# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:03:47 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-ethyl-1-(2-fluoro-5-nitrobenzyl)-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc2n(Cc3cc(ccc3F)[N+]([O-])=O)c(C(O)=O)c(C4=CC=CNC4=O)c2c1
#
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
 HI4  HI4  '5-ethyl-1-(2-fluoro-5-nitrobenzyl)-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid'  ligand  49  32  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HI4
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
 HI4  C1    C  CR6    0  -0.081  -2.5429   0.6799   0.6748
 HI4  N1    N  NR5    0  -0.583  -0.1257   0.6234   1.1469
 HI4  O1    O  OC    -1  -0.592  -0.9981  -2.0344   1.9861
 HI4  C2    C  CR16   0  -0.300  -3.4449  -0.3664   0.7878
 HI4  N2    N  NR16   0  -0.657   3.6675  -3.4602  -0.2707
 HI4  O2    O  O      0  -0.493   2.5638  -2.6952   1.5465
 HI4  C3    C  CR6    0   0.260  -4.4518  -0.5226  -0.1548
 HI4  N3    N  N      1   0.329  -5.3866  -1.6244  -0.0129
 HI4  O3    O  O      0  -0.580  -0.2302  -2.7435   0.0119
 HI4  C4    C  CR16   0  -0.261  -4.5862   0.3423  -1.2312
 HI4  O4    O  O      0  -0.379  -5.2520  -2.3693   0.9294
 HI4  C5    C  CR16   0  -0.401  -3.6923   1.3882  -1.3568
 HI4  O5    O  O     -1  -0.380  -6.2558  -1.7417  -0.8449
 HI4  C6    C  CR6    0   0.568  -2.6981   1.5366  -0.4080
 HI4  C7    C  CR6    0  -0.218   2.4307  -1.4389  -0.4779
 HI4  C8    C  CR16   0  -0.455   2.9665   1.7566  -0.2208
 HI4  C9    C  CR6    0   0.118   2.9721   3.1189   0.0169
 HI4  C10   C  CR56   0   0.087   1.8689   0.9841   0.1761
 HI4  C11   C  CR56   0   0.337   0.7844   1.6005   0.8286
 HI4  C12   C  CR5    0   0.162   0.3456  -0.5930   0.7023
 HI4  C13   C  CR5    0  -0.007   1.5641  -0.4113   0.0963
 HI4  C14   C  CR16   0  -0.330   1.8679   3.7082   0.6644
 HI4  C15   C  CR16   0  -0.291   0.7734   2.9729   1.0736
 HI4  C16   C  C      0   0.403  -0.3670  -1.9070   0.9183
 HI4  C17   C  CH2    0  -0.395  -1.4443   0.8735   1.6901
 HI4  C18   C  CR6    0   0.509   2.8536  -2.5444   0.3641
 HI4  C19   C  CR16   0   0.035   4.1115  -3.3755  -1.5472
 HI4  C20   C  CR16   0  -0.385   3.7534  -2.3248  -2.3225
 HI4  C21   C  CR16   0  -0.187   2.8948  -1.3497  -1.7588
 HI4  C22   C  CH2    0  -0.501   4.1158   3.9826  -0.4441
 HI4  C23   C  CH3    0  -0.653   3.8247   4.6667  -1.7787
 HI4  H2    H  HCR6   0   0.303  -3.3382  -1.0601   1.6081
 HI4  HN2   H  HNR6   0   0.417   3.9778  -4.2419   0.2902
 HI4  H4    H  HCR6   0   0.308  -5.3685   0.2157  -1.9645
 HI4  H5    H  HCR6   0   0.300  -3.7678   2.0857  -2.1799
 HI4  F1    F  F      0  -0.290  -1.8503   2.5570  -0.5398
 HI4  H8    H  HCR6   0   0.230   3.8138   1.2875  -0.7095
 HI4  H14   H  HCR6   0   0.238   1.8805   4.7756   0.8527
 HI4  H15   H  HCR6   0   0.257  -0.0509   3.4601   1.5779
 HI4  H17   H  HCH2   0   0.289  -1.4617   1.8928   2.0741
 HI4  H17A  H  HCH2   0   0.294  -1.6197   0.2127   2.5336
 HI4  H19   H  HCR6   0   0.304   4.7503  -4.1797  -1.8812
 HI4  H20   H  HCR6   0   0.270   4.1029  -2.2468  -3.3404
 HI4  H21   H  HCR6   0   0.262   2.5806  -0.5142  -2.3733
 HI4  H22   H  HCH2   0   0.232   4.3305   4.7439   0.3105
 HI4  H22A  H  HCH2   0   0.234   5.0194   3.3759  -0.5377
 HI4  H23   H  HCH3   0   0.226   4.6632   5.2906  -2.0915
 HI4  H23A  H  HCH3   0   0.222   3.6431   3.9305  -2.5631
 HI4  H23B  H  HCH3   0   0.222   2.9425   5.3049  -1.7105

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
 HI4  C1   C2    aromatic  1.386  0.020  1.386
 HI4  C1   C6    aromatic  1.389  0.020  1.389
 HI4  C1   C17   single    1.508  0.020  1.508
 HI4  N1   C11   aromatic  1.373  0.020  1.373
 HI4  O1   C16   deloc     1.247  0.020  1.247
 HI4  C2   C3    aromatic  1.388  0.020  1.388
 HI4  C2   H2    single    0.930  0.020  1.080
 HI4  N2   C19   single    1.354  0.020  1.354
 HI4  N2   HN2   single    0.860  0.020  1.020
 HI4  O2   C18   double    1.227  0.020  1.227
 HI4  C3   C4    aromatic  1.387  0.020  1.387
 HI4  N3   C3    single    1.452  0.020  1.452
 HI4  O3   C16   deloc     1.241  0.020  1.241
 HI4  C4   C5    aromatic  1.382  0.020  1.382
 HI4  C4   H4    single    0.930  0.020  1.080
 HI4  O4   N3    double    1.209  0.020  1.209
 HI4  C5   C6    aromatic  1.382  0.020  1.382
 HI4  C5   H5    single    0.930  0.020  1.080
 HI4  O5   N3    single    1.209  0.020  1.209
 HI4  C6   F1    single    1.333  0.020  1.333
 HI4  C7   C21   double    1.365  0.020  1.365
 HI4  C8   C9    aromatic  1.383  0.020  1.383
 HI4  C8   H8    single    0.930  0.020  1.080
 HI4  C9   C22   single    1.505  0.020  1.505
 HI4  C10  C8    aromatic  1.400  0.020  1.400
 HI4  C11  C10   aromatic  1.408  0.020  1.408
 HI4  C11  C15   aromatic  1.394  0.020  1.394
 HI4  C12  N1    aromatic  1.378  0.020  1.378
 HI4  C12  C13   aromatic  1.373  0.020  1.373
 HI4  C13  C7    single    1.462  0.020  1.462
 HI4  C13  C10   aromatic  1.431  0.020  1.431
 HI4  C14  C9    aromatic  1.409  0.020  1.409
 HI4  C14  H14   single    0.930  0.020  1.080
 HI4  C15  C14   aromatic  1.381  0.020  1.381
 HI4  C15  H15   single    0.930  0.020  1.080
 HI4  C16  C12   single    1.510  0.020  1.510
 HI4  C17  N1    single    1.448  0.020  1.448
 HI4  C17  H17   single    0.970  0.020  1.090
 HI4  C17  H17A  single    0.970  0.020  1.090
 HI4  C18  N2    single    1.380  0.020  1.380
 HI4  C18  C7    single    1.453  0.020  1.453
 HI4  C19  C20   double    1.354  0.020  1.354
 HI4  C19  H19   single    0.930  0.020  1.080
 HI4  C20  H20   single    0.930  0.020  1.080
 HI4  C21  C20   single    1.416  0.020  1.416
 HI4  C21  H21   single    0.930  0.020  1.080
 HI4  C22  C23   single    1.528  0.020  1.528
 HI4  C22  H22   single    0.970  0.020  1.090
 HI4  C22  H22A  single    0.970  0.020  1.090
 HI4  C23  H23   single    0.970  0.020  1.090
 HI4  C23  H23A  single    0.970  0.020  1.090
 HI4  C23  H23B  single    0.970  0.020  1.090

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
 HI4  C17   C1   C6    121.79  3.000
 HI4  C17   C1   C2    121.07  3.000
 HI4  C6    C1   C2    117.15  3.000
 HI4  C17   N1   C12   125.80  3.000
 HI4  C17   N1   C11   124.60  3.000
 HI4  C12   N1   C11   109.07  3.000
 HI4  H2    C2   C3    121.02  3.000
 HI4  H2    C2   C1    118.86  3.000
 HI4  C3    C2   C1    120.11  3.000
 HI4  HN2   N2   C19   118.08  3.000
 HI4  HN2   N2   C18   116.04  3.000
 HI4  C19   N2   C18   125.84  3.000
 HI4  C4    C3   N3    119.11  3.000
 HI4  N3    C3   C2    119.08  3.000
 HI4  C4    C3   C2    121.81  3.000
 HI4  O5    N3   O4    123.84  3.000
 HI4  O5    N3   C3    117.99  3.000
 HI4  O4    N3   C3    118.17  3.000
 HI4  H4    C4   C5    119.72  3.000
 HI4  H4    C4   C3    121.61  3.000
 HI4  C5    C4   C3    118.67  3.000
 HI4  H5    C5   C6    120.22  3.000
 HI4  H5    C5   C4    120.81  3.000
 HI4  C6    C5   C4    118.96  3.000
 HI4  F1    C6   C5    118.14  3.000
 HI4  F1    C6   C1    118.55  3.000
 HI4  C5    C6   C1    123.30  3.000
 HI4  C21   C7   C18   119.64  3.000
 HI4  C18   C7   C13   118.68  3.000
 HI4  C21   C7   C13   121.61  3.000
 HI4  H8    C8   C10   120.11  3.000
 HI4  C10   C8   C9    119.87  3.000
 HI4  H8    C8   C9    120.01  3.000
 HI4  C22   C9   C14   119.74  3.000
 HI4  C14   C9   C8    119.19  3.000
 HI4  C22   C9   C8    121.04  3.000
 HI4  C13   C10  C11   106.79  3.000
 HI4  C13   C10  C8    133.60  3.000
 HI4  C11   C10  C8    119.60  3.000
 HI4  C15   C11  C10   121.24  3.000
 HI4  C15   C11  N1    130.90  3.000
 HI4  C10   C11  N1    107.85  3.000
 HI4  C16   C12  C13   126.65  3.000
 HI4  C16   C12  N1    124.08  3.000
 HI4  C13   C12  N1    109.22  3.000
 HI4  C12   C13  C10   107.07  3.000
 HI4  C10   C13  C7    125.54  3.000
 HI4  C12   C13  C7    127.34  3.000
 HI4  H14   C14  C15   118.83  3.000
 HI4  C15   C14  C9    122.32  3.000
 HI4  H14   C14  C9    118.85  3.000
 HI4  H15   C15  C14   120.14  3.000
 HI4  H15   C15  C11   122.08  3.000
 HI4  C14   C15  C11   117.77  3.000
 HI4  C12   C16  O3    115.47  3.000
 HI4  C12   C16  O1    116.75  3.000
 HI4  O3    C16  O1    127.77  3.000
 HI4  H17A  C17  H17   107.04  3.000
 HI4  H17A  C17  N1    109.48  3.000
 HI4  H17   C17  N1    107.96  3.000
 HI4  H17A  C17  C1    109.09  3.000
 HI4  H17   C17  C1    110.23  3.000
 HI4  N1    C17  C1    112.87  3.000
 HI4  C7    C18  O2    125.70  3.000
 HI4  C7    C18  N2    114.22  3.000
 HI4  O2    C18  N2    120.07  3.000
 HI4  H19   C19  C20   123.86  3.000
 HI4  H19   C19  N2    116.04  3.000
 HI4  C20   C19  N2    120.11  3.000
 HI4  H20   C20  C21   121.47  3.000
 HI4  C21   C20  C19   117.82  3.000
 HI4  H20   C20  C19   120.70  3.000
 HI4  H21   C21  C20   118.74  3.000
 HI4  H21   C21  C7    118.94  3.000
 HI4  C20   C21  C7    122.31  3.000
 HI4  H22A  C22  H22   106.47  3.000
 HI4  H22A  C22  C23   109.35  3.000
 HI4  H22   C22  C23   109.18  3.000
 HI4  H22A  C22  C9    109.64  3.000
 HI4  H22   C22  C9    109.72  3.000
 HI4  C23   C22  C9    112.31  3.000
 HI4  H23B  C23  H23A  107.76  3.000
 HI4  H23B  C23  H23   107.74  3.000
 HI4  H23A  C23  H23   107.92  3.000
 HI4  H23B  C23  C22   111.19  3.000
 HI4  H23A  C23  C22   110.96  3.000
 HI4  H23   C23  C22   111.11  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
 HI4  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 HI4  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 HI4  CONST_03  C8   C10  C11  N1   180.00   0.0  0
 HI4  CONST_04  C13  C10  C11  N1     0.00   0.0  0
 HI4  CONST_05  C14  C15  C11  N1   180.00   0.0  0
 HI4  CONST_06  C10  C13  C12  N1     0.00   0.0  0
 HI4  CONST_07  C5   C6   C1   C2     0.00   0.0  0
 HI4  CONST_08  C5   C4   C3   C2     0.00   0.0  0
 HI4  CONST_09  C6   C1   C2   C3     0.00   0.0  0
 HI4  CONST_10  C6   C5   C4   C3     0.00   0.0  0
 HI4  CONST_11  C15  C14  C9   C8     0.00   0.0  0
 HI4  CONST_12  C15  C11  C10  C8     0.00   0.0  0
 HI4  CONST_13  C12  C13  C10  C8   180.00   0.0  0
 HI4  CONST_14  C11  C10  C8   C9     0.00   0.0  0
 HI4  CONST_15  C13  C10  C8   C9   180.00   0.0  0
 HI4  CONST_16  C11  C15  C14  C9     0.00   0.0  0
 HI4  CONST_17  C14  C9   C8   C10    0.00   0.0  0
 HI4  CONST_18  C12  N1   C11  C10    0.00   0.0  0
 HI4  CONST_19  C14  C15  C11  C10    0.00   0.0  0
 HI4  CONST_20  C13  C12  N1   C11    0.00   0.0  0
 HI4  CONST_21  C12  C13  C10  C11    0.00   0.0  0
 HI4  CONST_22  C15  C11  N1   C12  180.00   0.0  0
 HI4  CONST_23  C15  C11  C10  C13  180.00   0.0  0
 HI4  CONST_24  C7   C13  C12  N1   180.00   0.0  0
 HI4  CONST_25  C8   C10  C13  C7     0.00   0.0  0
 HI4  CONST_26  C11  C10  C13  C7   180.00   0.0  0
 HI4  CONST_27  C19  N2   C18  C7     0.00   0.0  0
 HI4  CONST_28  N3   C3   C2   C1   180.00   0.0  0
 HI4  CONST_29  F1   C6   C1   C2   180.00   0.0  0
 HI4  CONST_30  C17  C1   C2   C3   180.00   0.0  0
 HI4  CONST_31  C5   C4   C3   N3   180.00   0.0  0
 HI4  CONST_32  F1   C6   C5   C4   180.00   0.0  0
 HI4  CONST_33  C17  C1   C6   C5   180.00   0.0  0
 HI4  CONST_34  C16  C12  C13  C7     0.00   0.0  0
 HI4  CONST_35  C22  C9   C8   C10  180.00   0.0  0
 HI4  CONST_36  C17  N1   C11  C10  180.00   0.0  0
 HI4  CONST_37  C16  C12  C13  C10  180.00   0.0  0
 HI4  CONST_38  C16  C12  N1   C11  180.00   0.0  0
 HI4  CONST_39  C17  N1   C12  C13  180.00   0.0  0
 HI4  CONST_40  C17  N1   C11  C15    0.00   0.0  0
 HI4  CONST_41  C22  C9   C14  C15  180.00   0.0  0
 HI4  CONST_42  C19  N2   C18  O2   180.00   0.0  0
 HI4  CONST_43  H5   C5   C6   C1   180.00   0.0  0
 HI4  CONST_44  H15  C15  C11  N1     0.00   0.0  0
 HI4  CONST_45  H4   C4   C3   C2   180.00   0.0  0
 HI4  CONST_46  H2   C2   C3   C4   180.00   0.0  0
 HI4  CONST_47  H14  C14  C9   C8   180.00   0.0  0
 HI4  CONST_48  H8   C8   C10  C11  180.00   0.0  0
 HI4  CONST_49  HN2  N2   C18  C7   180.00   0.0  0
 HI4  CONST_50  O4   N3   C3   C2     0.00   0.0  0
 HI4  CONST_51  O5   N3   C3   C2   180.00   0.0  0
 HI4  CONST_52  O4   N3   C3   C4   180.00   0.0  0
 HI4  CONST_53  O5   N3   C3   C4     0.00   0.0  0
 HI4  Var_01    C21  C7   C13  C10  -55.90  30.0  2
 HI4  Var_02    C11  N1   C17  C1   105.09  30.0  2
 HI4  Var_03    C2   C1   C17  N1   111.74  30.0  2
 HI4  Var_04    O1   C16  C12  N1   -34.24  30.0  2
 HI4  Var_05    C23  C22  C9   C8    96.84  30.0  2
 HI4  Var_06    H23  C23  C22  C9   179.72  30.0  3

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
 HI4  plan-1  C1   0.020
 HI4  plan-1  C2   0.020
 HI4  plan-1  C3   0.020
 HI4  plan-1  N3   0.020
 HI4  plan-1  C4   0.020
 HI4  plan-1  C5   0.020
 HI4  plan-1  C6   0.020
 HI4  plan-1  C17  0.020
 HI4  plan-1  H2   0.020
 HI4  plan-1  H4   0.020
 HI4  plan-1  H5   0.020
 HI4  plan-1  F1   0.020
 HI4  plan-2  N2   0.020
 HI4  plan-2  O2   0.020
 HI4  plan-2  C7   0.020
 HI4  plan-2  C13  0.020
 HI4  plan-2  C18  0.020
 HI4  plan-2  C19  0.020
 HI4  plan-2  C20  0.020
 HI4  plan-2  C21  0.020
 HI4  plan-2  HN2  0.020
 HI4  plan-2  H19  0.020
 HI4  plan-2  H20  0.020
 HI4  plan-2  H21  0.020
 HI4  plan-3  N1   0.020
 HI4  plan-3  C7   0.020
 HI4  plan-3  C8   0.020
 HI4  plan-3  C9   0.020
 HI4  plan-3  C10  0.020
 HI4  plan-3  C11  0.020
 HI4  plan-3  C12  0.020
 HI4  plan-3  C13  0.020
 HI4  plan-3  C14  0.020
 HI4  plan-3  C15  0.020
 HI4  plan-3  C16  0.020
 HI4  plan-3  C17  0.020
 HI4  plan-3  C22  0.020
 HI4  plan-3  H8   0.020
 HI4  plan-3  H14  0.020
 HI4  plan-3  H15  0.020
 HI4  plan-4  C3   0.020
 HI4  plan-4  N3   0.020
 HI4  plan-4  O4   0.020
 HI4  plan-4  O5   0.020
 HI4  plan-5  O1   0.020
 HI4  plan-5  O3   0.020
 HI4  plan-5  C12  0.020
 HI4  plan-5  C16  0.020

