# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:58:59 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[(1-{2-[(3-chloro-1-methyl-1H-indazol-5-yl)amino]pyrimidin-4-yl}-3-methyl-1H-pyrazol-4-yl)methyl]azetidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(Cl)c2cc(Nc3nccc(n3)n4cc(CN5CC(O)C5)c(C)n4)ccc12
#
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
 X8G  X8G  1-[(1-{2-[(3-chloro-1-methyl-1H-indazol-5-yl)amino]pyrimidin-4-yl}-3-methyl-1H-pyrazol-4-yl)methyl]azetidin-3-ol  ligand  51  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X8G
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
 X8G  C4   C   CR6   0   0.578  -1.3771   1.5842   0.0601
 X8G  C5   C   CR16  0  -0.426  -0.8576   2.7669  -0.4668
 X8G  C6   C   CR16  0   0.014   0.4943   2.7359  -0.7301
 X8G  N1   N   N     0  -0.481   1.2685   1.6785  -0.5094
 X8G  N3   N   N     0  -0.510  -0.6379   0.5238   0.2943
 X8G  CAL  C   CH2   0  -0.294  -6.4940  -0.8885  -0.8530
 X8G  CBA  C   CH1   0  -0.006  -7.4198  -2.1094  -0.8307
 X8G  OAC  O   OH1   0  -0.671  -6.8407  -3.1931  -1.5075
 X8G  CAM  C   CH2   0  -0.298  -7.1997  -2.0966   0.6928
 X8G  NBB  N   NT    0  -0.405  -6.0265  -1.2414   0.4906
 X8G  CAU  C   CR5   0  -0.195  -4.6812   0.7070   0.9823
 X8G  CAJ  C   CR15  0   0.063  -3.3680   0.3629   0.8388
 X8G  CAS  C   CR5   0   0.300  -4.7442   2.0634   0.5560
 X8G  CAA  C   CH3   0  -0.746  -5.9459   2.9399   0.5033
 X8G  NAP  N   N     0  -0.306  -3.5613   2.4997   0.1921
 X8G  NBD  N   NR5   0  -0.399  -2.7266   1.4638   0.3656
 X8G  C2   C   CR6   0   0.624   0.6631   0.6118  -0.0009
 X8G  NAR  N   NH1   0  -0.773   1.3695  -0.5158   0.2676
 X8G  CAT  C   CR6   0   0.361   2.7167  -0.8222   0.0869
 X8G  CAI  C   CR16  0  -0.396   3.6521   0.0072  -0.5006
 X8G  CAY  C   CR56  0   0.009   4.9630  -0.4727  -0.6109
 X8G  CAV  C   CR5   0   0.087   6.1765   0.0345  -1.1274
 X8G  CL1  CL  CL    0  -0.110   6.4033   1.5658  -1.8523
 X8G  NAQ  N   N     0  -0.230   7.1588  -0.8155  -1.0065
 X8G  NBC  N   NR5   0  -0.398   6.6477  -1.9026  -0.4257
 X8G  CAB  C   CH3   0  -0.523   7.4997  -3.0047  -0.0569
 X8G  CAZ  C   CR56  0   0.453   5.3279  -1.7453  -0.1533
 X8G  CAH  C   CR16  0  -0.290   4.3838  -2.5863   0.4481
 X8G  CAG  C   CR16  0  -0.352   3.1042  -2.1097   0.5554
 X8G  H1   H   HCR6  0   0.288  -1.4612   3.6382  -0.6606
 X8G  H2   H   HCR6  0   0.280   0.9845   3.6097  -1.1432
 X8G  H3   H   HCH2  0   0.234  -5.7261  -0.8514  -1.6298
 X8G  H4   H   HCH2  0   0.212  -7.0718   0.0458  -0.8829
 X8G  H5   H   HCH1  0   0.224  -8.4492  -1.9299  -1.1542
 X8G  H6   H   HOH1  0   0.452  -7.3715  -3.9754  -1.3284
 X8G  H7   H   HCH2  0   0.208  -8.0234  -1.5876   1.2109
 X8G  H8   H   HCH2  0   0.232  -7.0061  -3.0519   1.1888
 X8G  H10  H   HCH2  0   0.208  -6.7126   0.4523   1.5574
 X8G  H11  H   HCH2  0   0.252  -5.5888  -0.5992   2.4065
 X8G  H12  H   HCR5  0   0.299  -2.8469  -0.5594   1.0325
 X8G  H13  H   HCH3  0   0.254  -6.3780   3.0783   1.4953
 X8G  H14  H   HCH3  0   0.258  -5.6931   3.9197   0.1026
 X8G  H15  H   HCH3  0   0.250  -6.7230   2.5056  -0.1271
 X8G  H16  H   HNH1  0   0.413   0.8085  -1.2507   0.6704
 X8G  H17  H   HCR6  0   0.286   3.3894   0.9870  -0.8642
 X8G  H18  H   HCH3  0   0.258   7.9450  -2.8518   0.9262
 X8G  H19  H   HCH3  0   0.261   6.9153  -3.9214  -0.0404
 X8G  H20  H   HCH3  0   0.270   8.2881  -3.1095  -0.7968
 X8G  H21  H   HCR6  0   0.283   4.6393  -3.5694   0.8199
 X8G  H22  H   HCR6  0   0.279   2.3532  -2.7390   1.0187
 X8G  CAK  C   CH2   0  -0.383  -5.8081  -0.1655   1.4269

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
 X8G  CL1  CAV  single    1.709  0.020  1.709
 X8G  CAI  CAT  aromatic  1.381  0.020  1.381
 X8G  CAI  CAY  aromatic  1.400  0.020  1.400
 X8G  NAR  CAT  single    1.393  0.020  1.393
 X8G  NAR  C2   single    1.357  0.020  1.357
 X8G  CAV  CAY  aromatic  1.413  0.020  1.413
 X8G  CAV  NAQ  aromatic  1.305  0.020  1.305
 X8G  CAT  CAG  aromatic  1.424  0.020  1.424
 X8G  CAY  CAZ  aromatic  1.401  0.020  1.401
 X8G  N1   C2   aromatic  1.328  0.020  1.328
 X8G  N1   C6   aromatic  1.329  0.020  1.329
 X8G  C2   N3   aromatic  1.337  0.020  1.337
 X8G  NAQ  NBC  aromatic  1.334  0.020  1.334
 X8G  CAG  CAH  aromatic  1.370  0.020  1.370
 X8G  CAZ  NBC  aromatic  1.357  0.020  1.357
 X8G  CAZ  CAH  aromatic  1.400  0.020  1.400
 X8G  C6   C5   aromatic  1.378  0.020  1.378
 X8G  N3   C4   aromatic  1.314  0.020  1.314
 X8G  NBC  CAB  single    1.441  0.020  1.441
 X8G  C5   C4   aromatic  1.395  0.020  1.395
 X8G  C4   NBD  single    1.389  0.020  1.389
 X8G  NBD  CAJ  aromatic  1.359  0.020  1.359
 X8G  NBD  NAP  aromatic  1.342  0.020  1.342
 X8G  CAJ  CAU  aromatic  1.365  0.020  1.365
 X8G  NAP  CAS  aromatic  1.312  0.020  1.312
 X8G  CAU  CAS  aromatic  1.423  0.020  1.423
 X8G  CAU  CAK  single    1.493  0.020  1.493
 X8G  CAS  CAA  single    1.488  0.020  1.488
 X8G  CAK  NBB  single    1.443  0.020  1.443
 X8G  NBB  CAM  single    1.466  0.020  1.466
 X8G  NBB  CAL  single    1.466  0.020  1.466
 X8G  CAM  CBA  single    1.539  0.020  1.539
 X8G  CAL  CBA  single    1.532  0.020  1.532
 X8G  OAC  CBA  single    1.403  0.020  1.403
 X8G  C5   H1   single    0.930  0.020  1.080
 X8G  C6   H2   single    0.930  0.020  1.080
 X8G  CAL  H3   single    0.970  0.020  1.090
 X8G  CAL  H4   single    0.970  0.020  1.090
 X8G  CBA  H5   single    0.970  0.020  1.090
 X8G  OAC  H6   single    0.850  0.020  0.980
 X8G  CAM  H7   single    0.970  0.020  1.090
 X8G  CAM  H8   single    0.970  0.020  1.090
 X8G  CAK  H10  single    0.970  0.020  1.090
 X8G  CAK  H11  single    0.970  0.020  1.090
 X8G  CAJ  H12  single    0.930  0.020  1.080
 X8G  CAA  H13  single    0.970  0.020  1.090
 X8G  CAA  H14  single    0.970  0.020  1.090
 X8G  CAA  H15  single    0.970  0.020  1.090
 X8G  NAR  H16  single    0.860  0.020  1.020
 X8G  CAI  H17  single    0.930  0.020  1.080
 X8G  CAB  H18  single    0.970  0.020  1.090
 X8G  CAB  H19  single    0.970  0.020  1.090
 X8G  CAB  H20  single    0.970  0.020  1.090
 X8G  CAH  H21  single    0.930  0.020  1.080
 X8G  CAG  H22  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
 X8G  NBD  C4   N3   115.95  3.000
 X8G  NBD  C4   C5   121.22  3.000
 X8G  N3   C4   C5   122.82  3.000
 X8G  H1   C5   C6   122.25  3.000
 X8G  H1   C5   C4   123.01  3.000
 X8G  C6   C5   C4   114.74  3.000
 X8G  H2   C6   N1   116.18  3.000
 X8G  H2   C6   C5   119.91  3.000
 X8G  N1   C6   C5   123.91  3.000
 X8G  C2   N1   C6   115.92  3.000
 X8G  C2   N3   C4   117.07  3.000
 X8G  H4   CAL  H3   108.73  3.000
 X8G  H4   CAL  NBB  113.41  3.000
 X8G  H3   CAL  NBB  115.83  3.000
 X8G  H4   CAL  CBA  111.11  3.000
 X8G  H3   CAL  CBA  117.51  3.000
 X8G  NBB  CAL  CBA   89.29  3.000
 X8G  H5   CBA  CAM  115.21  3.000
 X8G  H5   CBA  OAC  111.88  3.000
 X8G  CAM  CBA  OAC  115.14  3.000
 X8G  H5   CBA  CAL  115.70  3.000
 X8G  OAC  CBA  CAL  111.04  3.000
 X8G  CAM  CBA  CAL   85.49  3.000
 X8G  H6   OAC  CBA  108.09  3.000
 X8G  H8   CAM  H7   108.89  3.000
 X8G  H8   CAM  NBB  115.50  3.000
 X8G  H7   CAM  NBB  113.26  3.000
 X8G  H8   CAM  CBA  117.84  3.000
 X8G  H7   CAM  CBA  111.31  3.000
 X8G  NBB  CAM  CBA   89.02  3.000
 X8G  CAK  NBB  CAM  117.82  3.000
 X8G  CAM  NBB  CAL   90.66  3.000
 X8G  CAK  NBB  CAL  117.62  3.000
 X8G  CAS  CAU  CAJ  104.56  3.000
 X8G  CAS  CAU  CAK  127.79  3.000
 X8G  CAJ  CAU  CAK  127.60  3.000
 X8G  H12  CAJ  NBD  121.87  3.000
 X8G  H12  CAJ  CAU  131.50  3.000
 X8G  NBD  CAJ  CAU  106.64  3.000
 X8G  NAP  CAS  CAA  121.47  3.000
 X8G  CAA  CAS  CAU  127.42  3.000
 X8G  NAP  CAS  CAU  111.10  3.000
 X8G  H15  CAA  H14  108.12  3.000
 X8G  H15  CAA  H13  107.08  3.000
 X8G  H14  CAA  H13  108.22  3.000
 X8G  H15  CAA  CAS  111.17  3.000
 X8G  H14  CAA  CAS  110.84  3.000
 X8G  H13  CAA  CAS  111.25  3.000
 X8G  NBD  NAP  CAS  105.56  3.000
 X8G  NAP  NBD  CAJ  112.14  3.000
 X8G  NAP  NBD  C4   120.61  3.000
 X8G  CAJ  NBD  C4   127.25  3.000
 X8G  NAR  C2   N3   114.08  3.000
 X8G  N3   C2   N1   125.53  3.000
 X8G  NAR  C2   N1   120.39  3.000
 X8G  H16  NAR  CAT  115.43  3.000
 X8G  H16  NAR  C2   113.26  3.000
 X8G  CAT  NAR  C2   131.31  3.000
 X8G  CAG  CAT  CAI  119.91  3.000
 X8G  CAG  CAT  NAR  114.79  3.000
 X8G  CAI  CAT  NAR  125.30  3.000
 X8G  H17  CAI  CAY  120.88  3.000
 X8G  H17  CAI  CAT  121.63  3.000
 X8G  CAY  CAI  CAT  117.49  3.000
 X8G  CAZ  CAY  CAV  102.82  3.000
 X8G  CAZ  CAY  CAI  121.97  3.000
 X8G  CAV  CAY  CAI  135.21  3.000
 X8G  NAQ  CAV  CL1  121.54  3.000
 X8G  NAQ  CAV  CAY  112.26  3.000
 X8G  CL1  CAV  CAY  126.20  3.000
 X8G  NBC  NAQ  CAV  106.43  3.000
 X8G  CAZ  NBC  CAB  127.77  3.000
 X8G  CAB  NBC  NAQ  120.53  3.000
 X8G  CAZ  NBC  NAQ  111.44  3.000
 X8G  H20  CAB  H19  108.61  3.000
 X8G  H20  CAB  H18  109.35  3.000
 X8G  H19  CAB  H18  108.91  3.000
 X8G  H20  CAB  NBC  109.19  3.000
 X8G  H19  CAB  NBC  109.32  3.000
 X8G  H18  CAB  NBC  111.41  3.000
 X8G  CAH  CAZ  NBC  132.26  3.000
 X8G  CAH  CAZ  CAY  120.69  3.000
 X8G  NBC  CAZ  CAY  107.05  3.000
 X8G  H21  CAH  CAG  120.66  3.000
 X8G  H21  CAH  CAZ  122.30  3.000
 X8G  CAG  CAH  CAZ  117.04  3.000
 X8G  H22  CAG  CAH  118.61  3.000
 X8G  H22  CAG  CAT  118.50  3.000
 X8G  CAH  CAG  CAT  122.90  3.000
 X8G  H11  CAK  H10  106.30  3.000
 X8G  H11  CAK  CAU  110.32  3.000
 X8G  H10  CAK  CAU  109.08  3.000
 X8G  H11  CAK  NBB  108.41  3.000
 X8G  H10  CAK  NBB  111.73  3.000
 X8G  CAU  CAK  NBB  110.90  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
 X8G  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 X8G  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 X8G  CONST_03  CAU  CAJ  NBD  C4   180.00   0.0  0
 X8G  CONST_04  CAS  NAP  NBD  C4   180.00   0.0  0
 X8G  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 X8G  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 X8G  CONST_07  CAJ  NBD  C4   C5   180.00   0.0  0
 X8G  CONST_08  NAP  NBD  C4   C5     0.00   0.0  0
 X8G  CONST_09  N3   C2   N1   C6     0.00   0.0  0
 X8G  CONST_10  N3   C4   C5   C6     0.00   0.0  0
 X8G  CONST_11  NBD  C4   C5   C6   180.00   0.0  0
 X8G  CONST_12  CAJ  NBD  C4   N3     0.00   0.0  0
 X8G  CONST_13  NAP  NBD  C4   N3   180.00   0.0  0
 X8G  CONST_14  NAP  NBD  CAJ  CAU    0.00   0.0  0
 X8G  CONST_15  NBD  NAP  CAS  CAU    0.00   0.0  0
 X8G  CONST_16  CAS  NAP  NBD  CAJ    0.00   0.0  0
 X8G  CONST_17  NAP  CAS  CAU  CAJ    0.00   0.0  0
 X8G  CONST_18  NBD  CAJ  CAU  CAS    0.00   0.0  0
 X8G  CONST_19  C2   N3   C4   NBD  180.00   0.0  0
 X8G  CONST_20  CAV  CAY  CAI  CAT  180.00   0.0  0
 X8G  CONST_21  CAZ  CAY  CAI  CAT    0.00   0.0  0
 X8G  CONST_22  CAZ  CAH  CAG  CAT    0.00   0.0  0
 X8G  CONST_23  CAH  CAG  CAT  CAI    0.00   0.0  0
 X8G  CONST_24  NAQ  CAV  CAY  CAI  180.00   0.0  0
 X8G  CONST_25  NBC  CAZ  CAY  CAI  180.00   0.0  0
 X8G  CONST_26  CAH  CAZ  CAY  CAI    0.00   0.0  0
 X8G  CONST_27  CAG  CAT  CAI  CAY    0.00   0.0  0
 X8G  CONST_28  NBC  NAQ  CAV  CAY    0.00   0.0  0
 X8G  CONST_29  NAQ  NBC  CAZ  CAY    0.00   0.0  0
 X8G  CONST_30  CAG  CAH  CAZ  CAY    0.00   0.0  0
 X8G  CONST_31  NBC  CAZ  CAY  CAV    0.00   0.0  0
 X8G  CONST_32  CAH  CAZ  CAY  CAV  180.00   0.0  0
 X8G  CONST_33  CAZ  NBC  NAQ  CAV    0.00   0.0  0
 X8G  CONST_34  CAZ  CAY  CAV  NAQ    0.00   0.0  0
 X8G  CONST_35  CAH  CAZ  NBC  NAQ  180.00   0.0  0
 X8G  CONST_36  CAG  CAH  CAZ  NBC  180.00   0.0  0
 X8G  CONST_37  NAR  C2   N3   C4   180.00   0.0  0
 X8G  CONST_38  NAR  C2   N1   C6   180.00   0.0  0
 X8G  CONST_39  NBD  CAJ  CAU  CAK  180.00   0.0  0
 X8G  CONST_40  NAP  CAS  CAU  CAK  180.00   0.0  0
 X8G  CONST_41  CAA  CAS  CAU  CAJ  180.00   0.0  0
 X8G  CONST_42  NBD  NAP  CAS  CAA  180.00   0.0  0
 X8G  CONST_43  CAY  CAI  CAT  NAR  180.00   0.0  0
 X8G  CONST_44  CAH  CAG  CAT  NAR  180.00   0.0  0
 X8G  CONST_45  CL1  CAV  CAY  CAI    0.00   0.0  0
 X8G  CONST_46  CAB  NBC  CAZ  CAY  180.00   0.0  0
 X8G  CONST_47  CAB  NBC  NAQ  CAV  180.00   0.0  0
 X8G  CONST_48  CAZ  CAY  CAV  CL1  180.00   0.0  0
 X8G  CONST_49  NBC  NAQ  CAV  CL1  180.00   0.0  0
 X8G  CONST_50  CAH  CAZ  NBC  CAB    0.00   0.0  0
 X8G  CONST_51  H2   C6   C5   C4   180.00   0.0  0
 X8G  CONST_52  H12  CAJ  NBD  C4     0.00   0.0  0
 X8G  CONST_53  H1   C5   C6   N1   180.00   0.0  0
 X8G  CONST_54  H21  CAH  CAG  CAT  180.00   0.0  0
 X8G  CONST_55  H22  CAG  CAT  CAI  180.00   0.0  0
 X8G  CONST_56  H17  CAI  CAY  CAV    0.00   0.0  0
 X8G  Var_01    CBA  CAM  NBB  CAL   18.04  30.0  1
 X8G  Var_02    CAT  NAR  C2   N1    -1.14  30.0  2
 X8G  Var_03    CAU  CAK  NBB  CAL  -65.88  30.0  2
 X8G  Var_04    CAJ  CAU  CAK  NBB  -63.67  30.0  2
 X8G  Var_05    CAI  CAT  NAR  C2    -3.30  30.0  2
 X8G  Var_06    H13  CAA  CAS  CAU   61.42  30.0  2
 X8G  Var_07    H18  CAB  NBC  NAQ   85.45  30.0  2

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
 X8G  chir_01  CBA  CAM  CAL  OAC  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
 X8G  plan-1  C4   0.020
 X8G  plan-1  CAU  0.020
 X8G  plan-1  CAJ  0.020
 X8G  plan-1  CAS  0.020
 X8G  plan-1  CAA  0.020
 X8G  plan-1  NAP  0.020
 X8G  plan-1  NBD  0.020
 X8G  plan-1  H12  0.020
 X8G  plan-1  CAK  0.020
 X8G  plan-2  C4   0.020
 X8G  plan-2  C5   0.020
 X8G  plan-2  C6   0.020
 X8G  plan-2  N1   0.020
 X8G  plan-2  N3   0.020
 X8G  plan-2  NBD  0.020
 X8G  plan-2  C2   0.020
 X8G  plan-2  NAR  0.020
 X8G  plan-2  H1   0.020
 X8G  plan-2  H2   0.020
 X8G  plan-3  NAR  0.020
 X8G  plan-3  CAT  0.020
 X8G  plan-3  CAI  0.020
 X8G  plan-3  CAY  0.020
 X8G  plan-3  CAV  0.020
 X8G  plan-3  CL1  0.020
 X8G  plan-3  NAQ  0.020
 X8G  plan-3  NBC  0.020
 X8G  plan-3  CAB  0.020
 X8G  plan-3  CAZ  0.020
 X8G  plan-3  CAH  0.020
 X8G  plan-3  CAG  0.020
 X8G  plan-3  H17  0.020
 X8G  plan-3  H21  0.020
 X8G  plan-3  H22  0.020

