# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 08:56:41 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (3R)-6,8-dihydroxy-3-{[(2S,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
 9CC  9CC  (3R)-6,8-dihydroxy-3-{[(2S,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 OK
;

data_comp_9CC
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
 9CC  C1   C  CR6   0   0.396  -3.3921  -1.1983  -0.2317
 9CC  C8   C  C     0   0.612  -0.9930  -1.1094  -0.8651
 9CC  C4   C  CR16  0  -0.493  -3.3620   1.5523   0.2840
 9CC  C3   C  CR6   0   0.408  -4.5282   0.7992   0.4684
 9CC  C7   C  CH1   0   0.039   0.2595   0.7971  -0.1375
 9CC  C6   C  CH2   0  -0.541  -0.9451   1.6800  -0.3941
 9CC  C2   C  CR16  0  -0.453  -4.5457  -0.5664   0.2124
 9CC  C5   C  CR6   0   0.176  -2.2134   0.9247  -0.1445
 9CC  C9   C  CR6   0  -0.344  -2.2029  -0.4541  -0.3927
 9CC  C10  C  CH2   0  -0.477   1.5619   1.4672  -0.5351
 9CC  C11  C  CH1   0   0.060   2.8137   0.8796   0.0944
 9CC  C12  C  CH1   0   0.018   4.0710  -1.1568   0.1787
 9CC  C13  C  CH2   0  -0.449   5.3733  -0.4071  -0.0970
 9CC  C14  C  CH2   0  -0.457   5.2951   1.0469   0.3565
 9CC  O3   O  O2    0  -0.432   0.1404  -0.4331  -0.8820
 9CC  C15  C  CH2   0  -0.444   4.0520   1.7061  -0.2295
 9CC  C16  C  CH3   0  -0.695   3.8821  -1.5049   1.6513
 9CC  O5   O  O2    0  -0.494   2.9611  -0.4505  -0.3578
 9CC  O4   O  O     0  -0.490  -0.9766  -2.2655  -1.2671
 9CC  O2   O  OH1   0  -0.617  -5.6673   1.3559   0.8923
 9CC  O1   O  OH1   0  -0.624  -3.4495  -2.5016  -0.4897
 9CC  H1   H  HCR6  0   0.274  -3.3626   2.6190   0.4773
 9CC  H2   H  HCH1  0   0.254   0.2865   0.5344   0.9265
 9CC  H3   H  HCH2  0   0.279  -0.8885   2.5544   0.2551
 9CC  H4   H  HCH2  0   0.276  -0.9304   2.0477  -1.4261
 9CC  H5   H  HCR6  0   0.278  -5.4562  -1.1366   0.3481
 9CC  H6   H  HCH2  0   0.245   1.6484   1.4876  -1.6261
 9CC  H7   H  HCH2  0   0.253   1.4980   2.5104  -0.2142
 9CC  H8   H  HCH1  0   0.200   2.6726   0.8972   1.1871
 9CC  H9   H  HCH1  0   0.228   4.0886  -2.0964  -0.3810
 9CC  H10  H  HCH2  0   0.231   6.2038  -0.9243   0.3891
 9CC  H11  H  HCH2  0   0.227   5.5747  -0.4337  -1.1724
 9CC  H12  H  HCH2  0   0.221   5.2612   1.1089   1.4483
 9CC  H13  H  HCH2  0   0.237   6.1940   1.5838   0.0469
 9CC  H14  H  HCH2  0   0.217   4.1559   1.7923  -1.3167
 9CC  H15  H  HCH2  0   0.232   3.9266   2.7188   0.1620
 9CC  H16  H  HCH3  0   0.225   3.9598  -0.6428   2.3146
 9CC  H17  H  HCH3  0   0.234   2.9079  -1.9681   1.8140
 9CC  H18  H  HCH3  0   0.232   4.6448  -2.2211   1.9596
 9CC  H19  H  HOH1  0   0.482  -5.5536   2.3033   1.0329
 9CC  H20  H  HOH1  0   0.476  -2.5760  -2.7764  -0.8459

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
 9CC  O1   C1   single    1.330  0.020  1.330
 9CC  O4   C8   double    1.224  0.020  1.224
 9CC  C1   C2   aromatic  1.388  0.020  1.388
 9CC  C1   C9   aromatic  1.412  0.020  1.412
 9CC  C2   C3   aromatic  1.389  0.020  1.389
 9CC  C8   C9   single    1.455  0.020  1.455
 9CC  C8   O3   single    1.320  0.020  1.320
 9CC  C9   C5   aromatic  1.401  0.020  1.401
 9CC  O3   C7   single    1.443  0.020  1.443
 9CC  C3   O2   single    1.337  0.020  1.337
 9CC  C3   C4   aromatic  1.400  0.020  1.400
 9CC  C5   C4   aromatic  1.377  0.020  1.377
 9CC  C5   C6   single    1.497  0.020  1.497
 9CC  C7   C6   single    1.515  0.020  1.515
 9CC  C7   C10  single    1.518  0.020  1.518
 9CC  C10  C11  single    1.519  0.020  1.519
 9CC  C11  C15  single    1.524  0.020  1.524
 9CC  C11  O5   single    1.413  0.020  1.413
 9CC  C15  C14  single    1.524  0.020  1.524
 9CC  O5   C12  single    1.421  0.020  1.421
 9CC  C14  C13  single    1.525  0.020  1.525
 9CC  C12  C13  single    1.528  0.020  1.528
 9CC  C12  C16  single    1.525  0.020  1.525
 9CC  C4   H1   single    0.930  0.020  1.080
 9CC  C7   H2   single    0.970  0.020  1.090
 9CC  C6   H3   single    0.970  0.020  1.090
 9CC  C6   H4   single    0.970  0.020  1.090
 9CC  C2   H5   single    0.930  0.020  1.080
 9CC  C10  H6   single    0.970  0.020  1.090
 9CC  C10  H7   single    0.970  0.020  1.090
 9CC  C11  H8   single    0.970  0.020  1.090
 9CC  C12  H9   single    0.970  0.020  1.090
 9CC  C13  H10  single    0.970  0.020  1.090
 9CC  C13  H11  single    0.970  0.020  1.090
 9CC  C14  H12  single    0.970  0.020  1.090
 9CC  C14  H13  single    0.970  0.020  1.090
 9CC  C15  H14  single    0.970  0.020  1.090
 9CC  C15  H15  single    0.970  0.020  1.090
 9CC  C16  H16  single    0.970  0.020  1.090
 9CC  C16  H17  single    0.970  0.020  1.090
 9CC  C16  H18  single    0.970  0.020  1.090
 9CC  O2   H19  single    0.850  0.020  0.980
 9CC  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
 9CC  O1   C1   C9   122.05  3.000
 9CC  C9   C1   C2   119.76  3.000
 9CC  O1   C1   C2   118.19  3.000
 9CC  O4   C8   O3   117.92  3.000
 9CC  O3   C8   C9   119.17  3.000
 9CC  O4   C8   C9   122.90  3.000
 9CC  H1   C4   C5   120.29  3.000
 9CC  H1   C4   C3   120.35  3.000
 9CC  C5   C4   C3   119.37  3.000
 9CC  O2   C3   C2   117.19  3.000
 9CC  O2   C3   C4   121.83  3.000
 9CC  C2   C3   C4   120.98  3.000
 9CC  H2   C7   O3   107.37  3.000
 9CC  H2   C7   C10  109.81  3.000
 9CC  O3   C7   C10  108.19  3.000
 9CC  H2   C7   C6   108.88  3.000
 9CC  C10  C7   C6   112.36  3.000
 9CC  O3   C7   C6   110.11  3.000
 9CC  H4   C6   H3   106.91  3.000
 9CC  H4   C6   C5   109.74  3.000
 9CC  H3   C6   C5   110.44  3.000
 9CC  H4   C6   C7   110.14  3.000
 9CC  H3   C6   C7   108.97  3.000
 9CC  C5   C6   C7   110.56  3.000
 9CC  H5   C2   C3   120.33  3.000
 9CC  H5   C2   C1   119.94  3.000
 9CC  C3   C2   C1   119.72  3.000
 9CC  C9   C5   C6   117.43  3.000
 9CC  C6   C5   C4   121.90  3.000
 9CC  C9   C5   C4   120.65  3.000
 9CC  C5   C9   C8   120.47  3.000
 9CC  C5   C9   C1   119.48  3.000
 9CC  C8   C9   C1   120.00  3.000
 9CC  H7   C10  H6   106.22  3.000
 9CC  H7   C10  C11  107.19  3.000
 9CC  H6   C10  C11  110.79  3.000
 9CC  H7   C10  C7   107.12  3.000
 9CC  H6   C10  C7   109.71  3.000
 9CC  C11  C10  C7   115.32  3.000
 9CC  H8   C11  O5   110.23  3.000
 9CC  H8   C11  C15  107.83  3.000
 9CC  O5   C11  C15  110.97  3.000
 9CC  H8   C11  C10  107.41  3.000
 9CC  O5   C11  C10  108.51  3.000
 9CC  C15  C11  C10  111.83  3.000
 9CC  H9   C12  O5   104.27  3.000
 9CC  H9   C12  C16  107.46  3.000
 9CC  O5   C12  C16  112.42  3.000
 9CC  H9   C12  C13  108.39  3.000
 9CC  C16  C12  C13  113.07  3.000
 9CC  O5   C12  C13  110.72  3.000
 9CC  H11  C13  H10  106.61  3.000
 9CC  H11  C13  C14  108.95  3.000
 9CC  H10  C13  C14  110.98  3.000
 9CC  H11  C13  C12  108.80  3.000
 9CC  H10  C13  C12  109.60  3.000
 9CC  C14  C13  C12  111.75  3.000
 9CC  H13  C14  H12  106.30  3.000
 9CC  H13  C14  C15  110.48  3.000
 9CC  H12  C14  C15  109.50  3.000
 9CC  H13  C14  C13  110.02  3.000
 9CC  H12  C14  C13  110.63  3.000
 9CC  C15  C14  C13  109.87  3.000
 9CC  C7   O3   C8   120.07  3.000
 9CC  H15  C15  H14  107.06  3.000
 9CC  H15  C15  C14  110.89  3.000
 9CC  H14  C15  C14  109.76  3.000
 9CC  H15  C15  C11  109.47  3.000
 9CC  H14  C15  C11  109.31  3.000
 9CC  C14  C15  C11  110.28  3.000
 9CC  H18  C16  H17  107.67  3.000
 9CC  H18  C16  H16  107.30  3.000
 9CC  H17  C16  H16  107.97  3.000
 9CC  H18  C16  C12  109.65  3.000
 9CC  H17  C16  C12  110.58  3.000
 9CC  H16  C16  C12  113.46  3.000
 9CC  C12  O5   C11  115.39  3.000
 9CC  H19  O2   C3   110.78  3.000
 9CC  H20  O1   C1   107.83  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
 9CC  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 9CC  CONST_02  C4   C5   C9   C1      0.00   0.0  0
 9CC  CONST_03  C9   C1   C2   C3      0.00   0.0  0
 9CC  CONST_04  C9   C5   C4   C3      0.00   0.0  0
 9CC  CONST_05  C5   C9   C1   C2      0.00   0.0  0
 9CC  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 9CC  CONST_07  O2   C3   C2   C1    180.00   0.0  0
 9CC  CONST_08  O1   C1   C9   C8      0.00   0.0  0
 9CC  CONST_09  O1   C1   C2   C3    180.00   0.0  0
 9CC  CONST_10  O1   C1   C9   C5    180.00   0.0  0
 9CC  CONST_11  O2   C3   C4   C5    180.00   0.0  0
 9CC  CONST_12  H5   C2   C3   C4    180.00   0.0  0
 9CC  CONST_13  H1   C4   C5   C6      0.00   0.0  0
 9CC  Var_01    O3   C8   C9   C1   -173.24  30.0  1
 9CC  Var_02    C7   C6   C5   C4    150.26  30.0  1
 9CC  Var_03    C9   C8   O3   C7     15.75  30.0  1
 9CC  Var_04    C13  C14  C15  C11    53.07  30.0  1
 9CC  Var_05    C15  C14  C13  C12   -51.85  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
 9CC  chir_01  C7   O3  C6   C10  positiv
 9CC  chir_02  C11  O5  C10  C15  positiv
 9CC  chir_03  C12  O5  C16  C13  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
 9CC  plan-1  C8  0.020
 9CC  plan-1  C9  0.020
 9CC  plan-1  O3  0.020
 9CC  plan-1  O4  0.020
 9CC  plan-2  C1  0.020
 9CC  plan-2  C8  0.020
 9CC  plan-2  C4  0.020
 9CC  plan-2  C3  0.020
 9CC  plan-2  C6  0.020
 9CC  plan-2  C2  0.020
 9CC  plan-2  C5  0.020
 9CC  plan-2  C9  0.020
 9CC  plan-2  O2  0.020
 9CC  plan-2  O1  0.020
 9CC  plan-2  H1  0.020
 9CC  plan-2  H5  0.020

