# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:17:13 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: alpha-D-glucopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)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
 GCU  GCU  'alpha-D-glucopyranuronic acid'  D-saccharide  22  13  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GCU
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
 GCU  C1   C  CH1    0   0.231  39.7603  20.4839  29.3666
 GCU  C2   C  CH1    0   0.014  39.1736  20.3823  30.7730
 GCU  C3   C  CH1    0  -0.006  40.2353  20.6961  31.8189
 GCU  C4   C  CH1    0   0.020  41.4389  19.7901  31.6048
 GCU  C5   C  CH1    0  -0.153  41.9294  19.9274  30.1548
 GCU  C6   C  C      0   0.431  43.1243  18.9938  29.8693
 GCU  O1   O  OH1    0  -0.662  40.0481  21.8188  29.0971
 GCU  O2   O  OH1    0  -0.669  38.0581  21.2314  30.8572
 GCU  O3   O  OH1    0  -0.675  39.6368  20.5073  33.0830
 GCU  O4   O  OH1    0  -0.704  42.4465  20.1359  32.5161
 GCU  O5   O  O2     0  -0.495  40.8800  19.6519  29.2492
 GCU  O6A  O  O      0  -0.614  43.9952  18.9840  30.7818
 GCU  O6B  O  OC    -1  -0.555  43.1596  18.3688  28.8077
 GCU  H1   H  HCH1   0   0.228  39.0395  20.0844  28.6423
 GCU  H2   H  HCH1   0   0.211  38.8737  19.3308  30.9054
 GCU  H3   H  HCH1   0   0.204  40.5636  21.7397  31.7003
 GCU  H4   H  HCH1   0   0.182  41.1068  18.7468  31.7545
 GCU  H5   H  HCH1   0   0.221  42.2919  20.9592  30.0222
 GCU  HO1  H  HOH1   0   0.457  40.2413  21.9119  28.1579
 GCU  HO2  H  HOH1   0   0.447  37.6828  21.1330  31.7379
 GCU  HO3  H  HOH1   0   0.451  40.2451  20.8263  33.7566
 GCU  HO4  H  HOH1   0   0.437  43.2536  19.7389  32.1082

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
 GCU  C1  C2   single  1.527  0.020  1.527
 GCU  C1  O1   single  1.392  0.020  1.392
 GCU  C1  O5   single  1.400  0.020  1.400
 GCU  C1  H1   single  0.970  0.020  1.090
 GCU  C2  C3   single  1.523  0.020  1.523
 GCU  C2  O2   single  1.404  0.020  1.404
 GCU  C2  H2   single  0.970  0.020  1.090
 GCU  C3  C4   single  1.522  0.020  1.522
 GCU  C3  O3   single  1.411  0.020  1.411
 GCU  C3  H3   single  0.970  0.020  1.090
 GCU  C4  C5   single  1.537  0.020  1.537
 GCU  C4  O4   single  1.402  0.020  1.402
 GCU  C4  H4   single  0.970  0.020  1.090
 GCU  C5  C6   single  1.543  0.020  1.543
 GCU  C5  O5   single  1.413  0.020  1.413
 GCU  C5  H5   single  0.970  0.020  1.090
 GCU  C6  O6A  deloc   1.261  0.020  1.261
 GCU  C6  O6B  deloc   1.232  0.020  1.232
 GCU  O1  HO1  single  0.850  0.020  0.980
 GCU  O2  HO2  single  0.850  0.020  0.980
 GCU  O3  HO3  single  0.850  0.020  0.980
 GCU  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
 GCU  H1   C1  O5   104.70  3.000
 GCU  H1   C1  O1   110.93  3.000
 GCU  O5   C1  O1   112.86  3.000
 GCU  H1   C1  C2   109.34  3.000
 GCU  O5   C1  C2   110.18  3.000
 GCU  O1   C1  C2   108.75  3.000
 GCU  H2   C2  O2   110.72  3.000
 GCU  H2   C2  C3   107.69  3.000
 GCU  O2   C2  C3   112.83  3.000
 GCU  H2   C2  C1   106.19  3.000
 GCU  O2   C2  C1   108.67  3.000
 GCU  C3   C2  C1   110.54  3.000
 GCU  H3   C3  O3   110.48  3.000
 GCU  H3   C3  C4   108.27  3.000
 GCU  O3   C3  C4   112.45  3.000
 GCU  H3   C3  C2   109.23  3.000
 GCU  O3   C3  C2   106.97  3.000
 GCU  C4   C3  C2   109.40  3.000
 GCU  H4   C4  O4   111.15  3.000
 GCU  H4   C4  C5   107.94  3.000
 GCU  O4   C4  C5   111.22  3.000
 GCU  H4   C4  C3   107.78  3.000
 GCU  O4   C4  C3   109.28  3.000
 GCU  C5   C4  C3   109.39  3.000
 GCU  H5   C5  O5   110.48  3.000
 GCU  H5   C5  C6   106.83  3.000
 GCU  O5   C5  C6   109.79  3.000
 GCU  H5   C5  C4   107.59  3.000
 GCU  O5   C5  C4   110.50  3.000
 GCU  C6   C5  C4   111.57  3.000
 GCU  O6B  C6  O6A  126.82  3.000
 GCU  O6B  C6  C5   119.24  3.000
 GCU  O6A  C6  C5   113.92  3.000
 GCU  HO1  O1  C1   108.83  3.000
 GCU  HO2  O2  C2   107.62  3.000
 GCU  HO3  O3  C3   108.34  3.000
 GCU  HO4  O4  C4   102.69  3.000
 GCU  C5   O5  C1   115.11  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
 GCU  chir_01  C1  C2  O1  O5  negativ
 GCU  chir_02  C2  O2  C1  C3  negativ
 GCU  chir_03  C3  O3  C2  C4  positiv
 GCU  chir_04  C4  O4  C3  C5  negativ
 GCU  chir_05  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
 GCU  plan-1  C5   0.020
 GCU  plan-1  C6   0.020
 GCU  plan-1  O6A  0.020
 GCU  plan-1  O6B  0.020

