# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:27:07 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (2S,3S,4S,5R,6S)-6-[3-(4-hydroxyphenyl)-4-oxidanylidene-chromen-7-yl]oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]([C@H]1O)C(O)=O)Oc2ccc3c(OC=C(C3=O)c4ccc(O)cc4)c2
#
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
 D75  D75  '(2S,3S,4S,5R,6S)-6-[3-(4-hydroxyphenyl)-4-oxidanylidene-chromen-7-yl]oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid'  ligand  48  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D75
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
 D75  C1    C  CH1    0   0.262  -3.3095  -0.6223  -0.0651
 D75  C2    C  CH1    0  -0.030  -4.4007  -1.6874  -0.0090
 D75  O2    O  OH1    0  -0.667  -4.0163  -2.8578  -0.6842
 D75  C3    C  CH1    0   0.012  -5.6517  -1.1475  -0.6943
 D75  O3    O  OH1    0  -0.669  -6.7343  -2.0335  -0.5632
 D75  C4    C  CH1    0   0.037  -6.0423   0.1918  -0.0915
 D75  O4    O  OH1    0  -0.701  -7.1077   0.7351  -0.8186
 D75  C5    C  CH1    0  -0.165  -4.8273   1.1383  -0.1140
 D75  O5    O  O2     0  -0.484  -3.7304   0.5517   0.5522
 D75  C6    C  C      0   0.440  -5.1534   2.5017   0.5266
 D75  O10   O  O2     0  -0.495  -2.2089  -1.1109   0.6467
 D75  C11   C  CR16   0  -0.437   0.0763  -1.4297   0.8214
 D75  C12   C  CR6    0   0.390  -0.9739  -0.6404   0.3826
 D75  C13   C  CR16   0  -0.343  -0.7242   0.5689  -0.2855
 D75  C14   C  CR16   0  -0.282   0.5757   0.9498  -0.5254
 D75  C15   C  CR66   0  -0.136   1.6583   0.1711  -0.1044
 D75  C16   C  CR66   0   0.392   1.3753  -1.0120   0.5754
 D75  C17   C  CR6    0   0.431   3.0434   0.5641  -0.3693
 D75  C18   C  CR6    0  -0.227   4.0439  -0.3774   0.1310
 D75  C19   C  CR16   0   0.041   3.6366  -1.4820   0.7853
 D75  O20   O  O      0  -0.428   2.3654  -1.8172   1.0153
 D75  C21   C  CR6    0   0.065   5.4816  -0.1519  -0.1008
 D75  C22   C  CR16   0  -0.288   6.2751  -1.1524  -0.6614
 D75  C23   C  CR16   0  -0.325   7.6357  -0.9759  -0.8511
 D75  C24   C  CR6    0   0.347   8.2360   0.2259  -0.4858
 D75  C25   C  CR16   0  -0.372   7.4549   1.2394   0.0663
 D75  C26   C  CR16   0  -0.274   6.0958   1.0494   0.2512
 D75  O27   O  O      0  -0.424   3.3312   1.5882  -0.9712
 D75  O28   O  OH1    0  -0.630   9.5612   0.3575  -0.6862
 D75  O6A   O  OC    -1  -0.615  -6.2662   2.9812   0.1805
 D75  O6B   O  O      0  -0.554  -4.3295   3.0125   1.2850
 D75  H1    H  HCH1   0   0.215  -3.0292  -0.4368  -1.1168
 D75  H2    H  HCH1   0   0.231  -4.6316  -1.8873   1.0476
 D75  H3    H  HCH1   0   0.206  -5.4091  -0.9806  -1.7573
 D75  H4    H  HCH1   0   0.197  -6.3186   0.0235   0.9645
 D75  H5    H  HCH1   0   0.234  -4.5694   1.3250  -1.1717
 D75  H22   H  HCR6   0   0.256   5.8220  -2.0872  -0.9684
 D75  H13   H  HCR6   0   0.298  -1.5302   1.2174  -0.5975
 D75  H23   H  HCR6   0   0.265   8.2314  -1.7664  -1.2903
 D75  H14   H  HCR6   0   0.276   0.7702   1.8783  -1.0451
 D75  H25   H  HCR6   0   0.272   7.9089   2.1787   0.3610
 D75  H26   H  HCR6   0   0.255   5.5171   1.8468   0.6978
 D75  HO28  H  HOH1   0   0.475   9.8620   1.2244  -0.3913
 D75  HO2   H  HOH1   0   0.460  -3.4070  -3.3543  -0.1294
 D75  HO3   H  HOH1   0   0.450  -6.4905  -2.8662  -0.9804
 D75  HO4   H  HOH1   0   0.439  -7.0763   1.6911  -0.5789
 D75  H19   H  HCR6   0   0.307   4.3192  -2.2127   1.1994
 D75  H11   H  HCR6   0   0.293  -0.1134  -2.3616   1.3386

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
 D75  O10   C1   single    1.399  0.020  1.399
 D75  H1    C1   single    0.970  0.020  1.090
 D75  C1    C2   single    1.526  0.020  1.526
 D75  C1    O5   single    1.392  0.020  1.392
 D75  O2    C2   single    1.405  0.020  1.405
 D75  H2    C2   single    0.970  0.020  1.090
 D75  C2    C3   single    1.525  0.020  1.525
 D75  HO2   O2   single    0.850  0.020  0.980
 D75  C3    H3   single    0.970  0.020  1.090
 D75  C3    O3   single    1.405  0.020  1.405
 D75  C3    C4   single    1.520  0.020  1.520
 D75  HO3   O3   single    0.850  0.020  0.980
 D75  C5    C4   single    1.540  0.020  1.540
 D75  H4    C4   single    0.970  0.020  1.090
 D75  C4    O4   single    1.400  0.020  1.400
 D75  O4    HO4  single    0.850  0.020  0.980
 D75  O5    C5   single    1.411  0.020  1.411
 D75  C5    H5   single    0.970  0.020  1.090
 D75  C5    C6   single    1.541  0.020  1.541
 D75  C6    O6B  deloc     1.231  0.020  1.231
 D75  C6    O6A  deloc     1.260  0.020  1.260
 D75  C12   O10  single    1.348  0.020  1.348
 D75  C16   C11  aromatic  1.386  0.020  1.386
 D75  C11   H11  single    0.930  0.020  1.080
 D75  C11   C12  aromatic  1.385  0.020  1.385
 D75  C13   C12  aromatic  1.404  0.020  1.404
 D75  C14   C13  aromatic  1.376  0.020  1.376
 D75  C13   H13  single    0.930  0.020  1.080
 D75  C15   C14  aromatic  1.398  0.020  1.398
 D75  H14   C14  single    0.930  0.020  1.080
 D75  C17   C15  single    1.464  0.020  1.464
 D75  C15   C16  aromatic  1.394  0.020  1.394
 D75  O20   C16  single    1.350  0.020  1.350
 D75  O27   C17  double    1.222  0.020  1.222
 D75  C18   C17  single    1.462  0.020  1.462
 D75  C21   C18  single    1.474  0.020  1.474
 D75  C18   C19  double    1.347  0.020  1.347
 D75  C19   O20  single    1.335  0.020  1.335
 D75  H19   C19  single    0.930  0.020  1.080
 D75  C22   C21  aromatic  1.395  0.020  1.395
 D75  C26   C21  aromatic  1.394  0.020  1.394
 D75  C23   C22  aromatic  1.385  0.020  1.385
 D75  C22   H22  single    0.930  0.020  1.080
 D75  C24   C23  aromatic  1.392  0.020  1.392
 D75  H23   C23  single    0.930  0.020  1.080
 D75  O28   C24  single    1.347  0.020  1.347
 D75  C24   C25  aromatic  1.394  0.020  1.394
 D75  H25   C25  single    0.930  0.020  1.080
 D75  C25   C26  aromatic  1.385  0.020  1.385
 D75  C26   H26  single    0.930  0.020  1.080
 D75  HO28  O28  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
 D75  H1    C1   O10  110.09  3.000
 D75  H1    C1   O5   110.95  3.000
 D75  O10   C1   O5   107.87  3.000
 D75  O5    C1   C2   110.87  3.000
 D75  H1    C1   C2   109.50  3.000
 D75  O10   C1   C2   107.47  3.000
 D75  H2    C2   C3   108.89  3.000
 D75  C3    C2   O2   107.66  3.000
 D75  H2    C2   O2   111.57  3.000
 D75  C3    C2   C1   108.84  3.000
 D75  H2    C2   C1   108.20  3.000
 D75  O2    C2   C1   111.60  3.000
 D75  HO2   O2   C2   109.03  3.000
 D75  H3    C3   C4   107.78  3.000
 D75  C4    C3   O3   108.70  3.000
 D75  H3    C3   O3   110.78  3.000
 D75  C4    C3   C2   110.15  3.000
 D75  O3    C3   C2   111.52  3.000
 D75  H3    C3   C2   107.83  3.000
 D75  HO3   O3   C3   108.05  3.000
 D75  H4    C4   C5   107.76  3.000
 D75  H4    C4   O4   111.43  3.000
 D75  C5    C4   O4   110.75  3.000
 D75  O4    C4   C3   109.37  3.000
 D75  H4    C4   C3   108.02  3.000
 D75  C5    C4   C3   109.45  3.000
 D75  HO4   O4   C4   103.05  3.000
 D75  H5    C5   C6   107.33  3.000
 D75  C6    C5   O5   109.63  3.000
 D75  H5    C5   O5   109.93  3.000
 D75  C6    C5   C4   111.75  3.000
 D75  H5    C5   C4   107.58  3.000
 D75  O5    C5   C4   110.54  3.000
 D75  C5    O5   C1   112.11  3.000
 D75  O6B   C6   O6A  127.04  3.000
 D75  O6A   C6   C5   114.16  3.000
 D75  O6B   C6   C5   118.79  3.000
 D75  C12   O10  C1   119.96  3.000
 D75  H11   C11  C16  120.55  3.000
 D75  H11   C11  C12  120.60  3.000
 D75  C16   C11  C12  118.85  3.000
 D75  C13   C12  C11  120.45  3.000
 D75  C13   C12  O10  123.84  3.000
 D75  C11   C12  O10  115.71  3.000
 D75  H13   C13  C14  119.23  3.000
 D75  H13   C13  C12  121.45  3.000
 D75  C14   C13  C12  119.31  3.000
 D75  H14   C14  C15  118.90  3.000
 D75  H14   C14  C13  119.43  3.000
 D75  C15   C14  C13  121.66  3.000
 D75  C17   C15  C16  120.55  3.000
 D75  C16   C15  C14  117.54  3.000
 D75  C17   C15  C14  121.91  3.000
 D75  O20   C16  C15  121.09  3.000
 D75  O20   C16  C11  116.72  3.000
 D75  C15   C16  C11  122.18  3.000
 D75  O27   C17  C18  123.16  3.000
 D75  C18   C17  C15  114.37  3.000
 D75  O27   C17  C15  122.47  3.000
 D75  C21   C18  C19  119.80  3.000
 D75  C19   C18  C17  119.17  3.000
 D75  C21   C18  C17  121.02  3.000
 D75  H19   C19  O20  111.43  3.000
 D75  H19   C19  C18  123.28  3.000
 D75  O20   C19  C18  125.29  3.000
 D75  C19   O20  C16  119.52  3.000
 D75  C26   C21  C22  117.97  3.000
 D75  C26   C21  C18  121.46  3.000
 D75  C22   C21  C18  120.56  3.000
 D75  H22   C22  C23  118.82  3.000
 D75  H22   C22  C21  119.68  3.000
 D75  C23   C22  C21  121.50  3.000
 D75  H23   C23  C24  119.96  3.000
 D75  H23   C23  C22  120.19  3.000
 D75  C24   C23  C22  119.84  3.000
 D75  O28   C24  C25  122.64  3.000
 D75  C25   C24  C23  119.35  3.000
 D75  O28   C24  C23  118.01  3.000
 D75  H25   C25  C26  119.58  3.000
 D75  C26   C25  C24  120.21  3.000
 D75  H25   C25  C24  120.21  3.000
 D75  H26   C26  C25  118.62  3.000
 D75  H26   C26  C21  120.24  3.000
 D75  C25   C26  C21  121.12  3.000
 D75  HO28  O28  C24  110.46  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
 D75  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 D75  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 D75  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 D75  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 D75  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 D75  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 D75  CONST_07  C24  C23  C22  C21     0.00   0.0  0
 D75  CONST_08  C24  C25  C26  C21     0.00   0.0  0
 D75  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 D75  CONST_10  C25  C24  C23  C22     0.00   0.0  0
 D75  CONST_11  C26  C21  C22  C23     0.00   0.0  0
 D75  CONST_12  C26  C25  C24  C23     0.00   0.0  0
 D75  CONST_13  C23  C22  C21  C18   180.00   0.0  0
 D75  CONST_14  C25  C26  C21  C18   180.00   0.0  0
 D75  CONST_15  C16  C11  C12  O10   180.00   0.0  0
 D75  CONST_16  C14  C13  C12  O10   180.00   0.0  0
 D75  CONST_17  O28  C24  C23  C22   180.00   0.0  0
 D75  CONST_18  O28  C24  C25  C26   180.00   0.0  0
 D75  CONST_19  H13  C13  C12  C11   180.00   0.0  0
 D75  CONST_20  H14  C14  C13  C12   180.00   0.0  0
 D75  CONST_21  H11  C11  C12  C13   180.00   0.0  0
 D75  CONST_22  H22  C22  C21  C18     0.00   0.0  0
 D75  CONST_23  H26  C26  C21  C18     0.00   0.0  0
 D75  CONST_24  H23  C23  C22  C21   180.00   0.0  0
 D75  CONST_25  H25  C25  C26  C21   180.00   0.0  0
 D75  Var_01    C18  C17  C15  C14  -179.36  30.0  1
 D75  Var_02    C21  C18  C17  C15   177.64  30.0  1
 D75  Var_03    C18  C19  O20  C16    -0.08  30.0  1
 D75  Var_04    C22  C21  C18  C17  -127.75  30.0  2
 D75  Var_05    O20  C19  C18  C17     0.80  30.0  1
 D75  Var_06    C11  C12  O10  C1   -161.48  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
 D75  chir_01  C1  O10  C2  O5  negativ
 D75  chir_02  C2  O2   C1  C3  negativ
 D75  chir_03  C3  O3   C2  C4  positiv
 D75  chir_04  C4  O4   C3  C5  negativ
 D75  chir_05  C5  O5   C4  C6  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
 D75  plan-1  C18  0.020
 D75  plan-1  C21  0.020
 D75  plan-1  C22  0.020
 D75  plan-1  C23  0.020
 D75  plan-1  C24  0.020
 D75  plan-1  C25  0.020
 D75  plan-1  C26  0.020
 D75  plan-1  O28  0.020
 D75  plan-1  H22  0.020
 D75  plan-1  H23  0.020
 D75  plan-1  H25  0.020
 D75  plan-1  H26  0.020
 D75  plan-2  O10  0.020
 D75  plan-2  C11  0.020
 D75  plan-2  C12  0.020
 D75  plan-2  C13  0.020
 D75  plan-2  C14  0.020
 D75  plan-2  C15  0.020
 D75  plan-2  C16  0.020
 D75  plan-2  C17  0.020
 D75  plan-2  O20  0.020
 D75  plan-2  H13  0.020
 D75  plan-2  H14  0.020
 D75  plan-2  H11  0.020
 D75  plan-3  C15  0.020
 D75  plan-3  C17  0.020
 D75  plan-3  C18  0.020
 D75  plan-3  O27  0.020
 D75  plan-4  C5   0.020
 D75  plan-4  C6   0.020
 D75  plan-4  O6A  0.020
 D75  plan-4  O6B  0.020

