# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:19:37 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 1-benzyl-1H-imidazo[4,5-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(n1cnc2ncccc12)c3ccccc3
#
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
 EXG  EXG  1-benzyl-1H-imidazo[4,5-b]pyridine  ligand  27  16  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EXG
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
 EXG  C1   C  CR6   0   0.102  -1.8288  -0.1151   0.6809
 EXG  C2   C  CR16  0  -0.305  -2.4461   1.0585   1.0956
 EXG  C3   C  CR16  0  -0.241  -3.3877   1.6843   0.2870
 EXG  C11  C  CR16  0  -0.197   1.2963   1.2481   0.2964
 EXG  C12  C  CR56  0   0.267   1.2832  -0.1355   0.3526
 EXG  C10  C  CR16  0  -0.336   2.3900   1.8010  -0.3489
 EXG  C9   C  CR16  0  -0.098   3.3844   0.9751  -0.8884
 EXG  N2   N  N     0  -0.417   3.3726  -0.3481  -0.8340
 EXG  C8   C  CR56  0   0.261   2.3279  -0.8855  -0.2181
 EXG  N1   N  N     0  -0.466   2.0990  -2.2238  -0.0377
 EXG  C7   C  CR15  0   0.119   0.9697  -2.2760   0.6108
 EXG  N    N  NR5   0  -0.503   0.4261  -1.0623   0.8804
 EXG  C    C  CH2   0  -0.389  -0.8199  -0.7979   1.5686
 EXG  C6   C  CR16  0  -0.277  -2.1621  -0.6570  -0.5581
 EXG  C5   C  CR16  0  -0.241  -3.0979  -0.0324  -1.3681
 EXG  C4   C  CR16  0  -0.263  -3.7138   1.1409  -0.9468
 EXG  H1   H  HCR6  0   0.259  -2.1906   1.4908   2.0561
 EXG  H2   H  HCR6  0   0.259  -3.8597   2.5994   0.6202
 EXG  H4   H  HCR6  0   0.272   2.4866   2.8735  -0.4431
 EXG  H5   H  HCR6  0   0.260   4.2317   1.4295  -1.3892
 EXG  H6   H  HCR5  0   0.299   0.4755  -3.1836   0.9272
 EXG  H7   H  HCH2  0   0.287  -0.6164  -0.1929   2.4537
 EXG  H8   H  HCH2  0   0.295  -1.2024  -1.7580   1.9179
 EXG  H9   H  HCR6  0   0.253  -1.6890  -1.5723  -0.8948
 EXG  H10  H  HCR6  0   0.259  -3.3493  -0.4612  -2.3296
 EXG  H11  H  HCR6  0   0.259  -4.4438   1.6281  -1.5799
 EXG  H3   H  HCR6  0   0.282   0.5139   1.8621   0.7222

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
 EXG  C11  C10  aromatic  1.385  0.020  1.385
 EXG  C11  C12  aromatic  1.385  0.020  1.385
 EXG  C    N    single    1.448  0.020  1.448
 EXG  C    C1   single    1.507  0.020  1.507
 EXG  C10  C9   aromatic  1.401  0.020  1.401
 EXG  C12  N    aromatic  1.368  0.020  1.368
 EXG  C12  C8   aromatic  1.407  0.020  1.407
 EXG  N    C7   aromatic  1.357  0.020  1.357
 EXG  C9   N2   aromatic  1.324  0.020  1.324
 EXG  C7   N1   aromatic  1.303  0.020  1.303
 EXG  C8   N2   aromatic  1.326  0.020  1.326
 EXG  C8   N1   aromatic  1.370  0.020  1.370
 EXG  C1   C6   aromatic  1.393  0.020  1.393
 EXG  C1   C2   aromatic  1.389  0.020  1.389
 EXG  C6   C5   aromatic  1.386  0.020  1.386
 EXG  C2   C3   aromatic  1.390  0.020  1.390
 EXG  C5   C4   aromatic  1.391  0.020  1.391
 EXG  C3   C4   aromatic  1.387  0.020  1.387
 EXG  C2   H1   single    0.930  0.020  1.080
 EXG  C3   H2   single    0.930  0.020  1.080
 EXG  C11  H3   single    0.930  0.020  1.080
 EXG  C10  H4   single    0.930  0.020  1.080
 EXG  C9   H5   single    0.930  0.020  1.080
 EXG  C7   H6   single    0.930  0.020  1.080
 EXG  C    H7   single    0.970  0.020  1.090
 EXG  C    H8   single    0.970  0.020  1.090
 EXG  C6   H9   single    0.930  0.020  1.080
 EXG  C5   H10  single    0.930  0.020  1.080
 EXG  C4   H11  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
 EXG  C6   C1   C    120.52  3.000
 EXG  C6   C1   C2   119.20  3.000
 EXG  C    C1   C2   120.28  3.000
 EXG  H1   C2   C3   119.72  3.000
 EXG  H1   C2   C1   119.77  3.000
 EXG  C3   C2   C1   120.51  3.000
 EXG  H2   C3   C4   120.17  3.000
 EXG  H2   C3   C2   119.80  3.000
 EXG  C4   C3   C2   120.02  3.000
 EXG  H3   C11  C10  121.86  3.000
 EXG  H3   C11  C12  122.98  3.000
 EXG  C10  C11  C12  115.16  3.000
 EXG  N    C12  C8   105.10  3.000
 EXG  C8   C12  C11  120.61  3.000
 EXG  N    C12  C11  134.29  3.000
 EXG  H4   C10  C9   119.21  3.000
 EXG  H4   C10  C11  120.48  3.000
 EXG  C9   C10  C11  120.31  3.000
 EXG  H5   C9   N2   116.40  3.000
 EXG  H5   C9   C10  119.06  3.000
 EXG  N2   C9   C10  124.54  3.000
 EXG  C8   N2   C9   115.52  3.000
 EXG  N1   C8   N2   126.06  3.000
 EXG  N1   C8   C12  110.08  3.000
 EXG  N2   C8   C12  123.85  3.000
 EXG  C7   N1   C8   104.45  3.000
 EXG  H6   C7   N    120.65  3.000
 EXG  H6   C7   N1   125.14  3.000
 EXG  N    C7   N1   114.22  3.000
 EXG  C    N    C7   127.05  3.000
 EXG  C7   N    C12  106.16  3.000
 EXG  C    N    C12  126.79  3.000
 EXG  H8   C    H7   107.08  3.000
 EXG  H8   C    N    107.06  3.000
 EXG  H7   C    N    109.04  3.000
 EXG  H8   C    C1   110.64  3.000
 EXG  H7   C    C1   110.57  3.000
 EXG  N    C    C1   112.26  3.000
 EXG  H9   C6   C5   119.58  3.000
 EXG  H9   C6   C1   120.03  3.000
 EXG  C5   C6   C1   120.40  3.000
 EXG  H10  C5   C4   120.04  3.000
 EXG  H10  C5   C6   119.82  3.000
 EXG  C4   C5   C6   120.14  3.000
 EXG  H11  C4   C5   120.09  3.000
 EXG  H11  C4   C3   120.18  3.000
 EXG  C5   C4   C3   119.73  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
 EXG  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 EXG  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 EXG  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 EXG  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 EXG  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 EXG  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 EXG  CONST_07  N2   C9   C10  C11     0.00   0.0  0
 EXG  CONST_08  C7   N    C12  C11   180.00   0.0  0
 EXG  CONST_09  N2   C8   C12  C11     0.00   0.0  0
 EXG  CONST_10  N1   C8   C12  C11   180.00   0.0  0
 EXG  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 EXG  CONST_12  N1   C7   N    C12     0.00   0.0  0
 EXG  CONST_13  C9   N2   C8   C12     0.00   0.0  0
 EXG  CONST_14  C7   N1   C8   C12     0.00   0.0  0
 EXG  CONST_15  N    C12  C11  C10   180.00   0.0  0
 EXG  CONST_16  C8   C12  C11  C10     0.00   0.0  0
 EXG  CONST_17  C8   N2   C9   C10     0.00   0.0  0
 EXG  CONST_18  N1   C8   N2   C9    180.00   0.0  0
 EXG  CONST_19  N    C12  C8   N2    180.00   0.0  0
 EXG  CONST_20  C7   N1   C8   N2    180.00   0.0  0
 EXG  CONST_21  C7   N    C12  C8      0.00   0.0  0
 EXG  CONST_22  N    C7   N1   C8      0.00   0.0  0
 EXG  CONST_23  N    C12  C8   N1      0.00   0.0  0
 EXG  CONST_24  C    C1   C2   C3    180.00   0.0  0
 EXG  CONST_25  C    N    C12  C11     0.00   0.0  0
 EXG  CONST_26  C    N    C12  C8    180.00   0.0  0
 EXG  CONST_27  C    N    C7   N1    180.00   0.0  0
 EXG  CONST_28  C5   C6   C1   C     180.00   0.0  0
 EXG  CONST_29  H10  C5   C6   C1    180.00   0.0  0
 EXG  CONST_30  H2   C3   C2   C1    180.00   0.0  0
 EXG  CONST_31  H9   C6   C1   C2    180.00   0.0  0
 EXG  CONST_32  H11  C4   C3   C2    180.00   0.0  0
 EXG  CONST_33  H5   C9   C10  C11   180.00   0.0  0
 EXG  CONST_34  H4   C10  C11  C12   180.00   0.0  0
 EXG  CONST_35  H6   C7   N    C12   180.00   0.0  0
 EXG  CONST_36  H3   C11  C10  C9    180.00   0.0  0
 EXG  CONST_37  H1   C2   C1   C6    180.00   0.0  0
 EXG  Var_01    C12  N    C    C1     62.56  30.0  2
 EXG  Var_02    N    C    C1   C2   -127.58  30.0  2

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
 EXG  plan-1  C1   0.020
 EXG  plan-1  C2   0.020
 EXG  plan-1  C3   0.020
 EXG  plan-1  C    0.020
 EXG  plan-1  C6   0.020
 EXG  plan-1  C5   0.020
 EXG  plan-1  C4   0.020
 EXG  plan-1  H1   0.020
 EXG  plan-1  H2   0.020
 EXG  plan-1  H9   0.020
 EXG  plan-1  H10  0.020
 EXG  plan-1  H11  0.020
 EXG  plan-2  C11  0.020
 EXG  plan-2  C12  0.020
 EXG  plan-2  C10  0.020
 EXG  plan-2  C9   0.020
 EXG  plan-2  N2   0.020
 EXG  plan-2  C8   0.020
 EXG  plan-2  N1   0.020
 EXG  plan-2  C7   0.020
 EXG  plan-2  N    0.020
 EXG  plan-2  C    0.020
 EXG  plan-2  H4   0.020
 EXG  plan-2  H5   0.020
 EXG  plan-2  H6   0.020
 EXG  plan-2  H3   0.020

