# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:08:06 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  41  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  -3.0429  -0.7733  -0.2057
 J7G  C11  C   CR6   0   0.473  -0.6878  -1.5209  -0.0711
 J7G  C12  C   CR16  0  -0.436   0.6254  -1.0494  -0.0033
 J7G  C13  C   CR6   0   0.062   1.6738  -1.9575   0.0174
 J7G  C15  C   CR16  0  -0.087   0.2525  -3.7135  -0.0841
 J7G  C16  C   CR16  0  -0.360  -0.8730  -2.9033  -0.1132
 J7G  C18  C   CSP   0   0.121   3.0193  -1.4820   0.0778
 J7G  C19  C   CSP   0   0.158   4.1562  -1.0815   0.1213
 J7G  C20  C   CR6   0  -0.099   5.5012  -0.6209   0.1630
 J7G  C21  C   CR16  0  -0.310   5.7800   0.7445   0.1196
 J7G  C22  C   CR6   0  -0.071   7.0949   1.1932   0.1537
 J7G  C23  C   CR16  0  -0.253   8.1404   0.2743   0.2338
 J7G  C24  C   CR16  0  -0.235   7.8642  -1.0843   0.2799
 J7G  C25  C   CR16  0  -0.276   6.5564  -1.5355   0.2444
 J7G  C26  C   C     0   0.537   7.3307   2.6598   0.1041
 J7G  N1   N   NH1   0  -0.799  -1.6918  -0.5707  -0.0805
 J7G  N3   N   NH1   0  -0.796  -3.7443   0.4057  -0.1286
 J7G  O4   O   O     0  -0.470  -3.5564  -1.8597  -0.3661
 J7G  C5   C   CR6   0   0.486  -5.1055   0.5941  -0.2562
 J7G  C6   C   CR16  0  -0.372  -5.5695   1.9085  -0.1545
 J7G  C7   C   CR6   0   0.164  -6.9252   2.1289  -0.2805
 J7G  N8   N   N     0  -0.407  -7.8310   1.2033  -0.4900
 J7G  C9   C   CR16  0  -0.067  -7.3790  -0.0442  -0.5858
 J7G  C10  C   CR16  0  -0.369  -6.0511  -0.4119  -0.4795
 J7G  N14  N   N     0  -0.427   1.5017  -3.2824  -0.0212
 J7G  CL7  CL  CL    0  -0.105  -7.5059   3.7609  -0.1579
 J7G  O27  O   OH1   0  -0.592   8.6159   2.9767   0.1221
 J7G  O28  O   O     0  -0.434   6.4445   3.4779   0.0533
 J7G  H1   H   HCR6  0   0.294   0.8312   0.0130   0.0308
 J7G  H2   H   HCR6  0   0.272   0.1189  -4.7889  -0.1138
 J7G  H3   H   HCR6  0   0.296  -1.8472  -3.3573  -0.1660
 J7G  H4   H   HCR6  0   0.274   4.9647   1.4525   0.0581
 J7G  H5   H   HCR6  0   0.277   9.1689   0.6054   0.2616
 J7G  H6   H   HCR6  0   0.276   8.6755  -1.7962   0.3436
 J7G  H7   H   HCR6  0   0.275   6.3454  -2.5959   0.2792
 J7G  H8   H   HNH1  0   0.427  -1.3675   0.3821  -0.0014
 J7G  H9   H   HNH1  0   0.427  -3.2189   1.2491   0.0488
 J7G  H10  H   HCR6  0   0.306  -4.8882   2.7318   0.0144
 J7G  H11  H   HCR6  0   0.279  -8.1262  -0.8093  -0.7594
 J7G  H12  H   HCR6  0   0.299  -5.7831  -1.4499  -0.5694
 J7G  H13  H   HOH1  0   0.490   8.7210   3.9396   0.0927

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  1.395  0.020  1.395
 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    1.382  0.020  1.382
 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    1.737  0.020  1.737
 J7G  N14  C13  aromatic  1.337  0.020  1.337
 J7G  C12  C13  aromatic  1.387  0.020  1.387
 J7G  C13  C18  single    1.428  0.020  1.428
 J7G  C18  C19  triple    1.206  0.020  1.206
 J7G  C19  C20  single    1.422  0.020  1.422
 J7G  C20  C25  aromatic  1.399  0.020  1.399
 J7G  C20  C21  aromatic  1.394  0.020  1.394
 J7G  C25  C24  aromatic  1.384  0.020  1.384
 J7G  C21  C22  aromatic  1.390  0.020  1.390
 J7G  C24  C23  aromatic  1.387  0.020  1.387
 J7G  C22  C23  aromatic  1.394  0.020  1.394
 J7G  C22  C26  single    1.486  0.020  1.486
 J7G  O28  C26  double    1.207  0.020  1.207
 J7G  C26  O27  single    1.324  0.020  1.324
 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
 J7G  O27  H13  single    0.850  0.020  0.980

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   124.07  3.000
 J7G  O4   C2   N1   124.16  3.000
 J7G  N3   C2   N1   111.77  3.000
 J7G  N1   C11  C16  125.76  3.000
 J7G  N1   C11  C12  116.82  3.000
 J7G  C16  C11  C12  117.42  3.000
 J7G  H1   C12  C13  119.88  3.000
 J7G  H1   C12  C11  120.76  3.000
 J7G  C13  C12  C11  119.36  3.000
 J7G  N14  C13  C18  116.91  3.000
 J7G  C18  C13  C12  119.65  3.000
 J7G  N14  C13  C12  123.45  3.000
 J7G  H2   C15  N14  116.16  3.000
 J7G  H2   C15  C16  118.61  3.000
 J7G  N14  C15  C16  125.23  3.000
 J7G  H3   C16  C15  119.29  3.000
 J7G  H3   C16  C11  122.65  3.000
 J7G  C15  C16  C11  118.06  3.000
 J7G  C19  C18  C13  180.00  3.000
 J7G  C20  C19  C18  180.00  3.000
 J7G  C25  C20  C21  119.42  3.000
 J7G  C21  C20  C19  120.35  3.000
 J7G  C25  C20  C19  120.22  3.000
 J7G  H4   C21  C22  120.22  3.000
 J7G  H4   C21  C20  119.48  3.000
 J7G  C22  C21  C20  120.30  3.000
 J7G  C26  C22  C23  122.22  3.000
 J7G  C26  C22  C21  117.90  3.000
 J7G  C23  C22  C21  119.88  3.000
 J7G  H5   C23  C24  119.25  3.000
 J7G  H5   C23  C22  120.88  3.000
 J7G  C24  C23  C22  119.87  3.000
 J7G  H6   C24  C25  119.74  3.000
 J7G  H6   C24  C23  119.83  3.000
 J7G  C25  C24  C23  120.44  3.000
 J7G  H7   C25  C24  120.20  3.000
 J7G  H7   C25  C20  119.72  3.000
 J7G  C24  C25  C20  120.08  3.000
 J7G  O28  C26  O27  123.44  3.000
 J7G  O27  C26  C22  112.94  3.000
 J7G  O28  C26  C22  123.62  3.000
 J7G  H8   N1   C11  114.51  3.000
 J7G  H8   N1   C2   117.57  3.000
 J7G  C11  N1   C2   127.91  3.000
 J7G  H9   N3   C5   114.56  3.000
 J7G  H9   N3   C2   117.46  3.000
 J7G  C5   N3   C2   127.98  3.000
 J7G  C10  C5   C6   117.62  3.000
 J7G  C6   C5   N3   116.69  3.000
 J7G  C10  C5   N3   125.69  3.000
 J7G  H10  C6   C7   120.77  3.000
 J7G  H10  C6   C5   121.20  3.000
 J7G  C7   C6   C5   118.03  3.000
 J7G  CL7  C7   N8   116.33  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   124.78  3.000
 J7G  H12  C10  C9   119.32  3.000
 J7G  H12  C10  C5   122.61  3.000
 J7G  C9   C10  C5   118.07  3.000
 J7G  C15  N14  C13  116.48  3.000
 J7G  H13  O27  C26  110.05  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  CONST_51  H13  O27  C26  C22  180.00   0.0  0
 J7G  Var_01    O28  C26  C22  C21    0.98  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-2  H13  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

