# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:47:50 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 7-bromo-5-methyl-1H-indole-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Br)c2NC(=O)C(=O)c2c1
#
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
 2AK  2AK  7-bromo-5-methyl-1H-indole-2,3-dione  ligand  19  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2AK
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
 2AK  BR1  BR  BR    0  -0.004  -2.3220   0.9441  -0.0976
 2AK  C5   C   CR6   0  -0.159  -0.8722  -0.2496  -0.0369
 2AK  C4   C   CR16  0  -0.262  -1.0832  -1.6252  -0.0073
 2AK  C3   C   CR6   0   0.085  -0.0288  -2.5397   0.0407
 2AK  C12  C   CH3   0  -0.719  -0.3122  -4.0133   0.0519
 2AK  C2   C   CR16  0  -0.330   1.2739  -2.0507   0.0626
 2AK  C6   C   CR56  0   0.479   0.4234   0.2238  -0.0180
 2AK  N7   N   NR15  0  -0.767   0.8856   1.5343  -0.0370
 2AK  C8   C   CR5   0   0.458   2.2428   1.5841   0.0006
 2AK  O11  O   O     0  -0.392   2.9580   2.5516  -0.0024
 2AK  C9   C   CR5   0   0.253   2.7099   0.1044   0.0492
 2AK  C1   C   CR56  0  -0.065   1.4830  -0.6838   0.0328
 2AK  O10  O   O     0  -0.330   3.8622  -0.2312   0.0903
 2AK  H1   H   HCR6  0   0.288  -2.0993  -2.0011  -0.0203
 2AK  H2   H   HCH3  0   0.257  -0.6612  -4.3519  -0.9247
 2AK  H3   H   HCH3  0   0.252   0.5807  -4.5847   0.3001
 2AK  H4   H   HCH3  0   0.253  -1.0853  -4.2648   0.7778
 2AK  H5   H   HCR6  0   0.277   2.1166  -2.7295   0.1020
 2AK  H6   H   HNR5  0   0.427   0.2934   2.3514  -0.0749

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
 2AK  BR1  C5   single    1.879  0.020  1.879
 2AK  C4   C5   aromatic  1.392  0.020  1.392
 2AK  C4   C3   aromatic  1.397  0.020  1.397
 2AK  C5   C6   aromatic  1.380  0.020  1.380
 2AK  C12  C3   single    1.501  0.020  1.501
 2AK  C3   C2   aromatic  1.392  0.020  1.392
 2AK  C6   N7   single    1.390  0.020  1.390
 2AK  C6   C1   aromatic  1.396  0.020  1.396
 2AK  N7   C8   single    1.359  0.020  1.359
 2AK  C2   C1   aromatic  1.383  0.020  1.383
 2AK  C1   C9   single    1.458  0.020  1.458
 2AK  C8   C9   single    1.552  0.020  1.552
 2AK  C8   O11  double    1.203  0.020  1.203
 2AK  C9   O10  double    1.201  0.020  1.201
 2AK  C4   H1   single    0.930  0.020  1.080
 2AK  C12  H2   single    0.970  0.020  1.090
 2AK  C12  H3   single    0.970  0.020  1.090
 2AK  C12  H4   single    0.970  0.020  1.090
 2AK  C2   H5   single    0.930  0.020  1.080
 2AK  N7   H6   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
 2AK  C6   C5   C4   118.76  3.000
 2AK  C6   C5   BR1  120.47  3.000
 2AK  C4   C5   BR1  120.77  3.000
 2AK  H1   C4   C3   118.77  3.000
 2AK  H1   C4   C5   119.00  3.000
 2AK  C3   C4   C5   122.23  3.000
 2AK  C2   C3   C12  121.45  3.000
 2AK  C2   C3   C4   118.50  3.000
 2AK  C12  C3   C4   120.04  3.000
 2AK  H4   C12  H3   107.99  3.000
 2AK  H4   C12  H2   107.31  3.000
 2AK  H3   C12  H2   107.67  3.000
 2AK  H4   C12  C3   111.44  3.000
 2AK  H3   C12  C3   111.23  3.000
 2AK  H2   C12  C3   111.00  3.000
 2AK  H5   C2   C1   120.18  3.000
 2AK  H5   C2   C3   120.58  3.000
 2AK  C1   C2   C3   119.24  3.000
 2AK  C1   C6   N7   111.17  3.000
 2AK  C1   C6   C5   119.36  3.000
 2AK  N7   C6   C5   129.47  3.000
 2AK  H6   N7   C8   123.86  3.000
 2AK  H6   N7   C6   124.64  3.000
 2AK  C8   N7   C6   111.49  3.000
 2AK  C9   C8   O11  125.99  3.000
 2AK  O11  C8   N7   128.55  3.000
 2AK  C9   C8   N7   105.46  3.000
 2AK  O10  C9   C1   131.04  3.000
 2AK  O10  C9   C8   123.79  3.000
 2AK  C1   C9   C8   105.17  3.000
 2AK  C9   C1   C6   106.71  3.000
 2AK  C9   C1   C2   131.38  3.000
 2AK  C6   C1   C2   121.90  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
 2AK  CONST_01  C2   C3   C4  C5     0.00   0.0  0
 2AK  CONST_02  C2   C1   C6  C5     0.00   0.0  0
 2AK  CONST_03  C1   C6   C5  C4     0.00   0.0  0
 2AK  CONST_04  C1   C2   C3  C4     0.00   0.0  0
 2AK  CONST_05  C6   C5   C4  C3     0.00   0.0  0
 2AK  CONST_06  C6   C1   C2  C3     0.00   0.0  0
 2AK  CONST_07  C9   C8   N7  C6     0.00   0.0  0
 2AK  CONST_08  C3   C4   C5  BR1  180.00   0.0  0
 2AK  CONST_09  N7   C6   C5  BR1    0.00   0.0  0
 2AK  CONST_10  C1   C6   C5  BR1  180.00   0.0  0
 2AK  CONST_11  C12  C3   C4  C5   180.00   0.0  0
 2AK  CONST_12  C1   C2   C3  C12  180.00   0.0  0
 2AK  CONST_13  O11  C8   N7  C6   180.00   0.0  0
 2AK  CONST_14  H5   C2   C3  C4   180.00   0.0  0
 2AK  CONST_15  H1   C4   C3  C2   180.00   0.0  0
 2AK  CONST_16  H6   N7   C8  C9   180.00   0.0  0
 2AK  Var_01    H2   C12  C3  C4    72.08  30.0  2

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
 2AK  plan-1  BR1  0.020
 2AK  plan-1  C5   0.020
 2AK  plan-1  C4   0.020
 2AK  plan-1  C3   0.020
 2AK  plan-1  C12  0.020
 2AK  plan-1  C2   0.020
 2AK  plan-1  C6   0.020
 2AK  plan-1  N7   0.020
 2AK  plan-1  C8   0.020
 2AK  plan-1  O11  0.020
 2AK  plan-1  C9   0.020
 2AK  plan-1  C1   0.020
 2AK  plan-1  O10  0.020
 2AK  plan-1  H1   0.020
 2AK  plan-1  H5   0.020
 2AK  plan-1  H6   0.020

