# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:42:10 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (3E)-3-(pyridin-3-ylmethylidene)-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C/1Nc2ccccc2C/1=C/c3cccnc3
#
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
 EVO  EVO  (3E)-3-(pyridin-3-ylmethylidene)-1,3-dihydro-2H-indol-2-one  ligand  27  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EVO
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
 EVO  O    O  O     0  -0.445  -1.9033  -2.9391  -0.0089
 EVO  C1   C  CR5   0   0.527  -1.8650  -1.7254   0.0106
 EVO  C8   C  CR5   0  -0.002  -0.6496  -0.8435   0.0164
 EVO  C7   C  CR56  0   0.044  -1.1496   0.5283   0.0673
 EVO  C6   C  CR16  0  -0.374  -0.5524   1.7753   0.1816
 EVO  C5   C  CR16  0  -0.257  -1.3520   2.9111   0.2580
 EVO  C4   C  CR16  0  -0.264  -2.7375   2.8034   0.2253
 EVO  C3   C  CR16  0  -0.302  -3.3594   1.5615   0.1348
 EVO  C2   C  CR56  0   0.379  -2.5508   0.4442   0.0659
 EVO  N1   N  NR15  0  -0.771  -2.9372  -0.8861   0.0136
 EVO  C9   C  C1    0  -0.345   0.5678  -1.4054   0.0091
 EVO  C10  C  CR6   0  -0.008   1.8710  -0.7568  -0.0863
 EVO  C14  C  CR16  0  -0.074   2.9355  -1.2453   0.6754
 EVO  N2   N  N     0  -0.399   4.1575  -0.7376   0.6494
 EVO  C13  C  CR16  0  -0.062   4.3915   0.2809  -0.1713
 EVO  C12  C  CR16  0  -0.313   3.4212   0.8225  -1.0021
 EVO  C11  C  CR16  0  -0.206   2.1433   0.2936  -0.9609
 EVO  H1   H  HCR6  0   0.262   0.5222   1.8813   0.2196
 EVO  H2   H  HCR6  0   0.259  -0.8891   3.8849   0.3429
 EVO  H3   H  HCR6  0   0.264  -3.3474   3.6955   0.2798
 EVO  H4   H  HCR6  0   0.272  -4.4380   1.4759   0.1302
 EVO  H5   H  HNR5  0   0.415  -3.8949  -1.2026   0.0113
 EVO  H6   H  H     0   0.285   0.5938  -2.4891   0.0868
 EVO  H7   H  HCR6  0   0.270   2.7746  -2.0852   1.3441
 EVO  H8   H  HCR6  0   0.272   5.4008   0.6764  -0.1790
 EVO  H9   H  HCR6  0   0.280   3.6658   1.6349  -1.6720
 EVO  H10  H  HCR6  0   0.292   1.3756   0.6744  -1.6221

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
 EVO  C5   C6   aromatic  1.391  0.020  1.391
 EVO  C5   C4   aromatic  1.390  0.020  1.390
 EVO  C13  C12  aromatic  1.387  0.020  1.387
 EVO  C13  N2   aromatic  1.329  0.020  1.329
 EVO  C12  C11  aromatic  1.384  0.020  1.384
 EVO  C6   C7   aromatic  1.387  0.020  1.387
 EVO  C4   C3   aromatic  1.392  0.020  1.392
 EVO  N2   C14  aromatic  1.324  0.020  1.324
 EVO  C11  C10  aromatic  1.394  0.020  1.394
 EVO  C14  C10  aromatic  1.397  0.020  1.397
 EVO  C10  C9   single    1.459  0.020  1.459
 EVO  C7   C2   aromatic  1.404  0.020  1.404
 EVO  C7   C8   single    1.461  0.020  1.461
 EVO  C3   C2   aromatic  1.381  0.020  1.381
 EVO  C2   N1   single    1.386  0.020  1.386
 EVO  C9   C8   double    1.341  0.020  1.341
 EVO  C8   C1   single    1.502  0.020  1.502
 EVO  N1   C1   single    1.362  0.020  1.362
 EVO  C1   O    double    1.214  0.020  1.214
 EVO  C6   H1   single    0.930  0.020  1.080
 EVO  C5   H2   single    0.930  0.020  1.080
 EVO  C4   H3   single    0.930  0.020  1.080
 EVO  C3   H4   single    0.930  0.020  1.080
 EVO  N1   H5   single    0.860  0.020  1.020
 EVO  C9   H6   single    0.930  0.020  1.080
 EVO  C14  H7   single    0.930  0.020  1.080
 EVO  C13  H8   single    0.930  0.020  1.080
 EVO  C12  H9   single    0.930  0.020  1.080
 EVO  C11  H10  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
 EVO  N1   C1   C8   105.98  3.000
 EVO  N1   C1   O    126.25  3.000
 EVO  C8   C1   O    127.77  3.000
 EVO  C9   C8   C7   134.78  3.000
 EVO  C9   C8   C1   119.26  3.000
 EVO  C7   C8   C1   105.94  3.000
 EVO  C2   C7   C6   118.92  3.000
 EVO  C2   C7   C8   106.58  3.000
 EVO  C6   C7   C8   134.39  3.000
 EVO  H1   C6   C5   119.31  3.000
 EVO  H1   C6   C7   121.28  3.000
 EVO  C5   C6   C7   119.41  3.000
 EVO  H2   C5   C4   119.88  3.000
 EVO  H2   C5   C6   119.56  3.000
 EVO  C4   C5   C6   120.55  3.000
 EVO  H3   C4   C3   119.14  3.000
 EVO  H3   C4   C5   119.79  3.000
 EVO  C3   C4   C5   121.07  3.000
 EVO  H4   C3   C2   121.30  3.000
 EVO  H4   C3   C4   121.09  3.000
 EVO  C2   C3   C4   117.61  3.000
 EVO  N1   C2   C3   127.96  3.000
 EVO  N1   C2   C7   109.62  3.000
 EVO  C3   C2   C7   122.41  3.000
 EVO  H5   N1   C2   124.47  3.000
 EVO  H5   N1   C1   123.65  3.000
 EVO  C2   N1   C1   111.85  3.000
 EVO  H6   C9   C10  115.26  3.000
 EVO  H6   C9   C8   116.05  3.000
 EVO  C10  C9   C8   128.69  3.000
 EVO  C11  C10  C14  117.18  3.000
 EVO  C14  C10  C9   119.31  3.000
 EVO  C11  C10  C9   123.41  3.000
 EVO  H7   C14  N2   116.47  3.000
 EVO  H7   C14  C10  119.56  3.000
 EVO  N2   C14  C10  123.96  3.000
 EVO  C13  N2   C14  117.95  3.000
 EVO  H8   C13  C12  120.30  3.000
 EVO  H8   C13  N2   116.61  3.000
 EVO  C12  C13  N2   123.08  3.000
 EVO  H9   C12  C11  120.98  3.000
 EVO  H9   C12  C13  120.41  3.000
 EVO  C11  C12  C13  118.61  3.000
 EVO  H10  C11  C12  120.16  3.000
 EVO  H10  C11  C10  120.66  3.000
 EVO  C12  C11  C10  119.16  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
 EVO  CONST_01  C4   C5   C6   C7     0.00   0.0  0
 EVO  CONST_02  C4   C3   C2   C7     0.00   0.0  0
 EVO  CONST_03  C3   C4   C5   C6     0.00   0.0  0
 EVO  CONST_04  C3   C2   C7   C6     0.00   0.0  0
 EVO  CONST_05  C2   C7   C6   C5     0.00   0.0  0
 EVO  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 EVO  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 EVO  CONST_08  C13  N2   C14  C10    0.00   0.0  0
 EVO  CONST_09  C12  C13  N2   C14    0.00   0.0  0
 EVO  CONST_10  C12  C11  C10  C14    0.00   0.0  0
 EVO  CONST_11  C11  C12  C13  N2     0.00   0.0  0
 EVO  CONST_12  C11  C10  C14  N2     0.00   0.0  0
 EVO  CONST_13  C2   N1   C1   C8     0.00   0.0  0
 EVO  CONST_14  C12  C11  C10  C9   180.00   0.0  0
 EVO  CONST_15  N2   C14  C10  C9   180.00   0.0  0
 EVO  CONST_16  C2   N1   C1   O    180.00   0.0  0
 EVO  CONST_17  H1   C6   C7   C8     0.00   0.0  0
 EVO  CONST_18  H2   C5   C6   C7   180.00   0.0  0
 EVO  CONST_19  H4   C3   C2   C7   180.00   0.0  0
 EVO  CONST_20  H3   C4   C5   C6   180.00   0.0  0
 EVO  CONST_21  H9   C12  C11  C10  180.00   0.0  0
 EVO  CONST_22  H8   C13  N2   C14  180.00   0.0  0
 EVO  CONST_23  H10  C11  C10  C14  180.00   0.0  0
 EVO  CONST_24  H7   C14  N2   C13  180.00   0.0  0
 EVO  CONST_25  H5   N1   C1   C8   180.00   0.0  0
 EVO  Var_01    C10  C9   C8   C1   175.02  30.0  2
 EVO  Var_02    C11  C10  C9   C8   -42.64  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
 EVO  plan-1  C9   0.020
 EVO  plan-1  C10  0.020
 EVO  plan-1  C14  0.020
 EVO  plan-1  N2   0.020
 EVO  plan-1  C13  0.020
 EVO  plan-1  C12  0.020
 EVO  plan-1  C11  0.020
 EVO  plan-1  H7   0.020
 EVO  plan-1  H8   0.020
 EVO  plan-1  H9   0.020
 EVO  plan-1  H10  0.020
 EVO  plan-2  O    0.020
 EVO  plan-2  C1   0.020
 EVO  plan-2  C8   0.020
 EVO  plan-2  C7   0.020
 EVO  plan-2  C6   0.020
 EVO  plan-2  C5   0.020
 EVO  plan-2  C4   0.020
 EVO  plan-2  C3   0.020
 EVO  plan-2  C2   0.020
 EVO  plan-2  N1   0.020
 EVO  plan-2  C9   0.020
 EVO  plan-2  H1   0.020
 EVO  plan-2  H2   0.020
 EVO  plan-2  H3   0.020
 EVO  plan-2  H4   0.020
 EVO  plan-2  H5   0.020

