# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 21:37:15 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 6-deoxy-2,4-di-O-sulfo-alpha-L-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](O)[C@@H](O[S](O)(=O)=O)[C@H](O)[C@@H]1O[S](O)(=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
 X2Y  X2Y  6-deoxy-2,4-di-O-sulfo-alpha-L-galactopyranose  L-saccharide  29  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X2Y
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
 X2Y  C5   C  CH1    0   0.028   0.8366  -16.4231   2.1831
 X2Y  C4   C  CH1    0  -0.072   0.0983  -17.7534   2.0949
 X2Y  C3   C  CH1    0   0.040   0.7385  -18.6295   1.0160
 X2Y  C2   C  CH1    0  -0.015   0.7217  -17.8539  -0.3030
 X2Y  C1   C  CH1    0   0.241   1.3883  -16.4819  -0.1381
 X2Y  O5   O  O2     0  -0.497   0.8045  -15.7718   0.9216
 X2Y  C6   C  CH3    0  -0.684   0.2518  -15.4761   3.2102
 X2Y  O3   O  OH1    0  -0.689   0.1647  -19.9004   0.8960
 X2Y  O6   O  OS    -1  -0.738  -0.4933  -19.4730  -2.6214
 X2Y  O7   O  OS     0  -0.728   1.8060  -19.4158  -3.5020
 X2Y  O8   O  OS     0  -0.736   0.5272  -17.3250  -3.2219
 X2Y  O2   O  OC2    0  -0.622   1.4096  -18.6074  -1.2854
 X2Y  O9   O  OS     0  -0.713  -3.6360  -17.5880   1.9104
 X2Y  O10  O  OS     0  -0.742  -2.3209  -19.6609   2.1297
 X2Y  O11  O  OS    -1  -0.722  -2.2929  -18.0078   3.9393
 X2Y  O4   O  OC2    0  -0.622  -1.2568  -17.4652   1.7463
 X2Y  H5   H  HCH1   0   0.225   1.8717  -16.6473   2.4716
 X2Y  H4   H  HCH1   0   0.265   0.1595  -18.2576   3.0666
 X2Y  H3   H  HCH1   0   0.226   1.7823  -18.7806   1.3164
 X2Y  H2   H  HCH1   0   0.241  -0.3220  -17.6864  -0.5917
 X2Y  H1   H  HCH1   0   0.227   1.1902  -15.8704  -1.0243
 X2Y  H61  H  HCH3   0   0.231   0.2574  -15.9429   4.1951
 X2Y  H63  H  HCH3   0   0.239   0.8501  -14.5672   3.2711
 X2Y  H62  H  HCH3   0   0.232  -0.7734  -15.1972   2.9712
 X2Y  HO3  H  HOH1   0   0.445  -0.7703  -19.8696   1.1625
 X2Y  O1   O  OH1    0  -0.662   2.7533  -16.6797   0.0437
 X2Y  HO1  H  HOH1   0   0.458   3.2051  -15.8346  -0.0515
 X2Y  S1   S  S      0   1.560   0.7453  -18.7097  -2.7890
 X2Y  S2   S  S      0   1.583  -2.4813  -18.2430   2.5091

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
 X2Y  O7   S1   deloc   1.460  0.020  1.460
 X2Y  O8   S1   deloc   1.467  0.020  1.467
 X2Y  O6   S1   deloc   1.465  0.020  1.465
 X2Y  S1   O2   single  1.647  0.020  1.647
 X2Y  O2   C2   single  1.416  0.020  1.416
 X2Y  C2   C1   single  1.534  0.020  1.534
 X2Y  C2   C3   single  1.530  0.020  1.530
 X2Y  C1   O5   single  1.403  0.020  1.403
 X2Y  O5   C5   single  1.420  0.020  1.420
 X2Y  O3   C3   single  1.400  0.020  1.400
 X2Y  C3   C4   single  1.530  0.020  1.530
 X2Y  O4   C4   single  1.429  0.020  1.429
 X2Y  O4   S2   single  1.639  0.020  1.639
 X2Y  C5   C4   single  1.524  0.020  1.524
 X2Y  C5   C6   single  1.515  0.020  1.515
 X2Y  O9   S2   deloc   1.456  0.020  1.456
 X2Y  O10  S2   deloc   1.477  0.020  1.477
 X2Y  S2   O11  deloc   1.462  0.020  1.462
 X2Y  C5   H5   single  0.970  0.020  1.090
 X2Y  C4   H4   single  0.970  0.020  1.090
 X2Y  C3   H3   single  0.970  0.020  1.090
 X2Y  C2   H2   single  0.970  0.020  1.090
 X2Y  C1   H1   single  0.970  0.020  1.090
 X2Y  C6   H61  single  0.970  0.020  1.090
 X2Y  C6   H63  single  0.970  0.020  1.090
 X2Y  C6   H62  single  0.970  0.020  1.090
 X2Y  O3   HO3  single  0.850  0.020  0.980
 X2Y  C1   O1   single  1.391  0.020  1.391
 X2Y  O1   HO1  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
 X2Y  H5   C5  C6   108.27  3.000
 X2Y  H5   C5  O5   110.40  3.000
 X2Y  C6   C5  O5   107.87  3.000
 X2Y  H5   C5  C4   107.08  3.000
 X2Y  C6   C5  C4   113.45  3.000
 X2Y  O5   C5  C4   109.76  3.000
 X2Y  H4   C4  O4   111.22  3.000
 X2Y  H4   C4  C3   109.77  3.000
 X2Y  O4   C4  C3   109.89  3.000
 X2Y  H4   C4  C5   108.85  3.000
 X2Y  O4   C4  C5   107.31  3.000
 X2Y  C3   C4  C5   109.75  3.000
 X2Y  H3   C3  O3   106.78  3.000
 X2Y  H3   C3  C2   108.45  3.000
 X2Y  O3   C3  C2   112.45  3.000
 X2Y  H3   C3  C4   106.49  3.000
 X2Y  O3   C3  C4   114.13  3.000
 X2Y  C2   C3  C4   108.24  3.000
 X2Y  H2   C2  O2   111.17  3.000
 X2Y  H2   C2  C1   107.79  3.000
 X2Y  O2   C2  C1   109.83  3.000
 X2Y  H2   C2  C3   108.37  3.000
 X2Y  C1   C2  C3   110.84  3.000
 X2Y  O2   C2  C3   108.84  3.000
 X2Y  O1   C1  H1   111.27  3.000
 X2Y  O1   C1  O5   112.44  3.000
 X2Y  H1   C1  O5   104.69  3.000
 X2Y  O1   C1  C2   108.25  3.000
 X2Y  H1   C1  C2   109.50  3.000
 X2Y  O5   C1  C2   110.67  3.000
 X2Y  C1   O5  C5   115.43  3.000
 X2Y  H62  C6  H63  108.39  3.000
 X2Y  H62  C6  H61  108.23  3.000
 X2Y  H63  C6  H61  107.69  3.000
 X2Y  H62  C6  C5   112.01  3.000
 X2Y  H63  C6  C5   110.33  3.000
 X2Y  H61  C6  C5   110.06  3.000
 X2Y  HO3  O3  C3   109.99  3.000
 X2Y  S1   O2  C2   118.06  3.000
 X2Y  S2   O4  C4   119.96  3.000
 X2Y  HO1  O1  C1   108.82  3.000
 X2Y  O2   S1  O8   105.71  3.000
 X2Y  O2   S1  O7   100.54  3.000
 X2Y  O8   S1  O7   114.86  3.000
 X2Y  O2   S1  O6   105.60  3.000
 X2Y  O8   S1  O6   113.58  3.000
 X2Y  O7   S1  O6   114.72  3.000
 X2Y  O4   S2  O11  106.43  3.000
 X2Y  O11  S2  O10  113.08  3.000
 X2Y  O4   S2  O10  104.77  3.000
 X2Y  O11  S2  O9   115.60  3.000
 X2Y  O10  S2  O9   114.36  3.000
 X2Y  O4   S2  O9   100.81  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
 X2Y  Var_01  O9  S2  O4  C4  176.57  30.0  3
 X2Y  Var_02  O7  S1  O2  C2  173.96  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
 X2Y  chir_01  C5  O5  C4  C6  positiv
 X2Y  chir_02  C4  O4  C5  C3  positiv
 X2Y  chir_03  C3  O3  C4  C2  positiv
 X2Y  chir_04  C2  O2  C3  C1  negativ
 X2Y  chir_05  C1  O5  O1  C2  negativ

