# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 23:49:39 2021
#   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  30  18  .  2023-02-15  2023-02-16
;
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  -0.658  66.2215  -1.8896  -14.5166
 Z9K  C4   C  CR16  0   0.018  67.2703  -0.9586  -14.5226
 Z9K  C5   C  CR16  0  -0.125  67.0007   0.2369  -15.4641
 Z9K  O5   O  O     0  -0.482  67.4285  -0.0598  -16.7749
 Z9K  C6   C  C     0   0.518  65.5265   0.5688  -15.4495
 Z9K  O10  O  O     0  -0.440  64.9733   0.9085  -14.4344
 Z9K  O6   O  OH1   0  -0.568  64.9397   0.4468  -16.6205
 Z9K  C3   C  CR16  0   0.062  68.5393  -1.6868  -14.9813
 Z9K  O3   O  O2    0  -0.489  69.1356  -2.3028  -13.8796
 Z9K  C7   C  CH3   0  -0.413  69.5632  -3.6326  -14.0896
 Z9K  C2   C  CR16  0  -0.123  69.4636  -0.6587  -15.6260
 Z9K  O2   O  OC2   0  -0.579  70.7110  -1.2919  -15.9360
 Z9K  S1   S  S     0   1.646  72.0592  -0.4268  -15.9740
 Z9K  O7   O  OS    0  -0.726  71.9319   0.3631  -17.3268
 Z9K  O8   O  OS    0  -0.631  72.0672   0.4874  -14.8597
 Z9K  O9   O  OS    0  -0.618  73.1123  -1.3838  -16.1485
 Z9K  C1   C  CR16  0   0.286  68.8081  -0.1487  -16.9138
 Z9K  O1   O  OH1   0  -0.680  69.3904   1.0986  -17.2174
 Z9K  HO1  H  HOH1  0   0.491  69.0844   1.3933  -18.0868
 Z9K  H4   H  HCR6  0   0.261  67.4578  -0.5527  -13.5229
 Z9K  H5   H  HCR6  0   0.299  67.5185   1.1243  -15.0753
 Z9K  HO6  H  HOH1  0   0.491  63.9985   0.6675  -16.5417
 Z9K  H3   H  HCR6  0   0.253  68.2564  -2.4279  -15.7423
 Z9K  H51  H  HCH3  0   0.239  69.9011  -4.0178  -13.1289
 Z9K  H52  H  HCH3  0   0.217  68.7465  -4.2670  -14.4478
 Z9K  H53  H  HCH3  0   0.217  70.3911  -3.7033  -14.7996
 Z9K  H2   H  HCR6  0   0.296  69.6333   0.1619  -14.9187
 Z9K  H7O  H  H     0   0.502  71.0601   0.8506  -17.3837
 Z9K  H1   H  HCR6  0   0.270  68.9818  -0.8625  -17.7259
 Z9K  HO4  H  HOH1  0   0.465  65.6473  -1.7176  -13.7648

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  1.402  0.020  1.402
 Z9K  C4   C5   single  1.545  0.020  1.545
 Z9K  C4   C3   single  1.533  0.020  1.533
 Z9K  C4   H4   single  0.970  0.020  1.090
 Z9K  C5   O5   single  1.410  0.020  1.410
 Z9K  C5   C6   single  1.511  0.020  1.511
 Z9K  C5   H5   single  0.970  0.020  1.090
 Z9K  O5   C1   single  1.389  0.020  1.389
 Z9K  C6   O10  double  1.205  0.020  1.205
 Z9K  C6   O6   single  1.315  0.020  1.315
 Z9K  O6   HO6  single  0.850  0.020  0.980
 Z9K  C3   O3   single  1.396  0.020  1.396
 Z9K  C3   C2   single  1.525  0.020  1.525
 Z9K  C3   H3   single  0.970  0.020  1.090
 Z9K  O3   C7   single  1.413  0.020  1.413
 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  1.433  0.020  1.433
 Z9K  C2   C1   single  1.532  0.020  1.532
 Z9K  C2   H2   single  0.970  0.020  1.090
 Z9K  O2   S1   single  1.602  0.020  1.602
 Z9K  S1   O7   single  1.572  0.020  1.572
 Z9K  S1   O8   double  1.441  0.020  1.441
 Z9K  S1   O9   double  1.434  0.020  1.434
 Z9K  O7   H7O  single  0.850  0.020  0.980
 Z9K  C1   O1   single  1.410  0.020  1.410
 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   109.34  3.000
 Z9K  H4   C4  C3   107.90  3.000
 Z9K  H4   C4  C5   107.41  3.000
 Z9K  C3   C4  C5   109.24  3.000
 Z9K  H4   C4  O4   111.74  3.000
 Z9K  C3   C4  O4   107.76  3.000
 Z9K  C5   C4  O4   112.68  3.000
 Z9K  H5   C5  C6   106.20  3.000
 Z9K  H5   C5  O5   110.85  3.000
 Z9K  C6   C5  O5   110.55  3.000
 Z9K  H5   C5  C4   109.09  3.000
 Z9K  C6   C5  C4   109.52  3.000
 Z9K  O5   C5  C4   110.52  3.000
 Z9K  C1   O5  C5   114.05  3.000
 Z9K  O6   C6  O10  124.85  3.000
 Z9K  O6   C6  C5   113.97  3.000
 Z9K  O10  C6  C5   121.19  3.000
 Z9K  HO6  O6  C6   109.84  3.000
 Z9K  H3   C3  C2   108.52  3.000
 Z9K  H3   C3  O3   111.03  3.000
 Z9K  C2   C3  O3   111.84  3.000
 Z9K  H3   C3  C4   108.32  3.000
 Z9K  C2   C3  C4   107.93  3.000
 Z9K  O3   C3  C4   109.08  3.000
 Z9K  C7   O3  C3   115.30  3.000
 Z9K  H53  C7  H52  108.37  3.000
 Z9K  H53  C7  H51  108.38  3.000
 Z9K  H52  C7  H51  108.38  3.000
 Z9K  H53  C7  O3   112.76  3.000
 Z9K  H52  C7  O3   111.62  3.000
 Z9K  H51  C7  O3   107.20  3.000
 Z9K  H2   C2  C1   111.05  3.000
 Z9K  H2   C2  O2   109.60  3.000
 Z9K  C1   C2  O2   109.73  3.000
 Z9K  H2   C2  C3   109.00  3.000
 Z9K  C1   C2  C3   108.68  3.000
 Z9K  O2   C2  C3   108.73  3.000
 Z9K  S1   O2  C2   119.94  3.000
 Z9K  O9   S1  O8   120.89  3.000
 Z9K  O9   S1  O7   106.87  3.000
 Z9K  O8   S1  O7   110.31  3.000
 Z9K  O9   S1  O2   105.10  3.000
 Z9K  O8   S1  O2   109.19  3.000
 Z9K  O7   S1  O2   102.92  3.000
 Z9K  H7O  O7  S1   111.38  3.000
 Z9K  H1   C1  O1   110.58  3.000
 Z9K  H1   C1  C2   109.78  3.000
 Z9K  O1   C1  C2   107.39  3.000
 Z9K  H1   C1  O5   105.86  3.000
 Z9K  O1   C1  O5   112.03  3.000
 Z9K  C2   C1  O5   111.22  3.000
 Z9K  HO1  O1  C1   109.42  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  CONST_01  HO6  O6  C6  C5   180.00   0.0  0
 Z9K  Var_01    O7   S1  O2  C2   -75.04  30.0  3
 Z9K  Var_02    H51  C7  O3  C3  -173.82  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
 Z9K  plan-1  HO6  0.020

