# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 07:05:17 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-benzyl-1H-indole-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N(Cc2ccccc2)c3ccccc3C1=O
#
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
 3AK  3AK  1-benzyl-1H-indole-2,3-dione  ligand  29  18  .  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_3AK
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
 3AK  O11  O  O     0  -0.406   0.4031  -2.8694  -1.3530
 3AK  C8   C  CR5   0   0.452   0.8580  -1.8436  -0.9133
 3AK  C9   C  CR5   0   0.265   2.1943  -1.6996  -0.1429
 3AK  O10  O  O     0  -0.336   2.9255  -2.6228   0.0984
 3AK  C1   C  CR56  0  -0.088   2.2977  -0.2838   0.1700
 3AK  N7   N  NR5   0  -0.617   0.3255  -0.5936  -0.9823
 3AK  C6   C  CR56  0   0.443   1.1575   0.3364  -0.3499
 3AK  C5   C  CR16  0  -0.292   0.9641   1.6960  -0.2152
 3AK  C4   C  CR16  0  -0.235   1.9500   2.4178   0.4568
 3AK  C3   C  CR16  0  -0.266   3.0890   1.8104   0.9786
 3AK  C2   C  CR16  0  -0.277   3.2705   0.4413   0.8365
 3AK  C12  C  CH2   0  -0.392  -0.9229  -0.2557  -1.6247
 3AK  C13  C  CR6   0   0.096  -1.9783   0.2154  -0.6546
 3AK  C18  C  CR16  0  -0.306  -2.8141   1.2696  -1.0074
 3AK  C17  C  CR16  0  -0.241  -3.8156   1.6971  -0.1455
 3AK  C16  C  CR16  0  -0.266  -3.9842   1.0775   1.0850
 3AK  C15  C  CR16  0  -0.239  -3.1492   0.0269   1.4451
 3AK  C14  C  CR16  0  -0.281  -2.1533  -0.4029   0.5797
 3AK  H3   H  HCR6  0   0.285   0.0888   2.1965  -0.6051
 3AK  H4   H  HCR6  0   0.279   1.8192   3.4853   0.5754
 3AK  H5   H  HCR6  0   0.272   3.8294   2.4068   1.4932
 3AK  H6   H  HCR6  0   0.278   4.1487  -0.0506   1.2338
 3AK  H7   H  HCH2  0   0.286  -0.7426   0.5079  -2.3847
 3AK  H8   H  HCH2  0   0.298  -1.2642  -1.1472  -2.1522
 3AK  H9   H  HCR6  0   0.257  -2.6799   1.7635  -1.9629
 3AK  H10  H  HCR6  0   0.259  -4.4569   2.5201  -0.4333
 3AK  H11  H  HCR6  0   0.258  -4.7579   1.4147   1.7623
 3AK  H12  H  HCR6  0   0.259  -3.2729  -0.4596   2.4039
 3AK  H13  H  HCR6  0   0.252  -1.5124  -1.2244   0.8778

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
 3AK  C16  C17  aromatic  1.388  0.020  1.388
 3AK  C16  C15  aromatic  1.389  0.020  1.389
 3AK  C17  C18  aromatic  1.389  0.020  1.389
 3AK  C15  C14  aromatic  1.388  0.020  1.388
 3AK  C18  C13  aromatic  1.391  0.020  1.391
 3AK  O11  C8   double    1.205  0.020  1.205
 3AK  C14  C13  aromatic  1.392  0.020  1.392
 3AK  C13  C12  single    1.509  0.020  1.509
 3AK  O10  C9   double    1.202  0.020  1.202
 3AK  C8   C9   single    1.549  0.020  1.549
 3AK  C8   N7   single    1.360  0.020  1.360
 3AK  C9   C1   single    1.454  0.020  1.454
 3AK  C12  N7   single    1.444  0.020  1.444
 3AK  N7   C6   single    1.399  0.020  1.399
 3AK  C1   C6   aromatic  1.398  0.020  1.398
 3AK  C1   C2   aromatic  1.384  0.020  1.384
 3AK  C6   C5   aromatic  1.380  0.020  1.380
 3AK  C2   C3   aromatic  1.388  0.020  1.388
 3AK  C5   C4   aromatic  1.394  0.020  1.394
 3AK  C3   C4   aromatic  1.392  0.020  1.392
 3AK  C5   H3   single    0.930  0.020  1.080
 3AK  C4   H4   single    0.930  0.020  1.080
 3AK  C3   H5   single    0.930  0.020  1.080
 3AK  C2   H6   single    0.930  0.020  1.080
 3AK  C12  H7   single    0.970  0.020  1.090
 3AK  C12  H8   single    0.970  0.020  1.090
 3AK  C18  H9   single    0.930  0.020  1.080
 3AK  C17  H10  single    0.930  0.020  1.080
 3AK  C16  H11  single    0.930  0.020  1.080
 3AK  C15  H12  single    0.930  0.020  1.080
 3AK  C14  H13  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
 3AK  N7   C8   C9   106.11  3.000
 3AK  N7   C8   O11  128.01  3.000
 3AK  C9   C8   O11  125.88  3.000
 3AK  C1   C9   O10  131.41  3.000
 3AK  C1   C9   C8   105.01  3.000
 3AK  O10  C9   C8   123.58  3.000
 3AK  C2   C1   C6   121.31  3.000
 3AK  C2   C1   C9   131.59  3.000
 3AK  C6   C1   C9   107.10  3.000
 3AK  C12  N7   C6   124.03  3.000
 3AK  C6   N7   C8   110.80  3.000
 3AK  C12  N7   C8   125.17  3.000
 3AK  C5   C6   N7   128.01  3.000
 3AK  C5   C6   C1   121.00  3.000
 3AK  N7   C6   C1   110.99  3.000
 3AK  H3   C5   C4   120.44  3.000
 3AK  H3   C5   C6   122.31  3.000
 3AK  C4   C5   C6   117.25  3.000
 3AK  H4   C4   C3   119.22  3.000
 3AK  H4   C4   C5   118.56  3.000
 3AK  C3   C4   C5   122.22  3.000
 3AK  H5   C3   C2   120.21  3.000
 3AK  H5   C3   C4   119.87  3.000
 3AK  C2   C3   C4   119.92  3.000
 3AK  H6   C2   C3   121.12  3.000
 3AK  H6   C2   C1   120.59  3.000
 3AK  C3   C2   C1   118.29  3.000
 3AK  H8   C12  H7   106.65  3.000
 3AK  H8   C12  C13  110.32  3.000
 3AK  H7   C12  C13  110.15  3.000
 3AK  H8   C12  N7   107.12  3.000
 3AK  H7   C12  N7   109.30  3.000
 3AK  C13  C12  N7   113.07  3.000
 3AK  C14  C13  C18  119.09  3.000
 3AK  C14  C13  C12  121.29  3.000
 3AK  C18  C13  C12  119.60  3.000
 3AK  H9   C18  C17  119.74  3.000
 3AK  H9   C18  C13  119.64  3.000
 3AK  C17  C18  C13  120.62  3.000
 3AK  H10  C17  C16  120.21  3.000
 3AK  H10  C17  C18  119.76  3.000
 3AK  C16  C17  C18  120.03  3.000
 3AK  H11  C16  C15  120.20  3.000
 3AK  H11  C16  C17  120.17  3.000
 3AK  C15  C16  C17  119.63  3.000
 3AK  H12  C15  C14  119.69  3.000
 3AK  H12  C15  C16  120.06  3.000
 3AK  C14  C15  C16  120.25  3.000
 3AK  H13  C14  C15  119.19  3.000
 3AK  H13  C14  C13  120.43  3.000
 3AK  C15  C14  C13  120.38  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
 3AK  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 3AK  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 3AK  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 3AK  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 3AK  CONST_05  C2   C1   C6   C5     0.00   0.0  0
 3AK  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 3AK  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 3AK  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 3AK  CONST_09  C15  C16  C17  C18    0.00   0.0  0
 3AK  CONST_10  C15  C14  C13  C18    0.00   0.0  0
 3AK  CONST_11  C14  C15  C16  C17    0.00   0.0  0
 3AK  CONST_12  C14  C13  C18  C17    0.00   0.0  0
 3AK  CONST_13  C6   N7   C8   C9     0.00   0.0  0
 3AK  CONST_14  C17  C18  C13  C12  180.00   0.0  0
 3AK  CONST_15  C15  C14  C13  C12  180.00   0.0  0
 3AK  CONST_16  C6   N7   C8   O11  180.00   0.0  0
 3AK  CONST_17  C12  N7   C8   C9   180.00   0.0  0
 3AK  CONST_18  H6   C2   C1   C9     0.00   0.0  0
 3AK  CONST_19  H3   C5   C6   C1   180.00   0.0  0
 3AK  CONST_20  H5   C3   C2   C1   180.00   0.0  0
 3AK  CONST_21  H4   C4   C5   C6   180.00   0.0  0
 3AK  CONST_22  H10  C17  C18  C13  180.00   0.0  0
 3AK  CONST_23  H12  C15  C14  C13  180.00   0.0  0
 3AK  CONST_24  H11  C16  C17  C18  180.00   0.0  0
 3AK  CONST_25  H13  C14  C13  C18  180.00   0.0  0
 3AK  CONST_26  H9   C18  C17  C16  180.00   0.0  0
 3AK  CONST_27  C12  N7   C8   O11    0.00   0.0  0
 3AK  Var_01    C13  C12  N7   C8   113.71  30.0  2
 3AK  Var_02    C18  C13  C12  N7   140.38  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
 3AK  plan-1  C12  0.020
 3AK  plan-1  C13  0.020
 3AK  plan-1  C18  0.020
 3AK  plan-1  C17  0.020
 3AK  plan-1  C16  0.020
 3AK  plan-1  C15  0.020
 3AK  plan-1  C14  0.020
 3AK  plan-1  H9   0.020
 3AK  plan-1  H10  0.020
 3AK  plan-1  H11  0.020
 3AK  plan-1  H12  0.020
 3AK  plan-1  H13  0.020
 3AK  plan-2  O11  0.020
 3AK  plan-2  C8   0.020
 3AK  plan-2  C9   0.020
 3AK  plan-2  O10  0.020
 3AK  plan-2  C1   0.020
 3AK  plan-2  N7   0.020
 3AK  plan-2  C6   0.020
 3AK  plan-2  C5   0.020
 3AK  plan-2  C4   0.020
 3AK  plan-2  C3   0.020
 3AK  plan-2  C2   0.020
 3AK  plan-2  C12  0.020
 3AK  plan-2  H3   0.020
 3AK  plan-2  H4   0.020
 3AK  plan-2  H5   0.020
 3AK  plan-2  H6   0.020

