# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 06:31:46 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: a 3 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@@H](O)C[C@H]2[C@@H]1[C@@H](OC=C2C(O)=O)O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O
#
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
 EQV  EQV  '(1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxyl ic acid'  D-saccharide  50  26  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EQV
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
 EQV  C01  C  CH3   0  -0.661  12.9676  8.8065  -20.5963
 EQV  C02  C  CR15  0  -0.242  12.5144  7.5033  -21.2333
 EQV  C03  C  CR15  0   0.038  11.0316  7.1572  -21.0551
 EQV  C04  C  CH2   0  -0.466  10.7535  6.2171  -22.2234
 EQV  C3   C  CR15  0  -0.252  11.4569  6.9219  -23.3866
 EQV  C2   C  CR15  0  -0.331  12.7702  7.4284  -22.7600
 EQV  C1   C  CH1   0   0.331  13.8902  6.4522  -23.0544
 EQV  O5   O  O2    0  -0.452  14.0395  6.2150  -24.4539
 EQV  C5   C  C1    0   0.067  12.9229  5.9064  -25.1085
 EQV  C4   C  C     0  -0.189  11.6836  6.1358  -24.6420
 EQV  C11  C  C     0   0.521  10.5121  5.7610  -25.4355
 EQV  O12  O  O     0  -0.455   9.3803  6.0901  -25.1531
 EQV  O13  O  OH1   0  -0.608  10.7894  5.0163  -26.5060
 EQV  O1   O  O2    0  -0.497  15.0882  6.9724  -22.6075
 EQV  C15  C  CH1   0   0.302  16.0766  6.0534  -22.2783
 EQV  C16  C  CH1   0  -0.002  17.4008  6.7950  -22.1570
 EQV  C17  C  CH1   0  -0.016  18.4636  5.8197  -21.6601
 EQV  C18  C  CH1   0   0.011  18.0037  5.1357  -20.3780
 EQV  C19  C  CH1   0  -0.018  16.6411  4.4802  -20.6308
 EQV  O20  O  O2    0  -0.491  15.7295  5.4794  -21.0506
 EQV  C21  C  CH2   0  -0.191  16.0619  3.7686  -19.4292
 EQV  O22  O  OH1   0  -0.670  16.0043  4.6462  -18.3311
 EQV  O23  O  OH1   0  -0.675  18.9814  4.1843  -20.0273
 EQV  O24  O  OH1   0  -0.672  19.6496  6.5546  -21.4786
 EQV  O25  O  OH1   0  -0.668  17.7219  7.3254  -23.4145
 EQV  O26  O  OH1   0  -0.674  10.2691  8.3433  -21.1528
 EQV  H1A  H  HCH3  0   0.228  14.0461  8.9210  -20.7089
 EQV  H2A  H  HCH3  0   0.224  12.4937  9.6726  -21.0575
 EQV  H3A  H  HCH3  0   0.226  12.7449  8.8274  -19.5284
 EQV  H4   H  HCR5  0   0.247  13.0688  6.6913  -20.7501
 EQV  H5A  H  HCR5  0   0.218  10.8589  6.6684  -20.0873
 EQV  H6   H  HCH2  0   0.229  11.2121  5.2428  -22.0275
 EQV  H7   H  HCH2  0   0.252   9.6895  6.0466  -22.3955
 EQV  H3   H  HCR5  0   0.267  10.8567  7.7965  -23.6537
 EQV  H2   H  HCR5  0   0.266  13.0461  8.4035  -23.1729
 EQV  H1   H  HCH1  0   0.225  13.6670  5.4798  -22.5907
 EQV  H5   H  H     0   0.289  13.1278  5.4626  -26.0748
 EQV  H16  H  HOH1  0   0.482   9.9727  4.8375  -26.9936
 EQV  H17  H  HCH1  0   0.206  16.1658  5.2676  -23.0490
 EQV  H18  H  HCH1  0   0.220  17.2756  7.5885  -21.4027
 EQV  H19  H  HCH1  0   0.215  18.6021  5.0441  -22.4318
 EQV  H20  H  HCH1  0   0.228  17.8916  5.8977  -19.5963
 EQV  H21  H  HCH1  0   0.229  16.7590  3.7202  -21.4203
 EQV  H22  H  HCH2  0   0.221  15.0700  3.3840  -19.7004
 EQV  H23  H  HCH2  0   0.211  16.6884  2.8931  -19.2224
 EQV  H24  H  HOH1  0   0.460  15.7903  4.1315  -17.5483
 EQV  H25  H  HOH1  0   0.461  18.9433  4.0340  -19.0785
 EQV  H26  H  HOH1  0   0.456  20.3646  5.9355  -21.3002
 EQV  H27  H  HOH1  0   0.454  18.5948  7.7278  -23.3539
 EQV  H28  H  HOH1  0   0.449   9.3382  8.0999  -21.1475

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
 EQV  C01  C02  single  1.520  0.020  1.520
 EQV  C02  C03  single  1.533  0.020  1.533
 EQV  C02  C2   single  1.550  0.020  1.550
 EQV  C03  C04  single  1.525  0.020  1.525
 EQV  C03  O26  single  1.413  0.020  1.413
 EQV  C04  C3   single  1.531  0.020  1.531
 EQV  C3   C4   single  1.498  0.020  1.498
 EQV  C2   C1   single  1.515  0.020  1.515
 EQV  C1   O1   single  1.380  0.020  1.380
 EQV  O5   C5   single  1.331  0.020  1.331
 EQV  C5   C4   double  1.344  0.020  1.344
 EQV  C4   C11  single  1.464  0.020  1.464
 EQV  C11  O12  double  1.212  0.020  1.212
 EQV  C11  O13  single  1.333  0.020  1.333
 EQV  O1   C15  single  1.389  0.020  1.389
 EQV  C15  C16  single  1.523  0.020  1.523
 EQV  C15  O20  single  1.399  0.020  1.399
 EQV  C16  C17  single  1.526  0.020  1.526
 EQV  C16  O25  single  1.402  0.020  1.402
 EQV  C17  C18  single  1.524  0.020  1.524
 EQV  C17  O24  single  1.407  0.020  1.407
 EQV  C18  C19  single  1.533  0.020  1.533
 EQV  C18  O23  single  1.409  0.020  1.409
 EQV  C19  O20  single  1.416  0.020  1.416
 EQV  C19  C21  single  1.512  0.020  1.512
 EQV  C21  O22  single  1.407  0.020  1.407
 EQV  C01  H1A  single  0.970  0.020  1.090
 EQV  C01  H2A  single  0.970  0.020  1.090
 EQV  C01  H3A  single  0.970  0.020  1.090
 EQV  C02  H4   single  0.970  0.020  1.090
 EQV  C03  H5A  single  0.970  0.020  1.090
 EQV  C04  H6   single  0.970  0.020  1.090
 EQV  C04  H7   single  0.970  0.020  1.090
 EQV  C3   H3   single  0.970  0.020  1.090
 EQV  C2   H2   single  0.970  0.020  1.090
 EQV  C2   C3   single  1.541  0.020  1.541
 EQV  C1   O5   single  1.427  0.020  1.427
 EQV  C1   H1   single  0.970  0.020  1.090
 EQV  C5   H5   single  0.930  0.020  1.080
 EQV  O13  H16  single  0.850  0.020  0.980
 EQV  C15  H17  single  0.970  0.020  1.090
 EQV  C16  H18  single  0.970  0.020  1.090
 EQV  C17  H19  single  0.970  0.020  1.090
 EQV  C18  H20  single  0.970  0.020  1.090
 EQV  C19  H21  single  0.970  0.020  1.090
 EQV  C21  H22  single  0.970  0.020  1.090
 EQV  C21  H23  single  0.970  0.020  1.090
 EQV  O22  H24  single  0.850  0.020  0.980
 EQV  O23  H25  single  0.850  0.020  0.980
 EQV  O24  H26  single  0.850  0.020  0.980
 EQV  O25  H27  single  0.850  0.020  0.980
 EQV  O26  H28  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
 EQV  H3A  C01  H2A  108.07  3.000
 EQV  H3A  C01  H1A  107.52  3.000
 EQV  H2A  C01  H1A  107.64  3.000
 EQV  H3A  C01  C02  111.46  3.000
 EQV  H2A  C01  C02  111.99  3.000
 EQV  H1A  C01  C02  109.98  3.000
 EQV  H4   C02  C2   108.37  3.000
 EQV  H4   C02  C03  105.71  3.000
 EQV  C2   C02  C03  105.26  3.000
 EQV  H4   C02  C01  107.45  3.000
 EQV  C2   C02  C01  113.90  3.000
 EQV  C03  C02  C01  115.68  3.000
 EQV  H5A  C03  O26  110.47  3.000
 EQV  H5A  C03  C04  111.85  3.000
 EQV  O26  C03  C04  111.46  3.000
 EQV  H5A  C03  C02  110.80  3.000
 EQV  O26  C03  C02  108.92  3.000
 EQV  C04  C03  C02  103.09  3.000
 EQV  H7   C04  H6   107.32  3.000
 EQV  H7   C04  C3   113.58  3.000
 EQV  H6   C04  C3   110.68  3.000
 EQV  H7   C04  C03  113.26  3.000
 EQV  H6   C04  C03  109.59  3.000
 EQV  C3   C04  C03  102.39  3.000
 EQV  H3   C3   C4   107.34  3.000
 EQV  H3   C3   C2   107.71  3.000
 EQV  C4   C3   C2   112.59  3.000
 EQV  C2   C3   C04  103.52  3.000
 EQV  H3   C3   C04  107.54  3.000
 EQV  C4   C3   C04  117.68  3.000
 EQV  H2   C2   C1   108.33  3.000
 EQV  H2   C2   C3   110.75  3.000
 EQV  C1   C2   C3   109.84  3.000
 EQV  C3   C2   C02  106.02  3.000
 EQV  H2   C2   C02  111.73  3.000
 EQV  C1   C2   C02  110.16  3.000
 EQV  H1   C1   O1   111.88  3.000
 EQV  H1   C1   O5   106.71  3.000
 EQV  O1   C1   O5   106.81  3.000
 EQV  H1   C1   C2   109.74  3.000
 EQV  O5   C1   C2   112.03  3.000
 EQV  O1   C1   C2   109.63  3.000
 EQV  C5   O5   C1   115.67  3.000
 EQV  H5   C5   C4   123.65  3.000
 EQV  H5   C5   O5   112.04  3.000
 EQV  C4   C5   O5   124.29  3.000
 EQV  C11  C4   C5   120.41  3.000
 EQV  C11  C4   C3   117.86  3.000
 EQV  C5   C4   C3   121.33  3.000
 EQV  O13  C11  O12  122.21  3.000
 EQV  O13  C11  C4   114.32  3.000
 EQV  O12  C11  C4   123.47  3.000
 EQV  H16  O13  C11  109.40  3.000
 EQV  C15  O1   C1   116.41  3.000
 EQV  H17  C15  O20  109.91  3.000
 EQV  H17  C15  C16  109.39  3.000
 EQV  O20  C15  C16  110.23  3.000
 EQV  H17  C15  O1   111.28  3.000
 EQV  O20  C15  O1   107.63  3.000
 EQV  C16  C15  O1   108.39  3.000
 EQV  H18  C16  O25  111.57  3.000
 EQV  H18  C16  C17  108.45  3.000
 EQV  O25  C16  C17  111.99  3.000
 EQV  H18  C16  C15  107.84  3.000
 EQV  O25  C16  C15  108.18  3.000
 EQV  C17  C16  C15  108.69  3.000
 EQV  H19  C17  O24  110.60  3.000
 EQV  H19  C17  C18  108.11  3.000
 EQV  O24  C17  C18  112.35  3.000
 EQV  H19  C17  C16  108.01  3.000
 EQV  O24  C17  C16  107.18  3.000
 EQV  C18  C17  C16  110.53  3.000
 EQV  H20  C18  O23  111.26  3.000
 EQV  H20  C18  C19  108.88  3.000
 EQV  O23  C18  C19  111.67  3.000
 EQV  H20  C18  C17  108.57  3.000
 EQV  O23  C18  C17  107.65  3.000
 EQV  C19  C18  C17  108.74  3.000
 EQV  H21  C19  C21  106.60  3.000
 EQV  H21  C19  O20  110.06  3.000
 EQV  C21  C19  O20  108.73  3.000
 EQV  H21  C19  C18  108.54  3.000
 EQV  C21  C19  C18  114.25  3.000
 EQV  O20  C19  C18  108.62  3.000
 EQV  C19  O20  C15  112.95  3.000
 EQV  H23  C21  H22  106.44  3.000
 EQV  H23  C21  O22  111.98  3.000
 EQV  H22  C21  O22  111.99  3.000
 EQV  H23  C21  C19  107.87  3.000
 EQV  H22  C21  C19  108.34  3.000
 EQV  O22  C21  C19  110.03  3.000
 EQV  H24  O22  C21  108.11  3.000
 EQV  H25  O23  C18  108.89  3.000
 EQV  H26  O24  C17  108.31  3.000
 EQV  H27  O25  C16  108.01  3.000
 EQV  H28  O26  C03  108.01  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
 EQV  CONST_01  H16  O13  C11  C4  180.00   0.0  0
 EQV  Var_01    O5   C5   C4   C3    7.42  30.0  1
 EQV  Var_02    C4   C5   O5   C1   17.73  30.0  1
 EQV  Var_03    O12  C11  C4   C3    2.51  30.0  2

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
 EQV  chir_01  C02  C01  C03  C2   negativ
 EQV  chir_02  C03  O26  C02  C04  positiv
 EQV  chir_03  C3   C2   C4   C04  negativ
 EQV  chir_04  C2   C02  C1   C3   negativ
 EQV  chir_05  C1   O5   O1   C2   negativ
 EQV  chir_06  C15  O1   O20  C16  positiv
 EQV  chir_07  C16  O25  C15  C17  negativ
 EQV  chir_08  C17  O24  C16  C18  positiv
 EQV  chir_09  C18  O23  C17  C19  negativ
 EQV  chir_10  C19  O20  C18  C21  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
 EQV  plan-1  C4   0.020
 EQV  plan-1  C11  0.020
 EQV  plan-1  O12  0.020
 EQV  plan-1  O13  0.020
 EQV  plan-1  H16  0.020

