# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 22:18:33 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C(=O)Nc2ccc(F)cc12
#
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
 D4Y  D4Y  (3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one  ligand  18  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D4Y
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
 D4Y  C7  C  CR56  0   0.010  -0.0107  -0.3992   0.1347
 D4Y  C4  C  CR16  0  -0.418   2.2620   1.1443  -0.1463
 D4Y  C5  C  CR6   0   0.522   2.3381  -0.2260   0.0082
 D4Y  C6  C  CR16  0  -0.466   1.2150  -1.0278   0.1528
 D4Y  C3  C  CR16  0  -0.287   1.0178   1.7712  -0.1678
 D4Y  C2  C  CR56  0   0.402  -0.1050   0.9799  -0.0315
 D4Y  C1  C  CR5   0   0.507  -2.2751   0.2847   0.0540
 D4Y  F   F  F     0  -0.320   3.5507  -0.8095   0.0200
 D4Y  C   C  CR15  0  -0.123  -1.3909  -0.9542   0.2988
 D4Y  O   O  OH1   0  -0.645  -1.6538  -1.9989  -0.5881
 D4Y  N   N  NR15  0  -0.743  -1.4471   1.3563  -0.0453
 D4Y  O1  O  O     0  -0.446  -3.4836   0.2911  -0.0252
 D4Y  H4  H  HCR6  0   0.285   3.1662   1.7287  -0.2550
 D4Y  H5  H  HCR6  0   0.283   1.3071  -2.0994   0.2771
 D4Y  H3  H  HCR6  0   0.282   0.9474   2.8429  -0.2950
 D4Y  H1  H  HCR5  0   0.277  -1.5459  -1.2539   1.3459
 D4Y  H   H  HOH1  0   0.465  -2.4912  -2.4054  -0.3420
 D4Y  H2  H  HNR5  0   0.415  -1.7707   2.2940  -0.2317

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
 D4Y  F   C5  single    1.346  0.020  1.346
 D4Y  C5  C6  aromatic  1.387  0.020  1.387
 D4Y  C5  C4  aromatic  1.381  0.020  1.381
 D4Y  C6  C7  aromatic  1.378  0.020  1.378
 D4Y  C4  C3  aromatic  1.393  0.020  1.393
 D4Y  C7  C   single    1.497  0.020  1.497
 D4Y  C7  C2  aromatic  1.392  0.020  1.392
 D4Y  C3  C2  aromatic  1.380  0.020  1.380
 D4Y  C   O   single    1.395  0.020  1.395
 D4Y  C   C1  single    1.542  0.020  1.542
 D4Y  C2  N   single    1.394  0.020  1.394
 D4Y  N   C1  single    1.358  0.020  1.358
 D4Y  C1  O1  double    1.211  0.020  1.211
 D4Y  C4  H4  single    0.930  0.020  1.080
 D4Y  C6  H5  single    0.930  0.020  1.080
 D4Y  C3  H3  single    0.930  0.020  1.080
 D4Y  C   H1  single    0.970  0.020  1.090
 D4Y  O   H   single    0.850  0.020  0.980
 D4Y  N   H2  single    0.860  0.020  1.020

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
 D4Y  C   C7  C2  108.54  3.000
 D4Y  C2  C7  C6  120.92  3.000
 D4Y  C   C7  C6  130.53  3.000
 D4Y  H4  C4  C3  120.10  3.000
 D4Y  H4  C4  C5  120.07  3.000
 D4Y  C3  C4  C5  119.82  3.000
 D4Y  F   C5  C6  118.54  3.000
 D4Y  C6  C5  C4  122.71  3.000
 D4Y  F   C5  C4  118.74  3.000
 D4Y  H5  C6  C5  121.00  3.000
 D4Y  H5  C6  C7  121.92  3.000
 D4Y  C5  C6  C7  117.07  3.000
 D4Y  H3  C3  C2  121.78  3.000
 D4Y  H3  C3  C4  120.38  3.000
 D4Y  C2  C3  C4  117.83  3.000
 D4Y  N   C2  C3  128.86  3.000
 D4Y  N   C2  C7  109.50  3.000
 D4Y  C3  C2  C7  121.64  3.000
 D4Y  O1  C1  N   126.83  3.000
 D4Y  O1  C1  C   125.94  3.000
 D4Y  N   C1  C   107.23  3.000
 D4Y  H1  C   O   111.99  3.000
 D4Y  H1  C   C1  106.82  3.000
 D4Y  O   C   C1  113.12  3.000
 D4Y  H1  C   C7  109.59  3.000
 D4Y  C1  C   C7  102.33  3.000
 D4Y  O   C   C7  112.44  3.000
 D4Y  H   O   C   108.51  3.000
 D4Y  H2  N   C1  123.45  3.000
 D4Y  H2  N   C2  124.15  3.000
 D4Y  C1  N   C2  111.92  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
 D4Y  CONST_01  C4  C5  C6  C7    0.00  0.0  0
 D4Y  CONST_02  C4  C3  C2  C7    0.00  0.0  0
 D4Y  CONST_03  C2  C7  C6  C5    0.00  0.0  0
 D4Y  CONST_04  C2  C3  C4  C5    0.00  0.0  0
 D4Y  CONST_05  C3  C4  C5  C6    0.00  0.0  0
 D4Y  CONST_06  C3  C2  C7  C6    0.00  0.0  0
 D4Y  CONST_07  C   C1  N   C2    0.00  0.0  0
 D4Y  CONST_08  F   C5  C6  C7  180.00  0.0  0
 D4Y  CONST_09  F   C5  C4  C3  180.00  0.0  0
 D4Y  CONST_10  O1  C1  N   C2  180.00  0.0  0
 D4Y  CONST_11  H3  C3  C2  C7  180.00  0.0  0
 D4Y  CONST_12  H5  C6  C5  C4  180.00  0.0  0
 D4Y  CONST_13  H4  C4  C5  C6  180.00  0.0  0
 D4Y  CONST_14  H2  N   C1  C   180.00  0.0  0

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
 D4Y  chir_01  C  C7  O  C1  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
 D4Y  plan-1  C7  0.020
 D4Y  plan-1  C4  0.020
 D4Y  plan-1  C5  0.020
 D4Y  plan-1  C6  0.020
 D4Y  plan-1  C3  0.020
 D4Y  plan-1  C2  0.020
 D4Y  plan-1  C1  0.020
 D4Y  plan-1  F   0.020
 D4Y  plan-1  C   0.020
 D4Y  plan-1  N   0.020
 D4Y  plan-1  O1  0.020
 D4Y  plan-1  H4  0.020
 D4Y  plan-1  H5  0.020
 D4Y  plan-1  H3  0.020
 D4Y  plan-1  H2  0.020

