# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 10:55:30 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  46  31  .  2021-08-04  2022-09-22
;
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   0.397   8.0069  -0.1875   0.8728
 4NY  C23  C   CSP    0  -0.016   2.2064   0.9880  -2.0104
 4NY  C22  C   C1     0  -0.263  -3.2963   2.5646  -0.1707
 4NY  C14  C   CR16   0  -0.381  -0.7761  -2.3641   1.0665
 4NY  C15  C   CR56   0   0.059  -0.8987  -1.3194   0.1496
 4NY  C16  C   CH2    0  -0.418  -3.1063   0.7408  -1.8961
 4NY  C17  C   C      0   0.111  -3.9141   1.5800  -0.9380
 4NY  C18  C   C1     0  -0.296  -5.2837   1.3885  -0.8066
 4NY  C19  C   C1     0  -0.398  -6.0347   2.1597   0.0715
 4NY  C20  C   C      0   0.520  -5.3880   3.1236   0.8170
 4NY  C21  C   C1     0  -0.395  -4.0263   3.3428   0.7129
 4NY  O    O   O      0  -0.592   8.2003  -0.3427   2.0936
 4NY  O1   O   OC    -1  -0.592   8.8741  -0.1164  -0.0188
 4NY  C1   C   C      0  -0.109   6.5564  -0.0767   0.4225
 4NY  C2   C   C1     0  -0.272   6.2337   0.1386  -0.9143
 4NY  C3   C   C1     0  -0.296   4.9152   0.2417  -1.3269
 4NY  C4   C   C      0   0.126   3.8687   0.1228  -0.4105
 4NY  C5   C   C1     0  -0.312   4.1906  -0.0787   0.9336
 4NY  C    C   C1     0  -0.273   5.5111  -0.1805   1.3374
 4NY  C6   C   C      0   0.000   2.4635   0.2051  -0.8506
 4NY  N1   N   NS     0  -0.257   2.0112   1.6262  -2.9525
 4NY  C7   C   C1     0  -0.324   1.4478  -0.4326  -0.2190
 4NY  C8   C   CR5    0   0.027   0.0406  -0.4265  -0.4804
 4NY  C13  C   CR16   0  -0.217  -1.9086  -3.0434   1.4689
 4NY  C12  C   CR6    0  -0.065  -3.1616  -2.6863   0.9555
 4NY  CL   CL  CL     0  -0.129  -4.5575  -3.5696   1.4867
 4NY  C11  C   CR16   0  -0.249  -3.3280  -1.6628   0.0456
 4NY  C10  C   CR56   0   0.390  -2.1729  -0.9920  -0.3442
 4NY  N    N   NR5    0  -0.522  -2.0231   0.0450  -1.2313
 4NY  C9   C   CR15   0  -0.039  -0.7153   0.3821  -1.3081
 4NY  F    F   F      0  -0.314  -6.1019   3.8746   1.6700
 4NY  H2   H   HCR6   0   0.261   0.1877  -2.6526   1.4663
 4NY  H3   H   HCH2   0   0.295  -3.7422   0.0125  -2.4016
 4NY  H4   H   HCH2   0   0.301  -2.6602   1.3600  -2.6746
 4NY  H5   H   H      0   0.270  -5.7833   0.6278  -1.3940
 4NY  H6   H   H      0   0.283  -7.1007   2.0058   0.1740
 4NY  H7   H   H      0   0.283  -3.5455   4.1096   1.3058
 4NY  H9   H   H      0   0.248   7.0256   0.2229  -1.6463
 4NY  H10  H   H      0   0.251   4.7041   0.4010  -2.3779
 4NY  H11  H   H      0   0.251   3.4068  -0.1308   1.6790
 4NY  H12  H   H      0   0.247   5.7335  -0.3297   2.3856
 4NY  H13  H   H      0   0.269   1.7436  -1.0612   0.6142
 4NY  H14  H   HCR6   0   0.278  -1.8310  -3.8542   2.1798
 4NY  H15  H   HCR6   0   0.287  -4.3066  -1.4061  -0.3363
 4NY  H16  H   HCR5   0   0.307  -0.4153   1.1984  -1.9451
 4NY  H1   H   H      0   0.267  -2.2300   2.7362  -0.2562

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  1.373  0.020  1.373
 4NY  C10  C15  aromatic  1.405  0.020  1.405
 4NY  C16  N    single    1.449  0.020  1.449
 4NY  C14  C15  aromatic  1.395  0.020  1.395
 4NY  N    C9   aromatic  1.353  0.020  1.353
 4NY  C15  C8   aromatic  1.441  0.020  1.441
 4NY  C9   C8   aromatic  1.382  0.020  1.382
 4NY  C8   C7   single    1.431  0.020  1.431
 4NY  C7   C6   double    1.356  0.020  1.356
 4NY  C6   C23  single    1.423  0.020  1.423
 4NY  C6   C4   single    1.475  0.020  1.475
 4NY  C23  N1   triple    1.155  0.020  1.155
 4NY  C3   C4   aromatic  1.396  0.020  1.396
 4NY  C3   C2   aromatic  1.385  0.020  1.385
 4NY  C4   C5   aromatic  1.397  0.020  1.397
 4NY  C2   C1   aromatic  1.392  0.020  1.392
 4NY  C5   C    aromatic  1.385  0.020  1.385
 4NY  C1   C    aromatic  1.393  0.020  1.393
 4NY  C1   C24  single    1.523  0.020  1.523
 4NY  C24  O    deloc     1.246  0.020  1.246
 4NY  C24  O1   deloc     1.246  0.020  1.246
 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  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   116.57  3.000
 4NY  O1   C24  O    126.90  3.000
 4NY  C1   C24  O    116.53  3.000
 4NY  N1   C23  C6   180.00  3.000
 4NY  H1   C22  C21  118.69  3.000
 4NY  H1   C22  C17  120.33  3.000
 4NY  C21  C22  C17  120.98  3.000
 4NY  H2   C14  C13  119.45  3.000
 4NY  H2   C14  C15  121.36  3.000
 4NY  C13  C14  C15  119.20  3.000
 4NY  C10  C15  C8   107.04  3.000
 4NY  C8   C15  C14  133.94  3.000
 4NY  C10  C15  C14  119.02  3.000
 4NY  H4   C16  H3   106.67  3.000
 4NY  H4   C16  N    107.13  3.000
 4NY  H3   C16  N    109.13  3.000
 4NY  H4   C16  C17  110.90  3.000
 4NY  H3   C16  C17  110.71  3.000
 4NY  N    C16  C17  112.09  3.000
 4NY  C18  C17  C16  120.76  3.000
 4NY  C18  C17  C22  118.86  3.000
 4NY  C16  C17  C22  120.38  3.000
 4NY  H5   C18  C19  118.90  3.000
 4NY  H5   C18  C17  120.02  3.000
 4NY  C19  C18  C17  121.09  3.000
 4NY  H6   C19  C20  120.67  3.000
 4NY  H6   C19  C18  120.90  3.000
 4NY  C20  C19  C18  118.43  3.000
 4NY  F    C20  C21  118.87  3.000
 4NY  F    C20  C19  119.02  3.000
 4NY  C21  C20  C19  122.11  3.000
 4NY  H7   C21  C20  120.57  3.000
 4NY  H7   C21  C22  120.89  3.000
 4NY  C20  C21  C22  118.54  3.000
 4NY  C    C1   C2   117.92  3.000
 4NY  C    C1   C24  121.01  3.000
 4NY  C2   C1   C24  121.07  3.000
 4NY  H9   C2   C3   119.30  3.000
 4NY  H9   C2   C1   119.49  3.000
 4NY  C3   C2   C1   121.21  3.000
 4NY  H10  C3   C4   120.21  3.000
 4NY  H10  C3   C2   119.02  3.000
 4NY  C4   C3   C2   120.76  3.000
 4NY  C6   C4   C5   120.99  3.000
 4NY  C5   C4   C3   118.12  3.000
 4NY  C6   C4   C3   120.90  3.000
 4NY  H11  C5   C    119.08  3.000
 4NY  H11  C5   C4   120.17  3.000
 4NY  C    C5   C4   120.73  3.000
 4NY  H12  C    C5   119.26  3.000
 4NY  H12  C    C1   119.49  3.000
 4NY  C5   C    C1   121.24  3.000
 4NY  C7   C6   C4   123.27  3.000
 4NY  C4   C6   C23  116.50  3.000
 4NY  C7   C6   C23  120.22  3.000
 4NY  H13  C7   C8   114.26  3.000
 4NY  H13  C7   C6   115.23  3.000
 4NY  C8   C7   C6   130.51  3.000
 4NY  C9   C8   C7   130.51  3.000
 4NY  C7   C8   C15  123.94  3.000
 4NY  C9   C8   C15  105.53  3.000
 4NY  H14  C13  C12  119.77  3.000
 4NY  H14  C13  C14  120.12  3.000
 4NY  C12  C13  C14  120.11  3.000
 4NY  C11  C12  CL   118.85  3.000
 4NY  C11  C12  C13  122.61  3.000
 4NY  CL   C12  C13  118.54  3.000
 4NY  H15  C11  C10  122.53  3.000
 4NY  H15  C11  C12  121.21  3.000
 4NY  C10  C11  C12  116.25  3.000
 4NY  N    C10  C11  129.48  3.000
 4NY  N    C10  C15  107.70  3.000
 4NY  C11  C10  C15  122.81  3.000
 4NY  C9   N    C10  109.30  3.000
 4NY  C9   N    C16  125.24  3.000
 4NY  C10  N    C16  125.28  3.000
 4NY  H16  C9   N    119.43  3.000
 4NY  H16  C9   C8   130.14  3.000
 4NY  N    C9   C8   110.42  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  Var_01    N    C16  C17  C22   57.02  30.0  2
 4NY  Var_02    C10  N    C16  C17   69.42  30.0  2
 4NY  Var_03    C8   C7   C6   C4   177.67   0.0  2
 4NY  Var_04    C3   C4   C6   C23  -28.38  30.0  2
 4NY  Var_05    C6   C7   C8   C15  169.92  30.0  2
 4NY  Var_06    C2   C1   C24  O    178.05  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-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

