# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:21:10 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: (5~{S})-5-[[4-[2-(5-ethylpyridin-2-yl)ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(CCOc2ccc(C[C@@H]3SC(=O)NC3=O)cc2)nc1
#
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
 8N6  8N6  (5~{S})-5-[[4-[2-(5-ethylpyridin-2-yl)ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione  ligand  45  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8N6
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
 8N6  O4   O  O     0  -0.411   6.9901  -1.0230  -0.8553
 8N6  C4   C  C     0   0.623   6.2834  -0.2129  -0.3114
 8N6  N3   N  NH1   0  -0.658   6.6676   1.0572   0.0147
 8N6  C5   C  CH1   0  -0.551   4.8441  -0.4791   0.0873
 8N6  S1   S  S2    0   0.086   4.2130   1.0621   0.8164
 8N6  C2   C  C     0   0.403   5.7539   1.8959   0.6064
 8N6  O2   O  O     0  -0.401   5.9615   3.0319   0.9337
 8N6  C6   C  CH2   0  -0.498   4.0016  -0.9430  -1.1028
 8N6  C21  C  CR16  0  -0.188  -6.8487  -0.1934  -0.6334
 8N6  C7   C  CR6   0   0.089   2.5744  -1.1955  -0.7080
 8N6  C12  C  CR16  0  -0.284   1.5751  -0.2750  -0.9892
 8N6  C11  C  CR16  0  -0.369   0.2560  -0.4863  -0.6015
 8N6  C10  C  CR6   0   0.376  -0.0802  -1.6460   0.0901
 8N6  C9   C  CR16  0  -0.331   0.9161  -2.5815   0.3813
 8N6  C8   C  CR16  0  -0.280   2.2197  -2.3532  -0.0135
 8N6  O13  O  O2    0  -0.477  -1.3236  -1.9502   0.5103
 8N6  C14  C  CH2   0  -0.169  -2.3840  -1.0586   0.2131
 8N6  C15  C  CH2   0  -0.524  -3.6583  -1.6440   0.7977
 8N6  C24  C  CH3   0  -0.655  -7.7239   2.8879  -1.3769
 8N6  C20  C  CR6   0   0.037  -6.9071   1.0039   0.0710
 8N6  C19  C  CR16  0  -0.123  -5.8785   1.2398   0.9776
 8N6  N18  N  N     0  -0.417  -4.8727   0.4059   1.2035
 8N6  C22  C  CR16  0  -0.332  -5.8018  -1.0719  -0.4077
 8N6  C17  C  CR6   0   0.233  -4.8263  -0.7386   0.5258
 8N6  H1   H  HNH1  0   0.440   7.6002   1.3930  -0.1969
 8N6  H2   H  HCH1  0   0.353   4.8504  -1.2488   0.8635
 8N6  H3   H  HCH2  0   0.278   4.0489  -0.1935  -1.8951
 8N6  H4   H  HCH2  0   0.282   4.4547  -1.8575  -1.4919
 8N6  H5   H  HCR6  0   0.263  -7.6212  -0.4414  -1.3523
 8N6  H6   H  HCR6  0   0.255   1.8201   0.6316  -1.5295
 8N6  H7   H  HCR6  0   0.279  -0.4854   0.2617  -0.8468
 8N6  H8   H  HCR6  0   0.262   0.6560  -3.4874   0.9148
 8N6  H9   H  HCR6  0   0.254   2.9761  -3.0945   0.2184
 8N6  H10  H  HCH2  0   0.229  -2.1933  -0.0717   0.6480
 8N6  H11  H  HCH2  0   0.230  -2.4871  -0.9330  -0.8711
 8N6  H12  H  HCH2  0   0.256  -3.8418  -2.6304   0.3678
 8N6  H13  H  HCH2  0   0.259  -3.5377  -1.7691   1.8765
 8N6  H14  H  HCH3  0   0.227  -6.7880   3.4369  -1.2664
 8N6  H15  H  HCH3  0   0.227  -7.6523   2.2891  -2.2858
 8N6  H16  H  HCH3  0   0.234  -8.5241   3.6151  -1.5184
 8N6  H17  H  HCH2  0   0.243  -8.0999   2.6429   0.7293
 8N6  H18  H  HCH2  0   0.245  -8.9508   1.4963  -0.2830
 8N6  H19  H  HCR6  0   0.252  -5.8782   2.1576   1.5591
 8N6  H20  H  HCR6  0   0.264  -5.7426  -2.0097  -0.9449
 8N6  C23  C  CH2   0  -0.507  -7.9960   2.0114  -0.1560

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
 8N6  C24  C23  single    1.527  0.020  1.527
 8N6  C23  C20  single    1.501  0.020  1.501
 8N6  C20  C19  aromatic  1.391  0.020  1.391
 8N6  C20  C21  aromatic  1.390  0.020  1.390
 8N6  C19  N18  aromatic  1.326  0.020  1.326
 8N6  C21  C22  aromatic  1.385  0.020  1.385
 8N6  N18  C17  aromatic  1.331  0.020  1.331
 8N6  C22  C17  aromatic  1.391  0.020  1.391
 8N6  C17  C15  single    1.503  0.020  1.503
 8N6  C15  C14  single    1.519  0.020  1.519
 8N6  C14  O13  single    1.417  0.020  1.417
 8N6  O13  C10  single    1.347  0.020  1.347
 8N6  C10  C9   aromatic  1.397  0.020  1.397
 8N6  C10  C11  aromatic  1.391  0.020  1.391
 8N6  C9   C8   aromatic  1.381  0.020  1.381
 8N6  C11  C12  aromatic  1.391  0.020  1.391
 8N6  C8   C7   aromatic  1.396  0.020  1.396
 8N6  S1   C2   single    1.765  0.020  1.765
 8N6  S1   C5   single    1.818  0.020  1.818
 8N6  C12  C7   aromatic  1.387  0.020  1.387
 8N6  C7   C6   single    1.502  0.020  1.502
 8N6  O2   C2   double    1.200  0.020  1.200
 8N6  C2   N3   single    1.374  0.020  1.374
 8N6  C5   C6   single    1.530  0.020  1.530
 8N6  C5   C4   single    1.517  0.020  1.517
 8N6  N3   C4   single    1.366  0.020  1.366
 8N6  C4   O4   double    1.205  0.020  1.205
 8N6  N3   H1   single    0.860  0.020  1.020
 8N6  C5   H2   single    0.970  0.020  1.090
 8N6  C6   H3   single    0.970  0.020  1.090
 8N6  C6   H4   single    0.970  0.020  1.090
 8N6  C21  H5   single    0.930  0.020  1.080
 8N6  C12  H6   single    0.930  0.020  1.080
 8N6  C11  H7   single    0.930  0.020  1.080
 8N6  C9   H8   single    0.930  0.020  1.080
 8N6  C8   H9   single    0.930  0.020  1.080
 8N6  C14  H10  single    0.970  0.020  1.090
 8N6  C14  H11  single    0.970  0.020  1.090
 8N6  C15  H12  single    0.970  0.020  1.090
 8N6  C15  H13  single    0.970  0.020  1.090
 8N6  C24  H14  single    0.970  0.020  1.090
 8N6  C24  H15  single    0.970  0.020  1.090
 8N6  C24  H16  single    0.970  0.020  1.090
 8N6  C23  H17  single    0.970  0.020  1.090
 8N6  C23  H18  single    0.970  0.020  1.090
 8N6  C19  H19  single    0.930  0.020  1.080
 8N6  C22  H20  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
 8N6  C5   C4   N3   111.54  3.000
 8N6  N3   C4   O4   124.60  3.000
 8N6  C5   C4   O4   123.87  3.000
 8N6  H1   N3   C2   119.97  3.000
 8N6  H1   N3   C4   121.12  3.000
 8N6  C2   N3   C4   118.89  3.000
 8N6  H2   C5   C6   109.99  3.000
 8N6  H2   C5   S1   108.31  3.000
 8N6  C6   C5   S1   112.20  3.000
 8N6  H2   C5   C4   107.74  3.000
 8N6  C6   C5   C4   111.79  3.000
 8N6  S1   C5   C4   106.62  3.000
 8N6  C2   S1   C5    92.85  3.000
 8N6  O2   C2   S1   124.46  3.000
 8N6  O2   C2   N3   125.45  3.000
 8N6  S1   C2   N3   110.09  3.000
 8N6  H4   C6   H3   107.35  3.000
 8N6  H4   C6   C7   110.31  3.000
 8N6  H3   C6   C7   110.32  3.000
 8N6  H4   C6   C5   107.61  3.000
 8N6  H3   C6   C5   109.42  3.000
 8N6  C7   C6   C5   111.70  3.000
 8N6  H5   C21  C22  120.10  3.000
 8N6  H5   C21  C20  120.20  3.000
 8N6  C22  C21  C20  119.70  3.000
 8N6  C8   C7   C12  117.91  3.000
 8N6  C12  C7   C6   121.30  3.000
 8N6  C8   C7   C6   120.77  3.000
 8N6  H6   C12  C11  118.73  3.000
 8N6  H6   C12  C7   119.56  3.000
 8N6  C11  C12  C7   121.71  3.000
 8N6  H7   C11  C10  121.57  3.000
 8N6  H7   C11  C12  118.80  3.000
 8N6  C10  C11  C12  119.63  3.000
 8N6  O13  C10  C9   116.22  3.000
 8N6  C9   C10  C11  119.29  3.000
 8N6  O13  C10  C11  124.49  3.000
 8N6  H8   C9   C8   120.39  3.000
 8N6  H8   C9   C10  119.43  3.000
 8N6  C8   C9   C10  120.18  3.000
 8N6  H9   C8   C9   118.96  3.000
 8N6  H9   C8   C7   119.76  3.000
 8N6  C9   C8   C7   121.28  3.000
 8N6  C14  O13  C10  118.89  3.000
 8N6  H11  C14  H10  107.81  3.000
 8N6  H11  C14  C15  110.23  3.000
 8N6  H10  C14  C15  109.90  3.000
 8N6  H11  C14  O13  110.49  3.000
 8N6  H10  C14  O13  110.69  3.000
 8N6  C15  C14  O13  107.73  3.000
 8N6  H13  C15  H12  107.69  3.000
 8N6  H13  C15  C17  109.48  3.000
 8N6  H12  C15  C17  110.03  3.000
 8N6  H13  C15  C14  109.36  3.000
 8N6  H12  C15  C14  109.73  3.000
 8N6  C17  C15  C14  110.50  3.000
 8N6  H16  C24  H15  107.83  3.000
 8N6  H16  C24  H14  107.88  3.000
 8N6  H15  C24  H14  107.73  3.000
 8N6  H16  C24  C23  110.84  3.000
 8N6  H15  C24  C23  111.27  3.000
 8N6  H14  C24  C23  111.14  3.000
 8N6  C19  C20  C23  121.41  3.000
 8N6  C19  C20  C21  116.43  3.000
 8N6  C23  C20  C21  122.14  3.000
 8N6  H19  C19  N18  116.09  3.000
 8N6  H19  C19  C20  119.48  3.000
 8N6  N18  C19  C20  124.42  3.000
 8N6  C17  N18  C19  118.71  3.000
 8N6  H20  C22  C17  120.16  3.000
 8N6  H20  C22  C21  120.66  3.000
 8N6  C17  C22  C21  119.17  3.000
 8N6  C22  C17  N18  121.57  3.000
 8N6  C22  C17  C15  121.48  3.000
 8N6  N18  C17  C15  116.94  3.000
 8N6  H18  C23  H17  106.49  3.000
 8N6  H18  C23  C20  109.58  3.000
 8N6  H17  C23  C20  109.54  3.000
 8N6  H18  C23  C24  109.47  3.000
 8N6  H17  C23  C24  109.46  3.000
 8N6  C20  C23  C24  112.14  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
 8N6  CONST_01  N18  C19  C20  C21    0.00   0.0  0
 8N6  CONST_02  N18  C17  C22  C21    0.00   0.0  0
 8N6  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 8N6  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 8N6  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 8N6  CONST_06  C9   C8   C7   C12    0.00   0.0  0
 8N6  CONST_07  C8   C9   C10  C11    0.00   0.0  0
 8N6  CONST_08  C8   C7   C12  C11    0.00   0.0  0
 8N6  CONST_09  C17  N18  C19  C20    0.00   0.0  0
 8N6  CONST_10  C17  C22  C21  C20    0.00   0.0  0
 8N6  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 8N6  CONST_12  C22  C17  N18  C19    0.00   0.0  0
 8N6  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 8N6  CONST_14  C9   C8   C7   C6   180.00   0.0  0
 8N6  CONST_15  C11  C12  C7   C6   180.00   0.0  0
 8N6  CONST_16  C15  C17  C22  C21  180.00   0.0  0
 8N6  CONST_17  O13  C10  C11  C12  180.00   0.0  0
 8N6  CONST_18  O13  C10  C9   C8   180.00   0.0  0
 8N6  CONST_19  C19  N18  C17  C15  180.00   0.0  0
 8N6  CONST_20  N18  C19  C20  C23  180.00   0.0  0
 8N6  CONST_21  C22  C21  C20  C23  180.00   0.0  0
 8N6  CONST_22  C2   N3   C4   O4   180.00   0.0  0
 8N6  CONST_23  H19  C19  C20  C21  180.00   0.0  0
 8N6  CONST_24  H8   C9   C8   C7   180.00   0.0  0
 8N6  CONST_25  H7   C11  C12  C7   180.00   0.0  0
 8N6  CONST_26  H9   C8   C7   C12  180.00   0.0  0
 8N6  CONST_27  H6   C12  C11  C10  180.00   0.0  0
 8N6  CONST_28  H20  C22  C21  C20  180.00   0.0  0
 8N6  CONST_29  H5   C21  C20  C19  180.00   0.0  0
 8N6  CONST_30  H1   N3   C4   C5   180.00   0.0  0
 8N6  Var_01    S1   C2   N3   C4     0.27  30.0  1
 8N6  Var_02    C8   C7   C6   C5   -76.62  30.0  2
 8N6  Var_03    C24  C23  C20  C21  -81.28  30.0  2
 8N6  Var_04    N18  C17  C15  C14  -71.51  30.0  2
 8N6  Var_05    C15  C14  O13  C10  179.94  30.0  2
 8N6  Var_06    C17  C15  C14  O13  179.58  30.0  2
 8N6  Var_07    H14  C24  C23  C20  -59.70  30.0  3

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
 8N6  chir_01  C5  S1  C6  C4  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
 8N6  plan-1  C6   0.020
 8N6  plan-1  C7   0.020
 8N6  plan-1  C12  0.020
 8N6  plan-1  C11  0.020
 8N6  plan-1  C10  0.020
 8N6  plan-1  C9   0.020
 8N6  plan-1  C8   0.020
 8N6  plan-1  O13  0.020
 8N6  plan-1  H6   0.020
 8N6  plan-1  H7   0.020
 8N6  plan-1  H8   0.020
 8N6  plan-1  H9   0.020
 8N6  plan-2  C21  0.020
 8N6  plan-2  C15  0.020
 8N6  plan-2  C20  0.020
 8N6  plan-2  C19  0.020
 8N6  plan-2  N18  0.020
 8N6  plan-2  C22  0.020
 8N6  plan-2  C17  0.020
 8N6  plan-2  H5   0.020
 8N6  plan-2  H19  0.020
 8N6  plan-2  H20  0.020
 8N6  plan-2  C23  0.020
 8N6  plan-3  O4   0.020
 8N6  plan-3  C4   0.020
 8N6  plan-3  N3   0.020
 8N6  plan-3  C5   0.020
 8N6  plan-3  C2   0.020
 8N6  plan-3  H1   0.020
 8N6  plan-4  N3   0.020
 8N6  plan-4  S1   0.020
 8N6  plan-4  C2   0.020
 8N6  plan-4  O2   0.020

