# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:29:36 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2~{R})-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
 E9N  E9N  '(2~{R})-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 PERFECT
;

data_comp_E9N
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
 E9N  CAJ  C  C      0   0.444   2.9200   1.7548  -0.0861
 E9N  OAL  O  OC    -1  -0.760   3.2440   2.4630  -1.0614
 E9N  CAK  C  CH2    0  -0.568   2.9273   0.2290  -0.3000
 E9N  CAM  C  CH1    0  -0.441   1.7744  -0.5092   0.3741
 E9N  CAN  C  C      0   0.423   2.0209  -2.0366   0.3993
 E9N  OAP  O  O      0  -0.519   2.9670  -2.3861   1.1355
 E9N  OAO  O  OC    -1  -0.695   1.3001  -2.7789  -0.2887
 E9N  SAQ  S  S2     0  -0.025   0.2447  -0.0023  -0.4624
 E9N  CAR  C  CH2    0  -0.717  -1.0089  -0.7443   0.6253
 E9N  CAW  C  CR6    0   0.346  -2.3609  -0.2270   0.2393
 E9N  CAV  C  CR16   0  -0.365  -3.1655  -0.9365  -0.6474
 E9N  CAU  C  CR16   0  -0.200  -4.4145  -0.4511  -1.0200
 E9N  CAT  C  CR16   0  -0.319  -4.8691   0.7589  -0.5129
 E9N  CAS  C  CR16   0  -0.149  -4.0690   1.4793   0.3664
 E9N  CAX  C  CR16   0  -0.381  -2.8242   0.9906   0.7354
 E9N  H2   H  HCH2   0   0.283   2.9581  -0.0089  -1.3675
 E9N  H3   H  HCH1   0   0.272   1.7111  -0.1531   1.4060
 E9N  H5   H  HCH2   0   0.238  -0.9606  -1.8284   0.5320
 E9N  H6   H  HCH2   0   0.279  -0.7750  -0.4784   1.6584
 E9N  H7   H  HCR6   0   0.246  -2.8184  -1.8828  -1.0453
 E9N  H8   H  HCR6   0   0.259  -5.0296  -1.0182  -1.7066
 E9N  H9   H  HCR6   0   0.219  -5.8415   1.1383  -0.7992
 E9N  H10  H  HCR6   0   0.266  -4.4159   2.4233   0.7668
 E9N  H11  H  HCR6   0   0.231  -2.2044   1.5559   1.4214
 E9N  O1   O  O      0  -0.617   2.6325   2.1590   1.0579
 E9N  H12  H  HCH2   0   0.248   3.8561  -0.1614   0.1290

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
 E9N  CAT  CAS  aromatic  1.390  0.020  1.390
 E9N  CAT  CAU  aromatic  1.388  0.020  1.388
 E9N  CAS  CAX  aromatic  1.387  0.020  1.387
 E9N  CAU  CAV  aromatic  1.391  0.020  1.391
 E9N  CAX  CAW  aromatic  1.394  0.020  1.394
 E9N  OAP  CAN  deloc     1.249  0.020  1.249
 E9N  CAV  CAW  aromatic  1.392  0.020  1.392
 E9N  CAW  CAR  single    1.498  0.020  1.498
 E9N  CAN  CAM  single    1.547  0.020  1.547
 E9N  CAN  OAO  deloc     1.243  0.020  1.243
 E9N  CAM  SAQ  single    1.816  0.020  1.816
 E9N  CAM  CAK  single    1.526  0.020  1.526
 E9N  CAR  SAQ  single    1.818  0.020  1.818
 E9N  CAK  CAJ  single    1.541  0.020  1.541
 E9N  OAL  CAJ  deloc     1.248  0.020  1.248
 E9N  CAK  H2   single    0.970  0.020  1.090
 E9N  CAM  H3   single    0.970  0.020  1.090
 E9N  CAR  H5   single    0.970  0.020  1.090
 E9N  CAR  H6   single    0.970  0.020  1.090
 E9N  CAV  H7   single    0.930  0.020  1.080
 E9N  CAU  H8   single    0.930  0.020  1.080
 E9N  CAT  H9   single    0.930  0.020  1.080
 E9N  CAS  H10  single    0.930  0.020  1.080
 E9N  CAX  H11  single    0.930  0.020  1.080
 E9N  CAJ  O1   deloc     1.247  0.020  1.247
 E9N  CAK  H12  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
 E9N  O1   CAJ  CAK  116.71  3.000
 E9N  O1   CAJ  OAL  126.36  3.000
 E9N  CAK  CAJ  OAL  116.89  3.000
 E9N  H12  CAK  H2   106.31  3.000
 E9N  H12  CAK  CAM  107.17  3.000
 E9N  H2   CAK  CAM  110.31  3.000
 E9N  H12  CAK  CAJ  107.62  3.000
 E9N  H2   CAK  CAJ  110.54  3.000
 E9N  CAM  CAK  CAJ  114.47  3.000
 E9N  H3   CAM  SAQ  107.16  3.000
 E9N  H3   CAM  CAN  108.38  3.000
 E9N  SAQ  CAM  CAN  114.67  3.000
 E9N  H3   CAM  CAK  107.64  3.000
 E9N  SAQ  CAM  CAK  107.33  3.000
 E9N  CAN  CAM  CAK  111.37  3.000
 E9N  OAO  CAN  OAP  126.78  3.000
 E9N  OAO  CAN  CAM  119.23  3.000
 E9N  OAP  CAN  CAM  113.99  3.000
 E9N  CAR  SAQ  CAM  101.03  3.000
 E9N  H6   CAR  H5   108.30  3.000
 E9N  H6   CAR  CAW  110.67  3.000
 E9N  H5   CAR  CAW  111.20  3.000
 E9N  H6   CAR  SAQ  108.60  3.000
 E9N  H5   CAR  SAQ  108.93  3.000
 E9N  CAW  CAR  SAQ  109.10  3.000
 E9N  CAX  CAW  CAV  118.68  3.000
 E9N  CAV  CAW  CAR  120.65  3.000
 E9N  CAX  CAW  CAR  120.65  3.000
 E9N  H7   CAV  CAU  119.61  3.000
 E9N  H7   CAV  CAW  119.60  3.000
 E9N  CAU  CAV  CAW  120.79  3.000
 E9N  H8   CAU  CAT  120.15  3.000
 E9N  H8   CAU  CAV  119.83  3.000
 E9N  CAT  CAU  CAV  120.02  3.000
 E9N  H9   CAT  CAS  120.18  3.000
 E9N  H9   CAT  CAU  120.20  3.000
 E9N  CAS  CAT  CAU  119.62  3.000
 E9N  H10  CAS  CAX  119.76  3.000
 E9N  H10  CAS  CAT  120.10  3.000
 E9N  CAX  CAS  CAT  120.14  3.000
 E9N  H11  CAX  CAS  119.85  3.000
 E9N  H11  CAX  CAW  119.40  3.000
 E9N  CAS  CAX  CAW  120.75  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
 E9N  CONST_01  CAT  CAS  CAX  CAW     0.00   0.0  0
 E9N  CONST_02  CAT  CAU  CAV  CAW     0.00   0.0  0
 E9N  CONST_03  CAS  CAT  CAU  CAV     0.00   0.0  0
 E9N  CONST_04  CAS  CAX  CAW  CAV     0.00   0.0  0
 E9N  CONST_05  CAX  CAS  CAT  CAU     0.00   0.0  0
 E9N  CONST_06  CAX  CAW  CAV  CAU     0.00   0.0  0
 E9N  CONST_07  CAS  CAX  CAW  CAR   180.00   0.0  0
 E9N  CONST_08  CAU  CAV  CAW  CAR   180.00   0.0  0
 E9N  CONST_09  H10  CAS  CAX  CAW   180.00   0.0  0
 E9N  CONST_10  H8   CAU  CAV  CAW   180.00   0.0  0
 E9N  CONST_11  H9   CAT  CAU  CAV   180.00   0.0  0
 E9N  CONST_12  H11  CAX  CAW  CAV   180.00   0.0  0
 E9N  CONST_13  H7   CAV  CAU  CAT   180.00   0.0  0
 E9N  Var_01    CAX  CAW  CAR  SAQ   -84.26  30.0  2
 E9N  Var_02    CAW  CAR  SAQ  CAM   169.79  30.0  1
 E9N  Var_03    CAM  CAK  CAJ  OAL  -140.73  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
 E9N  chir_01  CAM  CAN  SAQ  CAK  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
 E9N  plan-1  CAR  0.020
 E9N  plan-1  CAW  0.020
 E9N  plan-1  CAV  0.020
 E9N  plan-1  CAU  0.020
 E9N  plan-1  CAT  0.020
 E9N  plan-1  CAS  0.020
 E9N  plan-1  CAX  0.020
 E9N  plan-1  H7   0.020
 E9N  plan-1  H8   0.020
 E9N  plan-1  H9   0.020
 E9N  plan-1  H10  0.020
 E9N  plan-1  H11  0.020
 E9N  plan-2  CAJ  0.020
 E9N  plan-2  OAL  0.020
 E9N  plan-2  CAK  0.020
 E9N  plan-2  O1   0.020
 E9N  plan-3  CAM  0.020
 E9N  plan-3  CAN  0.020
 E9N  plan-3  OAP  0.020
 E9N  plan-3  OAO  0.020

