# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 09:43:40 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (3S)-6,8-dihydroxy-3-{[(2R,6S)-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
 9CX  9CX  (3S)-6,8-dihydroxy-3-{[(2R,6S)-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_9CX
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
 9CX  C8   C  C     0   0.612  -1.0178  -1.0638   0.7463
 9CX  C5   C  CR6   0   0.172  -2.1787   1.0036   0.0149
 9CX  C6   C  CH2   0  -0.541  -0.9021   1.7284   0.3083
 9CX  C2   C  CR16  0  -0.494  -4.5267  -0.4368  -0.4235
 9CX  C4   C  CR16  0  -0.446  -3.2993   1.6583  -0.4405
 9CX  C15  C  CH2   0  -0.444   4.0924   1.6754   0.2344
 9CX  C14  C  CH2   0  -0.458   5.3350   1.0069  -0.3414
 9CX  C13  C  CH2   0  -0.449   5.3873  -0.4528   0.0969
 9CX  C12  C  CH1   0   0.018   4.0801  -1.1826  -0.2083
 9CX  C16  C  CH3   0  -0.695   3.9109  -1.5107  -1.6875
 9CX  O5   O  O2    0  -0.494   2.9706  -0.4683   0.3180
 9CX  C11  C  CH1   0   0.060   2.8483   0.8696  -0.1178
 9CX  C7   C  CH1   0   0.039   0.2899   0.8239   0.0693
 9CX  O3   O  O2    0  -0.432   0.1295  -0.4126   0.7960
 9CX  O4   O  O     0  -0.491  -1.0354  -2.2245   1.1357
 9CX  C9   C  CR6   0  -0.344  -2.2016  -0.3788   0.2513
 9CX  C3   C  CR6   0   0.409  -4.4745   0.9297  -0.6668
 9CX  O2   O  OH1   0  -0.617  -5.5320   1.6094  -1.1209
 9CX  C1   C  CR6   0   0.397  -3.3984  -1.0975   0.0494
 9CX  O1   O  OH1   0  -0.622  -3.4901  -2.4006   0.2938
 9CX  H1   H  HCH2  0   0.278  -0.8106   2.6102  -0.3266
 9CX  H2   H  HCH2  0   0.275  -0.9054   2.0812   1.3455
 9CX  H3   H  HCR6  0   0.284  -5.4390  -0.9974  -0.5931
 9CX  H4   H  HCR6  0   0.265  -3.2806   2.7247  -0.6267
 9CX  H6   H  HCH2  0   0.232   3.9858   2.6942  -0.1464
 9CX  H7   H  HCH2  0   0.221   5.3173   1.0810  -1.4330
 9CX  H8   H  HCH2  0   0.237   6.2364   1.5288  -0.0139
 9CX  H9   H  HCH2  0   0.231   6.2191  -0.9753  -0.3814
 9CX  H10  H  HCH2  0   0.227   5.5709  -0.4937   1.1751
 9CX  H11  H  HCH1  0   0.228   4.0772  -2.1286   0.3407
 9CX  H12  H  HCH3  0   0.232   4.6725  -2.2289  -1.9940
 9CX  H13  H  HCH3  0   0.234   2.9356  -1.9637  -1.8711
 9CX  H14  H  HCH3  0   0.225   4.0052  -0.6407  -2.3383
 9CX  H15  H  HCH1  0   0.200   2.7221   0.9046  -1.2121
 9CX  H18  H  HCH1  0   0.254   0.3365   0.5726  -0.9969
 9CX  H19  H  HOH1  0   0.482  -6.2918   1.0266  -1.2370
 9CX  H20  H  HOH1  0   0.477  -2.6299  -2.6963   0.6669
 9CX  C10  C  CH2   0  -0.478   1.5957   1.4644   0.5029
 9CX  H5   H  HCH2  0   0.217   4.1816   1.7471   1.3241
 9CX  H16  H  HCH2  0   0.245   1.6647   1.4617   1.5953
 9CX  H17  H  HCH2  0   0.253   1.5547   2.5152   0.2029

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
 9CX  C16  C12  single    1.525  0.020  1.525
 9CX  C13  C12  single    1.528  0.020  1.528
 9CX  C13  C14  single    1.525  0.020  1.525
 9CX  C12  O5   single    1.421  0.020  1.421
 9CX  C14  C15  single    1.524  0.020  1.524
 9CX  O5   C11  single    1.412  0.020  1.412
 9CX  C15  C11  single    1.523  0.020  1.523
 9CX  C11  C10  single    1.519  0.020  1.519
 9CX  C10  C7   single    1.518  0.020  1.518
 9CX  C6   C7   single    1.515  0.020  1.515
 9CX  C6   C5   single    1.497  0.020  1.497
 9CX  C7   O3   single    1.443  0.020  1.443
 9CX  C4   C5   aromatic  1.375  0.020  1.375
 9CX  C4   C3   aromatic  1.401  0.020  1.401
 9CX  C5   C9   aromatic  1.403  0.020  1.403
 9CX  O3   C8   single    1.320  0.020  1.320
 9CX  O2   C3   single    1.337  0.020  1.337
 9CX  C3   C2   aromatic  1.389  0.020  1.389
 9CX  C9   C8   single    1.455  0.020  1.455
 9CX  C9   C1   aromatic  1.411  0.020  1.411
 9CX  C8   O4   double    1.224  0.020  1.224
 9CX  C2   C1   aromatic  1.390  0.020  1.390
 9CX  C1   O1   single    1.329  0.020  1.329
 9CX  C6   H1   single    0.970  0.020  1.090
 9CX  C6   H2   single    0.970  0.020  1.090
 9CX  C2   H3   single    0.930  0.020  1.080
 9CX  C4   H4   single    0.930  0.020  1.080
 9CX  C15  H5   single    0.970  0.020  1.090
 9CX  C15  H6   single    0.970  0.020  1.090
 9CX  C14  H7   single    0.970  0.020  1.090
 9CX  C14  H8   single    0.970  0.020  1.090
 9CX  C13  H9   single    0.970  0.020  1.090
 9CX  C13  H10  single    0.970  0.020  1.090
 9CX  C12  H11  single    0.970  0.020  1.090
 9CX  C16  H12  single    0.970  0.020  1.090
 9CX  C16  H13  single    0.970  0.020  1.090
 9CX  C16  H14  single    0.970  0.020  1.090
 9CX  C11  H15  single    0.970  0.020  1.090
 9CX  C10  H16  single    0.970  0.020  1.090
 9CX  C10  H17  single    0.970  0.020  1.090
 9CX  C7   H18  single    0.970  0.020  1.090
 9CX  O2   H19  single    0.850  0.020  0.980
 9CX  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
 9CX  C9   C8   O4   122.88  3.000
 9CX  O4   C8   O3   117.92  3.000
 9CX  C9   C8   O3   119.20  3.000
 9CX  C9   C5   C4   120.78  3.000
 9CX  C9   C5   C6   117.26  3.000
 9CX  C4   C5   C6   121.95  3.000
 9CX  H2   C6   H1   106.92  3.000
 9CX  H2   C6   C7   110.12  3.000
 9CX  H1   C6   C7   108.96  3.000
 9CX  H2   C6   C5   109.81  3.000
 9CX  H1   C6   C5   110.42  3.000
 9CX  C7   C6   C5   110.54  3.000
 9CX  H3   C2   C1   119.37  3.000
 9CX  H3   C2   C3   120.86  3.000
 9CX  C1   C2   C3   119.78  3.000
 9CX  H4   C4   C3   119.93  3.000
 9CX  H4   C4   C5   120.78  3.000
 9CX  C3   C4   C5   119.29  3.000
 9CX  H6   C15  H5   107.07  3.000
 9CX  H6   C15  C11  109.45  3.000
 9CX  H5   C15  C11  109.33  3.000
 9CX  H6   C15  C14  110.90  3.000
 9CX  H5   C15  C14  109.76  3.000
 9CX  C11  C15  C14  110.27  3.000
 9CX  H8   C14  H7   106.27  3.000
 9CX  H8   C14  C13  110.06  3.000
 9CX  H7   C14  C13  110.62  3.000
 9CX  H8   C14  C15  110.50  3.000
 9CX  H7   C14  C15  109.52  3.000
 9CX  C13  C14  C15  109.83  3.000
 9CX  H10  C13  H9   106.60  3.000
 9CX  H10  C13  C12  108.81  3.000
 9CX  H9   C13  C12  109.60  3.000
 9CX  H10  C13  C14  108.95  3.000
 9CX  H9   C13  C14  110.98  3.000
 9CX  C12  C13  C14  111.74  3.000
 9CX  H11  C12  O5   104.29  3.000
 9CX  H11  C12  C16  107.49  3.000
 9CX  O5   C12  C16  112.39  3.000
 9CX  H11  C12  C13  108.37  3.000
 9CX  O5   C12  C13  110.73  3.000
 9CX  C16  C12  C13  113.05  3.000
 9CX  H14  C16  H13  107.95  3.000
 9CX  H14  C16  H12  107.29  3.000
 9CX  H13  C16  H12  107.67  3.000
 9CX  H14  C16  C12  113.43  3.000
 9CX  H13  C16  C12  110.60  3.000
 9CX  H12  C16  C12  109.68  3.000
 9CX  C11  O5   C12  115.44  3.000
 9CX  H15  C11  C10  107.39  3.000
 9CX  H15  C11  O5   110.26  3.000
 9CX  C10  C11  O5   108.43  3.000
 9CX  H15  C11  C15  107.83  3.000
 9CX  C10  C11  C15  111.82  3.000
 9CX  O5   C11  C15  111.04  3.000
 9CX  H18  C7   O3   107.34  3.000
 9CX  H18  C7   C10  109.76  3.000
 9CX  O3   C7   C10  108.26  3.000
 9CX  H18  C7   C6   108.88  3.000
 9CX  O3   C7   C6   110.15  3.000
 9CX  C10  C7   C6   112.32  3.000
 9CX  C7   O3   C8   120.02  3.000
 9CX  C1   C9   C5   119.46  3.000
 9CX  C1   C9   C8   119.95  3.000
 9CX  C5   C9   C8   120.55  3.000
 9CX  O2   C3   C4   117.00  3.000
 9CX  O2   C3   C2   122.01  3.000
 9CX  C4   C3   C2   120.98  3.000
 9CX  H19  O2   C3   110.91  3.000
 9CX  O1   C1   C9   122.13  3.000
 9CX  O1   C1   C2   118.19  3.000
 9CX  C9   C1   C2   119.68  3.000
 9CX  H20  O1   C1   107.71  3.000
 9CX  H17  C10  H16  106.18  3.000
 9CX  H17  C10  C7   107.15  3.000
 9CX  H16  C10  C7   109.77  3.000
 9CX  H17  C10  C11  107.16  3.000
 9CX  H16  C10  C11  110.78  3.000
 9CX  C7   C10  C11  115.30  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
 9CX  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 9CX  CONST_02  C2   C1   C9   C5      0.00   0.0  0
 9CX  CONST_03  C1   C9   C5   C4      0.00   0.0  0
 9CX  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 9CX  CONST_05  C3   C4   C5   C9      0.00   0.0  0
 9CX  CONST_06  C3   C2   C1   C9      0.00   0.0  0
 9CX  CONST_07  O1   C1   C9   C8      0.00   0.0  0
 9CX  CONST_08  O2   C3   C4   C5    180.00   0.0  0
 9CX  CONST_09  O1   C1   C9   C5    180.00   0.0  0
 9CX  CONST_10  O1   C1   C2   C3    180.00   0.0  0
 9CX  CONST_11  C1   C2   C3   O2    180.00   0.0  0
 9CX  CONST_12  H4   C4   C5   C6      0.00   0.0  0
 9CX  CONST_13  H3   C2   C3   C4    180.00   0.0  0
 9CX  Var_01    O3   C8   C9   C5     -9.31  30.0  1
 9CX  Var_02    C7   C6   C5   C4   -149.85  30.0  1
 9CX  Var_03    C12  C13  C14  C15    51.98  30.0  1
 9CX  Var_04    C11  C15  C14  C13   -53.14  30.0  1
 9CX  Var_05    C9   C8   O3   C7    -15.48  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
 9CX  chir_01  C12  C16  C13  O5   negativ
 9CX  chir_02  C11  O5   C15  C10  positiv
 9CX  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
 9CX  plan-1  C8  0.020
 9CX  plan-1  O3  0.020
 9CX  plan-1  O4  0.020
 9CX  plan-1  C9  0.020
 9CX  plan-2  C8  0.020
 9CX  plan-2  C5  0.020
 9CX  plan-2  C6  0.020
 9CX  plan-2  C2  0.020
 9CX  plan-2  C4  0.020
 9CX  plan-2  C9  0.020
 9CX  plan-2  C3  0.020
 9CX  plan-2  O2  0.020
 9CX  plan-2  C1  0.020
 9CX  plan-2  O1  0.020
 9CX  plan-2  H3  0.020
 9CX  plan-2  H4  0.020

