# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:13:53 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cccc(NC(=O)[C@@H]2SCCN2C(=O)Cn3ncc4ccccc34)n1
#
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
 J56  J56  (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide  ligand  43  27  .  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_J56
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
 J56  O1   O   O     0  -0.406  -1.2684   1.8308   1.4914
 J56  C2   C   C     0   0.547  -0.4155   2.0068   0.6577
 J56  N1   N   NH1   0  -0.717  -0.4249   1.4968  -0.6100
 J56  C1   C   CR6   0   0.524  -1.2091   0.4771  -1.1249
 J56  N    N   N     0  -0.403  -1.8811  -0.2968  -0.2888
 J56  C15  C   CR16  0  -0.389  -1.2166   0.2742  -2.5071
 J56  C16  C   CR16  0  -0.141  -1.9517  -0.7837  -3.0024
 J56  C17  C   CR16  0  -0.290  -2.6628  -1.6038  -2.1342
 J56  C    C   CR6   0   0.086  -2.5755  -1.2877  -0.7915
 J56  BR   BR  BR    0  -0.040  -3.5114  -2.3578   0.4652
 J56  C3   C   CH1   0  -0.337   0.7939   2.9082   0.9335
 J56  N2   N   NT    0  -0.490   2.0320   2.3581   0.4121
 J56  C5   C   CH2   0  -0.281   2.8254   3.2160  -0.4639
 J56  C4   C   CH2   0  -0.581   2.3732   4.6315  -0.1722
 J56  S    S   S2    0   0.039   0.5805   4.4932   0.0596
 J56  C6   C   C     0   0.562   2.3566   1.1005   0.7784
 J56  O    O   O     0  -0.452   1.6773   0.4664   1.5634
 J56  C7   C   CH2   0  -0.450   3.5870   0.4928   0.1150
 J56  N3   N   NR5   0  -0.392   3.6157  -0.9200   0.3237
 J56  C10  C   CR56  0   0.475   2.7626  -1.8286  -0.2145
 J56  C11  C   CR16  0  -0.288   1.7750  -1.7017  -1.1961
 J56  C12  C   CR16  0  -0.260   1.0663  -2.8387  -1.5128
 J56  C13  C   CR16  0  -0.271   1.3252  -4.0745  -0.8849
 J56  C14  C   CR16  0  -0.322   2.3018  -4.1933   0.0785
 J56  C9   C   CR56  0  -0.110   3.0312  -3.0484   0.4255
 J56  C8   C   CR15  0  -0.109   4.0601  -2.7295   1.3545
 J56  N4   N   N     0  -0.239   4.3754  -1.4631   1.2849
 J56  H1   H   HNH1  0   0.418   0.2178   1.9176  -1.2652
 J56  H2   H   HCR6  0   0.295  -0.6584   0.9236  -3.1683
 J56  H3   H   HCR6  0   0.292  -1.9776  -0.9742  -4.0668
 J56  H4   H   HCR6  0   0.292  -3.2451  -2.4386  -2.4948
 J56  H5   H   HCH1  0   0.332   0.8483   3.0653   2.0127
 J56  H6   H   HCH2  0   0.291   3.8878   3.1084  -0.2462
 J56  H7   H   HCH2  0   0.273   2.6591   2.9683  -1.5150
 J56  H8   H   HCH2  0   0.297   2.8402   5.0251   0.7297
 J56  H9   H   HCH2  0   0.314   2.5745   5.3045  -1.0029
 J56  H10  H   HCH2  0   0.299   3.5983   0.7068  -0.9567
 J56  H11  H   HCH2  0   0.333   4.4972   0.9251   0.5333
 J56  H12  H   HCR6  0   0.253   1.5689  -0.7600  -1.6883
 J56  H13  H   HCR6  0   0.258   0.2867  -2.7838  -2.2612
 J56  H14  H   HCR6  0   0.257   0.7399  -4.9392  -1.1681
 J56  H15  H   HCR6  0   0.258   2.4952  -5.1431   0.5605
 J56  H16  H   HCR5  0   0.273   4.5619  -3.3825   2.0523

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
 J56  C13  C14  aromatic  1.377  0.020  1.377
 J56  C13  C12  aromatic  1.410  0.020  1.410
 J56  C14  C9   aromatic  1.401  0.020  1.401
 J56  BR   C    single    1.897  0.020  1.897
 J56  C12  C11  aromatic  1.377  0.020  1.377
 J56  C9   C8   aromatic  1.422  0.020  1.422
 J56  C9   C10  aromatic  1.403  0.020  1.403
 J56  C17  C    aromatic  1.382  0.020  1.382
 J56  C17  C16  aromatic  1.390  0.020  1.390
 J56  C8   N4   aromatic  1.307  0.020  1.307
 J56  C    N    aromatic  1.310  0.020  1.310
 J56  C16  C15  aromatic  1.380  0.020  1.380
 J56  C11  C10  aromatic  1.398  0.020  1.398
 J56  C10  N3   aromatic  1.358  0.020  1.358
 J56  N    C1   aromatic  1.323  0.020  1.323
 J56  N4   N3   aromatic  1.340  0.020  1.340
 J56  C15  C1   aromatic  1.397  0.020  1.397
 J56  N3   C7   single    1.428  0.020  1.428
 J56  C1   N1   single    1.386  0.020  1.386
 J56  O    C6   double    1.216  0.020  1.216
 J56  C7   C6   single    1.524  0.020  1.524
 J56  N1   C2   single    1.366  0.020  1.366
 J56  C6   N2   single    1.349  0.020  1.349
 J56  O1   C2   double    1.206  0.020  1.206
 J56  C2   C3   single    1.533  0.020  1.533
 J56  N2   C3   single    1.452  0.020  1.452
 J56  N2   C5   single    1.460  0.020  1.460
 J56  C3   S    single    1.822  0.020  1.822
 J56  C5   C4   single    1.514  0.020  1.514
 J56  S    C4   single    1.813  0.020  1.813
 J56  N1   H1   single    0.860  0.020  1.020
 J56  C15  H2   single    0.930  0.020  1.080
 J56  C16  H3   single    0.930  0.020  1.080
 J56  C17  H4   single    0.930  0.020  1.080
 J56  C3   H5   single    0.970  0.020  1.090
 J56  C5   H6   single    0.970  0.020  1.090
 J56  C5   H7   single    0.970  0.020  1.090
 J56  C4   H8   single    0.970  0.020  1.090
 J56  C4   H9   single    0.970  0.020  1.090
 J56  C7   H10  single    0.970  0.020  1.090
 J56  C7   H11  single    0.970  0.020  1.090
 J56  C11  H12  single    0.930  0.020  1.080
 J56  C12  H13  single    0.930  0.020  1.080
 J56  C13  H14  single    0.930  0.020  1.080
 J56  C14  H15  single    0.930  0.020  1.080
 J56  C8   H16  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
 J56  C3   C2   N1   113.06  3.000
 J56  C3   C2   O1   121.29  3.000
 J56  N1   C2   O1   125.61  3.000
 J56  H1   N1   C1   115.20  3.000
 J56  H1   N1   C2   116.24  3.000
 J56  C1   N1   C2   128.56  3.000
 J56  C15  C1   N    122.53  3.000
 J56  C15  C1   N1   118.52  3.000
 J56  N    C1   N1   118.90  3.000
 J56  C    N    C1   117.98  3.000
 J56  H2   C15  C16  121.04  3.000
 J56  H2   C15  C1   120.98  3.000
 J56  C16  C15  C1   117.98  3.000
 J56  H3   C16  C17  119.90  3.000
 J56  H3   C16  C15  120.06  3.000
 J56  C17  C16  C15  120.04  3.000
 J56  H4   C17  C    122.36  3.000
 J56  H4   C17  C16  121.56  3.000
 J56  C    C17  C16  116.07  3.000
 J56  BR   C    C17  118.90  3.000
 J56  C17  C    N    125.39  3.000
 J56  BR   C    N    115.71  3.000
 J56  H5   C3   S    110.77  3.000
 J56  H5   C3   N2   111.54  3.000
 J56  S    C3   N2   104.90  3.000
 J56  H5   C3   C2   107.56  3.000
 J56  S    C3   C2   109.43  3.000
 J56  N2   C3   C2   112.66  3.000
 J56  C6   N2   C5   125.42  3.000
 J56  C5   N2   C3   117.14  3.000
 J56  C6   N2   C3   117.44  3.000
 J56  H7   C5   H6   108.55  3.000
 J56  H7   C5   C4   110.59  3.000
 J56  H6   C5   C4   110.18  3.000
 J56  H7   C5   N2   111.18  3.000
 J56  H6   C5   N2   110.59  3.000
 J56  C4   C5   N2   105.75  3.000
 J56  H9   C4   H8   109.23  3.000
 J56  H9   C4   S    109.14  3.000
 J56  H8   C4   S    110.22  3.000
 J56  H9   C4   C5   112.08  3.000
 J56  H8   C4   C5   111.66  3.000
 J56  S    C4   C5   104.39  3.000
 J56  C4   S    C3    90.68  3.000
 J56  C7   C6   O    121.59  3.000
 J56  C7   C6   N2   116.59  3.000
 J56  O    C6   N2   121.78  3.000
 J56  H11  C7   H10  106.84  3.000
 J56  H11  C7   N3   108.61  3.000
 J56  H10  C7   N3   109.68  3.000
 J56  H11  C7   C6   110.40  3.000
 J56  H10  C7   C6   110.92  3.000
 J56  N3   C7   C6   110.30  3.000
 J56  N4   N3   C10  111.68  3.000
 J56  N4   N3   C7   121.13  3.000
 J56  C10  N3   C7   126.26  3.000
 J56  C9   C10  C11  122.29  3.000
 J56  C11  C10  N3   131.40  3.000
 J56  C9   C10  N3   106.30  3.000
 J56  H12  C11  C12  121.06  3.000
 J56  H12  C11  C10  122.19  3.000
 J56  C12  C11  C10  116.75  3.000
 J56  H13  C12  C13  118.99  3.000
 J56  H13  C12  C11  119.22  3.000
 J56  C13  C12  C11  121.79  3.000
 J56  H14  C13  C14  119.86  3.000
 J56  H14  C13  C12  118.98  3.000
 J56  C14  C13  C12  121.16  3.000
 J56  H15  C14  C9   120.91  3.000
 J56  H15  C14  C13  120.92  3.000
 J56  C9   C14  C13  118.16  3.000
 J56  C8   C9   C14  136.18  3.000
 J56  C8   C9   C10  103.97  3.000
 J56  C14  C9   C10  119.84  3.000
 J56  H16  C8   N4   120.56  3.000
 J56  H16  C8   C9   128.52  3.000
 J56  N4   C8   C9   110.91  3.000
 J56  C8   N4   N3   107.10  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
 J56  CONST_01  C17  C    N    C1      0.00   0.0  0
 J56  CONST_02  C17  C16  C15  C1      0.00   0.0  0
 J56  CONST_03  C16  C17  C    N       0.00   0.0  0
 J56  CONST_04  C16  C15  C1   N       0.00   0.0  0
 J56  CONST_05  C    C17  C16  C15     0.00   0.0  0
 J56  CONST_06  C    N    C1   C15     0.00   0.0  0
 J56  CONST_07  C14  C9   C10  N3    180.00   0.0  0
 J56  CONST_08  C8   C9   C10  N3      0.00   0.0  0
 J56  CONST_09  C12  C11  C10  N3    180.00   0.0  0
 J56  CONST_10  C9   C8   N4   N3      0.00   0.0  0
 J56  CONST_11  C13  C14  C9   C10     0.00   0.0  0
 J56  CONST_12  N4   C8   C9   C10     0.00   0.0  0
 J56  CONST_13  C13  C12  C11  C10     0.00   0.0  0
 J56  CONST_14  C8   N4   N3   C10     0.00   0.0  0
 J56  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 J56  CONST_16  C14  C9   C10  C11     0.00   0.0  0
 J56  CONST_17  C8   C9   C10  C11   180.00   0.0  0
 J56  CONST_18  N4   N3   C10  C11   180.00   0.0  0
 J56  CONST_19  C9   C14  C13  C12     0.00   0.0  0
 J56  CONST_20  C9   C10  C11  C12     0.00   0.0  0
 J56  CONST_21  C8   C9   C14  C13   180.00   0.0  0
 J56  CONST_22  N4   C8   C9   C14   180.00   0.0  0
 J56  CONST_23  N4   N3   C10  C9      0.00   0.0  0
 J56  CONST_24  C    N    C1   N1    180.00   0.0  0
 J56  CONST_25  C16  C15  C1   N1    180.00   0.0  0
 J56  CONST_26  BR   C    N    C1    180.00   0.0  0
 J56  CONST_27  BR   C    C17  C16   180.00   0.0  0
 J56  CONST_28  C9   C10  N3   C7    180.00   0.0  0
 J56  CONST_29  C11  C10  N3   C7      0.00   0.0  0
 J56  CONST_30  C8   N4   N3   C7    180.00   0.0  0
 J56  CONST_31  H3   C16  C15  C1    180.00   0.0  0
 J56  CONST_32  H4   C17  C    N     180.00   0.0  0
 J56  CONST_33  H2   C15  C1   N     180.00   0.0  0
 J56  CONST_34  H12  C11  C10  N3      0.00   0.0  0
 J56  CONST_35  H16  C8   N4   N3    180.00   0.0  0
 J56  CONST_36  H15  C14  C9   C10   180.00   0.0  0
 J56  CONST_37  H13  C12  C11  C10   180.00   0.0  0
 J56  CONST_38  H14  C13  C12  C11   180.00   0.0  0
 J56  CONST_39  C3   C2   N1   C1    180.00   0.0  0
 J56  CONST_40  O    C6   N2   C3      0.00   0.0  0
 J56  CONST_41  C7   C6   N2   C3    180.00   0.0  0
 J56  CONST_42  O    C6   N2   C5    180.00   0.0  0
 J56  CONST_43  C7   C6   N2   C5      0.00   0.0  0
 J56  CONST_44  N    C1   N1   C2      0.00   0.0  0
 J56  CONST_45  C15  C1   N1   C2    180.00   0.0  0
 J56  CONST_46  H1   N1   C1   N     180.00   0.0  0
 J56  Var_01    C4   C5   N2   C3     20.58  30.0  1
 J56  Var_02    C5   C4   S    C3     38.45  30.0  1
 J56  Var_03    S    C4   C5   N2    -38.83  30.0  1
 J56  Var_04    N3   C7   C6   N2   -165.21  30.0  2
 J56  Var_05    C10  N3   C7   C6     68.84  30.0  1

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
 J56  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
 J56  plan-1  N1   0.020
 J56  plan-1  C1   0.020
 J56  plan-1  N    0.020
 J56  plan-1  C15  0.020
 J56  plan-1  C16  0.020
 J56  plan-1  C17  0.020
 J56  plan-1  C    0.020
 J56  plan-1  BR   0.020
 J56  plan-1  H2   0.020
 J56  plan-1  H3   0.020
 J56  plan-1  H4   0.020
 J56  plan-2  C7   0.020
 J56  plan-2  N3   0.020
 J56  plan-2  C10  0.020
 J56  plan-2  C11  0.020
 J56  plan-2  C12  0.020
 J56  plan-2  C13  0.020
 J56  plan-2  C14  0.020
 J56  plan-2  C9   0.020
 J56  plan-2  C8   0.020
 J56  plan-2  N4   0.020
 J56  plan-2  H12  0.020
 J56  plan-2  H13  0.020
 J56  plan-2  H14  0.020
 J56  plan-2  H15  0.020
 J56  plan-2  H16  0.020
 J56  plan-3  C3   0.020
 J56  plan-3  N2   0.020
 J56  plan-3  C5   0.020
 J56  plan-3  C6   0.020
 J56  plan-3  O    0.020
 J56  plan-3  C7   0.020
 J56  plan-4  O1   0.020
 J56  plan-4  C2   0.020
 J56  plan-4  N1   0.020
 J56  plan-4  C1   0.020
 J56  plan-4  C3   0.020
 J56  plan-4  H1   0.020

