# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:29:38 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: (Z)-3-(carboxymethylsulfanyl)-2-hydroxy-prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CS\C=C(/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
 XYM  XYM  '(Z)-3-(carboxymethylsulfanyl)-2-hydroxy-prop-2-enoic 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_XYM
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
 XYM  OAA   O  OC    -1  -0.613   4.3749  -1.0109   0.0184
 XYM  OAB   O  O      0  -0.577  -3.1858  -1.7020  -0.0623
 XYM  OAC   O  O      0  -0.594   3.5706   1.0736  -0.0138
 XYM  OAD   O  OC    -1  -0.619  -4.1805   0.3052  -0.0310
 XYM  OAE   O  OH1    0  -0.645  -1.9970   1.6238   0.0161
 XYM  CAF   C  C1     0  -0.510  -0.6703  -0.3102  -0.0167
 XYM  CAG   C  CH2    0  -0.692   2.0338  -0.7392   0.0312
 XYM  SAH   S  S2     0   0.004   0.8251   0.6070  -0.0017
 XYM  CAI   C  C      0   0.431   3.4625  -0.1649   0.0098
 XYM  CAJ   C  C      0   0.374  -3.1890  -0.4634  -0.0378
 XYM  CAK   C  C      0   0.190  -1.8679   0.2795  -0.0113
 XYM  HOAE  H  HOH1   0   0.445  -2.9663   1.7500   0.0121
 XYM  HAF   H  H      0   0.273  -0.6102  -1.3896  -0.0406
 XYM  HAG   H  HCH2   0   0.267   1.8930  -1.3491   0.9270
 XYM  HAGA  H  HCH2   0   0.267   1.8854  -1.3964  -0.8292

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
 XYM  OAA  CAI   deloc   1.244  0.020  1.244
 XYM  OAB  CAJ   deloc   1.239  0.020  1.239
 XYM  OAC  CAI   deloc   1.243  0.020  1.243
 XYM  OAD  CAJ   deloc   1.255  0.020  1.255
 XYM  OAE  CAK   single  1.351  0.020  1.351
 XYM  CAF  SAH   single  1.754  0.020  1.754
 XYM  CAF  CAK   double  1.335  0.020  1.335
 XYM  CAG  SAH   single  1.810  0.020  1.810
 XYM  CAG  CAI   single  1.540  0.020  1.540
 XYM  CAJ  CAK   single  1.516  0.020  1.516
 XYM  OAE  HOAE  single  0.850  0.020  0.980
 XYM  CAF  HAF   single  0.930  0.020  1.080
 XYM  CAG  HAG   single  0.970  0.020  1.090
 XYM  CAG  HAGA  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
 XYM  HOAE  OAE  CAK  102.90  3.000
 XYM  HAF   CAF  CAK  119.40  3.000
 XYM  HAF   CAF  SAH  118.34  3.000
 XYM  CAK   CAF  SAH  122.25  3.000
 XYM  HAGA  CAG  HAG  107.00  3.000
 XYM  HAGA  CAG  CAI  109.83  3.000
 XYM  HAG   CAG  CAI  109.82  3.000
 XYM  HAGA  CAG  SAH  110.02  3.000
 XYM  HAG   CAG  SAH  110.12  3.000
 XYM  CAI   CAG  SAH  110.00  3.000
 XYM  CAG   SAH  CAF  100.40  3.000
 XYM  CAG   CAI  OAC  116.89  3.000
 XYM  CAG   CAI  OAA  115.25  3.000
 XYM  OAC   CAI  OAA  127.85  3.000
 XYM  CAK   CAJ  OAD  112.86  3.000
 XYM  CAK   CAJ  OAB  119.22  3.000
 XYM  OAD   CAJ  OAB  127.93  3.000
 XYM  CAJ   CAK  CAF  124.42  3.000
 XYM  CAJ   CAK  OAE  113.88  3.000
 XYM  CAF   CAK  OAE  121.70  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
 XYM  Var_01  SAH  CAF  CAK  OAE    -0.50   0.0  2
 XYM  Var_02  SAH  CAG  CAI  OAA  -179.42  30.0  3
 XYM  Var_03  OAE  CAK  CAJ  OAB  -179.91  30.0  2
 XYM  Var_04  CAI  CAG  SAH  CAF   178.47  30.0  2
 XYM  Var_05  CAK  CAF  SAH  CAG   178.45  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
 XYM  plan-1  OAA  0.020
 XYM  plan-1  OAC  0.020
 XYM  plan-1  CAG  0.020
 XYM  plan-1  CAI  0.020
 XYM  plan-2  OAB  0.020
 XYM  plan-2  OAD  0.020
 XYM  plan-2  CAJ  0.020
 XYM  plan-2  CAK  0.020
 XYM  plan-3  OAE  0.020
 XYM  plan-3  CAF  0.020
 XYM  plan-3  SAH  0.020
 XYM  plan-3  CAJ  0.020
 XYM  plan-3  CAK  0.020
 XYM  plan-3  HAF  0.020

