# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:49:40 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R,3S)-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
 KXN  KXN  (2R,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol  ligand  35  21  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KXN
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
 KXN  O94   O  OH1   0  -0.632  -2.5073   8.0806  15.8279
 KXN  C94   C  CR6   0   0.286  -2.3066   6.9230  15.1661
 KXN  C93   C  CR6   0   0.279  -1.0915   6.2264  15.2554
 KXN  O93   O  OH1   0  -0.644  -0.1437   6.7880  16.0392
 KXN  C92   C  CR16  0  -0.415  -0.9201   5.0393  14.5671
 KXN  C95   C  CR16  0  -0.332  -3.3213   6.4087  14.3772
 KXN  C96   C  CR16  0  -0.319  -3.1409   5.2185  13.6814
 KXN  C91   C  CR6   0   0.046  -1.9434   4.5253  13.7690
 KXN  C2    C  CH1   0  -0.045  -1.7843   3.2013  13.0823
 KXN  O1    O  O2    0  -0.494  -0.5035   3.1693  12.4683
 KXN  C3    C  CH1   0   0.035  -1.9158   2.0267  14.0610
 KXN  O3    O  OH1   0  -0.662  -3.1479   2.0582  14.7319
 KXN  C4    C  CH2   0  -0.486  -1.8295   0.7277  13.2832
 KXN  C10   C  CR6   0  -0.155  -0.7050   0.7854  12.2864
 KXN  C9    C  CR6   0   0.413  -0.0938   1.9899  11.9470
 KXN  C8    C  CR16  0  -0.483   0.9767   2.0574  11.0600
 KXN  C5    C  CR6   0   0.344  -0.2201  -0.3710  11.6691
 KXN  O51   O  OH1   0  -0.624  -0.8373  -1.5247  11.9867
 KXN  C6    C  CR16  0  -0.541   0.8445  -0.3361  10.7765
 KXN  C7    C  CR6   0   0.379   1.4448   0.8861  10.4837
 KXN  O71   O  OH1   0  -0.636   2.4825   0.9824   9.6300
 KXN  HO94  H  HOH1  0   0.473  -1.7316   8.3097  16.3532
 KXN  HO93  H  HOH1  0   0.483   0.6576   6.2529  16.0489
 KXN  H92   H  HCR6  0   0.272   0.0255   4.5139  14.6509
 KXN  H95   H  HCR6  0   0.267  -4.2585   6.9466  14.3066
 KXN  H96   H  HCR6  0   0.255  -3.9438   4.8371  13.0628
 KXN  H2    H  HCH1  0   0.253  -2.5609   3.0948  12.3118
 KXN  H3    H  HCH1  0   0.223  -1.0738   2.0868  14.7672
 KXN  HO3   H  HOH1  0   0.454  -3.1709   2.8393  15.2953
 KXN  H4    H  HCH2  0   0.261  -1.6888  -0.1059  13.9749
 KXN  H4A   H  HCH2  0   0.251  -2.7853   0.5561  12.7755
 KXN  H8    H  HCR6  0   0.264   1.4302   3.0114  10.8228
 KXN  HO51  H  HOH1  0   0.477  -0.4313  -2.2646  11.5215
 KXN  H6    H  HCR6  0   0.278   1.2024  -1.2508  10.3143
 KXN  HO71  H  HOH1  0   0.475   2.7102   0.1142   9.2798

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
 KXN  C94  O94   single    1.348  0.020  1.348
 KXN  O94  HO94  single    0.850  0.020  0.980
 KXN  C95  C94   aromatic  1.384  0.020  1.384
 KXN  C94  C93   aromatic  1.403  0.020  1.403
 KXN  C92  C93   aromatic  1.383  0.020  1.383
 KXN  C93  O93   single    1.352  0.020  1.352
 KXN  O93  HO93  single    0.850  0.020  0.980
 KXN  C91  C92   aromatic  1.396  0.020  1.396
 KXN  C92  H92   single    0.930  0.020  1.080
 KXN  C96  C95   aromatic  1.390  0.020  1.390
 KXN  C95  H95   single    0.930  0.020  1.080
 KXN  C96  C91   aromatic  1.386  0.020  1.386
 KXN  C96  H96   single    0.930  0.020  1.080
 KXN  C2   C91   single    1.500  0.020  1.500
 KXN  O1   C2    single    1.421  0.020  1.421
 KXN  C2   C3    single    1.535  0.020  1.535
 KXN  C2   H2    single    0.970  0.020  1.090
 KXN  C9   O1    single    1.353  0.020  1.353
 KXN  C4   C3    single    1.517  0.020  1.517
 KXN  C3   O3    single    1.403  0.020  1.403
 KXN  C3   H3    single    0.970  0.020  1.090
 KXN  O3   HO3   single    0.850  0.020  0.980
 KXN  C10  C4    single    1.504  0.020  1.504
 KXN  C4   H4    single    0.970  0.020  1.090
 KXN  C4   H4A   single    0.970  0.020  1.090
 KXN  C5   C10   aromatic  1.398  0.020  1.398
 KXN  C9   C10   aromatic  1.393  0.020  1.393
 KXN  C8   C9    aromatic  1.392  0.020  1.392
 KXN  C7   C8    aromatic  1.387  0.020  1.387
 KXN  C8   H8    single    0.930  0.020  1.080
 KXN  C6   C5    aromatic  1.390  0.020  1.390
 KXN  C5   O51   single    1.346  0.020  1.346
 KXN  O51  HO51  single    0.850  0.020  0.980
 KXN  C7   C6    aromatic  1.393  0.020  1.393
 KXN  C6   H6    single    0.930  0.020  1.080
 KXN  O71  C7    single    1.347  0.020  1.347
 KXN  O71  HO71  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
 KXN  HO94  O94  C94  110.59  3.000
 KXN  C95   C94  C93  119.11  3.000
 KXN  C93   C94  O94  121.58  3.000
 KXN  C95   C94  O94  119.31  3.000
 KXN  C92   C93  O93  123.93  3.000
 KXN  O93   C93  C94  115.96  3.000
 KXN  C92   C93  C94  120.11  3.000
 KXN  HO93  O93  C93  110.98  3.000
 KXN  H92   C92  C91  120.32  3.000
 KXN  H92   C92  C93  119.03  3.000
 KXN  C91   C92  C93  120.65  3.000
 KXN  H95   C95  C96  120.33  3.000
 KXN  H95   C95  C94  119.14  3.000
 KXN  C96   C95  C94  120.53  3.000
 KXN  H96   C96  C91  120.03  3.000
 KXN  H96   C96  C95  119.41  3.000
 KXN  C91   C96  C95  120.56  3.000
 KXN  C2    C91  C96  120.27  3.000
 KXN  C2    C91  C92  120.60  3.000
 KXN  C96   C91  C92  119.03  3.000
 KXN  H2    C2   C3   108.20  3.000
 KXN  H2    C2   O1   109.38  3.000
 KXN  C3    C2   O1   109.61  3.000
 KXN  H2    C2   C91  109.36  3.000
 KXN  C3    C2   C91  112.00  3.000
 KXN  O1    C2   C91  108.26  3.000
 KXN  C9    O1   C2   117.33  3.000
 KXN  H3    C3   C4   109.41  3.000
 KXN  H3    C3   O3   111.33  3.000
 KXN  C4    C3   O3   108.33  3.000
 KXN  H3    C3   C2   107.57  3.000
 KXN  O3    C3   C2   111.28  3.000
 KXN  C4    C3   C2   108.89  3.000
 KXN  HO3   O3   C3   108.59  3.000
 KXN  H4A   C4   H4   106.64  3.000
 KXN  H4A   C4   C10  110.56  3.000
 KXN  H4    C4   C10  110.65  3.000
 KXN  H4A   C4   C3   108.79  3.000
 KXN  H4    C4   C3   109.65  3.000
 KXN  C10   C4   C3   110.46  3.000
 KXN  C5    C10  C9   117.11  3.000
 KXN  C9    C10  C4   121.53  3.000
 KXN  C5    C10  C4   121.36  3.000
 KXN  C8    C9   C10  122.33  3.000
 KXN  C8    C9   O1   115.86  3.000
 KXN  C10   C9   O1   121.81  3.000
 KXN  H8    C8   C7   120.79  3.000
 KXN  H8    C8   C9   120.30  3.000
 KXN  C7    C8   C9   118.91  3.000
 KXN  C6    C5   O51  121.62  3.000
 KXN  O51   C5   C10  116.47  3.000
 KXN  C6    C5   C10  121.91  3.000
 KXN  HO51  O51  C5   110.54  3.000
 KXN  H6    C6   C7   120.51  3.000
 KXN  H6    C6   C5   120.32  3.000
 KXN  C7    C6   C5   119.16  3.000
 KXN  O71   C7   C6   121.87  3.000
 KXN  O71   C7   C8   117.57  3.000
 KXN  C6    C7   C8   120.55  3.000
 KXN  HO71  O71  C7   110.36  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
 KXN  CONST_01  C91  C96  C95  C94    0.00   0.0  0
 KXN  CONST_02  C91  C92  C93  C94    0.00   0.0  0
 KXN  CONST_03  C96  C95  C94  C93    0.00   0.0  0
 KXN  CONST_04  C96  C91  C92  C93    0.00   0.0  0
 KXN  CONST_05  C95  C94  C93  C92    0.00   0.0  0
 KXN  CONST_06  C95  C96  C91  C92    0.00   0.0  0
 KXN  CONST_07  C7   C6   C5   C10    0.00   0.0  0
 KXN  CONST_08  C7   C8   C9   C10    0.00   0.0  0
 KXN  CONST_09  C6   C5   C10  C9     0.00   0.0  0
 KXN  CONST_10  C6   C7   C8   C9     0.00   0.0  0
 KXN  CONST_11  C5   C10  C9   C8     0.00   0.0  0
 KXN  CONST_12  C5   C6   C7   C8     0.00   0.0  0
 KXN  CONST_13  C2   C91  C92  C93  180.00   0.0  0
 KXN  CONST_14  C2   C91  C96  C95  180.00   0.0  0
 KXN  CONST_15  C96  C95  C94  O94  180.00   0.0  0
 KXN  CONST_16  C92  C93  C94  O94  180.00   0.0  0
 KXN  CONST_17  C95  C94  C93  O93  180.00   0.0  0
 KXN  CONST_18  C91  C92  C93  O93  180.00   0.0  0
 KXN  CONST_19  O51  C5   C10  C4     0.00   0.0  0
 KXN  CONST_20  O51  C5   C10  C9   180.00   0.0  0
 KXN  CONST_21  O71  C7   C8   C9   180.00   0.0  0
 KXN  CONST_22  O71  C7   C6   C5   180.00   0.0  0
 KXN  CONST_23  C7   C6   C5   O51  180.00   0.0  0
 KXN  CONST_24  H96  C96  C95  C94  180.00   0.0  0
 KXN  CONST_25  H92  C92  C93  C94  180.00   0.0  0
 KXN  CONST_26  H95  C95  C94  C93  180.00   0.0  0
 KXN  CONST_27  H8   C8   C9   O1     0.00   0.0  0
 KXN  CONST_28  H6   C6   C5   C10  180.00   0.0  0
 KXN  Var_01    C10  C9   O1   C2   -16.58  30.0  1
 KXN  Var_02    C5   C10  C4   C3   165.08  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
 KXN  chir_01  C2  C91  O1  C3  negativ
 KXN  chir_02  C3  O3   C2  C4  positiv

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
 KXN  plan-1  O94  0.020
 KXN  plan-1  C94  0.020
 KXN  plan-1  C93  0.020
 KXN  plan-1  O93  0.020
 KXN  plan-1  C92  0.020
 KXN  plan-1  C95  0.020
 KXN  plan-1  C96  0.020
 KXN  plan-1  C91  0.020
 KXN  plan-1  C2   0.020
 KXN  plan-1  H92  0.020
 KXN  plan-1  H95  0.020
 KXN  plan-1  H96  0.020
 KXN  plan-2  O1   0.020
 KXN  plan-2  C4   0.020
 KXN  plan-2  C10  0.020
 KXN  plan-2  C9   0.020
 KXN  plan-2  C8   0.020
 KXN  plan-2  C5   0.020
 KXN  plan-2  O51  0.020
 KXN  plan-2  C6   0.020
 KXN  plan-2  C7   0.020
 KXN  plan-2  O71  0.020
 KXN  plan-2  H8   0.020
 KXN  plan-2  H6   0.020

