# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 03:03:18 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-[(2R)-1-azanyl-1-oxo-propan-2-yl]-3-[6-methyl-4-[[3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propyl]amino]indazol-1-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cccc(c1)n2ncc3c(NCC(O)(C(F)(F)F)C(F)(F)F)cc(C)cc23)C(N)=O
#
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
 JZS  JZS  N-[(2R)-1-azanyl-1-oxo-propan-2-yl]-3-[6-methyl-4-[[3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propyl]amino]indazol-1-yl]benzamide  ligand  57  36  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JZS
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
 JZS  C1    C  CH3   0  -0.655   8.7466   1.2057  -1.8524
 JZS  F1    F  F     0  -0.289  -7.9820   1.0371   0.7608
 JZS  N1    N  NH1   0  -0.666   7.1779   0.4754  -0.0978
 JZS  O1    O  O     0  -0.488   5.5442   1.7021  -1.0482
 JZS  C2    C  CH1   0  -0.191   8.2472   1.3884  -0.4167
 JZS  F2    F  F     0  -0.302  -7.1853  -0.8600   1.3406
 JZS  N2    N  NR5   0  -0.526   1.2759  -0.5888   0.3862
 JZS  O2    O  OH1   0  -0.648  -5.4169   1.3387   1.6840
 JZS  C3    C  C     0   0.557   5.9059   0.6914  -0.4599
 JZS  F3    F  F     0  -0.297  -7.3888  -0.3792  -0.7500
 JZS  N3    N  N     0  -0.244   0.9614   0.6210   0.8882
 JZS  C4    C  CR6   0  -0.023   4.9247  -0.3795  -0.0919
 JZS  F4    F  F     0  -0.288  -4.3288   2.4834  -0.4117
 JZS  C5    C  CR16  0  -0.306   5.2985  -1.7015   0.1401
 JZS  F5    F  F     0  -0.297  -6.4477   2.6944  -0.5645
 JZS  N5    N  NH2   0  -0.797  10.2888   2.1209   0.6366
 JZS  C6    C  CR16  0  -0.236   4.3358  -2.6454   0.4614
 JZS  F6    F  F     0  -0.295  -5.4229   1.2911  -1.8300
 JZS  C7    C  CR16  0  -0.309   3.0010  -2.2868   0.5626
 JZS  C8    C  CR6   0   0.375   2.6249  -0.9732   0.3027
 JZS  C9    C  CR16  0  -0.323   3.5826  -0.0241  -0.0289
 JZS  C10   C  CR15  0  -0.085  -0.3385   0.7227   0.8416
 JZS  C11   C  CR56  0  -0.220  -0.9213  -0.4467   0.2901
 JZS  C12   C  CR6   0   0.350  -2.2427  -0.8597   0.0048
 JZS  C13   C  CH2   0  -0.319  -4.6404  -0.4654   0.2310
 JZS  C14   C  CT    0  -0.221  -5.6254   0.6937   0.4693
 JZS  C15   C  CT    0   1.038  -7.0697   0.1249   0.4434
 JZS  C16   C  CT    0   1.036  -5.4545   1.8034  -0.5996
 JZS  C17   C  CR16  0  -0.424  -2.3952  -2.1018  -0.5899
 JZS  C18   C  CR6   0   0.105  -1.2878  -2.9157  -0.9168
 JZS  C19   C  CH3   0  -0.726  -1.5460  -4.2371  -1.5812
 JZS  C20   C  CR16  0  -0.397   0.0035  -2.5235  -0.6311
 JZS  C21   C  CR56  0   0.475   0.1633  -1.2789  -0.0066
 JZS  C22   C  C     0   0.519   9.3888   1.1373   0.5651
 JZS  H1    H  HCH3  0   0.242   9.5384   1.9156  -2.0884
 JZS  H1A   H  HCH3  0   0.238   9.1308   0.1963  -2.0010
 JZS  H1B   H  HCH3  0   0.252   7.9316   1.3714  -2.5549
 JZS  HN1   H  HNH1  0   0.407   7.4304  -0.3319   0.4523
 JZS  H2    H  HCH1  0   0.281   7.8902   2.4135  -0.2914
 JZS  HO2   H  HOH1  0   0.481  -5.3153   0.6965   2.3978
 JZS  HN4   H  HNH1  0   0.387  -3.0904   0.6304   1.0520
 JZS  H5    H  HCR6  0   0.263   6.3296  -2.0192   0.0556
 JZS  HN5   H  HNH2  0   0.414  10.1888   2.9775   0.1190
 JZS  HN5A  H  HNH2  0   0.408  11.1144   2.0166   1.2041
 JZS  H6    H  HCR6  0   0.274   4.6271  -3.6698   0.6491
 JZS  H7    H  HCR6  0   0.287   2.2662  -3.0240   0.8564
 JZS  H9    H  HCR6  0   0.272   3.2818   0.9934  -0.2363
 JZS  H10   H  HCR5  0   0.273  -0.8220   1.6182   1.2024
 JZS  H13   H  HCH2  0   0.280  -4.8313  -0.9126  -0.7444
 JZS  H13A  H  HCH2  0   0.275  -4.8367  -1.2469   0.9762
 JZS  H17   H  HCR6  0   0.264  -3.3822  -2.4806  -0.8222
 JZS  H19   H  HCH3  0   0.247  -2.0659  -4.1042  -2.5315
 JZS  H19A  H  HCH3  0   0.246  -0.6197  -4.7749  -1.7774
 JZS  H19B  H  HCH3  0   0.247  -2.1780  -4.8721  -0.9582
 JZS  H20   H  HCR6  0   0.264   0.8414  -3.1538  -0.8930
 JZS  O3    O  O     0  -0.483   9.4700   0.0946   1.1987
 JZS  N4    N  NH1   0  -0.703  -3.2792  -0.0054   0.2918

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
 JZS  C1   C2    single    1.531  0.020  1.531
 JZS  F1   C15   single    1.329  0.020  1.329
 JZS  N1   C2    single    1.442  0.020  1.442
 JZS  N1   C3    single    1.340  0.020  1.340
 JZS  O1   C3    double    1.224  0.020  1.224
 JZS  C2   C22   single    1.526  0.020  1.526
 JZS  F2   C15   single    1.337  0.020  1.337
 JZS  N2   N3    aromatic  1.347  0.020  1.347
 JZS  N2   C8    single    1.405  0.020  1.405
 JZS  N2   C21   aromatic  1.367  0.020  1.367
 JZS  O2   C14   single    1.391  0.020  1.391
 JZS  C3   C4    single    1.498  0.020  1.498
 JZS  F3   C15   single    1.334  0.020  1.334
 JZS  N3   C10   aromatic  1.305  0.020  1.305
 JZS  O3   C22   double    1.223  0.020  1.223
 JZS  C4   C5    aromatic  1.393  0.020  1.393
 JZS  C4   C9    aromatic  1.390  0.020  1.390
 JZS  F4   C16   single    1.328  0.020  1.328
 JZS  N4   C12   single    1.373  0.020  1.373
 JZS  N4   C13   single    1.438  0.020  1.438
 JZS  C5   C6    aromatic  1.386  0.020  1.386
 JZS  F5   C16   single    1.335  0.020  1.335
 JZS  N5   C22   single    1.335  0.020  1.335
 JZS  C6   C7    aromatic  1.386  0.020  1.386
 JZS  F6   C16   single    1.333  0.020  1.333
 JZS  C7   C8    aromatic  1.391  0.020  1.391
 JZS  C8   C9    aromatic  1.389  0.020  1.389
 JZS  C10  C11   aromatic  1.418  0.020  1.418
 JZS  C11  C12   aromatic  1.414  0.020  1.414
 JZS  C11  C21   aromatic  1.399  0.020  1.399
 JZS  C12  C17   aromatic  1.385  0.020  1.385
 JZS  C13  C14   single    1.540  0.020  1.540
 JZS  C14  C15   single    1.552  0.020  1.552
 JZS  C14  C16   single    1.550  0.020  1.550
 JZS  C17  C18   aromatic  1.413  0.020  1.413
 JZS  C18  C19   single    1.501  0.020  1.501
 JZS  C18  C20   aromatic  1.379  0.020  1.379
 JZS  C20  C21   aromatic  1.402  0.020  1.402
 JZS  C1   H1    single    0.970  0.020  1.090
 JZS  C1   H1A   single    0.970  0.020  1.090
 JZS  C1   H1B   single    0.970  0.020  1.090
 JZS  N1   HN1   single    0.860  0.020  1.020
 JZS  C2   H2    single    0.970  0.020  1.090
 JZS  O2   HO2   single    0.850  0.020  0.980
 JZS  N4   HN4   single    0.890  0.020  1.040
 JZS  C5   H5    single    0.930  0.020  1.080
 JZS  N5   HN5   single    0.860  0.020  1.020
 JZS  N5   HN5A  single    0.860  0.020  1.020
 JZS  C6   H6    single    0.930  0.020  1.080
 JZS  C7   H7    single    0.930  0.020  1.080
 JZS  C9   H9    single    0.930  0.020  1.080
 JZS  C10  H10   single    0.930  0.020  1.080
 JZS  C13  H13   single    0.970  0.020  1.090
 JZS  C13  H13A  single    0.970  0.020  1.090
 JZS  C17  H17   single    0.930  0.020  1.080
 JZS  C19  H19   single    0.970  0.020  1.090
 JZS  C19  H19A  single    0.970  0.020  1.090
 JZS  C19  H19B  single    0.970  0.020  1.090
 JZS  C20  H20   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
 JZS  H1B   C1   H1A   108.47  3.000
 JZS  H1B   C1   H1    107.77  3.000
 JZS  H1A   C1   H1    108.52  3.000
 JZS  H1B   C1   C2    110.05  3.000
 JZS  H1A   C1   C2    110.69  3.000
 JZS  H1    C1   C2    111.25  3.000
 JZS  HN1   N1   C3    120.92  3.000
 JZS  HN1   N1   C2    116.20  3.000
 JZS  C3    N1   C2    122.84  3.000
 JZS  H2    C2   C22   108.96  3.000
 JZS  H2    C2   N1    109.05  3.000
 JZS  C22   C2   N1    107.96  3.000
 JZS  H2    C2   C1    109.03  3.000
 JZS  C22   C2   C1    109.85  3.000
 JZS  N1    C2   C1    111.95  3.000
 JZS  C21   N2   C8    128.77  3.000
 JZS  C21   N2   N3    111.74  3.000
 JZS  C8    N2   N3    119.47  3.000
 JZS  HO2   O2   C14   110.67  3.000
 JZS  C4    C3   O1    120.97  3.000
 JZS  C4    C3   N1    116.11  3.000
 JZS  O1    C3   N1    122.92  3.000
 JZS  C10   N3   N2    106.82  3.000
 JZS  C9    C4   C5    119.61  3.000
 JZS  C9    C4   C3    117.44  3.000
 JZS  C5    C4   C3    122.91  3.000
 JZS  H5    C5   C6    118.68  3.000
 JZS  H5    C5   C4    121.41  3.000
 JZS  C6    C5   C4    119.90  3.000
 JZS  HN5A  N5   HN5   117.36  3.000
 JZS  HN5A  N5   C22   120.42  3.000
 JZS  HN5   N5   C22   122.20  3.000
 JZS  H6    C6   C7    119.47  3.000
 JZS  H6    C6   C5    119.89  3.000
 JZS  C7    C6   C5    120.64  3.000
 JZS  H7    C7   C8    120.72  3.000
 JZS  H7    C7   C6    119.85  3.000
 JZS  C8    C7   C6    119.42  3.000
 JZS  C9    C8   C7    120.24  3.000
 JZS  C9    C8   N2    119.30  3.000
 JZS  C7    C8   N2    120.46  3.000
 JZS  H9    C9   C8    119.81  3.000
 JZS  H9    C9   C4    120.05  3.000
 JZS  C8    C9   C4    120.14  3.000
 JZS  H10   C10  C11   129.03  3.000
 JZS  H10   C10  N3    119.92  3.000
 JZS  C11   C10  N3    111.05  3.000
 JZS  C21   C11  C12   120.54  3.000
 JZS  C21   C11  C10   104.73  3.000
 JZS  C12   C11  C10   134.72  3.000
 JZS  C17   C12  C11   116.83  3.000
 JZS  C17   C12  N4    124.35  3.000
 JZS  C11   C12  N4    118.79  3.000
 JZS  H13A  C13  H13   106.51  3.000
 JZS  H13A  C13  C14   108.46  3.000
 JZS  H13   C13  C14   109.59  3.000
 JZS  H13A  C13  N4    111.61  3.000
 JZS  H13   C13  N4    109.56  3.000
 JZS  C14   C13  N4    110.99  3.000
 JZS  C16   C14  C15   110.69  3.000
 JZS  C16   C14  C13   111.20  3.000
 JZS  C15   C14  C13   108.47  3.000
 JZS  C16   C14  O2    104.69  3.000
 JZS  C15   C14  O2    108.90  3.000
 JZS  C13   C14  O2    112.85  3.000
 JZS  C14   C15  F3    112.08  3.000
 JZS  C14   C15  F2    109.82  3.000
 JZS  F3    C15  F2    107.52  3.000
 JZS  C14   C15  F1    112.54  3.000
 JZS  F3    C15  F1    107.99  3.000
 JZS  F2    C15  F1    106.62  3.000
 JZS  C14   C16  F6    111.34  3.000
 JZS  C14   C16  F5    112.19  3.000
 JZS  F6    C16  F5    107.37  3.000
 JZS  C14   C16  F4    111.24  3.000
 JZS  F6    C16  F4    107.89  3.000
 JZS  F5    C16  F4    106.56  3.000
 JZS  H17   C17  C18   117.61  3.000
 JZS  H17   C17  C12   120.41  3.000
 JZS  C18   C17  C12   121.98  3.000
 JZS  C20   C18  C19   120.19  3.000
 JZS  C20   C18  C17   121.47  3.000
 JZS  C19   C18  C17   118.34  3.000
 JZS  H19B  C19  H19A  107.95  3.000
 JZS  H19B  C19  H19   106.98  3.000
 JZS  H19A  C19  H19   107.97  3.000
 JZS  H19B  C19  C18   111.05  3.000
 JZS  H19A  C19  C18   111.60  3.000
 JZS  H19   C19  C18   111.10  3.000
 JZS  H20   C20  C21   122.51  3.000
 JZS  H20   C20  C18   120.64  3.000
 JZS  C21   C20  C18   116.84  3.000
 JZS  C20   C21  C11   122.30  3.000
 JZS  C20   C21  N2    132.00  3.000
 JZS  C11   C21  N2    105.65  3.000
 JZS  N5    C22  O3    123.76  3.000
 JZS  N5    C22  C2    114.67  3.000
 JZS  O3    C22  C2    121.54  3.000
 JZS  HN4   N4   C13   114.24  3.000
 JZS  HN4   N4   C12   114.09  3.000
 JZS  C13   N4   C12   120.43  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
 JZS  CONST_01  C11   C10  N3   N2      0.00   0.0  0
 JZS  CONST_02  C6    C7   C8   N2    180.00   0.0  0
 JZS  CONST_03  C4    C9   C8   N2    180.00   0.0  0
 JZS  CONST_04  C10   C11  C21  N2      0.00   0.0  0
 JZS  CONST_05  C12   C11  C21  N2    180.00   0.0  0
 JZS  CONST_06  C18   C20  C21  N2    180.00   0.0  0
 JZS  CONST_09  C11   C21  N2   N3      0.00   0.0  0
 JZS  CONST_10  C20   C21  N2   N3    180.00   0.0  0
 JZS  CONST_11  C12   C11  C10  N3    180.00   0.0  0
 JZS  CONST_12  C21   C11  C10  N3      0.00   0.0  0
 JZS  CONST_13  C7    C6   C5   C4      0.00   0.0  0
 JZS  CONST_14  C7    C8   C9   C4      0.00   0.0  0
 JZS  CONST_15  C8    C9   C4   C5      0.00   0.0  0
 JZS  CONST_16  C8    C7   C6   C5      0.00   0.0  0
 JZS  CONST_17  C9    C4   C5   C6      0.00   0.0  0
 JZS  CONST_18  C9    C8   C7   C6      0.00   0.0  0
 JZS  CONST_20  C10   N3   N2   C8    180.00   0.0  0
 JZS  CONST_21  C11   C21  N2   C8    180.00   0.0  0
 JZS  CONST_22  C20   C21  N2   C8      0.00   0.0  0
 JZS  CONST_24  C21   N2   N3   C10     0.00   0.0  0
 JZS  CONST_25  C17   C12  C11  C10   180.00   0.0  0
 JZS  CONST_26  C20   C21  C11  C10   180.00   0.0  0
 JZS  CONST_27  C18   C17  C12  C11     0.00   0.0  0
 JZS  CONST_28  C18   C20  C21  C11     0.00   0.0  0
 JZS  CONST_29  C20   C21  C11  C12     0.00   0.0  0
 JZS  CONST_30  C20   C18  C17  C12     0.00   0.0  0
 JZS  CONST_31  C21   C11  C12  C17     0.00   0.0  0
 JZS  CONST_32  C21   C20  C18  C17     0.00   0.0  0
 JZS  CONST_33  C6    C5   C4   C3    180.00   0.0  0
 JZS  CONST_34  C8    C9   C4   C3    180.00   0.0  0
 JZS  CONST_35  C10   C11  C12  N4      0.00   0.0  0
 JZS  CONST_36  C21   C11  C12  N4    180.00   0.0  0
 JZS  CONST_37  C18   C17  C12  N4    180.00   0.0  0
 JZS  CONST_38  C19   C18  C17  C12   180.00   0.0  0
 JZS  CONST_39  C21   C20  C18  C19   180.00   0.0  0
 JZS  CONST_40  H10   C10  N3   N2    180.00   0.0  0
 JZS  CONST_41  H7    C7   C8   N2      0.00   0.0  0
 JZS  CONST_42  H9    C9   C8   N2      0.00   0.0  0
 JZS  CONST_43  H20   C20  C21  N2      0.00   0.0  0
 JZS  CONST_44  H6    C6   C5   C4    180.00   0.0  0
 JZS  CONST_45  H5    C5   C6   C7    180.00   0.0  0
 JZS  CONST_46  H17   C17  C12  C11   180.00   0.0  0
 JZS  CONST_47  C13   N4   C12  C11   180.00   0.0  0
 JZS  CONST_48  C17   C12  N4   C13     0.00   0.0  0
 JZS  CONST_50  C4    C3   N1   C2    180.00   0.0  0
 JZS  CONST_51  HN1   N1   C3   C4      0.00   0.0  0
 JZS  CONST_52  C2    N1   C3   O1      0.00   0.0  0
 JZS  CONST_53  HN5   N5   C22  C2      0.00   0.0  0
 JZS  CONST_54  HN5A  N5   C22  C2    180.00   0.0  0
 JZS  Var_01    C5    C4   C3   N1    -23.44  30.0  2
 JZS  Var_02    H19   C19  C18  C17    59.80  30.0  2
 JZS  Var_03    C14   C13  N4   C12  -174.99  30.0  3
 JZS  Var_04    O2    C14  C15  F1     51.15  30.0  3
 JZS  Var_05    N4    C13  C14  O2    -57.19  30.0  2
 JZS  Var_06    F4    C16  C14  O2     49.98  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JZS  chir_01  C2  C1  N1  C22  negativ

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
 JZS  plan-1  N2    0.020
 JZS  plan-1  C3    0.020
 JZS  plan-1  C4    0.020
 JZS  plan-1  C5    0.020
 JZS  plan-1  C6    0.020
 JZS  plan-1  C7    0.020
 JZS  plan-1  C8    0.020
 JZS  plan-1  C9    0.020
 JZS  plan-1  H5    0.020
 JZS  plan-1  H6    0.020
 JZS  plan-1  H7    0.020
 JZS  plan-1  H9    0.020
 JZS  plan-2  N2    0.020
 JZS  plan-2  N3    0.020
 JZS  plan-2  C8    0.020
 JZS  plan-2  C10   0.020
 JZS  plan-2  C11   0.020
 JZS  plan-2  C12   0.020
 JZS  plan-2  C17   0.020
 JZS  plan-2  C18   0.020
 JZS  plan-2  C19   0.020
 JZS  plan-2  C20   0.020
 JZS  plan-2  C21   0.020
 JZS  plan-2  H10   0.020
 JZS  plan-2  H17   0.020
 JZS  plan-2  H20   0.020
 JZS  plan-2  N4    0.020
 JZS  plan-3  N1    0.020
 JZS  plan-3  O1    0.020
 JZS  plan-3  C2    0.020
 JZS  plan-3  C3    0.020
 JZS  plan-3  C4    0.020
 JZS  plan-3  HN1   0.020
 JZS  plan-4  C2    0.020
 JZS  plan-4  N5    0.020
 JZS  plan-4  C22   0.020
 JZS  plan-4  HN5   0.020
 JZS  plan-4  HN5A  0.020
 JZS  plan-4  O3    0.020
 JZS  plan-5  C12   0.020
 JZS  plan-5  C13   0.020
 JZS  plan-5  HN4   0.020
 JZS  plan-5  N4    0.020

