# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 03:44:48 2022
#   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  26  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.413  13.7237  22.5465  -25.1380
 PKD  O1    O   OC    -1  -0.582  13.4426  21.5334  -25.7962
 PKD  O3    O   O      0  -0.600  12.9594  23.4344  -24.7181
 PKD  C11   C   CR6    0  -0.064  17.0698  20.8431  -27.3820
 PKD  C12   C   CR16   0  -0.278  18.1606  21.1187  -28.1996
 PKD  C13   C   CR16   0  -0.201  18.7936  20.1014  -28.8955
 PKD  C14   C   CR6    0  -0.041  18.3028  18.8079  -28.7943
 PKD  C16   C   CR16   0  -0.200  17.2008  18.5158  -28.0062
 PKD  C17   C   CR16   0  -0.261  16.5918  19.5395  -27.2972
 PKD  C4    C   CH1    0  -0.153  15.2054  22.7370  -24.7147
 PKD  C5    C   CH2    0  -0.608  15.3386  22.4705  -23.2091
 PKD  C7    C   CH2    0  -0.403  16.7858  20.8775  -24.5168
 PKD  N8    N   NT     0  -0.453  16.1123  21.8182  -25.3843
 PKD  O10   O   O      0  -0.478  15.9823  22.9363  -27.3411
 PKD  S6    S   S2     0  -0.009  17.0050  21.7935  -22.9660
 PKD  CL15  CL  CL     0  -0.121  19.0784  17.5343  -29.6734
 PKD  H2    H   HCR6   0   0.270  18.5328  22.1312  -28.2878
 PKD  H3    H   HCR6   0   0.282  19.6534  20.3160  -29.5155
 PKD  H4    H   HCR6   0   0.283  16.8168  17.5066  -27.9459
 PKD  H5    H   HCR6   0   0.274  15.7229  19.3141  -26.6912
 PKD  H6    H   HCH1   0   0.257  15.5172  23.7636  -24.9220
 PKD  H7    H   HCH2   0   0.294  15.2171  23.3795  -22.6247
 PKD  H8    H   HCH2   0   0.278  14.6086  21.7371  -22.8623
 PKD  H9    H   HCH2   0   0.277  16.1848  19.9848  -24.3292
 PKD  H10   H   HCH2   0   0.297  17.7557  20.5776  -24.9074
 PKD  C9    C   C      0   0.527  16.3491  21.9611  -26.7003

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    1.731  0.020  1.731
 PKD  C14   C16  aromatic  1.386  0.020  1.386
 PKD  C14   C13  aromatic  1.387  0.020  1.387
 PKD  C16   C17  aromatic  1.386  0.020  1.386
 PKD  C13   C12  aromatic  1.386  0.020  1.386
 PKD  C17   C11  aromatic  1.391  0.020  1.391
 PKD  C12   C11  aromatic  1.391  0.020  1.391
 PKD  C11   C9   single    1.495  0.020  1.495
 PKD  O10   C9   double    1.223  0.020  1.223
 PKD  C9    N8   single    1.345  0.020  1.345
 PKD  O3    C2   deloc     1.244  0.020  1.244
 PKD  N8    C4   single    1.454  0.020  1.454
 PKD  N8    C7   single    1.446  0.020  1.446
 PKD  C2    C4   single    1.553  0.020  1.553
 PKD  C2    O1   deloc     1.240  0.020  1.240
 PKD  C4    C5   single    1.535  0.020  1.535
 PKD  C7    S6   single    1.814  0.020  1.814
 PKD  C5    S6   single    1.815  0.020  1.815
 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   113.99  3.000
 PKD  C4    C2   O1   117.46  3.000
 PKD  O3    C2   O1   128.50  3.000
 PKD  C9    C11  C17  120.49  3.000
 PKD  C9    C11  C12  119.88  3.000
 PKD  C17   C11  C12  119.41  3.000
 PKD  H2    C12  C13  119.26  3.000
 PKD  H2    C12  C11  120.19  3.000
 PKD  C13   C12  C11  120.54  3.000
 PKD  H3    C13  C14  120.54  3.000
 PKD  H3    C13  C12  120.36  3.000
 PKD  C14   C13  C12  119.10  3.000
 PKD  CL15  C14  C16  119.35  3.000
 PKD  C16   C14  C13  121.28  3.000
 PKD  CL15  C14  C13  119.37  3.000
 PKD  H4    C16  C17  120.30  3.000
 PKD  H4    C16  C14  120.71  3.000
 PKD  C17   C16  C14  118.99  3.000
 PKD  H5    C17  C16  119.01  3.000
 PKD  H5    C17  C11  120.32  3.000
 PKD  C16   C17  C11  120.65  3.000
 PKD  H6    C4   N8   109.16  3.000
 PKD  H6    C4   C5   108.94  3.000
 PKD  N8    C4   C5   106.73  3.000
 PKD  H6    C4   C2   109.63  3.000
 PKD  C5    C4   C2   109.20  3.000
 PKD  N8    C4   C2   113.08  3.000
 PKD  H8    C5   H7   108.44  3.000
 PKD  H8    C5   S6   108.72  3.000
 PKD  H7    C5   S6   110.02  3.000
 PKD  H8    C5   C4   111.74  3.000
 PKD  H7    C5   C4   111.85  3.000
 PKD  S6    C5   C4   106.01  3.000
 PKD  H10   C7   H9   109.08  3.000
 PKD  H10   C7   S6   109.78  3.000
 PKD  H9    C7   S6   109.40  3.000
 PKD  H10   C7   N8   112.29  3.000
 PKD  H9    C7   N8   112.23  3.000
 PKD  S6    C7   N8   103.92  3.000
 PKD  C9    N8   C7   125.04  3.000
 PKD  C7    N8   C4   115.16  3.000
 PKD  C9    N8   C4   119.55  3.000
 PKD  C7    S6   C5    87.88  3.000
 PKD  O10   C9   N8   123.00  3.000
 PKD  N8    C9   C11  116.86  3.000
 PKD  O10   C9   C11  120.13  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_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  Var_01    S6    C7   N8   C4    -32.68  30.0  1
 PKD  Var_02    N8    C7   S6   C5     40.12  30.0  1
 PKD  Var_03    N8    C9   C11  C12  -131.19  30.0  2
 PKD  Var_04    H7    C5   S6   C7   -159.68  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

