# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:41:42 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: beta-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
 BDP  BDP  'beta-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_BDP
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
 BDP  C1   C  CH1    0   0.279   8.6815  -11.6303  3.3746
 BDP  C2   C  CH1    0   0.004   9.0749  -11.1056  4.7519
 BDP  C3   C  CH1    0  -0.014   8.4353  -11.9802  5.8233
 BDP  C4   C  CH1    0   0.028   6.9353  -12.0959  5.6020
 BDP  C5   C  CH1    0  -0.161   6.6839  -12.5696  4.1619
 BDP  C6   C  C      0   0.437   5.1801  -12.7266  3.8565
 BDP  O2   O  OH1    0  -0.669  10.4774  -11.1134  4.8428
 BDP  O3   O  OH1    0  -0.673   8.7597  -11.4122  7.0732
 BDP  O4   O  OH1    0  -0.705   6.4032  -12.9907  6.5404
 BDP  O5   O  O2     0  -0.491   7.2809  -11.6720  3.2577
 BDP  O6A  O  O      0  -0.613   4.5220  -13.2662  4.7876
 BDP  O1   O  OH1    0  -0.655   9.1756  -10.7729  2.4141
 BDP  O6B  O  OC    -1  -0.553   4.7503  -12.3564  2.7631
 BDP  H1   H  HCH1   0   0.178   9.0853  -12.6525  3.2521
 BDP  H2   H  HCH1   0   0.206   8.6738  -10.0832  4.8508
 BDP  H3   H  HCH1   0   0.201   8.8626  -12.9929  5.7363
 BDP  H4   H  HCH1   0   0.184   6.4911  -11.0902  5.7096
 BDP  H5   H  HCH1   0   0.218   7.1373  -13.5732  4.0561
 BDP  HO2  H  HOH1   0   0.448  10.7129  -10.9013  5.7523
 BDP  HO3  H  HOH1   0   0.452   8.5160  -12.0369  7.7633
 BDP  HO4  H  HOH1   0   0.438   5.5480  -13.2577  6.1236
 BDP  HO1  H  HOH1   0   0.459   9.1670  -11.2157  1.5589

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
 BDP  C1  C2   single  1.525  0.020  1.525
 BDP  C1  O5   single  1.406  0.020  1.406
 BDP  C1  O1   single  1.379  0.020  1.379
 BDP  C1  H1   single  0.970  0.020  1.090
 BDP  C2  C3   single  1.524  0.020  1.524
 BDP  C2  O2   single  1.405  0.020  1.405
 BDP  C2  H2   single  0.970  0.020  1.090
 BDP  C3  C4   single  1.521  0.020  1.521
 BDP  C3  O3   single  1.411  0.020  1.411
 BDP  C3  H3   single  0.970  0.020  1.090
 BDP  C4  C5   single  1.537  0.020  1.537
 BDP  C4  O4   single  1.402  0.020  1.402
 BDP  C4  H4   single  0.970  0.020  1.090
 BDP  C5  C6   single  1.543  0.020  1.543
 BDP  C5  O5   single  1.407  0.020  1.407
 BDP  C5  H5   single  0.970  0.020  1.090
 BDP  C6  O6A  deloc   1.261  0.020  1.261
 BDP  C6  O6B  deloc   1.232  0.020  1.232
 BDP  O2  HO2  single  0.850  0.020  0.980
 BDP  O3  HO3  single  0.850  0.020  0.980
 BDP  O4  HO4  single  0.850  0.020  0.980
 BDP  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
 BDP  H1   C1  O1   111.52  3.000
 BDP  H1   C1  O5   109.09  3.000
 BDP  O1   C1  O5   108.50  3.000
 BDP  H1   C1  C2   108.89  3.000
 BDP  O1   C1  C2   108.82  3.000
 BDP  O5   C1  C2   110.01  3.000
 BDP  H2   C2  O2   111.24  3.000
 BDP  H2   C2  C3   108.45  3.000
 BDP  O2   C2  C3   111.73  3.000
 BDP  H2   C2  C1   107.82  3.000
 BDP  O2   C2  C1   108.29  3.000
 BDP  C3   C2  C1   109.22  3.000
 BDP  H3   C3  O3   110.52  3.000
 BDP  H3   C3  C4   107.51  3.000
 BDP  O3   C3  C4   112.73  3.000
 BDP  H3   C3  C2   108.00  3.000
 BDP  O3   C3  C2   107.18  3.000
 BDP  C4   C3  C2   110.82  3.000
 BDP  H4   C4  O4   111.31  3.000
 BDP  H4   C4  C5   107.82  3.000
 BDP  O4   C4  C5   111.62  3.000
 BDP  H4   C4  C3   108.25  3.000
 BDP  O4   C4  C3   109.01  3.000
 BDP  C5   C4  C3   108.73  3.000
 BDP  H5   C5  O5   110.08  3.000
 BDP  H5   C5  C6   106.75  3.000
 BDP  O5   C5  C6   110.57  3.000
 BDP  H5   C5  C4   107.59  3.000
 BDP  O5   C5  C4   109.65  3.000
 BDP  C6   C5  C4   112.11  3.000
 BDP  O6B  C6  O6A  127.00  3.000
 BDP  O6B  C6  C5   119.03  3.000
 BDP  O6A  C6  C5   113.95  3.000
 BDP  HO2  O2  C2   107.69  3.000
 BDP  HO3  O3  C3   108.41  3.000
 BDP  HO4  O4  C4   102.63  3.000
 BDP  C5   O5  C1   112.84  3.000
 BDP  HO1  O1  C1   109.23  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
 BDP  chir_01  C1  C2  O5  O1  negativ
 BDP  chir_02  C2  O2  C1  C3  negativ
 BDP  chir_03  C3  O3  C2  C4  positiv
 BDP  chir_04  C4  O4  C3  C5  negativ
 BDP  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
 BDP  plan-1  C5   0.020
 BDP  plan-1  C6   0.020
 BDP  plan-1  O6A  0.020
 BDP  plan-1  O6B  0.020

