# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:22:44 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N-{4-[3-(6-methoxypyridin-3-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(cn1)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
 J2V  J2V  N-{4-[3-(6-methoxypyridin-3-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_J2V
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
 J2V  C17  C  CR16  0  -0.101  -1.1035  -1.7460  -0.7011
 J2V  C16  C  CR6   0  -0.090  -1.8489  -0.8684   0.0715
 J2V  C15  C  CR16  0  -0.475   2.1230   1.1219  -0.1371
 J2V  C19  C  CR6   0   0.528  -2.3180  -3.5581  -0.0638
 J2V  C20  C  CR16  0  -0.385  -3.1622  -2.7737   0.7319
 J2V  C21  C  CR16  0  -0.186  -2.9156  -1.4219   0.7928
 J2V  C23  C  C     0   0.497   5.8056   0.8028  -0.3839
 J2V  C11  C  CR16  0  -0.392   1.1691  -0.4921   1.3402
 J2V  C12  C  CR16  0  -0.051   2.4453  -0.9785   1.5265
 J2V  C27  C  CH3   0  -0.416  -1.7142  -5.6845  -0.9010
 J2V  C1   C  CR56  0   0.138  -2.4976   1.6201  -0.0665
 J2V  C2   C  CR56  0   0.308  -1.7810   2.8354  -0.0450
 J2V  C3   C  CR16  0  -0.216  -2.4491   4.0446  -0.1847
 J2V  C4   C  CR16  0  -0.335  -3.8174   3.9595  -0.3550
 J2V  C5   C  CR16  0  -0.115  -4.4480   2.7058  -0.3805
 J2V  N6   N  N     0  -0.418  -3.8189   1.5533  -0.2428
 J2V  C7   C  CR5   0  -0.043  -1.5508   0.5620   0.1113
 J2V  C8   C  CR5   0   0.355  -0.3216   1.1733   0.2406
 J2V  N9   N  NR15  0  -0.742  -0.4675   2.5307   0.1242
 J2V  C10  C  CR6   0   0.130   0.9988   0.5927   0.4750
 J2V  N13  N  N     0  -0.426   3.5315  -0.4828   0.9382
 J2V  C14  C  CR6   0   0.552   3.3727   0.5477   0.1281
 J2V  N18  N  N     0  -0.456  -1.3233  -3.0565  -0.7636
 J2V  N22  N  NH1   0  -0.722   4.4726   1.0996  -0.5138
 J2V  O24  O  O     0  -0.440   6.2483  -0.0426   0.3621
 J2V  C25  C  CH3   0  -0.799   6.6738   1.6499  -1.2815
 J2V  O26  O  O2    0  -0.473  -2.5576  -4.8705  -0.0991
 J2V  H35  H  HCR6  0   0.257  -0.2846  -1.3726  -1.3073
 J2V  H34  H  HCR6  0   0.283   2.0423   1.9532  -0.8269
 J2V  H36  H  HCR6  0   0.273  -3.9770  -3.2246   1.2821
 J2V  H37  H  HCR6  0   0.262  -3.5413  -0.7886   1.4074
 J2V  H32  H  HCR6  0   0.270   0.3352  -0.9318   1.8678
 J2V  H33  H  HCR6  0   0.267   2.6086  -1.8177   2.1932
 J2V  H42  H  HCH3  0   0.229  -0.6711  -5.6208  -0.5887
 J2V  H44  H  HCH3  0   0.246  -2.0678  -6.7033  -0.7652
 J2V  H43  H  HCH3  0   0.229  -1.7790  -5.4191  -1.9570
 J2V  H28  H  HCR6  0   0.279  -1.9338   4.9961  -0.1640
 J2V  H29  H  HCR6  0   0.270  -4.4133   4.8539  -0.4723
 J2V  H30  H  HCR6  0   0.254  -5.5222   2.6570  -0.5204
 J2V  H31  H  HNR5  0   0.421   0.2681   3.2016   0.2803
 J2V  H38  H  HNH1  0   0.424   4.2572   1.8506  -1.1521
 J2V  H39  H  HCH3  0   0.269   7.7223   1.4192  -1.1157
 J2V  H40  H  HCH3  0   0.273   6.4360   1.4662  -2.3304
 J2V  H41  H  HCH3  0   0.270   6.5126   2.7120  -1.0924

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
 J2V  C25  C23  single    1.509  0.020  1.509
 J2V  N13  C12  aromatic  1.331  0.020  1.331
 J2V  N13  C14  aromatic  1.320  0.020  1.320
 J2V  N22  C23  single    1.372  0.020  1.372
 J2V  N22  C14  single    1.388  0.020  1.388
 J2V  C12  C11  aromatic  1.378  0.020  1.378
 J2V  C23  O24  double    1.211  0.020  1.211
 J2V  C14  C15  aromatic  1.401  0.020  1.401
 J2V  C11  C10  aromatic  1.398  0.020  1.398
 J2V  C15  C10  aromatic  1.385  0.020  1.385
 J2V  C20  C21  aromatic  1.375  0.020  1.375
 J2V  C20  C19  aromatic  1.400  0.020  1.400
 J2V  C10  C8   single    1.461  0.020  1.461
 J2V  O26  C19  single    1.335  0.020  1.335
 J2V  O26  C27  single    1.420  0.020  1.420
 J2V  C21  C16  aromatic  1.402  0.020  1.402
 J2V  C19  N18  aromatic  1.316  0.020  1.316
 J2V  C8   C7   aromatic  1.379  0.020  1.379
 J2V  C8   N9   aromatic  1.370  0.020  1.370
 J2V  C16  C7   single    1.462  0.020  1.462
 J2V  C16  C17  aromatic  1.387  0.020  1.387
 J2V  N18  C17  aromatic  1.330  0.020  1.330
 J2V  C7   C1   aromatic  1.431  0.020  1.431
 J2V  N9   C2   aromatic  1.359  0.020  1.359
 J2V  C1   C2   aromatic  1.411  0.020  1.411
 J2V  C1   N6   aromatic  1.335  0.020  1.335
 J2V  C2   C3   aromatic  1.388  0.020  1.388
 J2V  N6   C5   aromatic  1.320  0.020  1.320
 J2V  C3   C4   aromatic  1.382  0.020  1.382
 J2V  C5   C4   aromatic  1.404  0.020  1.404
 J2V  C17  H35  single    0.930  0.020  1.080
 J2V  C15  H34  single    0.930  0.020  1.080
 J2V  C20  H36  single    0.930  0.020  1.080
 J2V  C21  H37  single    0.930  0.020  1.080
 J2V  C11  H32  single    0.930  0.020  1.080
 J2V  C12  H33  single    0.930  0.020  1.080
 J2V  C27  H42  single    0.970  0.020  1.090
 J2V  C27  H44  single    0.970  0.020  1.090
 J2V  C27  H43  single    0.970  0.020  1.090
 J2V  C3   H28  single    0.930  0.020  1.080
 J2V  C4   H29  single    0.930  0.020  1.080
 J2V  C5   H30  single    0.930  0.020  1.080
 J2V  N9   H31  single    0.860  0.020  1.020
 J2V  N22  H38  single    0.860  0.020  1.020
 J2V  C25  H39  single    0.970  0.020  1.090
 J2V  C25  H40  single    0.970  0.020  1.090
 J2V  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
 J2V  H35  C17  N18  115.95  3.000
 J2V  H35  C17  C16  119.94  3.000
 J2V  N18  C17  C16  124.11  3.000
 J2V  C7   C16  C21  121.85  3.000
 J2V  C7   C16  C17  121.66  3.000
 J2V  C21  C16  C17  116.48  3.000
 J2V  H34  C15  C14  120.12  3.000
 J2V  H34  C15  C10  120.94  3.000
 J2V  C14  C15  C10  118.94  3.000
 J2V  O26  C19  N18  119.78  3.000
 J2V  N18  C19  C20  122.98  3.000
 J2V  O26  C19  C20  117.24  3.000
 J2V  H36  C20  C21  121.48  3.000
 J2V  H36  C20  C19  120.64  3.000
 J2V  C21  C20  C19  117.88  3.000
 J2V  H37  C21  C20  119.78  3.000
 J2V  H37  C21  C16  120.09  3.000
 J2V  C20  C21  C16  120.12  3.000
 J2V  C25  C23  O24  123.22  3.000
 J2V  O24  C23  N22  124.37  3.000
 J2V  C25  C23  N22  112.42  3.000
 J2V  H32  C11  C10  121.60  3.000
 J2V  H32  C11  C12  120.34  3.000
 J2V  C10  C11  C12  118.05  3.000
 J2V  H33  C12  N13  115.92  3.000
 J2V  H33  C12  C11  119.72  3.000
 J2V  N13  C12  C11  124.36  3.000
 J2V  H43  C27  H44  109.24  3.000
 J2V  H43  C27  H42  108.65  3.000
 J2V  H44  C27  H42  109.27  3.000
 J2V  H43  C27  O26  111.84  3.000
 J2V  H44  C27  O26  105.88  3.000
 J2V  H42  C27  O26  111.89  3.000
 J2V  C7   C1   N6   129.38  3.000
 J2V  N6   C1   C2   123.22  3.000
 J2V  C7   C1   C2   107.40  3.000
 J2V  N9   C2   C3   132.29  3.000
 J2V  C3   C2   C1   120.28  3.000
 J2V  N9   C2   C1   107.43  3.000
 J2V  H28  C3   C4   121.87  3.000
 J2V  H28  C3   C2   122.32  3.000
 J2V  C4   C3   C2   115.81  3.000
 J2V  H29  C4   C5   119.30  3.000
 J2V  H29  C4   C3   120.56  3.000
 J2V  C5   C4   C3   120.15  3.000
 J2V  H30  C5   N6   116.50  3.000
 J2V  H30  C5   C4   119.18  3.000
 J2V  N6   C5   C4   124.32  3.000
 J2V  C5   N6   C1   116.22  3.000
 J2V  C8   C7   C1   105.88  3.000
 J2V  C1   C7   C16  125.83  3.000
 J2V  C8   C7   C16  128.18  3.000
 J2V  C10  C8   N9   120.23  3.000
 J2V  N9   C8   C7   109.65  3.000
 J2V  C10  C8   C7   130.12  3.000
 J2V  H31  N9   C8   124.66  3.000
 J2V  H31  N9   C2   125.14  3.000
 J2V  C8   N9   C2   109.61  3.000
 J2V  C8   C10  C11  121.17  3.000
 J2V  C8   C10  C15  120.71  3.000
 J2V  C11  C10  C15  118.10  3.000
 J2V  C14  N13  C12  117.63  3.000
 J2V  N22  C14  N13  119.92  3.000
 J2V  N22  C14  C15  117.16  3.000
 J2V  N13  C14  C15  122.92  3.000
 J2V  C19  N18  C17  118.40  3.000
 J2V  H38  N22  C14  114.80  3.000
 J2V  H38  N22  C23  115.37  3.000
 J2V  C14  N22  C23  129.81  3.000
 J2V  H41  C25  H40  107.36  3.000
 J2V  H41  C25  H39  108.84  3.000
 J2V  H40  C25  H39  108.74  3.000
 J2V  H41  C25  C23  111.01  3.000
 J2V  H40  C25  C23  110.61  3.000
 J2V  H39  C25  C23  110.20  3.000
 J2V  C27  O26  C19  118.16  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
 J2V  CONST_01  C20  C21  C16  C17    0.00   0.0  0
 J2V  CONST_04  C20  C19  N18  C17    0.00   0.0  0
 J2V  CONST_05  C19  C20  C21  C16    0.00   0.0  0
 J2V  CONST_06  C10  C8   C7   C16    0.00   0.0  0
 J2V  CONST_07  N9   C8   C7   C16  180.00   0.0  0
 J2V  CONST_08  C2   C1   C7   C16  180.00   0.0  0
 J2V  CONST_09  N6   C1   C7   C16    0.00   0.0  0
 J2V  CONST_10  C19  N18  C17  C16    0.00   0.0  0
 J2V  CONST_11  C12  N13  C14  C15    0.00   0.0  0
 J2V  CONST_12  C12  C11  C10  C15    0.00   0.0  0
 J2V  CONST_15  C7   C16  C21  C20  180.00   0.0  0
 J2V  CONST_16  N18  C19  C20  C21    0.00   0.0  0
 J2V  CONST_19  N18  C17  C16  C21    0.00   0.0  0
 J2V  CONST_20  C14  N13  C12  C11    0.00   0.0  0
 J2V  CONST_21  C14  C15  C10  C11    0.00   0.0  0
 J2V  CONST_24  C8   C10  C11  C12  180.00   0.0  0
 J2V  CONST_25  C10  C8   C7   C1   180.00   0.0  0
 J2V  CONST_26  N9   C8   C7   C1     0.00   0.0  0
 J2V  CONST_27  C8   N9   C2   C1     0.00   0.0  0
 J2V  CONST_28  C4   C3   C2   C1     0.00   0.0  0
 J2V  CONST_29  C4   C5   N6   C1     0.00   0.0  0
 J2V  CONST_30  C10  C8   N9   C2   180.00   0.0  0
 J2V  CONST_31  C7   C8   N9   C2     0.00   0.0  0
 J2V  CONST_32  C8   C7   C1   C2     0.00   0.0  0
 J2V  CONST_33  C5   N6   C1   C2     0.00   0.0  0
 J2V  CONST_34  C5   C4   C3   C2     0.00   0.0  0
 J2V  CONST_35  C8   N9   C2   C3   180.00   0.0  0
 J2V  CONST_36  C7   C1   C2   C3   180.00   0.0  0
 J2V  CONST_37  N6   C1   C2   C3     0.00   0.0  0
 J2V  CONST_38  N6   C5   C4   C3     0.00   0.0  0
 J2V  CONST_39  N9   C2   C3   C4   180.00   0.0  0
 J2V  CONST_40  C7   C1   N6   C5   180.00   0.0  0
 J2V  CONST_41  C8   C7   C1   N6   180.00   0.0  0
 J2V  CONST_42  N9   C2   C1   N6   180.00   0.0  0
 J2V  CONST_43  N18  C17  C16  C7   180.00   0.0  0
 J2V  CONST_44  N9   C2   C1   C7     0.00   0.0  0
 J2V  CONST_45  C14  C15  C10  C8   180.00   0.0  0
 J2V  CONST_46  N13  C12  C11  C10    0.00   0.0  0
 J2V  CONST_47  N13  C14  C15  C10    0.00   0.0  0
 J2V  CONST_48  O26  C19  N18  C17  180.00   0.0  0
 J2V  CONST_49  O26  C19  C20  C21  180.00   0.0  0
 J2V  CONST_50  N22  C14  N13  C12  180.00   0.0  0
 J2V  CONST_51  N22  C14  C15  C10  180.00   0.0  0
 J2V  CONST_52  H37  C21  C16  C17  180.00   0.0  0
 J2V  CONST_53  H36  C20  C21  C16  180.00   0.0  0
 J2V  CONST_54  H32  C11  C10  C15  180.00   0.0  0
 J2V  CONST_55  H35  C17  N18  C19  180.00   0.0  0
 J2V  CONST_56  H34  C15  C10  C11  180.00   0.0  0
 J2V  CONST_57  H31  N9   C2   C1   180.00   0.0  0
 J2V  CONST_58  H28  C3   C2   C1   180.00   0.0  0
 J2V  CONST_59  H30  C5   N6   C1   180.00   0.0  0
 J2V  CONST_60  H29  C4   C3   C2   180.00   0.0  0
 J2V  CONST_61  H33  C12  C11  C10  180.00   0.0  0
 J2V  CONST_62  C23  N22  C14  C15  180.00   0.0  0
 J2V  CONST_63  N13  C14  N22  C23    0.00   0.0  0
 J2V  CONST_64  H38  N22  C14  C15    0.00   0.0  0
 J2V  CONST_65  C25  C23  N22  C14  180.00   0.0  0
 J2V  CONST_66  O24  C23  N22  C14    0.00   0.0  0
 J2V  Var_01    N18  C19  O26  C27    0.12  30.0  2
 J2V  Var_02    H42  C27  O26  C19   59.71  30.0  3
 J2V  Var_03    H39  C25  C23  N22  177.30  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
 J2V  plan-1  C17  0.020
 J2V  plan-1  C16  0.020
 J2V  plan-1  C19  0.020
 J2V  plan-1  C20  0.020
 J2V  plan-1  C21  0.020
 J2V  plan-1  C7   0.020
 J2V  plan-1  N18  0.020
 J2V  plan-1  O26  0.020
 J2V  plan-1  H35  0.020
 J2V  plan-1  H36  0.020
 J2V  plan-1  H37  0.020
 J2V  plan-2  C15  0.020
 J2V  plan-2  C11  0.020
 J2V  plan-2  C12  0.020
 J2V  plan-2  C8   0.020
 J2V  plan-2  C10  0.020
 J2V  plan-2  N13  0.020
 J2V  plan-2  C14  0.020
 J2V  plan-2  N22  0.020
 J2V  plan-2  H34  0.020
 J2V  plan-2  H32  0.020
 J2V  plan-2  H33  0.020
 J2V  plan-3  C16  0.020
 J2V  plan-3  C1   0.020
 J2V  plan-3  C2   0.020
 J2V  plan-3  C3   0.020
 J2V  plan-3  C4   0.020
 J2V  plan-3  C5   0.020
 J2V  plan-3  N6   0.020
 J2V  plan-3  C7   0.020
 J2V  plan-3  C8   0.020
 J2V  plan-3  N9   0.020
 J2V  plan-3  C10  0.020
 J2V  plan-3  H28  0.020
 J2V  plan-3  H29  0.020
 J2V  plan-3  H30  0.020
 J2V  plan-3  H31  0.020
 J2V  plan-4  C23  0.020
 J2V  plan-4  C14  0.020
 J2V  plan-4  N22  0.020
 J2V  plan-4  O24  0.020
 J2V  plan-4  C25  0.020
 J2V  plan-4  H38  0.020

