# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 16:32:00 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C[C@@H](OC(=O)c3cc(O)c(O)c(O)c3)[C@H](Oc2c1)c4cc(O)c(O)c(O)c4
#
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
 KDH  KDH  '(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate'  ligand  51  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDH
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
 KDH  O1    O  OH1   0  -0.643   1.9253   2.7214  -1.7459
 KDH  C3    C  CR6   0   0.298   0.8761   2.8469  -0.9011
 KDH  C6    C  CR6   0   0.198   0.8029   4.0491  -0.2003
 KDH  O7    O  OH1   0  -0.630   1.7102   5.0409  -0.3458
 KDH  C9    C  CR6   0   0.302  -0.2543   4.2494   0.6868
 KDH  O10   O  OH1   0  -0.630  -0.2886   5.4364   1.3264
 KDH  C12   C  CR16  0  -0.450  -1.2025   3.2530   0.8790
 KDH  C14   C  CR6   0   0.066  -1.1123   2.0539   0.1860
 KDH  C15   C  CH1   0   0.004  -2.0624   0.9462   0.5389
 KDH  C20   C  CR6   0   0.425  -2.8881  -1.0374  -0.4926
 KDH  C21   C  CR16  0  -0.529  -3.3494  -1.6172  -1.6728
 KDH  C24   C  CR6   0   0.377  -3.9574  -2.8623  -1.6164
 KDH  C26   C  CR16  0  -0.498  -4.1122  -3.5214  -0.3990
 KDH  C29   C  CR6   0   0.338  -3.6369  -2.9209   0.7580
 KDH  C31   C  CR6   0  -0.142  -3.0068  -1.6722   0.7380
 KDH  C33   C  CH1   0  -0.058  -1.5010   0.0719   1.6610
 KDH  C38   C  CR6   0  -0.076   2.0159  -0.4840   0.7479
 KDH  C39   C  CR16  0  -0.398   3.2925  -0.0547   1.0922
 KDH  C41   C  CR16  0  -0.413   1.8116  -1.3350  -0.3342
 KDH  C01   C  CH2   0  -0.457  -2.4703  -1.0427   1.9905
 KDH  O01   O  O2    0  -0.498  -2.3079   0.1767  -0.6243
 KDH  O02   O  OH1   0  -0.634  -4.4307  -3.4806  -2.7156
 KDH  O03   O  OH1   0  -0.624  -3.7571  -3.5094   1.9631
 KDH  C4    C  CR16  0  -0.465  -0.0781   1.8551  -0.7189
 KDH  O35   O  O2    0  -0.470  -0.2815  -0.5031   1.1889
 KDH  O37   O  O     0  -0.432   1.0085   0.8042   2.4718
 KDH  C43   C  CR6   0   0.355   2.9023  -1.7482  -1.0884
 KDH  O44   O  OH1   0  -0.628   2.6947  -2.5678  -2.1317
 KDH  C46   C  CR6   0   0.099   4.1850  -1.3106  -0.7585
 KDH  O47   O  OH1   0  -0.657   5.2603  -1.7462  -1.4852
 KDH  C49   C  CR6   0   0.353   4.3806  -0.4717   0.3385
 KDH  O50   O  OH1   0  -0.628   5.6094  -0.0547   0.6842
 KDH  HO1   H  HOH1  0   0.476   1.9558   1.8351  -2.1216
 KDH  H21   H  HCR6  0   0.273  -3.2305  -1.0918  -2.6134
 KDH  H33   H  HCH1  0   0.289  -1.3213   0.6891   2.5415
 KDH  H4    H  HCR6  0   0.276  -0.0040   0.9352  -1.2858
 KDH  HO7   H  HOH1  0   0.472   2.4185   4.7598  -0.9363
 KDH  H01   H  HCH2  0   0.266  -3.2793  -0.6174   2.5917
 KDH  H01A  H  HCH2  0   0.270  -1.9733  -1.7769   2.6276
 KDH  HO03  H  HOH1  0   0.478  -4.1766  -4.3728   1.8773
 KDH  HO10  H  HOH1  0   0.476  -1.0560   5.4747   1.9079
 KDH  H12   H  HCR6  0   0.265  -2.0093   3.4154   1.5859
 KDH  H15   H  HCH1  0   0.267  -3.0071   1.3709   0.9052
 KDH  H26   H  HCR6  0   0.271  -4.6009  -4.4888  -0.3632
 KDH  H39   H  HCR6  0   0.268   3.4475   0.6058   1.9345
 KDH  H41   H  HCR6  0   0.271   0.8229  -1.6734  -0.6113
 KDH  HO02  H  HOH1  0   0.475  -4.2789  -2.9368  -3.4963
 KDH  HO44  H  HOH1  0   0.472   3.5385  -2.8189  -2.5289
 KDH  HO47  H  HOH1  0   0.487   5.4467  -1.1304  -2.2065
 KDH  HO50  H  HOH1  0   0.472   6.2702  -0.4579   0.1068
 KDH  C36   C  C     0   0.622   0.8817   0.0204   1.5648

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
 KDH  O1   C3    single    1.353  0.020  1.353
 KDH  O1   HO1   single    0.850  0.020  0.980
 KDH  C3   C6    aromatic  1.393  0.020  1.393
 KDH  C3   C4    aromatic  1.388  0.020  1.388
 KDH  C6   O7    single    1.352  0.020  1.352
 KDH  C6   C9    aromatic  1.395  0.020  1.395
 KDH  O7   HO7   single    0.850  0.020  0.980
 KDH  C9   O10   single    1.349  0.020  1.349
 KDH  C9   C12   aromatic  1.389  0.020  1.389
 KDH  O10  HO10  single    0.850  0.020  0.980
 KDH  C12  C14   aromatic  1.388  0.020  1.388
 KDH  C12  H12   single    0.930  0.020  1.080
 KDH  C14  C15   single    1.501  0.020  1.501
 KDH  C14  C4    aromatic  1.388  0.020  1.388
 KDH  C15  C33   single    1.529  0.020  1.529
 KDH  C15  O01   single    1.416  0.020  1.416
 KDH  C15  H15   single    0.970  0.020  1.090
 KDH  C20  C21   aromatic  1.394  0.020  1.394
 KDH  C20  C31   aromatic  1.390  0.020  1.390
 KDH  C20  O01   single    1.352  0.020  1.352
 KDH  C21  C24   aromatic  1.387  0.020  1.387
 KDH  C21  H21   single    0.930  0.020  1.080
 KDH  C24  C26   aromatic  1.393  0.020  1.393
 KDH  C24  O02   single    1.347  0.020  1.347
 KDH  C26  C29   aromatic  1.388  0.020  1.388
 KDH  C26  H26   single    0.930  0.020  1.080
 KDH  C29  C31   aromatic  1.399  0.020  1.399
 KDH  C29  O03   single    1.346  0.020  1.346
 KDH  C31  C01   single    1.501  0.020  1.501
 KDH  C33  C01   single    1.513  0.020  1.513
 KDH  C33  O35   single    1.429  0.020  1.429
 KDH  C33  H33   single    0.970  0.020  1.090
 KDH  C36  C38   single    1.486  0.020  1.486
 KDH  C36  O35   single    1.330  0.020  1.330
 KDH  C36  O37   double    1.205  0.020  1.205
 KDH  C38  C39   aromatic  1.390  0.020  1.390
 KDH  C38  C41   aromatic  1.392  0.020  1.392
 KDH  C39  C49   aromatic  1.388  0.020  1.388
 KDH  C39  H39   single    0.930  0.020  1.080
 KDH  C41  C43   aromatic  1.389  0.020  1.389
 KDH  C41  H41   single    0.930  0.020  1.080
 KDH  C01  H01   single    0.970  0.020  1.090
 KDH  C01  H01A  single    0.970  0.020  1.090
 KDH  O02  HO02  single    0.850  0.020  0.980
 KDH  O03  HO03  single    0.850  0.020  0.980
 KDH  C4   H4    single    0.930  0.020  1.080
 KDH  C43  O44   single    1.343  0.020  1.343
 KDH  C43  C46   aromatic  1.395  0.020  1.395
 KDH  O44  HO44  single    0.850  0.020  0.980
 KDH  C46  O47   single    1.369  0.020  1.369
 KDH  C46  C49   aromatic  1.395  0.020  1.395
 KDH  O47  HO47  single    0.850  0.020  0.980
 KDH  C49  O50   single    1.343  0.020  1.343
 KDH  O50  HO50  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
 KDH  HO1   O1   C3   110.70  3.000
 KDH  C4    C3   C6   120.94  3.000
 KDH  C4    C3   O1   123.28  3.000
 KDH  C6    C3   O1   115.77  3.000
 KDH  C9    C6   O7   118.15  3.000
 KDH  C9    C6   C3   118.93  3.000
 KDH  O7    C6   C3   122.92  3.000
 KDH  HO7   O7   C6   110.18  3.000
 KDH  C12   C9   O10  123.26  3.000
 KDH  C12   C9   C6   120.17  3.000
 KDH  O10   C9   C6   116.58  3.000
 KDH  HO10  O10  C9   109.97  3.000
 KDH  H12   C12  C14  120.20  3.000
 KDH  H12   C12  C9   119.37  3.000
 KDH  C14   C12  C9   120.43  3.000
 KDH  C4    C14  C15  121.26  3.000
 KDH  C4    C14  C12  119.83  3.000
 KDH  C15   C14  C12  118.61  3.000
 KDH  H15   C15  O01  109.56  3.000
 KDH  H15   C15  C33  106.98  3.000
 KDH  O01   C15  C33  110.83  3.000
 KDH  H15   C15  C14  109.72  3.000
 KDH  O01   C15  C14  108.51  3.000
 KDH  C33   C15  C14  111.22  3.000
 KDH  O01   C20  C31  122.22  3.000
 KDH  O01   C20  C21  115.67  3.000
 KDH  C31   C20  C21  122.11  3.000
 KDH  H21   C21  C24  121.24  3.000
 KDH  H21   C21  C20  119.79  3.000
 KDH  C24   C21  C20  118.96  3.000
 KDH  O02   C24  C26  117.19  3.000
 KDH  O02   C24  C21  122.20  3.000
 KDH  C26   C24  C21  120.61  3.000
 KDH  H26   C26  C29  120.87  3.000
 KDH  H26   C26  C24  120.07  3.000
 KDH  C29   C26  C24  119.07  3.000
 KDH  O03   C29  C31  116.31  3.000
 KDH  O03   C29  C26  121.77  3.000
 KDH  C31   C29  C26  121.92  3.000
 KDH  C01   C31  C29  121.56  3.000
 KDH  C01   C31  C20  121.11  3.000
 KDH  C29   C31  C20  117.32  3.000
 KDH  H33   C33  O35  110.73  3.000
 KDH  H33   C33  C01  110.28  3.000
 KDH  O35   C33  C01  108.80  3.000
 KDH  H33   C33  C15  109.24  3.000
 KDH  O35   C33  C15  107.52  3.000
 KDH  C01   C33  C15  110.23  3.000
 KDH  C41   C38  C39  121.08  3.000
 KDH  C41   C38  C36  121.53  3.000
 KDH  C39   C38  C36  117.38  3.000
 KDH  H39   C39  C49  119.61  3.000
 KDH  H39   C39  C38  120.87  3.000
 KDH  C49   C39  C38  119.52  3.000
 KDH  H41   C41  C43  119.07  3.000
 KDH  H41   C41  C38  121.67  3.000
 KDH  C43   C41  C38  119.26  3.000
 KDH  H01A  C01  H01  106.10  3.000
 KDH  H01A  C01  C33  109.32  3.000
 KDH  H01   C01  C33  107.87  3.000
 KDH  H01A  C01  C31  111.57  3.000
 KDH  H01   C01  C31  110.94  3.000
 KDH  C33   C01  C31  110.86  3.000
 KDH  C20   O01  C15  118.84  3.000
 KDH  HO02  O02  C24  110.29  3.000
 KDH  HO03  O03  C29  110.54  3.000
 KDH  H4    C4   C14  120.91  3.000
 KDH  H4    C4   C3   119.41  3.000
 KDH  C14   C4   C3   119.68  3.000
 KDH  C36   O35  C33  119.66  3.000
 KDH  C46   C43  O44  121.15  3.000
 KDH  C46   C43  C41  120.03  3.000
 KDH  O44   C43  C41  118.82  3.000
 KDH  HO44  O44  C43  110.07  3.000
 KDH  C49   C46  O47  119.91  3.000
 KDH  C49   C46  C43  120.24  3.000
 KDH  O47   C46  C43  119.80  3.000
 KDH  HO47  O47  C46  110.18  3.000
 KDH  O50   C49  C46  121.17  3.000
 KDH  O50   C49  C39  118.97  3.000
 KDH  C46   C49  C39  119.86  3.000
 KDH  HO50  O50  C49  110.03  3.000
 KDH  O37   C36  O35  124.10  3.000
 KDH  O37   C36  C38  123.65  3.000
 KDH  O35   C36  C38  112.25  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
 KDH  CONST_01  C12  C9   C6   C3      0.00   0.0  0
 KDH  CONST_02  C12  C14  C4   C3      0.00   0.0  0
 KDH  CONST_03  C14  C4   C3   C6      0.00   0.0  0
 KDH  CONST_04  C14  C12  C9   C6      0.00   0.0  0
 KDH  CONST_05  C4   C3   C6   C9      0.00   0.0  0
 KDH  CONST_06  C4   C14  C12  C9      0.00   0.0  0
 KDH  CONST_07  C26  C24  C21  C20     0.00   0.0  0
 KDH  CONST_08  C26  C29  C31  C20     0.00   0.0  0
 KDH  CONST_09  C29  C31  C20  C21     0.00   0.0  0
 KDH  CONST_10  C29  C26  C24  C21     0.00   0.0  0
 KDH  CONST_11  C31  C20  C21  C24     0.00   0.0  0
 KDH  CONST_12  C31  C29  C26  C24     0.00   0.0  0
 KDH  CONST_13  C46  C49  C39  C38     0.00   0.0  0
 KDH  CONST_14  C46  C43  C41  C38     0.00   0.0  0
 KDH  CONST_15  C43  C41  C38  C39     0.00   0.0  0
 KDH  CONST_16  C43  C46  C49  C39     0.00   0.0  0
 KDH  CONST_17  C49  C39  C38  C41     0.00   0.0  0
 KDH  CONST_18  C49  C46  C43  C41     0.00   0.0  0
 KDH  CONST_19  C15  C14  C4   C3    180.00   0.0  0
 KDH  CONST_20  C15  C14  C12  C9    180.00   0.0  0
 KDH  CONST_21  C9   C6   C3   O1    180.00   0.0  0
 KDH  CONST_22  C14  C4   C3   O1    180.00   0.0  0
 KDH  CONST_23  O10  C9   C6   C3    180.00   0.0  0
 KDH  CONST_24  C4   C3   C6   O7    180.00   0.0  0
 KDH  CONST_25  C12  C9   C6   O7    180.00   0.0  0
 KDH  CONST_26  C14  C12  C9   O10   180.00   0.0  0
 KDH  CONST_27  O02  C24  C21  C20   180.00   0.0  0
 KDH  CONST_28  O03  C29  C31  C20   180.00   0.0  0
 KDH  CONST_29  O03  C29  C26  C24   180.00   0.0  0
 KDH  CONST_30  O02  C24  C26  C29   180.00   0.0  0
 KDH  CONST_31  C49  C39  C38  C36   180.00   0.0  0
 KDH  CONST_32  C43  C41  C38  C36   180.00   0.0  0
 KDH  CONST_33  O50  C49  C39  C38   180.00   0.0  0
 KDH  CONST_34  O44  C43  C41  C38   180.00   0.0  0
 KDH  CONST_35  O47  C46  C49  C39   180.00   0.0  0
 KDH  CONST_36  O47  C46  C43  C41   180.00   0.0  0
 KDH  CONST_37  O03  C29  C31  C01     0.00   0.0  0
 KDH  CONST_38  O50  C49  C46  C43   180.00   0.0  0
 KDH  CONST_39  C49  C46  C43  O44   180.00   0.0  0
 KDH  CONST_40  H4   C4   C3   C6    180.00   0.0  0
 KDH  CONST_41  H12  C12  C9   C6    180.00   0.0  0
 KDH  CONST_42  H26  C26  C24  C21   180.00   0.0  0
 KDH  CONST_43  H21  C21  C24  C26   180.00   0.0  0
 KDH  CONST_44  H41  C41  C38  C39   180.00   0.0  0
 KDH  CONST_45  H39  C39  C38  C41   180.00   0.0  0
 KDH  Var_01    C21  C20  O01  C15   167.29  30.0  1
 KDH  Var_02    C33  C01  C31  C20   -16.27  30.0  1
 KDH  Var_03    C38  C36  O35  C33  -166.64  30.0  1
 KDH  Var_04    O35  C36  C38  C39  -176.97  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
 KDH  chir_01  C15  C14  C33  O01  positiv
 KDH  chir_02  C33  O35  C15  C01  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
 KDH  plan-1  O1   0.020
 KDH  plan-1  C3   0.020
 KDH  plan-1  C6   0.020
 KDH  plan-1  O7   0.020
 KDH  plan-1  C9   0.020
 KDH  plan-1  O10  0.020
 KDH  plan-1  C12  0.020
 KDH  plan-1  C14  0.020
 KDH  plan-1  C15  0.020
 KDH  plan-1  C4   0.020
 KDH  plan-1  H4   0.020
 KDH  plan-1  H12  0.020
 KDH  plan-2  C38  0.020
 KDH  plan-2  C39  0.020
 KDH  plan-2  C41  0.020
 KDH  plan-2  C43  0.020
 KDH  plan-2  O44  0.020
 KDH  plan-2  C46  0.020
 KDH  plan-2  O47  0.020
 KDH  plan-2  C49  0.020
 KDH  plan-2  O50  0.020
 KDH  plan-2  H39  0.020
 KDH  plan-2  H41  0.020
 KDH  plan-2  C36  0.020
 KDH  plan-3  C20  0.020
 KDH  plan-3  C21  0.020
 KDH  plan-3  C24  0.020
 KDH  plan-3  C26  0.020
 KDH  plan-3  C29  0.020
 KDH  plan-3  C31  0.020
 KDH  plan-3  C01  0.020
 KDH  plan-3  O01  0.020
 KDH  plan-3  O02  0.020
 KDH  plan-3  O03  0.020
 KDH  plan-3  H21  0.020
 KDH  plan-3  H26  0.020
 KDH  plan-4  C38  0.020
 KDH  plan-4  O35  0.020
 KDH  plan-4  O37  0.020
 KDH  plan-4  C36  0.020

