# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 19:25:58 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-L-gulopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 GUP  GUP  'alpha-L-gulopyranose     '  L-saccharide  24  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GUP
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
 GUP  O5   O  O2    0  -0.499  19.3187  -11.6511  22.2246
 GUP  C1   C  CH1   0   0.237  18.1274  -11.1811  22.7514
 GUP  O1   O  OH1   0  -0.667  17.1363  -12.1666  22.5647
 GUP  C2   C  CH1   0   0.001  18.2852  -10.8119  24.2294
 GUP  O2   O  OH1   0  -0.669  17.0183  -10.4003  24.6772
 GUP  C3   C  CH1   0  -0.073  18.8673  -11.9805  25.0306
 GUP  O3   O  OH1   0  -0.669  17.9794  -13.0606  25.1835
 GUP  C4   C  CH1   0   0.006  20.1823  -12.4305  24.3655
 GUP  O4   O  OH1   0  -0.668  21.1704  -11.4302  24.4507
 GUP  C5   C  CH1   0  -0.032  19.9297  -12.7479  22.8998
 GUP  C6   C  CH2   0  -0.167  21.1956  -13.0788  22.1262
 GUP  O6   O  OH1   0  -0.662  20.9253  -13.5614  20.8310
 GUP  H1   H  HCH1  0   0.240  17.8786  -10.2808  22.1754
 GUP  HO1  H  HOH1  0   0.462  16.2816  -11.7928  22.8098
 GUP  H2   H  HCH1  0   0.223  19.0095   -9.9887  24.2765
 GUP  HO2  H  HOH1  0   0.457  17.0819  -10.1335  25.5999
 GUP  H3   H  HCH1  0   0.247  19.1003  -11.6298  26.0452
 GUP  HO3  H  HOH1  0   0.441  17.4977  -13.1814  24.3561
 GUP  H4   H  HCH1  0   0.232  20.5105  -13.3590  24.8539
 GUP  HO4  H  HOH1  0   0.454  21.3862  -11.2937  25.3790
 GUP  H5   H  HCH1  0   0.231  19.2799  -13.6319  22.8594
 GUP  H61  H  HCH2  0   0.225  21.7245  -13.8737  22.6567
 GUP  H62  H  HCH2  0   0.208  21.8574  -12.2062  22.1026
 GUP  HO6  H  HOH1  0   0.445  20.5132  -12.8516  20.3288

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
 GUP  O5  C1   single  1.385  0.020  1.385
 GUP  O5  C5   single  1.426  0.020  1.426
 GUP  C1  O1   single  1.410  0.020  1.410
 GUP  C1  C2   single  1.532  0.020  1.532
 GUP  C1  H1   single  0.970  0.020  1.090
 GUP  O1  HO1  single  0.850  0.020  0.980
 GUP  C2  O2   single  1.405  0.020  1.405
 GUP  C2  C3   single  1.532  0.020  1.532
 GUP  C2  H2   single  0.970  0.020  1.090
 GUP  O2  HO2  single  0.850  0.020  0.980
 GUP  C3  O3   single  1.407  0.020  1.407
 GUP  C3  C4   single  1.541  0.020  1.541
 GUP  C3  H3   single  0.970  0.020  1.090
 GUP  O3  HO3  single  0.850  0.020  0.980
 GUP  C4  O4   single  1.409  0.020  1.409
 GUP  C4  C5   single  1.521  0.020  1.521
 GUP  C4  H4   single  0.970  0.020  1.090
 GUP  O4  HO4  single  0.850  0.020  0.980
 GUP  C5  C6   single  1.520  0.020  1.520
 GUP  C5  H5   single  0.970  0.020  1.090
 GUP  C6  O6   single  1.408  0.020  1.408
 GUP  C6  H61  single  0.970  0.020  1.090
 GUP  C6  H62  single  0.970  0.020  1.090
 GUP  O6  HO6  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
 GUP  C5   O5  C1   116.72  3.000
 GUP  H1   C1  C2   109.40  3.000
 GUP  H1   C1  O1   110.15  3.000
 GUP  C2   C1  O1   111.64  3.000
 GUP  H1   C1  O5   105.89  3.000
 GUP  C2   C1  O5   111.12  3.000
 GUP  O1   C1  O5   108.49  3.000
 GUP  HO1  O1  C1   108.56  3.000
 GUP  H2   C2  C3   107.39  3.000
 GUP  H2   C2  O2   111.20  3.000
 GUP  C3   C2  O2   113.54  3.000
 GUP  H2   C2  C1   106.87  3.000
 GUP  C3   C2  C1   111.10  3.000
 GUP  O2   C2  C1   106.57  3.000
 GUP  HO2  O2  C2   109.09  3.000
 GUP  H3   C3  C4   108.11  3.000
 GUP  H3   C3  O3   106.18  3.000
 GUP  C4   C3  O3   111.18  3.000
 GUP  H3   C3  C2   108.67  3.000
 GUP  C4   C3  C2   108.75  3.000
 GUP  O3   C3  C2   113.75  3.000
 GUP  HO3  O3  C3   108.55  3.000
 GUP  H4   C4  C5   107.55  3.000
 GUP  H4   C4  O4   111.32  3.000
 GUP  C5   C4  O4   108.84  3.000
 GUP  H4   C4  C3   108.04  3.000
 GUP  C5   C4  C3   109.59  3.000
 GUP  O4   C4  C3   111.41  3.000
 GUP  HO4  O4  C4   108.43  3.000
 GUP  H5   C5  C6   107.39  3.000
 GUP  H5   C5  C4   107.57  3.000
 GUP  C6   C5  C4   113.43  3.000
 GUP  H5   C5  O5   110.39  3.000
 GUP  C6   C5  O5   106.46  3.000
 GUP  C4   C5  O5   111.54  3.000
 GUP  H62  C6  H61  107.32  3.000
 GUP  H62  C6  O6   111.66  3.000
 GUP  H61  C6  O6   106.87  3.000
 GUP  H62  C6  C5   109.92  3.000
 GUP  H61  C6  C5   108.33  3.000
 GUP  O6   C6  C5   112.51  3.000
 GUP  HO6  O6  C6   108.03  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
 GUP  chir_01  C1  O5  O1  C2  negativ
 GUP  chir_02  C2  O2  C1  C3  positiv
 GUP  chir_03  C3  O3  C2  C4  positiv
 GUP  chir_04  C4  O4  C5  C3  positiv
 GUP  chir_05  C5  O5  C4  C6  positiv

