# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 01:55:04 2021
#   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  49  31  .  2021-08-08  2022-11-17
;
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   0.293  22.2011  42.6043  63.8516
 D75  C2    C  CH1   0  -0.007  23.6355  42.4694  64.3461
 D75  O2    O  OH1   0  -0.662  24.4398  42.1679  63.2399
 D75  C3    C  CH1   0  -0.017  23.6884  41.3811  65.4100
 D75  O3    O  OH1   0  -0.666  25.0077  41.3267  65.8851
 D75  C4    C  CH1   0  -0.003  22.6932  41.6760  66.5294
 D75  O4    O  OH1   0  -0.660  22.7285  40.5892  67.4119
 D75  C5    C  CH1   0  -0.085  21.2995  41.8727  65.8885
 D75  O5    O  O2    0  -0.480  21.3477  42.8872  64.9183
 D75  C6    C  C     0   0.503  20.2714  42.3151  66.9085
 D75  O10   O  O2    0  -0.491  22.0701  43.7189  63.0173
 D75  C11   C  CR16  0  -0.450  22.2589  42.5033  60.9389
 D75  C12   C  CR6   0   0.397  21.8963  43.6084  61.6878
 D75  C13   C  CR16  0  -0.337  21.3296  44.7341  61.0649
 D75  C14   C  CR16  0  -0.282  21.1351  44.7423  59.7081
 D75  C15   C  CR66  0  -0.140  21.4834  43.6367  58.9198
 D75  C16   C  CR66  0   0.402  22.0366  42.5366  59.5654
 D75  C17   C  CR6   0   0.429  21.2773  43.6252  57.4716
 D75  C18   C  CR6   0  -0.225  21.7203  42.4006  56.8077
 D75  C19   C  CR16  0   0.040  22.2507  41.4090  57.5488
 D75  O20   O  O     0  -0.428  22.4081  41.4388  58.8738
 D75  C21   C  CR6   0   0.066  21.5672  42.2345  55.3517
 D75  C22   C  CR16  0  -0.274  22.0498  43.1965  54.4616
 D75  C23   C  CR16  0  -0.325  21.9352  43.0302  53.0939
 D75  C24   C  CR6   0   0.347  21.3247  41.8880  52.5766
 D75  C25   C  CR16  0  -0.371  20.8360  40.9214  53.4498
 D75  C26   C  CR16  0  -0.289  20.9559  41.1020  54.8201
 D75  O27   O  O     0  -0.425  20.7705  44.5640  56.8743
 D75  O28   O  OH1   0  -0.629  21.2345  41.7761  51.2380
 D75  O6A   O  OH1   0  -0.587  19.9243  41.3169  67.7053
 D75  O6B   O  O     0  -0.419  19.8467  43.4352  66.9965
 D75  H1    H  HCH1  0   0.230  21.8825  41.6832  63.3381
 D75  H2    H  HCH1  0   0.235  23.9236  43.4274  64.8059
 D75  H3    H  HCH1  0   0.227  23.3962  40.4247  64.9461
 D75  H4    H  HCH1  0   0.247  22.9834  42.6132  67.0236
 D75  H5    H  HCH1  0   0.277  20.9807  40.9149  65.4503
 D75  H22   H  HCR6  0   0.252  22.5419  44.0841  54.8358
 D75  H13   H  HCR6  0   0.280  21.0517  45.5895  61.6662
 D75  H23   H  HCR6  0   0.265  22.3221  43.7845  52.4200
 D75  H14   H  HCR6  0   0.274  20.7028  45.6124  59.2333
 D75  H25   H  HCR6  0   0.273  20.3537  40.0295  53.0666
 D75  H26   H  HCR6  0   0.258  20.5499  40.3463  55.4817
 D75  HO28  H  HOH1  0   0.475  20.7984  40.9512  50.9971
 D75  HO2   H  HOH1  0   0.462  25.3493  42.0690  63.5411
 D75  HO3   H  HOH1  0   0.459  25.1012  40.5464  66.4415
 D75  HO4   H  HOH1  0   0.464  22.4466  40.8723  68.2862
 D75  HO6A  H  HOH1  0   0.490  19.3059  41.6293  68.3837
 D75  H19   H  HCR6  0   0.307  22.6137  40.4807  57.1276
 D75  H11   H  HCR6  0   0.299  22.7348  41.6351  61.3712

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    1.398  0.020  1.398
 D75  H1    C1    single    0.970  0.020  1.090
 D75  C1    C2    single    1.523  0.020  1.523
 D75  C1    O5    single    1.395  0.020  1.395
 D75  O2    C2    single    1.400  0.020  1.400
 D75  H2    C2    single    0.970  0.020  1.090
 D75  C2    C3    single    1.523  0.020  1.523
 D75  HO2   O2    single    0.850  0.020  0.980
 D75  C3    H3    single    0.970  0.020  1.090
 D75  C3    O3    single    1.403  0.020  1.403
 D75  C3    C4    single    1.527  0.020  1.527
 D75  HO3   O3    single    0.850  0.020  0.980
 D75  C5    C4    single    1.547  0.020  1.547
 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    1.405  0.020  1.405
 D75  C5    H5    single    0.970  0.020  1.090
 D75  C5    C6    single    1.514  0.020  1.514
 D75  C6    O6B   double    1.201  0.020  1.201
 D75  C6    O6A   single    1.324  0.020  1.324
 D75  C12   O10   single    1.345  0.020  1.345
 D75  C16   C11   aromatic  1.392  0.020  1.392
 D75  C11   H11   single    0.930  0.020  1.080
 D75  C11   C12   aromatic  1.383  0.020  1.383
 D75  C13   C12   aromatic  1.406  0.020  1.406
 D75  C14   C13   aromatic  1.371  0.020  1.371
 D75  C13   H13   single    0.930  0.020  1.080
 D75  C15   C14   aromatic  1.402  0.020  1.402
 D75  H14   C14   single    0.930  0.020  1.080
 D75  C17   C15   single    1.463  0.020  1.463
 D75  C15   C16   aromatic  1.390  0.020  1.390
 D75  O20   C16   single    1.350  0.020  1.350
 D75  O27   C17   double    1.223  0.020  1.223
 D75  C18   C17   single    1.462  0.020  1.462
 D75  C21   C18   single    1.473  0.020  1.473
 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  1.397  0.020  1.397
 D75  C26   C21   aromatic  1.392  0.020  1.392
 D75  C23   C22   aromatic  1.383  0.020  1.383
 D75  C22   H22   single    0.930  0.020  1.080
 D75  C24   C23   aromatic  1.395  0.020  1.395
 D75  H23   C23   single    0.930  0.020  1.080
 D75  O28   C24   single    1.346  0.020  1.346
 D75  C24   C25   aromatic  1.391  0.020  1.391
 D75  H25   C25   single    0.930  0.020  1.080
 D75  C25   C26   aromatic  1.387  0.020  1.387
 D75  C26   H26   single    0.930  0.020  1.080
 D75  HO28  O28   single    0.850  0.020  0.980
 D75  O6A   HO6A  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  111.18  3.000
 D75  H1    C1   O5   110.43  3.000
 D75  O10   C1   O5   103.72  3.000
 D75  O5    C1   C2   110.23  3.000
 D75  H1    C1   C2   110.46  3.000
 D75  O10   C1   C2   110.63  3.000
 D75  H2    C2   C3   108.72  3.000
 D75  C3    C2   O2   112.21  3.000
 D75  H2    C2   O2   111.53  3.000
 D75  C3    C2   C1   108.83  3.000
 D75  H2    C2   C1   107.76  3.000
 D75  O2    C2   C1   107.66  3.000
 D75  HO2   O2   C2   108.51  3.000
 D75  H3    C3   C4   107.66  3.000
 D75  C4    C3   O3   111.85  3.000
 D75  H3    C3   O3   110.98  3.000
 D75  C4    C3   C2   110.58  3.000
 D75  O3    C3   C2   107.27  3.000
 D75  H3    C3   C2   108.47  3.000
 D75  HO3   O3   C3   108.57  3.000
 D75  H4    C4   C5   108.42  3.000
 D75  H4    C4   O4   111.84  3.000
 D75  C5    C4   O4   112.49  3.000
 D75  O4    C4   C3   107.20  3.000
 D75  H4    C4   C3   108.81  3.000
 D75  C5    C4   C3   107.95  3.000
 D75  HO4   O4   C4   109.70  3.000
 D75  H5    C5   C6   109.01  3.000
 D75  C6    C5   O5   106.12  3.000
 D75  H5    C5   O5   111.31  3.000
 D75  C6    C5   C4   111.71  3.000
 D75  H5    C5   C4   108.38  3.000
 D75  O5    C5   C4   110.31  3.000
 D75  C5    O5   C1   113.75  3.000
 D75  O6B   C6   O6A  124.50  3.000
 D75  O6A   C6   C5   111.30  3.000
 D75  O6B   C6   C5   124.18  3.000
 D75  C12   O10  C1   122.42  3.000
 D75  H11   C11  C16  118.98  3.000
 D75  H11   C11  C12  122.74  3.000
 D75  C16   C11  C12  118.25  3.000
 D75  C13   C12  C11  120.36  3.000
 D75  C13   C12  O10  115.10  3.000
 D75  C11   C12  O10  124.52  3.000
 D75  H13   C13  C14  120.60  3.000
 D75  H13   C13  C12  119.37  3.000
 D75  C14   C13  C12  120.04  3.000
 D75  H14   C14  C15  119.14  3.000
 D75  H14   C14  C13  119.75  3.000
 D75  C15   C14  C13  121.11  3.000
 D75  C17   C15  C16  120.63  3.000
 D75  C16   C15  C14  117.50  3.000
 D75  C17   C15  C14  121.86  3.000
 D75  O20   C16  C15  121.01  3.000
 D75  O20   C16  C11  116.25  3.000
 D75  C15   C16  C11  122.73  3.000
 D75  O27   C17  C18  123.16  3.000
 D75  C18   C17  C15  114.42  3.000
 D75  O27   C17  C15  122.41  3.000
 D75  C21   C18  C19  120.11  3.000
 D75  C19   C18  C17  119.10  3.000
 D75  C21   C18  C17  120.78  3.000
 D75  H19   C19  O20  111.47  3.000
 D75  H19   C19  C18  123.34  3.000
 D75  O20   C19  C18  125.19  3.000
 D75  C19   O20  C16  119.64  3.000
 D75  C26   C21  C22  117.94  3.000
 D75  C26   C21  C18  120.97  3.000
 D75  C22   C21  C18  121.08  3.000
 D75  H22   C22  C23  118.60  3.000
 D75  H22   C22  C21  120.13  3.000
 D75  C23   C22  C21  121.26  3.000
 D75  H23   C23  C24  119.74  3.000
 D75  H23   C23  C22  120.14  3.000
 D75  C24   C23  C22  120.11  3.000
 D75  O28   C24  C25  122.88  3.000
 D75  C25   C24  C23  119.34  3.000
 D75  O28   C24  C23  117.78  3.000
 D75  H25   C25  C26  119.65  3.000
 D75  C26   C25  C24  119.94  3.000
 D75  H25   C25  C24  120.40  3.000
 D75  H26   C26  C25  118.68  3.000
 D75  H26   C26  C21  119.92  3.000
 D75  C25   C26  C21  121.39  3.000
 D75  HO28  O28  C24  110.49  3.000
 D75  HO6A  O6A  C6   110.21  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  CONST_26  HO6A  O6A  C6   C5   180.00   0.0  0
 D75  Var_01    C18   C17  C15  C14  178.95  30.0  1
 D75  Var_02    C21   C18  C17  C15  179.43  30.0  1
 D75  Var_03    C18   C19  O20  C16   -0.94  30.0  1
 D75  Var_04    C22   C21  C18  C17   52.58  30.0  2
 D75  Var_05    O20   C19  C18  C17    0.36  30.0  1
 D75  Var_06    C11   C12  O10  C1   -22.56  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
 D75  plan-4  HO6A  0.020

