# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:10:02 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: (2S)-2-sulfanylbutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](S)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
 JYD  JYD  '(2S)-2-sulfanylbutanedioic acid'  ligand  15  9  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JYD
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
 JYD  C01  C  CH2   0  -0.555  -0.6441   0.8810   0.1842
 JYD  C02  C  CH1   0  -0.518   0.4942   0.0162  -0.3190
 JYD  C03  C  C     0   0.592   1.8442   0.6363  -0.0425
 JYD  C07  C  C     0   0.561  -1.9892   0.3688  -0.2587
 JYD  O04  O  OH1   0  -0.582   2.7787   0.1660  -0.8515
 JYD  O05  O  O     0  -0.430   2.0483   1.4432   0.8285
 JYD  O08  O  O     0  -0.437  -2.1753  -0.3424  -1.2131
 JYD  O09  O  OH1   0  -0.589  -2.9644   0.8338   0.5098
 JYD  S06  S  S2    0  -0.178   0.4741  -1.6541   0.4210
 JYD  H1   H  HCH2  0   0.289  -0.6155   0.9797   1.2697
 JYD  H2   H  HCH2  0   0.312  -0.5433   1.8962  -0.2167
 JYD  H3   H  HCH1  0   0.336   0.3941  -0.1637  -1.3908
 JYD  H4   H  HOH1  0   0.486   3.6417   0.5396  -0.6170
 JYD  H5   H  HOH1  0   0.482  -3.8233   0.5356   0.1734
 JYD  H6   H  HSH1  0   0.231   0.6104  -1.2633   1.6953

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
 JYD  O05  C03  double  1.205  0.020  1.205
 JYD  O04  C03  single  1.322  0.020  1.322
 JYD  C03  C02  single  1.511  0.020  1.511
 JYD  C02  S06  single  1.827  0.020  1.827
 JYD  C02  C01  single  1.516  0.020  1.516
 JYD  C01  C07  single  1.506  0.020  1.506
 JYD  C07  O08  double  1.205  0.020  1.205
 JYD  C07  O09  single  1.326  0.020  1.326
 JYD  C01  H1   single  0.970  0.020  1.090
 JYD  C01  H2   single  0.970  0.020  1.090
 JYD  C02  H3   single  0.970  0.020  1.090
 JYD  O04  H4   single  0.850  0.020  0.980
 JYD  O09  H5   single  0.850  0.020  0.980
 JYD  S06  H6   single  1.200  0.020  1.300

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
 JYD  H2   C01  H1   106.13  3.000
 JYD  H2   C01  C07  106.84  3.000
 JYD  H1   C01  C07  110.31  3.000
 JYD  H2   C01  C02  109.75  3.000
 JYD  H1   C01  C02  111.26  3.000
 JYD  C07  C01  C02  112.28  3.000
 JYD  H3   C02  S06  104.25  3.000
 JYD  H3   C02  C03  109.22  3.000
 JYD  S06  C02  C03  108.11  3.000
 JYD  H3   C02  C01  110.57  3.000
 JYD  S06  C02  C01  112.26  3.000
 JYD  C03  C02  C01  112.09  3.000
 JYD  O05  C03  O04  124.11  3.000
 JYD  O04  C03  C02  111.93  3.000
 JYD  O05  C03  C02  123.95  3.000
 JYD  O09  C07  O08  123.55  3.000
 JYD  O09  C07  C01  111.55  3.000
 JYD  O08  C07  C01  124.87  3.000
 JYD  H4   O04  C03  110.13  3.000
 JYD  H5   O09  C07  110.04  3.000
 JYD  H6   S06  C02   96.74  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
 JYD  CONST_01  H5   O09  C07  C01  180.00   0.0  0
 JYD  CONST_02  H4   O04  C03  C02  180.00   0.0  0
 JYD  Var_01    O08  C07  C01  C02  -22.63  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
 JYD  chir_01  C02  C03  S06  C01  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
 JYD  plan-1  C02  0.020
 JYD  plan-1  C03  0.020
 JYD  plan-1  O04  0.020
 JYD  plan-1  O05  0.020
 JYD  plan-1  H4   0.020
 JYD  plan-2  C01  0.020
 JYD  plan-2  C07  0.020
 JYD  plan-2  O08  0.020
 JYD  plan-2  O09  0.020
 JYD  plan-2  H5   0.020

