2KR  N04  N  N     0  -0.524   4.7271  -0.6435  -0.5760
 2KR  C05  C  CR56  0   0.113   4.6681   0.6365  -0.0748
 2KR  C06  C  CR16  0  -0.224   5.6383   1.6013   0.1286
 2KR  C07  C  CR16  0  -0.341   5.2115   2.8097   0.6728
 2KR  C08  C  CR16  0  -0.097   3.8689   3.0049   0.9859
 2KR  N09  N  N     0  -0.416   2.9185   2.0869   0.7975
 2KR  C10  C  CR56  0   0.441   3.3482   0.9606   0.2839
 2KR  N11  N  NR5   0  -0.670   2.6055  -0.1648  -0.0125
 2KR  C12  C  CR6   0   0.275   1.2156  -0.3460   0.1808
 2KR  C13  C  CR16  0  -0.254   0.7500  -1.2612   1.1169
 2KR  C14  C  CR16  0  -0.376  -0.6064  -1.4217   1.3080
 2KR  C15  C  CR6   0   0.384  -1.5389  -0.6614   0.5847
 2KR  N16  N  NH1   0  -0.786  -2.8712  -0.8910   0.8673
 2KR  C17  C  CR6   0   0.542  -4.0231  -0.3420   0.3534
 2KR  C18  C  CR16  0  -0.414  -5.2513  -0.7675   0.8910
 2KR  C19  C  CR16  0  -0.163  -6.4099  -0.2307   0.3844
 2KR  C20  C  CR6   0  -0.020  -6.3618   0.7182  -0.6439
 2KR  C21  C  CH3   0  -0.726  -7.6045   1.3206  -1.2238
 2KR  C22  C  CR16  0  -0.086  -5.0994   1.0605  -1.0902
 2KR  N23  N  N     0  -0.469  -3.9611   0.5541  -0.6159
 2KR  C24  C  CR16  0  -0.330  -1.0578   0.2628  -0.3502
 2KR  C25  C  CR16  0  -0.255   0.3072   0.4070  -0.5449
 2KR  H1   H  HCH3  0   0.242   4.4664  -2.7938  -2.3109
 2KR  H2   H  HCH3  0   0.242   4.7797  -3.3730  -0.6594
 2KR  H3   H  HCH3  0   0.258   3.4527  -4.0762  -1.6114
 2KR  H4   H  HCR6  0   0.270   6.6774   1.4278  -0.1194
 2KR  H5   H  HCR6  0   0.267   5.9189   3.6058   0.8590
 2KR  H6   H  HCR6  0   0.257   3.5452   3.9478   1.4095
 2KR  H7   H  HCR6  0   0.271   1.4455  -1.8475   1.7031
 2KR  H8   H  HCR6  0   0.272  -0.9550  -2.1419   2.0387
 2KR  H9   H  HNH1  0   0.412  -3.0270  -1.5756   1.5905
 2KR  H10  H  HCR6  0   0.275  -5.2821  -1.5001   1.6875
 2KR  H11  H  HCR6  0   0.264  -7.3648  -0.5460   0.7882
 2KR  H12  H  HCH3  0   0.246  -8.2089   1.8049  -0.4555
 2KR  H13  H  HCH3  0   0.244  -7.3685   2.0688  -1.9797
 2KR  H14  H  HCH3  0   0.246  -8.2317   0.5622  -1.6952
 2KR  H15  H  HCR6  0   0.251  -4.9892   1.7924  -1.8849
 2KR  H16  H  HCR6  0   0.290  -1.7438   0.8610  -0.9256
 2KR  H17  H  HCR6  0   0.268   0.6625   1.1186  -1.2792

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
 2KR  C07  C06  aromatic  1.392  0.020  1.392
 2KR  C07  C08  aromatic  1.392  0.020  1.392
 2KR  C06  C05  aromatic  1.383  0.020  1.383
 2KR  C08  N09  aromatic  1.335  0.020  1.335
 2KR  C05  N04  aromatic  1.376  0.020  1.376
 2KR  C05  C10  aromatic  1.406  0.020  1.406
 2KR  N09  C10  aromatic  1.310  0.020  1.310
 2KR  N04  C03  aromatic  1.299  0.020  1.299
 2KR  C10  N11  aromatic  1.381  0.020  1.381
 2KR  C03  N11  aromatic  1.368  0.020  1.368
 2KR  C03  O02  single    1.310  0.020  1.310
 2KR  N11  C12  single    1.415  0.020  1.415
 2KR  C01  O02  single    1.428  0.020  1.428
 2KR  C12  C13  aromatic  1.389  0.020  1.389
 2KR  C12  C25  aromatic  1.385  0.020  1.385
 2KR  C13  C14  aromatic  1.379  0.020  1.379
 2KR  C25  C24  aromatic  1.386  0.020  1.386
 2KR  C14  C15  aromatic  1.404  0.020  1.404
 2KR  C24  C15  aromatic  1.400  0.020  1.400
 2KR  C15  N16  single    1.381  0.020  1.381
 2KR  N23  C22  aromatic  1.333  0.020  1.333
 2KR  N23  C17  aromatic  1.321  0.020  1.321
 2KR  C22  C20  aromatic  1.382  0.020  1.382
 2KR  N16  C17  single    1.376  0.020  1.376
 2KR  C17  C18  aromatic  1.407  0.020  1.407
 2KR  C20  C21  single    1.498  0.020  1.498
 2KR  C20  C19  aromatic  1.400  0.020  1.400
 2KR  C18  C19  aromatic  1.374  0.020  1.374
 2KR  C01  H1   single    0.970  0.020  1.090
 2KR  C01  H2   single    0.970  0.020  1.090
 2KR  C01  H3   single    0.970  0.020  1.090
 2KR  C06  H4   single    0.930  0.020  1.080
 2KR  C07  H5   single    0.930  0.020  1.080
 2KR  C08  H6   single    0.930  0.020  1.080
 2KR  C13  H7   single    0.930  0.020  1.080
 2KR  C14  H8   single    0.930  0.020  1.080
 2KR  N16  H9   single    0.860  0.020  1.020
 2KR  C18  H10  single    0.930  0.020  1.080
 2KR  C19  H11  single    0.930  0.020  1.080
 2KR  C21  H12  single    0.970  0.020  1.090
 2KR  C21  H13  single    0.970  0.020  1.090
 2KR  C21  H14  single    0.970  0.020  1.090
 2KR  C22  H15  single    0.930  0.020  1.080
 2KR  C24  H16  single    0.930  0.020  1.080
 2KR  C25  H17  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
 2KR  H3   C01  H2   109.68  3.000
 2KR  H3   C01  H1   109.66  3.000
 2KR  H2   C01  H1   109.35  3.000
 2KR  H3   C01  O02  105.88  3.000
 2KR  H2   C01  O02  111.11  3.000
 2KR  H1   C01  O02  111.10  3.000
 2KR  C03  O02  C01  116.67  3.000
 2KR  N11  C03  N04  114.80  3.000
 2KR  N11  C03  O02  117.85  3.000
 2KR  N04  C03  O02  127.35  3.000
 2KR  C05  N04  C03  104.27  3.000
 2KR  C10  C05  C06  117.41  3.000
 2KR  C10  C05  N04  110.35  3.000
 2KR  C06  C05  N04  132.25  3.000
 2KR  H4   C06  C07  121.54  3.000
 2KR  H4   C06  C05  121.86  3.000
 2KR  C07  C06  C05  116.60  3.000
 2KR  H5   C07  C08  119.27  3.000
 2KR  H5   C07  C06  120.39  3.000
 2KR  C08  C07  C06  120.34  3.000
 2KR  H6   C08  N09  116.17  3.000
 2KR  H6   C08  C07  119.88  3.000
 2KR  N09  C08  C07  123.95  3.000
 2KR  C10  N09  C08  114.39  3.000
 2KR  N11  C10  N09  127.48  3.000
 2KR  N11  C10  C05  105.22  3.000
 2KR  N09  C10  C05  127.31  3.000
 2KR  C12  N11  C10  127.12  3.000
 2KR  C12  N11  C03  127.51  3.000
 2KR  C10  N11  C03  105.37  3.000
 2KR  C25  C12  C13  119.42  3.000
 2KR  C25  C12  N11  120.20  3.000
 2KR  C13  C12  N11  120.37  3.000
 2KR  H7   C13  C14  119.60  3.000
 2KR  H7   C13  C12  120.42  3.000
 2KR  C14  C13  C12  119.97  3.000
 2KR  H8   C14  C15  119.59  3.000
 2KR  H8   C14  C13  119.16  3.000
 2KR  C15  C14  C13  121.26  3.000
 2KR  C24  C15  N16  125.30  3.000
 2KR  N16  C15  C14  116.45  3.000
 2KR  C24  C15  C14  118.25  3.000
 2KR  H9   N16  C17  114.19  3.000
 2KR  H9   N16  C15  114.13  3.000
 2KR  C17  N16  C15  131.68  3.000
 2KR  N23  C17  C18  121.77  3.000
 2KR  C18  C17  N16  117.88  3.000
 2KR  N23  C17  N16  120.36  3.000
 2KR  H10  C18  C19  120.78  3.000
 2KR  H10  C18  C17  120.71  3.000
 2KR  C19  C18  C17  118.51  3.000
 2KR  H11  C19  C20  120.07  3.000
 2KR  H11  C19  C18  119.48  3.000
 2KR  C20  C19  C18  120.45  3.000
 2KR  C22  C20  C21  122.22  3.000
 2KR  C21  C20  C19  121.90  3.000
 2KR  C22  C20  C19  115.87  3.000
 2KR  H14  C21  H13  107.59  3.000
 2KR  H14  C21  H12  107.12  3.000
 2KR  H13  C21  H12  107.68  3.000
 2KR  H14  C21  C20  111.38  3.000
 2KR  H13  C21  C20  111.41  3.000
 2KR  H12  C21  C20  111.44  3.000
 2KR  H15  C22  N23  115.45  3.000
 2KR  H15  C22  C20  119.73  3.000
 2KR  N23  C22  C20  124.82  3.000
 2KR  C22  N23  C17  118.59  3.000
 2KR  H16  C24  C25  119.63  3.000
 2KR  H16  C24  C15  120.32  3.000
 2KR  C25  C24  C15  120.05  3.000
 2KR  H17  C25  C24  119.13  3.000
 2KR  H17  C25  C12  119.83  3.000
 2KR  C24  C25  C12  121.04  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
 2KR  CONST_01  C06  C05  N04  C03   180.00   0.0  0
 2KR  CONST_02  C10  C05  N04  C03     0.00   0.0  0
 2KR  CONST_03  C05  C10  N11  C03     0.00   0.0  0
 2KR  CONST_04  N09  C10  N11  C03   180.00   0.0  0
 2KR  CONST_07  C07  C06  C05  N04   180.00   0.0  0
 2KR  CONST_08  N09  C10  C05  N04   180.00   0.0  0
 2KR  CONST_09  N11  C10  C05  N04     0.00   0.0  0
 2KR  CONST_10  C10  N11  C03  N04     0.00   0.0  0
 2KR  CONST_11  C12  N11  C03  N04   180.00   0.0  0
 2KR  CONST_12  C08  C07  C06  C05     0.00   0.0  0
 2KR  CONST_13  N11  C03  N04  C05     0.00   0.0  0
 2KR  CONST_14  C08  N09  C10  C05     0.00   0.0  0
 2KR  CONST_15  C12  N11  C10  C05   180.00   0.0  0
 2KR  CONST_16  N09  C08  C07  C06     0.00   0.0  0
 2KR  CONST_17  N09  C10  C05  C06     0.00   0.0  0
 2KR  CONST_18  N11  C10  C05  C06   180.00   0.0  0
 2KR  CONST_19  C10  C05  C06  C07     0.00   0.0  0
 2KR  CONST_20  C10  N09  C08  C07     0.00   0.0  0
 2KR  CONST_21  N11  C10  N09  C08   180.00   0.0  0
 2KR  CONST_22  C12  N11  C10  N09     0.00   0.0  0
 2KR  CONST_25  C14  C13  C12  N11   180.00   0.0  0
 2KR  CONST_26  C24  C25  C12  N11   180.00   0.0  0
 2KR  CONST_27  C15  C14  C13  C12     0.00   0.0  0
 2KR  CONST_28  C15  C24  C25  C12     0.00   0.0  0
 2KR  CONST_29  C24  C25  C12  C13     0.00   0.0  0
 2KR  CONST_30  C24  C15  C14  C13     0.00   0.0  0
 2KR  CONST_31  C25  C12  C13  C14     0.00   0.0  0
 2KR  CONST_32  C25  C24  C15  C14     0.00   0.0  0
 2KR  CONST_33  C20  C22  N23  C17     0.00   0.0  0
 2KR  CONST_34  C20  C19  C18  C17     0.00   0.0  0
 2KR  CONST_35  C22  N23  C17  C18     0.00   0.0  0
 2KR  CONST_36  C22  C20  C19  C18     0.00   0.0  0
 2KR  CONST_37  N23  C22  C20  C19     0.00   0.0  0
 2KR  CONST_38  N23  C17  C18  C19     0.00   0.0  0
 2KR  CONST_39  C05  N04  C03  O02   180.00   0.0  0
 2KR  CONST_40  C10  N11  C03  O02   180.00   0.0  0
 2KR  CONST_41  C12  N11  C03  O02     0.00   0.0  0
 2KR  CONST_42  N16  C15  C14  C13   180.00   0.0  0
 2KR  CONST_43  C25  C24  C15  N16   180.00   0.0  0
 2KR  CONST_44  C22  N23  C17  N16   180.00   0.0  0
 2KR  CONST_45  C19  C18  C17  N16   180.00   0.0  0
 2KR  CONST_46  C21  C20  C19  C18   180.00   0.0  0
 2KR  CONST_47  N23  C22  C20  C21   180.00   0.0  0
 2KR  CONST_48  H4   C06  C05  N04     0.00   0.0  0
 2KR  CONST_49  H5   C07  C06  C05   180.00   0.0  0
 2KR  CONST_50  H6   C08  C07  C06   180.00   0.0  0
 2KR  CONST_51  H7   C13  C12  N11     0.00   0.0  0
 2KR  CONST_52  H17  C25  C12  N11     0.00   0.0  0
 2KR  CONST_53  H8   C14  C13  C12   180.00   0.0  0
 2KR  CONST_54  H16  C24  C25  C12   180.00   0.0  0
 2KR  CONST_55  H15  C22  N23  C17   180.00   0.0  0
 2KR  CONST_56  H11  C19  C18  C17   180.00   0.0  0
 2KR  CONST_57  H10  C18  C19  C20   180.00   0.0  0
 2KR  Var_01    C17  N16  C15  C14  -179.58  30.0  2
 2KR  Var_02    N23  C17  N16  C15     2.04  30.0  2
 2KR  Var_03    N04  C03  O02  C01     0.95  30.0  1
 2KR  Var_04    H12  C21  C20  C19    57.16  30.0  2
 2KR  Var_05    H1   C01  O02  C03   -63.08  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
 2KR  plan-1  N11  0.020
 2KR  plan-1  C12  0.020
 2KR  plan-1  C13  0.020
 2KR  plan-1  C14  0.020
 2KR  plan-1  C15  0.020
 2KR  plan-1  N16  0.020
 2KR  plan-1  C24  0.020
 2KR  plan-1  C25  0.020
 2KR  plan-1  H7   0.020
 2KR  plan-1  H8   0.020
 2KR  plan-1  H16  0.020
 2KR  plan-1  H17  0.020
 2KR  plan-2  N16  0.020
 2KR  plan-2  C17  0.020
 2KR  plan-2  C18  0.020
 2KR  plan-2  C19  0.020
 2KR  plan-2  C20  0.020
 2KR  plan-2  C21  0.020
 2KR  plan-2  C22  0.020
 2KR  plan-2  N23  0.020
 2KR  plan-2  H10  0.020
 2KR  plan-2  H11  0.020
 2KR  plan-2  H15  0.020
 2KR  plan-3  O02  0.020
 2KR  plan-3  C03  0.020
 2KR  plan-3  N04  0.020
 2KR  plan-3  C05  0.020
 2KR  plan-3  C06  0.020
 2KR  plan-3  C07  0.020
 2KR  plan-3  C08  0.020
 2KR  plan-3  N09  0.020
 2KR  plan-3  C10  0.020
 2KR  plan-3  N11  0.020
 2KR  plan-3  C12  0.020
 2KR  plan-3  H4   0.020
 2KR  plan-3  H5   0.020
 2KR  plan-3  H6   0.020

