# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:23:22 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c3ccc(O)c(O)c3
#
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
 28E  28E  (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol  ligand  35  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_28E
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
 28E  OAB  O  OH1   0  -0.636   4.8342  -2.5482   0.1991
 28E  CAT  C  CR6   0   0.375   4.0108  -1.4821   0.1553
 28E  CAK  C  CR16  0  -0.458   4.6004  -0.2245   0.0902
 28E  CAY  C  CR6   0   0.335   3.7891   0.9015   0.0415
 28E  OAG  O  OH1   0  -0.631   4.4196   2.0916  -0.0252
 28E  CBD  C  CR6   0  -0.157   2.3928   0.8085   0.0518
 28E  CAP  C  CH2   0  -0.540   1.5047   2.0182  -0.0511
 28E  CAN  C  CR16  0  -0.530   2.6293  -1.6143   0.1857
 28E  CBC  C  CR6   0   0.426   1.8403  -0.4683   0.1368
 28E  OAR  O  O2    0  -0.496   0.5074  -0.6767   0.1690
 28E  CBF  C  CH1   0  -0.027  -0.3487   0.4394   0.3551
 28E  CBE  C  CH1   0   0.009   0.1087   1.6113  -0.5056
 28E  OAQ  O  OH1   0  -0.656   0.0866   1.1913  -1.8439
 28E  CBA  C  CR6   0   0.081  -1.7552   0.0031   0.0564
 28E  CAO  C  CR16  0  -0.429  -2.7977   0.5777   0.7795
 28E  CAV  C  CR6   0   0.278  -4.1176   0.2547   0.5119
 28E  OAD  O  OH1   0  -0.646  -5.1725   0.7823   1.1757
 28E  CAU  C  CR6   0   0.280  -4.4177  -0.6756  -0.4905
 28E  OAC  O  OH1   0  -0.635  -5.6895  -1.0271  -0.7775
 28E  CAI  C  CR16  0  -0.332  -3.3781  -1.2510  -1.2040
 28E  CAJ  C  CR16  0  -0.313  -2.0566  -0.9125  -0.9415
 28E  H1   H  HOH1  0   0.474   4.3231  -3.3640   0.2373
 28E  H2   H  HCR6  0   0.263   5.6783  -0.1214   0.0793
 28E  H3   H  HOH1  0   0.480   3.7962   2.8247   0.0091
 28E  H4   H  HCH2  0   0.267   1.4277   2.5403   0.9082
 28E  H5   H  HCH2  0   0.258   1.9006   2.7510  -0.7633
 28E  H6   H  HCR6  0   0.270   2.1578  -2.5883   0.2512
 28E  H7   H  HCH1  0   0.261  -0.2901   0.7669   1.4018
 28E  H8   H  HCH1  0   0.244  -0.5812   2.4465  -0.3278
 28E  H9   H  HOH1  0   0.456   0.3875   1.9212  -2.3943
 28E  H10  H  HCR6  0   0.268  -2.5796   1.2893   1.5703
 28E  H11  H  HOH1  0   0.481  -4.8764   1.3709   1.8786
 28E  H12  H  HOH1  0   0.472  -6.3037  -0.5980  -0.1707
 28E  H13  H  HCR6  0   0.263  -3.6091  -1.9724  -1.9783
 28E  H14  H  HCR6  0   0.246  -1.2731  -1.3802  -1.5204

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
 28E  OAG  CAY  single    1.348  0.020  1.348
 28E  CAY  CAK  aromatic  1.389  0.020  1.389
 28E  CAY  CBD  aromatic  1.399  0.020  1.399
 28E  CAK  CAT  aromatic  1.390  0.020  1.390
 28E  CAP  CBD  single    1.504  0.020  1.504
 28E  CAP  CBE  single    1.523  0.020  1.523
 28E  CBD  CBC  aromatic  1.394  0.020  1.394
 28E  CAT  OAB  single    1.348  0.020  1.348
 28E  CAT  CAN  aromatic  1.388  0.020  1.388
 28E  OAQ  CBE  single    1.403  0.020  1.403
 28E  CBE  CBF  single    1.524  0.020  1.524
 28E  CBC  CAN  aromatic  1.392  0.020  1.392
 28E  CBC  OAR  single    1.349  0.020  1.349
 28E  CBF  OAR  single    1.419  0.020  1.419
 28E  CBF  CBA  single    1.503  0.020  1.503
 28E  CBA  CAJ  aromatic  1.388  0.020  1.388
 28E  CBA  CAO  aromatic  1.393  0.020  1.393
 28E  CAJ  CAI  aromatic  1.389  0.020  1.389
 28E  CAO  CAV  aromatic  1.385  0.020  1.385
 28E  CAI  CAU  aromatic  1.386  0.020  1.386
 28E  CAV  CAU  aromatic  1.400  0.020  1.400
 28E  CAV  OAD  single    1.353  0.020  1.353
 28E  CAU  OAC  single    1.350  0.020  1.350
 28E  OAB  H1   single    0.850  0.020  0.980
 28E  CAK  H2   single    0.930  0.020  1.080
 28E  OAG  H3   single    0.850  0.020  0.980
 28E  CAP  H4   single    0.970  0.020  1.090
 28E  CAP  H5   single    0.970  0.020  1.090
 28E  CAN  H6   single    0.930  0.020  1.080
 28E  CBF  H7   single    0.970  0.020  1.090
 28E  CBE  H8   single    0.970  0.020  1.090
 28E  OAQ  H9   single    0.850  0.020  0.980
 28E  CAO  H10  single    0.930  0.020  1.080
 28E  OAD  H11  single    0.850  0.020  0.980
 28E  OAC  H12  single    0.850  0.020  0.980
 28E  CAI  H13  single    0.930  0.020  1.080
 28E  CAJ  H14  single    0.930  0.020  1.080

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
 28E  H1   OAB  CAT  110.30  3.000
 28E  CAN  CAT  CAK  120.61  3.000
 28E  CAN  CAT  OAB  122.14  3.000
 28E  CAK  CAT  OAB  117.25  3.000
 28E  H2   CAK  CAY  120.26  3.000
 28E  H2   CAK  CAT  120.58  3.000
 28E  CAY  CAK  CAT  119.16  3.000
 28E  CBD  CAY  OAG  121.70  3.000
 28E  CBD  CAY  CAK  121.92  3.000
 28E  OAG  CAY  CAK  116.37  3.000
 28E  H3   OAG  CAY  111.56  3.000
 28E  CBC  CBD  CAP  120.45  3.000
 28E  CBC  CBD  CAY  117.18  3.000
 28E  CAP  CBD  CAY  122.36  3.000
 28E  H5   CAP  H4   106.01  3.000
 28E  H5   CAP  CBE  108.41  3.000
 28E  H4   CAP  CBE  108.92  3.000
 28E  H5   CAP  CBD  111.64  3.000
 28E  H4   CAP  CBD  111.41  3.000
 28E  CBE  CAP  CBD  110.29  3.000
 28E  H6   CAN  CBC  119.68  3.000
 28E  H6   CAN  CAT  121.31  3.000
 28E  CBC  CAN  CAT  119.01  3.000
 28E  OAR  CBC  CAN  115.59  3.000
 28E  OAR  CBC  CBD  122.31  3.000
 28E  CAN  CBC  CBD  122.11  3.000
 28E  CBF  OAR  CBC  118.53  3.000
 28E  H7   CBF  CBA  109.02  3.000
 28E  H7   CBF  CBE  107.03  3.000
 28E  CBA  CBF  CBE  113.07  3.000
 28E  H7   CBF  OAR  109.11  3.000
 28E  CBA  CBF  OAR  108.08  3.000
 28E  CBE  CBF  OAR  110.47  3.000
 28E  H8   CBE  OAQ  111.86  3.000
 28E  H8   CBE  CBF  107.75  3.000
 28E  OAQ  CBE  CBF  107.68  3.000
 28E  H8   CBE  CAP  108.93  3.000
 28E  CBF  CBE  CAP  108.17  3.000
 28E  OAQ  CBE  CAP  112.28  3.000
 28E  H9   OAQ  CBE  108.27  3.000
 28E  CAJ  CBA  CAO  118.88  3.000
 28E  CAO  CBA  CBF  118.53  3.000
 28E  CAJ  CBA  CBF  122.54  3.000
 28E  H10  CAO  CAV  119.01  3.000
 28E  H10  CAO  CBA  119.87  3.000
 28E  CAV  CAO  CBA  121.12  3.000
 28E  CAU  CAV  OAD  116.30  3.000
 28E  OAD  CAV  CAO  123.86  3.000
 28E  CAU  CAV  CAO  119.84  3.000
 28E  H11  OAD  CAV  110.88  3.000
 28E  CAI  CAU  OAC  119.27  3.000
 28E  OAC  CAU  CAV  121.80  3.000
 28E  CAI  CAU  CAV  118.92  3.000
 28E  H12  OAC  CAU  110.51  3.000
 28E  H13  CAI  CAJ  120.01  3.000
 28E  H13  CAI  CAU  118.98  3.000
 28E  CAJ  CAI  CAU  121.00  3.000
 28E  H14  CAJ  CAI  118.89  3.000
 28E  H14  CAJ  CBA  120.89  3.000
 28E  CAI  CAJ  CBA  120.22  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
 28E  CONST_01  CBD  CAY  CAK  CAT    0.00   0.0  0
 28E  CONST_02  CBD  CBC  CAN  CAT    0.00   0.0  0
 28E  CONST_03  CBC  CBD  CAY  CAK    0.00   0.0  0
 28E  CONST_04  CBC  CAN  CAT  CAK    0.00   0.0  0
 28E  CONST_05  CAN  CAT  CAK  CAY    0.00   0.0  0
 28E  CONST_06  CAN  CBC  CBD  CAY    0.00   0.0  0
 28E  CONST_07  CAU  CAI  CAJ  CBA    0.00   0.0  0
 28E  CONST_08  CAU  CAV  CAO  CBA    0.00   0.0  0
 28E  CONST_09  CAI  CAJ  CBA  CAO    0.00   0.0  0
 28E  CONST_10  CAI  CAU  CAV  CAO    0.00   0.0  0
 28E  CONST_11  CAJ  CBA  CAO  CAV    0.00   0.0  0
 28E  CONST_12  CAJ  CAI  CAU  CAV    0.00   0.0  0
 28E  CONST_13  CAI  CAJ  CBA  CBF  180.00   0.0  0
 28E  CONST_14  CAV  CAO  CBA  CBF  180.00   0.0  0
 28E  CONST_15  CAY  CAK  CAT  OAB  180.00   0.0  0
 28E  CONST_16  CBC  CAN  CAT  OAB  180.00   0.0  0
 28E  CONST_17  OAG  CAY  CAK  CAT  180.00   0.0  0
 28E  CONST_18  CAP  CBD  CAY  OAG    0.00   0.0  0
 28E  CONST_19  CBC  CBD  CAY  OAG  180.00   0.0  0
 28E  CONST_20  OAD  CAV  CAO  CBA  180.00   0.0  0
 28E  CONST_21  OAC  CAU  CAV  CAO  180.00   0.0  0
 28E  CONST_22  CAI  CAU  CAV  OAD  180.00   0.0  0
 28E  CONST_23  CAJ  CAI  CAU  OAC  180.00   0.0  0
 28E  CONST_24  H6   CAN  CAT  CAK  180.00   0.0  0
 28E  CONST_25  H2   CAK  CAY  CBD  180.00   0.0  0
 28E  CONST_26  H14  CAJ  CBA  CBF    0.00   0.0  0
 28E  CONST_27  H10  CAO  CBA  CBF    0.00   0.0  0
 28E  CONST_28  H13  CAI  CAJ  CBA  180.00   0.0  0
 28E  Var_01    CBE  CAP  CBD  CAY  159.94  30.0  1

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
 28E  chir_01  CBF  CBE  OAR  CBA  positiv
 28E  chir_02  CBE  OAQ  CBF  CAP  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
 28E  plan-1  CBF  0.020
 28E  plan-1  CBA  0.020
 28E  plan-1  CAO  0.020
 28E  plan-1  CAV  0.020
 28E  plan-1  OAD  0.020
 28E  plan-1  CAU  0.020
 28E  plan-1  OAC  0.020
 28E  plan-1  CAI  0.020
 28E  plan-1  CAJ  0.020
 28E  plan-1  H10  0.020
 28E  plan-1  H13  0.020
 28E  plan-1  H14  0.020
 28E  plan-2  OAB  0.020
 28E  plan-2  CAT  0.020
 28E  plan-2  CAK  0.020
 28E  plan-2  CAY  0.020
 28E  plan-2  OAG  0.020
 28E  plan-2  CBD  0.020
 28E  plan-2  CAP  0.020
 28E  plan-2  CAN  0.020
 28E  plan-2  CBC  0.020
 28E  plan-2  OAR  0.020
 28E  plan-2  H2   0.020
 28E  plan-2  H6   0.020

