# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 07:27:46 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[3-[2-(6-bromanylpyridin-2-yl)oxyethyl]-2-methyl-imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2ccc(nc2n1CCOc3cccc(Br)n3)c4cc(N)nc(N)c4
#
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
 RJZ  RJZ  4-[3-[2-(6-bromanylpyridin-2-yl)oxyethyl]-2-methyl-imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine  ligand  46  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJZ
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
 RJZ  C1   C   CH3   0  -0.767   4.1035  7.0824  38.8101
 RJZ  N1   N   N     0  -0.475   1.8399  6.1571  38.4368
 RJZ  O1   O   O2    0  -0.472   4.7896  3.3707  36.2976
 RJZ  C2   C   CR5   0   0.443   3.0705  6.3512  38.0375
 RJZ  N2   N   N     0  -0.456   1.9398  4.6040  35.2573
 RJZ  C3   C   CR56  0   0.107   1.2404  5.4566  37.4243
 RJZ  N3   N   NR5   0  -0.527   3.3244  5.8189  36.8024
 RJZ  C4   C   CR16  0  -0.223  -0.0435  4.9638  37.2445
 RJZ  N4   N   N     0  -0.453   5.1209  3.4956  34.0332
 RJZ  C5   C   CR16  0  -0.345  -0.2966  4.2877  36.0608
 RJZ  N5   N   NH2   0  -0.838  -1.8403  1.0065  32.2852
 RJZ  C6   C   CR6   0   0.204   0.7078  4.1212  35.0928
 RJZ  N6   N   N     0  -0.504  -0.0150  2.0868  31.4149
 RJZ  C7   C   CR56  0   0.467   2.1590  5.2315  36.3878
 RJZ  N7   N   NH2   0  -0.838   1.7959  3.1019  30.4423
 RJZ  C8   C   CH2   0  -0.373   4.5760  5.8016  36.0796
 RJZ  C9   C   CH2   0  -0.203   5.4525  4.6174  36.4516
 RJZ  C10  C   CR6   0   0.566   4.6489  2.8479  35.0792
 RJZ  C11  C   CR16  0  -0.389   4.0029  1.6124  34.9770
 RJZ  C12  C   CR16  0  -0.141   3.8644  1.0698  33.7188
 RJZ  C13  C   CR16  0  -0.286   4.3528  1.7451  32.6011
 RJZ  C14  C   CR6   0   0.093   4.9653  2.9544  32.8449
 RJZ  C15  C   CR6   0   0.188   0.4465  3.4079  33.8210
 RJZ  C16  C   CR16  0  -0.509  -0.6004  2.4993  33.7049
 RJZ  C17  C   CR6   0   0.461  -0.7929  1.8651  32.4719
 RJZ  C18  C   CR6   0   0.469   0.9924  2.9497  31.5358
 RJZ  C19  C   CR16  0  -0.459   1.2612  3.6422  32.7212
 RJZ  BR1  BR  BR    0  -0.044   5.6386  3.9681  31.3886
 RJZ  H1   H   HCH3  0   0.275   3.6652  7.4609  39.7296
 RJZ  H2   H   HCH3  0   0.269   4.9438  6.4368  39.0714
 RJZ  H3   H   HCH3  0   0.269   4.5014  7.9261  38.2443
 RJZ  H4   H   HCR6  0   0.267  -0.8192  5.1014  37.9867
 RJZ  H5   H   HCR6  0   0.265  -1.2903  3.9044  35.8782
 RJZ  H6   H   HNH2  0   0.376  -1.7575  0.3724  31.5074
 RJZ  H7   H   HNH2  0   0.385  -2.2508  0.5942  33.1065
 RJZ  H8   H   HNH2  0   0.377   1.4040  2.8322  29.5551
 RJZ  H9   H   HNH2  0   0.384   2.3826  3.9185  30.4062
 RJZ  H10  H   HCH2  0   0.289   5.1277  6.7182  36.2902
 RJZ  H11  H   HCH2  0   0.288   4.3508  5.8005  35.0147
 RJZ  H12  H   HCH2  0   0.254   6.3724  4.6560  35.8649
 RJZ  H13  H   HCH2  0   0.266   5.7224  4.6611  37.5063
 RJZ  H14  H   HCR6  0   0.280   3.6253  1.1116  35.8575
 RJZ  H15  H   HCR6  0   0.284   3.3687  0.1163  33.5930
 RJZ  H16  H   HCR6  0   0.282   4.2406  1.3449  31.6049
 RJZ  H17  H   HCR6  0   0.248  -1.2480  2.2560  34.5364
 RJZ  H18  H   HCR6  0   0.246   2.0869  4.3373  32.7739

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
 RJZ  N7   C18  single    1.365  0.020  1.365
 RJZ  N6   C18  aromatic  1.332  0.020  1.332
 RJZ  N6   C17  aromatic  1.331  0.020  1.331
 RJZ  BR1  C14  single    1.898  0.020  1.898
 RJZ  C18  C19  aromatic  1.399  0.020  1.399
 RJZ  N5   C17  single    1.367  0.020  1.367
 RJZ  C17  C16  aromatic  1.400  0.020  1.400
 RJZ  C13  C14  aromatic  1.377  0.020  1.377
 RJZ  C13  C12  aromatic  1.394  0.020  1.394
 RJZ  C14  N4   aromatic  1.315  0.020  1.315
 RJZ  C19  C15  aromatic  1.389  0.020  1.389
 RJZ  C12  C11  aromatic  1.377  0.020  1.377
 RJZ  C16  C15  aromatic  1.391  0.020  1.391
 RJZ  C15  C6   single    1.481  0.020  1.481
 RJZ  N4   C10  aromatic  1.318  0.020  1.318
 RJZ  C11  C10  aromatic  1.398  0.020  1.398
 RJZ  C10  O1   single    1.333  0.020  1.333
 RJZ  C6   N2   aromatic  1.333  0.020  1.333
 RJZ  C6   C5   aromatic  1.405  0.020  1.405
 RJZ  N2   C7   aromatic  1.311  0.020  1.311
 RJZ  C8   C9   single    1.520  0.020  1.520
 RJZ  C8   N3   single    1.445  0.020  1.445
 RJZ  C5   C4   aromatic  1.387  0.020  1.387
 RJZ  O1   C9   single    1.420  0.020  1.420
 RJZ  C7   N3   aromatic  1.369  0.020  1.369
 RJZ  C7   C3   aromatic  1.403  0.020  1.403
 RJZ  N3   C2   aromatic  1.369  0.020  1.369
 RJZ  C4   C3   aromatic  1.387  0.020  1.387
 RJZ  C3   N1   aromatic  1.369  0.020  1.369
 RJZ  C2   N1   aromatic  1.308  0.020  1.308
 RJZ  C2   C1   single    1.483  0.020  1.483
 RJZ  C1   H1   single    0.970  0.020  1.090
 RJZ  C1   H2   single    0.970  0.020  1.090
 RJZ  C1   H3   single    0.970  0.020  1.090
 RJZ  C4   H4   single    0.930  0.020  1.080
 RJZ  C5   H5   single    0.930  0.020  1.080
 RJZ  N5   H6   single    0.890  0.020  1.040
 RJZ  N5   H7   single    0.890  0.020  1.040
 RJZ  N7   H8   single    0.890  0.020  1.040
 RJZ  N7   H9   single    0.890  0.020  1.040
 RJZ  C8   H10  single    0.970  0.020  1.090
 RJZ  C8   H11  single    0.970  0.020  1.090
 RJZ  C9   H12  single    0.970  0.020  1.090
 RJZ  C9   H13  single    0.970  0.020  1.090
 RJZ  C11  H14  single    0.930  0.020  1.080
 RJZ  C12  H15  single    0.930  0.020  1.080
 RJZ  C13  H16  single    0.930  0.020  1.080
 RJZ  C16  H17  single    0.930  0.020  1.080
 RJZ  C19  H18  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
 RJZ  H3   C1   H2   107.50  3.000
 RJZ  H3   C1   H1   108.45  3.000
 RJZ  H2   C1   H1   108.30  3.000
 RJZ  H3   C1   C2   111.42  3.000
 RJZ  H2   C1   C2   111.68  3.000
 RJZ  H1   C1   C2   109.37  3.000
 RJZ  C3   N1   C2   105.19  3.000
 RJZ  C10  O1   C9   119.50  3.000
 RJZ  N3   C2   N1   113.09  3.000
 RJZ  N1   C2   C1   124.71  3.000
 RJZ  N3   C2   C1   122.19  3.000
 RJZ  C7   N2   C6   115.73  3.000
 RJZ  C7   C3   C4   116.95  3.000
 RJZ  C4   C3   N1   133.07  3.000
 RJZ  C7   C3   N1   109.98  3.000
 RJZ  C8   N3   C7   125.48  3.000
 RJZ  C7   N3   C2   106.39  3.000
 RJZ  C8   N3   C2   128.06  3.000
 RJZ  H4   C4   C5   121.10  3.000
 RJZ  H4   C4   C3   121.97  3.000
 RJZ  C5   C4   C3   116.93  3.000
 RJZ  C14  N4   C10  118.21  3.000
 RJZ  H5   C5   C6   119.93  3.000
 RJZ  H5   C5   C4   119.02  3.000
 RJZ  C6   C5   C4   121.03  3.000
 RJZ  H7   N5   H6   113.94  3.000
 RJZ  H7   N5   C17  117.28  3.000
 RJZ  H6   N5   C17  115.97  3.000
 RJZ  C15  C6   C5   121.50  3.000
 RJZ  C5   C6   N2   122.18  3.000
 RJZ  C15  C6   N2   116.32  3.000
 RJZ  C18  N6   C17  118.55  3.000
 RJZ  N3   C7   C3   105.35  3.000
 RJZ  C3   C7   N2   127.17  3.000
 RJZ  N3   C7   N2   127.48  3.000
 RJZ  H9   N7   H8   114.38  3.000
 RJZ  H9   N7   C18  117.54  3.000
 RJZ  H8   N7   C18  116.54  3.000
 RJZ  H11  C8   H10  107.13  3.000
 RJZ  H11  C8   C9   110.98  3.000
 RJZ  H10  C8   C9   108.42  3.000
 RJZ  H11  C8   N3   108.07  3.000
 RJZ  H10  C8   N3   109.36  3.000
 RJZ  C9   C8   N3   112.73  3.000
 RJZ  H13  C9   H12  108.07  3.000
 RJZ  H13  C9   C8   110.40  3.000
 RJZ  H12  C9   C8   109.08  3.000
 RJZ  H13  C9   O1   104.82  3.000
 RJZ  H12  C9   O1   111.47  3.000
 RJZ  C8   C9   O1   112.85  3.000
 RJZ  C11  C10  N4   122.81  3.000
 RJZ  C11  C10  O1   117.52  3.000
 RJZ  N4   C10  O1   119.66  3.000
 RJZ  H14  C11  C12  121.77  3.000
 RJZ  H14  C11  C10  120.75  3.000
 RJZ  C12  C11  C10  117.48  3.000
 RJZ  H15  C12  C13  119.62  3.000
 RJZ  H15  C12  C11  119.96  3.000
 RJZ  C13  C12  C11  120.42  3.000
 RJZ  H16  C13  C14  122.35  3.000
 RJZ  H16  C13  C12  121.59  3.000
 RJZ  C14  C13  C12  116.05  3.000
 RJZ  BR1  C14  C13  119.40  3.000
 RJZ  C13  C14  N4   125.02  3.000
 RJZ  BR1  C14  N4   115.57  3.000
 RJZ  C19  C15  C16  119.05  3.000
 RJZ  C16  C15  C6   121.26  3.000
 RJZ  C19  C15  C6   119.69  3.000
 RJZ  H17  C16  C17  119.53  3.000
 RJZ  H17  C16  C15  122.23  3.000
 RJZ  C17  C16  C15  118.23  3.000
 RJZ  C16  C17  N6   122.93  3.000
 RJZ  C16  C17  N5   120.67  3.000
 RJZ  N6   C17  N5   116.36  3.000
 RJZ  C19  C18  N7   120.69  3.000
 RJZ  C19  C18  N6   122.88  3.000
 RJZ  N7   C18  N6   116.40  3.000
 RJZ  H18  C19  C18  120.44  3.000
 RJZ  H18  C19  C15  121.21  3.000
 RJZ  C18  C19  C15  118.35  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
 RJZ  CONST_01  N2   C7   C3   N1   180.00   0.0  0
 RJZ  CONST_02  N3   C7   C3   N1     0.00   0.0  0
 RJZ  CONST_03  C5   C4   C3   N1   180.00   0.0  0
 RJZ  CONST_04  C7   N3   C2   N1     0.00   0.0  0
 RJZ  CONST_05  N2   C7   N3   C2   180.00   0.0  0
 RJZ  CONST_06  C3   C7   N3   C2     0.00   0.0  0
 RJZ  CONST_07  C7   C3   N1   C2     0.00   0.0  0
 RJZ  CONST_08  C4   C3   N1   C2   180.00   0.0  0
 RJZ  CONST_11  C4   C5   C6   N2     0.00   0.0  0
 RJZ  CONST_12  C4   C3   C7   N2     0.00   0.0  0
 RJZ  CONST_13  C6   N2   C7   C3     0.00   0.0  0
 RJZ  CONST_14  C6   C5   C4   C3     0.00   0.0  0
 RJZ  CONST_15  N3   C2   N1   C3     0.00   0.0  0
 RJZ  CONST_16  C6   N2   C7   N3   180.00   0.0  0
 RJZ  CONST_17  C4   C3   C7   N3   180.00   0.0  0
 RJZ  CONST_18  C15  C6   C5   C4   180.00   0.0  0
 RJZ  CONST_19  C12  C13  C14  N4     0.00   0.0  0
 RJZ  CONST_20  C12  C11  C10  N4     0.00   0.0  0
 RJZ  CONST_23  C7   N2   C6   C5     0.00   0.0  0
 RJZ  CONST_24  C7   C3   C4   C5     0.00   0.0  0
 RJZ  CONST_25  C18  C19  C15  C6   180.00   0.0  0
 RJZ  CONST_26  C17  C16  C15  C6   180.00   0.0  0
 RJZ  CONST_27  C15  C19  C18  N6     0.00   0.0  0
 RJZ  CONST_28  C15  C16  C17  N6     0.00   0.0  0
 RJZ  CONST_29  C15  C6   N2   C7   180.00   0.0  0
 RJZ  CONST_30  C13  C14  N4   C10    0.00   0.0  0
 RJZ  CONST_31  C13  C12  C11  C10    0.00   0.0  0
 RJZ  CONST_32  C14  C13  C12  C11    0.00   0.0  0
 RJZ  CONST_33  C14  N4   C10  C11    0.00   0.0  0
 RJZ  CONST_34  C18  N6   C17  C16    0.00   0.0  0
 RJZ  CONST_35  C18  C19  C15  C16    0.00   0.0  0
 RJZ  CONST_36  C19  C18  N6   C17    0.00   0.0  0
 RJZ  CONST_37  C19  C15  C16  C17    0.00   0.0  0
 RJZ  CONST_38  C7   N3   C2   C1   180.00   0.0  0
 RJZ  CONST_39  C3   N1   C2   C1   180.00   0.0  0
 RJZ  CONST_40  C8   N3   C2   N1   180.00   0.0  0
 RJZ  CONST_41  C14  N4   C10  O1   180.00   0.0  0
 RJZ  CONST_42  C12  C11  C10  O1   180.00   0.0  0
 RJZ  CONST_43  C8   N3   C7   N2     0.00   0.0  0
 RJZ  CONST_44  C8   N3   C7   C3   180.00   0.0  0
 RJZ  CONST_45  C18  N6   C17  N5   180.00   0.0  0
 RJZ  CONST_46  C15  C16  C17  N5   180.00   0.0  0
 RJZ  CONST_47  C17  N6   C18  N7   180.00   0.0  0
 RJZ  CONST_48  C15  C19  C18  N7   180.00   0.0  0
 RJZ  CONST_49  BR1  C14  N4   C10  180.00   0.0  0
 RJZ  CONST_50  BR1  C14  C13  C12  180.00   0.0  0
 RJZ  CONST_51  H4   C4   C3   N1     0.00   0.0  0
 RJZ  CONST_52  H5   C5   C6   N2   180.00   0.0  0
 RJZ  CONST_53  H16  C13  C14  N4   180.00   0.0  0
 RJZ  CONST_54  H14  C11  C10  N4   180.00   0.0  0
 RJZ  CONST_55  H18  C19  C15  C6     0.00   0.0  0
 RJZ  CONST_56  H17  C16  C15  C6     0.00   0.0  0
 RJZ  CONST_57  H15  C12  C11  C10  180.00   0.0  0
 RJZ  Var_01    C9   C8   N3   C2    86.13  30.0  1
 RJZ  Var_02    C11  C10  O1   C9   179.31  30.0  1
 RJZ  Var_03    H1   C1   C2   N1    -2.34  30.0  2
 RJZ  Var_04    N3   C8   C9   O1    54.84  30.0  1

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
 RJZ  plan-1  N5   0.020
 RJZ  plan-1  C6   0.020
 RJZ  plan-1  N6   0.020
 RJZ  plan-1  N7   0.020
 RJZ  plan-1  C15  0.020
 RJZ  plan-1  C16  0.020
 RJZ  plan-1  C17  0.020
 RJZ  plan-1  C18  0.020
 RJZ  plan-1  C19  0.020
 RJZ  plan-1  H17  0.020
 RJZ  plan-1  H18  0.020
 RJZ  plan-2  O1   0.020
 RJZ  plan-2  N4   0.020
 RJZ  plan-2  C10  0.020
 RJZ  plan-2  C11  0.020
 RJZ  plan-2  C12  0.020
 RJZ  plan-2  C13  0.020
 RJZ  plan-2  C14  0.020
 RJZ  plan-2  BR1  0.020
 RJZ  plan-2  H14  0.020
 RJZ  plan-2  H15  0.020
 RJZ  plan-2  H16  0.020
 RJZ  plan-3  C1   0.020
 RJZ  plan-3  N1   0.020
 RJZ  plan-3  C2   0.020
 RJZ  plan-3  N2   0.020
 RJZ  plan-3  C3   0.020
 RJZ  plan-3  N3   0.020
 RJZ  plan-3  C4   0.020
 RJZ  plan-3  C5   0.020
 RJZ  plan-3  C6   0.020
 RJZ  plan-3  C7   0.020
 RJZ  plan-3  C8   0.020
 RJZ  plan-3  C15  0.020
 RJZ  plan-3  H4   0.020
 RJZ  plan-3  H5   0.020
 RJZ  plan-4  N5   0.020
 RJZ  plan-4  C17  0.020
 RJZ  plan-4  H6   0.020
 RJZ  plan-4  H7   0.020
 RJZ  plan-5  N7   0.020
 RJZ  plan-5  C18  0.020
 RJZ  plan-5  H8   0.020
 RJZ  plan-5  H9   0.020

