# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 19:42:40 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 2,3-di-O-methyl-beta-D-glucopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)O[C@@H]([C@@H](O)[C@@H]1OC)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
 GU1  GU1  '2,3-di-O-methyl-beta-D-glucopyranuronic acid'  D-saccharide  28  15  .  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_GU1
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
 GU1  O1   O  OH1    0  -0.653  56.9496  -2.2759  -12.6079
 GU1  C1   C  CH1    0   0.282  57.0954  -2.3811  -11.2398
 GU1  C2   C  CH1    0  -0.011  57.8634  -1.1617  -10.7239
 GU1  O2   O  O2     0  -0.491  59.1790  -1.1528  -11.2136
 GU1  C7   C  CH3    0  -0.403  59.4130  -0.3027  -12.3101
 GU1  C3   C  CH1    0  -0.001  57.9274  -1.2204   -9.1948
 GU1  O3   O  O2     0  -0.481  58.6617  -0.1561   -8.6414
 GU1  C8   C  CH3    0  -0.415  58.0919   1.1284   -8.7153
 GU1  O5   O  O2     0  -0.487  55.8165  -2.4309  -10.6618
 GU1  C5   C  CH1    0  -0.151  55.8574  -2.6021   -9.2677
 GU1  C6   C  C      0   0.437  54.4323  -2.8415   -8.7252
 GU1  O6B  O  OC    -1  -0.611  54.3157  -2.6877   -7.4794
 GU1  O6A  O  O      0  -0.554  53.5504  -3.1807   -9.5155
 GU1  C4   C  CH1    0   0.014  56.5305  -1.3868   -8.6071
 GU1  O4   O  OH1    0  -0.699  56.6302  -1.5486   -7.2211
 GU1  HO1  H  HOH1   0   0.460  56.7156  -3.1373  -12.9701
 GU1  H1   H  HCH1   0   0.177  57.6563  -3.2925  -10.9614
 GU1  H2   H  HCH1   0   0.221  57.3163  -0.2619  -11.0444
 GU1  H71  H  HCH3   0   0.227  60.4868  -0.3007  -12.4974
 GU1  H72  H  HCH3   0   0.209  58.9060  -0.6311  -13.2208
 GU1  H73  H  HCH3   0   0.205  59.1036   0.7276  -12.1002
 GU1  H3   H  HCH1   0   0.229  58.5007  -2.1174   -8.9224
 GU1  H81  H  HCH3   0   0.234  58.8474   1.8305   -8.3639
 GU1  H82  H  HCH3   0   0.206  57.8139   1.4210   -9.7330
 GU1  H83  H  HCH3   0   0.210  57.2082   1.2391   -8.0793
 GU1  H5   H  HCH1   0   0.218  56.4554  -3.4964   -9.0090
 GU1  H4   H  HCH1   0   0.191  55.9206  -0.5031   -8.8666
 GU1  HO4  H  HOH1   0   0.435  55.7612  -1.9555   -6.9883

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
 GU1  O1  C1   single  1.380  0.020  1.380
 GU1  O1  HO1  single  0.850  0.020  0.980
 GU1  C1  C2   single  1.531  0.020  1.531
 GU1  C1  O5   single  1.404  0.020  1.404
 GU1  C1  H1   single  0.970  0.020  1.090
 GU1  C2  O2   single  1.404  0.020  1.404
 GU1  C2  C3   single  1.532  0.020  1.532
 GU1  C2  H2   single  0.970  0.020  1.090
 GU1  O2  C7   single  1.407  0.020  1.407
 GU1  C7  H71  single  0.970  0.020  1.090
 GU1  C7  H72  single  0.970  0.020  1.090
 GU1  C7  H73  single  0.970  0.020  1.090
 GU1  C3  O3   single  1.407  0.020  1.407
 GU1  C3  C4   single  1.525  0.020  1.525
 GU1  C3  H3   single  0.970  0.020  1.090
 GU1  O3  C8   single  1.407  0.020  1.407
 GU1  C8  H81  single  0.970  0.020  1.090
 GU1  C8  H82  single  0.970  0.020  1.090
 GU1  C8  H83  single  0.970  0.020  1.090
 GU1  O5  C5   single  1.405  0.020  1.405
 GU1  C5  C6   single  1.544  0.020  1.544
 GU1  C5  C4   single  1.538  0.020  1.538
 GU1  C5  H5   single  0.970  0.020  1.090
 GU1  C6  O6B  deloc   1.261  0.020  1.261
 GU1  C6  O6A  deloc   1.232  0.020  1.232
 GU1  C4  O4   single  1.399  0.020  1.399
 GU1  C4  H4   single  0.970  0.020  1.090
 GU1  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
 GU1  HO1  O1  C1   109.29  3.000
 GU1  H1   C1  O5   109.21  3.000
 GU1  H1   C1  C2   108.50  3.000
 GU1  O5   C1  C2   110.27  3.000
 GU1  H1   C1  O1   111.47  3.000
 GU1  O5   C1  O1   108.34  3.000
 GU1  C2   C1  O1   109.06  3.000
 GU1  H2   C2  C3   110.05  3.000
 GU1  H2   C2  O2   111.04  3.000
 GU1  C3   C2  O2   108.02  3.000
 GU1  H2   C2  C1   107.68  3.000
 GU1  C3   C2  C1   109.08  3.000
 GU1  O2   C2  C1   110.96  3.000
 GU1  C7   O2  C2   115.57  3.000
 GU1  H73  C7  H72  108.12  3.000
 GU1  H73  C7  H71  108.02  3.000
 GU1  H72  C7  H71  108.32  3.000
 GU1  H73  C7  O2   111.83  3.000
 GU1  H72  C7  O2   113.00  3.000
 GU1  H71  C7  O2   107.39  3.000
 GU1  H3   C3  C4   107.06  3.000
 GU1  H3   C3  O3   104.35  3.000
 GU1  C4   C3  O3   114.16  3.000
 GU1  H3   C3  C2   107.49  3.000
 GU1  C4   C3  C2   110.53  3.000
 GU1  O3   C3  C2   112.68  3.000
 GU1  C8   O3  C3   117.30  3.000
 GU1  H83  C8  H82  107.95  3.000
 GU1  H83  C8  H81  107.90  3.000
 GU1  H82  C8  H81  107.68  3.000
 GU1  H83  C8  O3   112.88  3.000
 GU1  H82  C8  O3   113.31  3.000
 GU1  H81  C8  O3   106.88  3.000
 GU1  C5   O5  C1   112.72  3.000
 GU1  H5   C5  C4   107.56  3.000
 GU1  H5   C5  C6   106.94  3.000
 GU1  C4   C5  C6   112.06  3.000
 GU1  H5   C5  O5   110.25  3.000
 GU1  C4   C5  O5   110.03  3.000
 GU1  C6   C5  O5   109.92  3.000
 GU1  O6A  C6  O6B  126.97  3.000
 GU1  O6A  C6  C5   118.57  3.000
 GU1  O6B  C6  C5   114.45  3.000
 GU1  H4   C4  O4   111.38  3.000
 GU1  H4   C4  C5   106.83  3.000
 GU1  O4   C4  C5   111.42  3.000
 GU1  H4   C4  C3   109.15  3.000
 GU1  O4   C4  C3   109.22  3.000
 GU1  C5   C4  C3   108.76  3.000
 GU1  HO4  O4  C4   102.62  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
 GU1  Var_01  H71  C7  O2  C2   172.87  30.0  3
 GU1  Var_02  H81  C8  O3  C3  -172.63  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
 GU1  chir_01  C1  O1  C2  O5  negativ
 GU1  chir_02  C2  O2  C3  C1  positiv
 GU1  chir_03  C3  O3  C4  C2  negativ
 GU1  chir_04  C5  O5  C6  C4  positiv
 GU1  chir_05  C4  O4  C5  C3  positiv

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
 GU1  plan-1  C5   0.020
 GU1  plan-1  C6   0.020
 GU1  plan-1  O6B  0.020
 GU1  plan-1  O6A  0.020

