# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 01:09:47 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 2,2'-sulfanediyldiacetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSCC(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
 9X6  9X6  '2,2'-sulfanediyldiacetic acid'  ligand  13  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9X6
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
 9X6  C3    C  C      0   0.424  -2.6916   0.0409   0.0271
 9X6  C4    C  CH2    0  -0.680  -1.3335   0.7664   0.0343
 9X6  C2    C  CH2    0  -0.680   1.4179   0.7562   0.0278
 9X6  C1    C  C      0   0.424   2.7704   0.0209   0.0066
 9X6  S2    S  S2     0  -0.055   0.0377  -0.4139   0.0152
 9X6  O4    O  O      0  -0.600  -2.6711  -1.2030   0.0094
 9X6  O3    O  OC    -1  -0.619  -3.6941   0.7802   0.0398
 9X6  O2    O  OC    -1  -0.619   3.7781   0.7529  -0.0147
 9X6  O1    O  O      0  -0.600   2.7411  -1.2229   0.0144
 9X6  H41C  H  HCH2   0   0.252  -1.2708   1.4315  -0.8327
 9X6  H42C  H  HCH2   0   0.252  -1.2674   1.4077   0.9187
 9X6  H21C  H  HCH2   0   0.252   1.3641   1.3923   0.9167
 9X6  H22C  H  HCH2   0   0.251   1.3526   1.4267  -0.8344

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
 9X6  O4  C3    deloc   1.244  0.020  1.244
 9X6  C3  O3    deloc   1.246  0.020  1.246
 9X6  C3  C4    single  1.540  0.020  1.540
 9X6  C4  S2    single  1.809  0.020  1.809
 9X6  S2  C2    single  1.809  0.020  1.809
 9X6  C2  C1    single  1.540  0.020  1.540
 9X6  C1  O1    deloc   1.244  0.020  1.244
 9X6  C1  O2    deloc   1.246  0.020  1.246
 9X6  C4  H41C  single  0.970  0.020  1.090
 9X6  C4  H42C  single  0.970  0.020  1.090
 9X6  C2  H21C  single  0.970  0.020  1.090
 9X6  C2  H22C  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
 9X6  O3    C3  O4    127.36  3.000
 9X6  O3    C3  C4    115.48  3.000
 9X6  O4    C3  C4    117.17  3.000
 9X6  H42C  C4  H41C  106.30  3.000
 9X6  H42C  C4  S2    110.18  3.000
 9X6  H41C  C4  S2    110.16  3.000
 9X6  H42C  C4  C3    109.46  3.000
 9X6  H41C  C4  C3    109.46  3.000
 9X6  S2    C4  C3    111.16  3.000
 9X6  H22C  C2  H21C  106.32  3.000
 9X6  H22C  C2  S2    110.20  3.000
 9X6  H21C  C2  S2    110.12  3.000
 9X6  H22C  C2  C1    109.52  3.000
 9X6  H21C  C2  C1    109.39  3.000
 9X6  S2    C2  C1    111.17  3.000
 9X6  O1    C1  O2    127.35  3.000
 9X6  O2    C1  C2    115.48  3.000
 9X6  O1    C1  C2    117.17  3.000
 9X6  C2    S2  C4     98.98  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
 9X6  Var_01  C1    C2  S2  C4  -179.67  30.0  3
 9X6  Var_02  O4    C3  C4  S2    -0.03  30.0  2
 9X6  Var_03  O1    C1  C2  S2    -1.55  30.0  3
 9X6  Var_04  H41C  C4  S2  C2    58.47  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
 9X6  plan-1  C3  0.020
 9X6  plan-1  C4  0.020
 9X6  plan-1  O4  0.020
 9X6  plan-1  O3  0.020
 9X6  plan-2  C2  0.020
 9X6  plan-2  C1  0.020
 9X6  plan-2  O2  0.020
 9X6  plan-2  O1  0.020

