# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:49:06 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 5-[(2,3-dichlorophenyl)sulfanyl]-3H-imidazo[4,5-b]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c2nc(Sc3cccc(Cl)c3Cl)ccc2n1
#
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
 JE7  JE7  5-[(2,3-dichlorophenyl)sulfanyl]-3H-imidazo[4,5-b]pyridin-2-amine  ligand  27  19  .  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_JE7
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
 JE7  C1   C   CR56  0   0.448   2.3440  -0.2390  -0.3829
 JE7  C2   C   CR56  0   0.115   3.3660   0.2883   0.4312
 JE7  C12  C   CR6   0  -0.073  -1.5926   1.0863  -0.8593
 JE7  C13  C   CR6   0   0.028  -1.9692   0.1958   0.1495
 JE7  C14  C   CR16  0  -0.253  -2.1734   0.9784  -2.1163
 JE7  C15  C   CR6   0   0.010  -2.9006  -0.7997  -0.1251
 JE7  C17  C   CR16  0  -0.244  -3.1192  -0.0022  -2.3735
 JE7  C18  C   CR16  0  -0.225  -3.4795  -0.8979  -1.3823
 JE7  C5   C   CR16  0  -0.238   3.1507   1.5446   0.9703
 JE7  C7   C   CR6   0   0.025   1.0260   1.5340  -0.1646
 JE7  C8   C   CR5   0   0.629   4.0362  -1.6269  -0.1987
 JE7  C9   C   CR16  0  -0.300   1.9432   2.1691   0.6694
 JE7  N11  N   NH2   0  -0.844   4.7403  -2.7663  -0.3445
 JE7  N3   N   N     0  -0.402   1.2108   0.3363  -0.7052
 JE7  N4   N   NR15  0  -0.707   2.8044  -1.4694  -0.7695
 JE7  N6   N   N     0  -0.519   4.4079  -0.5970   0.5258
 JE7  S10  S   S2    0   0.090  -0.4668   2.4101  -0.5657
 JE7  CL2  CL  CL    0  -0.075  -1.2877   0.3228   1.7181
 JE7  CL1  CL  CL    0  -0.091  -3.3639  -1.9214   1.0981
 JE7  H1   H   HCR6  0   0.283  -1.8760   1.6651  -2.8970
 JE7  H2   H   HCR6  0   0.280  -3.5678  -0.0783  -3.3543
 JE7  H3   H   HCR6  0   0.293  -4.2057  -1.6748  -1.5777
 JE7  H4   H   HCR6  0   0.268   3.8764   2.0233   1.6146
 JE7  H5   H   HCR6  0   0.273   1.7115   3.1379   1.0907
 JE7  H6   H   HNH2  0   0.403   5.7134  -2.7187  -0.0916
 JE7  H7   H   HNH2  0   0.405   4.5424  -3.3574  -1.1346
 JE7  H8   H   HNR5  0   0.422   2.3243  -2.1314  -1.3594

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
 JE7  N11  C8   single    1.347  0.020  1.347
 JE7  C8   N6   aromatic  1.313  0.020  1.313
 JE7  C8   N4   aromatic  1.367  0.020  1.367
 JE7  N6   C2   aromatic  1.370  0.020  1.370
 JE7  N4   C1   aromatic  1.369  0.020  1.369
 JE7  C17  C18  aromatic  1.384  0.020  1.384
 JE7  C17  C14  aromatic  1.386  0.020  1.386
 JE7  C2   C1   aromatic  1.409  0.020  1.409
 JE7  C2   C5   aromatic  1.384  0.020  1.384
 JE7  C1   N3   aromatic  1.311  0.020  1.311
 JE7  C18  C15  aromatic  1.388  0.020  1.388
 JE7  C14  C12  aromatic  1.389  0.020  1.389
 JE7  C5   C9   aromatic  1.392  0.020  1.392
 JE7  N3   C7   aromatic  1.327  0.020  1.327
 JE7  C7   C9   aromatic  1.393  0.020  1.393
 JE7  C7   S10  single    1.777  0.020  1.777
 JE7  C15  C13  aromatic  1.391  0.020  1.391
 JE7  C15  CL1  single    1.723  0.020  1.723
 JE7  C12  C13  aromatic  1.397  0.020  1.397
 JE7  C12  S10  single    1.762  0.020  1.762
 JE7  C13  CL2  single    1.715  0.020  1.715
 JE7  C14  H1   single    0.930  0.020  1.080
 JE7  C17  H2   single    0.930  0.020  1.080
 JE7  C18  H3   single    0.930  0.020  1.080
 JE7  C5   H4   single    0.930  0.020  1.080
 JE7  C9   H5   single    0.930  0.020  1.080
 JE7  N11  H6   single    0.890  0.020  1.040
 JE7  N11  H7   single    0.890  0.020  1.040
 JE7  N4   H8   single    0.860  0.020  1.020

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
 JE7  N4   C1   N3   127.98  3.000
 JE7  N3   C1   C2   127.22  3.000
 JE7  N4   C1   C2   104.80  3.000
 JE7  N6   C2   C5   132.67  3.000
 JE7  C5   C2   C1   116.87  3.000
 JE7  N6   C2   C1   110.46  3.000
 JE7  S10  C12  C14  118.44  3.000
 JE7  S10  C12  C13  122.04  3.000
 JE7  C14  C12  C13  119.42  3.000
 JE7  CL2  C13  C15  119.98  3.000
 JE7  CL2  C13  C12  120.40  3.000
 JE7  C15  C13  C12  119.62  3.000
 JE7  H1   C14  C17  120.18  3.000
 JE7  H1   C14  C12  119.27  3.000
 JE7  C17  C14  C12  120.54  3.000
 JE7  CL1  C15  C18  119.01  3.000
 JE7  CL1  C15  C13  120.39  3.000
 JE7  C18  C15  C13  120.60  3.000
 JE7  H2   C17  C18  119.74  3.000
 JE7  H2   C17  C14  120.08  3.000
 JE7  C18  C17  C14  120.17  3.000
 JE7  H3   C18  C17  120.71  3.000
 JE7  H3   C18  C15  119.65  3.000
 JE7  C17  C18  C15  119.64  3.000
 JE7  H4   C5   C9   120.79  3.000
 JE7  H4   C5   C2   121.95  3.000
 JE7  C9   C5   C2   117.25  3.000
 JE7  S10  C7   N3   118.04  3.000
 JE7  S10  C7   C9   117.62  3.000
 JE7  N3   C7   C9   124.32  3.000
 JE7  N6   C8   N4   113.28  3.000
 JE7  N4   C8   N11  121.56  3.000
 JE7  N6   C8   N11  125.11  3.000
 JE7  H5   C9   C7   120.04  3.000
 JE7  H5   C9   C5   120.22  3.000
 JE7  C7   C9   C5   119.74  3.000
 JE7  H7   N11  H6   114.53  3.000
 JE7  H7   N11  C8   118.61  3.000
 JE7  H6   N11  C8   115.98  3.000
 JE7  C7   N3   C1   114.59  3.000
 JE7  H8   N4   C8   126.71  3.000
 JE7  H8   N4   C1   126.51  3.000
 JE7  C8   N4   C1   106.78  3.000
 JE7  C8   N6   C2   104.68  3.000
 JE7  C7   S10  C12  101.76  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
 JE7  CONST_01  N6   C8   N4   C1     0.00   0.0  0
 JE7  CONST_02  C8   N6   C2   C1     0.00   0.0  0
 JE7  CONST_03  C9   C5   C2   C1     0.00   0.0  0
 JE7  CONST_04  C9   C7   N3   C1     0.00   0.0  0
 JE7  CONST_05  N4   C8   N6   C2     0.00   0.0  0
 JE7  CONST_06  C8   N4   C1   C2     0.00   0.0  0
 JE7  CONST_07  C7   N3   C1   C2     0.00   0.0  0
 JE7  CONST_08  C7   C9   C5   C2     0.00   0.0  0
 JE7  CONST_09  C18  C17  C14  C12    0.00   0.0  0
 JE7  CONST_10  C18  C15  C13  C12    0.00   0.0  0
 JE7  CONST_11  C17  C18  C15  C13    0.00   0.0  0
 JE7  CONST_12  C17  C14  C12  C13    0.00   0.0  0
 JE7  CONST_13  C15  C18  C17  C14    0.00   0.0  0
 JE7  CONST_14  C15  C13  C12  C14    0.00   0.0  0
 JE7  CONST_15  C8   N6   C2   C5   180.00   0.0  0
 JE7  CONST_16  N4   C1   C2   C5   180.00   0.0  0
 JE7  CONST_17  N3   C1   C2   C5     0.00   0.0  0
 JE7  CONST_18  N3   C7   C9   C5     0.00   0.0  0
 JE7  CONST_19  N4   C1   N3   C7   180.00   0.0  0
 JE7  CONST_20  N3   C1   N4   C8   180.00   0.0  0
 JE7  CONST_21  N6   C2   C5   C9   180.00   0.0  0
 JE7  CONST_22  N6   C2   C1   N3   180.00   0.0  0
 JE7  CONST_23  N6   C2   C1   N4     0.00   0.0  0
 JE7  CONST_24  N11  C8   N4   C1   180.00   0.0  0
 JE7  CONST_25  S10  C7   N3   C1   180.00   0.0  0
 JE7  CONST_26  N11  C8   N6   C2   180.00   0.0  0
 JE7  CONST_27  CL1  C15  C13  C12  180.00   0.0  0
 JE7  CONST_28  CL2  C13  C12  C14  180.00   0.0  0
 JE7  CONST_29  S10  C12  C13  C15  180.00   0.0  0
 JE7  CONST_30  CL1  C15  C18  C17  180.00   0.0  0
 JE7  CONST_31  S10  C12  C14  C17  180.00   0.0  0
 JE7  CONST_32  CL2  C13  C15  C18  180.00   0.0  0
 JE7  CONST_33  S10  C7   C9   C5   180.00   0.0  0
 JE7  CONST_34  H4   C5   C2   C1   180.00   0.0  0
 JE7  CONST_35  H8   N4   C1   C2   180.00   0.0  0
 JE7  CONST_36  H5   C9   C5   C2   180.00   0.0  0
 JE7  CONST_37  H2   C17  C14  C12  180.00   0.0  0
 JE7  CONST_38  H3   C18  C15  C13  180.00   0.0  0
 JE7  CONST_39  H1   C14  C12  C13  180.00   0.0  0
 JE7  CONST_40  H6   N11  C8   N4   180.00   0.0  0
 JE7  Var_01    N3   C7   S10  C12   29.41  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
 JE7  plan-1  C12  0.020
 JE7  plan-1  C13  0.020
 JE7  plan-1  C14  0.020
 JE7  plan-1  C15  0.020
 JE7  plan-1  C17  0.020
 JE7  plan-1  C18  0.020
 JE7  plan-1  S10  0.020
 JE7  plan-1  CL2  0.020
 JE7  plan-1  CL1  0.020
 JE7  plan-1  H1   0.020
 JE7  plan-1  H2   0.020
 JE7  plan-1  H3   0.020
 JE7  plan-2  C1   0.020
 JE7  plan-2  C2   0.020
 JE7  plan-2  C5   0.020
 JE7  plan-2  C7   0.020
 JE7  plan-2  C8   0.020
 JE7  plan-2  C9   0.020
 JE7  plan-2  N11  0.020
 JE7  plan-2  N3   0.020
 JE7  plan-2  N4   0.020
 JE7  plan-2  N6   0.020
 JE7  plan-2  S10  0.020
 JE7  plan-2  H4   0.020
 JE7  plan-2  H5   0.020
 JE7  plan-2  H8   0.020
 JE7  plan-3  C8   0.020
 JE7  plan-3  N11  0.020
 JE7  plan-3  H6   0.020
 JE7  plan-3  H7   0.020

