# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:42:57 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{4-[3-(5-methoxypyridin-2-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(nc1)c2c([nH]c3cccnc23)c4ccnc(NC(C)=O)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
 J2Y  J2Y  N-{4-[3-(5-methoxypyridin-2-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide  ligand  44  27  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J2Y
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
 J2Y  C18  C  CR16  0  -0.150  -0.9899   3.0684   0.5341
 J2Y  C16  C  CR6   0   0.254  -1.7888   0.9887  -0.0271
 J2Y  C15  C  CR16  0  -0.405   2.0770  -1.2195   0.0736
 J2Y  C19  C  CR6   0   0.289  -2.1184   3.7130   0.0295
 J2Y  C20  C  CR16  0  -0.222  -3.1222   2.9184  -0.5221
 J2Y  C21  C  CR16  0  -0.390  -2.9569   1.5504  -0.5521
 J2Y  C23  C  C     0   0.422   5.7683  -1.0424   0.2879
 J2Y  C11  C  CR16  0  -0.308   1.1720   0.3895  -1.4374
 J2Y  C12  C  CR16  0  -0.088   2.4691   0.7679  -1.7070
 J2Y  C27  C  CH3   0  -0.435  -1.3103   5.8683   0.5915
 J2Y  C1   C  CR56  0   0.081  -2.5601  -1.4663   0.1910
 J2Y  C2   C  CR56  0   0.407  -1.9011  -2.7140   0.1755
 J2Y  C3   C  CR16  0  -0.272  -2.6136  -3.8881   0.3768
 J2Y  C4   C  CR16  0  -0.258  -3.9687  -3.7389   0.6003
 J2Y  C5   C  CR16  0  -0.137  -4.5416  -2.4581   0.6158
 J2Y  N6   N  N     0  -0.467  -3.8690  -1.3388   0.4204
 J2Y  C7   C  CR5   0  -0.048  -1.5711  -0.4581  -0.0468
 J2Y  C8   C  CR5   0   0.275  -0.3758  -1.1300  -0.2035
 J2Y  N9   N  NR15  0  -0.661  -0.5826  -2.4746  -0.0514
 J2Y  C10  C  CR6   0   0.148   0.9655  -0.6379  -0.5132
 J2Y  N13  N  N     0  -0.423   3.5452   0.2160  -1.1487
 J2Y  C14  C  CR6   0   0.459   3.3511  -0.7566  -0.2785
 J2Y  N17  N  N     0  -0.440  -0.8426   1.7508   0.5094
 J2Y  N22  N  NH1   0  -0.547   4.4389  -1.3750   0.3248
 J2Y  O24  O  O     0  -0.620   6.2235  -0.1080  -0.3349
 J2Y  C25  C  CH3   0  -0.709   6.6179  -1.9572   1.1357
 J2Y  O26  O  O2    0  -0.534  -2.3155   5.0406   0.0359
 J2Y  H35  H  HCR6  0   0.284  -0.1757   3.6244   0.9843
 J2Y  H34  H  HCR6  0   0.287   1.9706  -2.0058   0.8107
 J2Y  H36  H  HCR6  0   0.285  -4.0159   3.3765  -0.9270
 J2Y  H37  H  HCR6  0   0.272  -3.7227   0.9221  -0.9843
 J2Y  H32  H  HCR6  0   0.286   0.3489   0.8663  -1.9485
 J2Y  H33  H  HCR6  0   0.297   2.6603   1.5586  -2.4237
 J2Y  H42  H  HCH3  0   0.243  -0.3630   5.7755   0.0541
 J2Y  H43  H  HCH3  0   0.213  -1.6670   6.8908   0.4988
 J2Y  H44  H  HCH3  0   0.248  -1.1413   5.6484   1.6488
 J2Y  H28  H  HCR6  0   0.277  -2.1404  -4.8613   0.3628
 J2Y  H29  H  HCR6  0   0.260  -4.5967  -4.6026   0.7684
 J2Y  H30  H  HCR6  0   0.232  -5.6058  -2.3566   0.7977
 J2Y  H31  H  HNR5  0   0.378   0.1147  -3.1831  -0.2185
 J2Y  H38  H  HNH1  0   0.422   4.2052  -2.1637   0.9088
 J2Y  H40  H  HCH3  0   0.292   7.6709  -1.7875   0.9285
 J2Y  H39  H  HCH3  0   0.251   6.4375  -1.7582   2.1938
 J2Y  H41  H  HCH3  0   0.250   6.3861  -3.0070   0.9565

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
 J2Y  N13  C12  aromatic  1.332  0.020  1.332
 J2Y  N13  C14  aromatic  1.319  0.020  1.319
 J2Y  C25  C23  single    1.509  0.020  1.509
 J2Y  N22  C14  single    1.389  0.020  1.389
 J2Y  N22  C23  single    1.371  0.020  1.371
 J2Y  C12  C11  aromatic  1.378  0.020  1.378
 J2Y  C14  C15  aromatic  1.401  0.020  1.401
 J2Y  C23  O24  double    1.212  0.020  1.212
 J2Y  C11  C10  aromatic  1.397  0.020  1.397
 J2Y  C15  C10  aromatic  1.385  0.020  1.385
 J2Y  C20  C21  aromatic  1.378  0.020  1.378
 J2Y  C20  C19  aromatic  1.394  0.020  1.394
 J2Y  O26  C27  single    1.416  0.020  1.416
 J2Y  O26  C19  single    1.342  0.020  1.342
 J2Y  C10  C8   single    1.462  0.020  1.462
 J2Y  C21  C16  aromatic  1.398  0.020  1.398
 J2Y  C19  C18  aromatic  1.394  0.020  1.394
 J2Y  C16  C7   single    1.463  0.020  1.463
 J2Y  C16  N17  aromatic  1.328  0.020  1.328
 J2Y  C8   C7   aromatic  1.380  0.020  1.380
 J2Y  C8   N9   aromatic  1.369  0.020  1.369
 J2Y  C18  N17  aromatic  1.326  0.020  1.326
 J2Y  C7   C1   aromatic  1.432  0.020  1.432
 J2Y  N9   C2   aromatic  1.359  0.020  1.359
 J2Y  C1   C2   aromatic  1.411  0.020  1.411
 J2Y  C1   N6   aromatic  1.335  0.020  1.335
 J2Y  C2   C3   aromatic  1.388  0.020  1.388
 J2Y  N6   C5   aromatic  1.320  0.020  1.320
 J2Y  C3   C4   aromatic  1.381  0.020  1.381
 J2Y  C5   C4   aromatic  1.403  0.020  1.403
 J2Y  C18  H35  single    0.930  0.020  1.080
 J2Y  C15  H34  single    0.930  0.020  1.080
 J2Y  C20  H36  single    0.930  0.020  1.080
 J2Y  C21  H37  single    0.930  0.020  1.080
 J2Y  C11  H32  single    0.930  0.020  1.080
 J2Y  C12  H33  single    0.930  0.020  1.080
 J2Y  C27  H42  single    0.970  0.020  1.090
 J2Y  C27  H43  single    0.970  0.020  1.090
 J2Y  C27  H44  single    0.970  0.020  1.090
 J2Y  C3   H28  single    0.930  0.020  1.080
 J2Y  C4   H29  single    0.930  0.020  1.080
 J2Y  C5   H30  single    0.930  0.020  1.080
 J2Y  N9   H31  single    0.860  0.020  1.020
 J2Y  N22  H38  single    0.860  0.020  1.020
 J2Y  C25  H40  single    0.970  0.020  1.090
 J2Y  C25  H39  single    0.970  0.020  1.090
 J2Y  C25  H41  single    0.970  0.020  1.090

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
 J2Y  H35  C18  N17  115.72  3.000
 J2Y  H35  C18  C19  121.42  3.000
 J2Y  N17  C18  C19  122.86  3.000
 J2Y  N17  C16  C7   117.82  3.000
 J2Y  N17  C16  C21  121.08  3.000
 J2Y  C7   C16  C21  121.09  3.000
 J2Y  H34  C15  C14  120.03  3.000
 J2Y  H34  C15  C10  120.96  3.000
 J2Y  C14  C15  C10  119.00  3.000
 J2Y  O26  C19  C20  117.39  3.000
 J2Y  O26  C19  C18  125.06  3.000
 J2Y  C20  C19  C18  117.55  3.000
 J2Y  H36  C20  C21  120.71  3.000
 J2Y  H36  C20  C19  120.07  3.000
 J2Y  C21  C20  C19  119.21  3.000
 J2Y  H37  C21  C20  120.05  3.000
 J2Y  H37  C21  C16  120.56  3.000
 J2Y  C20  C21  C16  119.38  3.000
 J2Y  C25  C23  O24  123.00  3.000
 J2Y  O24  C23  N22  124.42  3.000
 J2Y  C25  C23  N22  112.56  3.000
 J2Y  H32  C11  C10  121.67  3.000
 J2Y  H32  C11  C12  120.25  3.000
 J2Y  C10  C11  C12  118.07  3.000
 J2Y  H33  C12  N13  115.90  3.000
 J2Y  H33  C12  C11  119.72  3.000
 J2Y  N13  C12  C11  124.38  3.000
 J2Y  H44  C27  H43  108.81  3.000
 J2Y  H44  C27  H42  108.93  3.000
 J2Y  H43  C27  H42  108.80  3.000
 J2Y  H44  C27  O26  111.83  3.000
 J2Y  H43  C27  O26  106.47  3.000
 J2Y  H42  C27  O26  111.88  3.000
 J2Y  C7   C1   N6   129.67  3.000
 J2Y  N6   C1   C2   122.97  3.000
 J2Y  C7   C1   C2   107.35  3.000
 J2Y  N9   C2   C3   132.16  3.000
 J2Y  C3   C2   C1   120.44  3.000
 J2Y  N9   C2   C1   107.40  3.000
 J2Y  H28  C3   C4   121.88  3.000
 J2Y  H28  C3   C2   122.30  3.000
 J2Y  C4   C3   C2   115.83  3.000
 J2Y  H29  C4   C5   119.37  3.000
 J2Y  H29  C4   C3   120.58  3.000
 J2Y  C5   C4   C3   120.06  3.000
 J2Y  H30  C5   N6   116.45  3.000
 J2Y  H30  C5   C4   119.20  3.000
 J2Y  N6   C5   C4   124.35  3.000
 J2Y  C5   N6   C1   116.36  3.000
 J2Y  C8   C7   C1   105.91  3.000
 J2Y  C1   C7   C16  126.23  3.000
 J2Y  C8   C7   C16  127.72  3.000
 J2Y  C10  C8   N9   119.52  3.000
 J2Y  N9   C8   C7   109.56  3.000
 J2Y  C10  C8   C7   130.91  3.000
 J2Y  H31  N9   C8   124.58  3.000
 J2Y  H31  N9   C2   125.09  3.000
 J2Y  C8   N9   C2   109.77  3.000
 J2Y  C8   C10  C11  121.55  3.000
 J2Y  C8   C10  C15  120.35  3.000
 J2Y  C11  C10  C15  118.07  3.000
 J2Y  C14  N13  C12  117.58  3.000
 J2Y  N22  C14  N13  119.96  3.000
 J2Y  N22  C14  C15  117.13  3.000
 J2Y  N13  C14  C15  122.90  3.000
 J2Y  C16  N17  C18  119.90  3.000
 J2Y  H38  N22  C14  114.71  3.000
 J2Y  H38  N22  C23  115.46  3.000
 J2Y  C14  N22  C23  129.77  3.000
 J2Y  H41  C25  H39  107.44  3.000
 J2Y  H41  C25  H40  108.97  3.000
 J2Y  H39  C25  H40  108.45  3.000
 J2Y  H41  C25  C23  111.83  3.000
 J2Y  H39  C25  C23  109.94  3.000
 J2Y  H40  C25  C23  110.11  3.000
 J2Y  C27  O26  C19  118.42  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
 J2Y  CONST_01  C21  C20  C19  C18    0.00   0.0  0
 J2Y  CONST_02  C21  C16  N17  C18    0.00   0.0  0
 J2Y  CONST_03  C7   C16  N17  C18  180.00   0.0  0
 J2Y  CONST_04  C19  C20  C21  C16    0.00   0.0  0
 J2Y  CONST_05  C10  C8   C7   C16    0.00   0.0  0
 J2Y  CONST_06  N9   C8   C7   C16  180.00   0.0  0
 J2Y  CONST_07  C2   C1   C7   C16  180.00   0.0  0
 J2Y  CONST_08  N6   C1   C7   C16    0.00   0.0  0
 J2Y  CONST_09  C19  C18  N17  C16    0.00   0.0  0
 J2Y  CONST_10  C12  N13  C14  C15    0.00   0.0  0
 J2Y  CONST_11  C12  C11  C10  C15    0.00   0.0  0
 J2Y  CONST_14  C7   C16  C21  C20  180.00   0.0  0
 J2Y  CONST_15  N17  C16  C21  C20    0.00   0.0  0
 J2Y  CONST_16  N17  C18  C19  C20    0.00   0.0  0
 J2Y  CONST_19  C14  N13  C12  C11    0.00   0.0  0
 J2Y  CONST_20  C14  C15  C10  C11    0.00   0.0  0
 J2Y  CONST_23  C8   C10  C11  C12  180.00   0.0  0
 J2Y  CONST_25  C10  C8   C7   C1   180.00   0.0  0
 J2Y  CONST_26  N9   C8   C7   C1     0.00   0.0  0
 J2Y  CONST_27  C8   N9   C2   C1     0.00   0.0  0
 J2Y  CONST_28  C4   C3   C2   C1     0.00   0.0  0
 J2Y  CONST_29  C4   C5   N6   C1     0.00   0.0  0
 J2Y  CONST_30  C10  C8   N9   C2   180.00   0.0  0
 J2Y  CONST_31  C7   C8   N9   C2     0.00   0.0  0
 J2Y  CONST_32  C8   C7   C1   C2     0.00   0.0  0
 J2Y  CONST_33  C5   N6   C1   C2     0.00   0.0  0
 J2Y  CONST_34  C5   C4   C3   C2     0.00   0.0  0
 J2Y  CONST_35  C8   N9   C2   C3   180.00   0.0  0
 J2Y  CONST_36  C7   C1   C2   C3   180.00   0.0  0
 J2Y  CONST_37  N6   C1   C2   C3     0.00   0.0  0
 J2Y  CONST_38  N6   C5   C4   C3     0.00   0.0  0
 J2Y  CONST_39  N9   C2   C3   C4   180.00   0.0  0
 J2Y  CONST_40  C7   C1   N6   C5   180.00   0.0  0
 J2Y  CONST_41  C8   C7   C1   N6   180.00   0.0  0
 J2Y  CONST_42  N9   C2   C1   N6   180.00   0.0  0
 J2Y  CONST_43  N9   C2   C1   C7     0.00   0.0  0
 J2Y  CONST_44  C14  C15  C10  C8   180.00   0.0  0
 J2Y  CONST_46  N13  C12  C11  C10    0.00   0.0  0
 J2Y  CONST_47  N13  C14  C15  C10    0.00   0.0  0
 J2Y  CONST_48  O26  C19  C20  C21  180.00   0.0  0
 J2Y  CONST_49  N22  C14  N13  C12  180.00   0.0  0
 J2Y  CONST_50  N22  C14  C15  C10  180.00   0.0  0
 J2Y  CONST_51  O26  C19  C18  N17  180.00   0.0  0
 J2Y  CONST_52  H36  C20  C19  C18  180.00   0.0  0
 J2Y  CONST_53  H35  C18  N17  C16  180.00   0.0  0
 J2Y  CONST_54  H32  C11  C10  C15  180.00   0.0  0
 J2Y  CONST_55  H37  C21  C20  C19  180.00   0.0  0
 J2Y  CONST_56  H34  C15  C10  C11  180.00   0.0  0
 J2Y  CONST_57  H31  N9   C2   C1   180.00   0.0  0
 J2Y  CONST_58  H28  C3   C2   C1   180.00   0.0  0
 J2Y  CONST_59  H30  C5   N6   C1   180.00   0.0  0
 J2Y  CONST_60  H29  C4   C3   C2   180.00   0.0  0
 J2Y  CONST_61  H33  C12  C11  C10  180.00   0.0  0
 J2Y  CONST_62  C23  N22  C14  C15  180.00   0.0  0
 J2Y  CONST_63  N13  C14  N22  C23    0.00   0.0  0
 J2Y  CONST_64  H38  N22  C14  C15    0.00   0.0  0
 J2Y  CONST_65  C25  C23  N22  C14  180.00   0.0  0
 J2Y  CONST_66  O24  C23  N22  C14    0.00   0.0  0
 J2Y  Var_01    H42  C27  O26  C19   61.38  30.0  3
 J2Y  Var_02    H40  C25  C23  N22  168.90  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
 J2Y  plan-1  C18  0.020
 J2Y  plan-1  C16  0.020
 J2Y  plan-1  C19  0.020
 J2Y  plan-1  C20  0.020
 J2Y  plan-1  C21  0.020
 J2Y  plan-1  C7   0.020
 J2Y  plan-1  N17  0.020
 J2Y  plan-1  O26  0.020
 J2Y  plan-1  H35  0.020
 J2Y  plan-1  H36  0.020
 J2Y  plan-1  H37  0.020
 J2Y  plan-2  C15  0.020
 J2Y  plan-2  C11  0.020
 J2Y  plan-2  C12  0.020
 J2Y  plan-2  C8   0.020
 J2Y  plan-2  C10  0.020
 J2Y  plan-2  N13  0.020
 J2Y  plan-2  C14  0.020
 J2Y  plan-2  N22  0.020
 J2Y  plan-2  H34  0.020
 J2Y  plan-2  H32  0.020
 J2Y  plan-2  H33  0.020
 J2Y  plan-3  C16  0.020
 J2Y  plan-3  C1   0.020
 J2Y  plan-3  C2   0.020
 J2Y  plan-3  C3   0.020
 J2Y  plan-3  C4   0.020
 J2Y  plan-3  C5   0.020
 J2Y  plan-3  N6   0.020
 J2Y  plan-3  C7   0.020
 J2Y  plan-3  C8   0.020
 J2Y  plan-3  N9   0.020
 J2Y  plan-3  C10  0.020
 J2Y  plan-3  H28  0.020
 J2Y  plan-3  H29  0.020
 J2Y  plan-3  H30  0.020
 J2Y  plan-3  H31  0.020
 J2Y  plan-4  C23  0.020
 J2Y  plan-4  C14  0.020
 J2Y  plan-4  N22  0.020
 J2Y  plan-4  O24  0.020
 J2Y  plan-4  C25  0.020
 J2Y  plan-4  H38  0.020

