# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 08:56:33 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: (3R,4R)-3-[4-(2-chlorophenyl)piperazin-1-yl]-4-hydroxy-1lambda~6~-thiolane-1,1-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[S](=O)(=O)C[C@@H]1N2CCN(CC2)c3ccccc3Cl
#
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
 PZJ  PZJ  (3R,4R)-3-[4-(2-chlorophenyl)piperazin-1-yl]-4-hydroxy-1lambda~6~-thiolane-1,1-dione  ligand  40  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PZJ
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
 PZJ  C13   C   CH1   0   0.073  -0.9841   8.9850   9.3014
 PZJ  C15   C   CR6   0   0.384   2.9273   4.4427   9.7579
 PZJ  C17   C   CR16  0  -0.249   5.3336   4.7694   9.6621
 PZJ  C20   C   CR6   0  -0.096   3.1689   3.1282  10.1670
 PZJ  C01   C   CH2   0  -0.250  -0.1250   5.5708   8.0707
 PZJ  C02   C   CH2   0  -0.347   0.6860   4.4298   8.6915
 PZJ  C04   C   CH2   0  -0.243   1.0658   5.6418  10.7642
 PZJ  C05   C   CH2   0  -0.368  -0.3283   6.1519  10.4017
 PZJ  C07   C   CH1   0  -0.138  -1.2817   7.6215   8.6629
 PZJ  C08   C   CH2   0  -0.636  -2.7546   7.3118   8.9792
 PZJ  C12   C   CH2   0  -0.637  -2.0723   9.9184   8.7905
 PZJ  C16   C   CR16  0  -0.289   4.0414   5.2486   9.5186
 PZJ  C18   C   CR16  0  -0.269   5.5411   3.4501  10.0410
 PZJ  C19   C   CR16  0  -0.224   4.4561   2.6250  10.2935
 PZJ  N03   N   NT    0  -0.516   1.6517   5.0023   9.6006
 PZJ  N06   N   NT    0  -0.438  -0.2978   6.6484   9.0400
 PZJ  O14   O   OH1   0  -0.656   0.2830   9.4498   8.9483
 PZJ  S09   S   S     0   1.224  -3.5787   8.9187   8.8683
 PZJ  CL21  CL  CL    0  -0.119   1.8370   2.0879  10.5564
 PZJ  H1    H   HCH1  0   0.227  -1.0873   8.9008  10.3934
 PZJ  H3    H   HCR6  0   0.261   6.1761   5.4189   9.4649
 PZJ  H4    H   HCH2  0   0.235   0.3929   5.9711   7.1955
 PZJ  H5    H   HCH2  0   0.210  -1.0851   5.1634   7.7243
 PZJ  H6    H   HCH2  0   0.217   0.0116   3.7126   9.1755
 PZJ  H7    H   HCH2  0   0.262   1.2033   3.8864   7.9009
 PZJ  H8    H   HCH2  0   0.231   1.6967   6.4818  11.0685
 PZJ  H9    H   HCH2  0   0.209   0.9833   4.9650  11.6261
 PZJ  H10   H   HCH2  0   0.231  -1.0772   5.3589  10.5401
 PZJ  H11   H   HCH2  0   0.268  -0.5968   6.9481  11.0968
 PZJ  H12   H   HCH1  0   0.282  -1.1919   7.7587   7.5791
 PZJ  H14   H   HCH2  0   0.323  -3.2275   6.6239   8.2804
 PZJ  H15   H   HCH2  0   0.309  -2.8943   6.9498   9.9985
 PZJ  H16   H   HCH2  0   0.325  -2.2202  10.8171   9.3878
 PZJ  H17   H   HCH2  0   0.311  -1.8971  10.1856   7.7472
 PZJ  H18   H   HCR6  0   0.261   3.8657   6.2699   9.2046
 PZJ  H19   H   HCR6  0   0.267   6.5443   3.0591  10.1457
 PZJ  H20   H   HCR6  0   0.278   4.6091   1.5988  10.6000
 PZJ  H22   H   HOH1  0   0.446   0.8667   8.6783   8.9917
 PZJ  O10   O   OS    0  -0.681  -4.2876   9.1939  10.1166
 PZJ  O11   O   OS    0  -0.679  -4.3158   9.0339   7.6122

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
 PZJ  C13  C12   single    1.522  0.020  1.522
 PZJ  C13  O14   single    1.395  0.020  1.395
 PZJ  C15  C20   aromatic  1.398  0.020  1.398
 PZJ  C15  C16   aromatic  1.396  0.020  1.396
 PZJ  C15  N03   single    1.402  0.020  1.402
 PZJ  C17  C16   aromatic  1.386  0.020  1.386
 PZJ  C17  C18   aromatic  1.388  0.020  1.388
 PZJ  C20  C19   aromatic  1.388  0.020  1.388
 PZJ  C20  CL21  single    1.734  0.020  1.734
 PZJ  C01  C02   single    1.531  0.020  1.531
 PZJ  C01  N06   single    1.460  0.020  1.460
 PZJ  C02  N03   single    1.445  0.020  1.445
 PZJ  C04  C05   single    1.528  0.020  1.528
 PZJ  C04  N03   single    1.451  0.020  1.451
 PZJ  C05  N06   single    1.450  0.020  1.450
 PZJ  C07  C08   single    1.538  0.020  1.538
 PZJ  C07  N06   single    1.434  0.020  1.434
 PZJ  C08  S09   single    1.809  0.020  1.809
 PZJ  C12  S09   single    1.810  0.020  1.810
 PZJ  C18  C19   aromatic  1.386  0.020  1.386
 PZJ  O10  S09   double    1.462  0.020  1.462
 PZJ  O11  S09   double    1.461  0.020  1.461
 PZJ  C13  H1    single    0.970  0.020  1.090
 PZJ  C17  H3    single    0.930  0.020  1.080
 PZJ  C01  H4    single    0.970  0.020  1.090
 PZJ  C01  H5    single    0.970  0.020  1.090
 PZJ  C02  H6    single    0.970  0.020  1.090
 PZJ  C02  H7    single    0.970  0.020  1.090
 PZJ  C04  H8    single    0.970  0.020  1.090
 PZJ  C04  H9    single    0.970  0.020  1.090
 PZJ  C05  H10   single    0.970  0.020  1.090
 PZJ  C05  H11   single    0.970  0.020  1.090
 PZJ  C07  H12   single    0.970  0.020  1.090
 PZJ  C08  H14   single    0.970  0.020  1.090
 PZJ  C08  H15   single    0.970  0.020  1.090
 PZJ  C12  H16   single    0.970  0.020  1.090
 PZJ  C12  H17   single    0.970  0.020  1.090
 PZJ  C16  H18   single    0.930  0.020  1.080
 PZJ  C18  H19   single    0.930  0.020  1.080
 PZJ  C19  H20   single    0.930  0.020  1.080
 PZJ  O14  H22   single    0.850  0.020  0.980
 PZJ  C13  C07   single    1.535  0.020  1.535

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
 PZJ  H1    C13  O14  111.23  3.000
 PZJ  H1    C13  C12  108.24  3.000
 PZJ  O14   C13  C12  111.11  3.000
 PZJ  H1    C13  C07  109.07  3.000
 PZJ  O14   C13  C07  111.52  3.000
 PZJ  C12   C13  C07  105.45  3.000
 PZJ  N03   C15  C16  118.46  3.000
 PZJ  N03   C15  C20  124.44  3.000
 PZJ  C16   C15  C20  117.09  3.000
 PZJ  H3    C17  C18  120.26  3.000
 PZJ  H3    C17  C16  119.98  3.000
 PZJ  C18   C17  C16  119.76  3.000
 PZJ  CL21  C20  C19  118.32  3.000
 PZJ  CL21  C20  C15  119.81  3.000
 PZJ  C19   C20  C15  121.87  3.000
 PZJ  H5    C01  H4   107.29  3.000
 PZJ  H5    C01  N06  112.31  3.000
 PZJ  H4    C01  N06  108.52  3.000
 PZJ  H5    C01  C02  108.31  3.000
 PZJ  H4    C01  C02  110.28  3.000
 PZJ  N06   C01  C02  110.10  3.000
 PZJ  H7    C02  H6   106.61  3.000
 PZJ  H7    C02  N03  109.68  3.000
 PZJ  H6    C02  N03  113.10  3.000
 PZJ  H7    C02  C01  109.19  3.000
 PZJ  H6    C02  C01  109.90  3.000
 PZJ  N03   C02  C01  108.29  3.000
 PZJ  H9    C04  H8   107.34  3.000
 PZJ  H9    C04  N03  112.82  3.000
 PZJ  H8    C04  N03  109.18  3.000
 PZJ  H9    C04  C05  108.85  3.000
 PZJ  H8    C04  C05  109.62  3.000
 PZJ  N03   C04  C05  108.98  3.000
 PZJ  H11   C05  H10  106.18  3.000
 PZJ  H11   C05  N06  110.72  3.000
 PZJ  H10   C05  N06  112.31  3.000
 PZJ  H11   C05  C04  108.49  3.000
 PZJ  H10   C05  C04  110.53  3.000
 PZJ  N06   C05  C04  108.54  3.000
 PZJ  H12   C07  N06  106.78  3.000
 PZJ  H12   C07  C08  107.88  3.000
 PZJ  N06   C07  C08  117.79  3.000
 PZJ  H12   C07  C13  106.51  3.000
 PZJ  N06   C07  C13  111.12  3.000
 PZJ  C08   C07  C13  106.21  3.000
 PZJ  H15   C08  H14  109.54  3.000
 PZJ  H15   C08  S09  107.08  3.000
 PZJ  H14   C08  S09  108.90  3.000
 PZJ  H15   C08  C07  112.44  3.000
 PZJ  H14   C08  C07  114.28  3.000
 PZJ  S09   C08  C07  104.17  3.000
 PZJ  H17   C12  H16  110.12  3.000
 PZJ  H17   C12  S09  108.06  3.000
 PZJ  H16   C12  S09  108.62  3.000
 PZJ  H17   C12  C13  110.88  3.000
 PZJ  H16   C12  C13  114.77  3.000
 PZJ  S09   C12  C13  104.00  3.000
 PZJ  H18   C16  C17  120.50  3.000
 PZJ  H18   C16  C15  117.70  3.000
 PZJ  C17   C16  C15  121.80  3.000
 PZJ  H19   C18  C19  119.55  3.000
 PZJ  H19   C18  C17  120.56  3.000
 PZJ  C19   C18  C17  119.89  3.000
 PZJ  H20   C19  C18  120.36  3.000
 PZJ  H20   C19  C20  120.06  3.000
 PZJ  C18   C19  C20  119.58  3.000
 PZJ  C04   N03  C02  114.16  3.000
 PZJ  C04   N03  C15  116.96  3.000
 PZJ  C02   N03  C15  121.38  3.000
 PZJ  C07   N06  C05  117.70  3.000
 PZJ  C07   N06  C01  114.05  3.000
 PZJ  C05   N06  C01  111.92  3.000
 PZJ  H22   O14  C13  105.70  3.000
 PZJ  O11   S09  O10  118.34  3.000
 PZJ  O11   S09  C12  109.84  3.000
 PZJ  O10   S09  C12  109.65  3.000
 PZJ  O11   S09  C08  110.65  3.000
 PZJ  O10   S09  C08  109.62  3.000
 PZJ  C12   S09  C08   96.55  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
 PZJ  CONST_01  C18   C19  C20  C15     0.00   0.0  0
 PZJ  CONST_02  C18   C17  C16  C15     0.00   0.0  0
 PZJ  CONST_03  C20   C15  C16  C17     0.00   0.0  0
 PZJ  CONST_04  C20   C19  C18  C17     0.00   0.0  0
 PZJ  CONST_05  C19   C20  C15  C16     0.00   0.0  0
 PZJ  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 PZJ  CONST_07  N03   C15  C16  C17   180.00   0.0  0
 PZJ  CONST_08  N03   C15  C20  C19   180.00   0.0  0
 PZJ  CONST_09  CL21  C20  C15  C16   180.00   0.0  0
 PZJ  CONST_10  CL21  C20  C19  C18   180.00   0.0  0
 PZJ  CONST_11  CL21  C20  C15  N03     0.00   0.0  0
 PZJ  CONST_12  H20   C19  C20  C15   180.00   0.0  0
 PZJ  CONST_13  H3    C17  C16  C15   180.00   0.0  0
 PZJ  CONST_14  H18   C16  C15  C20   180.00   0.0  0
 PZJ  CONST_15  H19   C18  C19  C20   180.00   0.0  0
 PZJ  Var_01    C08   S09  C12  C13   -17.66  30.0  1
 PZJ  Var_02    C01   C02  N03  C15  -144.68  30.0  1
 PZJ  Var_03    C05   C04  N03  C15  -178.54  30.0  1
 PZJ  Var_04    C02   N03  C15  C20   -58.54  30.0  2
 PZJ  Var_05    C04   C05  N06  C01    68.97  30.0  1
 PZJ  Var_06    C05   N06  C01  C02   -30.18  30.0  1
 PZJ  Var_07    C12   S09  C08  C07   -11.10  30.0  1
 PZJ  Var_08    N06   C01  C02  N03   -34.01  30.0  1
 PZJ  Var_09    N06   C05  C04  N03   -37.21  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
 PZJ  chir_01  C13  C12  O14  C07  positiv
 PZJ  chir_02  C07  N06  C13  C08  positiv

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
 PZJ  plan-1  C15   0.020
 PZJ  plan-1  C17   0.020
 PZJ  plan-1  C20   0.020
 PZJ  plan-1  C16   0.020
 PZJ  plan-1  C18   0.020
 PZJ  plan-1  C19   0.020
 PZJ  plan-1  N03   0.020
 PZJ  plan-1  CL21  0.020
 PZJ  plan-1  H3    0.020
 PZJ  plan-1  H18   0.020
 PZJ  plan-1  H19   0.020
 PZJ  plan-1  H20   0.020

