# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:49:31 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-chloro-2-(2-fluoro-4,5-dimethoxyphenyl)-N-(piperidin-4-ylmethyl)-3H-imidazo[4,5-b]pyridin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(F)c(cc1OC)c2[nH]c3ncc(Cl)c(NCC4CCNCC4)c3n2
#
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
 5JG  5JG  6-chloro-2-(2-fluoro-4,5-dimethoxyphenyl)-N-(piperidin-4-ylmethyl)-3H-imidazo[4,5-b]pyridin-7-amine  ligand  52  29  .  2022-07-23  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_5JG
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
 5JG  C1   C   CH3   0  -0.442  -2.1442   3.6718   0.0673
 5JG  C3   C   CR6   0   0.346  -3.3849   1.6912   0.4276
 5JG  C7   C   CR16  0  -0.536  -4.7406  -0.2646   0.8439
 5JG  C8   C   CR6   0   0.337  -4.6261   1.1132   0.7862
 5JG  C10  C   CH3   0  -0.443  -6.8781   1.4522   1.4221
 5JG  C12  C   CR5   0   0.541  -1.2281  -1.3151  -0.1197
 5JG  C14  C   CR56  0   0.435   0.0876  -3.0224  -0.5633
 5JG  C15  C   CR56  0   0.035   0.7921  -1.8133  -0.5926
 5JG  C19  C   CR16  0  -0.089   1.8442  -4.2675  -1.0633
 5JG  C22  C   CH2   0  -0.228   2.5687   0.6256  -0.8048
 5JG  C24  C   CH2   0  -0.428   3.3719   2.9852  -0.6002
 5JG  N26  N   NH1   0  -0.576   5.2142   3.5935   0.9769
 5JG  C27  C   CH2   0  -0.316   5.5917   2.1912   1.0658
 5JG  O2   O   O2    0  -0.463  -3.3628   3.0347   0.3940
 5JG  C4   C   CR16  0  -0.442  -2.3156   0.8736   0.1429
 5JG  C5   C   CR6   0  -0.225  -2.4156  -0.5288   0.1928
 5JG  C6   C   CR6   0   0.548  -3.6406  -1.0533   0.5478
 5JG  O9   O   O2    0  -0.451  -5.6147   1.9716   1.0478
 5JG  F11  F   F     0  -0.316  -3.8042  -2.3871   0.6280
 5JG  N13  N   NR15  0  -0.729  -1.1942  -2.6721  -0.2572
 5JG  N16  N   N     0  -0.480  -0.0533  -0.7747  -0.3147
 5JG  C17  C   CR6   0   0.498   2.1730  -1.8357  -0.8806
 5JG  C18  C   CR6   0  -0.244   2.6556  -3.1411  -1.1199
 5JG  N20  N   N     0  -0.450   0.5479  -4.2439  -0.7843
 5JG  CL   CL  CL    0  -0.130   4.3403  -3.3571  -1.4920
 5JG  N21  N   NH1   0  -0.685   2.9744  -0.7613  -0.9180
 5JG  C23  C   CH1   0  -0.292   3.7766   1.5133  -0.5382
 5JG  C25  C   CH2   0  -0.315   4.5606   3.8915  -0.2881
 5JG  C28  C   CH2   0  -0.419   4.4415   1.2195   0.8064
 5JG  H1   H   HCH3  0   0.229  -1.3594   3.4456   0.7943
 5JG  H2   H   HCH3  0   0.231  -1.7917   3.3951  -0.9300
 5JG  H3   H   HCH3  0   0.264  -2.3409   4.7406   0.0856
 5JG  H4   H   HCR6  0   0.310  -5.6676  -0.7491   1.1191
 5JG  H5   H   HCH3  0   0.268  -7.5254   2.3092   1.5868
 5JG  H6   H   HCH3  0   0.236  -7.3081   0.8277   0.6353
 5JG  H7   H   HCH3  0   0.236  -6.8185   0.8715   2.3459
 5JG  H8   H   HCR6  0   0.273   2.2857  -5.2386  -1.2573
 5JG  H9   H   HCH2  0   0.232   2.0659   0.9572  -1.7208
 5JG  H10  H   HCH2  0   0.244   1.8509   0.7312   0.0072
 5JG  H11  H   HCH2  0   0.229   2.9687   3.2276  -1.5878
 5JG  H12  H   HCH2  0   0.213   2.5718   3.1739   0.1257
 5JG  H13  H   HNH1  0   0.337   4.5699   3.8033   1.7314
 5JG  H15  H   HCH2  0   0.214   6.3869   2.0077   0.3345
 5JG  H16  H   HCH2  0   0.234   6.0262   2.0069   2.0506
 5JG  H17  H   HCR6  0   0.292  -1.3581   1.2916  -0.1347
 5JG  H18  H   HNR5  0   0.419  -1.9644  -3.3153  -0.1713
 5JG  H20  H   HNH1  0   0.385   3.9068  -0.9140  -1.2703
 5JG  H21  H   HCH1  0   0.225   4.5157   1.3381  -1.3339
 5JG  H22  H   HCH2  0   0.214   5.3048   3.7896  -1.0853
 5JG  H23  H   HCH2  0   0.234   4.2477   4.9377  -0.2847
 5JG  H24  H   HCH2  0   0.227   4.8123   0.1918   0.8461
 5JG  H25  H   HCH2  0   0.213   3.6963   1.3171   1.6047

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
 5JG  N20  C19  aromatic  1.326  0.020  1.326
 5JG  N20  C14  aromatic  1.324  0.020  1.324
 5JG  F11  C6   single    1.346  0.020  1.346
 5JG  C19  C18  aromatic  1.389  0.020  1.389
 5JG  N13  C14  aromatic  1.364  0.020  1.364
 5JG  N13  C12  aromatic  1.364  0.020  1.364
 5JG  C14  C15  aromatic  1.400  0.020  1.400
 5JG  C6   C7   aromatic  1.386  0.020  1.386
 5JG  C6   C5   aromatic  1.379  0.020  1.379
 5JG  C18  CL   single    1.739  0.020  1.739
 5JG  C18  C17  aromatic  1.412  0.020  1.412
 5JG  C7   C8   aromatic  1.384  0.020  1.384
 5JG  C12  C5   single    1.458  0.020  1.458
 5JG  C12  N16  aromatic  1.308  0.020  1.308
 5JG  C15  C17  aromatic  1.411  0.020  1.411
 5JG  C15  N16  aromatic  1.368  0.020  1.368
 5JG  C5   C4   aromatic  1.407  0.020  1.407
 5JG  C10  O9   single    1.416  0.020  1.416
 5JG  C17  N21  single    1.341  0.020  1.341
 5JG  C8   O9   single    1.335  0.020  1.335
 5JG  C8   C3   aromatic  1.415  0.020  1.415
 5JG  C4   C3   aromatic  1.376  0.020  1.376
 5JG  N21  C22  single    1.449  0.020  1.449
 5JG  C3   O2   single    1.344  0.020  1.344
 5JG  C22  C23  single    1.523  0.020  1.523
 5JG  O2   C1   single    1.413  0.020  1.413
 5JG  C28  C23  single    1.529  0.020  1.529
 5JG  C28  C27  single    1.528  0.020  1.528
 5JG  C23  C24  single    1.528  0.020  1.528
 5JG  C27  N26  single    1.455  0.020  1.455
 5JG  C24  C25  single    1.527  0.020  1.527
 5JG  N26  C25  single    1.455  0.020  1.455
 5JG  C1   H1   single    0.970  0.020  1.090
 5JG  C1   H2   single    0.970  0.020  1.090
 5JG  C1   H3   single    0.970  0.020  1.090
 5JG  C7   H4   single    0.930  0.020  1.080
 5JG  C10  H5   single    0.970  0.020  1.090
 5JG  C10  H6   single    0.970  0.020  1.090
 5JG  C10  H7   single    0.970  0.020  1.090
 5JG  C19  H8   single    0.930  0.020  1.080
 5JG  C22  H9   single    0.970  0.020  1.090
 5JG  C22  H10  single    0.970  0.020  1.090
 5JG  C24  H11  single    0.970  0.020  1.090
 5JG  C24  H12  single    0.970  0.020  1.090
 5JG  N26  H13  single    0.890  0.020  1.040
 5JG  C27  H15  single    0.970  0.020  1.090
 5JG  C27  H16  single    0.970  0.020  1.090
 5JG  C4   H17  single    0.930  0.020  1.080
 5JG  N13  H18  single    0.860  0.020  1.020
 5JG  N21  H20  single    0.860  0.020  1.020
 5JG  C23  H21  single    0.970  0.020  1.090
 5JG  C25  H22  single    0.970  0.020  1.090
 5JG  C25  H23  single    0.970  0.020  1.090
 5JG  C28  H24  single    0.970  0.020  1.090
 5JG  C28  H25  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
 5JG  H3   C1   H2   108.82  3.000
 5JG  H3   C1   H1   108.79  3.000
 5JG  H2   C1   H1   108.83  3.000
 5JG  H3   C1   O2   106.46  3.000
 5JG  H2   C1   O2   112.01  3.000
 5JG  H1   C1   O2   111.83  3.000
 5JG  C4   C3   O2   125.17  3.000
 5JG  O2   C3   C8   115.40  3.000
 5JG  C4   C3   C8   119.43  3.000
 5JG  H4   C7   C6   118.68  3.000
 5JG  H4   C7   C8   121.84  3.000
 5JG  C6   C7   C8   119.48  3.000
 5JG  O9   C8   C7   124.80  3.000
 5JG  O9   C8   C3   115.88  3.000
 5JG  C7   C8   C3   119.32  3.000
 5JG  H7   C10  H6   109.05  3.000
 5JG  H7   C10  H5   108.88  3.000
 5JG  H6   C10  H5   108.99  3.000
 5JG  H7   C10  O9   111.70  3.000
 5JG  H6   C10  O9   111.73  3.000
 5JG  H5   C10  O9   106.39  3.000
 5JG  N16  C12  N13  111.94  3.000
 5JG  N16  C12  C5   122.74  3.000
 5JG  N13  C12  C5   125.32  3.000
 5JG  N20  C14  N13  126.97  3.000
 5JG  N13  C14  C15  104.83  3.000
 5JG  N20  C14  C15  128.21  3.000
 5JG  C17  C15  N16  131.19  3.000
 5JG  N16  C15  C14  109.91  3.000
 5JG  C17  C15  C14  118.90  3.000
 5JG  H8   C19  N20  116.85  3.000
 5JG  H8   C19  C18  118.75  3.000
 5JG  N20  C19  C18  124.40  3.000
 5JG  H10  C22  H9   106.94  3.000
 5JG  H10  C22  C23  109.62  3.000
 5JG  H9   C22  C23  109.49  3.000
 5JG  H10  C22  N21  109.61  3.000
 5JG  H9   C22  N21  110.65  3.000
 5JG  C23  C22  N21  110.45  3.000
 5JG  H12  C24  H11  106.89  3.000
 5JG  H12  C24  C25  109.30  3.000
 5JG  H11  C24  C25  109.87  3.000
 5JG  H12  C24  C23  109.40  3.000
 5JG  H11  C24  C23  110.35  3.000
 5JG  C25  C24  C23  110.94  3.000
 5JG  H13  N26  C25  108.61  3.000
 5JG  H13  N26  C27  108.59  3.000
 5JG  C25  N26  C27  111.54  3.000
 5JG  H16  C27  H15  106.54  3.000
 5JG  H16  C27  C28  110.20  3.000
 5JG  H15  C27  C28  109.06  3.000
 5JG  H16  C27  N26  108.72  3.000
 5JG  H15  C27  N26  107.99  3.000
 5JG  C28  C27  N26  114.03  3.000
 5JG  C3   O2   C1   118.07  3.000
 5JG  H17  C4   C5   117.23  3.000
 5JG  H17  C4   C3   120.78  3.000
 5JG  C5   C4   C3   121.99  3.000
 5JG  C6   C5   C4   116.83  3.000
 5JG  C4   C5   C12  118.17  3.000
 5JG  C6   C5   C12  125.00  3.000
 5JG  F11  C6   C5   120.01  3.000
 5JG  C5   C6   C7   122.94  3.000
 5JG  F11  C6   C7   117.05  3.000
 5JG  C10  O9   C8   118.46  3.000
 5JG  H18  N13  C14  125.02  3.000
 5JG  H18  N13  C12  127.42  3.000
 5JG  C14  N13  C12  107.55  3.000
 5JG  C15  N16  C12  105.77  3.000
 5JG  N21  C17  C18  122.12  3.000
 5JG  N21  C17  C15  125.31  3.000
 5JG  C18  C17  C15  112.57  3.000
 5JG  CL   C18  C17  118.83  3.000
 5JG  C17  C18  C19  122.89  3.000
 5JG  CL   C18  C19  118.28  3.000
 5JG  C19  N20  C14  113.04  3.000
 5JG  H20  N21  C17  116.17  3.000
 5JG  H20  N21  C22  115.53  3.000
 5JG  C17  N21  C22  126.67  3.000
 5JG  H21  C23  C28  108.26  3.000
 5JG  H21  C23  C24  107.58  3.000
 5JG  C28  C23  C24  109.64  3.000
 5JG  H21  C23  C22  108.27  3.000
 5JG  C24  C23  C22  110.15  3.000
 5JG  C28  C23  C22  112.77  3.000
 5JG  H23  C25  H22  106.63  3.000
 5JG  H23  C25  N26  108.80  3.000
 5JG  H22  C25  N26  107.97  3.000
 5JG  H23  C25  C24  110.26  3.000
 5JG  H22  C25  C24  108.96  3.000
 5JG  N26  C25  C24  113.95  3.000
 5JG  H25  C28  H24  106.72  3.000
 5JG  H25  C28  C23  109.13  3.000
 5JG  H24  C28  C23  111.11  3.000
 5JG  H25  C28  C27  109.35  3.000
 5JG  H24  C28  C27  109.65  3.000
 5JG  C23  C28  C27  110.77  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
 5JG  CONST_01  C6   C7   C8   C3     0.00   0.0  0
 5JG  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 5JG  CONST_03  C12  C5   C4   C3   180.00   0.0  0
 5JG  CONST_04  C12  C5   C6   C7   180.00   0.0  0
 5JG  CONST_05  C4   C5   C6   C7     0.00   0.0  0
 5JG  CONST_06  C4   C3   C8   C7     0.00   0.0  0
 5JG  CONST_07  C5   C6   C7   C8     0.00   0.0  0
 5JG  CONST_08  C5   C4   C3   C8     0.00   0.0  0
 5JG  CONST_09  N20  C14  N13  C12  180.00   0.0  0
 5JG  CONST_10  C15  C14  N13  C12    0.00   0.0  0
 5JG  CONST_11  C14  C15  N16  C12    0.00   0.0  0
 5JG  CONST_12  C17  C15  N16  C12  180.00   0.0  0
 5JG  CONST_13  C18  C19  N20  C14    0.00   0.0  0
 5JG  CONST_14  C5   C12  N13  C14  180.00   0.0  0
 5JG  CONST_15  N16  C12  N13  C14    0.00   0.0  0
 5JG  CONST_16  C18  C17  C15  C14    0.00   0.0  0
 5JG  CONST_17  C19  N20  C14  C15    0.00   0.0  0
 5JG  CONST_18  C19  C18  C17  C15    0.00   0.0  0
 5JG  CONST_19  N13  C12  N16  C15    0.00   0.0  0
 5JG  CONST_20  C5   C12  N16  C15  180.00   0.0  0
 5JG  CONST_21  N13  C14  N20  C19  180.00   0.0  0
 5JG  CONST_22  N13  C12  C5   C4   180.00   0.0  0
 5JG  CONST_23  N16  C12  C5   C4     0.00   0.0  0
 5JG  CONST_24  N13  C12  C5   C6     0.00   0.0  0
 5JG  CONST_25  N16  C12  C5   C6   180.00   0.0  0
 5JG  CONST_26  C17  C15  C14  N13  180.00   0.0  0
 5JG  CONST_27  N16  C15  C14  N13    0.00   0.0  0
 5JG  CONST_28  N20  C14  C15  N16  180.00   0.0  0
 5JG  CONST_29  C18  C17  C15  N16  180.00   0.0  0
 5JG  CONST_30  N20  C19  C18  C17    0.00   0.0  0
 5JG  CONST_31  N20  C14  C15  C17    0.00   0.0  0
 5JG  CONST_32  O2   C3   C8   C7   180.00   0.0  0
 5JG  CONST_33  F11  C6   C7   C8   180.00   0.0  0
 5JG  CONST_34  F11  C6   C5   C12    0.00   0.0  0
 5JG  CONST_35  N21  C17  C15  C14  180.00   0.0  0
 5JG  CONST_36  CL   C18  C17  C15  180.00   0.0  0
 5JG  CONST_37  N21  C17  C18  C19  180.00   0.0  0
 5JG  CONST_38  C5   C4   C3   O2   180.00   0.0  0
 5JG  CONST_39  F11  C6   C5   C4   180.00   0.0  0
 5JG  CONST_40  O9   C8   C3   C4   180.00   0.0  0
 5JG  CONST_41  O9   C8   C7   C6   180.00   0.0  0
 5JG  CONST_42  N21  C17  C15  N16    0.00   0.0  0
 5JG  CONST_43  CL   C18  C19  N20  180.00   0.0  0
 5JG  CONST_44  H4   C7   C8   C3   180.00   0.0  0
 5JG  CONST_45  H17  C4   C3   C8   180.00   0.0  0
 5JG  CONST_46  H8   C19  N20  C14  180.00   0.0  0
 5JG  CONST_47  H18  N13  C14  C15  180.00   0.0  0
 5JG  CONST_48  C22  N21  C17  C15    0.00   0.0  0
 5JG  CONST_49  C18  C17  N21  C22  180.00   0.0  0
 5JG  CONST_50  H20  N21  C17  C15  180.00   0.0  0
 5JG  Var_01    C27  N26  C25  C24   53.42  30.0  1
 5JG  Var_02    C23  C28  C27  N26   54.47  30.0  1
 5JG  Var_03    C23  C24  C25  N26  -54.42  30.0  1
 5JG  Var_04    C28  C27  N26  C25  -53.52  30.0  1
 5JG  Var_05    C8   C3   O2   C1   178.82  30.0  3
 5JG  Var_06    C23  C22  N21  C17  165.55  30.0  3
 5JG  Var_07    H1   C1   O2   C3   -61.84  30.0  3
 5JG  Var_08    H5   C10  O9   C8   179.96  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5JG  chir_01  C23  C22  C28  C24  positiv

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
 5JG  plan-1  C3   0.020
 5JG  plan-1  C7   0.020
 5JG  plan-1  C8   0.020
 5JG  plan-1  C12  0.020
 5JG  plan-1  O2   0.020
 5JG  plan-1  C4   0.020
 5JG  plan-1  C5   0.020
 5JG  plan-1  C6   0.020
 5JG  plan-1  O9   0.020
 5JG  plan-1  F11  0.020
 5JG  plan-1  H4   0.020
 5JG  plan-1  H17  0.020
 5JG  plan-2  C12  0.020
 5JG  plan-2  C14  0.020
 5JG  plan-2  C15  0.020
 5JG  plan-2  C19  0.020
 5JG  plan-2  C5   0.020
 5JG  plan-2  N13  0.020
 5JG  plan-2  N16  0.020
 5JG  plan-2  C17  0.020
 5JG  plan-2  C18  0.020
 5JG  plan-2  N20  0.020
 5JG  plan-2  CL   0.020
 5JG  plan-2  N21  0.020
 5JG  plan-2  H8   0.020
 5JG  plan-2  H18  0.020
 5JG  plan-3  C22  0.020
 5JG  plan-3  C17  0.020
 5JG  plan-3  N21  0.020
 5JG  plan-3  H20  0.020

