# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 09:00:05 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (3R)-6,8-dihydroxy-3-{[(2R,6S)-6-methyltetrahydro-2H-pyran-2-yl]methyl}-3,4-dihydro-1H-isochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC[C@H](C[C@H]2Cc3cc(O)cc(O)c3C(=O)O2)O1
#
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
 KRS  KRS  (3R)-6,8-dihydroxy-3-{[(2R,6S)-6-methyltetrahydro-2H-pyran-2-yl]methyl}-3,4-dihydro-1H-isochromen-1-one  ligand  41  21  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KRS
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
 KRS  O4   O  O     0  -0.437   0.9532  -2.2056   1.5198
 KRS  C8   C  C     0   0.557   0.9398  -1.0968   1.0401
 KRS  C9   C  CR6   0  -0.293   2.1011  -0.4173   0.4482
 KRS  C5   C  CR6   0   0.171   2.0824   0.9788   0.2913
 KRS  C4   C  CR16  0  -0.446   3.1801   1.6637  -0.1843
 KRS  C3   C  CR6   0   0.409   4.3326   0.9559  -0.5285
 KRS  O2   O  OH1   0  -0.619   5.3737   1.6563  -0.9906
 KRS  C2   C  CR16  0  -0.540   4.3716  -0.4269  -0.4000
 KRS  C1   C  CR6   0   0.397   3.2675  -1.1176   0.0871
 KRS  O1   O  OH1   0  -0.601   3.2942  -2.4479   0.1975
 KRS  O3   O  O2    0  -0.456  -0.2097  -0.4189   1.0876
 KRS  C7   C  CH1   0   0.042  -0.3643   0.8169   0.3721
 KRS  C6   C  CH2   0  -0.530   0.8250   1.7057   0.6588
 KRS  C10  C  CH2   0  -0.480  -1.6836   1.4269   0.8030
 KRS  C11  C  CH1   0   0.062  -2.9050   0.5727   0.5036
 KRS  O5   O  O2    0  -0.505  -2.9414   0.3651  -0.8963
 KRS  C12  C  CH1   0   0.017  -3.9967  -0.4666  -1.3566
 KRS  C16  C  CH3   0  -0.695  -3.8033  -1.9255  -0.9566
 KRS  C13  C  CH2   0  -0.447  -5.3503   0.0979  -0.9271
 KRS  C14  C  CH2   0  -0.458  -5.3955   0.3811   0.5711
 KRS  C15  C  CH2   0  -0.439  -4.1940   1.2241   0.9865
 KRS  H1   H  HCR6  0   0.265   3.1499   2.7397  -0.3006
 KRS  H2   H  HOH1  0   0.482   6.1138   1.0744  -1.2014
 KRS  H3   H  HCR6  0   0.290   5.2645  -0.9743  -0.6849
 KRS  H4   H  HOH1  0   0.481   4.1373  -2.7903  -0.1235
 KRS  H5   H  HCH1  0   0.252  -0.3923   0.5902  -0.6987
 KRS  H6   H  HCH2  0   0.270   0.8423   1.9834   1.7183
 KRS  H7   H  HCH2  0   0.274   0.7417   2.6307   0.0874
 KRS  H8   H  HCH2  0   0.243  -1.6528   1.6350   1.8764
 KRS  H9   H  HCH2  0   0.241  -1.7879   2.3934   0.3003
 KRS  H10  H  HCH1  0   0.207  -2.7988  -0.3890   1.0259
 KRS  H11  H  HCH1  0   0.229  -3.9300  -0.4133  -2.4471
 KRS  H12  H  HCH3  0   0.226  -3.9520  -2.1034   0.1088
 KRS  H13  H  HCH3  0   0.233  -4.5185  -2.5498  -1.4933
 KRS  H14  H  HCH3  0   0.234  -2.8011  -2.2681  -1.2177
 KRS  H15  H  HCH2  0   0.227  -5.5358   1.0290  -1.4714
 KRS  H16  H  HCH2  0   0.231  -6.1426  -0.5968  -1.2166
 KRS  H17  H  HCH2  0   0.238  -6.3268   0.8896   0.8286
 KRS  H18  H  HCH2  0   0.221  -5.3927  -0.5547   1.1380
 KRS  H19  H  HCH2  0   0.232  -4.1604   1.3344   2.0731
 KRS  H20  H  HCH2  0   0.215  -4.2776   2.2318   0.5648

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
 KRS  O1   C1   single    1.335  0.020  1.335
 KRS  O4   C8   double    1.208  0.020  1.208
 KRS  C1   C2   aromatic  1.390  0.020  1.390
 KRS  C1   C9   aromatic  1.408  0.020  1.408
 KRS  C8   C9   single    1.470  0.020  1.470
 KRS  C8   O3   single    1.335  0.020  1.335
 KRS  C2   C3   aromatic  1.389  0.020  1.389
 KRS  C9   C5   aromatic  1.405  0.020  1.405
 KRS  O3   C7   single    1.436  0.020  1.436
 KRS  C3   O2   single    1.337  0.020  1.337
 KRS  C3   C4   aromatic  1.396  0.020  1.396
 KRS  C5   C4   aromatic  1.378  0.020  1.378
 KRS  C5   C6   single    1.498  0.020  1.498
 KRS  C6   C7   single    1.512  0.020  1.512
 KRS  C7   C10  single    1.516  0.020  1.516
 KRS  C10  C11  single    1.520  0.020  1.520
 KRS  C11  C15  single    1.523  0.020  1.523
 KRS  C11  O5   single    1.416  0.020  1.416
 KRS  C15  C14  single    1.525  0.020  1.525
 KRS  O5   C12  single    1.420  0.020  1.420
 KRS  C14  C13  single    1.525  0.020  1.525
 KRS  C12  C13  single    1.528  0.020  1.528
 KRS  C12  C16  single    1.525  0.020  1.525
 KRS  C4   H1   single    0.930  0.020  1.080
 KRS  O2   H2   single    0.850  0.020  0.980
 KRS  C2   H3   single    0.930  0.020  1.080
 KRS  O1   H4   single    0.850  0.020  0.980
 KRS  C7   H5   single    0.970  0.020  1.090
 KRS  C6   H6   single    0.970  0.020  1.090
 KRS  C6   H7   single    0.970  0.020  1.090
 KRS  C10  H8   single    0.970  0.020  1.090
 KRS  C10  H9   single    0.970  0.020  1.090
 KRS  C11  H10  single    0.970  0.020  1.090
 KRS  C12  H11  single    0.970  0.020  1.090
 KRS  C16  H12  single    0.970  0.020  1.090
 KRS  C16  H13  single    0.970  0.020  1.090
 KRS  C16  H14  single    0.970  0.020  1.090
 KRS  C13  H15  single    0.970  0.020  1.090
 KRS  C13  H16  single    0.970  0.020  1.090
 KRS  C14  H17  single    0.970  0.020  1.090
 KRS  C14  H18  single    0.970  0.020  1.090
 KRS  C15  H19  single    0.970  0.020  1.090
 KRS  C15  H20  single    0.970  0.020  1.090

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
 KRS  O3   C8   C9   117.37  3.000
 KRS  O3   C8   O4   117.47  3.000
 KRS  C9   C8   O4   125.12  3.000
 KRS  C1   C9   C5   118.47  3.000
 KRS  C5   C9   C8   119.59  3.000
 KRS  C1   C9   C8   121.87  3.000
 KRS  C6   C5   C4   120.79  3.000
 KRS  C6   C5   C9   117.76  3.000
 KRS  C4   C5   C9   121.44  3.000
 KRS  H1   C4   C3   120.04  3.000
 KRS  H1   C4   C5   120.57  3.000
 KRS  C3   C4   C5   119.39  3.000
 KRS  C2   C3   O2   122.11  3.000
 KRS  O2   C3   C4   117.55  3.000
 KRS  C2   C3   C4   120.34  3.000
 KRS  H2   O2   C3   110.91  3.000
 KRS  H3   C2   C1   119.65  3.000
 KRS  H3   C2   C3   120.05  3.000
 KRS  C1   C2   C3   120.30  3.000
 KRS  O1   C1   C2   120.53  3.000
 KRS  C2   C1   C9   120.05  3.000
 KRS  O1   C1   C9   119.41  3.000
 KRS  H4   O1   C1   110.09  3.000
 KRS  C7   O3   C8   120.78  3.000
 KRS  H5   C7   C10  109.82  3.000
 KRS  H5   C7   C6   109.10  3.000
 KRS  C10  C7   C6   113.20  3.000
 KRS  H5   C7   O3   108.17  3.000
 KRS  C10  C7   O3   107.36  3.000
 KRS  C6   C7   O3   109.06  3.000
 KRS  H7   C6   H6   107.04  3.000
 KRS  H7   C6   C7   109.83  3.000
 KRS  H6   C6   C7   110.17  3.000
 KRS  H7   C6   C5   110.31  3.000
 KRS  H6   C6   C5   110.30  3.000
 KRS  C7   C6   C5   109.17  3.000
 KRS  H9   C10  H8   106.59  3.000
 KRS  H9   C10  C11  109.22  3.000
 KRS  H8   C10  C11  108.83  3.000
 KRS  H9   C10  C7   107.92  3.000
 KRS  H8   C10  C7   109.33  3.000
 KRS  C11  C10  C7   114.65  3.000
 KRS  H10  C11  C15  107.78  3.000
 KRS  H10  C11  O5   110.12  3.000
 KRS  C15  C11  O5   110.76  3.000
 KRS  H10  C11  C10  108.68  3.000
 KRS  O5   C11  C10  107.33  3.000
 KRS  C15  C11  C10  112.16  3.000
 KRS  C12  O5   C11  115.18  3.000
 KRS  H11  C12  C13  108.43  3.000
 KRS  H11  C12  C16  107.48  3.000
 KRS  C13  C12  C16  113.08  3.000
 KRS  H11  C12  O5   104.43  3.000
 KRS  C16  C12  O5   112.39  3.000
 KRS  C13  C12  O5   110.53  3.000
 KRS  H14  C16  H13  107.75  3.000
 KRS  H14  C16  H12  107.93  3.000
 KRS  H13  C16  H12  107.34  3.000
 KRS  H14  C16  C12  110.75  3.000
 KRS  H13  C16  C12  109.60  3.000
 KRS  H12  C16  C12  113.27  3.000
 KRS  H16  C13  H15  106.64  3.000
 KRS  H16  C13  C14  110.90  3.000
 KRS  H15  C13  C14  108.99  3.000
 KRS  H16  C13  C12  109.45  3.000
 KRS  H15  C13  C12  108.94  3.000
 KRS  C14  C13  C12  111.77  3.000
 KRS  H18  C14  H17  106.16  3.000
 KRS  H18  C14  C15  109.24  3.000
 KRS  H17  C14  C15  110.50  3.000
 KRS  H18  C14  C13  110.49  3.000
 KRS  H17  C14  C13  110.08  3.000
 KRS  C15  C14  C13  110.29  3.000
 KRS  H20  C15  H19  106.99  3.000
 KRS  H20  C15  C14  110.08  3.000
 KRS  H19  C15  C14  110.53  3.000
 KRS  H20  C15  C11  109.63  3.000
 KRS  H19  C15  C11  109.42  3.000
 KRS  C14  C15  C11  110.12  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
 KRS  CONST_01  C3   C2   C1   C9     0.00   0.0  0
 KRS  CONST_02  C3   C4   C5   C9     0.00   0.0  0
 KRS  CONST_03  C2   C1   C9   C5     0.00   0.0  0
 KRS  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 KRS  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 KRS  CONST_06  C1   C9   C5   C4     0.00   0.0  0
 KRS  CONST_07  O1   C1   C9   C8     0.00   0.0  0
 KRS  CONST_08  O1   C1   C9   C5   180.00   0.0  0
 KRS  CONST_09  O2   C3   C4   C5   180.00   0.0  0
 KRS  CONST_10  O1   C1   C2   C3   180.00   0.0  0
 KRS  CONST_11  C1   C2   C3   O2   180.00   0.0  0
 KRS  CONST_12  H3   C2   C1   C9   180.00   0.0  0
 KRS  CONST_13  H1   C4   C5   C9   180.00   0.0  0
 KRS  Var_01    C7   C6   C5   C9   -32.44  30.0  1
 KRS  Var_02    O3   C8   C9   C5    16.89  30.0  1
 KRS  Var_03    C13  C14  C15  C11  -52.58  30.0  1
 KRS  Var_04    C15  C14  C13  C12   51.22  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
 KRS  chir_01  C7   O3  C6   C10  positiv
 KRS  chir_02  C11  O5  C10  C15  negativ
 KRS  chir_03  C12  O5  C16  C13  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
 KRS  plan-1  O4  0.020
 KRS  plan-1  C8  0.020
 KRS  plan-1  C9  0.020
 KRS  plan-1  O3  0.020
 KRS  plan-2  C8  0.020
 KRS  plan-2  C9  0.020
 KRS  plan-2  C5  0.020
 KRS  plan-2  C4  0.020
 KRS  plan-2  C3  0.020
 KRS  plan-2  O2  0.020
 KRS  plan-2  C2  0.020
 KRS  plan-2  C1  0.020
 KRS  plan-2  O1  0.020
 KRS  plan-2  C6  0.020
 KRS  plan-2  H1  0.020
 KRS  plan-2  H3  0.020

