# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:54:37 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-[(4-{[(2-chloropyridin-4-yl)carbamoyl]amino}pyridin-2-yl)ethynyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)C#Cc2cc(NC(=O)Nc3ccnc(Cl)c3)ccn2
#
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
 J7G  J7G  '3-[(4-{[(2-chloropyridin-4-yl)carbamoyl]amino}pyridin-2-yl)ethynyl]benzoic acid'  ligand  40  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J7G
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
 J7G  C2   C   C      0   0.770  -3.0483  -0.7710  -0.2229
 J7G  C11  C   CR6    0   0.473  -0.6888  -1.5128  -0.1300
 J7G  C12  C   CR16   0  -0.439   0.6225  -1.0384  -0.0535
 J7G  C13  C   CR6    0   0.065   1.6753  -1.9425  -0.0409
 J7G  C15  C   CR16   0  -0.088   0.2578  -3.7014  -0.1700
 J7G  C16  C   CR16   0  -0.363  -0.8703  -2.8952  -0.1917
 J7G  C18  C   CSP    0   0.106   3.0182  -1.4636   0.0340
 J7G  C19  C   CSP    0   0.150   4.1519  -1.0541   0.0976
 J7G  C20  C   C      0  -0.099   5.4938  -0.5867   0.1711
 J7G  C21  C   C1     0  -0.344   5.7720   0.7806   0.0899
 J7G  C22  C   C      0  -0.089   7.0779   1.2484   0.1588
 J7G  C23  C   C1     0  -0.284   8.1115   0.3273   0.3132
 J7G  C24  C   C1     0  -0.238   7.8466  -1.0337   0.3956
 J7G  C25  C   C1     0  -0.296   6.5442  -1.4974   0.3242
 J7G  C26  C   C      0   0.403   7.3706   2.7437   0.0658
 J7G  N1   N   NH1    0  -0.798  -1.6956  -0.5648  -0.1291
 J7G  N3   N   NH1    0  -0.796  -3.7518   0.4054  -0.1228
 J7G  O4   O   O      0  -0.471  -3.5628  -1.8579  -0.3772
 J7G  C5   C   C      0   0.486  -5.1151   0.5910  -0.2274
 J7G  C6   C   C1     0  -0.372  -5.5805   1.9039  -0.1127
 J7G  C7   C   C      0   0.164  -6.9386   2.1217  -0.2157
 J7G  N8   N   N      0  -0.407  -7.8455   1.1948  -0.4141
 J7G  C9   C   C1     0  -0.067  -7.3923  -0.0512  -0.5224
 J7G  C10  C   C1     0  -0.369  -6.0620  -0.4163  -0.4393
 J7G  N14  N   N      0  -0.429   1.5057  -3.2675  -0.0970
 J7G  CL7  CL  CL     0  -0.105  -7.5209   3.7517  -0.0773
 J7G  O27  O   OC    -1  -0.589   8.5670   3.0790   0.1380
 J7G  O28  O   O      0  -0.589   6.3869   3.4941  -0.0747
 J7G  H1   H   HCR6   0   0.293   0.8243   0.0243  -0.0035
 J7G  H2   H   HCR6   0   0.271   0.1280  -4.7768  -0.2149
 J7G  H3   H   HCR6   0   0.295  -1.8427  -3.3517  -0.2548
 J7G  H4   H   H      0   0.250   4.9578   1.4831  -0.0285
 J7G  H5   H   H      0   0.252   9.1323   0.6807   0.3697
 J7G  H6   H   H      0   0.259   8.6594  -1.7380   0.5156
 J7G  H7   H   H      0   0.260   6.3348  -2.5573   0.3865
 J7G  H8   H   HNH1   0   0.427  -1.3720   0.3887  -0.0533
 J7G  H9   H   HNH1   0   0.427  -3.2256   1.2487   0.0525
 J7G  H10  H   H      0   0.306  -4.8984   2.7280   0.0483
 J7G  H11  H   H      0   0.279  -8.1404  -0.8172  -0.6871
 J7G  H12  H   H      0   0.299  -5.7932  -1.4532  -0.5373

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
 J7G  C10  C9   aromatic  1.382  0.020  1.382
 J7G  C10  C5   aromatic  1.399  0.020  1.399
 J7G  C9   N8   aromatic  1.330  0.020  1.330
 J7G  C16  C15  aromatic  1.387  0.020  1.387
 J7G  C16  C11  aromatic  1.396  0.020  1.396
 J7G  N3   C5   single    1.380  0.020  1.380
 J7G  N3   C2   single    1.374  0.020  1.374
 J7G  C5   C6   aromatic  1.398  0.020  1.398
 J7G  N8   C7   aromatic  1.312  0.020  1.312
 J7G  N1   C2   single    1.372  0.020  1.372
 J7G  N1   C11  single    1.383  0.020  1.383
 J7G  C15  N14  aromatic  1.323  0.020  1.323
 J7G  C2   O4   double    1.212  0.020  1.212
 J7G  C11  C12  aromatic  1.397  0.020  1.397
 J7G  C6   C7   aromatic  1.379  0.020  1.379
 J7G  C7   CL7  single    1.736  0.020  1.736
 J7G  N14  C13  aromatic  1.337  0.020  1.337
 J7G  C12  C13  aromatic  1.388  0.020  1.388
 J7G  C13  C18  single    1.428  0.020  1.428
 J7G  C18  C19  triple    1.207  0.020  1.207
 J7G  C19  C20  single    1.423  0.020  1.423
 J7G  C20  C25  aromatic  1.399  0.020  1.399
 J7G  C20  C21  aromatic  1.398  0.020  1.398
 J7G  C25  C24  aromatic  1.384  0.020  1.384
 J7G  C21  C22  aromatic  1.389  0.020  1.389
 J7G  C24  C23  aromatic  1.389  0.020  1.389
 J7G  C22  C23  aromatic  1.393  0.020  1.393
 J7G  C22  C26  single    1.526  0.020  1.526
 J7G  O28  C26  deloc     1.245  0.020  1.245
 J7G  C26  O27  deloc     1.245  0.020  1.245
 J7G  C12  H1   single    0.930  0.020  1.080
 J7G  C15  H2   single    0.930  0.020  1.080
 J7G  C16  H3   single    0.930  0.020  1.080
 J7G  C21  H4   single    0.930  0.020  1.080
 J7G  C23  H5   single    0.930  0.020  1.080
 J7G  C24  H6   single    0.930  0.020  1.080
 J7G  C25  H7   single    0.930  0.020  1.080
 J7G  N1   H8   single    0.860  0.020  1.020
 J7G  N3   H9   single    0.860  0.020  1.020
 J7G  C6   H10  single    0.930  0.020  1.080
 J7G  C9   H11  single    0.930  0.020  1.080
 J7G  C10  H12  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
 J7G  O4   C2   N3   124.01  3.000
 J7G  O4   C2   N1   124.20  3.000
 J7G  N3   C2   N1   111.79  3.000
 J7G  N1   C11  C16  125.76  3.000
 J7G  N1   C11  C12  116.78  3.000
 J7G  C16  C11  C12  117.46  3.000
 J7G  H1   C12  C13  119.84  3.000
 J7G  H1   C12  C11  120.72  3.000
 J7G  C13  C12  C11  119.44  3.000
 J7G  N14  C13  C18  117.00  3.000
 J7G  C18  C13  C12  119.70  3.000
 J7G  N14  C13  C12  123.30  3.000
 J7G  H2   C15  N14  116.14  3.000
 J7G  H2   C15  C16  118.59  3.000
 J7G  N14  C15  C16  125.27  3.000
 J7G  H3   C16  C15  119.30  3.000
 J7G  H3   C16  C11  122.71  3.000
 J7G  C15  C16  C11  117.99  3.000
 J7G  C19  C18  C13  180.00  3.000
 J7G  C20  C19  C18  180.00  3.000
 J7G  C25  C20  C21  119.60  3.000
 J7G  C21  C20  C19  120.40  3.000
 J7G  C25  C20  C19  120.00  3.000
 J7G  H4   C21  C22  119.63  3.000
 J7G  H4   C21  C20  119.46  3.000
 J7G  C22  C21  C20  120.91  3.000
 J7G  C26  C22  C23  120.81  3.000
 J7G  C26  C22  C21  120.48  3.000
 J7G  C23  C22  C21  118.71  3.000
 J7G  H5   C23  C24  119.80  3.000
 J7G  H5   C23  C22  119.33  3.000
 J7G  C24  C23  C22  120.87  3.000
 J7G  H6   C24  C25  119.63  3.000
 J7G  H6   C24  C23  120.07  3.000
 J7G  C25  C24  C23  120.30  3.000
 J7G  H7   C25  C24  120.47  3.000
 J7G  H7   C25  C20  119.92  3.000
 J7G  C24  C25  C20  119.61  3.000
 J7G  O28  C26  O27  127.13  3.000
 J7G  O27  C26  C22  116.40  3.000
 J7G  O28  C26  C22  116.47  3.000
 J7G  H8   N1   C11  114.46  3.000
 J7G  H8   N1   C2   117.59  3.000
 J7G  C11  N1   C2   127.94  3.000
 J7G  H9   N3   C5   114.57  3.000
 J7G  H9   N3   C2   117.45  3.000
 J7G  C5   N3   C2   127.98  3.000
 J7G  C10  C5   C6   117.61  3.000
 J7G  C6   C5   N3   116.69  3.000
 J7G  C10  C5   N3   125.70  3.000
 J7G  H10  C6   C7   120.78  3.000
 J7G  H10  C6   C5   121.19  3.000
 J7G  C7   C6   C5   118.04  3.000
 J7G  CL7  C7   N8   116.32  3.000
 J7G  CL7  C7   C6   118.19  3.000
 J7G  N8   C7   C6   125.48  3.000
 J7G  C9   N8   C7   116.01  3.000
 J7G  H11  C9   C10  119.15  3.000
 J7G  H11  C9   N8   116.07  3.000
 J7G  C10  C9   N8   124.79  3.000
 J7G  H12  C10  C9   119.33  3.000
 J7G  H12  C10  C5   122.61  3.000
 J7G  C9   C10  C5   118.07  3.000
 J7G  C15  N14  C13  116.55  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
 J7G  CONST_01  N14  C15  C16  C11    0.00   0.0  0
 J7G  CONST_02  N14  C13  C12  C11    0.00   0.0  0
 J7G  CONST_03  C15  C16  C11  C12    0.00   0.0  0
 J7G  CONST_04  C15  N14  C13  C12    0.00   0.0  0
 J7G  CONST_05  C16  C15  N14  C13    0.00   0.0  0
 J7G  CONST_06  C16  C11  C12  C13    0.00   0.0  0
 J7G  CONST_07  C23  C24  C25  C20    0.00   0.0  0
 J7G  CONST_08  C23  C22  C21  C20    0.00   0.0  0
 J7G  CONST_09  C24  C25  C20  C21    0.00   0.0  0
 J7G  CONST_10  C24  C23  C22  C21    0.00   0.0  0
 J7G  CONST_11  C25  C20  C21  C22    0.00   0.0  0
 J7G  CONST_12  C25  C24  C23  C22    0.00   0.0  0
 J7G  CONST_13  N8   C9   C10  C5     0.00   0.0  0
 J7G  CONST_14  N8   C7   C6   C5     0.00   0.0  0
 J7G  CONST_15  C9   C10  C5   C6     0.00   0.0  0
 J7G  CONST_16  C9   N8   C7   C6     0.00   0.0  0
 J7G  CONST_17  C10  C9   N8   C7     0.00   0.0  0
 J7G  CONST_18  C10  C5   C6   C7     0.00   0.0  0
 J7G  CONST_19  C18  C13  C12  C11  180.00   0.0  0
 J7G  CONST_20  N1   C11  C12  C13  180.00   0.0  0
 J7G  CONST_21  N1   C11  C16  C15  180.00   0.0  0
 J7G  CONST_22  C18  C13  N14  C15  180.00   0.0  0
 J7G  CONST_23  C24  C25  C20  C19  180.00   0.0  0
 J7G  CONST_24  C22  C21  C20  C19  180.00   0.0  0
 J7G  CONST_25  C26  C22  C21  C20  180.00   0.0  0
 J7G  CONST_26  C26  C22  C23  C24  180.00   0.0  0
 J7G  CONST_27  C9   C10  C5   N3   180.00   0.0  0
 J7G  CONST_28  C7   C6   C5   N3   180.00   0.0  0
 J7G  CONST_29  CL7  C7   C6   C5   180.00   0.0  0
 J7G  CONST_30  CL7  C7   N8   C9   180.00   0.0  0
 J7G  CONST_31  H2   C15  C16  C11  180.00   0.0  0
 J7G  CONST_32  H3   C16  C11  C12  180.00   0.0  0
 J7G  CONST_33  H1   C12  C11  C16  180.00   0.0  0
 J7G  CONST_34  H6   C24  C25  C20  180.00   0.0  0
 J7G  CONST_35  H7   C25  C20  C21  180.00   0.0  0
 J7G  CONST_36  H5   C23  C22  C21  180.00   0.0  0
 J7G  CONST_37  H4   C21  C22  C23  180.00   0.0  0
 J7G  CONST_38  H11  C9   C10  C5   180.00   0.0  0
 J7G  CONST_39  H12  C10  C5   C6   180.00   0.0  0
 J7G  CONST_40  H10  C6   C7   N8   180.00   0.0  0
 J7G  CONST_41  C10  C5   N3   C2     0.00   0.0  0
 J7G  CONST_42  C6   C5   N3   C2   180.00   0.0  0
 J7G  CONST_43  C16  C11  N1   C2     0.00   0.0  0
 J7G  CONST_44  C12  C11  N1   C2   180.00   0.0  0
 J7G  CONST_45  H8   N1   C11  C12    0.00   0.0  0
 J7G  CONST_46  H9   N3   C5   C6     0.00   0.0  0
 J7G  CONST_47  O4   C2   N1   C11    0.00   0.0  0
 J7G  CONST_48  C5   N3   C2   O4     0.00   0.0  0
 J7G  CONST_49  N3   C2   N1   C11  180.00   0.0  0
 J7G  CONST_50  C5   N3   C2   N1   180.00   0.0  0
 J7G  Var_01    O28  C26  C22  C21   -0.13  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
 J7G  plan-1  C11  0.020
 J7G  plan-1  C12  0.020
 J7G  plan-1  C13  0.020
 J7G  plan-1  C15  0.020
 J7G  plan-1  C16  0.020
 J7G  plan-1  C18  0.020
 J7G  plan-1  C19  0.020
 J7G  plan-1  N1   0.020
 J7G  plan-1  N14  0.020
 J7G  plan-1  H1   0.020
 J7G  plan-1  H2   0.020
 J7G  plan-1  H3   0.020
 J7G  plan-2  C22  0.020
 J7G  plan-2  C26  0.020
 J7G  plan-2  O27  0.020
 J7G  plan-2  O28  0.020
 J7G  plan-3  C18  0.020
 J7G  plan-3  C19  0.020
 J7G  plan-3  C20  0.020
 J7G  plan-3  C21  0.020
 J7G  plan-3  C22  0.020
 J7G  plan-3  C23  0.020
 J7G  plan-3  C24  0.020
 J7G  plan-3  C25  0.020
 J7G  plan-3  C26  0.020
 J7G  plan-3  H4   0.020
 J7G  plan-3  H5   0.020
 J7G  plan-3  H6   0.020
 J7G  plan-3  H7   0.020
 J7G  plan-4  N3   0.020
 J7G  plan-4  C5   0.020
 J7G  plan-4  C6   0.020
 J7G  plan-4  C7   0.020
 J7G  plan-4  N8   0.020
 J7G  plan-4  C9   0.020
 J7G  plan-4  C10  0.020
 J7G  plan-4  CL7  0.020
 J7G  plan-4  H10  0.020
 J7G  plan-4  H11  0.020
 J7G  plan-4  H12  0.020
 J7G  plan-5  C2   0.020
 J7G  plan-5  C11  0.020
 J7G  plan-5  N1   0.020
 J7G  plan-5  N3   0.020
 J7G  plan-5  O4   0.020
 J7G  plan-5  C5   0.020
 J7G  plan-5  H8   0.020
 J7G  plan-5  H9   0.020

