# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 20:13:41 2021
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-O-beta-D-glucopyranosyl-D-gluconic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)[C@H](O)[C@@H](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
 CEZ  CEZ  '4-O-beta-D-glucopyranosyl-D-gluconic acid'  D-saccharide  46  24  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CEZ
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
 CEZ  O1   O  O2    0  -0.511  60.1023  -44.3808  -3.4285
 CEZ  C1   C  CH1   0   0.273  58.7986  -43.9304  -3.4295
 CEZ  C2   C  CH1   0   0.003  58.2547  -44.0470  -4.8536
 CEZ  O2   O  OH1   0  -0.678  58.9339  -43.1710  -5.7124
 CEZ  O5   O  O2    0  -0.509  58.0716  -44.7434  -2.5431
 CEZ  C5   C  CH1   0  -0.014  56.7082  -44.3654  -2.4418
 CEZ  C4   C  CH1   0   0.003  56.0449  -44.5362  -3.8133
 CEZ  O4   O  OH1   0  -0.675  54.7044  -44.1013  -3.7882
 CEZ  C3   C  CH1   0   0.009  56.7790  -43.6911  -4.8521
 CEZ  O3   O  OH1   0  -0.669  56.2683  -43.8975  -6.1436
 CEZ  C6   C  CH2   0  -0.193  56.0646  -45.1746  -1.3383
 CEZ  O6   O  OH1   0  -0.670  56.0240  -46.5316  -1.7055
 CEZ  C11  C  C     0   0.523  62.6650  -44.5493   0.6977
 CEZ  O11  O  O     0  -0.449  62.9010  -45.7311   0.7414
 CEZ  C21  C  CH1   0  -0.098  62.5410  -43.7934  -0.6215
 CEZ  O21  O  OH1   0  -0.657  62.3428  -42.4202  -0.4730
 CEZ  C31  C  CH1   0   0.011  61.3653  -44.3914  -1.3911
 CEZ  O31  O  OH1   0  -0.679  60.2499  -44.3269  -0.5356
 CEZ  C41  C  CH1   0  -0.029  61.0866  -43.6561  -2.7082
 CEZ  C51  C  CH1   0  -0.003  62.2855  -43.4715  -3.6443
 CEZ  O51  O  OH1   0  -0.665  61.8947  -42.7419  -4.7909
 CEZ  C61  C  CH2   0  -0.153  62.8796  -44.7837  -4.1202
 CEZ  O61  O  OH1   0  -0.669  64.0654  -44.5059  -4.8256
 CEZ  H1   H  HCH1  0   0.203  58.7403  -42.8752  -3.1076
 CEZ  H2   H  HCH1  0   0.216  58.3656  -45.0968  -5.1712
 CEZ  HO2  H  HOH1  0   0.442  59.8859  -43.2786  -5.5758
 CEZ  H5   H  HCH1  0   0.233  56.6328  -43.3076  -2.1424
 CEZ  H4   H  HCH1  0   0.232  56.1124  -45.5888  -4.1158
 CEZ  HO4  H  HOH1  0   0.462  54.1404  -44.8426  -3.5509
 CEZ  H3   H  HCH1  0   0.208  56.6827  -42.6320  -4.5570
 CEZ  HO3  H  HOH1  0   0.450  55.3272  -43.6934  -6.1229
 CEZ  H61  H  HCH2  0   0.223  56.6372  -45.0159  -0.4148
 CEZ  H62  H  HCH2  0   0.212  55.0640  -44.7638  -1.1579
 CEZ  HO6  H  HOH1  0   0.461  55.5829  -47.0193  -1.0044
 CEZ  H12  H  HOH1  0   0.485  62.6108  -44.3156   2.5655
 CEZ  H13  H  HCH1  0   0.272  63.4623  -44.0179  -1.1766
 CEZ  H14  H  HOH1  0   0.466  63.1719  -42.0057  -0.2156
 CEZ  H15  H  HCH1  0   0.236  61.6230  -45.4344  -1.6171
 CEZ  H16  H  HOH1  0   0.455  59.5038  -44.7796  -0.9495
 CEZ  H17  H  HCH1  0   0.257  60.7042  -42.6585  -2.4576
 CEZ  H18  H  HCH1  0   0.237  63.0570  -42.9176  -3.0950
 CEZ  H19  H  HOH1  0   0.460  61.7536  -41.8234  -4.5383
 CEZ  H20  H  HCH2  0   0.210  62.1484  -45.3119  -4.7444
 CEZ  H21  H  HCH2  0   0.198  63.0767  -45.4266  -3.2529
 CEZ  H22  H  HOH1  0   0.456  64.4378  -45.3424  -5.1185
 CEZ  O12  O  OH1   0  -0.575  62.5095  -43.7840   1.7610

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
 CEZ  O2   C2   single  1.402  0.020  1.402
 CEZ  O3   C3   single  1.404  0.020  1.404
 CEZ  C3   C2   single  1.518  0.020  1.518
 CEZ  C3   C4   single  1.527  0.020  1.527
 CEZ  C2   C1   single  1.529  0.020  1.529
 CEZ  O61  C61  single  1.407  0.020  1.407
 CEZ  C61  C51  single  1.517  0.020  1.517
 CEZ  O4   C4   single  1.410  0.020  1.410
 CEZ  O51  C51  single  1.414  0.020  1.414
 CEZ  C1   O1   single  1.379  0.020  1.379
 CEZ  C1   O5   single  1.405  0.020  1.405
 CEZ  C4   C5   single  1.533  0.020  1.533
 CEZ  O1   C41  single  1.419  0.020  1.419
 CEZ  C51  C41  single  1.532  0.020  1.532
 CEZ  C5   O5   single  1.418  0.020  1.418
 CEZ  C5   C6   single  1.512  0.020  1.512
 CEZ  C41  C31  single  1.534  0.020  1.534
 CEZ  C31  O31  single  1.407  0.020  1.407
 CEZ  C31  C21  single  1.527  0.020  1.527
 CEZ  C6   O6   single  1.406  0.020  1.406
 CEZ  C21  O21  single  1.395  0.020  1.395
 CEZ  C21  C11  single  1.525  0.020  1.525
 CEZ  O11  C11  double  1.206  0.020  1.206
 CEZ  C11  O12  single  1.319  0.020  1.319
 CEZ  C1   H1   single  0.970  0.020  1.090
 CEZ  C2   H2   single  0.970  0.020  1.090
 CEZ  O2   HO2  single  0.850  0.020  0.980
 CEZ  C5   H5   single  0.970  0.020  1.090
 CEZ  C4   H4   single  0.970  0.020  1.090
 CEZ  O4   HO4  single  0.850  0.020  0.980
 CEZ  C3   H3   single  0.970  0.020  1.090
 CEZ  O3   HO3  single  0.850  0.020  0.980
 CEZ  C6   H61  single  0.970  0.020  1.090
 CEZ  C6   H62  single  0.970  0.020  1.090
 CEZ  O6   HO6  single  0.850  0.020  0.980
 CEZ  O12  H12  single  0.850  0.020  0.980
 CEZ  C21  H13  single  0.970  0.020  1.090
 CEZ  O21  H14  single  0.850  0.020  0.980
 CEZ  C31  H15  single  0.970  0.020  1.090
 CEZ  O31  H16  single  0.850  0.020  0.980
 CEZ  C41  H17  single  0.970  0.020  1.090
 CEZ  C51  H18  single  0.970  0.020  1.090
 CEZ  O51  H19  single  0.850  0.020  0.980
 CEZ  C61  H20  single  0.970  0.020  1.090
 CEZ  C61  H21  single  0.970  0.020  1.090
 CEZ  O61  H22  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
 CEZ  C41  O1   C1   119.30  3.000
 CEZ  H1   C1   O5   109.97  3.000
 CEZ  H1   C1   C2   109.00  3.000
 CEZ  O5   C1   C2   111.06  3.000
 CEZ  H1   C1   O1   111.19  3.000
 CEZ  O5   C1   O1   107.43  3.000
 CEZ  C2   C1   O1   108.18  3.000
 CEZ  H2   C2   C3   108.75  3.000
 CEZ  H2   C2   O2   111.69  3.000
 CEZ  C3   C2   O2   108.97  3.000
 CEZ  H2   C2   C1   107.77  3.000
 CEZ  C3   C2   C1   109.09  3.000
 CEZ  O2   C2   C1   110.52  3.000
 CEZ  HO2  O2   C2   108.70  3.000
 CEZ  C5   O5   C1   112.83  3.000
 CEZ  H5   C5   C6   106.63  3.000
 CEZ  H5   C5   C4   108.69  3.000
 CEZ  C6   C5   C4   114.15  3.000
 CEZ  H5   C5   O5   109.94  3.000
 CEZ  C6   C5   O5   108.58  3.000
 CEZ  C4   C5   O5   108.81  3.000
 CEZ  H4   C4   C3   108.28  3.000
 CEZ  H4   C4   O4   111.06  3.000
 CEZ  C3   C4   O4   107.37  3.000
 CEZ  H4   C4   C5   109.08  3.000
 CEZ  O4   C4   C5   111.18  3.000
 CEZ  C3   C4   C5   109.81  3.000
 CEZ  HO4  O4   C4   108.94  3.000
 CEZ  H3   C3   O3   110.80  3.000
 CEZ  H3   C3   C4   107.89  3.000
 CEZ  O3   C3   C4   111.69  3.000
 CEZ  H3   C3   C2   108.07  3.000
 CEZ  C4   C3   C2   109.77  3.000
 CEZ  O3   C3   C2   108.56  3.000
 CEZ  HO3  O3   C3   107.73  3.000
 CEZ  H62  C6   H61  106.46  3.000
 CEZ  H62  C6   O6   112.21  3.000
 CEZ  H61  C6   O6   111.97  3.000
 CEZ  H62  C6   C5   107.93  3.000
 CEZ  H61  C6   C5   108.33  3.000
 CEZ  O6   C6   C5   109.75  3.000
 CEZ  HO6  O6   C6   108.20  3.000
 CEZ  C21  C11  O11  122.20  3.000
 CEZ  O11  C11  O12  124.21  3.000
 CEZ  C21  C11  O12  113.58  3.000
 CEZ  H13  C21  C31  108.12  3.000
 CEZ  H13  C21  O21  111.96  3.000
 CEZ  C31  C21  O21  109.24  3.000
 CEZ  H13  C21  C11  105.52  3.000
 CEZ  O21  C21  C11  114.03  3.000
 CEZ  C31  C21  C11  107.72  3.000
 CEZ  H14  O21  C21  109.27  3.000
 CEZ  H15  C31  C41  108.74  3.000
 CEZ  H15  C31  O31  110.78  3.000
 CEZ  C41  C31  O31  110.86  3.000
 CEZ  H15  C31  C21  107.15  3.000
 CEZ  O31  C31  C21  106.62  3.000
 CEZ  C41  C31  C21  112.64  3.000
 CEZ  H16  O31  C31  109.29  3.000
 CEZ  H17  C41  C51  107.62  3.000
 CEZ  H17  C41  C31  107.63  3.000
 CEZ  C51  C41  C31  116.11  3.000
 CEZ  H17  C41  O1   109.79  3.000
 CEZ  C31  C41  O1   108.49  3.000
 CEZ  C51  C41  O1   107.11  3.000
 CEZ  H18  C51  C61  108.57  3.000
 CEZ  H18  C51  O51  109.86  3.000
 CEZ  C61  C51  O51  107.47  3.000
 CEZ  H18  C51  C41  107.76  3.000
 CEZ  O51  C51  C41  109.95  3.000
 CEZ  C61  C51  C41  113.20  3.000
 CEZ  H19  O51  C51  108.66  3.000
 CEZ  H21  C61  H20  106.70  3.000
 CEZ  H21  C61  O61  111.12  3.000
 CEZ  H20  C61  O61  111.81  3.000
 CEZ  H21  C61  C51  109.21  3.000
 CEZ  H20  C61  C51  109.52  3.000
 CEZ  O61  C61  C51  108.45  3.000
 CEZ  H22  O61  C61  107.90  3.000
 CEZ  H12  O12  C11  109.78  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
 CEZ  CONST_01  H12  O12  C11  O11  0.00  0.0  0

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
 CEZ  chir_01  C1   C2   O1   O5   positiv
 CEZ  chir_02  C2   O2   C1   C3   negativ
 CEZ  chir_03  C5   O5   C4   C6   negativ
 CEZ  chir_04  C4   O4   C5   C3   positiv
 CEZ  chir_05  C3   O3   C2   C4   positiv
 CEZ  chir_06  C21  O21  C11  C31  negativ
 CEZ  chir_07  C31  O31  C21  C41  positiv
 CEZ  chir_08  C41  O1   C51  C31  positiv
 CEZ  chir_09  C51  O51  C41  C61  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
 CEZ  plan-1  C11  0.020
 CEZ  plan-1  O11  0.020
 CEZ  plan-1  C21  0.020
 CEZ  plan-1  H12  0.020
 CEZ  plan-1  O12  0.020

