# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:52:59 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2~{S})-2-(phenylmethylsulfanyl)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](SCc1ccccc1)C(O)=O
#
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
 DZK  DZK  '(2~{S})-2-(phenylmethylsulfanyl)butanedioic acid'  ligand  26  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DZK
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
 DZK  CAJ  C  C      0   0.406  -2.8642   1.7769  -0.0488
 DZK  OAL  O  O      0  -0.613  -2.5959   2.1217   1.1198
 DZK  CAK  C  CH2    0  -0.561  -2.8973   0.2656  -0.3411
 DZK  CAM  C  CH1    0  -0.452  -1.8013  -0.5296   0.3473
 DZK  CAN  C  C      0   0.443  -1.9395  -2.0585   0.2283
 DZK  OAP  O  O      0  -0.614  -1.4920  -2.7253   1.1847
 DZK  OAO  O  OC    -1  -0.607  -2.4585  -2.5099  -0.8107
 DZK  SAQ  S  S2     0  -0.039  -0.2161  -0.0225  -0.4134
 DZK  CAR  C  CH2    0  -0.614   1.0042  -0.7000   0.7573
 DZK  CAW  C  CR6    0   0.114   2.3600  -0.2112   0.3472
 DZK  CAV  C  CR16   0  -0.291   2.8500   1.0032   0.8232
 DZK  CAU  C  CR16   0  -0.242   4.0948   1.4706   0.4257
 DZK  CAT  C  CR16   0  -0.269   4.8647   0.7319  -0.4642
 DZK  CAS  C  CR16   0  -0.243   4.3817  -0.4759  -0.9509
 DZK  CAX  C  CR16   0  -0.292   3.1372  -0.9421  -0.5479
 DZK  H2   H  HCH2   0   0.236  -3.8615  -0.1168   0.0164
 DZK  H3   H  HCH2   0   0.209  -2.8849   0.0822  -1.4171
 DZK  H4   H  HCH1   0   0.246  -1.7486  -0.2377   1.3977
 DZK  H6   H  HCH2   0   0.269   0.7528  -0.3578   1.7625
 DZK  H7   H  HCH2   0   0.274   0.9573  -1.7879   0.7499
 DZK  H8   H  HCR6   0   0.251   2.2521   1.5836   1.5161
 DZK  H9   H  HCR6   0   0.254   4.4637   2.4122   0.8118
 DZK  H10  H  HCR6   0   0.254   5.8361   1.0940  -0.7752
 DZK  H11  H  HCR6   0   0.255   4.9752  -1.0573  -1.6448
 DZK  H12  H  HCR6   0   0.251   2.7679  -1.8862  -0.9309
 DZK  O1   O  OC    -1  -0.625  -3.1518   2.5394  -0.9949

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
 DZK  CAT  CAS  aromatic  1.389  0.020  1.389
 DZK  CAT  CAU  aromatic  1.389  0.020  1.389
 DZK  CAS  CAX  aromatic  1.389  0.020  1.389
 DZK  CAU  CAV  aromatic  1.388  0.020  1.388
 DZK  CAX  CAW  aromatic  1.393  0.020  1.393
 DZK  CAV  CAW  aromatic  1.393  0.020  1.393
 DZK  OAP  CAN  deloc     1.249  0.020  1.249
 DZK  CAW  CAR  single    1.498  0.020  1.498
 DZK  OAO  CAN  deloc     1.246  0.020  1.246
 DZK  CAN  CAM  single    1.540  0.020  1.540
 DZK  CAR  SAQ  single    1.822  0.020  1.822
 DZK  SAQ  CAM  single    1.830  0.020  1.830
 DZK  CAM  CAK  single    1.519  0.020  1.519
 DZK  CAK  CAJ  single    1.540  0.020  1.540
 DZK  OAL  CAJ  deloc     1.248  0.020  1.248
 DZK  CAK  H2   single    0.970  0.020  1.090
 DZK  CAK  H3   single    0.970  0.020  1.090
 DZK  CAM  H4   single    0.970  0.020  1.090
 DZK  CAR  H6   single    0.970  0.020  1.090
 DZK  CAR  H7   single    0.970  0.020  1.090
 DZK  CAV  H8   single    0.930  0.020  1.080
 DZK  CAU  H9   single    0.930  0.020  1.080
 DZK  CAT  H10  single    0.930  0.020  1.080
 DZK  CAS  H11  single    0.930  0.020  1.080
 DZK  CAX  H12  single    0.930  0.020  1.080
 DZK  CAJ  O1   deloc     1.249  0.020  1.249

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
 DZK  O1   CAJ  CAK  116.78  3.000
 DZK  O1   CAJ  OAL  126.19  3.000
 DZK  CAK  CAJ  OAL  116.98  3.000
 DZK  H3   CAK  H2   105.82  3.000
 DZK  H3   CAK  CAM  110.52  3.000
 DZK  H2   CAK  CAM  107.69  3.000
 DZK  H3   CAK  CAJ  110.60  3.000
 DZK  H2   CAK  CAJ  107.41  3.000
 DZK  CAM  CAK  CAJ  114.35  3.000
 DZK  H4   CAM  SAQ  106.51  3.000
 DZK  H4   CAM  CAN  110.14  3.000
 DZK  SAQ  CAM  CAN  108.71  3.000
 DZK  H4   CAM  CAK  109.33  3.000
 DZK  SAQ  CAM  CAK  106.95  3.000
 DZK  CAN  CAM  CAK  114.83  3.000
 DZK  OAO  CAN  OAP  126.47  3.000
 DZK  OAO  CAN  CAM  117.49  3.000
 DZK  OAP  CAN  CAM  116.03  3.000
 DZK  CAR  SAQ  CAM  102.13  3.000
 DZK  H7   CAR  H6   108.03  3.000
 DZK  H7   CAR  CAW  111.28  3.000
 DZK  H6   CAR  CAW  110.99  3.000
 DZK  H7   CAR  SAQ  109.78  3.000
 DZK  H6   CAR  SAQ  108.73  3.000
 DZK  CAW  CAR  SAQ  108.00  3.000
 DZK  CAX  CAW  CAV  118.73  3.000
 DZK  CAV  CAW  CAR  120.60  3.000
 DZK  CAX  CAW  CAR  120.64  3.000
 DZK  H8   CAV  CAU  119.84  3.000
 DZK  H8   CAV  CAW  119.42  3.000
 DZK  CAU  CAV  CAW  120.74  3.000
 DZK  H9   CAU  CAT  120.14  3.000
 DZK  H9   CAU  CAV  119.77  3.000
 DZK  CAT  CAU  CAV  120.09  3.000
 DZK  H10  CAT  CAS  120.15  3.000
 DZK  H10  CAT  CAU  120.23  3.000
 DZK  CAS  CAT  CAU  119.61  3.000
 DZK  H11  CAS  CAX  119.81  3.000
 DZK  H11  CAS  CAT  120.07  3.000
 DZK  CAX  CAS  CAT  120.13  3.000
 DZK  H12  CAX  CAS  119.69  3.000
 DZK  H12  CAX  CAW  119.61  3.000
 DZK  CAS  CAX  CAW  120.70  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
 DZK  CONST_01  CAT  CAS  CAX  CAW     0.00   0.0  0
 DZK  CONST_02  CAT  CAU  CAV  CAW     0.00   0.0  0
 DZK  CONST_03  CAS  CAT  CAU  CAV     0.00   0.0  0
 DZK  CONST_04  CAS  CAX  CAW  CAV     0.00   0.0  0
 DZK  CONST_05  CAX  CAS  CAT  CAU     0.00   0.0  0
 DZK  CONST_06  CAX  CAW  CAV  CAU     0.00   0.0  0
 DZK  CONST_07  CAS  CAX  CAW  CAR   180.00   0.0  0
 DZK  CONST_08  CAU  CAV  CAW  CAR   180.00   0.0  0
 DZK  CONST_09  H11  CAS  CAX  CAW   180.00   0.0  0
 DZK  CONST_10  H9   CAU  CAV  CAW   180.00   0.0  0
 DZK  CONST_11  H10  CAT  CAU  CAV   180.00   0.0  0
 DZK  CONST_12  H12  CAX  CAW  CAV   180.00   0.0  0
 DZK  CONST_13  H8   CAV  CAU  CAT   180.00   0.0  0
 DZK  Var_01    CAX  CAW  CAR  SAQ   -89.89  30.0  2
 DZK  Var_02    CAW  CAR  SAQ  CAM  -173.07  30.0  1
 DZK  Var_03    CAM  CAK  CAJ  OAL   -39.98  30.0  2

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
 DZK  chir_01  CAM  CAN  SAQ  CAK  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
 DZK  plan-1  CAR  0.020
 DZK  plan-1  CAW  0.020
 DZK  plan-1  CAV  0.020
 DZK  plan-1  CAU  0.020
 DZK  plan-1  CAT  0.020
 DZK  plan-1  CAS  0.020
 DZK  plan-1  CAX  0.020
 DZK  plan-1  H8   0.020
 DZK  plan-1  H9   0.020
 DZK  plan-1  H10  0.020
 DZK  plan-1  H11  0.020
 DZK  plan-1  H12  0.020
 DZK  plan-2  CAJ  0.020
 DZK  plan-2  OAL  0.020
 DZK  plan-2  CAK  0.020
 DZK  plan-2  O1   0.020
 DZK  plan-3  CAM  0.020
 DZK  plan-3  CAN  0.020
 DZK  plan-3  OAP  0.020
 DZK  plan-3  OAO  0.020

