# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 07:31:47 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Oc1cc(ccc1c2c([nH]c3cc(F)c(F)cc23)C(N)=O)N4CCNCC4
#
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
 HZE  HZE  5,6-bis(fluoranyl)-3-(4-piperazin-1-yl-2-propan-2-yloxy-phenyl)-1~{H}-indole-2-carboxamide  ligand  54  30  .  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_HZE
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
 HZE  C1   C  CR6   0   0.400   3.7895  -2.4246  -1.1667
 HZE  C2   C  CR6   0   0.378   4.9677  -1.6666  -1.0917
 HZE  C3   C  CR16  0  -0.457   4.9493  -0.3213  -0.8326
 HZE  C8   C  CR5   0   0.186   1.9938   1.6552  -0.3020
 HZE  C9   C  CR5   0   0.058   1.4139   0.4315  -0.5267
 HZE  C10  C  C     0   0.462   1.3254   2.9521  -0.0504
 HZE  C13  C  CR6   0  -0.104  -0.0064   0.0752  -0.4867
 HZE  C16  C  CR16  0  -0.293  -0.5884  -0.6459  -1.5183
 HZE  C19  C  CR16  0  -0.489  -2.1548   0.0243   0.6385
 HZE  C20  C  CR6   0   0.396  -0.8220   0.4046   0.6129
 HZE  C22  C  CH2   0  -0.300  -4.5975  -1.9094  -1.4057
 HZE  C30  C  CH3   0  -0.681  -1.7639   2.7926   2.3285
 HZE  C4   C  CR16  0  -0.530   2.5555  -1.8577  -0.9973
 HZE  C5   C  CR56  0   0.058   2.4957  -0.4800  -0.7477
 HZE  C6   C  CR56  0   0.353   3.6927   0.2585  -0.6528
 HZE  N7   N  NR15  0  -0.741   3.3601   1.5430  -0.3610
 HZE  N11  N  NH2   0  -0.814   1.9893   3.7837   0.7722
 HZE  O12  O  O     0  -0.469   0.2692   3.2326  -0.5919
 HZE  F14  F  F     0  -0.316   3.9075  -3.7392  -1.4094
 HZE  F15  F  F     0  -0.311   6.1330  -2.2999  -1.2755
 HZE  C17  C  CR16  0  -0.388  -1.9255  -1.0189  -1.5115
 HZE  C18  C  CR6   0   0.389  -2.7373  -0.6871  -0.4239
 HZE  N21  N  NT    0  -0.521  -4.0757  -1.0626  -0.3485
 HZE  C23  C  CH2   0  -0.299  -5.9299  -2.5124  -0.9991
 HZE  N24  N  NH1   0  -0.598  -6.8651  -1.4605  -0.6577
 HZE  C25  C  CH2   0  -0.299  -6.3579  -0.6952   0.4628
 HZE  C26  C  CH2   0  -0.295  -5.0376  -0.0538   0.0825
 HZE  O27  O  O2    0  -0.482  -0.2081   1.0522   1.6169
 HZE  C28  C  CH1   0   0.000  -0.9342   1.5828   2.7259
 HZE  C29  C  CH3   0  -0.664   0.1081   1.9346   3.7698
 HZE  H1   H  HCR6  0   0.297   5.8675   0.2473  -0.7649
 HZE  H2   H  HCR6  0   0.249   0.0127  -0.9012  -2.3830
 HZE  H3   H  HCR6  0   0.277  -2.7543   0.2434   1.5100
 HZE  H4   H  HCH2  0   0.210  -4.7176  -1.3547  -2.3488
 HZE  H5   H  HCH2  0   0.248  -3.8972  -2.7241  -1.5921
 HZE  H6   H  HCH3  0   0.235  -2.2746   3.1877   3.2072
 HZE  H7   H  HCH3  0   0.235  -1.1297   3.5796   1.9200
 HZE  H8   H  HCH3  0   0.238  -2.5257   2.5549   1.5861
 HZE  H9   H  HCR6  0   0.279   1.6638  -2.4687  -1.0577
 HZE  H10  H  HNR5  0   0.417   4.0078   2.3146  -0.3433
 HZE  H11  H  HNH2  0   0.408   1.5848   4.6756   1.0085
 HZE  H12  H  HNH2  0   0.409   2.7525   3.4677   1.3462
 HZE  H13  H  HCR6  0   0.261  -2.3192  -1.5415  -2.3710
 HZE  H14  H  HCH2  0   0.239  -6.3212  -3.0907  -1.8381
 HZE  H15  H  HCH2  0   0.195  -5.7581  -3.2147  -0.1677
 HZE  H16  H  HNH1  0   0.356  -7.7635  -1.8615  -0.4233
 HZE  H18  H  HCH2  0   0.238  -7.0680   0.0928   0.7205
 HZE  H19  H  HCH2  0   0.196  -6.2047  -1.3098   1.3643
 HZE  H20  H  HCH2  0   0.249  -4.6598   0.4863   0.9474
 HZE  H21  H  HCH2  0   0.215  -5.2052   0.6829  -0.7166
 HZE  H22  H  HCH1  0   0.226  -1.5877   0.8062   3.1416
 HZE  H23  H  HCH3  0   0.232  -0.3772   2.3527   4.6511
 HZE  H24  H  HCH3  0   0.238   0.6691   1.0537   4.0832
 HZE  H25  H  HCH3  0   0.225   0.8110   2.6755   3.3859

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
 HZE  C29  C28  single    1.516  0.020  1.516
 HZE  C30  C28  single    1.520  0.020  1.520
 HZE  C28  O27  single    1.428  0.020  1.428
 HZE  C25  C26  single    1.516  0.020  1.516
 HZE  C25  N24  single    1.449  0.020  1.449
 HZE  C26  N21  single    1.459  0.020  1.459
 HZE  O27  C20  single    1.343  0.020  1.343
 HZE  N24  C23  single    1.448  0.020  1.448
 HZE  C19  C20  aromatic  1.386  0.020  1.386
 HZE  C19  C18  aromatic  1.405  0.020  1.405
 HZE  C20  C13  aromatic  1.408  0.020  1.408
 HZE  N21  C18  single    1.392  0.020  1.392
 HZE  N21  C22  single    1.452  0.020  1.452
 HZE  C18  C17  aromatic  1.397  0.020  1.397
 HZE  C23  C22  single    1.518  0.020  1.518
 HZE  N11  C10  single    1.345  0.020  1.345
 HZE  C13  C9   single    1.465  0.020  1.465
 HZE  C13  C16  aromatic  1.387  0.020  1.387
 HZE  C10  O12  double    1.220  0.020  1.220
 HZE  C10  C8   single    1.480  0.020  1.480
 HZE  C9   C8   aromatic  1.373  0.020  1.373
 HZE  C9   C5   aromatic  1.432  0.020  1.432
 HZE  C8   N7   aromatic  1.372  0.020  1.372
 HZE  C17  C16  aromatic  1.388  0.020  1.388
 HZE  C5   C4   aromatic  1.401  0.020  1.401
 HZE  C5   C6   aromatic  1.410  0.020  1.410
 HZE  N7   C6   aromatic  1.359  0.020  1.359
 HZE  C4   C1   aromatic  1.369  0.020  1.369
 HZE  C6   C3   aromatic  1.395  0.020  1.395
 HZE  C1   F14  single    1.342  0.020  1.342
 HZE  C1   C2   aromatic  1.403  0.020  1.403
 HZE  C3   C2   aromatic  1.370  0.020  1.370
 HZE  C2   F15  single    1.339  0.020  1.339
 HZE  C3   H1   single    0.930  0.020  1.080
 HZE  C16  H2   single    0.930  0.020  1.080
 HZE  C19  H3   single    0.930  0.020  1.080
 HZE  C22  H4   single    0.970  0.020  1.090
 HZE  C22  H5   single    0.970  0.020  1.090
 HZE  C30  H6   single    0.970  0.020  1.090
 HZE  C30  H7   single    0.970  0.020  1.090
 HZE  C30  H8   single    0.970  0.020  1.090
 HZE  C4   H9   single    0.930  0.020  1.080
 HZE  N7   H10  single    0.860  0.020  1.020
 HZE  N11  H11  single    0.860  0.020  1.020
 HZE  N11  H12  single    0.860  0.020  1.020
 HZE  C17  H13  single    0.930  0.020  1.080
 HZE  C23  H14  single    0.970  0.020  1.090
 HZE  C23  H15  single    0.970  0.020  1.090
 HZE  N24  H16  single    0.890  0.020  1.040
 HZE  C25  H18  single    0.970  0.020  1.090
 HZE  C25  H19  single    0.970  0.020  1.090
 HZE  C26  H20  single    0.970  0.020  1.090
 HZE  C26  H21  single    0.970  0.020  1.090
 HZE  C28  H22  single    0.970  0.020  1.090
 HZE  C29  H23  single    0.970  0.020  1.090
 HZE  C29  H24  single    0.970  0.020  1.090
 HZE  C29  H25  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
 HZE  F14  C1   C4   120.49  3.000
 HZE  F14  C1   C2   117.72  3.000
 HZE  C4   C1   C2   121.79  3.000
 HZE  F15  C2   C3   120.13  3.000
 HZE  F15  C2   C1   117.90  3.000
 HZE  C3   C2   C1   121.96  3.000
 HZE  H1   C3   C6   122.53  3.000
 HZE  H1   C3   C2   121.09  3.000
 HZE  C6   C3   C2   116.38  3.000
 HZE  N7   C8   C10  121.90  3.000
 HZE  N7   C8   C9   109.91  3.000
 HZE  C10  C8   C9   128.17  3.000
 HZE  C5   C9   C13  125.59  3.000
 HZE  C5   C9   C8   105.88  3.000
 HZE  C13  C9   C8   128.45  3.000
 HZE  O12  C10  N11  123.84  3.000
 HZE  O12  C10  C8   121.13  3.000
 HZE  N11  C10  C8   115.00  3.000
 HZE  C20  C13  C16  117.35  3.000
 HZE  C16  C13  C9   120.87  3.000
 HZE  C20  C13  C9   121.74  3.000
 HZE  H2   C16  C17  118.36  3.000
 HZE  H2   C16  C13  118.90  3.000
 HZE  C17  C16  C13  122.71  3.000
 HZE  H3   C19  C18  118.86  3.000
 HZE  H3   C19  C20  119.52  3.000
 HZE  C18  C19  C20  121.57  3.000
 HZE  O27  C20  C19  123.91  3.000
 HZE  C19  C20  C13  120.47  3.000
 HZE  O27  C20  C13  115.58  3.000
 HZE  H5   C22  H4   107.47  3.000
 HZE  H5   C22  C23  108.22  3.000
 HZE  H4   C22  C23  109.51  3.000
 HZE  H5   C22  N21  109.24  3.000
 HZE  H4   C22  N21  111.67  3.000
 HZE  C23  C22  N21  110.62  3.000
 HZE  H8   C30  H7   107.99  3.000
 HZE  H8   C30  H6   107.50  3.000
 HZE  H7   C30  H6   108.23  3.000
 HZE  H8   C30  C28  112.71  3.000
 HZE  H7   C30  C28  110.79  3.000
 HZE  H6   C30  C28  109.47  3.000
 HZE  H9   C4   C5   121.98  3.000
 HZE  H9   C4   C1   120.13  3.000
 HZE  C5   C4   C1   117.89  3.000
 HZE  C6   C5   C4   119.39  3.000
 HZE  C6   C5   C9   107.32  3.000
 HZE  C4   C5   C9   133.28  3.000
 HZE  N7   C6   C5   107.57  3.000
 HZE  N7   C6   C3   129.86  3.000
 HZE  C5   C6   C3   122.57  3.000
 HZE  H10  N7   C6   124.78  3.000
 HZE  H10  N7   C8   125.21  3.000
 HZE  C6   N7   C8   109.29  3.000
 HZE  H12  N11  H11  116.67  3.000
 HZE  H12  N11  C10  121.96  3.000
 HZE  H11  N11  C10  119.51  3.000
 HZE  H13  C17  C18  121.50  3.000
 HZE  H13  C17  C16  118.50  3.000
 HZE  C18  C17  C16  119.98  3.000
 HZE  N21  C18  C17  122.46  3.000
 HZE  C17  C18  C19  117.90  3.000
 HZE  N21  C18  C19  119.62  3.000
 HZE  C26  N21  C18  117.60  3.000
 HZE  C18  N21  C22  117.62  3.000
 HZE  C26  N21  C22  112.43  3.000
 HZE  H15  C23  H14  107.35  3.000
 HZE  H15  C23  N24  112.69  3.000
 HZE  H14  C23  N24  109.54  3.000
 HZE  H15  C23  C22  108.57  3.000
 HZE  H14  C23  C22  108.62  3.000
 HZE  N24  C23  C22  109.96  3.000
 HZE  H16  N24  C25  109.95  3.000
 HZE  H16  N24  C23  109.90  3.000
 HZE  C25  N24  C23  109.87  3.000
 HZE  H19  C25  H18  107.45  3.000
 HZE  H19  C25  C26  108.67  3.000
 HZE  H18  C25  C26  108.68  3.000
 HZE  H19  C25  N24  112.76  3.000
 HZE  H18  C25  N24  109.64  3.000
 HZE  C26  C25  N24  109.53  3.000
 HZE  H21  C26  H20  107.35  3.000
 HZE  H21  C26  C25  109.45  3.000
 HZE  H20  C26  C25  108.25  3.000
 HZE  H21  C26  N21  110.43  3.000
 HZE  H20  C26  N21  110.45  3.000
 HZE  C25  C26  N21  110.83  3.000
 HZE  C28  O27  C20  121.83  3.000
 HZE  H22  C28  C29  108.23  3.000
 HZE  H22  C28  O27  109.53  3.000
 HZE  C29  C28  O27  105.75  3.000
 HZE  H22  C28  C30  109.72  3.000
 HZE  O27  C28  C30  111.73  3.000
 HZE  C29  C28  C30  111.75  3.000
 HZE  H25  C29  H24  108.56  3.000
 HZE  H25  C29  H23  108.12  3.000
 HZE  H24  C29  H23  107.86  3.000
 HZE  H25  C29  C28  110.99  3.000
 HZE  H24  C29  C28  111.35  3.000
 HZE  H23  C29  C28  109.86  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
 HZE  CONST_01  C9   C5   C4   C1    180.00   0.0  0
 HZE  CONST_02  C6   C5   C4   C1      0.00   0.0  0
 HZE  CONST_03  C6   C3   C2   C1      0.00   0.0  0
 HZE  CONST_04  C5   C4   C1   C2      0.00   0.0  0
 HZE  CONST_05  C5   C6   C3   C2      0.00   0.0  0
 HZE  CONST_06  N7   C6   C3   C2    180.00   0.0  0
 HZE  CONST_07  C9   C5   C6   C3    180.00   0.0  0
 HZE  CONST_08  C4   C5   C6   C3      0.00   0.0  0
 HZE  CONST_09  C8   N7   C6   C3    180.00   0.0  0
 HZE  CONST_10  C4   C1   C2   C3      0.00   0.0  0
 HZE  CONST_13  C4   C5   C9   C8    180.00   0.0  0
 HZE  CONST_14  C6   C5   C9   C8      0.00   0.0  0
 HZE  CONST_15  C5   C6   N7   C8      0.00   0.0  0
 HZE  CONST_16  C19  C20  C13  C9    180.00   0.0  0
 HZE  CONST_17  C17  C16  C13  C9    180.00   0.0  0
 HZE  CONST_18  C6   N7   C8   C9      0.00   0.0  0
 HZE  CONST_19  N7   C6   C5   C9      0.00   0.0  0
 HZE  CONST_20  C18  C19  C20  C13     0.00   0.0  0
 HZE  CONST_21  N7   C8   C9   C13   180.00   0.0  0
 HZE  CONST_22  C4   C5   C9   C13     0.00   0.0  0
 HZE  CONST_23  C6   C5   C9   C13   180.00   0.0  0
 HZE  CONST_24  C18  C17  C16  C13     0.00   0.0  0
 HZE  CONST_25  C19  C20  C13  C16     0.00   0.0  0
 HZE  CONST_27  C19  C18  C17  C16     0.00   0.0  0
 HZE  CONST_28  C17  C18  C19  C20     0.00   0.0  0
 HZE  CONST_30  C17  C16  C13  C20     0.00   0.0  0
 HZE  CONST_31  N7   C6   C5   C4    180.00   0.0  0
 HZE  CONST_32  N7   C8   C9   C5      0.00   0.0  0
 HZE  CONST_33  N21  C18  C17  C16   180.00   0.0  0
 HZE  CONST_34  N21  C18  C19  C20   180.00   0.0  0
 HZE  CONST_35  F14  C1   C2   C3    180.00   0.0  0
 HZE  CONST_36  O27  C20  C13  C9      0.00   0.0  0
 HZE  CONST_37  C13  C9   C8   C10     0.00   0.0  0
 HZE  CONST_38  C5   C9   C8   C10   180.00   0.0  0
 HZE  CONST_39  C6   N7   C8   C10   180.00   0.0  0
 HZE  CONST_40  O27  C20  C13  C16   180.00   0.0  0
 HZE  CONST_41  F15  C2   C1   C4    180.00   0.0  0
 HZE  CONST_42  F14  C1   C4   C5    180.00   0.0  0
 HZE  CONST_43  F15  C2   C3   C6    180.00   0.0  0
 HZE  CONST_44  O27  C20  C19  C18   180.00   0.0  0
 HZE  CONST_45  H1   C3   C2   C1    180.00   0.0  0
 HZE  CONST_46  H9   C4   C1   C2    180.00   0.0  0
 HZE  CONST_47  H10  N7   C6   C3      0.00   0.0  0
 HZE  CONST_48  H2   C16  C13  C9      0.00   0.0  0
 HZE  CONST_49  H3   C19  C20  C13   180.00   0.0  0
 HZE  CONST_50  H13  C17  C16  C13   180.00   0.0  0
 HZE  CONST_51  H11  N11  C10  C8    180.00   0.0  0
 HZE  CONST_52  H12  N11  C10  C8      0.00   0.0  0
 HZE  Var_01    C26  N21  C18  C19    46.62  30.0  3
 HZE  Var_02    C25  C26  N21  C22    53.59  30.0  1
 HZE  Var_03    C25  N24  C23  C22   -61.18  30.0  1
 HZE  Var_04    C23  C22  N21  C18   165.33  30.0  1
 HZE  Var_05    N24  C25  C26  N21   -56.84  30.0  1
 HZE  Var_06    N24  C23  C22  N21    56.66  30.0  1
 HZE  Var_07    C26  C25  N24  C23    61.14  30.0  1
 HZE  Var_08    N11  C10  C8   C9    147.16  30.0  2
 HZE  Var_09    C29  C28  O27  C20   167.17  30.0  2
 HZE  Var_10    H23  C29  C28  C30    58.00  30.0  3
 HZE  Var_11    H6   C30  C28  O27  -178.07  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
 HZE  plan-1  C9   0.020
 HZE  plan-1  C13  0.020
 HZE  plan-1  C16  0.020
 HZE  plan-1  C19  0.020
 HZE  plan-1  C20  0.020
 HZE  plan-1  C17  0.020
 HZE  plan-1  C18  0.020
 HZE  plan-1  N21  0.020
 HZE  plan-1  O27  0.020
 HZE  plan-1  H2   0.020
 HZE  plan-1  H3   0.020
 HZE  plan-1  H13  0.020
 HZE  plan-2  C1   0.020
 HZE  plan-2  C2   0.020
 HZE  plan-2  C3   0.020
 HZE  plan-2  C8   0.020
 HZE  plan-2  C9   0.020
 HZE  plan-2  C10  0.020
 HZE  plan-2  C13  0.020
 HZE  plan-2  C4   0.020
 HZE  plan-2  C5   0.020
 HZE  plan-2  C6   0.020
 HZE  plan-2  N7   0.020
 HZE  plan-2  F14  0.020
 HZE  plan-2  F15  0.020
 HZE  plan-2  H1   0.020
 HZE  plan-2  H9   0.020
 HZE  plan-2  H10  0.020
 HZE  plan-3  C8   0.020
 HZE  plan-3  C10  0.020
 HZE  plan-3  N11  0.020
 HZE  plan-3  O12  0.020
 HZE  plan-3  H11  0.020
 HZE  plan-3  H12  0.020

