# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:16:17 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-{(Z)-2-[6-chloro-1-(4-fluorobenzyl)-1H-indol-3-yl]-1-cyanoethenyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)C(=C/c2cn(Cc3ccc(F)cc3)c4cc(Cl)ccc24)/C#N
#
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
 4NY  4NY  '4-{(Z)-2-[6-chloro-1-(4-fluorobenzyl)-1H-indol-3-yl]-1-cyanoethenyl}benzoic acid'  ligand  47  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4NY
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
 4NY  C24  C   C     0   0.533   7.9452  -0.3169   0.8323
 4NY  C23  C   CSP   0  -0.017   2.1826   1.1252  -1.8808
 4NY  C22  C   CR16  0  -0.262  -3.3254   2.5635  -0.2208
 4NY  C14  C   CR16  0  -0.381  -0.7786  -2.3523   1.1157
 4NY  C15  C   CR56  0   0.062  -0.9039  -1.3251   0.1801
 4NY  C16  C   CH2   0  -0.418  -3.1160   0.6989  -1.8993
 4NY  C17  C   CR6   0   0.110  -3.9328   1.5547  -0.9645
 4NY  C18  C   CR16  0  -0.295  -5.3015   1.3561  -0.8342
 4NY  C19  C   CR16  0  -0.398  -6.0620   2.1442   0.0202
 4NY  C20  C   CR6   0   0.521  -5.4256   3.1321   0.7431
 4NY  C21  C   CR16  0  -0.395  -4.0651   3.3589   0.6391
 4NY  O    O   O     0  -0.439   8.2543  -0.6893   1.9395
 4NY  O1   O   OH1   0  -0.593   8.8319  -0.0028  -0.1017
 4NY  C1   C   CR6   0  -0.098   6.5440  -0.1615   0.3774
 4NY  C2   C   CR16  0  -0.238   6.2167   0.2407  -0.9158
 4NY  C3   C   CR16  0  -0.295   4.8922   0.3737  -1.2922
 4NY  C4   C   CR6   0   0.149   3.8580   0.1077  -0.3921
 4NY  C5   C   CR16  0  -0.313   4.1951  -0.2779   0.9089
 4NY  C    C   CR16  0  -0.238   5.5166  -0.4177   1.2839
 4NY  C6   C   C     0   0.002   2.4507   0.2346  -0.8061
 4NY  N1   N   NS    0  -0.254   1.9767   1.8530  -2.7530
 4NY  C7   C   C1    0  -0.318   1.4402  -0.4618  -0.2251
 4NY  C8   C   CR5   0   0.031   0.0346  -0.4456  -0.4721
 4NY  C13  C   CR16  0  -0.215  -1.9114  -3.0172   1.5404
 4NY  C12  C   CR6   0  -0.066  -3.1670  -2.6619   1.0326
 4NY  CL   CL  CL    0  -0.127  -4.5630  -3.5242   1.5954
 4NY  C11  C   CR16  0  -0.246  -3.3357  -1.6542   0.1054
 4NY  C10  C   CR56  0   0.390  -2.1800  -0.9990  -0.3070
 4NY  N    N   NR5   0  -0.522  -2.0317   0.0229  -1.2141
 4NY  C9   C   CR15  0  -0.032  -0.7266   0.3529  -1.3086
 4NY  F    F   F     0  -0.313  -6.1489   3.8995   1.5729
 4NY  H2   H   HCR6  0   0.263   0.1867  -2.6384   1.5137
 4NY  H3   H   HCH2  0   0.297  -3.7444  -0.0447  -2.3915
 4NY  H4   H   HCH2  0   0.301  -2.6684   1.3031  -2.6885
 4NY  H5   H   HCR6  0   0.271  -5.7925   0.5763  -1.4035
 4NY  H6   H   HCR6  0   0.284  -7.1274   1.9856   0.1224
 4NY  H7   H   HCR6  0   0.284  -3.5931   4.1452   1.2132
 4NY  H8   H   HOH1  0   0.488   9.7301  -0.1214   0.2411
 4NY  H9   H   HCR6  0   0.272   6.9865   0.4484  -1.6457
 4NY  H10  H   HCR6  0   0.267   4.6688   0.6763  -2.3074
 4NY  H11  H   HCR6  0   0.264   3.4233  -0.4453   1.6485
 4NY  H12  H   HCR6  0   0.271   5.7503  -0.7131   2.2978
 4NY  H13  H   H     0   0.271   1.7422  -1.1602   0.5476
 4NY  H14  H   HCR6  0   0.280  -1.8320  -3.8147   2.2660
 4NY  H15  H   HCR6  0   0.290  -4.3166  -1.3975  -0.2704
 4NY  H16  H   HCR5  0   0.309  -0.4292   1.1501  -1.9703
 4NY  H1   H   HCR6  0   0.267  -2.2601   2.7411  -0.3072

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
 4NY  CL   C12  single    1.735  0.020  1.735
 4NY  C21  C22  aromatic  1.385  0.020  1.385
 4NY  C21  C20  aromatic  1.383  0.020  1.383
 4NY  C12  C11  aromatic  1.380  0.020  1.380
 4NY  C12  C13  aromatic  1.400  0.020  1.400
 4NY  F    C20  single    1.342  0.020  1.342
 4NY  C22  C17  aromatic  1.393  0.020  1.393
 4NY  C11  C10  aromatic  1.391  0.020  1.391
 4NY  C20  C19  aromatic  1.380  0.020  1.380
 4NY  C13  C14  aromatic  1.380  0.020  1.380
 4NY  C17  C16  single    1.508  0.020  1.508
 4NY  C17  C18  aromatic  1.389  0.020  1.389
 4NY  C19  C18  aromatic  1.389  0.020  1.389
 4NY  C10  N    aromatic  1.374  0.020  1.374
 4NY  C10  C15  aromatic  1.404  0.020  1.404
 4NY  C16  N    single    1.450  0.020  1.450
 4NY  C14  C15  aromatic  1.395  0.020  1.395
 4NY  N    C9   aromatic  1.349  0.020  1.349
 4NY  C15  C8   aromatic  1.442  0.020  1.442
 4NY  C9   C8   aromatic  1.385  0.020  1.385
 4NY  C8   C7   single    1.427  0.020  1.427
 4NY  C7   C6   double    1.358  0.020  1.358
 4NY  C6   C23  single    1.421  0.020  1.421
 4NY  C6   C4   single    1.472  0.020  1.472
 4NY  C23  N1   triple    1.154  0.020  1.154
 4NY  C3   C4   aromatic  1.397  0.020  1.397
 4NY  C3   C2   aromatic  1.383  0.020  1.383
 4NY  C4   C5   aromatic  1.398  0.020  1.398
 4NY  C2   C1   aromatic  1.393  0.020  1.393
 4NY  C5   C    aromatic  1.381  0.020  1.381
 4NY  C1   C    aromatic  1.394  0.020  1.394
 4NY  C1   C24  single    1.481  0.020  1.481
 4NY  C24  O    double    1.208  0.020  1.208
 4NY  C24  O1   single    1.326  0.020  1.326
 4NY  C22  H1   single    0.930  0.020  1.080
 4NY  C14  H2   single    0.930  0.020  1.080
 4NY  C16  H3   single    0.970  0.020  1.090
 4NY  C16  H4   single    0.970  0.020  1.090
 4NY  C18  H5   single    0.930  0.020  1.080
 4NY  C19  H6   single    0.930  0.020  1.080
 4NY  C21  H7   single    0.930  0.020  1.080
 4NY  O1   H8   single    0.850  0.020  0.980
 4NY  C2   H9   single    0.930  0.020  1.080
 4NY  C3   H10  single    0.930  0.020  1.080
 4NY  C5   H11  single    0.930  0.020  1.080
 4NY  C    H12  single    0.930  0.020  1.080
 4NY  C7   H13  single    0.930  0.020  1.080
 4NY  C13  H14  single    0.930  0.020  1.080
 4NY  C11  H15  single    0.930  0.020  1.080
 4NY  C9   H16  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
 4NY  C1   C24  O1   113.04  3.000
 4NY  O1   C24  O    123.20  3.000
 4NY  C1   C24  O    123.76  3.000
 4NY  N1   C23  C6   180.00  3.000
 4NY  H1   C22  C21  118.71  3.000
 4NY  H1   C22  C17  120.33  3.000
 4NY  C21  C22  C17  120.96  3.000
 4NY  H2   C14  C13  119.43  3.000
 4NY  H2   C14  C15  121.41  3.000
 4NY  C13  C14  C15  119.16  3.000
 4NY  C10  C15  C8   107.03  3.000
 4NY  C8   C15  C14  133.94  3.000
 4NY  C10  C15  C14  119.03  3.000
 4NY  H4   C16  H3   106.72  3.000
 4NY  H4   C16  N    107.07  3.000
 4NY  H3   C16  N    109.04  3.000
 4NY  H4   C16  C17  110.90  3.000
 4NY  H3   C16  C17  110.76  3.000
 4NY  N    C16  C17  112.13  3.000
 4NY  C18  C17  C16  120.72  3.000
 4NY  C18  C17  C22  118.89  3.000
 4NY  C16  C17  C22  120.39  3.000
 4NY  H5   C18  C19  118.92  3.000
 4NY  H5   C18  C17  120.01  3.000
 4NY  C19  C18  C17  121.07  3.000
 4NY  H6   C19  C20  120.65  3.000
 4NY  H6   C19  C18  120.93  3.000
 4NY  C20  C19  C18  118.42  3.000
 4NY  F    C20  C21  118.87  3.000
 4NY  F    C20  C19  119.00  3.000
 4NY  C21  C20  C19  122.13  3.000
 4NY  H7   C21  C20  120.56  3.000
 4NY  H7   C21  C22  120.91  3.000
 4NY  C20  C21  C22  118.53  3.000
 4NY  H8   O1   C24  109.99  3.000
 4NY  C    C1   C2   118.92  3.000
 4NY  C    C1   C24  118.56  3.000
 4NY  C2   C1   C24  122.52  3.000
 4NY  H9   C2   C3   118.66  3.000
 4NY  H9   C2   C1   120.99  3.000
 4NY  C3   C2   C1   120.35  3.000
 4NY  H10  C3   C4   120.32  3.000
 4NY  H10  C3   C2   118.66  3.000
 4NY  C4   C3   C2   121.02  3.000
 4NY  C6   C4   C5   121.06  3.000
 4NY  C5   C4   C3   118.28  3.000
 4NY  C6   C4   C3   120.67  3.000
 4NY  H11  C5   C    118.77  3.000
 4NY  H11  C5   C4   120.45  3.000
 4NY  C    C5   C4   120.76  3.000
 4NY  H12  C    C5   119.28  3.000
 4NY  H12  C    C1   120.04  3.000
 4NY  C5   C    C1   120.67  3.000
 4NY  C7   C6   C4   123.15  3.000
 4NY  C4   C6   C23  116.55  3.000
 4NY  C7   C6   C23  120.30  3.000
 4NY  H13  C7   C8   113.88  3.000
 4NY  H13  C7   C6   115.34  3.000
 4NY  C8   C7   C6   130.78  3.000
 4NY  C9   C8   C7   130.74  3.000
 4NY  C7   C8   C15  123.77  3.000
 4NY  C9   C8   C15  105.49  3.000
 4NY  H14  C13  C12  119.76  3.000
 4NY  H14  C13  C14  120.10  3.000
 4NY  C12  C13  C14  120.14  3.000
 4NY  C11  C12  CL   118.86  3.000
 4NY  C11  C12  C13  122.59  3.000
 4NY  CL   C12  C13  118.55  3.000
 4NY  H15  C11  C10  122.60  3.000
 4NY  H15  C11  C12  121.19  3.000
 4NY  C10  C11  C12  116.21  3.000
 4NY  N    C10  C11  129.46  3.000
 4NY  N    C10  C15  107.67  3.000
 4NY  C11  C10  C15  122.87  3.000
 4NY  C9   N    C10  109.41  3.000
 4NY  C9   N    C16  125.18  3.000
 4NY  C10  N    C16  125.30  3.000
 4NY  H16  C9   N    119.39  3.000
 4NY  H16  C9   C8   130.22  3.000
 4NY  N    C9   C8   110.39  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
 4NY  CONST_01  C19  C20  C21  C22     0.00   0.0  0
 4NY  CONST_02  C19  C18  C17  C22     0.00   0.0  0
 4NY  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 4NY  CONST_04  C11  C10  C15  C14     0.00   0.0  0
 4NY  CONST_05  N    C10  C15  C14   180.00   0.0  0
 4NY  CONST_06  C9   C8   C15  C14   180.00   0.0  0
 4NY  CONST_07  C12  C11  C10  C15     0.00   0.0  0
 4NY  CONST_08  C9   N    C10  C15     0.00   0.0  0
 4NY  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 4NY  CONST_10  N    C9   C8   C15     0.00   0.0  0
 4NY  CONST_11  C20  C21  C22  C17     0.00   0.0  0
 4NY  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 4NY  CONST_13  C21  C22  C17  C18     0.00   0.0  0
 4NY  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 4NY  CONST_15  C4   C3   C2   C1      0.00   0.0  0
 4NY  CONST_16  C4   C5   C    C1      0.00   0.0  0
 4NY  CONST_17  C5   C4   C3   C2      0.00   0.0  0
 4NY  CONST_18  C5   C    C1   C2      0.00   0.0  0
 4NY  CONST_19  C    C5   C4   C3      0.00   0.0  0
 4NY  CONST_20  C    C1   C2   C3      0.00   0.0  0
 4NY  CONST_21  C11  C10  C15  C8    180.00   0.0  0
 4NY  CONST_22  N    C10  C15  C8      0.00   0.0  0
 4NY  CONST_23  C13  C14  C15  C8    180.00   0.0  0
 4NY  CONST_24  C10  N    C9   C8      0.00   0.0  0
 4NY  CONST_25  C10  C11  C12  C13     0.00   0.0  0
 4NY  CONST_26  C10  C15  C14  C13     0.00   0.0  0
 4NY  CONST_27  N    C10  C11  C12   180.00   0.0  0
 4NY  CONST_28  C9   N    C10  C11   180.00   0.0  0
 4NY  CONST_29  C9   C8   C15  C10     0.00   0.0  0
 4NY  CONST_30  C3   C2   C1   C24   180.00   0.0  0
 4NY  CONST_31  C5   C    C1   C24   180.00   0.0  0
 4NY  CONST_32  F    C20  C21  C22   180.00   0.0  0
 4NY  CONST_33  CL   C12  C13  C14   180.00   0.0  0
 4NY  CONST_34  C7   C8   C15  C14     0.00   0.0  0
 4NY  CONST_35  C16  N    C10  C15   180.00   0.0  0
 4NY  CONST_36  C21  C22  C17  C16   180.00   0.0  0
 4NY  CONST_37  C19  C18  C17  C16   180.00   0.0  0
 4NY  CONST_38  C11  C10  N    C16     0.00   0.0  0
 4NY  CONST_39  C8   C9   N    C16   180.00   0.0  0
 4NY  CONST_40  F    C20  C19  C18   180.00   0.0  0
 4NY  CONST_41  C6   C4   C3   C2    180.00   0.0  0
 4NY  CONST_42  C6   C4   C5   C     180.00   0.0  0
 4NY  CONST_43  C10  C15  C8   C7    180.00   0.0  0
 4NY  CONST_44  N    C9   C8   C7    180.00   0.0  0
 4NY  CONST_45  C10  C11  C12  CL    180.00   0.0  0
 4NY  CONST_46  H5   C18  C17  C22   180.00   0.0  0
 4NY  CONST_47  H15  C11  C10  C15   180.00   0.0  0
 4NY  CONST_48  H14  C13  C14  C15   180.00   0.0  0
 4NY  CONST_49  H16  C9   C8   C15   180.00   0.0  0
 4NY  CONST_50  H7   C21  C22  C17   180.00   0.0  0
 4NY  CONST_51  H6   C19  C18  C17   180.00   0.0  0
 4NY  CONST_52  H1   C22  C17  C18   180.00   0.0  0
 4NY  CONST_53  H10  C3   C2   C1    180.00   0.0  0
 4NY  CONST_54  H11  C5   C    C1    180.00   0.0  0
 4NY  CONST_55  H12  C    C1   C2    180.00   0.0  0
 4NY  CONST_56  H9   C2   C3   C4    180.00   0.0  0
 4NY  CONST_57  H2   C14  C15  C8      0.00   0.0  0
 4NY  CONST_58  H8   O1   C24  C1    180.00   0.0  0
 4NY  Var_01    N    C16  C17  C22    57.32  30.0  2
 4NY  Var_02    C10  N    C16  C17    69.61  30.0  2
 4NY  Var_03    C8   C7   C6   C4    178.48   0.0  2
 4NY  Var_04    C3   C4   C6   C23   -25.42  30.0  2
 4NY  Var_05    C6   C7   C8   C15   175.56  30.0  2
 4NY  Var_06    C2   C1   C24  O    -178.49  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
 4NY  plan-1  C22  0.020
 4NY  plan-1  C16  0.020
 4NY  plan-1  C17  0.020
 4NY  plan-1  C18  0.020
 4NY  plan-1  C19  0.020
 4NY  plan-1  C20  0.020
 4NY  plan-1  C21  0.020
 4NY  plan-1  F    0.020
 4NY  plan-1  H5   0.020
 4NY  plan-1  H6   0.020
 4NY  plan-1  H7   0.020
 4NY  plan-1  H1   0.020
 4NY  plan-2  C24  0.020
 4NY  plan-2  C1   0.020
 4NY  plan-2  C2   0.020
 4NY  plan-2  C3   0.020
 4NY  plan-2  C4   0.020
 4NY  plan-2  C5   0.020
 4NY  plan-2  C    0.020
 4NY  plan-2  C6   0.020
 4NY  plan-2  H9   0.020
 4NY  plan-2  H10  0.020
 4NY  plan-2  H11  0.020
 4NY  plan-2  H12  0.020
 4NY  plan-3  C14  0.020
 4NY  plan-3  C15  0.020
 4NY  plan-3  C16  0.020
 4NY  plan-3  C7   0.020
 4NY  plan-3  C8   0.020
 4NY  plan-3  C13  0.020
 4NY  plan-3  C12  0.020
 4NY  plan-3  CL   0.020
 4NY  plan-3  C11  0.020
 4NY  plan-3  C10  0.020
 4NY  plan-3  N    0.020
 4NY  plan-3  C9   0.020
 4NY  plan-3  H2   0.020
 4NY  plan-3  H14  0.020
 4NY  plan-3  H15  0.020
 4NY  plan-3  H16  0.020
 4NY  plan-4  C24  0.020
 4NY  plan-4  O    0.020
 4NY  plan-4  O1   0.020
 4NY  plan-4  C1   0.020
 4NY  plan-4  H8   0.020
 4NY  plan-5  C23  0.020
 4NY  plan-5  C4   0.020
 4NY  plan-5  C6   0.020
 4NY  plan-5  C7   0.020
 4NY  plan-5  C8   0.020
 4NY  plan-5  H13  0.020

