# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 04:08:20 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-deoxy-D-lyxo-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
 RSH  RSH  '3-deoxy-D-lyxo-hexonic acid'  ligand  23  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RSH
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
 RSH  O2    O  O      0  -0.607  -3.6567   0.2329   0.7753
 RSH  C1    C  C      0   0.406  -2.9373  -0.4171  -0.0190
 RSH  O1    O  OC    -1  -0.589  -3.1314  -1.5570  -0.4621
 RSH  C2    C  CH1    0  -0.087  -1.6540   0.3199  -0.4598
 RSH  C3    C  CH2    0  -0.482  -0.4080  -0.4393  -0.0038
 RSH  C4    C  CH1    0   0.019   0.8891   0.2978  -0.3242
 RSH  O4    O  OH1    0  -0.708   0.9813   1.5280   0.3696
 RSH  C5    C  CH1    0  -0.001   2.1271  -0.5215   0.0462
 RSH  O5    O  OH1    0  -0.672   2.2155  -0.7181   1.4390
 RSH  C6    C  CH2    0  -0.154   3.3896   0.1089  -0.5225
 RSH  O6    O  OH1    0  -0.674   4.4814  -0.7423  -0.2580
 RSH  OT    O  OH1    0  -0.706  -1.6865   1.6312   0.0762
 RSH  H2C1  H  HCH1   0   0.215  -1.6415   0.3839  -1.5564
 RSH  H3C1  H  HCH2   0   0.233  -0.3971  -1.4084  -0.5062
 RSH  H3C2  H  HCH2   0   0.226  -0.4658  -0.6343   1.0722
 RSH  H4    H  HCH1   0   0.193   0.9181   0.4636  -1.4139
 RSH  HA    H  HOH1   0   0.453   0.0718   1.8585   0.4649
 RSH  H5    H  HCH1   0   0.224   2.0164  -1.5150  -0.4034
 RSH  HB    H  HOH1   0   0.436   2.0412   0.1351   1.8538
 RSH  H6C1  H  HCH2   0   0.194   3.5413   1.1050  -0.0858
 RSH  H6C2  H  HCH2   0   0.190   3.2450   0.2531  -1.6019
 RSH  H6    H  HOH1   0   0.453   5.2704  -0.3377  -0.6292
 RSH  HT    H  HOH1   0   0.439  -2.4722   1.5868   0.6614

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
 RSH  O2  C1    deloc   1.253  0.020  1.253
 RSH  C1  O1    deloc   1.238  0.020  1.238
 RSH  C1  C2    single  1.544  0.020  1.544
 RSH  C2  C3    single  1.529  0.020  1.529
 RSH  C2  OT    single  1.417  0.020  1.417
 RSH  C2  H2C1  single  0.970  0.020  1.090
 RSH  C3  C4    single  1.526  0.020  1.526
 RSH  C3  H3C1  single  0.970  0.020  1.090
 RSH  C3  H3C2  single  0.970  0.020  1.090
 RSH  C4  O4    single  1.415  0.020  1.415
 RSH  C4  C5    single  1.530  0.020  1.530
 RSH  C4  H4    single  0.970  0.020  1.090
 RSH  O4  HA    single  0.850  0.020  0.980
 RSH  C5  O5    single  1.409  0.020  1.409
 RSH  C5  C6    single  1.521  0.020  1.521
 RSH  C5  H5    single  0.970  0.020  1.090
 RSH  O5  HB    single  0.850  0.020  0.980
 RSH  C6  O6    single  1.409  0.020  1.409
 RSH  C6  H6C1  single  0.970  0.020  1.090
 RSH  C6  H6C2  single  0.970  0.020  1.090
 RSH  O6  H6    single  0.850  0.020  0.980
 RSH  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
 RSH  C2    C1  O1    117.87  3.000
 RSH  C2    C1  O2    114.23  3.000
 RSH  O1    C1  O2    127.89  3.000
 RSH  H2C1  C2  OT    108.90  3.000
 RSH  H2C1  C2  C3    108.51  3.000
 RSH  OT    C2  C3    111.43  3.000
 RSH  H2C1  C2  C1    108.80  3.000
 RSH  OT    C2  C1    108.34  3.000
 RSH  C3    C2  C1    110.81  3.000
 RSH  H3C2  C3  H3C1  107.14  3.000
 RSH  H3C2  C3  C4    109.70  3.000
 RSH  H3C1  C3  C4    108.89  3.000
 RSH  H3C2  C3  C2    109.79  3.000
 RSH  H3C1  C3  C2    108.16  3.000
 RSH  C4    C3  C2    112.97  3.000
 RSH  H4    C4  C5    107.37  3.000
 RSH  H4    C4  O4    110.61  3.000
 RSH  C5    C4  O4    107.10  3.000
 RSH  H4    C4  C3    107.61  3.000
 RSH  C5    C4  C3    112.23  3.000
 RSH  O4    C4  C3    111.86  3.000
 RSH  HA    O4  C4    106.42  3.000
 RSH  H5    C5  C6    107.83  3.000
 RSH  H5    C5  O5    106.57  3.000
 RSH  C6    C5  O5    112.03  3.000
 RSH  H5    C5  C4    107.72  3.000
 RSH  C6    C5  C4    111.04  3.000
 RSH  O5    C5  C4    111.39  3.000
 RSH  HB    O5  C5    106.87  3.000
 RSH  H6C2  C6  H6C1  106.85  3.000
 RSH  H6C2  C6  O6    111.44  3.000
 RSH  H6C1  C6  O6    111.48  3.000
 RSH  H6C2  C6  C5    108.20  3.000
 RSH  H6C1  C6  C5    109.99  3.000
 RSH  O6    C6  C5    108.81  3.000
 RSH  H6    O6  C6    108.01  3.000
 RSH  HT    OT  C2    101.66  3.000

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
 RSH  chir_01  C2  C1  C3  OT  positiv
 RSH  chir_02  C4  O4  C5  C3  negativ
 RSH  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
 RSH  plan-1  O2  0.020
 RSH  plan-1  C1  0.020
 RSH  plan-1  O1  0.020
 RSH  plan-1  C2  0.020

