# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 08:10:25 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-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
 9CF  9CF  (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one  ligand  41  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9CF
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
 9CF  C15  C  CH2   0  -0.445   4.0610   1.8282   0.1567
 9CF  C14  C  CH2   0  -0.451   5.3073   1.2019  -0.4586
 9CF  C13  C  CH2   0  -0.438   5.3795  -0.2803  -0.1079
 9CF  C12  C  CH1   0   0.050   4.0710  -0.9775  -0.4578
 9CF  C16  C  CH3   0  -0.677   4.0526  -2.4329  -0.0389
 9CF  O5   O  O2    0  -0.489   2.9773  -0.3344   0.1735
 9CF  C11  C  CH1   0   0.061   2.8230   1.0155  -0.2055
 9CF  C10  C  CH2   0  -0.481   1.5709   1.5724   0.4500
 9CF  C7   C  CH1   0   0.037   0.2694   0.9050   0.0450
 9CF  C6   C  CH2   0  -0.540  -0.9378   1.7684   0.3515
 9CF  O3   O  O2    0  -0.430   0.1719  -0.3531   0.7444
 9CF  C8   C  C     0   0.613  -0.9562  -1.0379   0.7158
 9CF  O4   O  O     0  -0.490  -0.9272  -2.2083   1.0732
 9CF  C9   C  CR6   0  -0.344  -2.1772  -0.3750   0.2833
 9CF  C5   C  CR6   0   0.171  -2.2041   1.0140   0.0896
 9CF  C4   C  CR16  0  -0.445  -3.3626   1.6483  -0.2956
 9CF  C3   C  CR6   0   0.409  -4.5258   0.8923  -0.4912
 9CF  O2   O  OH1   0  -0.617  -5.6239   1.5539  -0.8701
 9CF  C2   C  CR16  0  -0.494  -4.5269  -0.4823  -0.2921
 9CF  C1   C  CR6   0   0.396  -3.3603  -1.1225   0.1100
 9CF  O1   O  OH1   0  -0.623  -3.4049  -2.4351   0.3169
 9CF  H1   H  HCH2  0   0.218   4.1622   1.8636   1.2469
 9CF  H2   H  HCH2  0   0.233   3.9343   2.8579  -0.1865
 9CF  H3   H  HCH2  0   0.217   5.2727   1.3168  -1.5468
 9CF  H4   H  HCH2  0   0.236   6.2052   1.7219  -0.1188
 9CF  H5   H  HCH2  0   0.231   6.2021  -0.7644  -0.6399
 9CF  H6   H  HCH2  0   0.215   5.5760  -0.4025   0.9632
 9CF  H7   H  HCH1  0   0.190   3.9373  -0.9186  -1.5511
 9CF  H8   H  HCH3  0   0.222   4.2027  -2.5343   1.0376
 9CF  H9   H  HCH3  0   0.234   3.1068  -2.9094  -0.3000
 9CF  H10  H  HCH3  0   0.226   4.8527  -2.9773  -0.5408
 9CF  H11  H  HCH1  0   0.193   2.6894   1.0730  -1.3004
 9CF  H12  H  HCH2  0   0.245   1.6662   1.5597   1.5404
 9CF  H13  H  HCH2  0   0.254   1.4970   2.6247   0.1629
 9CF  H14  H  HCH1  0   0.254   0.2827   0.6831  -1.0286
 9CF  H15  H  HCH2  0   0.275  -0.9110   2.0947   1.3970
 9CF  H16  H  HCH2  0   0.278  -0.8960   2.6677  -0.2637
 9CF  H17  H  HCR6  0   0.265  -3.3836   2.7202  -0.4463
 9CF  H18  H  HOH1  0   0.482  -6.3702   0.9514  -0.9729
 9CF  H19  H  HCR6  0   0.284  -5.4300  -1.0642  -0.4366
 9CF  H20  H  HOH1  0   0.477  -2.5243  -2.7153   0.6521

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
 9CF  C16  C12  single    1.515  0.020  1.515
 9CF  C13  C12  single    1.523  0.020  1.523
 9CF  C13  C14  single    1.525  0.020  1.525
 9CF  C12  O5   single    1.417  0.020  1.417
 9CF  C14  C15  single    1.525  0.020  1.525
 9CF  O5   C11  single    1.411  0.020  1.411
 9CF  C15  C11  single    1.525  0.020  1.525
 9CF  C11  C10  single    1.519  0.020  1.519
 9CF  C10  C7   single    1.518  0.020  1.518
 9CF  C6   C7   single    1.516  0.020  1.516
 9CF  C6   C5   single    1.497  0.020  1.497
 9CF  C7   O3   single    1.443  0.020  1.443
 9CF  C4   C5   aromatic  1.376  0.020  1.376
 9CF  C4   C3   aromatic  1.401  0.020  1.401
 9CF  C5   C9   aromatic  1.403  0.020  1.403
 9CF  O3   C8   single    1.320  0.020  1.320
 9CF  O2   C3   single    1.337  0.020  1.337
 9CF  C3   C2   aromatic  1.389  0.020  1.389
 9CF  C9   C8   single    1.455  0.020  1.455
 9CF  C9   C1   aromatic  1.410  0.020  1.410
 9CF  C8   O4   double    1.224  0.020  1.224
 9CF  C2   C1   aromatic  1.390  0.020  1.390
 9CF  C1   O1   single    1.329  0.020  1.329
 9CF  C15  H1   single    0.970  0.020  1.090
 9CF  C15  H2   single    0.970  0.020  1.090
 9CF  C14  H3   single    0.970  0.020  1.090
 9CF  C14  H4   single    0.970  0.020  1.090
 9CF  C13  H5   single    0.970  0.020  1.090
 9CF  C13  H6   single    0.970  0.020  1.090
 9CF  C12  H7   single    0.970  0.020  1.090
 9CF  C16  H8   single    0.970  0.020  1.090
 9CF  C16  H9   single    0.970  0.020  1.090
 9CF  C16  H10  single    0.970  0.020  1.090
 9CF  C11  H11  single    0.970  0.020  1.090
 9CF  C10  H12  single    0.970  0.020  1.090
 9CF  C10  H13  single    0.970  0.020  1.090
 9CF  C7   H14  single    0.970  0.020  1.090
 9CF  C6   H15  single    0.970  0.020  1.090
 9CF  C6   H16  single    0.970  0.020  1.090
 9CF  C4   H17  single    0.930  0.020  1.080
 9CF  O2   H18  single    0.850  0.020  0.980
 9CF  C2   H19  single    0.930  0.020  1.080
 9CF  O1   H20  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
 9CF  H2   C15  H1   107.03  3.000
 9CF  H2   C15  C11  109.48  3.000
 9CF  H1   C15  C11  109.19  3.000
 9CF  H2   C15  C14  110.80  3.000
 9CF  H1   C15  C14  109.84  3.000
 9CF  C11  C15  C14  110.42  3.000
 9CF  H4   C14  H3   106.58  3.000
 9CF  H4   C14  C13  110.63  3.000
 9CF  H3   C14  C13  109.40  3.000
 9CF  H4   C14  C15  110.55  3.000
 9CF  H3   C14  C15  109.41  3.000
 9CF  C13  C14  C15  110.19  3.000
 9CF  H6   C13  H5   106.94  3.000
 9CF  H6   C13  C12  109.12  3.000
 9CF  H5   C13  C12  109.39  3.000
 9CF  H6   C13  C14  109.98  3.000
 9CF  H5   C13  C14  110.75  3.000
 9CF  C12  C13  C14  110.57  3.000
 9CF  H7   C12  O5   108.89  3.000
 9CF  H7   C12  C16  108.90  3.000
 9CF  O5   C12  C16  107.66  3.000
 9CF  H7   C12  C13  107.90  3.000
 9CF  O5   C12  C13  110.66  3.000
 9CF  C16  C12  C13  112.75  3.000
 9CF  H10  C16  H9   107.94  3.000
 9CF  H10  C16  H8   107.85  3.000
 9CF  H9   C16  H8   108.34  3.000
 9CF  H10  C16  C12  110.10  3.000
 9CF  H9   C16  C12  111.36  3.000
 9CF  H8   C16  C12  111.12  3.000
 9CF  C11  O5   C12  113.52  3.000
 9CF  H11  C11  C10  108.00  3.000
 9CF  H11  C11  O5   109.23  3.000
 9CF  C10  C11  O5   108.97  3.000
 9CF  H11  C11  C15  107.82  3.000
 9CF  C10  C11  C15  111.80  3.000
 9CF  O5   C11  C15  110.95  3.000
 9CF  H13  C10  H12  106.18  3.000
 9CF  H13  C10  C7   107.17  3.000
 9CF  H12  C10  C7   109.60  3.000
 9CF  H13  C10  C11  107.17  3.000
 9CF  H12  C10  C11  110.72  3.000
 9CF  C7   C10  C11  115.50  3.000
 9CF  H14  C7   O3   107.40  3.000
 9CF  H14  C7   C6   108.85  3.000
 9CF  O3   C7   C6   110.17  3.000
 9CF  H14  C7   C10  109.88  3.000
 9CF  O3   C7   C10  108.18  3.000
 9CF  C6   C7   C10  112.25  3.000
 9CF  H16  C6   H15  106.97  3.000
 9CF  H16  C6   C5   110.45  3.000
 9CF  H15  C6   C5   109.74  3.000
 9CF  H16  C6   C7   108.98  3.000
 9CF  H15  C6   C7   110.07  3.000
 9CF  C5   C6   C7   110.57  3.000
 9CF  C8   O3   C7   119.98  3.000
 9CF  C9   C8   O4   122.84  3.000
 9CF  O4   C8   O3   118.00  3.000
 9CF  C9   C8   O3   119.16  3.000
 9CF  C1   C9   C5   119.46  3.000
 9CF  C1   C9   C8   119.94  3.000
 9CF  C5   C9   C8   120.55  3.000
 9CF  C4   C5   C9   120.76  3.000
 9CF  C9   C5   C6   117.30  3.000
 9CF  C4   C5   C6   121.93  3.000
 9CF  H17  C4   C3   119.91  3.000
 9CF  H17  C4   C5   120.79  3.000
 9CF  C3   C4   C5   119.30  3.000
 9CF  C2   C3   O2   121.99  3.000
 9CF  C2   C3   C4   120.98  3.000
 9CF  O2   C3   C4   117.04  3.000
 9CF  H18  O2   C3   110.89  3.000
 9CF  H19  C2   C1   119.37  3.000
 9CF  H19  C2   C3   120.86  3.000
 9CF  C1   C2   C3   119.77  3.000
 9CF  O1   C1   C2   118.14  3.000
 9CF  O1   C1   C9   122.16  3.000
 9CF  C2   C1   C9   119.70  3.000
 9CF  H20  O1   C1   107.73  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
 9CF  CONST_01  C3   C4   C5   C9      0.00   0.0  0
 9CF  CONST_02  C3   C2   C1   C9      0.00   0.0  0
 9CF  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 9CF  CONST_04  C2   C1   C9   C5      0.00   0.0  0
 9CF  CONST_05  C1   C9   C5   C4      0.00   0.0  0
 9CF  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 9CF  CONST_07  O1   C1   C9   C8      0.00   0.0  0
 9CF  CONST_08  O2   C3   C4   C5    180.00   0.0  0
 9CF  CONST_09  O1   C1   C9   C5    180.00   0.0  0
 9CF  CONST_10  O1   C1   C2   C3    180.00   0.0  0
 9CF  CONST_11  C1   C2   C3   O2    180.00   0.0  0
 9CF  CONST_12  H17  C4   C5   C6      0.00   0.0  0
 9CF  CONST_13  H19  C2   C1   C9    180.00   0.0  0
 9CF  Var_01    C12  C13  C14  C15    51.86  30.0  1
 9CF  Var_02    C11  C15  C14  C13   -51.67  30.0  1
 9CF  Var_03    C4   C5   C6   C7   -150.41  30.0  1
 9CF  Var_04    C9   C8   O3   C7    -15.74  30.0  1
 9CF  Var_05    C5   C9   C8   O3     -9.40  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
 9CF  chir_01  C12  C16  C13  O5   positiv
 9CF  chir_02  C11  O5   C15  C10  positiv
 9CF  chir_03  C7   O3   C6   C10  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
 9CF  plan-1  O3   0.020
 9CF  plan-1  C8   0.020
 9CF  plan-1  O4   0.020
 9CF  plan-1  C9   0.020
 9CF  plan-2  C6   0.020
 9CF  plan-2  C8   0.020
 9CF  plan-2  C9   0.020
 9CF  plan-2  C5   0.020
 9CF  plan-2  C4   0.020
 9CF  plan-2  C3   0.020
 9CF  plan-2  O2   0.020
 9CF  plan-2  C2   0.020
 9CF  plan-2  C1   0.020
 9CF  plan-2  O1   0.020
 9CF  plan-2  H17  0.020
 9CF  plan-2  H19  0.020

