# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:52:33 2021
#   Inital geometry file: a 58 line input string
#   Ligand name: (3S)-3-hydroxy-2-methyl-2,3-dihydro-1H-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](O)c2ccccc2C1=O
#
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
 R8V  R8V  (3S)-3-hydroxy-2-methyl-2,3-dihydro-1H-isoindol-1-one  ligand  21  12  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R8V
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
 R8V  C4  C  CR16  0  -0.243  31.4420  -10.3347  82.5436
 R8V  C5  C  CR16  0  -0.255  32.7531  -10.5480  82.1218
 R8V  C6  C  CR16  0  -0.303  33.8196   -9.9760  82.8055
 R8V  C7  C  CR56  0  -0.058  33.5278   -9.1985  83.9112
 R8V  C8  C  CR5   0   0.546  34.4424   -8.4594  84.8125
 R8V  O   O  O     0  -0.472  35.6582   -8.4143  84.7534
 R8V  N   N  NR5   0  -0.530  33.6511   -7.8483  85.7270
 R8V  C   C  CH3   0  -0.529  34.1320   -7.0496  86.8229
 R8V  C2  C  CR56  0   0.073  32.2292   -8.9933  84.3369
 R8V  C1  C  CR15  0   0.192  32.2326   -8.1092  85.5514
 R8V  O1  O  OH1   0  -0.646  31.4842   -6.9594  85.3153
 R8V  C3  C  CR16  0  -0.314  31.1624   -9.5494  83.6587
 R8V  H1  H  HCR6  0   0.267  30.6278  -10.7875  81.9927
 R8V  H2  H  HCR6  0   0.266  32.9388  -11.1663  81.2536
 R8V  H3  H  HCR6  0   0.263  34.8399  -10.1289  82.4782
 R8V  H4  H  HCH3  0   0.247  33.7268   -7.4147  87.7676
 R8V  H5  H  HCH3  0   0.261  35.2160   -7.1121  86.8685
 R8V  H6  H  HCH3  0   0.247  33.8531   -6.0013  86.7078
 R8V  H7  H  HCR5  0   0.256  31.8571   -8.6426  86.4338
 R8V  H8  H  HOH1  0   0.469  31.1982   -6.5894  86.1567
 R8V  H9  H  HCR6  0   0.263  30.1410   -9.3896  83.9793

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
 R8V  C5  C4  aromatic  1.394  0.020  1.394
 R8V  C5  C6  aromatic  1.390  0.020  1.390
 R8V  C4  C3  aromatic  1.392  0.020  1.392
 R8V  C6  C7  aromatic  1.383  0.020  1.383
 R8V  C3  C2  aromatic  1.381  0.020  1.381
 R8V  C7  C2  aromatic  1.382  0.020  1.382
 R8V  C7  C8  single    1.482  0.020  1.482
 R8V  C2  C1  single    1.502  0.020  1.502
 R8V  O   C8  double    1.218  0.020  1.218
 R8V  C8  N   single    1.355  0.020  1.355
 R8V  C1  O1  single    1.392  0.020  1.392
 R8V  C1  N   single    1.453  0.020  1.453
 R8V  N   C   single    1.439  0.020  1.439
 R8V  C4  H1  single    0.930  0.020  1.080
 R8V  C5  H2  single    0.930  0.020  1.080
 R8V  C6  H3  single    0.930  0.020  1.080
 R8V  C   H4  single    0.970  0.020  1.090
 R8V  C   H5  single    0.970  0.020  1.090
 R8V  C   H6  single    0.970  0.020  1.090
 R8V  C1  H7  single    0.970  0.020  1.090
 R8V  O1  H8  single    0.850  0.020  0.980
 R8V  C3  H9  single    0.930  0.020  1.080

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
 R8V  H1  C4  C3  119.51  3.000
 R8V  H1  C4  C5  119.32  3.000
 R8V  C3  C4  C5  121.17  3.000
 R8V  H2  C5  C6  119.88  3.000
 R8V  H2  C5  C4  119.46  3.000
 R8V  C6  C5  C4  120.67  3.000
 R8V  H3  C6  C7  121.34  3.000
 R8V  H3  C6  C5  121.09  3.000
 R8V  C7  C6  C5  117.56  3.000
 R8V  C2  C7  C8  108.58  3.000
 R8V  C8  C7  C6  129.54  3.000
 R8V  C2  C7  C6  121.88  3.000
 R8V  N   C8  O   126.80  3.000
 R8V  N   C8  C7  105.97  3.000
 R8V  O   C8  C7  127.24  3.000
 R8V  C1  N   C   121.20  3.000
 R8V  C   N   C8  124.70  3.000
 R8V  C1  N   C8  114.05  3.000
 R8V  H6  C   H5  108.34  3.000
 R8V  H6  C   H4  108.54  3.000
 R8V  H5  C   H4  108.35  3.000
 R8V  H6  C   N   111.57  3.000
 R8V  H5  C   N   109.48  3.000
 R8V  H4  C   N   110.47  3.000
 R8V  C3  C2  C1  129.48  3.000
 R8V  C1  C2  C7  109.53  3.000
 R8V  C3  C2  C7  120.99  3.000
 R8V  H7  C1  O1  110.72  3.000
 R8V  H7  C1  C2  111.30  3.000
 R8V  O1  C1  C2  110.35  3.000
 R8V  H7  C1  N   108.92  3.000
 R8V  O1  C1  N   113.39  3.000
 R8V  C2  C1  N   101.86  3.000
 R8V  H8  O1  C1  109.21  3.000
 R8V  H9  C3  C2  121.61  3.000
 R8V  H9  C3  C4  120.66  3.000
 R8V  C2  C3  C4  117.73  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
 R8V  CONST_01  C7  C6  C5  C4     0.00   0.0  0
 R8V  CONST_02  C7  C2  C3  C4     0.00   0.0  0
 R8V  CONST_03  C2  C3  C4  C5     0.00   0.0  0
 R8V  CONST_04  C2  C7  C6  C5     0.00   0.0  0
 R8V  CONST_05  C3  C4  C5  C6     0.00   0.0  0
 R8V  CONST_06  C3  C2  C7  C6     0.00   0.0  0
 R8V  CONST_07  C1  N   C8  C7     0.00   0.0  0
 R8V  CONST_08  C   N   C8  C7   180.00   0.0  0
 R8V  CONST_09  C1  N   C8  O    180.00   0.0  0
 R8V  CONST_10  H3  C6  C5  C4   180.00   0.0  0
 R8V  CONST_11  H9  C3  C4  C5   180.00   0.0  0
 R8V  CONST_12  H1  C4  C5  C6   180.00   0.0  0
 R8V  CONST_13  H2  C5  C6  C7   180.00   0.0  0
 R8V  CONST_14  C   N   C8  O      0.00   0.0  0
 R8V  Var_01    H4  C   N   C8  -125.88  30.0  3

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
 R8V  chir_01  C1  C2  O1  N  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
 R8V  plan-1  C4  0.020
 R8V  plan-1  C5  0.020
 R8V  plan-1  C6  0.020
 R8V  plan-1  C7  0.020
 R8V  plan-1  C8  0.020
 R8V  plan-1  O   0.020
 R8V  plan-1  N   0.020
 R8V  plan-1  C   0.020
 R8V  plan-1  C2  0.020
 R8V  plan-1  C1  0.020
 R8V  plan-1  C3  0.020
 R8V  plan-1  H1  0.020
 R8V  plan-1  H2  0.020
 R8V  plan-1  H3  0.020
 R8V  plan-1  H9  0.020

