# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:12:28 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 3-[(E)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)\C=C/2C(=O)Nc3ccccc/23
#
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
 1TD  1TD  '3-[(E)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]benzoic acid'  ligand  30  20  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1TD
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
 1TD  C1   C  CR16   0  -0.259  -2.5002   2.8819  -0.4527
 1TD  C2   C  CR16   0  -0.267  -3.8598   2.6467  -0.6218
 1TD  C3   C  CR16   0  -0.230   2.1639   1.2882   1.6304
 1TD  C4   C  CR16   0  -0.375  -1.6237   1.8285  -0.2103
 1TD  C5   C  CR16   0  -0.322   0.9739   0.6248   1.3784
 1TD  C6   C  CR16   0  -0.293   3.3424   0.8656   1.0298
 1TD  C7   C  CR16   0  -0.303  -4.3755   1.3550  -0.5734
 1TD  C8   C  CR16   0  -0.340   2.1584  -0.9157  -0.0394
 1TD  C9   C  CR56   0   0.040  -2.1181   0.5342  -0.1353
 1TD  C10  C  CR6    0   0.112   0.9564  -0.4777   0.5212
 1TD  C11  C  CR6    0  -0.081   3.3534  -0.2448   0.1891
 1TD  C12  C  CR56   0   0.376  -3.4908   0.3206  -0.3401
 1TD  C13  C  CR5    0  -0.009  -1.5122  -0.7841   0.0411
 1TD  C14  C  CR5    0   0.521  -2.6294  -1.7730  -0.1053
 1TD  C15  C  C1     0  -0.339  -0.2630  -1.2319   0.2481
 1TD  C16  C  C      0   0.402   4.6497  -0.7253  -0.4559
 1TD  N17  N  NR15   0  -0.770  -3.7606  -1.0377  -0.2954
 1TD  O18  O  O      0  -0.589   4.5726  -1.7471  -1.1635
 1TD  O19  O  O      0  -0.451  -2.5666  -2.9859  -0.0532
 1TD  O20  O  OC    -1  -0.591   5.6702  -0.0528  -0.2180
 1TD  H1   H  HCR6   0   0.257  -2.1180   3.8924  -0.5081
 1TD  H2   H  HCR6   0   0.262  -4.5300   3.4769  -0.8023
 1TD  H4   H  HCR6   0   0.263  -0.5689   2.0291  -0.0911
 1TD  H6   H  HCR6   0   0.250   4.2670   1.3925   1.2243
 1TD  H7   H  HCR6   0   0.270  -5.4311   1.1687  -0.7218
 1TD  H8   H  HCR6   0   0.248   2.1575  -1.7904  -0.6781
 1TD  H9   H  H      0   0.277  -0.1393  -2.3110   0.2027
 1TD  H10  H  HNR5   0   0.413  -4.6734  -1.4432  -0.4343
 1TD  H3   H  HCR6   0   0.257   2.1718   2.1355   2.3039
 1TD  H5   H  HCR6   0   0.272   0.0661   0.9432   1.8750

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
 1TD  O18  C16  deloc     1.245  0.020  1.245
 1TD  O20  C16  deloc     1.245  0.020  1.245
 1TD  C16  C11  single    1.526  0.020  1.526
 1TD  C7   C12  aromatic  1.381  0.020  1.381
 1TD  C7   C2   aromatic  1.392  0.020  1.392
 1TD  N17  C12  single    1.386  0.020  1.386
 1TD  N17  C14  single    1.363  0.020  1.363
 1TD  C12  C9   aromatic  1.404  0.020  1.404
 1TD  C2   C1   aromatic  1.390  0.020  1.390
 1TD  C8   C11  aromatic  1.389  0.020  1.389
 1TD  C8   C10  aromatic  1.397  0.020  1.397
 1TD  C11  C6   aromatic  1.393  0.020  1.393
 1TD  C14  O19  double    1.216  0.020  1.216
 1TD  C14  C13  single    1.499  0.020  1.499
 1TD  C9   C13  single    1.462  0.020  1.462
 1TD  C9   C4   aromatic  1.388  0.020  1.388
 1TD  C1   C4   aromatic  1.392  0.020  1.392
 1TD  C13  C15  double    1.343  0.020  1.343
 1TD  C15  C10  single    1.460  0.020  1.460
 1TD  C10  C5   aromatic  1.397  0.020  1.397
 1TD  C6   C3   aromatic  1.389  0.020  1.389
 1TD  C5   C3   aromatic  1.386  0.020  1.386
 1TD  C1   H1   single    0.930  0.020  1.080
 1TD  C2   H2   single    0.930  0.020  1.080
 1TD  C3   H3   single    0.930  0.020  1.080
 1TD  C4   H4   single    0.930  0.020  1.080
 1TD  C5   H5   single    0.930  0.020  1.080
 1TD  C6   H6   single    0.930  0.020  1.080
 1TD  C7   H7   single    0.930  0.020  1.080
 1TD  C8   H8   single    0.930  0.020  1.080
 1TD  C15  H9   single    0.930  0.020  1.080
 1TD  N17  H10  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
 1TD  H1   C1   C4   119.57  3.000
 1TD  H1   C1   C2   119.82  3.000
 1TD  C4   C1   C2   120.61  3.000
 1TD  H2   C2   C7   119.23  3.000
 1TD  H2   C2   C1   119.75  3.000
 1TD  C7   C2   C1   121.01  3.000
 1TD  H3   C3   C6   120.08  3.000
 1TD  H3   C3   C5   119.63  3.000
 1TD  C6   C3   C5   120.30  3.000
 1TD  H4   C4   C9   121.00  3.000
 1TD  H4   C4   C1   119.58  3.000
 1TD  C9   C4   C1   119.42  3.000
 1TD  H5   C5   C10  120.21  3.000
 1TD  H5   C5   C3   119.73  3.000
 1TD  C10  C5   C3   120.03  3.000
 1TD  H6   C6   C11  119.34  3.000
 1TD  H6   C6   C3   119.96  3.000
 1TD  C11  C6   C3   120.69  3.000
 1TD  H7   C7   C12  121.28  3.000
 1TD  H7   C7   C2   121.10  3.000
 1TD  C12  C7   C2   117.62  3.000
 1TD  H8   C8   C11  119.18  3.000
 1TD  H8   C8   C10  119.29  3.000
 1TD  C11  C8   C10  121.52  3.000
 1TD  C13  C9   C12  106.60  3.000
 1TD  C13  C9   C4   134.45  3.000
 1TD  C12  C9   C4   118.83  3.000
 1TD  C15  C10  C8   118.81  3.000
 1TD  C15  C10  C5   122.22  3.000
 1TD  C8   C10  C5   118.88  3.000
 1TD  C16  C11  C8   120.61  3.000
 1TD  C8   C11  C6   118.52  3.000
 1TD  C16  C11  C6   120.87  3.000
 1TD  N17  C12  C9   109.56  3.000
 1TD  C9   C12  C7   122.48  3.000
 1TD  N17  C12  C7   127.95  3.000
 1TD  C15  C13  C14  119.23  3.000
 1TD  C15  C13  C9   134.82  3.000
 1TD  C14  C13  C9   105.92  3.000
 1TD  O19  C14  N17  125.97  3.000
 1TD  O19  C14  C13  127.99  3.000
 1TD  N17  C14  C13  106.04  3.000
 1TD  H9   C15  C13  115.49  3.000
 1TD  H9   C15  C10  115.19  3.000
 1TD  C13  C15  C10  129.32  3.000
 1TD  O20  C16  O18  127.05  3.000
 1TD  O20  C16  C11  116.46  3.000
 1TD  O18  C16  C11  116.49  3.000
 1TD  H10  N17  C14  123.62  3.000
 1TD  H10  N17  C12  124.47  3.000
 1TD  C14  N17  C12  111.83  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
 1TD  CONST_01  C12  C7   C2   C1     0.00   0.0  0
 1TD  CONST_02  C12  C9   C4   C1     0.00   0.0  0
 1TD  CONST_03  C9   C12  C7   C2     0.00   0.0  0
 1TD  CONST_04  C9   C4   C1   C2     0.00   0.0  0
 1TD  CONST_05  C8   C11  C6   C3     0.00   0.0  0
 1TD  CONST_06  C8   C10  C5   C3     0.00   0.0  0
 1TD  CONST_07  C7   C12  C9   C4     0.00   0.0  0
 1TD  CONST_08  C7   C2   C1   C4     0.00   0.0  0
 1TD  CONST_09  C11  C8   C10  C5     0.00   0.0  0
 1TD  CONST_10  C11  C6   C3   C5     0.00   0.0  0
 1TD  CONST_11  C10  C8   C11  C6     0.00   0.0  0
 1TD  CONST_12  C10  C5   C3   C6     0.00   0.0  0
 1TD  CONST_13  C13  C14  N17  C12    0.00   0.0  0
 1TD  CONST_14  C16  C11  C6   C3   180.00   0.0  0
 1TD  CONST_15  C15  C10  C5   C3   180.00   0.0  0
 1TD  CONST_16  C16  C11  C8   C10  180.00   0.0  0
 1TD  CONST_17  C15  C10  C8   C11  180.00   0.0  0
 1TD  CONST_18  O19  C14  N17  C12  180.00   0.0  0
 1TD  CONST_19  H7   C7   C2   C1   180.00   0.0  0
 1TD  CONST_20  H4   C4   C1   C2   180.00   0.0  0
 1TD  CONST_21  H2   C2   C1   C4   180.00   0.0  0
 1TD  CONST_22  H8   C8   C10  C5   180.00   0.0  0
 1TD  CONST_23  H6   C6   C3   C5   180.00   0.0  0
 1TD  CONST_24  H5   C5   C3   C6   180.00   0.0  0
 1TD  CONST_25  H1   C1   C2   C7   180.00   0.0  0
 1TD  CONST_26  H3   C3   C5   C10  180.00   0.0  0
 1TD  CONST_27  H10  N17  C14  C13  180.00   0.0  0
 1TD  Var_01    C13  C15  C10  C5    40.88  30.0  3
 1TD  Var_02    C10  C15  C13  C9     7.71  30.0  2
 1TD  Var_03    O18  C16  C11  C6   178.10  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
 1TD  plan-1  C3   0.020
 1TD  plan-1  C5   0.020
 1TD  plan-1  C6   0.020
 1TD  plan-1  C8   0.020
 1TD  plan-1  C10  0.020
 1TD  plan-1  C11  0.020
 1TD  plan-1  C15  0.020
 1TD  plan-1  C16  0.020
 1TD  plan-1  H6   0.020
 1TD  plan-1  H8   0.020
 1TD  plan-1  H3   0.020
 1TD  plan-1  H5   0.020
 1TD  plan-2  C1   0.020
 1TD  plan-2  C2   0.020
 1TD  plan-2  C4   0.020
 1TD  plan-2  C7   0.020
 1TD  plan-2  C9   0.020
 1TD  plan-2  C12  0.020
 1TD  plan-2  C13  0.020
 1TD  plan-2  C14  0.020
 1TD  plan-2  C15  0.020
 1TD  plan-2  N17  0.020
 1TD  plan-2  O19  0.020
 1TD  plan-2  H1   0.020
 1TD  plan-2  H2   0.020
 1TD  plan-2  H4   0.020
 1TD  plan-2  H7   0.020
 1TD  plan-2  H10  0.020
 1TD  plan-3  C11  0.020
 1TD  plan-3  C16  0.020
 1TD  plan-3  O18  0.020
 1TD  plan-3  O20  0.020

