# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:27:02 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid
#   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-carboxylic acid'  D-saccharide  49  26  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.662   3.0939   3.3842   0.4305
 EQV  C02  C  CH1    0  -0.269   2.9390   2.0153  -0.2224
 EQV  C03  C  CH1    0   0.083   4.1997   1.1370  -0.1203
 EQV  C04  C  CH2    0  -0.476   3.9517   0.2697   1.1068
 EQV  C05  C  CH1    0  -0.274   2.4804  -0.1352   0.9571
 EQV  C06  C  CH1    0  -0.304   1.8354   1.1879   0.4829
 EQV  C07  C  CH1    0   0.268   0.6306   0.9377  -0.3944
 EQV  O08  O  O2     0  -0.472   0.9503   0.1154  -1.4922
 EQV  C09  C  C1     0   0.002   1.6127  -1.0309  -1.1759
 EQV  C10  C  C      0  -0.193   2.3011  -1.2353  -0.0525
 EQV  C11  C  C      0   0.390   2.8857  -2.6079   0.2168
 EQV  O12  O  O      0  -0.606   2.8798  -3.4377  -0.7158
 EQV  O13  O  OC    -1  -0.598   3.3116  -2.8025   1.3738
 EQV  O14  O  O2     0  -0.508  -0.3337   0.3141   0.4111
 EQV  C15  C  CH1    0   0.285  -1.5885   0.0905  -0.1367
 EQV  C16  C  CH1    0  -0.025  -2.0905  -1.2492   0.3943
 EQV  C17  C  CH1    0  -0.011  -3.5231  -1.4647  -0.0687
 EQV  C18  C  CH1    0   0.033  -4.3882  -0.2613   0.2937
 EQV  C19  C  CH1    0  -0.018  -3.7393   1.0232  -0.2278
 EQV  O20  O  O2     0  -0.491  -2.4265   1.1296   0.2855
 EQV  C21  C  CH2    0  -0.157  -4.5050   2.2585   0.1947
 EQV  O22  O  OH1    0  -0.670  -3.9111   3.3857  -0.4038
 EQV  O23  O  OH1    0  -0.672  -5.6692  -0.3654  -0.2755
 EQV  O24  O  OH1    0  -0.672  -4.1119  -2.5985   0.5238
 EQV  O25  O  OH1    0  -0.669  -1.3105  -2.3140  -0.0881
 EQV  O26  O  OH1    0  -0.674   5.3684   1.9219  -0.0711
 EQV  H1   H  HCH3   0   0.230   3.8365   3.9992  -0.0767
 EQV  H2   H  HCH3   0   0.226   2.1450   3.9232   0.3960
 EQV  H3   H  HCH3   0   0.218   3.3831   3.3027   1.4803
 EQV  H4   H  HCH1   0   0.240   2.6874   2.1745  -1.2754
 EQV  H5   H  HCH1   0   0.205   4.2298   0.4790  -0.9997
 EQV  H6   H  HCH2   0   0.240   4.6250  -0.5833   1.1799
 EQV  H7   H  HCH2   0   0.224   4.0746   0.8719   2.0129
 EQV  H8   H  HCH1   0   0.246   2.0694  -0.4493   1.9186
 EQV  H10  H  HCH1   0   0.263   1.4902   1.7466   1.3575
 EQV  H13  H  HCH1   0   0.249   0.2410   1.8626  -0.8335
 EQV  H15  H  H      0   0.260   1.5127  -1.7830  -1.9483
 EQV  H17  H  HCH1   0   0.203  -1.5528   0.0574  -1.2385
 EQV  H18  H  HCH1   0   0.219  -2.0749  -1.2034   1.4946
 EQV  H19  H  HCH1   0   0.217  -3.5196  -1.5582  -1.1662
 EQV  H20  H  HCH1   0   0.213  -4.4474  -0.1942   1.3921
 EQV  H21  H  HCH1   0   0.224  -3.7135   0.9792  -1.3294
 EQV  H22  H  HCH2   0   0.214  -5.5488   2.1390  -0.1116
 EQV  H23  H  HCH2   0   0.196  -4.4960   2.3250   1.2917
 EQV  H24  H  HOH1   0   0.457  -4.4626   4.1485  -0.2097
 EQV  H25  H  HOH1   0   0.455  -6.0822  -1.1674   0.0610
 EQV  H26  H  HOH1   0   0.458  -3.7254  -3.3882   0.1332
 EQV  H27  H  HOH1   0   0.455  -0.4035  -2.1954   0.2184
 EQV  H28  H  HOH1   0   0.448   6.1238   1.3267  -0.0654

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  1.525  0.020  1.525
 EQV  C02  C03  single  1.540  0.020  1.540
 EQV  C02  C06  single  1.549  0.020  1.549
 EQV  C03  C04  single  1.523  0.020  1.523
 EQV  C03  O26  single  1.409  0.020  1.409
 EQV  C04  C05  single  1.533  0.020  1.533
 EQV  C05  C10  single  1.504  0.020  1.504
 EQV  C06  C07  single  1.511  0.020  1.511
 EQV  C07  O14  single  1.403  0.020  1.403
 EQV  O08  C09  single  1.361  0.020  1.361
 EQV  C09  C10  double  1.333  0.020  1.333
 EQV  C10  C11  single  1.516  0.020  1.516
 EQV  C11  O12  deloc   1.248  0.020  1.248
 EQV  C11  O13  deloc   1.248  0.020  1.248
 EQV  O14  C15  single  1.387  0.020  1.387
 EQV  C15  C16  single  1.526  0.020  1.526
 EQV  C15  O20  single  1.400  0.020  1.400
 EQV  C16  C17  single  1.521  0.020  1.521
 EQV  C16  O25  single  1.405  0.020  1.405
 EQV  C17  C18  single  1.526  0.020  1.526
 EQV  C17  O24  single  1.408  0.020  1.408
 EQV  C18  C19  single  1.531  0.020  1.531
 EQV  C18  O23  single  1.406  0.020  1.406
 EQV  C19  O20  single  1.414  0.020  1.414
 EQV  C19  C21  single  1.514  0.020  1.514
 EQV  C21  O22  single  1.408  0.020  1.408
 EQV  C01  H1   single  0.970  0.020  1.090
 EQV  C01  H2   single  0.970  0.020  1.090
 EQV  C01  H3   single  0.970  0.020  1.090
 EQV  C02  H4   single  0.970  0.020  1.090
 EQV  C03  H5   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  C05  H8   single  0.970  0.020  1.090
 EQV  C06  H10  single  0.970  0.020  1.090
 EQV  C06  C05  single  1.546  0.020  1.546
 EQV  C07  O08  single  1.408  0.020  1.408
 EQV  C07  H13  single  0.970  0.020  1.090
 EQV  C09  H15  single  0.930  0.020  1.080
 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  H3   C01  H2   107.30  3.000
 EQV  H3   C01  H1   108.01  3.000
 EQV  H2   C01  H1   107.40  3.000
 EQV  H3   C01  C02  111.81  3.000
 EQV  H2   C01  C02  109.96  3.000
 EQV  H1   C01  C02  112.13  3.000
 EQV  H4   C02  C06  110.61  3.000
 EQV  H4   C02  C03  109.57  3.000
 EQV  C06  C02  C03  104.38  3.000
 EQV  H4   C02  C01  107.75  3.000
 EQV  C06  C02  C01  110.92  3.000
 EQV  C03  C02  C01  113.62  3.000
 EQV  H5   C03  O26  109.81  3.000
 EQV  H5   C03  C04  107.96  3.000
 EQV  O26  C03  C04  115.10  3.000
 EQV  H5   C03  C02  108.12  3.000
 EQV  O26  C03  C02  111.33  3.000
 EQV  C04  C03  C02  104.18  3.000
 EQV  H7   C04  H6   107.81  3.000
 EQV  H7   C04  C05  109.49  3.000
 EQV  H6   C04  C05  113.14  3.000
 EQV  H7   C04  C03  109.60  3.000
 EQV  H6   C04  C03  113.54  3.000
 EQV  C05  C04  C03  103.18  3.000
 EQV  H8   C05  C10  109.62  3.000
 EQV  H8   C05  C06  111.05  3.000
 EQV  C10  C05  C06  111.73  3.000
 EQV  C06  C05  C04  101.78  3.000
 EQV  H8   C05  C04  110.56  3.000
 EQV  C10  C05  C04  111.91  3.000
 EQV  H10  C06  C07  107.28  3.000
 EQV  H10  C06  C05  108.88  3.000
 EQV  C07  C06  C05  111.65  3.000
 EQV  C05  C06  C02  107.43  3.000
 EQV  H10  C06  C02  108.42  3.000
 EQV  C07  C06  C02  113.08  3.000
 EQV  H13  C07  O14  111.16  3.000
 EQV  H13  C07  O08  105.14  3.000
 EQV  O14  C07  O08  110.12  3.000
 EQV  H13  C07  C06  112.12  3.000
 EQV  O08  C07  C06  111.60  3.000
 EQV  O14  C07  C06  106.76  3.000
 EQV  C09  O08  C07  114.90  3.000
 EQV  H15  C09  C10  122.84  3.000
 EQV  H15  C09  O08  111.98  3.000
 EQV  C10  C09  O08  125.18  3.000
 EQV  C11  C10  C09  119.18  3.000
 EQV  C11  C10  C05  119.80  3.000
 EQV  C09  C10  C05  121.00  3.000
 EQV  O13  C11  O12  126.19  3.000
 EQV  O13  C11  C10  115.94  3.000
 EQV  O12  C11  C10  117.86  3.000
 EQV  C15  O14  C07  117.83  3.000
 EQV  H17  C15  O20  110.05  3.000
 EQV  H17  C15  C16  109.39  3.000
 EQV  O20  C15  C16  110.47  3.000
 EQV  H17  C15  O14  111.72  3.000
 EQV  O20  C15  O14  107.62  3.000
 EQV  C16  C15  O14  107.56  3.000
 EQV  H18  C16  O25  111.51  3.000
 EQV  H18  C16  C17  108.87  3.000
 EQV  O25  C16  C17  108.11  3.000
 EQV  H18  C16  C15  107.85  3.000
 EQV  O25  C16  C15  111.29  3.000
 EQV  C17  C16  C15  109.17  3.000
 EQV  H19  C17  O24  110.62  3.000
 EQV  H19  C17  C18  107.79  3.000
 EQV  O24  C17  C18  107.34  3.000
 EQV  H19  C17  C16  108.20  3.000
 EQV  O24  C17  C16  112.32  3.000
 EQV  C18  C17  C16  110.48  3.000
 EQV  H20  C18  O23  111.05  3.000
 EQV  H20  C18  C19  108.14  3.000
 EQV  O23  C18  C19  108.09  3.000
 EQV  H20  C18  C17  108.37  3.000
 EQV  O23  C18  C17  111.23  3.000
 EQV  C19  C18  C17  109.91  3.000
 EQV  H21  C19  C21  108.86  3.000
 EQV  H21  C19  O20  110.12  3.000
 EQV  C21  C19  O20  107.88  3.000
 EQV  H21  C19  C18  108.47  3.000
 EQV  C21  C19  C18  112.04  3.000
 EQV  O20  C19  C18  109.46  3.000
 EQV  C19  O20  C15  112.98  3.000
 EQV  H23  C21  H22  107.09  3.000
 EQV  H23  C21  O22  111.87  3.000
 EQV  H22  C21  O22  111.77  3.000
 EQV  H23  C21  C19  108.89  3.000
 EQV  H22  C21  C19  108.37  3.000
 EQV  O22  C21  C19  108.75  3.000
 EQV  H24  O22  C21  107.91  3.000
 EQV  H25  O23  C18  108.13  3.000
 EQV  H26  O24  C17  108.79  3.000
 EQV  H27  O25  C16  108.64  3.000
 EQV  H28  O26  C03  107.88  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  Var_01  O08  C09  C10  C05    -4.15  30.0  1
 EQV  Var_02  C10  C09  O08  C07   -20.89  30.0  1
 EQV  Var_03  O12  C11  C10  C05  -170.25  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  C06  negativ
 EQV  chir_02  C03  O26  C02  C04  positiv
 EQV  chir_03  C05  C06  C10  C04  negativ
 EQV  chir_04  C06  C02  C07  C05  negativ
 EQV  chir_05  C07  O08  O14  C06  negativ
 EQV  chir_06  C15  O14  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  C10  0.020
 EQV  plan-1  C11  0.020
 EQV  plan-1  O12  0.020
 EQV  plan-1  O13  0.020

