# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 09:51:59 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-deoxy-D-arabino-hexonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)C[C@H](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
 SSH  SSH  '3-deoxy-D-arabino-hexonic acid'  D-saccharide  24  12  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SSH
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
 SSH  O2    O  OH1   0  -0.591  -3.1255   0.5846  -1.4414
 SSH  C1    C  C     0   0.505  -2.9680  -0.0949  -0.3144
 SSH  O1    O  O     0  -0.437  -3.7087  -0.9720   0.0510
 SSH  C2    C  CH1   0  -0.055  -1.7283   0.3454   0.4465
 SSH  C3    C  CH2   0  -0.513  -0.4763  -0.1083  -0.3136
 SSH  C4    C  CH1   0   0.010   0.8133   0.3082   0.3901
 SSH  O4    O  OH1   0  -0.663   0.8310   1.6903   0.6736
 SSH  C5    C  CH1   0  -0.018   2.0573  -0.0982  -0.4212
 SSH  O5    O  OH1   0  -0.660   1.9954  -1.4423  -0.8402
 SSH  C6    C  CH2   0  -0.159   3.3298   0.1848   0.3618
 SSH  O6    O  OH1   0  -0.671   4.4419  -0.0781  -0.4619
 SSH  OT    O  OH1   0  -0.653  -1.7670  -0.1178   1.7640
 SSH  H2    H  HOH1  0   0.485  -3.8965   0.2538  -1.9267
 SSH  H2C1  H  HCH1  0   0.272  -1.7388   1.4374   0.5003
 SSH  H3C1  H  HCH2  0   0.249  -0.4930   0.3074  -1.3259
 SSH  H3C2  H  HCH2  0   0.254  -0.4959  -1.1952  -0.4250
 SSH  H4    H  HCH1  0   0.230   0.8607  -0.1887   1.3652
 SSH  HA    H  HOH1  0   0.446   0.7781   2.1756  -0.1578
 SSH  H5    H  HCH1  0   0.226   2.0687   0.4987  -1.3425
 SSH  HB    H  HOH1  0   0.445   2.0382  -2.0089  -0.0615
 SSH  H6C1  H  HCH2  0   0.190   3.3347  -0.4492   1.2622
 SSH  H6C2  H  HCH2  0   0.205   3.3184   1.2242   0.7062
 SSH  H6    H  HOH1  0   0.455   5.2362   0.0870   0.0533
 SSH  HT    H  HOH1  0   0.447  -1.7875  -1.0813   1.7580

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
 SSH  O2  C1    single  1.325  0.020  1.325
 SSH  O2  H2    single  0.850  0.020  0.980
 SSH  C1  O1    double  1.205  0.020  1.205
 SSH  C1  C2    single  1.520  0.020  1.520
 SSH  C2  C3    single  1.533  0.020  1.533
 SSH  C2  OT    single  1.397  0.020  1.397
 SSH  C2  H2C1  single  0.970  0.020  1.090
 SSH  C3  C4    single  1.527  0.020  1.527
 SSH  C3  H3C1  single  0.970  0.020  1.090
 SSH  C3  H3C2  single  0.970  0.020  1.090
 SSH  C4  O4    single  1.411  0.020  1.411
 SSH  C4  C5    single  1.540  0.020  1.540
 SSH  C4  H4    single  0.970  0.020  1.090
 SSH  O4  HA    single  0.850  0.020  0.980
 SSH  C5  O5    single  1.409  0.020  1.409
 SSH  C5  C6    single  1.521  0.020  1.521
 SSH  C5  H5    single  0.970  0.020  1.090
 SSH  O5  HB    single  0.850  0.020  0.980
 SSH  C6  O6    single  1.409  0.020  1.409
 SSH  C6  H6C1  single  0.970  0.020  1.090
 SSH  C6  H6C2  single  0.970  0.020  1.090
 SSH  O6  H6    single  0.850  0.020  0.980
 SSH  OT  HT    single  0.850  0.020  0.980

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
 SSH  H2    O2  C1    110.20  3.000
 SSH  C2    C1  O1    124.10  3.000
 SSH  C2    C1  O2    111.97  3.000
 SSH  O1    C1  O2    123.93  3.000
 SSH  H2C1  C2  OT    106.52  3.000
 SSH  H2C1  C2  C3    109.13  3.000
 SSH  OT    C2  C3    113.08  3.000
 SSH  H2C1  C2  C1    107.83  3.000
 SSH  OT    C2  C1    110.70  3.000
 SSH  C3    C2  C1    109.40  3.000
 SSH  H3C2  C3  H3C1  106.46  3.000
 SSH  H3C2  C3  C4    109.47  3.000
 SSH  H3C1  C3  C4    109.61  3.000
 SSH  H3C2  C3  C2    109.28  3.000
 SSH  H3C1  C3  C2    109.49  3.000
 SSH  C4    C3  C2    112.36  3.000
 SSH  H4    C4  C5    108.33  3.000
 SSH  H4    C4  O4    105.36  3.000
 SSH  C5    C4  O4    110.75  3.000
 SSH  H4    C4  C3    108.85  3.000
 SSH  C5    C4  C3    111.56  3.000
 SSH  O4    C4  C3    111.73  3.000
 SSH  HA    O4  C4    108.61  3.000
 SSH  H5    C5  C6    108.80  3.000
 SSH  H5    C5  O5    105.64  3.000
 SSH  C6    C5  O5    111.55  3.000
 SSH  H5    C5  C4    107.89  3.000
 SSH  C6    C5  C4    110.83  3.000
 SSH  O5    C5  C4    111.90  3.000
 SSH  HB    O5  C5    108.57  3.000
 SSH  H6C2  C6  H6C1  106.82  3.000
 SSH  H6C2  C6  O6    111.67  3.000
 SSH  H6C1  C6  O6    111.54  3.000
 SSH  H6C2  C6  C5    109.26  3.000
 SSH  H6C1  C6  C5    108.52  3.000
 SSH  O6    C6  C5    108.95  3.000
 SSH  H6    O6  C6    107.87  3.000
 SSH  HT    OT  C2    109.04  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
 SSH  CONST_01  H2  O2  C1  O1  0.00  0.0  0

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
 SSH  chir_01  C2  C1  C3  OT  positiv
 SSH  chir_02  C4  O4  C5  C3  positiv
 SSH  chir_03  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
 SSH  plan-1  O2  0.020
 SSH  plan-1  C1  0.020
 SSH  plan-1  O1  0.020
 SSH  plan-1  C2  0.020
 SSH  plan-1  H2  0.020

