# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:30:37 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-(carboxymethylsulfanyl)-2-oxo-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSCC(=O)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
 XYN  XYN  '3-(carboxymethylsulfanyl)-2-oxo-propanoic acid'  ligand  15  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XYN
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
 XYN  OBA   O  O      0  -0.596   3.5560   1.0722  -0.0396
 XYN  OBB   O  O      0  -0.576  -3.1911  -1.6483   0.0616
 XYN  OBC   O  O      0  -0.384  -1.8463   1.5455   0.0602
 XYN  OBD   O  OC    -1  -0.615   4.4149  -0.9899  -0.0175
 XYN  OBE   O  OC    -1  -0.578  -4.2688   0.3116  -0.0601
 XYN  CBF   C  CH2    0  -0.681   2.0650  -0.7781   0.0203
 XYN  CBG   C  CH2    0  -0.654  -0.6592  -0.5080   0.0536
 XYN  SBH   S  S2     0  -0.028   0.8213   0.5329   0.0319
 XYN  CBI   C  C      0   0.429   3.4792  -0.1691  -0.0154
 XYN  CBJ   C  C      0   0.349  -3.2659  -0.4094   0.0114
 XYN  CBK   C  C      0   0.248  -1.9020   0.3394   0.0437
 XYN  HBF   H  HCH2   0   0.260   1.9563  -1.4114   0.9053
 XYN  HBFA  H  HCH2   0   0.260   1.9219  -1.4276  -0.8483
 XYN  HBG   H  HCH2   0   0.282  -0.6789  -1.1838  -0.8061
 XYN  HBGA  H  HCH2   0   0.284  -0.6766  -1.1501   0.9396

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
 XYN  OBA  CBI   deloc   1.244  0.020  1.244
 XYN  OBB  CBJ   deloc   1.242  0.020  1.242
 XYN  OBC  CBK   double  1.208  0.020  1.208
 XYN  OBD  CBI   deloc   1.245  0.020  1.245
 XYN  OBE  CBJ   deloc   1.237  0.020  1.237
 XYN  CBF  SBH   single  1.807  0.020  1.807
 XYN  CBF  CBI   single  1.540  0.020  1.540
 XYN  CBG  SBH   single  1.810  0.020  1.810
 XYN  CBG  CBK   single  1.504  0.020  1.504
 XYN  CBJ  CBK   single  1.556  0.020  1.556
 XYN  CBF  HBF   single  0.970  0.020  1.090
 XYN  CBF  HBFA  single  0.970  0.020  1.090
 XYN  CBG  HBG   single  0.970  0.020  1.090
 XYN  CBG  HBGA  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
 XYN  HBFA  CBF  HBF  106.60  3.000
 XYN  HBFA  CBF  CBI  109.66  3.000
 XYN  HBF   CBF  CBI  109.82  3.000
 XYN  HBFA  CBF  SBH  110.23  3.000
 XYN  HBF   CBF  SBH  110.27  3.000
 XYN  CBI   CBF  SBH  110.19  3.000
 XYN  HBGA  CBG  HBG  105.87  3.000
 XYN  HBGA  CBG  CBK  108.83  3.000
 XYN  HBG   CBG  CBK  109.15  3.000
 XYN  HBGA  CBG  SBH  111.11  3.000
 XYN  HBG   CBG  SBH  111.14  3.000
 XYN  CBK   CBG  SBH  110.60  3.000
 XYN  CBG   SBH  CBF   98.39  3.000
 XYN  CBF   CBI  OBD  115.43  3.000
 XYN  CBF   CBI  OBA  116.86  3.000
 XYN  OBD   CBI  OBA  127.71  3.000
 XYN  CBK   CBJ  OBE  115.55  3.000
 XYN  CBK   CBJ  OBB  115.23  3.000
 XYN  OBE   CBJ  OBB  129.22  3.000
 XYN  CBJ   CBK  CBG  116.95  3.000
 XYN  CBJ   CBK  OBC  121.41  3.000
 XYN  CBG   CBK  OBC  121.64  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
 XYN  Var_01  SBH  CBF  CBI  OBA    -0.48  30.0  3
 XYN  Var_02  OBC  CBK  CBJ  OBB  -176.69  30.0  2
 XYN  Var_03  SBH  CBG  CBK  OBC    -2.03  30.0  2
 XYN  Var_04  CBK  CBG  SBH  CBF  -179.07  30.0  1
 XYN  Var_05  CBI  CBF  SBH  CBG   179.36  30.0  1

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
 XYN  plan-1  OBC  0.020
 XYN  plan-1  CBG  0.020
 XYN  plan-1  CBJ  0.020
 XYN  plan-1  CBK  0.020
 XYN  plan-2  OBA  0.020
 XYN  plan-2  OBD  0.020
 XYN  plan-2  CBF  0.020
 XYN  plan-2  CBI  0.020
 XYN  plan-3  OBB  0.020
 XYN  plan-3  OBE  0.020
 XYN  plan-3  CBJ  0.020
 XYN  plan-3  CBK  0.020

