# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 19:28:09 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)[C@@H](O[C@@H](O)[C@@H]1O[S](O)(=O)=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
 Z9K  Z9K  '3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid'  L-saccharide  28  18  .  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_Z9K
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
 Z9K  O4   O  OH1    0  -0.664  66.1361  -1.7713  -14.3777
 Z9K  C4   C  CH1    0   0.039  67.2206  -0.8914  -14.5623
 Z9K  C5   C  CH1    0  -0.145  66.8574   0.1853  -15.5900
 Z9K  O5   O  O2     0  -0.494  67.2085  -0.2610  -16.8900
 Z9K  C6   C  C      0   0.393  65.3691   0.5919  -15.5076
 Z9K  O10  O  O      0  -0.611  65.0612   1.1434  -14.4336
 Z9K  O6   O  OC    -1  -0.584  64.6463   0.3550  -16.4863
 Z9K  C3   C  CH1    0   0.045  68.4709  -1.6510  -15.0311
 Z9K  O3   O  O2     0  -0.495  69.1252  -2.1675  -13.8986
 Z9K  C7   C  CH3    0  -0.403  69.7171  -3.4362  -14.0540
 Z9K  C2   C  CH1    0  -0.116  69.3471  -0.7020  -15.8372
 Z9K  O2   O  OC2    0  -0.616  70.5543  -1.3556  -16.2067
 Z9K  S1   S  S      0   1.579  71.9512  -0.4905  -16.1162
 Z9K  O7   O  OS    -1  -0.740  71.7092   0.7068  -16.9441
 Z9K  O8   O  OS     0  -0.722  72.1403  -0.1837  -14.7000
 Z9K  O9   O  OS     0  -0.711  72.9061  -1.4360  -16.6784
 Z9K  C1   C  CH1    0   0.298  68.5808  -0.2824  -17.1096
 Z9K  O1   O  OH1    0  -0.686  68.9787   0.9692  -17.5838
 Z9K  HO1  H  HOH1   0   0.449  69.9420   1.0452  -17.4668
 Z9K  H4   H  HCH1   0   0.209  67.4747  -0.3811  -13.6235
 Z9K  H5   H  HCH1   0   0.227  67.4373   1.0844  -15.3417
 Z9K  H3   H  HCH1   0   0.219  68.1440  -2.4727  -15.6868
 Z9K  H51  H  HCH3   0   0.227  70.0257  -3.7739  -13.0648
 Z9K  H52  H  HCH3   0   0.205  69.0092  -4.1690  -14.4571
 Z9K  H53  H  HCH3   0   0.212  70.5966  -3.4224  -14.7013
 Z9K  H2   H  HCH1   0   0.245  69.5643   0.1798  -15.2185
 Z9K  H1   H  HCH1   0   0.195  68.7486  -1.0604  -17.8700
 Z9K  HO4  H  HOH1   0   0.447  66.3616  -2.3813  -13.6679

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
 Z9K  O4   C4   single  1.409  0.020  1.409
 Z9K  C4   C5   single  1.532  0.020  1.532
 Z9K  C4   C3   single  1.536  0.020  1.536
 Z9K  C4   H4   single  0.970  0.020  1.090
 Z9K  C5   O5   single  1.419  0.020  1.419
 Z9K  C5   C6   single  1.545  0.020  1.545
 Z9K  C5   H5   single  0.970  0.020  1.090
 Z9K  O5   C1   single  1.390  0.020  1.390
 Z9K  C6   O10  deloc   1.246  0.020  1.246
 Z9K  C6   O6   deloc   1.239  0.020  1.239
 Z9K  C3   O3   single  1.406  0.020  1.406
 Z9K  C3   C2   single  1.523  0.020  1.523
 Z9K  C3   H3   single  0.970  0.020  1.090
 Z9K  O3   C7   single  1.409  0.020  1.409
 Z9K  C7   H51  single  0.970  0.020  1.090
 Z9K  C7   H52  single  0.970  0.020  1.090
 Z9K  C7   H53  single  0.970  0.020  1.090
 Z9K  C2   O2   single  1.422  0.020  1.422
 Z9K  C2   C1   single  1.543  0.020  1.543
 Z9K  C2   H2   single  0.970  0.020  1.090
 Z9K  O2   S1   single  1.646  0.020  1.646
 Z9K  S1   O7   deloc   1.476  0.020  1.476
 Z9K  S1   O8   deloc   1.461  0.020  1.461
 Z9K  S1   O9   deloc   1.457  0.020  1.457
 Z9K  C1   O1   single  1.396  0.020  1.396
 Z9K  C1   H1   single  0.970  0.020  1.090
 Z9K  HO1  O1   single  0.850  0.020  0.980
 Z9K  O4   HO4  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
 Z9K  HO4  O4  C4   108.18  3.000
 Z9K  H4   C4  C3   107.60  3.000
 Z9K  H4   C4  C5   107.56  3.000
 Z9K  C3   C4  C5   109.62  3.000
 Z9K  H4   C4  O4   110.87  3.000
 Z9K  C3   C4  O4   110.96  3.000
 Z9K  C5   C4  O4   110.14  3.000
 Z9K  H5   C5  C6   106.32  3.000
 Z9K  H5   C5  O5   109.51  3.000
 Z9K  C6   C5  O5   111.72  3.000
 Z9K  H5   C5  C4   107.37  3.000
 Z9K  C6   C5  C4   112.18  3.000
 Z9K  O5   C5  C4   109.57  3.000
 Z9K  C1   O5  C5   113.20  3.000
 Z9K  O6   C6  O10  128.39  3.000
 Z9K  O6   C6  C5   117.99  3.000
 Z9K  O10  C6  C5   113.61  3.000
 Z9K  H3   C3  C2   108.71  3.000
 Z9K  H3   C3  O3   110.10  3.000
 Z9K  C2   C3  O3   112.80  3.000
 Z9K  H3   C3  C4   108.01  3.000
 Z9K  C2   C3  C4   108.77  3.000
 Z9K  O3   C3  C4   108.33  3.000
 Z9K  C7   O3  C3   115.94  3.000
 Z9K  H53  C7  H52  108.11  3.000
 Z9K  H53  C7  H51  108.30  3.000
 Z9K  H52  C7  H51  108.04  3.000
 Z9K  H53  C7  O3   113.10  3.000
 Z9K  H52  C7  O3   111.80  3.000
 Z9K  H51  C7  O3   107.33  3.000
 Z9K  H2   C2  C1   110.13  3.000
 Z9K  H2   C2  O2   110.33  3.000
 Z9K  C1   C2  O2   109.41  3.000
 Z9K  H2   C2  C3   108.41  3.000
 Z9K  C1   C2  C3   108.67  3.000
 Z9K  O2   C2  C3   109.86  3.000
 Z9K  S1   O2  C2   117.70  3.000
 Z9K  O9   S1  O8   115.18  3.000
 Z9K  O9   S1  O7   114.68  3.000
 Z9K  O8   S1  O7   113.24  3.000
 Z9K  O9   S1  O2   101.19  3.000
 Z9K  O8   S1  O2   105.87  3.000
 Z9K  O7   S1  O2   104.86  3.000
 Z9K  H1   C1  O1   110.82  3.000
 Z9K  H1   C1  C2   107.56  3.000
 Z9K  O1   C1  C2   112.47  3.000
 Z9K  H1   C1  O5   105.70  3.000
 Z9K  O1   C1  O5   108.73  3.000
 Z9K  C2   C1  O5   111.35  3.000
 Z9K  HO1  O1  C1   108.13  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
 Z9K  Var_01  O7   S1  O2  C2   -55.42  30.0  3
 Z9K  Var_02  H51  C7  O3  C3  -170.33  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
 Z9K  chir_01  C4  O4  C5  C3  positiv
 Z9K  chir_02  C5  O5  C4  C6  positiv
 Z9K  chir_03  C3  O3  C4  C2  negativ
 Z9K  chir_04  C2  O2  C3  C1  positiv
 Z9K  chir_05  C1  O5  O1  C2  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
 Z9K  plan-1  C5   0.020
 Z9K  plan-1  C6   0.020
 Z9K  plan-1  O10  0.020
 Z9K  plan-1  O6   0.020

