# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:06:47 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: (4S)-3-(4-chlorobenzene-1-carbonyl)-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CSCN1C(=O)c2ccc(Cl)cc2
#
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
 PKD  PKD  '(4S)-3-(4-chlorobenzene-1-carbonyl)-1,3-thiazolidine-4-carboxylic acid'  ligand  27  17  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PKD
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
 PKD  C2    C   C     0   0.540  13.8045  22.6014  -24.8475
 PKD  O1    O   OH1   0  -0.582  13.5029  21.3161  -24.7784
 PKD  O3    O   O     0  -0.432  12.9953  23.4911  -24.8983
 PKD  C11   C   CR6   0  -0.050  16.7956  20.6047  -27.3919
 PKD  C12   C   CR16  0  -0.274  18.1626  20.8383  -27.4998
 PKD  C13   C   CR16  0  -0.198  18.9708  19.9678  -28.2138
 PKD  C14   C   CR6   0  -0.039  18.3991  18.8542  -28.8100
 PKD  C16   C   CR16  0  -0.200  17.0381  18.6064  -28.7162
 PKD  C17   C   CR16  0  -0.275  16.2373  19.4951  -28.0165
 PKD  C4    C   CH1   0  -0.141  15.2986  22.8486  -24.7552
 PKD  C5    C   CH2   0  -0.619  15.7173  22.8872  -23.2746
 PKD  C7    C   CH2   0  -0.398  16.9559  21.0686  -24.4992
 PKD  N8    N   NT    0  -0.471  16.0933  21.8146  -25.3951
 PKD  O10   O   O     0  -0.469  15.0164  22.1580  -27.3282
 PKD  S6    S   S2    0   0.026  17.4222  22.2773  -23.2391
 PKD  CL15  CL  CL    0  -0.117  19.4025  17.7559  -29.6937
 PKD  H1    H   HOH1  0   0.488  12.5409  21.1961  -24.7924
 PKD  H2    H   HCR6  0   0.285  18.6103  21.7101  -27.0388
 PKD  H3    H   HCR6  0   0.288  20.0311  20.1590  -28.3033
 PKD  H4    H   HCR6  0   0.288  16.6031  17.7361  -29.1876
 PKD  H5    H   HCR6  0   0.276  15.1733  19.3082  -27.9519
 PKD  H6    H   HCH1  0   0.317  15.5078  23.8134  -25.2208
 PKD  H7    H   HCH2  0   0.319  15.6714  23.8988  -22.8781
 PKD  H8    H   HCH2  0   0.299  15.0906  22.2421  -22.6577
 PKD  H9    H   HCH2  0   0.296  16.4210  20.2328  -24.0436
 PKD  H10   H   HCH2  0   0.308  17.8441  20.6894  -24.9941
 PKD  C9    C   C     0   0.535  15.8978  21.5815  -26.7085

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
 PKD  CL15  C14  single    1.730  0.020  1.730
 PKD  C14   C16  aromatic  1.387  0.020  1.387
 PKD  C14   C13  aromatic  1.386  0.020  1.386
 PKD  C16   C17  aromatic  1.386  0.020  1.386
 PKD  C13   C12  aromatic  1.386  0.020  1.386
 PKD  C17   C11  aromatic  1.390  0.020  1.390
 PKD  C12   C11  aromatic  1.391  0.020  1.391
 PKD  C11   C9   single    1.492  0.020  1.492
 PKD  O10   C9   double    1.222  0.020  1.222
 PKD  C9    N8   single    1.348  0.020  1.348
 PKD  O3    C2   double    1.204  0.020  1.204
 PKD  N8    C4   single    1.453  0.020  1.453
 PKD  N8    C7   single    1.450  0.020  1.450
 PKD  C2    C4   single    1.517  0.020  1.517
 PKD  C2    O1   single    1.322  0.020  1.322
 PKD  C4    C5   single    1.539  0.020  1.539
 PKD  C7    S6   single    1.807  0.020  1.807
 PKD  C5    S6   single    1.811  0.020  1.811
 PKD  O1    H1   single    0.850  0.020  0.980
 PKD  C12   H2   single    0.930  0.020  1.080
 PKD  C13   H3   single    0.930  0.020  1.080
 PKD  C16   H4   single    0.930  0.020  1.080
 PKD  C17   H5   single    0.930  0.020  1.080
 PKD  C4    H6   single    0.970  0.020  1.090
 PKD  C5    H7   single    0.970  0.020  1.090
 PKD  C5    H8   single    0.970  0.020  1.090
 PKD  C7    H9   single    0.970  0.020  1.090
 PKD  C7    H10  single    0.970  0.020  1.090

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
 PKD  C4    C2   O3   122.96  3.000
 PKD  C4    C2   O1   112.33  3.000
 PKD  O3    C2   O1   124.57  3.000
 PKD  H1    O1   C2   110.24  3.000
 PKD  C9    C11  C17  119.12  3.000
 PKD  C9    C11  C12  121.12  3.000
 PKD  C17   C11  C12  119.59  3.000
 PKD  H2    C12  C13  118.94  3.000
 PKD  H2    C12  C11  120.56  3.000
 PKD  C13   C12  C11  120.50  3.000
 PKD  H3    C13  C14  120.72  3.000
 PKD  H3    C13  C12  120.23  3.000
 PKD  C14   C13  C12  119.05  3.000
 PKD  CL15  C14  C16  119.36  3.000
 PKD  C16   C14  C13  121.28  3.000
 PKD  CL15  C14  C13  119.36  3.000
 PKD  H4    C16  C17  120.25  3.000
 PKD  H4    C16  C14  120.62  3.000
 PKD  C17   C16  C14  119.13  3.000
 PKD  H5    C17  C16  119.17  3.000
 PKD  H5    C17  C11  120.39  3.000
 PKD  C16   C17  C11  120.44  3.000
 PKD  H6    C4   N8   109.66  3.000
 PKD  H6    C4   C5   109.63  3.000
 PKD  N8    C4   C5   107.02  3.000
 PKD  H6    C4   C2   107.87  3.000
 PKD  C5    C4   C2   109.30  3.000
 PKD  N8    C4   C2   113.32  3.000
 PKD  H8    C5   H7   108.65  3.000
 PKD  H8    C5   S6   109.31  3.000
 PKD  H7    C5   S6   110.24  3.000
 PKD  H8    C5   C4   111.90  3.000
 PKD  H7    C5   C4   111.26  3.000
 PKD  S6    C5   C4   105.46  3.000
 PKD  H10   C7   H9   108.89  3.000
 PKD  H10   C7   S6   109.90  3.000
 PKD  H9    C7   S6   110.33  3.000
 PKD  H10   C7   N8   112.63  3.000
 PKD  H9    C7   N8   111.11  3.000
 PKD  S6    C7   N8   103.90  3.000
 PKD  C9    N8   C7   126.81  3.000
 PKD  C7    N8   C4   114.80  3.000
 PKD  C9    N8   C4   118.22  3.000
 PKD  C7    S6   C5    88.20  3.000
 PKD  O10   C9   N8   121.14  3.000
 PKD  N8    C9   C11  118.17  3.000
 PKD  O10   C9   C11  120.69  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
 PKD  CONST_01  C14   C16  C17  C11     0.00   0.0  0
 PKD  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 PKD  CONST_03  C16   C14  C13  C12     0.00   0.0  0
 PKD  CONST_04  C16   C17  C11  C12     0.00   0.0  0
 PKD  CONST_05  C17   C16  C14  C13     0.00   0.0  0
 PKD  CONST_06  C17   C11  C12  C13     0.00   0.0  0
 PKD  CONST_07  CL15  C14  C13  C12   180.00   0.0  0
 PKD  CONST_08  C9    C11  C12  C13   180.00   0.0  0
 PKD  CONST_09  C9    C11  C17  C16   180.00   0.0  0
 PKD  CONST_10  CL15  C14  C16  C17   180.00   0.0  0
 PKD  CONST_11  C4    N8   C9   C11   180.00   0.0  0
 PKD  CONST_12  C7    N8   C9   C11     0.00   0.0  0
 PKD  CONST_13  H4    C16  C17  C11   180.00   0.0  0
 PKD  CONST_14  H3    C13  C12  C11   180.00   0.0  0
 PKD  CONST_15  H5    C17  C11  C12   180.00   0.0  0
 PKD  CONST_16  H2    C12  C13  C14   180.00   0.0  0
 PKD  CONST_17  O10   C9   N8   C4      0.00   0.0  0
 PKD  CONST_18  O10   C9   N8   C7    180.00   0.0  0
 PKD  CONST_19  H1    O1   C2   C4    180.00   0.0  0
 PKD  Var_01    S6    C7   N8   C4    -32.55  30.0  1
 PKD  Var_02    N8    C7   S6   C5     40.50  30.0  1
 PKD  Var_03    N8    C9   C11  C12   -63.23  30.0  2
 PKD  Var_04    H7    C5   S6   C7   -159.13  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
 PKD  chir_01  C4  N8  C2  C5  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
 PKD  plan-1  C11   0.020
 PKD  plan-1  C12   0.020
 PKD  plan-1  C13   0.020
 PKD  plan-1  C14   0.020
 PKD  plan-1  C16   0.020
 PKD  plan-1  C17   0.020
 PKD  plan-1  CL15  0.020
 PKD  plan-1  H2    0.020
 PKD  plan-1  H3    0.020
 PKD  plan-1  H4    0.020
 PKD  plan-1  H5    0.020
 PKD  plan-1  C9    0.020
 PKD  plan-2  C11   0.020
 PKD  plan-2  C4    0.020
 PKD  plan-2  C7    0.020
 PKD  plan-2  N8    0.020
 PKD  plan-2  O10   0.020
 PKD  plan-2  C9    0.020
 PKD  plan-3  C2    0.020
 PKD  plan-3  O1    0.020
 PKD  plan-3  O3    0.020
 PKD  plan-3  C4    0.020
 PKD  plan-3  H1    0.020

