# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:10:54 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (3~{Z})-5-ethanoyl-3-[[(1-methylpiperidin-4-yl)amino]-phenyl-methylidene]-1~{H}-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)NC(/c2ccccc2)=C3\C(=O)Nc4ccc(cc34)C(C)=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
 F1B  F1B  (3~{Z})-5-ethanoyl-3-[[(1-methylpiperidin-4-yl)amino]-phenyl-methylidene]-1~{H}-indol-2-one  ligand  53  28  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F1B
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
 F1B  C4   C  CR5   0   0.531  -0.5592   2.7405  -0.0186
 F1B  C5   C  CR56  0   0.371  -2.7502   2.1392   0.0131
 F1B  C6   C  CR16  0  -0.441  -2.7387  -0.2596  -0.1283
 F1B  C7   C  CR6   0  -0.088   0.3441  -0.9833  -0.2202
 F1B  C13  C  CR16  0  -0.248   0.2278  -1.6197  -1.4513
 F1B  C15  C  CH1   0  -0.085   2.9783   0.2502  -0.1395
 F1B  C20  C  CH2   0  -0.442   4.0059   0.9165  -1.0466
 F1B  C21  C  CH2   0  -0.428   3.5311   0.1481   1.2788
 F1B  C22  C  CH3   0  -0.800  -6.3715  -1.5106  -0.0436
 F1B  C24  C  CR16  0  -0.247  -0.0457  -3.7290  -0.3281
 F1B  C26  C  CH2   0  -0.283   4.8827  -0.5493   1.2703
 F1B  C12  C  CR6   0  -0.027  -4.1393  -0.2414  -0.0745
 F1B  C16  C  CR16  0  -0.316  -4.8185   0.9765   0.0214
 F1B  C11  C  CR16  0  -0.290  -4.1315   2.1804   0.0647
 F1B  N9   N  NR15  0  -0.765  -1.8601   3.1832   0.0457
 F1B  O10  O  O     0  -0.504   0.4282   3.4759   0.0001
 F1B  C2   C  CR56  0   0.083  -2.0288   0.9274  -0.0826
 F1B  C1   C  CR5   0  -0.226  -0.6242   1.2919  -0.1032
 F1B  C3   C  C     0   0.392   0.5021   0.4906  -0.1624
 F1B  C18  C  CR16  0  -0.242   0.0316  -2.9923  -1.5027
 F1B  C19  C  CR16  0  -0.242   0.0759  -3.0929   0.8998
 F1B  C14  C  CR16  0  -0.244   0.2720  -1.7202   0.9563
 F1B  N8   N  NH1   0  -0.636   1.7306   0.9903  -0.1748
 F1B  C25  C  CH2   0  -0.282   5.3387   0.1893  -0.9575
 F1B  N27  N  NT    0  -0.410   5.8231   0.1407   0.4086
 F1B  H1   H  HCR6  0   0.263  -2.2304  -1.2103  -0.2068
 F1B  H2   H  HCR6  0   0.264   0.2810  -1.0422  -2.3658
 F1B  H3   H  HCH1  0   0.257   2.7907  -0.7586  -0.5145
 F1B  H4   H  HCH2  0   0.249   3.6556   0.9152  -2.0807
 F1B  H5   H  HCH2  0   0.230   4.1423   1.9599  -0.7445
 F1B  H6   H  HCH2  0   0.229   3.6372   1.1513   1.7023
 F1B  H7   H  HCH2  0   0.241   2.8381  -0.4054   1.9162
 F1B  H8   H  HCH3  0   0.263  -6.7102  -1.0272   0.8740
 F1B  H9   H  HCH3  0   0.264  -6.7963  -0.9491  -0.8774
 F1B  H10  H  HCH3  0   0.266  -6.7641  -2.5246  -0.0704
 F1B  H11  H  HCR6  0   0.263  -0.2023  -4.7989  -0.3701
 F1B  H12  H  HCH2  0   0.241   5.2848  -0.5745   2.2856
 F1B  H13  H  HCH2  0   0.190   4.7466  -1.6016   0.9592
 F1B  H14  H  HCH3  0   0.191   7.1645  -1.5005   0.1444
 F1B  H15  H  HCH3  0   0.232   7.8399   0.1113  -0.1364
 F1B  H16  H  HCH3  0   0.232   7.5058  -0.4255   1.5088
 F1B  H17  H  HCR6  0   0.259  -5.8987   1.0036   0.0625
 F1B  H18  H  HCR6  0   0.267  -4.6627   3.1201   0.1399
 F1B  H19  H  HNR5  0   0.408  -2.1145   4.1565   0.1134
 F1B  H21  H  HCR6  0   0.264  -0.0639  -3.4857  -2.4609
 F1B  H22  H  HCR6  0   0.264   0.0132  -3.6651   1.8160
 F1B  H23  H  HCR6  0   0.262   0.3509  -1.2221   1.9145
 F1B  H24  H  HCH2  0   0.191   5.2273  -0.8249  -1.3828
 F1B  H25  H  HCH2  0   0.241   6.0754   0.7082  -1.5747
 F1B  H20  H  HNH1  0   0.410   1.7949   2.0025  -0.1134
 F1B  C17  C  C     0   0.355  -4.8661  -1.5326  -0.1209
 F1B  C28  C  CH3   0  -0.517   7.1391  -0.4521   0.4815
 F1B  O23  O  O     0  -0.407  -4.2639  -2.5849  -0.2194

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
 F1B  C28  N27  single    1.445  0.020  1.445
 F1B  C26  N27  single    1.450  0.020  1.450
 F1B  C26  C21  single    1.521  0.020  1.521
 F1B  N27  C25  single    1.450  0.020  1.450
 F1B  C18  C24  aromatic  1.389  0.020  1.389
 F1B  C18  C13  aromatic  1.388  0.020  1.388
 F1B  C24  C19  aromatic  1.388  0.020  1.388
 F1B  C21  C15  single    1.526  0.020  1.526
 F1B  C25  C20  single    1.521  0.020  1.521
 F1B  C13  C7   aromatic  1.391  0.020  1.391
 F1B  C15  C20  single    1.524  0.020  1.524
 F1B  C15  N8   single    1.451  0.020  1.451
 F1B  C19  C14  aromatic  1.388  0.020  1.388
 F1B  C7   C14  aromatic  1.390  0.020  1.390
 F1B  C7   C3   single    1.483  0.020  1.483
 F1B  N8   C3   single    1.326  0.020  1.326
 F1B  C3   C1   double    1.384  0.020  1.384
 F1B  C22  C17  single    1.508  0.020  1.508
 F1B  C1   C2   single    1.451  0.020  1.451
 F1B  C1   C4   single    1.452  0.020  1.452
 F1B  C6   C2   aromatic  1.384  0.020  1.384
 F1B  C6   C12  aromatic  1.402  0.020  1.402
 F1B  C2   C5   aromatic  1.413  0.020  1.413
 F1B  O10  C4   double    1.231  0.020  1.231
 F1B  C17  C12  single    1.482  0.020  1.482
 F1B  C17  O23  double    1.216  0.020  1.216
 F1B  C4   N9   single    1.376  0.020  1.376
 F1B  C12  C16  aromatic  1.398  0.020  1.398
 F1B  C5   N9   single    1.372  0.020  1.372
 F1B  C5   C11  aromatic  1.383  0.020  1.383
 F1B  C16  C11  aromatic  1.387  0.020  1.387
 F1B  C6   H1   single    0.930  0.020  1.080
 F1B  C13  H2   single    0.930  0.020  1.080
 F1B  C15  H3   single    0.970  0.020  1.090
 F1B  C20  H4   single    0.970  0.020  1.090
 F1B  C20  H5   single    0.970  0.020  1.090
 F1B  C21  H6   single    0.970  0.020  1.090
 F1B  C21  H7   single    0.970  0.020  1.090
 F1B  C22  H8   single    0.970  0.020  1.090
 F1B  C22  H9   single    0.970  0.020  1.090
 F1B  C22  H10  single    0.970  0.020  1.090
 F1B  C24  H11  single    0.930  0.020  1.080
 F1B  C26  H12  single    0.970  0.020  1.090
 F1B  C26  H13  single    0.970  0.020  1.090
 F1B  C28  H14  single    0.970  0.020  1.090
 F1B  C28  H15  single    0.970  0.020  1.090
 F1B  C28  H16  single    0.970  0.020  1.090
 F1B  C16  H17  single    0.930  0.020  1.080
 F1B  C11  H18  single    0.930  0.020  1.080
 F1B  N9   H19  single    0.860  0.020  1.020
 F1B  C18  H21  single    0.930  0.020  1.080
 F1B  C19  H22  single    0.930  0.020  1.080
 F1B  C14  H23  single    0.930  0.020  1.080
 F1B  C25  H24  single    0.970  0.020  1.090
 F1B  C25  H25  single    0.970  0.020  1.090
 F1B  N8   H20  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
 F1B  C1   C4   O10  129.23  3.000
 F1B  O10  C4   N9   124.43  3.000
 F1B  C1   C4   N9   106.34  3.000
 F1B  C2   C5   N9   108.83  3.000
 F1B  N9   C5   C11  128.63  3.000
 F1B  C2   C5   C11  122.54  3.000
 F1B  H1   C6   C2   121.04  3.000
 F1B  H1   C6   C12  118.95  3.000
 F1B  C2   C6   C12  120.01  3.000
 F1B  C14  C7   C3   119.95  3.000
 F1B  C3   C7   C13  119.88  3.000
 F1B  C14  C7   C13  120.15  3.000
 F1B  H2   C13  C18  120.21  3.000
 F1B  H2   C13  C7   119.96  3.000
 F1B  C18  C13  C7   119.82  3.000
 F1B  H3   C15  N8   108.36  3.000
 F1B  H3   C15  C21  108.64  3.000
 F1B  N8   C15  C21  111.61  3.000
 F1B  H3   C15  C20  108.37  3.000
 F1B  N8   C15  C20  110.02  3.000
 F1B  C21  C15  C20  109.78  3.000
 F1B  H5   C20  H4   107.61  3.000
 F1B  H5   C20  C25  109.29  3.000
 F1B  H4   C20  C25  109.64  3.000
 F1B  H5   C20  C15  109.66  3.000
 F1B  H4   C20  C15  110.30  3.000
 F1B  C25  C20  C15  110.30  3.000
 F1B  H7   C21  H6   107.48  3.000
 F1B  H7   C21  C26  109.56  3.000
 F1B  H6   C21  C26  109.66  3.000
 F1B  H7   C21  C15  110.28  3.000
 F1B  H6   C21  C15  109.49  3.000
 F1B  C26  C21  C15  110.33  3.000
 F1B  H10  C22  H9   108.68  3.000
 F1B  H10  C22  H8   108.77  3.000
 F1B  H9   C22  H8   107.08  3.000
 F1B  H10  C22  C17  110.22  3.000
 F1B  H9   C22  C17  110.92  3.000
 F1B  H8   C22  C17  111.07  3.000
 F1B  H11  C24  C19  120.00  3.000
 F1B  H11  C24  C18  119.99  3.000
 F1B  C19  C24  C18  120.01  3.000
 F1B  H13  C26  H12  106.56  3.000
 F1B  H13  C26  N27  111.44  3.000
 F1B  H12  C26  N27  108.94  3.000
 F1B  H13  C26  C21  109.18  3.000
 F1B  H12  C26  C21  109.42  3.000
 F1B  N27  C26  C21  111.18  3.000
 F1B  C16  C12  C17  121.52  3.000
 F1B  C16  C12  C6   119.96  3.000
 F1B  C17  C12  C6   118.51  3.000
 F1B  H17  C16  C11  118.16  3.000
 F1B  H17  C16  C12  120.65  3.000
 F1B  C11  C16  C12  121.19  3.000
 F1B  H18  C11  C16  120.85  3.000
 F1B  H18  C11  C5   121.26  3.000
 F1B  C16  C11  C5   117.89  3.000
 F1B  H19  N9   C5   124.91  3.000
 F1B  H19  N9   C4   123.53  3.000
 F1B  C5   N9   C4   111.55  3.000
 F1B  C1   C2   C6   135.35  3.000
 F1B  C6   C2   C5   118.41  3.000
 F1B  C1   C2   C5   106.24  3.000
 F1B  C3   C1   C2   130.02  3.000
 F1B  C2   C1   C4   107.03  3.000
 F1B  C3   C1   C4   122.94  3.000
 F1B  N8   C3   C1   122.42  3.000
 F1B  C1   C3   C7   119.37  3.000
 F1B  N8   C3   C7   118.20  3.000
 F1B  H21  C18  C24  120.15  3.000
 F1B  H21  C18  C13  119.76  3.000
 F1B  C24  C18  C13  120.09  3.000
 F1B  H22  C19  C14  119.79  3.000
 F1B  H22  C19  C24  120.11  3.000
 F1B  C14  C19  C24  120.10  3.000
 F1B  H23  C14  C19  120.09  3.000
 F1B  H23  C14  C7   120.08  3.000
 F1B  C19  C14  C7   119.82  3.000
 F1B  H20  N8   C3   115.68  3.000
 F1B  H20  N8   C15  116.89  3.000
 F1B  C3   N8   C15  127.16  3.000
 F1B  H25  C25  H24  106.65  3.000
 F1B  H25  C25  N27  108.84  3.000
 F1B  H24  C25  N27  111.43  3.000
 F1B  H25  C25  C20  109.32  3.000
 F1B  H24  C25  C20  109.14  3.000
 F1B  N27  C25  C20  111.34  3.000
 F1B  C25  N27  C28  111.43  3.000
 F1B  C25  N27  C26  111.04  3.000
 F1B  C28  N27  C26  111.42  3.000
 F1B  C12  C17  O23  120.88  3.000
 F1B  O23  C17  C22  120.74  3.000
 F1B  C12  C17  C22  118.38  3.000
 F1B  H16  C28  H15  107.74  3.000
 F1B  H16  C28  H14  107.67  3.000
 F1B  H15  C28  H14  107.66  3.000
 F1B  H16  C28  N27  110.09  3.000
 F1B  H15  C28  N27  110.15  3.000
 F1B  H14  C28  N27  113.33  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
 F1B  CONST_01  C12  C6   C2   C5     0.00   0.0  0
 F1B  CONST_02  C12  C16  C11  C5     0.00   0.0  0
 F1B  CONST_03  C11  C5   C2   C6     0.00   0.0  0
 F1B  CONST_04  C11  C16  C12  C6     0.00   0.0  0
 F1B  CONST_05  C24  C18  C13  C7     0.00   0.0  0
 F1B  CONST_06  C24  C19  C14  C7     0.00   0.0  0
 F1B  CONST_07  C19  C24  C18  C13    0.00   0.0  0
 F1B  CONST_08  C19  C14  C7   C13    0.00   0.0  0
 F1B  CONST_09  C2   C6   C12  C16    0.00   0.0  0
 F1B  CONST_10  C2   C5   C11  C16    0.00   0.0  0
 F1B  CONST_11  C14  C19  C24  C18    0.00   0.0  0
 F1B  CONST_12  C14  C7   C13  C18    0.00   0.0  0
 F1B  CONST_13  C1   C4   N9   C5     0.00   0.0  0
 F1B  CONST_14  C2   C6   C12  C17  180.00   0.0  0
 F1B  CONST_15  C11  C16  C12  C17  180.00   0.0  0
 F1B  CONST_16  C18  C13  C7   C3   180.00   0.0  0
 F1B  CONST_17  C19  C14  C7   C3   180.00   0.0  0
 F1B  CONST_18  O10  C4   N9   C5   180.00   0.0  0
 F1B  CONST_19  H1   C6   C2   C5   180.00   0.0  0
 F1B  CONST_20  H17  C16  C11  C5   180.00   0.0  0
 F1B  CONST_21  H21  C18  C13  C7   180.00   0.0  0
 F1B  CONST_22  H22  C19  C14  C7   180.00   0.0  0
 F1B  CONST_23  H11  C24  C18  C13  180.00   0.0  0
 F1B  CONST_24  H23  C14  C7   C13  180.00   0.0  0
 F1B  CONST_25  H2   C13  C18  C24  180.00   0.0  0
 F1B  CONST_26  H18  C11  C16  C12  180.00   0.0  0
 F1B  CONST_27  H19  N9   C4   C1   180.00   0.0  0
 F1B  Var_01    N27  C26  C21  C15   57.10  30.0  1
 F1B  Var_02    N27  C25  C20  C15  -56.95  30.0  1
 F1B  Var_03    C26  N27  C25  C20   59.85  30.0  1
 F1B  Var_04    C25  N27  C26  C21  -59.88  30.0  1
 F1B  Var_05    C7   C3   C1   C4   178.79  30.0  2
 F1B  Var_06    C1   C3   C7   C13   89.28  30.0  2
 F1B  Var_07    C22  C17  C12  C6   179.17  30.0  2
 F1B  Var_08    C15  N8   C3   C7    -4.98  30.0  2
 F1B  Var_09    H14  C28  N27  C26   62.04  30.0  3
 F1B  Var_10    H8   C22  C17  C12  -58.33  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 F1B  chir_01  C15  C21  C20  N8  positiv

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
 F1B  plan-1  C7   0.020
 F1B  plan-1  C13  0.020
 F1B  plan-1  C24  0.020
 F1B  plan-1  C3   0.020
 F1B  plan-1  C18  0.020
 F1B  plan-1  C19  0.020
 F1B  plan-1  C14  0.020
 F1B  plan-1  H2   0.020
 F1B  plan-1  H11  0.020
 F1B  plan-1  H21  0.020
 F1B  plan-1  H22  0.020
 F1B  plan-1  H23  0.020
 F1B  plan-2  C4   0.020
 F1B  plan-2  C5   0.020
 F1B  plan-2  C6   0.020
 F1B  plan-2  C12  0.020
 F1B  plan-2  C16  0.020
 F1B  plan-2  C11  0.020
 F1B  plan-2  N9   0.020
 F1B  plan-2  O10  0.020
 F1B  plan-2  C2   0.020
 F1B  plan-2  C1   0.020
 F1B  plan-2  C3   0.020
 F1B  plan-2  H1   0.020
 F1B  plan-2  H17  0.020
 F1B  plan-2  H18  0.020
 F1B  plan-2  H19  0.020
 F1B  plan-2  C17  0.020
 F1B  plan-3  C22  0.020
 F1B  plan-3  C12  0.020
 F1B  plan-3  C17  0.020
 F1B  plan-3  O23  0.020

