# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:04:09 2021
#   Inital geometry file: a 59 line input string
#   Ligand name: (1S,3S)-2-methyl-2,3-dihydro-1H-isoindole-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](O)c2ccccc2[C@@H]1O
#
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
 USJ  USJ  (1S,3S)-2-methyl-2,3-dihydro-1H-isoindole-1,3-diol  ligand  23  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_USJ
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
 USJ  C4   C  CR16  0  -0.255   0.7449  12.6034  -36.0768
 USJ  C5   C  CR16  0  -0.256   0.1162  11.5811  -35.3701
 USJ  C6   C  CR16  0  -0.317  -1.0715  11.8185  -34.6865
 USJ  C7   C  CR56  0   0.089  -1.6021  13.0961  -34.7203
 USJ  C8   C  CR15  0   0.133  -2.8764  13.6122  -34.1206
 USJ  O1   O  OH1   0  -0.665  -0.9312  16.4439  -34.9515
 USJ  C1   C  CR15  0   0.207  -1.7722  15.3772  -35.2987
 USJ  N    N  NR5   0  -0.501  -2.7048  15.0385  -34.2469
 USJ  C    C  CH3   0  -0.539  -3.8750  15.8671  -34.1092
 USJ  O    O  OH1   0  -0.666  -3.9488  13.0656  -34.8638
 USJ  C2   C  CR56  0   0.022  -0.9828  14.1078  -35.4287
 USJ  C3   C  CR16  0  -0.317   0.1986  13.8821  -36.1128
 USJ  H1   H  HCR6  0   0.258   1.6697  12.3995  -36.6009
 USJ  H2   H  HCR6  0   0.258   0.5566  10.5926  -35.3549
 USJ  H3   H  HCR6  0   0.254  -1.5594  11.0228  -34.1375
 USJ  H4   H  HCR5  0   0.232  -2.9994  13.3435  -33.0638
 USJ  H5   H  HOH1  0   0.458  -1.3006  17.2611  -35.2976
 USJ  H6   H  HCR5  0   0.211  -2.2835  15.6164  -36.2459
 USJ  H8   H  HCH3  0   0.240  -4.4097  15.6110  -33.1930
 USJ  H9   H  HCH3  0   0.236  -3.5814  16.9131  -34.0186
 USJ  H10  H  HCH3  0   0.212  -4.5774  15.7880  -34.9479
 USJ  H11  H  HOH1  0   0.455  -4.7578  13.1612  -34.3510
 USJ  H12  H  HCR6  0   0.253   0.6890  14.6739  -36.6649

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
 USJ  C4  C3   aromatic  1.391  0.020  1.391
 USJ  C4  C5   aromatic  1.393  0.020  1.393
 USJ  C3  C2   aromatic  1.384  0.020  1.384
 USJ  C5  C6   aromatic  1.391  0.020  1.391
 USJ  C2  C1   single    1.500  0.020  1.500
 USJ  C2  C7   aromatic  1.382  0.020  1.382
 USJ  C1  O1   single    1.402  0.020  1.402
 USJ  C1  N    single    1.446  0.020  1.446
 USJ  C7  C6   aromatic  1.384  0.020  1.384
 USJ  C7  C8   single    1.500  0.020  1.500
 USJ  O   C8   single    1.415  0.020  1.415
 USJ  C   N    single    1.440  0.020  1.440
 USJ  N   C8   single    1.442  0.020  1.442
 USJ  C4  H1   single    0.930  0.020  1.080
 USJ  C5  H2   single    0.930  0.020  1.080
 USJ  C6  H3   single    0.930  0.020  1.080
 USJ  C8  H4   single    0.970  0.020  1.090
 USJ  O1  H5   single    0.850  0.020  0.980
 USJ  C1  H6   single    0.970  0.020  1.090
 USJ  C   H8   single    0.970  0.020  1.090
 USJ  C   H9   single    0.970  0.020  1.090
 USJ  C   H10  single    0.970  0.020  1.090
 USJ  O   H11  single    0.850  0.020  0.980
 USJ  C3  H12  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
 USJ  H1   C4  C3  119.75  3.000
 USJ  H1   C4  C5  119.54  3.000
 USJ  C3   C4  C5  120.71  3.000
 USJ  H2   C5  C6  119.77  3.000
 USJ  H2   C5  C4  119.59  3.000
 USJ  C6   C5  C4  120.63  3.000
 USJ  H3   C6  C7  121.21  3.000
 USJ  H3   C6  C5  120.56  3.000
 USJ  C7   C6  C5  118.23  3.000
 USJ  C2   C7  C8  109.50  3.000
 USJ  C8   C7  C6  129.32  3.000
 USJ  C2   C7  C6  121.11  3.000
 USJ  H4   C8  O   109.05  3.000
 USJ  H4   C8  N   109.86  3.000
 USJ  O    C8  N   115.24  3.000
 USJ  H4   C8  C7  113.33  3.000
 USJ  N    C8  C7  101.78  3.000
 USJ  O    C8  C7  107.52  3.000
 USJ  H5   O1  C1  109.09  3.000
 USJ  H6   C1  C2  110.68  3.000
 USJ  H6   C1  N   112.12  3.000
 USJ  C2   C1  N   101.78  3.000
 USJ  H6   C1  O1  109.01  3.000
 USJ  N    C1  O1  112.64  3.000
 USJ  C2   C1  O1  110.46  3.000
 USJ  C    N   C1  117.31  3.000
 USJ  C    N   C8  117.64  3.000
 USJ  C1   N   C8  111.85  3.000
 USJ  H10  C   H9  107.77  3.000
 USJ  H10  C   H8  108.14  3.000
 USJ  H9   C   H8  106.70  3.000
 USJ  H10  C   N   113.94  3.000
 USJ  H9   C   N   109.94  3.000
 USJ  H8   C   N   110.08  3.000
 USJ  H11  O   C8  108.59  3.000
 USJ  C3   C2  C1  129.05  3.000
 USJ  C1   C2  C7  109.83  3.000
 USJ  C3   C2  C7  121.11  3.000
 USJ  H12  C3  C2  121.30  3.000
 USJ  H12  C3  C4  120.51  3.000
 USJ  C2   C3  C4  118.20  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
 USJ  CONST_01  C7   C2  C3  C4    0.00   0.0  0
 USJ  CONST_02  C7   C6  C5  C4    0.00   0.0  0
 USJ  CONST_03  C2   C3  C4  C5    0.00   0.0  0
 USJ  CONST_04  C2   C7  C6  C5    0.00   0.0  0
 USJ  CONST_05  C3   C4  C5  C6    0.00   0.0  0
 USJ  CONST_06  C3   C2  C7  C6    0.00   0.0  0
 USJ  CONST_07  H3   C6  C5  C4  180.00   0.0  0
 USJ  CONST_08  H12  C3  C4  C5  180.00   0.0  0
 USJ  CONST_09  H1   C4  C5  C6  180.00   0.0  0
 USJ  CONST_10  H2   C5  C6  C7  180.00   0.0  0
 USJ  Var_01    H8   C   N   C8   51.05  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
 USJ  chir_01  C8  C7  O  N   positiv
 USJ  chir_02  C1  O1  N  C2  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
 USJ  plan-1  C4   0.020
 USJ  plan-1  C5   0.020
 USJ  plan-1  C6   0.020
 USJ  plan-1  C7   0.020
 USJ  plan-1  C8   0.020
 USJ  plan-1  C1   0.020
 USJ  plan-1  C2   0.020
 USJ  plan-1  C3   0.020
 USJ  plan-1  H1   0.020
 USJ  plan-1  H2   0.020
 USJ  plan-1  H3   0.020
 USJ  plan-1  H12  0.020

