# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 09:37:37 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-[2-methyl-3-(2-phenoxyethyl)imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2ccc(nc2n1CCOc3ccccc3)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
 RKQ  RKQ  4-[2-methyl-3-(2-phenoxyethyl)imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine  ligand  47  27  .  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_RKQ
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
 RKQ  C1   C  CH3   0  -0.768  44.9459   3.3093  18.0597
 RKQ  N1   N  N     0  -0.475  44.7348   5.6162  17.1872
 RKQ  O1   O  O2    0  -0.476  43.9910   0.9027  13.9654
 RKQ  C2   C  CR5   0   0.449  44.5095   4.3327  17.0792
 RKQ  N2   N  N     0  -0.452  42.9648   5.3330  14.1319
 RKQ  C3   C  CR56  0   0.107  44.1664   6.1774  16.0741
 RKQ  N3   N  NR5   0  -0.539  43.8097   4.0059  15.9488
 RKQ  C4   C  CR16  0  -0.221  44.0686   7.4826  15.6158
 RKQ  N4   N  NH2   0  -0.838  41.5391   5.0883   9.2475
 RKQ  C5   C  CR16  0  -0.347  43.4041   7.6759  14.4140
 RKQ  N5   N  N     0  -0.503  40.8667   7.1551   9.9832
 RKQ  C6   C  CR6   0   0.199  42.8671   6.5920  13.7014
 RKQ  N6   N  NH2   0  -0.839  40.1380   9.2349  10.6115
 RKQ  C7   C  CR56  0   0.462  43.5881   5.1781  15.2772
 RKQ  C8   C  CH2   0  -0.366  43.4029   2.6980  15.4910
 RKQ  C9   C  CH2   0  -0.212  44.4052   2.1499  14.4764
 RKQ  C10  C  CR6   0   0.390  43.0803   0.8538  12.9657
 RKQ  C11  C  CR16  0  -0.389  42.4744   1.9671  12.3887
 RKQ  C12  C  CR16  0  -0.245  41.5692   1.7936  11.3467
 RKQ  C13  C  CR16  0  -0.278  41.2528   0.5289  10.8770
 RKQ  C14  C  CR16  0  -0.239  41.8547  -0.5783  11.4657
 RKQ  C15  C  CR16  0  -0.346  42.7612  -0.4225  12.4998
 RKQ  C16  C  CR6   0   0.190  42.1748   6.7983  12.4099
 RKQ  C17  C  CR16  0  -0.475  42.2362   5.8181  11.4277
 RKQ  C18  C  CR6   0   0.461  41.5574   6.0433  10.2258
 RKQ  C19  C  CR6   0   0.466  40.8173   8.0947  10.9252
 RKQ  C20  C  CR16  0  -0.495  41.4554   7.9610  12.1654
 RKQ  H1   H  HCH3  0   0.276  45.5006   3.7894  18.8612
 RKQ  H2   H  HCH3  0   0.270  44.0924   2.7870  18.4947
 RKQ  H3   H  HCH3  0   0.269  45.5882   2.5597  17.5947
 RKQ  H4   H  HCR6  0   0.269  44.4936   8.3156  16.1607
 RKQ  H5   H  HNH2  0   0.378  41.2948   5.4059   8.3235
 RKQ  H6   H  HNH2  0   0.387  42.2773   4.4041   9.2609
 RKQ  H7   H  HCR6  0   0.267  43.3194   8.6744  14.0086
 RKQ  H8   H  HNH2  0   0.379  39.4834   9.1745   9.8493
 RKQ  H9   H  HNH2  0   0.388  39.8450   9.8307  11.3673
 RKQ  H10  H  HCH2  0   0.284  42.4052   2.7857  15.0596
 RKQ  H11  H  HCH2  0   0.292  43.3255   2.0283  16.3466
 RKQ  H12  H  HCH2  0   0.271  45.3612   1.9710  14.9701
 RKQ  H13  H  HCH2  0   0.242  44.5820   2.8769  13.6779
 RKQ  H14  H  HCR6  0   0.283  42.6788   2.9714  12.7373
 RKQ  H15  H  HCR6  0   0.253  41.1113   2.6685  10.9018
 RKQ  H16  H  HCR6  0   0.251  40.5473   0.4046  10.0664
 RKQ  H17  H  HCR6  0   0.255  41.6197  -1.5751  11.1151
 RKQ  H18  H  HCR6  0   0.260  43.2316  -1.2869  12.9521
 RKQ  H19  H  HCR6  0   0.252  42.8039   4.9104  11.5749
 RKQ  H20  H  HCR6  0   0.252  41.3566   8.7398  12.9099

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
 RKQ  N4   C18  single    1.367  0.020  1.367
 RKQ  N5   C18  aromatic  1.331  0.020  1.331
 RKQ  N5   C19  aromatic  1.331  0.020  1.331
 RKQ  N6   C19  single    1.364  0.020  1.364
 RKQ  C18  C17  aromatic  1.399  0.020  1.399
 RKQ  C14  C13  aromatic  1.391  0.020  1.391
 RKQ  C14  C15  aromatic  1.384  0.020  1.384
 RKQ  C19  C20  aromatic  1.401  0.020  1.401
 RKQ  C13  C12  aromatic  1.386  0.020  1.386
 RKQ  C15  C10  aromatic  1.396  0.020  1.396
 RKQ  C17  C16  aromatic  1.389  0.020  1.389
 RKQ  C20  C16  aromatic  1.389  0.020  1.389
 RKQ  C12  C11  aromatic  1.391  0.020  1.391
 RKQ  C16  C6   single    1.480  0.020  1.480
 RKQ  C10  C11  aromatic  1.393  0.020  1.393
 RKQ  C10  O1   single    1.353  0.020  1.353
 RKQ  C6   N2   aromatic  1.334  0.020  1.334
 RKQ  C6   C5   aromatic  1.404  0.020  1.404
 RKQ  O1   C9   single    1.410  0.020  1.410
 RKQ  C9   C8   single    1.528  0.020  1.528
 RKQ  N2   C7   aromatic  1.313  0.020  1.313
 RKQ  C5   C4   aromatic  1.387  0.020  1.387
 RKQ  C7   N3   aromatic  1.369  0.020  1.369
 RKQ  C7   C3   aromatic  1.403  0.020  1.403
 RKQ  C8   N3   single    1.444  0.020  1.444
 RKQ  C4   C3   aromatic  1.387  0.020  1.387
 RKQ  N3   C2   aromatic  1.369  0.020  1.369
 RKQ  C3   N1   aromatic  1.370  0.020  1.370
 RKQ  C2   N1   aromatic  1.308  0.020  1.308
 RKQ  C2   C1   single    1.483  0.020  1.483
 RKQ  C1   H1   single    0.970  0.020  1.090
 RKQ  C1   H2   single    0.970  0.020  1.090
 RKQ  C1   H3   single    0.970  0.020  1.090
 RKQ  C4   H4   single    0.930  0.020  1.080
 RKQ  N4   H5   single    0.890  0.020  1.040
 RKQ  N4   H6   single    0.890  0.020  1.040
 RKQ  C5   H7   single    0.930  0.020  1.080
 RKQ  N6   H8   single    0.890  0.020  1.040
 RKQ  N6   H9   single    0.890  0.020  1.040
 RKQ  C8   H10  single    0.970  0.020  1.090
 RKQ  C8   H11  single    0.970  0.020  1.090
 RKQ  C9   H12  single    0.970  0.020  1.090
 RKQ  C9   H13  single    0.970  0.020  1.090
 RKQ  C11  H14  single    0.930  0.020  1.080
 RKQ  C12  H15  single    0.930  0.020  1.080
 RKQ  C13  H16  single    0.930  0.020  1.080
 RKQ  C14  H17  single    0.930  0.020  1.080
 RKQ  C15  H18  single    0.930  0.020  1.080
 RKQ  C17  H19  single    0.930  0.020  1.080
 RKQ  C20  H20  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
 RKQ  H3   C1   H2   107.54  3.000
 RKQ  H3   C1   H1   108.51  3.000
 RKQ  H2   C1   H1   108.47  3.000
 RKQ  H3   C1   C2   111.44  3.000
 RKQ  H2   C1   C2   111.33  3.000
 RKQ  H1   C1   C2   109.46  3.000
 RKQ  C3   N1   C2   105.28  3.000
 RKQ  C10  O1   C9   119.82  3.000
 RKQ  N3   C2   N1   112.99  3.000
 RKQ  N1   C2   C1   124.90  3.000
 RKQ  N3   C2   C1   122.12  3.000
 RKQ  C7   N2   C6   115.31  3.000
 RKQ  C7   C3   C4   116.98  3.000
 RKQ  C4   C3   N1   133.10  3.000
 RKQ  C7   C3   N1   109.92  3.000
 RKQ  C8   N3   C7   125.05  3.000
 RKQ  C8   N3   C2   128.45  3.000
 RKQ  C7   N3   C2   106.47  3.000
 RKQ  H4   C4   C5   121.14  3.000
 RKQ  H4   C4   C3   122.03  3.000
 RKQ  C5   C4   C3   116.83  3.000
 RKQ  H6   N4   H5   113.86  3.000
 RKQ  H6   N4   C18  117.09  3.000
 RKQ  H5   N4   C18  116.07  3.000
 RKQ  H7   C5   C6   119.52  3.000
 RKQ  H7   C5   C4   119.43  3.000
 RKQ  C6   C5   C4   121.03  3.000
 RKQ  C19  N5   C18  118.67  3.000
 RKQ  C16  C6   C5   120.95  3.000
 RKQ  C5   C6   N2   122.46  3.000
 RKQ  C16  C6   N2   116.58  3.000
 RKQ  H9   N6   H8   114.52  3.000
 RKQ  H9   N6   C19  117.87  3.000
 RKQ  H8   N6   C19  116.61  3.000
 RKQ  N3   C7   C3   105.34  3.000
 RKQ  C3   C7   N2   127.38  3.000
 RKQ  N3   C7   N2   127.28  3.000
 RKQ  H11  C8   H10  107.16  3.000
 RKQ  H11  C8   C9   110.35  3.000
 RKQ  H10  C8   C9   111.49  3.000
 RKQ  H11  C8   N3   109.14  3.000
 RKQ  H10  C8   N3   108.08  3.000
 RKQ  C9   C8   N3   110.53  3.000
 RKQ  H13  C9   H12  107.32  3.000
 RKQ  H13  C9   C8   110.62  3.000
 RKQ  H12  C9   C8   109.46  3.000
 RKQ  H13  C9   O1   111.76  3.000
 RKQ  H12  C9   O1   106.05  3.000
 RKQ  C8   C9   O1   111.42  3.000
 RKQ  C15  C10  C11  119.56  3.000
 RKQ  C11  C10  O1   124.75  3.000
 RKQ  C15  C10  O1   115.69  3.000
 RKQ  H14  C11  C12  118.68  3.000
 RKQ  H14  C11  C10  121.74  3.000
 RKQ  C12  C11  C10  119.58  3.000
 RKQ  H15  C12  C13  120.10  3.000
 RKQ  H15  C12  C11  118.81  3.000
 RKQ  C13  C12  C11  121.09  3.000
 RKQ  H16  C13  C14  120.52  3.000
 RKQ  H16  C13  C12  120.51  3.000
 RKQ  C14  C13  C12  118.96  3.000
 RKQ  H17  C14  C15  119.20  3.000
 RKQ  H17  C14  C13  120.13  3.000
 RKQ  C15  C14  C13  120.67  3.000
 RKQ  H18  C15  C14  120.45  3.000
 RKQ  H18  C15  C10  119.41  3.000
 RKQ  C14  C15  C10  120.14  3.000
 RKQ  C20  C16  C17  119.28  3.000
 RKQ  C20  C16  C6   120.85  3.000
 RKQ  C17  C16  C6   119.87  3.000
 RKQ  H19  C17  C18  120.48  3.000
 RKQ  H19  C17  C16  121.31  3.000
 RKQ  C18  C17  C16  118.21  3.000
 RKQ  C17  C18  N5   122.88  3.000
 RKQ  C17  C18  N4   120.60  3.000
 RKQ  N5   C18  N4   116.48  3.000
 RKQ  C20  C19  N6   120.68  3.000
 RKQ  C20  C19  N5   122.82  3.000
 RKQ  N6   C19  N5   116.47  3.000
 RKQ  H20  C20  C19  119.92  3.000
 RKQ  H20  C20  C16  121.91  3.000
 RKQ  C19  C20  C16  118.14  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
 RKQ  CONST_01  N2   C7   C3   N1    180.00   0.0  0
 RKQ  CONST_02  N3   C7   C3   N1      0.00   0.0  0
 RKQ  CONST_03  C5   C4   C3   N1    180.00   0.0  0
 RKQ  CONST_04  C7   N3   C2   N1      0.00   0.0  0
 RKQ  CONST_05  N2   C7   N3   C2    180.00   0.0  0
 RKQ  CONST_06  C3   C7   N3   C2      0.00   0.0  0
 RKQ  CONST_07  C7   C3   N1   C2      0.00   0.0  0
 RKQ  CONST_08  C4   C3   N1   C2    180.00   0.0  0
 RKQ  CONST_11  C4   C5   C6   N2      0.00   0.0  0
 RKQ  CONST_12  C4   C3   C7   N2      0.00   0.0  0
 RKQ  CONST_13  C6   N2   C7   C3      0.00   0.0  0
 RKQ  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 RKQ  CONST_15  N3   C2   N1   C3      0.00   0.0  0
 RKQ  CONST_16  C6   N2   C7   N3    180.00   0.0  0
 RKQ  CONST_17  C4   C3   C7   N3    180.00   0.0  0
 RKQ  CONST_18  C16  C6   C5   C4    180.00   0.0  0
 RKQ  CONST_21  C7   N2   C6   C5      0.00   0.0  0
 RKQ  CONST_22  C7   C3   C4   C5      0.00   0.0  0
 RKQ  CONST_23  C16  C17  C18  N5      0.00   0.0  0
 RKQ  CONST_24  C16  C20  C19  N5      0.00   0.0  0
 RKQ  CONST_25  C18  C17  C16  C6    180.00   0.0  0
 RKQ  CONST_26  C19  C20  C16  C6    180.00   0.0  0
 RKQ  CONST_27  C16  C6   N2   C7    180.00   0.0  0
 RKQ  CONST_28  C13  C14  C15  C10     0.00   0.0  0
 RKQ  CONST_29  C13  C12  C11  C10     0.00   0.0  0
 RKQ  CONST_30  C14  C13  C12  C11     0.00   0.0  0
 RKQ  CONST_31  C14  C15  C10  C11     0.00   0.0  0
 RKQ  CONST_32  C15  C14  C13  C12     0.00   0.0  0
 RKQ  CONST_33  C15  C10  C11  C12     0.00   0.0  0
 RKQ  CONST_34  C19  N5   C18  C17     0.00   0.0  0
 RKQ  CONST_35  C19  C20  C16  C17     0.00   0.0  0
 RKQ  CONST_36  C20  C19  N5   C18     0.00   0.0  0
 RKQ  CONST_37  C20  C16  C17  C18     0.00   0.0  0
 RKQ  CONST_38  C7   N3   C2   C1    180.00   0.0  0
 RKQ  CONST_39  C3   N1   C2   C1    180.00   0.0  0
 RKQ  CONST_40  C8   N3   C2   N1    180.00   0.0  0
 RKQ  CONST_41  C14  C15  C10  O1    180.00   0.0  0
 RKQ  CONST_42  C12  C11  C10  O1    180.00   0.0  0
 RKQ  CONST_43  C8   N3   C7   N2      0.00   0.0  0
 RKQ  CONST_44  C8   N3   C7   C3    180.00   0.0  0
 RKQ  CONST_45  C19  N5   C18  N4    180.00   0.0  0
 RKQ  CONST_46  C16  C17  C18  N4    180.00   0.0  0
 RKQ  CONST_47  C18  N5   C19  N6    180.00   0.0  0
 RKQ  CONST_48  C16  C20  C19  N6    180.00   0.0  0
 RKQ  CONST_49  H4   C4   C3   N1      0.00   0.0  0
 RKQ  CONST_50  H7   C5   C6   N2    180.00   0.0  0
 RKQ  CONST_51  H19  C17  C18  N5    180.00   0.0  0
 RKQ  CONST_52  H20  C20  C19  N5    180.00   0.0  0
 RKQ  CONST_53  H17  C14  C15  C10   180.00   0.0  0
 RKQ  CONST_54  H15  C12  C11  C10   180.00   0.0  0
 RKQ  CONST_55  H16  C13  C12  C11   180.00   0.0  0
 RKQ  CONST_56  H18  C15  C10  C11   180.00   0.0  0
 RKQ  CONST_57  H14  C11  C12  C13   180.00   0.0  0
 RKQ  Var_01    C9   C8   N3   C2    -96.31  30.0  2
 RKQ  Var_02    C15  C10  O1   C9    178.23  30.0  2
 RKQ  Var_03    H1   C1   C2   N1     -1.48  30.0  2
 RKQ  Var_04    N3   C8   C9   O1   -176.99  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
 RKQ  plan-1  N4   0.020
 RKQ  plan-1  N5   0.020
 RKQ  plan-1  C6   0.020
 RKQ  plan-1  N6   0.020
 RKQ  plan-1  C16  0.020
 RKQ  plan-1  C17  0.020
 RKQ  plan-1  C18  0.020
 RKQ  plan-1  C19  0.020
 RKQ  plan-1  C20  0.020
 RKQ  plan-1  H19  0.020
 RKQ  plan-1  H20  0.020
 RKQ  plan-2  O1   0.020
 RKQ  plan-2  C10  0.020
 RKQ  plan-2  C11  0.020
 RKQ  plan-2  C12  0.020
 RKQ  plan-2  C13  0.020
 RKQ  plan-2  C14  0.020
 RKQ  plan-2  C15  0.020
 RKQ  plan-2  H14  0.020
 RKQ  plan-2  H15  0.020
 RKQ  plan-2  H16  0.020
 RKQ  plan-2  H17  0.020
 RKQ  plan-2  H18  0.020
 RKQ  plan-3  C1   0.020
 RKQ  plan-3  N1   0.020
 RKQ  plan-3  C2   0.020
 RKQ  plan-3  N2   0.020
 RKQ  plan-3  C3   0.020
 RKQ  plan-3  N3   0.020
 RKQ  plan-3  C4   0.020
 RKQ  plan-3  C5   0.020
 RKQ  plan-3  C6   0.020
 RKQ  plan-3  C7   0.020
 RKQ  plan-3  C8   0.020
 RKQ  plan-3  C16  0.020
 RKQ  plan-3  H4   0.020
 RKQ  plan-3  H7   0.020
 RKQ  plan-4  N4   0.020
 RKQ  plan-4  C18  0.020
 RKQ  plan-4  H5   0.020
 RKQ  plan-4  H6   0.020
 RKQ  plan-5  N6   0.020
 RKQ  plan-5  C19  0.020
 RKQ  plan-5  H8   0.020
 RKQ  plan-5  H9   0.020

