# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:40:06 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 5-hydroxy-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2NC(=O)Cc2c1
#
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
 8SD  8SD  5-hydroxy-1,3-dihydro-2H-indol-2-one  ligand  18  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SD
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
 8SD  N1  N  NR15  0  -0.740   1.6941   0.9660   0.0066
 8SD  C4  C  CR16  0  -0.304  -0.7390   1.5754  -0.0704
 8SD  C5  C  CR16  0  -0.296  -2.0255   1.0445  -0.1008
 8SD  C6  C  CR6   0   0.304  -2.2368  -0.3321  -0.0875
 8SD  C7  C  CR16  0  -0.317  -1.1466  -1.2070  -0.0472
 8SD  C8  C  CR56  0  -0.014   0.1250  -0.6776  -0.0184
 8SD  C1  C  CH2   0  -0.622   1.4661  -1.3410   0.0189
 8SD  C2  C  CR5   0   0.493   2.4395  -0.1721   0.0395
 8SD  C3  C  CR56  0   0.420   0.3270   0.6997  -0.0268
 8SD  O1  O  OH1   0  -0.698  -3.4728  -0.8796  -0.1104
 8SD  O2  O  O     0  -0.360   3.6524  -0.2257   0.0775
 8SD  H1  H  HNR5  0   0.374   2.0990   1.8889   0.0221
 8SD  H2  H  HCR6  0   0.243  -0.5916   2.6472  -0.0823
 8SD  H3  H  HCR6  0   0.248  -2.8724   1.7199  -0.1378
 8SD  H4  H  HCR6  0   0.248  -1.3071  -2.2785  -0.0446
 8SD  H5  H  HCH2  0   0.305   1.6158  -1.9671   0.9014
 8SD  H6  H  HCH2  0   0.286   1.6563  -1.9724  -0.8525
 8SD  H7  H  HOH1  0   0.427  -4.1389  -0.1840  -0.1419

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
 8SD  C5  C4  aromatic  1.392  0.020  1.392
 8SD  C5  C6  aromatic  1.393  0.020  1.393
 8SD  O1  C6  single    1.352  0.020  1.352
 8SD  C4  C3  aromatic  1.380  0.020  1.380
 8SD  C6  C7  aromatic  1.398  0.020  1.398
 8SD  C3  N1  single    1.393  0.020  1.393
 8SD  C3  C8  aromatic  1.392  0.020  1.392
 8SD  C7  C8  aromatic  1.378  0.020  1.378
 8SD  N1  C2  single    1.361  0.020  1.361
 8SD  C8  C1  single    1.497  0.020  1.497
 8SD  C2  C1  single    1.521  0.020  1.521
 8SD  C2  O2  double    1.215  0.020  1.215
 8SD  N1  H1  single    0.860  0.020  1.020
 8SD  C4  H2  single    0.930  0.020  1.080
 8SD  C5  H3  single    0.930  0.020  1.080
 8SD  C7  H4  single    0.930  0.020  1.080
 8SD  C1  H5  single    0.970  0.020  1.090
 8SD  C1  H6  single    0.970  0.020  1.090
 8SD  O1  H7  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
 8SD  H1  N1  C3  124.72  3.000
 8SD  H1  N1  C2  123.04  3.000
 8SD  C3  N1  C2  112.23  3.000
 8SD  H2  C4  C3  121.58  3.000
 8SD  H2  C4  C5  120.23  3.000
 8SD  C3  C4  C5  118.19  3.000
 8SD  H3  C5  C6  119.85  3.000
 8SD  H3  C5  C4  119.02  3.000
 8SD  C6  C5  C4  121.13  3.000
 8SD  O1  C6  C7  117.38  3.000
 8SD  C7  C6  C5  120.03  3.000
 8SD  O1  C6  C5  122.60  3.000
 8SD  H4  C7  C8  121.11  3.000
 8SD  H4  C7  C6  120.22  3.000
 8SD  C8  C7  C6  118.67  3.000
 8SD  C3  C8  C1  107.98  3.000
 8SD  C1  C8  C7  131.09  3.000
 8SD  C3  C8  C7  120.93  3.000
 8SD  H6  C1  H5  106.81  3.000
 8SD  H6  C1  C2  110.08  3.000
 8SD  H5  C1  C2  109.98  3.000
 8SD  H6  C1  C8  113.09  3.000
 8SD  H5  C1  C8  113.39  3.000
 8SD  C2  C1  C8  103.48  3.000
 8SD  O2  C2  C1  127.26  3.000
 8SD  O2  C2  N1  125.78  3.000
 8SD  C1  C2  N1  106.96  3.000
 8SD  C8  C3  C4  121.05  3.000
 8SD  C8  C3  N1  109.35  3.000
 8SD  C4  C3  N1  129.59  3.000
 8SD  H7  O1  C6  109.89  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
 8SD  CONST_01  C7  C6  C5  C4     0.00   0.0  0
 8SD  CONST_02  C7  C8  C3  C4     0.00   0.0  0
 8SD  CONST_03  C8  C3  C4  C5     0.00   0.0  0
 8SD  CONST_04  C8  C7  C6  C5     0.00   0.0  0
 8SD  CONST_05  C3  C4  C5  C6     0.00   0.0  0
 8SD  CONST_06  C3  C8  C7  C6     0.00   0.0  0
 8SD  CONST_07  C3  N1  C2  C1     0.00   0.0  0
 8SD  CONST_08  O1  C6  C5  C4   180.00   0.0  0
 8SD  CONST_09  O1  C6  C7  C8   180.00   0.0  0
 8SD  CONST_10  O2  C2  N1  C3   180.00   0.0  0
 8SD  CONST_11  H2  C4  C3  N1     0.00   0.0  0
 8SD  CONST_12  H4  C7  C6  C5   180.00   0.0  0
 8SD  CONST_13  H3  C5  C6  C7   180.00   0.0  0
 8SD  CONST_14  H1  N1  C2  C1   180.00   0.0  0
 8SD  Var_01    H5  C1  C2  N1  -121.84  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
 8SD  plan-1  N1  0.020
 8SD  plan-1  C4  0.020
 8SD  plan-1  C5  0.020
 8SD  plan-1  C6  0.020
 8SD  plan-1  C7  0.020
 8SD  plan-1  C8  0.020
 8SD  plan-1  C1  0.020
 8SD  plan-1  C2  0.020
 8SD  plan-1  C3  0.020
 8SD  plan-1  O1  0.020
 8SD  plan-1  O2  0.020
 8SD  plan-1  H1  0.020
 8SD  plan-1  H2  0.020
 8SD  plan-1  H3  0.020
 8SD  plan-1  H4  0.020

