# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:21:17 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: D-mannonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)[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
 CS2  CS2  'D-mannonic acid          '  ligand  24  13  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CS2
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
 CS2  C2   C  CH1    0  -0.116   1.5903  -0.6384  -0.2311
 CS2  C3   C  CH1    0   0.008   0.3563   0.2389   0.0473
 CS2  O1A  O  OC    -1  -0.602   2.9955   1.2816  -0.4195
 CS2  C1   C  C      0   0.430   2.8811   0.1414   0.0902
 CS2  O1B  O  O      0  -0.578   3.6967  -0.4300   0.8332
 CS2  O2   O  OH1    0  -0.691   1.5432  -1.8182   0.5242
 CS2  O3   O  OH1    0  -0.714   0.3962   1.4051  -0.7424
 CS2  C4   C  CH1    0  -0.017  -0.9485  -0.4885  -0.2749
 CS2  O4   O  OH1    0  -0.673  -1.0063  -0.8257  -1.6441
 CS2  C5   C  CH1    0  -0.013  -2.1905   0.3275   0.1349
 CS2  O5   O  OH1    0  -0.663  -2.1138   0.7551   1.4772
 CS2  C6   C  CH2    0  -0.159  -3.4594  -0.4707  -0.1194
 CS2  O6   O  OH1    0  -0.673  -4.5776   0.3384   0.1665
 CS2  H2   H  HCH1   0   0.209   1.6099  -0.8720  -1.3067
 CS2  H3   H  HCH1   0   0.197   0.3620   0.4781   1.1209
 CS2  HO2  H  HOH1   0   0.432   2.3808  -1.8069   1.0183
 CS2  HO3  H  HOH1   0   0.442   1.3504   1.6396  -0.7904
 CS2  H4   H  HCH1   0   0.231  -0.9623  -1.4324   0.2819
 CS2  HO4  H  HOH1   0   0.439  -0.7714  -0.0305  -2.1377
 CS2  H5   H  HCH1   0   0.227  -2.2233   1.2423  -0.4672
 CS2  HO5  H  HOH1   0   0.442  -2.1140  -0.0227   2.0463
 CS2  H61  H  HCH2   0   0.204  -3.4667  -0.8156  -1.1584
 CS2  H62  H  HCH2   0   0.185  -3.4415  -1.3709   0.5154
 CS2  HO6  H  HOH1   0   0.453  -5.3681  -0.1825   0.0012

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
 CS2  C2   O2   single  1.402  0.020  1.402
 CS2  C2   C1   single  1.542  0.020  1.542
 CS2  C2   C3   single  1.539  0.020  1.539
 CS2  C2   H2   single  0.970  0.020  1.090
 CS2  C3   C4   single  1.528  0.020  1.528
 CS2  C3   O3   single  1.409  0.020  1.409
 CS2  C3   H3   single  0.970  0.020  1.090
 CS2  O1A  C1   deloc   1.254  0.020  1.254
 CS2  C1   O1B  deloc   1.242  0.020  1.242
 CS2  O2   HO2  single  0.850  0.020  0.980
 CS2  O3   HO3  single  0.850  0.020  0.980
 CS2  C4   O4   single  1.411  0.020  1.411
 CS2  C4   C5   single  1.541  0.020  1.541
 CS2  C4   H4   single  0.970  0.020  1.090
 CS2  O4   HO4  single  0.850  0.020  0.980
 CS2  C5   C6   single  1.521  0.020  1.521
 CS2  C5   O5   single  1.411  0.020  1.411
 CS2  C5   H5   single  0.970  0.020  1.090
 CS2  O5   HO5  single  0.850  0.020  0.980
 CS2  C6   O6   single  1.409  0.020  1.409
 CS2  C6   H61  single  0.970  0.020  1.090
 CS2  C6   H62  single  0.970  0.020  1.090
 CS2  O6   HO6  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
 CS2  H2   C2  O2   110.40  3.000
 CS2  H2   C2  C1   107.22  3.000
 CS2  O2   C2  C1   109.97  3.000
 CS2  H2   C2  C3   108.17  3.000
 CS2  C1   C2  C3   110.19  3.000
 CS2  O2   C2  C3   110.81  3.000
 CS2  H3   C3  C4   108.28  3.000
 CS2  H3   C3  O3   111.52  3.000
 CS2  C4   C3  O3   107.46  3.000
 CS2  H3   C3  C2   107.24  3.000
 CS2  O3   C3  C2   110.34  3.000
 CS2  C4   C3  C2   112.03  3.000
 CS2  O1B  C1  O1A  126.96  3.000
 CS2  O1B  C1  C2   116.20  3.000
 CS2  O1A  C1  C2   116.84  3.000
 CS2  HO2  O2  C2   103.59  3.000
 CS2  HO3  O3  C3   104.60  3.000
 CS2  H4   C4  C5   108.10  3.000
 CS2  H4   C4  O4   106.65  3.000
 CS2  C5   C4  O4   110.57  3.000
 CS2  H4   C4  C3   108.27  3.000
 CS2  C5   C4  C3   112.33  3.000
 CS2  O4   C4  C3   110.68  3.000
 CS2  HO4  O4  C4   106.82  3.000
 CS2  H5   C5  C6   108.75  3.000
 CS2  H5   C5  O5   105.74  3.000
 CS2  C6   C5  O5   111.32  3.000
 CS2  H5   C5  C4   108.67  3.000
 CS2  O5   C5  C4   111.69  3.000
 CS2  C6   C5  C4   110.49  3.000
 CS2  HO5  O5  C5   108.49  3.000
 CS2  H62  C6  H61  106.83  3.000
 CS2  H62  C6  O6   111.41  3.000
 CS2  H61  C6  O6   111.60  3.000
 CS2  H62  C6  C5   108.60  3.000
 CS2  H61  C6  C5   109.25  3.000
 CS2  O6   C6  C5   109.07  3.000
 CS2  HO6  O6  C6   107.85  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
 CS2  chir_01  C2  O2  C1  C3  positiv
 CS2  chir_02  C3  O3  C2  C4  positiv
 CS2  chir_03  C4  O4  C3  C5  negativ
 CS2  chir_04  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
 CS2  plan-1  C2   0.020
 CS2  plan-1  O1A  0.020
 CS2  plan-1  C1   0.020
 CS2  plan-1  O1B  0.020

