# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 04:34:44 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 1-methyl-1,2-dihydro-3H-indol-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC(=O)c2ccccc12
#
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
 OMI  OMI  1-methyl-1,2-dihydro-3H-indol-3-one  ligand  20  11  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OMI
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
 OMI  CA   C  CH2   0  -0.379  -2.0441  -0.1131   0.0044
 OMI  C    C  CR5   0   0.320  -1.2500   1.1826   0.1022
 OMI  O    O  O     0  -0.418  -1.7271   2.2962   0.1918
 OMI  CAI  C  CR56  0  -0.127   0.1465   0.7899   0.0571
 OMI  CAE  C  CR16  0  -0.280   1.3052   1.5602   0.0772
 OMI  CAC  C  CR16  0  -0.289   2.5278   0.9234  -0.0067
 OMI  CAD  C  CR16  0  -0.234   2.5736  -0.4748  -0.1164
 OMI  CAF  C  CR16  0  -0.331   1.4350  -1.2583  -0.1344
 OMI  CAJ  C  CR56  0   0.436   0.1956  -0.6124  -0.0301
 OMI  N    N  NR5   0  -0.540  -1.0445  -1.1556   0.0162
 OMI  CAA  C  CH3   0  -0.526  -1.3657  -2.5111  -0.3391
 OMI  H1   H  HCH2  0   0.286  -2.7481  -0.2100   0.8355
 OMI  H2   H  HCH2  0   0.284  -2.6263  -0.1188  -0.9247
 OMI  H3   H  HCR6  0   0.262   1.2416   2.6388   0.1496
 OMI  H4   H  HCR6  0   0.256   3.4468   1.4930   0.0047
 OMI  H5   H  HCR6  0   0.265   3.5378  -0.9617  -0.1931
 OMI  H6   H  HCR6  0   0.271   1.5106  -2.3336  -0.2233
 OMI  H7   H  HCH3  0   0.234  -1.4558  -2.6507  -1.4208
 OMI  H8   H  HCH3  0   0.254  -0.6009  -3.1906   0.0337
 OMI  H9   H  HCH3  0   0.254  -2.3096  -2.7929   0.1242

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
 OMI  CA   N    single    1.444  0.020  1.444
 OMI  CA   C    single    1.523  0.020  1.523
 OMI  CAA  N    single    1.438  0.020  1.438
 OMI  O    C    double    1.215  0.020  1.215
 OMI  N    CAJ  single    1.355  0.020  1.355
 OMI  C    CAI  single    1.451  0.020  1.451
 OMI  CAJ  CAI  aromatic  1.406  0.020  1.406
 OMI  CAJ  CAF  aromatic  1.402  0.020  1.402
 OMI  CAI  CAE  aromatic  1.392  0.020  1.392
 OMI  CAF  CAD  aromatic  1.382  0.020  1.382
 OMI  CAE  CAC  aromatic  1.381  0.020  1.381
 OMI  CAD  CAC  aromatic  1.403  0.020  1.403
 OMI  CA   H1   single    0.970  0.020  1.090
 OMI  CA   H2   single    0.970  0.020  1.090
 OMI  CAE  H3   single    0.930  0.020  1.080
 OMI  CAC  H4   single    0.930  0.020  1.080
 OMI  CAD  H5   single    0.930  0.020  1.080
 OMI  CAF  H6   single    0.930  0.020  1.080
 OMI  CAA  H7   single    0.970  0.020  1.090
 OMI  CAA  H8   single    0.970  0.020  1.090
 OMI  CAA  H9   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
 OMI  H2   CA   H1   107.56  3.000
 OMI  H2   CA   N    111.76  3.000
 OMI  H1   CA   N    112.04  3.000
 OMI  H2   CA   C    109.62  3.000
 OMI  H1   CA   C    111.24  3.000
 OMI  N    CA   C    104.64  3.000
 OMI  CAI  C    O    128.92  3.000
 OMI  CAI  C    CA   105.64  3.000
 OMI  O    C    CA   125.45  3.000
 OMI  CAJ  CAI  CAE  121.59  3.000
 OMI  CAE  CAI  C    130.62  3.000
 OMI  CAJ  CAI  C    107.79  3.000
 OMI  H3   CAE  CAC  121.02  3.000
 OMI  H3   CAE  CAI  120.22  3.000
 OMI  CAC  CAE  CAI  118.76  3.000
 OMI  H4   CAC  CAD  119.87  3.000
 OMI  H4   CAC  CAE  120.59  3.000
 OMI  CAD  CAC  CAE  119.54  3.000
 OMI  H5   CAD  CAF  118.53  3.000
 OMI  H5   CAD  CAC  118.85  3.000
 OMI  CAF  CAD  CAC  122.61  3.000
 OMI  H6   CAF  CAJ  121.74  3.000
 OMI  H6   CAF  CAD  120.47  3.000
 OMI  CAJ  CAF  CAD  117.79  3.000
 OMI  N    CAJ  CAF  128.85  3.000
 OMI  CAF  CAJ  CAI  119.69  3.000
 OMI  N    CAJ  CAI  111.46  3.000
 OMI  CAA  N    CAJ  125.04  3.000
 OMI  CAJ  N    CA   110.11  3.000
 OMI  CAA  N    CA   121.59  3.000
 OMI  H9   CAA  H8   107.57  3.000
 OMI  H9   CAA  H7   108.43  3.000
 OMI  H8   CAA  H7   108.46  3.000
 OMI  H9   CAA  N    109.43  3.000
 OMI  H8   CAA  N    110.29  3.000
 OMI  H7   CAA  N    112.52  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
 OMI  CONST_01  CAD  CAF  CAJ  CAI    0.00   0.0  0
 OMI  CONST_02  CAD  CAC  CAE  CAI    0.00   0.0  0
 OMI  CONST_03  CAF  CAJ  CAI  CAE    0.00   0.0  0
 OMI  CONST_04  CAF  CAD  CAC  CAE    0.00   0.0  0
 OMI  CONST_05  CAJ  CAI  CAE  CAC    0.00   0.0  0
 OMI  CONST_06  CAJ  CAF  CAD  CAC    0.00   0.0  0
 OMI  CONST_07  H3   CAE  CAI  C      0.00   0.0  0
 OMI  CONST_08  H6   CAF  CAJ  CAI  180.00   0.0  0
 OMI  CONST_09  H4   CAC  CAE  CAI  180.00   0.0  0
 OMI  CONST_10  H5   CAD  CAC  CAE  180.00   0.0  0
 OMI  Var_01    CAI  CAJ  N    CA     5.82  30.0  1
 OMI  Var_02    CAJ  CAI  C    CA    -1.16  30.0  1
 OMI  Var_03    CAJ  N    CA   C     -6.19  30.0  1
 OMI  Var_04    N    CA   C    CAI    4.34  30.0  1
 OMI  Var_05    H7   CAA  N    CA    77.25  30.0  3

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
 OMI  plan-1  CA   0.020
 OMI  plan-1  C    0.020
 OMI  plan-1  O    0.020
 OMI  plan-1  CAI  0.020
 OMI  plan-2  C    0.020
 OMI  plan-2  CAI  0.020
 OMI  plan-2  CAE  0.020
 OMI  plan-2  CAC  0.020
 OMI  plan-2  CAD  0.020
 OMI  plan-2  CAF  0.020
 OMI  plan-2  CAJ  0.020
 OMI  plan-2  N    0.020
 OMI  plan-2  H3   0.020
 OMI  plan-2  H4   0.020
 OMI  plan-2  H5   0.020
 OMI  plan-2  H6   0.020

