# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 21:05:45 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2,3-dihydro-1H-inden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCc2ccccc12
#
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
 1ON  1ON  2,3-dihydro-1H-inden-1-one  ligand  18  10  .  2021-08-03  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1ON
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
 1ON  O10  O  O     0  -0.404   2.2234  -1.5174  -0.0501
 1ON  C7   C  CR5   0   0.342   1.5596  -0.5046  -0.0237
 1ON  C8   C  CH2   0  -0.588   2.0956   0.9156  -0.0021
 1ON  C9   C  CH2   0  -0.500   0.8710   1.8402  -0.0018
 1ON  C6   C  CR56  0  -0.022   0.0916  -0.4247  -0.0049
 1ON  C1   C  CR16  0  -0.270  -0.8281  -1.4695  -0.0018
 1ON  C2   C  CR16  0  -0.264  -2.1748  -1.1540   0.0174
 1ON  C5   C  CR56  0   0.083  -0.3065   0.9055   0.0092
 1ON  C4   C  CR16  0  -0.305  -1.6595   1.2192   0.0282
 1ON  C3   C  CR16  0  -0.235  -2.5826   0.1830   0.0322
 1ON  H1   H  HCH2  0   0.286   2.7187   1.0483   0.8849
 1ON  H2   H  HCH2  0   0.269   0.8543   2.4992   0.8676
 1ON  H3   H  HCR6  0   0.262  -0.4977  -2.5006  -0.0138
 1ON  H4   H  HCR6  0   0.265  -2.9186  -1.9395   0.0211
 1ON  H5   H  HCR6  0   0.259  -1.9931   2.2496   0.0395
 1ON  H6   H  HCR6  0   0.267  -3.6406   0.4114   0.0472
 1ON  H7   H  HCH2  0   0.285   2.7460   1.0740  -0.8644
 1ON  H8   H  HCH2  0   0.270   0.8454   2.4841  -0.8825

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
 1ON  C1   C2  aromatic  1.383  0.020  1.383
 1ON  C1   C6  aromatic  1.392  0.020  1.392
 1ON  C2   C3  aromatic  1.398  0.020  1.398
 1ON  O10  C7  double    1.211  0.020  1.211
 1ON  C6   C7  single    1.470  0.020  1.470
 1ON  C6   C5  aromatic  1.389  0.020  1.389
 1ON  C3   C4  aromatic  1.388  0.020  1.388
 1ON  C7   C8  single    1.518  0.020  1.518
 1ON  C5   C4  aromatic  1.389  0.020  1.389
 1ON  C5   C9  single    1.503  0.020  1.503
 1ON  C8   C9  single    1.534  0.020  1.534
 1ON  C8   H1  single    0.970  0.020  1.090
 1ON  C9   H2  single    0.970  0.020  1.090
 1ON  C1   H3  single    0.930  0.020  1.080
 1ON  C2   H4  single    0.930  0.020  1.080
 1ON  C4   H5  single    0.930  0.020  1.080
 1ON  C3   H6  single    0.930  0.020  1.080
 1ON  C8   H7  single    0.970  0.020  1.090
 1ON  C9   H8  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
 1ON  C6  C7  C8   107.55  3.000
 1ON  C8  C7  O10  126.10  3.000
 1ON  C6  C7  O10  126.36  3.000
 1ON  H7  C8  H1   106.50  3.000
 1ON  H7  C8  C9   112.85  3.000
 1ON  H1  C8  C9   112.46  3.000
 1ON  H7  C8  C7   109.56  3.000
 1ON  H1  C8  C7   109.06  3.000
 1ON  C9  C8  C7   106.38  3.000
 1ON  H8  C9  H2   106.64  3.000
 1ON  H8  C9  C5   110.76  3.000
 1ON  H2  C9  C5   110.96  3.000
 1ON  H8  C9  C8   111.97  3.000
 1ON  H2  C9  C8   112.10  3.000
 1ON  C5  C9  C8   104.50  3.000
 1ON  C5  C6  C1   121.98  3.000
 1ON  C5  C6  C7   109.78  3.000
 1ON  C1  C6  C7   128.24  3.000
 1ON  H3  C1  C2   120.96  3.000
 1ON  H3  C1  C6   120.87  3.000
 1ON  C2  C1  C6   118.17  3.000
 1ON  H4  C2  C3   119.60  3.000
 1ON  H4  C2  C1   120.25  3.000
 1ON  C3  C2  C1   120.15  3.000
 1ON  C4  C5  C6   119.72  3.000
 1ON  C4  C5  C9   128.50  3.000
 1ON  C6  C5  C9   111.78  3.000
 1ON  H5  C4  C3   120.36  3.000
 1ON  H5  C4  C5   121.00  3.000
 1ON  C3  C4  C5   118.64  3.000
 1ON  H6  C3  C4   119.51  3.000
 1ON  H6  C3  C2   119.15  3.000
 1ON  C4  C3  C2   121.34  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
 1ON  CONST_01  C3  C2  C1  C6     0.00   0.0  0
 1ON  CONST_02  C3  C4  C5  C6     0.00   0.0  0
 1ON  CONST_03  C4  C3  C2  C1     0.00   0.0  0
 1ON  CONST_04  C4  C5  C6  C1     0.00   0.0  0
 1ON  CONST_05  C5  C6  C1  C2     0.00   0.0  0
 1ON  CONST_06  C5  C4  C3  C2     0.00   0.0  0
 1ON  CONST_07  H3  C1  C6  C7     0.00   0.0  0
 1ON  CONST_08  H5  C4  C5  C9     0.00   0.0  0
 1ON  CONST_09  H4  C2  C1  C6   180.00   0.0  0
 1ON  CONST_10  H6  C3  C2  C1   180.00   0.0  0
 1ON  Var_01    C5  C9  C8  C7     1.28  30.0  1
 1ON  Var_02    C1  C6  C7  C8  -179.32  30.0  1
 1ON  Var_03    C6  C5  C9  C8    -0.90  30.0  1
 1ON  Var_04    C6  C7  C8  C9    -1.26  30.0  1

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
 1ON  plan-1  O10  0.020
 1ON  plan-1  C7   0.020
 1ON  plan-1  C8   0.020
 1ON  plan-1  C6   0.020
 1ON  plan-2  C7   0.020
 1ON  plan-2  C9   0.020
 1ON  plan-2  C6   0.020
 1ON  plan-2  C1   0.020
 1ON  plan-2  C2   0.020
 1ON  plan-2  C5   0.020
 1ON  plan-2  C4   0.020
 1ON  plan-2  C3   0.020
 1ON  plan-2  H3   0.020
 1ON  plan-2  H4   0.020
 1ON  plan-2  H5   0.020
 1ON  plan-2  H6   0.020

