# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:57:08 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  31  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  -0.258  -2.4846   2.8652  -0.4256
 1TD  C2   C  CR16  0  -0.264  -3.8453   2.6311  -0.5872
 1TD  C3   C  CR16  0  -0.224   2.1465   1.2874   1.6670
 1TD  C4   C  CR16  0  -0.371  -1.6072   1.8102  -0.1956
 1TD  C5   C  CR16  0  -0.301   0.9740   0.5940   1.4151
 1TD  C6   C  CR16  0  -0.265   3.3240   0.9309   1.0273
 1TD  C7   C  CR16  0  -0.302  -4.3625   1.3397  -0.5425
 1TD  C8   C  CR16  0  -0.305   2.1553  -0.8498  -0.0955
 1TD  C9   C  CR56  0   0.041  -2.1034   0.5165  -0.1246
 1TD  C10  C  CR6   0   0.106   0.9613  -0.4729   0.5145
 1TD  C11  C  CR6   0  -0.062   3.3307  -0.1458   0.1419
 1TD  C12  C  CR56  0   0.379  -3.4771   0.3036  -0.3204
 1TD  C13  C  CR5   0  -0.002  -1.4971  -0.8023   0.0430
 1TD  C14  C  CR5   0   0.526  -2.6171  -1.7921  -0.0997
 1TD  C15  C  C1    0  -0.339  -0.2492  -1.2479   0.2475
 1TD  C16  C  C     0   0.538   4.5618  -0.5845  -0.5646
 1TD  N17  N  NR15  0  -0.771  -3.7479  -1.0551  -0.2797
 1TD  O18  O  O     0  -0.435   4.5941  -1.5075  -1.3424
 1TD  O19  O  O     0  -0.446  -2.5508  -3.0040  -0.0516
 1TD  O20  O  OH1   0  -0.592   5.6229   0.1451  -0.2562
 1TD  H1   H  HCR6  0   0.259  -2.1026   3.8759  -0.4781
 1TD  H2   H  HCR6  0   0.264  -4.5160   3.4627  -0.7589
 1TD  H4   H  HCR6  0   0.262  -0.5512   2.0100  -0.0839
 1TD  H5   H  HCR6  0   0.285   0.0694   0.8660   1.9441
 1TD  H6   H  HCR6  0   0.275   4.2274   1.4880   1.2325
 1TD  H7   H  HCR6  0   0.271  -5.4192   1.1555  -0.6846
 1TD  H8   H  HCR6  0   0.270   2.1614  -1.6948  -0.7722
 1TD  H9   H  H     0   0.285  -0.1155  -2.3257   0.2091
 1TD  H10  H  HNR5  0   0.414  -4.6625  -1.4589  -0.4128
 1TD  H11  H  HOH1  0   0.490   6.3966  -0.1711  -0.7463
 1TD  H3   H  HCR6  0   0.274   2.1442   2.1077   2.3716

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  double    1.207  0.020  1.207
 1TD  O20  C16  single    1.324  0.020  1.324
 1TD  C16  C11  single    1.486  0.020  1.486
 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    1.362  0.020  1.362
 1TD  C12  C9   aromatic  1.404  0.020  1.404
 1TD  C2   C1   aromatic  1.390  0.020  1.390
 1TD  C8   C11  aromatic  1.391  0.020  1.391
 1TD  C8   C10  aromatic  1.393  0.020  1.393
 1TD  C11  C6   aromatic  1.394  0.020  1.394
 1TD  C14  O19  double    1.215  0.020  1.215
 1TD  C14  C13  single    1.502  0.020  1.502
 1TD  C9   C13  single    1.461  0.020  1.461
 1TD  C9   C4   aromatic  1.387  0.020  1.387
 1TD  C1   C4   aromatic  1.391  0.020  1.391
 1TD  C13  C15  double    1.341  0.020  1.341
 1TD  C15  C10  single    1.462  0.020  1.462
 1TD  C10  C5   aromatic  1.396  0.020  1.396
 1TD  C6   C3   aromatic  1.387  0.020  1.387
 1TD  C5   C3   aromatic  1.385  0.020  1.385
 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
 1TD  O20  H11  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
 1TD  H1   C1   C4   119.60  3.000
 1TD  H1   C1   C2   119.83  3.000
 1TD  C4   C1   C2   120.58  3.000
 1TD  H2   C2   C7   119.20  3.000
 1TD  H2   C2   C1   119.71  3.000
 1TD  C7   C2   C1   121.08  3.000
 1TD  H3   C3   C6   119.83  3.000
 1TD  H3   C3   C5   119.76  3.000
 1TD  C6   C3   C5   120.41  3.000
 1TD  H4   C4   C9   121.11  3.000
 1TD  H4   C4   C1   119.55  3.000
 1TD  C9   C4   C1   119.34  3.000
 1TD  H5   C5   C10  119.97  3.000
 1TD  H5   C5   C3   119.51  3.000
 1TD  C10  C5   C3   120.49  3.000
 1TD  H6   C6   C11  120.97  3.000
 1TD  H6   C6   C3   119.31  3.000
 1TD  C11  C6   C3   119.72  3.000
 1TD  H7   C7   C12  121.30  3.000
 1TD  H7   C7   C2   121.11  3.000
 1TD  C12  C7   C2   117.59  3.000
 1TD  H8   C8   C11  119.81  3.000
 1TD  H8   C8   C10  119.33  3.000
 1TD  C11  C8   C10  120.86  3.000
 1TD  C13  C9   C12  106.57  3.000
 1TD  C13  C9   C4   134.35  3.000
 1TD  C12  C9   C4   118.96  3.000
 1TD  C15  C10  C8   119.10  3.000
 1TD  C15  C10  C5   122.03  3.000
 1TD  C8   C10  C5   118.79  3.000
 1TD  C16  C11  C8   118.02  3.000
 1TD  C8   C11  C6   119.69  3.000
 1TD  C16  C11  C6   122.29  3.000
 1TD  N17  C12  C9   109.62  3.000
 1TD  C9   C12  C7   122.42  3.000
 1TD  N17  C12  C7   127.95  3.000
 1TD  C15  C13  C14  119.32  3.000
 1TD  C15  C13  C9   134.73  3.000
 1TD  C14  C13  C9   105.94  3.000
 1TD  O19  C14  N17  126.20  3.000
 1TD  O19  C14  C13  127.83  3.000
 1TD  N17  C14  C13  105.97  3.000
 1TD  H9   C15  C13  116.02  3.000
 1TD  H9   C15  C10  115.49  3.000
 1TD  C13  C15  C10  128.49  3.000
 1TD  O20  C16  O18  123.35  3.000
 1TD  O20  C16  C11  112.99  3.000
 1TD  O18  C16  C11  123.66  3.000
 1TD  H10  N17  C14  123.63  3.000
 1TD  H10  N17  C12  124.45  3.000
 1TD  C14  N17  C12  111.85  3.000
 1TD  H11  O20  C16  110.02  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  CONST_28  H11  O20  C16  C11   180.00   0.0  0
 1TD  Var_01    C13  C15  C10  C5     44.02  30.0  1
 1TD  Var_02    C10  C15  C13  C9      7.11  30.0  2
 1TD  Var_03    O18  C16  C11  C6   -179.52  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  H5   0.020
 1TD  plan-1  H6   0.020
 1TD  plan-1  H8   0.020
 1TD  plan-1  H3   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
 1TD  plan-3  H11  0.020

