# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:55:19 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: methyl 6-thio-beta-D-galacto-hexodialdo-1,5-pyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](C=S)[C@H](O)[C@H](O)[C@H]1O
#
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
 WIA  WIA  'methyl 6-thio-beta-D-galacto-hexodialdo-1,5-pyranoside'  D-saccharide  25  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WIA
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
 WIA  C1    C  CH1   0   0.289   1.1514   0.2547  -0.6451
 WIA  CM    C  CH3   0  -0.411   3.4389   0.1151  -0.1240
 WIA  O1    O  O2    0  -0.492   2.3190  -0.4576  -0.7739
 WIA  C2    C  CH1   0  -0.030   0.1440  -0.2591  -1.6722
 WIA  O2    O  OH1   0  -0.670   0.5659   0.0283  -2.9829
 WIA  C3    C  CH1   0   0.026  -1.1873   0.4570  -1.4610
 WIA  O3    O  OH1   0  -0.666  -2.1873  -0.0121  -2.3226
 WIA  C4    C  CH1   0  -0.014  -1.6622   0.2968  -0.0224
 WIA  O4    O  OH1   0  -0.659  -1.9719  -1.0490   0.2053
 WIA  C5    C  CH1   0   0.011  -0.5174   0.7851   0.8972
 WIA  O5    O  O2    0  -0.479   0.6561   0.0703   0.6623
 WIA  C6    C  C1    0  -0.320  -0.9292   0.6793   2.3199
 WIA  S1    S  S1    0  -0.103  -0.2494  -0.2531   3.4390
 WIA  H1    H  HCH1  0   0.187   1.3260   1.3352  -0.8187
 WIA  HMC1  H  HCH3  0   0.241   4.3184  -0.4406  -0.4433
 WIA  HMC2  H  HCH3  0   0.216   3.5681   1.1652  -0.4038
 WIA  HMC3  H  HCH3  0   0.222   3.3614   0.0520   0.9636
 WIA  H2    H  HCH1  0   0.232   0.0066  -1.3387  -1.5205
 WIA  HA    H  HOH1  0   0.459   1.2812  -0.5716  -3.2153
 WIA  H3    H  HCH1  0   0.221  -1.0120   1.5350  -1.6113
 WIA  HB    H  HOH1  0   0.452  -1.8835   0.1138  -3.2276
 WIA  H4    H  HCH1  0   0.254  -2.5286   0.9526   0.1354
 WIA  HC    H  HOH1  0   0.459  -2.4854  -1.1246   1.0154
 WIA  H5    H  HCH1  0   0.262  -0.3837   1.8646   0.6968
 WIA  H6    H  H     0   0.312  -1.7908   1.3015   2.5642

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
 WIA  C1  O1    single  1.374  0.020  1.374
 WIA  C1  C2    single  1.528  0.020  1.528
 WIA  C1  O5    single  1.410  0.020  1.410
 WIA  C1  H1    single  0.970  0.020  1.090
 WIA  CM  O1    single  1.416  0.020  1.416
 WIA  CM  HMC1  single  0.970  0.020  1.090
 WIA  CM  HMC2  single  0.970  0.020  1.090
 WIA  CM  HMC3  single  0.970  0.020  1.090
 WIA  C2  O2    single  1.407  0.020  1.407
 WIA  C2  C3    single  1.526  0.020  1.526
 WIA  C2  H2    single  0.970  0.020  1.090
 WIA  O2  HA    single  0.850  0.020  0.980
 WIA  C3  O3    single  1.401  0.020  1.401
 WIA  C3  C4    single  1.523  0.020  1.523
 WIA  C3  H3    single  0.970  0.020  1.090
 WIA  O3  HB    single  0.850  0.020  0.980
 WIA  C4  O4    single  1.400  0.020  1.400
 WIA  C4  C5    single  1.547  0.020  1.547
 WIA  C4  H4    single  0.970  0.020  1.090
 WIA  O4  HC    single  0.850  0.020  0.980
 WIA  C5  O5    single  1.394  0.020  1.394
 WIA  C5  C6    single  1.485  0.020  1.485
 WIA  C5  H5    single  0.970  0.020  1.090
 WIA  C6  S1    double  1.607  0.020  1.607
 WIA  C6  H6    single  0.930  0.020  1.080

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
 WIA  H1    C1  O5    109.15  3.000
 WIA  H1    C1  C2    109.06  3.000
 WIA  O5    C1  C2    110.35  3.000
 WIA  H1    C1  O1    110.91  3.000
 WIA  O5    C1  O1    108.52  3.000
 WIA  C2    C1  O1    108.85  3.000
 WIA  HMC3  CM  HMC2  108.57  3.000
 WIA  HMC3  CM  HMC1  108.67  3.000
 WIA  HMC2  CM  HMC1  108.63  3.000
 WIA  HMC3  CM  O1    112.19  3.000
 WIA  HMC2  CM  O1    111.35  3.000
 WIA  HMC1  CM  O1    107.33  3.000
 WIA  CM    O1  C1    114.80  3.000
 WIA  H2    C2  C3    109.44  3.000
 WIA  H2    C2  O2    111.53  3.000
 WIA  C3    C2  O2    107.14  3.000
 WIA  H2    C2  C1    108.67  3.000
 WIA  C3    C2  C1    108.92  3.000
 WIA  O2    C2  C1    111.10  3.000
 WIA  HA    O2  C2    108.70  3.000
 WIA  H3    C3  C4    106.33  3.000
 WIA  H3    C3  O3    110.92  3.000
 WIA  C4    C3  O3    108.85  3.000
 WIA  H3    C3  C2    107.53  3.000
 WIA  C4    C3  C2    110.69  3.000
 WIA  O3    C3  C2    112.36  3.000
 WIA  HB    O3  C3    108.00  3.000
 WIA  H4    C4  C5    108.05  3.000
 WIA  H4    C4  O4    112.10  3.000
 WIA  C5    C4  O4    111.74  3.000
 WIA  H4    C4  C3    108.60  3.000
 WIA  C5    C4  C3    107.30  3.000
 WIA  O4    C4  C3    108.89  3.000
 WIA  HC    O4  C4    109.31  3.000
 WIA  H5    C5  C6    106.06  3.000
 WIA  H5    C5  O5    111.60  3.000
 WIA  C6    C5  O5    111.00  3.000
 WIA  H5    C5  C4    106.84  3.000
 WIA  C6    C5  C4    109.98  3.000
 WIA  O5    C5  C4    111.15  3.000
 WIA  C5    O5  C1    112.64  3.000
 WIA  H6    C6  S1    120.60  3.000
 WIA  H6    C6  C5    113.15  3.000
 WIA  S1    C6  C5    126.24  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
 WIA  Var_01  HMC1  CM  O1  C1  -170.31  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
 WIA  chir_01  C1  O1  C2  O5  negativ
 WIA  chir_02  C2  O2  C1  C3  negativ
 WIA  chir_03  C3  O3  C2  C4  positiv
 WIA  chir_04  C4  O4  C3  C5  positiv
 WIA  chir_05  C5  O5  C4  C6  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
 WIA  plan-1  C5  0.020
 WIA  plan-1  C6  0.020
 WIA  plan-1  S1  0.020
 WIA  plan-1  H6  0.020

