# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:52:51 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: 6-(2-fluoro-6-methylphenyl)-1-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(cc2)n3ncc4cc(C#N)c(cc34)c5c(C)cccc5F
#
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
 XHM  XHM  6-(2-fluoro-6-methylphenyl)-1-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-5-carbonitrile  ligand  56  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XHM
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
 XHM  C1   C  CR6   0   0.123  -2.1379   8.2782  -52.4317
 XHM  C2   C  CR6   0  -0.017  -1.8963   7.0251  -53.0625
 XHM  C3   C  CR16  0  -0.305  -2.5157   5.8604  -52.6464
 XHM  C4   C  CR56  0  -0.105  -3.3836   5.9400  -51.5612
 XHM  C5   C  CR56  0   0.477  -3.5894   7.1716  -50.9159
 XHM  C6   C  CR16  0  -0.321  -2.9849   8.3548  -51.3526
 XHM  C11  C  CR16  0  -0.264  -6.3232   7.9435  -48.7159
 XHM  C12  C  CR16  0  -0.333  -6.8019   8.8363  -47.7786
 XHM  C15  C  CR16  0  -0.280  -4.0844   8.6485  -48.2415
 XHM  C17  C  CH2   0  -0.315  -5.5044  11.4785  -45.4798
 XHM  C18  C  CH2   0  -0.279  -6.2306  12.6337  -44.8177
 XHM  C21  C  CH2   0  -0.306  -7.5068  10.1540  -45.2460
 XHM  C23  C  CSP   0   0.004  -0.9745   6.9701  -54.1483
 XHM  C27  C  CR16  0  -0.313   0.1363  11.2744  -52.8003
 XHM  C30  C  CR6   0   0.556  -1.8860  10.0336  -54.1578
 XHM  N7   N  NR5   0  -0.512  -4.4627   6.9293  -49.9088
 XHM  N8   N  N     0  -0.225  -4.8342   5.6372  -49.8782
 XHM  C9   C  CR15  0  -0.091  -4.2096   5.0294  -50.8489
 XHM  C10  C  CR6   0   0.287  -4.9573   7.8439  -48.9545
 XHM  C13  C  CR6   0   0.384  -5.9375   9.6709  -47.0482
 XHM  C14  C  CR16  0  -0.362  -4.5645   9.5504  -47.3051
 XHM  N16  N  NT    0  -0.515  -6.4413  10.5900  -46.1392
 XHM  N19  N  NT    0  -0.409  -7.2323  12.1601  -43.8879
 XHM  C20  C  CH2   0  -0.284  -8.1910  11.3396  -44.5961
 XHM  C22  C  CH3   0  -0.517  -7.8719  13.2530  -43.1925
 XHM  N24  N  NS    0  -0.245  -0.2189   6.9200  -55.0174
 XHM  C25  C  CR6   0  -0.243  -1.4747   9.4978  -52.9473
 XHM  C26  C  CR6   0   0.114  -0.4387  10.1321  -52.2499
 XHM  C28  C  CR16  0  -0.226  -0.3007  11.7866  -54.0135
 XHM  C29  C  CR16  0  -0.423  -1.3259  11.1660  -54.7110
 XHM  H1   H  HCR6  0   0.284  -2.3281   4.9210  -53.1499
 XHM  H2   H  HCR6  0   0.289  -3.1761   9.3052  -50.8725
 XHM  H3   H  HCR6  0   0.268  -7.0182   7.3283  -49.2729
 XHM  H4   H  HCR6  0   0.268  -7.8723   8.9014  -47.6405
 XHM  H5   H  HCR6  0   0.279  -3.0149   8.5625  -48.3897
 XHM  H6   H  HCH2  0   0.217  -4.8982  10.9472  -44.7304
 XHM  H7   H  HCH2  0   0.253  -4.8193  11.8998  -46.2163
 XHM  H8   H  HCH2  0   0.242  -5.4964  13.2403  -44.2826
 XHM  H9   H  HCH2  0   0.194  -6.6746  13.2752  -45.5993
 XHM  H10  H  HCH2  0   0.256  -8.2567   9.5884  -45.7941
 XHM  H11  H  HCH2  0   0.220  -7.1039   9.4944  -44.4640
 XHM  H12  H  HCR6  0   0.257   0.9426  11.7657  -52.2704
 XHM  H13  H  HCH3  0   0.250   0.2518   8.5189  -50.9952
 XHM  H14  H  HCH3  0   0.257   0.9688  10.0896  -50.6345
 XHM  H15  H  HCH3  0   0.256  -0.6837   9.7340  -50.1457
 XHM  H16  H  HCR5  0   0.283  -4.3497   3.9733  -51.0212
 XHM  H17  H  HCR6  0   0.275  -3.8421  10.1377  -46.7579
 XHM  H19  H  HCH2  0   0.195  -8.7330  11.9164  -45.3664
 XHM  H20  H  HCH2  0   0.241  -8.9367  10.9626  -43.8926
 XHM  H21  H  HCH3  0   0.233  -8.5976  12.8669  -42.4755
 XHM  H22  H  HCH3  0   0.233  -7.1296  13.8289  -42.6380
 XHM  H23  H  HCH3  0   0.192  -8.3989  13.9457  -43.8666
 XHM  H24  H  HCR6  0   0.268   0.1615  12.6754  -54.4223
 XHM  H25  H  HCR6  0   0.279  -1.6813  11.5503  -55.6579
 XHM  F31  F  F     0  -0.303  -2.8778   9.4122  -54.8167
 XHM  C32  C  CH3   0  -0.742   0.0515   9.5894  -50.9393

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
 XHM  N24  C23  triple    1.153  0.020  1.153
 XHM  F31  C30  single    1.343  0.020  1.343
 XHM  C29  C30  aromatic  1.379  0.020  1.379
 XHM  C29  C28  aromatic  1.387  0.020  1.387
 XHM  C30  C25  aromatic  1.386  0.020  1.386
 XHM  C23  C2   single    1.425  0.020  1.425
 XHM  C28  C27  aromatic  1.388  0.020  1.388
 XHM  C2   C3   aromatic  1.383  0.020  1.383
 XHM  C2   C1   aromatic  1.424  0.020  1.424
 XHM  C25  C1   single    1.481  0.020  1.481
 XHM  C25  C26  aromatic  1.401  0.020  1.401
 XHM  C27  C26  aromatic  1.392  0.020  1.392
 XHM  C3   C4   aromatic  1.392  0.020  1.392
 XHM  C1   C6   aromatic  1.374  0.020  1.374
 XHM  C26  C32  single    1.501  0.020  1.501
 XHM  C4   C5   aromatic  1.406  0.020  1.406
 XHM  C4   C9   aromatic  1.421  0.020  1.421
 XHM  C6   C5   aromatic  1.399  0.020  1.399
 XHM  C5   N7   aromatic  1.355  0.020  1.355
 XHM  C9   N8   aromatic  1.305  0.020  1.305
 XHM  N8   N7   aromatic  1.345  0.020  1.345
 XHM  N7   C10  single    1.411  0.020  1.411
 XHM  C10  C11  aromatic  1.390  0.020  1.390
 XHM  C10  C15  aromatic  1.385  0.020  1.385
 XHM  C11  C12  aromatic  1.380  0.020  1.380
 XHM  C15  C14  aromatic  1.386  0.020  1.386
 XHM  C12  C13  aromatic  1.406  0.020  1.406
 XHM  C14  C13  aromatic  1.402  0.020  1.402
 XHM  C13  N16  single    1.387  0.020  1.387
 XHM  N16  C17  single    1.450  0.020  1.450
 XHM  N16  C21  single    1.457  0.020  1.457
 XHM  C17  C18  single    1.517  0.020  1.517
 XHM  C18  N19  single    1.446  0.020  1.446
 XHM  C21  C20  single    1.515  0.020  1.515
 XHM  C20  N19  single    1.447  0.020  1.447
 XHM  N19  C22  single    1.445  0.020  1.445
 XHM  C3   H1   single    0.930  0.020  1.080
 XHM  C6   H2   single    0.930  0.020  1.080
 XHM  C11  H3   single    0.930  0.020  1.080
 XHM  C12  H4   single    0.930  0.020  1.080
 XHM  C15  H5   single    0.930  0.020  1.080
 XHM  C17  H6   single    0.970  0.020  1.090
 XHM  C17  H7   single    0.970  0.020  1.090
 XHM  C18  H8   single    0.970  0.020  1.090
 XHM  C18  H9   single    0.970  0.020  1.090
 XHM  C21  H10  single    0.970  0.020  1.090
 XHM  C21  H11  single    0.970  0.020  1.090
 XHM  C27  H12  single    0.930  0.020  1.080
 XHM  C32  H13  single    0.970  0.020  1.090
 XHM  C32  H14  single    0.970  0.020  1.090
 XHM  C32  H15  single    0.970  0.020  1.090
 XHM  C9   H16  single    0.930  0.020  1.080
 XHM  C14  H17  single    0.930  0.020  1.080
 XHM  C20  H19  single    0.970  0.020  1.090
 XHM  C20  H20  single    0.970  0.020  1.090
 XHM  C22  H21  single    0.970  0.020  1.090
 XHM  C22  H22  single    0.970  0.020  1.090
 XHM  C22  H23  single    0.970  0.020  1.090
 XHM  C28  H24  single    0.930  0.020  1.080
 XHM  C29  H25  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
 XHM  C25  C1   C6   120.23  3.000
 XHM  C6   C1   C2   120.12  3.000
 XHM  C25  C1   C2   119.65  3.000
 XHM  C23  C2   C3   119.10  3.000
 XHM  C3   C2   C1   122.13  3.000
 XHM  C23  C2   C1   118.77  3.000
 XHM  H1   C3   C4   121.37  3.000
 XHM  H1   C3   C2   120.89  3.000
 XHM  C4   C3   C2   117.75  3.000
 XHM  C9   C4   C5   104.26  3.000
 XHM  C9   C4   C3   135.78  3.000
 XHM  C5   C4   C3   119.96  3.000
 XHM  N7   C5   C6   131.45  3.000
 XHM  N7   C5   C4   106.20  3.000
 XHM  C6   C5   C4   122.32  3.000
 XHM  H2   C6   C5   121.88  3.000
 XHM  H2   C6   C1   120.44  3.000
 XHM  C5   C6   C1   117.68  3.000
 XHM  H3   C11  C10  120.12  3.000
 XHM  H3   C11  C12  119.63  3.000
 XHM  C10  C11  C12  120.25  3.000
 XHM  H4   C12  C13  120.43  3.000
 XHM  H4   C12  C11  117.98  3.000
 XHM  C13  C12  C11  121.57  3.000
 XHM  H5   C15  C14  119.09  3.000
 XHM  H5   C15  C10  120.38  3.000
 XHM  C14  C15  C10  120.51  3.000
 XHM  H7   C17  H6   107.48  3.000
 XHM  H7   C17  N16  109.60  3.000
 XHM  H6   C17  N16  111.70  3.000
 XHM  H7   C17  C18  107.55  3.000
 XHM  H6   C17  C18  109.52  3.000
 XHM  N16  C17  C18  110.85  3.000
 XHM  H9   C18  H8   107.12  3.000
 XHM  H9   C18  N19  111.52  3.000
 XHM  H8   C18  N19  109.42  3.000
 XHM  H9   C18  C17  109.02  3.000
 XHM  H8   C18  C17  108.36  3.000
 XHM  N19  C18  C17  111.28  3.000
 XHM  H11  C21  H10  107.41  3.000
 XHM  H11  C21  C20  109.26  3.000
 XHM  H10  C21  C20  108.16  3.000
 XHM  H11  C21  N16  110.34  3.000
 XHM  H10  C21  N16  110.54  3.000
 XHM  C20  C21  N16  111.04  3.000
 XHM  N24  C23  C2   180.00  3.000
 XHM  H12  C27  C28  119.67  3.000
 XHM  H12  C27  C26  119.10  3.000
 XHM  C28  C27  C26  121.23  3.000
 XHM  F31  C30  C29  118.88  3.000
 XHM  C29  C30  C25  123.17  3.000
 XHM  F31  C30  C25  117.95  3.000
 XHM  C10  N7   N8   120.69  3.000
 XHM  C10  N7   C5   127.78  3.000
 XHM  N8   N7   C5   111.52  3.000
 XHM  C9   N8   N7   107.36  3.000
 XHM  H16  C9   N8   120.83  3.000
 XHM  H16  C9   C4   128.51  3.000
 XHM  N8   C9   C4   110.66  3.000
 XHM  N7   C10  C15  120.25  3.000
 XHM  C15  C10  C11  119.29  3.000
 XHM  N7   C10  C11  120.45  3.000
 XHM  N16  C13  C14  122.18  3.000
 XHM  N16  C13  C12  120.69  3.000
 XHM  C14  C13  C12  117.11  3.000
 XHM  H17  C14  C13  121.03  3.000
 XHM  H17  C14  C15  117.68  3.000
 XHM  C13  C14  C15  121.27  3.000
 XHM  C13  N16  C21  117.97  3.000
 XHM  C21  N16  C17  112.15  3.000
 XHM  C13  N16  C17  117.99  3.000
 XHM  C22  N19  C20  111.79  3.000
 XHM  C22  N19  C18  111.61  3.000
 XHM  C20  N19  C18  109.26  3.000
 XHM  H20  C20  H19  107.12  3.000
 XHM  H20  C20  N19  109.44  3.000
 XHM  H19  C20  N19  111.73  3.000
 XHM  H20  C20  C21  108.33  3.000
 XHM  H19  C20  C21  109.34  3.000
 XHM  N19  C20  C21  110.75  3.000
 XHM  H23  C22  H22  107.74  3.000
 XHM  H23  C22  H21  107.86  3.000
 XHM  H22  C22  H21  107.79  3.000
 XHM  H23  C22  N19  113.15  3.000
 XHM  H22  C22  N19  110.05  3.000
 XHM  H21  C22  N19  110.07  3.000
 XHM  C26  C25  C30  118.63  3.000
 XHM  C26  C25  C1   122.06  3.000
 XHM  C30  C25  C1   119.31  3.000
 XHM  C25  C26  C32  120.84  3.000
 XHM  C32  C26  C27  120.47  3.000
 XHM  C25  C26  C27  118.69  3.000
 XHM  H24  C28  C29  119.57  3.000
 XHM  H24  C28  C27  119.93  3.000
 XHM  C29  C28  C27  120.49  3.000
 XHM  H25  C29  C28  121.61  3.000
 XHM  H25  C29  C30  120.62  3.000
 XHM  C28  C29  C30  117.77  3.000
 XHM  H15  C32  H14  107.65  3.000
 XHM  H15  C32  H13  106.92  3.000
 XHM  H14  C32  H13  108.10  3.000
 XHM  H15  C32  C26  111.53  3.000
 XHM  H14  C32  C26  110.71  3.000
 XHM  H13  C32  C26  111.73  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
 XHM  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 XHM  CONST_02  C29  C30  C25  C1    180.00   0.0  0
 XHM  CONST_03  C27  C26  C25  C1    180.00   0.0  0
 XHM  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 XHM  CONST_05  N7   C5   C6   C1    180.00   0.0  0
 XHM  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 XHM  CONST_07  C9   C4   C3   C2    180.00   0.0  0
 XHM  CONST_10  C5   C6   C1   C2      0.00   0.0  0
 XHM  CONST_11  C25  C1   C2   C3    180.00   0.0  0
 XHM  CONST_12  C6   C1   C2   C3      0.00   0.0  0
 XHM  CONST_13  C6   C5   C4   C3      0.00   0.0  0
 XHM  CONST_14  N7   C5   C4   C3    180.00   0.0  0
 XHM  CONST_15  N8   C9   C4   C3    180.00   0.0  0
 XHM  CONST_16  N8   N7   C5   C4      0.00   0.0  0
 XHM  CONST_17  C10  N7   C5   C4    180.00   0.0  0
 XHM  CONST_18  N7   N8   C9   C4      0.00   0.0  0
 XHM  CONST_19  N8   C9   C4   C5      0.00   0.0  0
 XHM  CONST_20  C25  C1   C6   C5    180.00   0.0  0
 XHM  CONST_21  C9   N8   N7   C5      0.00   0.0  0
 XHM  CONST_26  C9   C4   C5   C6    180.00   0.0  0
 XHM  CONST_27  N8   N7   C5   C6    180.00   0.0  0
 XHM  CONST_28  C10  N7   C5   C6      0.00   0.0  0
 XHM  CONST_30  C14  C15  C10  C11     0.00   0.0  0
 XHM  CONST_31  C14  C13  C12  C11     0.00   0.0  0
 XHM  CONST_32  N7   C10  C11  C12   180.00   0.0  0
 XHM  CONST_33  C15  C10  C11  C12     0.00   0.0  0
 XHM  CONST_34  C15  C14  C13  C12     0.00   0.0  0
 XHM  CONST_36  C30  C29  C28  C27     0.00   0.0  0
 XHM  CONST_37  C30  C25  C26  C27     0.00   0.0  0
 XHM  CONST_38  C9   C4   C5   N7      0.00   0.0  0
 XHM  CONST_39  C14  C15  C10  N7    180.00   0.0  0
 XHM  CONST_40  C10  N7   N8   C9    180.00   0.0  0
 XHM  CONST_41  C13  C12  C11  C10     0.00   0.0  0
 XHM  CONST_42  C13  C14  C15  C10     0.00   0.0  0
 XHM  CONST_43  C28  C29  C30  C25     0.00   0.0  0
 XHM  CONST_44  C28  C27  C26  C25     0.00   0.0  0
 XHM  CONST_45  C29  C30  C25  C26     0.00   0.0  0
 XHM  CONST_46  C29  C28  C27  C26     0.00   0.0  0
 XHM  CONST_47  N16  C13  C12  C11   180.00   0.0  0
 XHM  CONST_48  N16  C13  C14  C15   180.00   0.0  0
 XHM  CONST_49  F31  C30  C25  C1      0.00   0.0  0
 XHM  CONST_50  C32  C26  C25  C1      0.00   0.0  0
 XHM  CONST_51  C23  C2   C3   C4    180.00   0.0  0
 XHM  CONST_52  C23  C2   C1   C6    180.00   0.0  0
 XHM  CONST_53  C25  C1   C2   C23     0.00   0.0  0
 XHM  CONST_54  C32  C26  C25  C30   180.00   0.0  0
 XHM  CONST_55  C28  C27  C26  C32   180.00   0.0  0
 XHM  CONST_56  F31  C30  C25  C26   180.00   0.0  0
 XHM  CONST_57  F31  C30  C29  C28   180.00   0.0  0
 XHM  CONST_58  H1   C3   C2   C1    180.00   0.0  0
 XHM  CONST_59  H2   C6   C1   C2    180.00   0.0  0
 XHM  CONST_60  H16  C9   C4   C3      0.00   0.0  0
 XHM  CONST_61  H5   C15  C10  C11   180.00   0.0  0
 XHM  CONST_62  H17  C14  C13  C12   180.00   0.0  0
 XHM  CONST_63  H3   C11  C10  C15   180.00   0.0  0
 XHM  CONST_64  H25  C29  C28  C27   180.00   0.0  0
 XHM  CONST_65  H24  C28  C29  C30   180.00   0.0  0
 XHM  CONST_66  H4   C12  C11  C10   180.00   0.0  0
 XHM  CONST_67  H12  C27  C26  C25   180.00   0.0  0
 XHM  Var_01    C17  N16  C13  C12  -176.20  30.0  2
 XHM  Var_02    C20  C21  N16  C17    53.18  30.0  1
 XHM  Var_03    C20  N19  C18  C17   -59.39  30.0  1
 XHM  Var_04    C13  N16  C17  C18   165.10  30.0  1
 XHM  Var_05    C21  C20  N19  C18    59.42  30.0  1
 XHM  Var_06    N19  C18  C17  N16    56.16  30.0  1
 XHM  Var_07    N19  C20  C21  N16   -56.53  30.0  1
 XHM  Var_08    H21  C22  N19  C18  -178.13  30.0  3
 XHM  Var_09    H13  C32  C26  C27  -130.65  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
 XHM  plan-1  C11  0.020
 XHM  plan-1  C12  0.020
 XHM  plan-1  C15  0.020
 XHM  plan-1  N7   0.020
 XHM  plan-1  C10  0.020
 XHM  plan-1  C13  0.020
 XHM  plan-1  C14  0.020
 XHM  plan-1  N16  0.020
 XHM  plan-1  H3   0.020
 XHM  plan-1  H4   0.020
 XHM  plan-1  H5   0.020
 XHM  plan-1  H17  0.020
 XHM  plan-2  C1   0.020
 XHM  plan-2  C27  0.020
 XHM  plan-2  C30  0.020
 XHM  plan-2  C25  0.020
 XHM  plan-2  C26  0.020
 XHM  plan-2  C28  0.020
 XHM  plan-2  C29  0.020
 XHM  plan-2  H12  0.020
 XHM  plan-2  H24  0.020
 XHM  plan-2  H25  0.020
 XHM  plan-2  F31  0.020
 XHM  plan-2  C32  0.020
 XHM  plan-3  C1   0.020
 XHM  plan-3  C2   0.020
 XHM  plan-3  C3   0.020
 XHM  plan-3  C4   0.020
 XHM  plan-3  C5   0.020
 XHM  plan-3  C6   0.020
 XHM  plan-3  C23  0.020
 XHM  plan-3  N7   0.020
 XHM  plan-3  N8   0.020
 XHM  plan-3  C9   0.020
 XHM  plan-3  C10  0.020
 XHM  plan-3  N24  0.020
 XHM  plan-3  C25  0.020
 XHM  plan-3  H1   0.020
 XHM  plan-3  H2   0.020
 XHM  plan-3  H16  0.020

