# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:08:24 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1nn(CC(=O)N2CCS[C@H]2C(=O)Nc3cccc(Br)n3)c4ncccc14
#
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
 J55  J55  1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide  ligand  46  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J55
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
 J55  O2   O   O     0  -0.414   2.3688   1.3243  -1.5429
 J55  C2   C   C     0   0.543   1.6450   1.8298  -0.7195
 J55  N1   N   NH1   0  -0.710   1.5051   1.4210   0.5724
 J55  C1   C   CR6   0   0.536   1.9817   0.2604   1.1614
 J55  N    N   N     0  -0.403   2.3037  -0.7629   0.3876
 J55  C15  C   CR16  0  -0.385   2.0703   0.2068   2.5538
 J55  C16  C   CR16  0  -0.148   2.5120  -0.9668   3.1304
 J55  C17  C   CR16  0  -0.288   2.8590  -2.0478   2.3282
 J55  C    C   CR6   0   0.084   2.7274  -1.8605   0.9648
 J55  BR   BR  BR    0  -0.040   3.1723  -3.2873  -0.2044
 J55  C3   C   CH1   0  -0.334   0.8315   3.0866  -1.0481
 J55  N2   N   NT    0  -0.494  -0.4962   3.0711  -0.4620
 J55  C5   C   CH2   0  -0.281  -0.8856   4.2322   0.3353
 J55  C4   C   CH2   0  -0.582   0.0497   5.3489  -0.0796
 J55  S    S   S2    0   0.039   1.6531   4.5357  -0.3076
 J55  C6   C   C     0   0.575  -1.2763   2.0013  -0.7172
 J55  O1   O   O     0  -0.455  -0.9219   1.1073  -1.4615
 J55  C7   C   CH2   0  -0.443  -2.6085   1.9465   0.0180
 J55  N3   N   NR5   0  -0.358  -3.0915   0.5993   0.0316
 J55  C11  C   CR56  0   0.586  -2.5206  -0.4403   0.6926
 J55  N6   N   N     0  -0.419  -1.4881  -0.3620   1.5197
 J55  C12  C   CR16  0  -0.060  -1.1215  -1.5219   2.0314
 J55  C13  C   CR16  0  -0.338  -1.7477  -2.7498   1.7487
 J55  C14  C   CR16  0  -0.211  -2.8221  -2.8019   0.8864
 J55  C10  C   CR56  0  -0.103  -3.2320  -1.5903   0.3242
 J55  C8   C   CR5   0   0.083  -4.2079  -1.1057  -0.5889
 J55  N4   N   N     0  -0.249  -4.0849   0.1920  -0.7461
 J55  C9   C   C     0   0.478  -5.2417  -1.8946  -1.2935
 J55  O    O   O     0  -0.477  -5.3169  -3.1022  -1.1090
 J55  N5   N   NH2   0  -0.810  -6.0462  -1.2043  -2.1089
 J55  H1   H   HNH1  0   0.418   1.0015   2.0380   1.1922
 J55  H2   H   HCR6  0   0.291   1.8011   1.0611   3.1600
 J55  H3   H   HCR6  0   0.291   2.5919  -1.0459   4.2060
 J55  H4   H   HCR6  0   0.292   3.2108  -2.9766   2.7518
 J55  H5   H   HCH1  0   0.331   0.7893   3.1799  -2.1352
 J55  H6   H   HCH2  0   0.291  -1.9186   4.5126   0.1285
 J55  H7   H   HCH2  0   0.274  -0.7896   4.0259   1.4042
 J55  H8   H   HCH2  0   0.296  -0.2703   5.8160  -1.0103
 J55  H9   H   HCH2  0   0.314   0.1414   6.1112   0.6910
 J55  H10  H   HCH2  0   0.306  -2.5097   2.3067   1.0431
 J55  H11  H   HCH2  0   0.335  -3.3473   2.5743  -0.4818
 J55  H12  H   HCR6  0   0.267  -0.2817  -1.5013   2.7155
 J55  H13  H   HCR6  0   0.277  -1.3723  -3.6475   2.2194
 J55  H14  H   HCR6  0   0.274  -3.3175  -3.7343   0.6567
 J55  H15  H   HNH2  0   0.413  -5.9459  -0.2110  -2.2332
 J55  H16  H   HNH2  0   0.408  -6.7746  -1.6747  -2.6204

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
 J55  O    C9   double    1.224  0.020  1.224
 J55  C13  C14  aromatic  1.379  0.020  1.379
 J55  C13  C12  aromatic  1.407  0.020  1.407
 J55  C14  C10  aromatic  1.397  0.020  1.397
 J55  BR   C    single    1.898  0.020  1.898
 J55  C9   C8   single    1.479  0.020  1.479
 J55  C9   N5   single    1.337  0.020  1.337
 J55  C17  C    aromatic  1.382  0.020  1.382
 J55  C17  C16  aromatic  1.390  0.020  1.390
 J55  C12  N6   aromatic  1.320  0.020  1.320
 J55  C10  C8   aromatic  1.422  0.020  1.422
 J55  C10  C11  aromatic  1.402  0.020  1.402
 J55  C    N    aromatic  1.311  0.020  1.311
 J55  C8   N4   aromatic  1.313  0.020  1.313
 J55  C16  C15  aromatic  1.380  0.020  1.380
 J55  N6   C11  aromatic  1.325  0.020  1.325
 J55  C11  N3   aromatic  1.358  0.020  1.358
 J55  N    C1   aromatic  1.323  0.020  1.323
 J55  C15  C1   aromatic  1.396  0.020  1.396
 J55  N4   N3   aromatic  1.326  0.020  1.326
 J55  C1   N1   single    1.386  0.020  1.386
 J55  N3   C7   single    1.431  0.020  1.431
 J55  O1   C6   double    1.216  0.020  1.216
 J55  N1   C2   single    1.362  0.020  1.362
 J55  O2   C2   double    1.207  0.020  1.207
 J55  C6   C7   single    1.523  0.020  1.523
 J55  C6   N2   single    1.348  0.020  1.348
 J55  C2   C3   single    1.533  0.020  1.533
 J55  N2   C3   single    1.451  0.020  1.451
 J55  N2   C5   single    1.461  0.020  1.461
 J55  C3   S    single    1.823  0.020  1.823
 J55  C5   C4   single    1.515  0.020  1.515
 J55  S    C4   single    1.812  0.020  1.812
 J55  N1   H1   single    0.860  0.020  1.020
 J55  C15  H2   single    0.930  0.020  1.080
 J55  C16  H3   single    0.930  0.020  1.080
 J55  C17  H4   single    0.930  0.020  1.080
 J55  C3   H5   single    0.970  0.020  1.090
 J55  C5   H6   single    0.970  0.020  1.090
 J55  C5   H7   single    0.970  0.020  1.090
 J55  C4   H8   single    0.970  0.020  1.090
 J55  C4   H9   single    0.970  0.020  1.090
 J55  C7   H10  single    0.970  0.020  1.090
 J55  C7   H11  single    0.970  0.020  1.090
 J55  C12  H12  single    0.930  0.020  1.080
 J55  C13  H13  single    0.930  0.020  1.080
 J55  C14  H14  single    0.930  0.020  1.080
 J55  N5   H15  single    0.860  0.020  1.020
 J55  N5   H16  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
 J55  C3   C2   N1   113.26  3.000
 J55  C3   C2   O2   121.02  3.000
 J55  N1   C2   O2   125.64  3.000
 J55  H1   N1   C1   114.99  3.000
 J55  H1   N1   C2   116.76  3.000
 J55  C1   N1   C2   128.24  3.000
 J55  C15  C1   N    122.56  3.000
 J55  C15  C1   N1   118.54  3.000
 J55  N    C1   N1   118.88  3.000
 J55  C    N    C1   117.97  3.000
 J55  H2   C15  C16  121.14  3.000
 J55  H2   C15  C1   120.85  3.000
 J55  C16  C15  C1   118.01  3.000
 J55  H3   C16  C17  119.91  3.000
 J55  H3   C16  C15  120.09  3.000
 J55  C17  C16  C15  120.00  3.000
 J55  H4   C17  C    122.31  3.000
 J55  H4   C17  C16  121.59  3.000
 J55  C    C17  C16  116.10  3.000
 J55  BR   C    C17  118.92  3.000
 J55  C17  C    N    125.35  3.000
 J55  BR   C    N    115.73  3.000
 J55  H5   C3   S    110.73  3.000
 J55  H5   C3   N2   111.56  3.000
 J55  S    C3   N2   104.88  3.000
 J55  H5   C3   C2   107.70  3.000
 J55  S    C3   C2   109.00  3.000
 J55  N2   C3   C2   112.97  3.000
 J55  C6   N2   C5   125.41  3.000
 J55  C5   N2   C3   117.11  3.000
 J55  C6   N2   C3   117.47  3.000
 J55  H7   C5   H6   108.50  3.000
 J55  H7   C5   C4   110.66  3.000
 J55  H6   C5   C4   110.09  3.000
 J55  H7   C5   N2   111.12  3.000
 J55  H6   C5   N2   110.70  3.000
 J55  C4   C5   N2   105.77  3.000
 J55  H9   C4   H8   109.23  3.000
 J55  H9   C4   S    109.21  3.000
 J55  H8   C4   S    110.17  3.000
 J55  H9   C4   C5   112.01  3.000
 J55  H8   C4   C5   111.64  3.000
 J55  S    C4   C5   104.48  3.000
 J55  C4   S    C3    90.52  3.000
 J55  C7   C6   O1   121.61  3.000
 J55  C7   C6   N2   116.32  3.000
 J55  O1   C6   N2   122.03  3.000
 J55  H11  C7   H10  107.57  3.000
 J55  H11  C7   N3   108.52  3.000
 J55  H10  C7   N3   109.41  3.000
 J55  H11  C7   C6   110.53  3.000
 J55  H10  C7   C6   111.26  3.000
 J55  N3   C7   C6   109.50  3.000
 J55  N4   N3   C11  111.43  3.000
 J55  N4   N3   C7   122.45  3.000
 J55  C11  N3   C7   125.69  3.000
 J55  C10  C11  N6   127.44  3.000
 J55  N6   C11  N3   125.89  3.000
 J55  C10  C11  N3   106.67  3.000
 J55  C12  N6   C11  113.99  3.000
 J55  H12  C12  C13  119.24  3.000
 J55  H12  C12  N6   116.33  3.000
 J55  C13  C12  N6   124.44  3.000
 J55  H13  C13  C14  120.77  3.000
 J55  H13  C13  C12  118.87  3.000
 J55  C14  C13  C12  120.36  3.000
 J55  H14  C14  C10  121.89  3.000
 J55  H14  C14  C13  121.52  3.000
 J55  C10  C14  C13  116.58  3.000
 J55  C8   C10  C14  139.06  3.000
 J55  C8   C10  C11  103.74  3.000
 J55  C14  C10  C11  117.19  3.000
 J55  C9   C8   N4   122.39  3.000
 J55  N4   C8   C10  110.45  3.000
 J55  C9   C8   C10  127.16  3.000
 J55  C8   N4   N3   107.68  3.000
 J55  N5   C9   O    124.35  3.000
 J55  N5   C9   C8   115.83  3.000
 J55  O    C9   C8   119.83  3.000
 J55  H16  N5   H15  118.08  3.000
 J55  H16  N5   C9   120.26  3.000
 J55  H15  N5   C9   121.66  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
 J55  CONST_01  C17  C    N    C1      0.00   0.0  0
 J55  CONST_02  C17  C16  C15  C1      0.00   0.0  0
 J55  CONST_03  C16  C17  C    N       0.00   0.0  0
 J55  CONST_04  C16  C15  C1   N       0.00   0.0  0
 J55  CONST_05  C    C17  C16  C15     0.00   0.0  0
 J55  CONST_06  C    N    C1   C15     0.00   0.0  0
 J55  CONST_07  C14  C10  C11  N3    180.00   0.0  0
 J55  CONST_08  C8   C10  C11  N3      0.00   0.0  0
 J55  CONST_09  C12  N6   C11  N3    180.00   0.0  0
 J55  CONST_10  C10  C8   N4   N3      0.00   0.0  0
 J55  CONST_11  C13  C14  C10  C11     0.00   0.0  0
 J55  CONST_12  N4   C8   C10  C11     0.00   0.0  0
 J55  CONST_13  C13  C12  N6   C11     0.00   0.0  0
 J55  CONST_14  C8   N4   N3   C11     0.00   0.0  0
 J55  CONST_15  C14  C13  C12  N6      0.00   0.0  0
 J55  CONST_16  C14  C10  C11  N6      0.00   0.0  0
 J55  CONST_17  C8   C10  C11  N6    180.00   0.0  0
 J55  CONST_18  N4   N3   C11  N6    180.00   0.0  0
 J55  CONST_19  C10  C14  C13  C12     0.00   0.0  0
 J55  CONST_20  C10  C11  N6   C12     0.00   0.0  0
 J55  CONST_21  C8   C10  C14  C13   180.00   0.0  0
 J55  CONST_22  N4   C8   C10  C14   180.00   0.0  0
 J55  CONST_23  N4   N3   C11  C10     0.00   0.0  0
 J55  CONST_24  C    N    C1   N1    180.00   0.0  0
 J55  CONST_25  C16  C15  C1   N1    180.00   0.0  0
 J55  CONST_26  BR   C    N    C1    180.00   0.0  0
 J55  CONST_27  BR   C    C17  C16   180.00   0.0  0
 J55  CONST_28  C10  C11  N3   C7    180.00   0.0  0
 J55  CONST_29  N6   C11  N3   C7      0.00   0.0  0
 J55  CONST_30  C8   N4   N3   C7    180.00   0.0  0
 J55  CONST_31  C9   C8   N4   N3    180.00   0.0  0
 J55  CONST_32  C9   C8   C10  C11   180.00   0.0  0
 J55  CONST_33  C9   C8   C10  C14     0.00   0.0  0
 J55  CONST_34  H3   C16  C15  C1    180.00   0.0  0
 J55  CONST_35  H4   C17  C    N     180.00   0.0  0
 J55  CONST_36  H2   C15  C1   N     180.00   0.0  0
 J55  CONST_37  H14  C14  C10  C11   180.00   0.0  0
 J55  CONST_38  H12  C12  N6   C11   180.00   0.0  0
 J55  CONST_39  H13  C13  C12  N6    180.00   0.0  0
 J55  CONST_40  C3   C2   N1   C1    180.00   0.0  0
 J55  CONST_41  O1   C6   N2   C3      0.00   0.0  0
 J55  CONST_42  C7   C6   N2   C3    180.00   0.0  0
 J55  CONST_43  O1   C6   N2   C5    180.00   0.0  0
 J55  CONST_44  C7   C6   N2   C5      0.00   0.0  0
 J55  CONST_48  C1   N1   C2   O2      0.00   0.0  0
 J55  CONST_49  H15  N5   C9   C8      0.00   0.0  0
 J55  CONST_50  H16  N5   C9   C8    180.00   0.0  0
 J55  Var_01    C4   C5   N2   C3     19.56  30.0  1
 J55  Var_02    C5   C4   S    C3     38.72  30.0  1
 J55  Var_03    S    C4   C5   N2    -38.53  30.0  1
 J55  Var_04    N3   C7   C6   N2   -159.67  30.0  3
 J55  Var_05    C11  N3   C7   C6     66.93  30.0  3
 J55  Var_06    O    C9   C8   C10     0.15  30.0  2

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
 J55  chir_01  C3  C2  N2  S  negativ

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
 J55  plan-1  N1   0.020
 J55  plan-1  C1   0.020
 J55  plan-1  N    0.020
 J55  plan-1  C15  0.020
 J55  plan-1  C16  0.020
 J55  plan-1  C17  0.020
 J55  plan-1  C    0.020
 J55  plan-1  BR   0.020
 J55  plan-1  H2   0.020
 J55  plan-1  H3   0.020
 J55  plan-1  H4   0.020
 J55  plan-2  C7   0.020
 J55  plan-2  N3   0.020
 J55  plan-2  C11  0.020
 J55  plan-2  N6   0.020
 J55  plan-2  C12  0.020
 J55  plan-2  C13  0.020
 J55  plan-2  C14  0.020
 J55  plan-2  C10  0.020
 J55  plan-2  C8   0.020
 J55  plan-2  N4   0.020
 J55  plan-2  C9   0.020
 J55  plan-2  H12  0.020
 J55  plan-2  H13  0.020
 J55  plan-2  H14  0.020
 J55  plan-3  C3   0.020
 J55  plan-3  N2   0.020
 J55  plan-3  C5   0.020
 J55  plan-3  C6   0.020
 J55  plan-3  O1   0.020
 J55  plan-3  C7   0.020
 J55  plan-4  C8   0.020
 J55  plan-4  C9   0.020
 J55  plan-4  O    0.020
 J55  plan-4  N5   0.020
 J55  plan-4  H15  0.020
 J55  plan-4  H16  0.020
 J55  plan-5  O2   0.020
 J55  plan-5  C2   0.020
 J55  plan-5  N1   0.020
 J55  plan-5  C1   0.020
 J55  plan-5  C3   0.020
 J55  plan-5  H1   0.020

