# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:35:25 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: trans-4-[(4-{4-[3-(methylsulfonyl)propoxy]-1H-indazol-1-yl}pyrimidin-2-yl)amino]cyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)CCCOc1cccc2n(ncc12)c3ccnc(N[C@@H]4CC[C@@H](O)CC4)n3
#
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
 1BK  1BK  trans-4-[(4-{4-[3-(methylsulfonyl)propoxy]-1H-indazol-1-yl}pyrimidin-2-yl)amino]cyclohexanol  ligand  58  31  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1BK
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
 1BK  N1   N  NH1   0  -0.666   -4.8719  -0.3183   0.5643
 1BK  C2   C  CR6   0   0.619   -4.1074   0.7827   0.4446
 1BK  N3   N  N     0  -0.476   -4.7061   1.9724   0.3594
 1BK  C4   C  CR16  0  -0.012   -3.8981   3.0200   0.2639
 1BK  C5   C  CR16  0  -0.438   -2.5214   2.9383   0.2419
 1BK  C6   C  CR6   0   0.556   -2.0122   1.6408   0.3338
 1BK  N7   N  N     0  -0.515   -2.7821   0.5814   0.4376
 1BK  N8   N  NR5   0  -0.508   -0.6427   1.4093   0.3101
 1BK  N9   N  N     0  -0.236    0.1958   2.4590   0.1635
 1BK  C10  C  CR15  0  -0.038    1.4037   1.9845   0.1442
 1BK  C11  C  CR56  0   0.458    0.0462   0.2178   0.3896
 1BK  C12  C  CR56  0  -0.244    1.3971   0.5694   0.2821
 1BK  C13  C  CR6   0   0.344    2.4044  -0.4070   0.3195
 1BK  C14  C  CR16  0  -0.410    2.0190  -1.7259   0.4738
 1BK  C15  C  CR16  0  -0.246    0.6564  -2.0511   0.5832
 1BK  C16  C  CR16  0  -0.305   -0.3543  -1.1146   0.5445
 1BK  C17  C  CH1   0  -0.048   -6.3051  -0.3452   0.3532
 1BK  C18  C  CH2   0  -0.458   -6.8836  -1.6039   0.9926
 1BK  C19  C  CH2   0  -0.463   -8.3893  -1.7011   0.7697
 1BK  C20  C  CH1   0   0.085   -8.7310  -1.6470  -0.7107
 1BK  C21  C  CH2   0  -0.481   -8.1768  -0.3698  -1.3314
 1BK  C22  C  CH2   0  -0.444   -6.6681  -0.2798  -1.1305
 1BK  O23  O  OH1   0  -0.679  -10.1350  -1.7426  -0.8397
 1BK  O24  O  O2    0  -0.463    3.6622   0.0370   0.1988
 1BK  C25  C  CH2   0  -0.170    4.7191  -0.9092   0.2063
 1BK  C26  C  CH2   0  -0.471    6.0141  -0.1481   0.0026
 1BK  C27  C  CH2   0  -0.619    7.1816  -1.1252   0.0080
 1BK  S28  S  S     0   1.196    8.7249  -0.2518  -0.2444
 1BK  C29  C  CH3   0  -0.786    9.9531  -1.5351  -0.1912
 1BK  O30  O  OS    0  -0.687    8.7135   0.3317  -1.5867
 1BK  O31  O  OS    0  -0.688    8.9368   0.6489   0.8896
 1BK  H1   H  HNH1  0   0.388   -4.3791  -1.1958   0.5000
 1BK  H2   H  HCR6  0   0.271   -4.3779   3.9904   0.1958
 1BK  H3   H  HCR6  0   0.282   -1.8981   3.8124   0.1541
 1BK  H4   H  HCR5  0   0.282    2.2493   2.6457   0.0340
 1BK  H5   H  HCR6  0   0.287    2.7444  -2.5259   0.5132
 1BK  H6   H  HCR6  0   0.267    0.3936  -3.0940   0.7039
 1BK  H7   H  HCR6  0   0.281   -1.3895  -1.3971   0.6313
 1BK  H8   H  HCH1  0   0.238   -6.7348   0.5263   0.8550
 1BK  H9   H  HCH2  0   0.223   -6.3934  -2.4849   0.5609
 1BK  H10  H  HCH2  0   0.249   -6.6622  -1.6121   2.0620
 1BK  H11  H  HCH2  0   0.241   -8.7671  -2.6271   1.2102
 1BK  H12  H  HCH2  0   0.221   -8.8909  -0.8725   1.2823
 1BK  H13  H  HCH1  0   0.186   -8.2416  -2.5030  -1.2037
 1BK  H14  H  HCH2  0   0.236   -8.4111  -0.3350  -2.3996
 1BK  H15  H  HCH2  0   0.220   -8.6666   0.4943  -0.8683
 1BK  H16  H  HCH2  0   0.242   -6.2845   0.6443  -1.5678
 1BK  H17  H  HCH2  0   0.218   -6.1757  -1.1090  -1.6509
 1BK  H18  H  HOH1  0   0.446  -10.3513  -1.7305  -1.7773
 1BK  H19  H  HCH2  0   0.236    4.7379  -1.4498   1.1588
 1BK  H20  H  HCH2  0   0.237    4.5777  -1.6444  -0.5933
 1BK  H21  H  HCH2  0   0.265    5.9785   0.3869  -0.9483
 1BK  H22  H  HCH2  0   0.266    6.1370   0.5862   0.8004
 1BK  H23  H  HCH2  0   0.303    7.2640  -1.6536   0.9598
 1BK  H24  H  HCH2  0   0.304    7.0970  -1.8625  -0.7923
 1BK  H25  H  HCH3  0   0.295    9.7753  -2.2410  -0.9987
 1BK  H26  H  HCH3  0   0.312   10.9234  -1.0576  -0.3203
 1BK  H27  H  HCH3  0   0.295    9.9124  -2.0380   0.7722

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
 1BK  C22  C21  single    1.525  0.020  1.525
 1BK  C22  C17  single    1.529  0.020  1.529
 1BK  C21  C20  single    1.524  0.020  1.524
 1BK  N1   C17  single    1.449  0.020  1.449
 1BK  N1   C2   single    1.346  0.020  1.346
 1BK  N3   C2   aromatic  1.335  0.020  1.335
 1BK  N3   C4   aromatic  1.326  0.020  1.326
 1BK  C17  C18  single    1.526  0.020  1.526
 1BK  C20  O23  single    1.413  0.020  1.413
 1BK  C20  C19  single    1.520  0.020  1.520
 1BK  C2   N7   aromatic  1.340  0.020  1.340
 1BK  C4   C5   aromatic  1.379  0.020  1.379
 1BK  C18  C19  single    1.525  0.020  1.525
 1BK  N7   C6   aromatic  1.314  0.020  1.314
 1BK  C5   C6   aromatic  1.397  0.020  1.397
 1BK  C6   N8   single    1.389  0.020  1.389
 1BK  N8   C11  aromatic  1.379  0.020  1.379
 1BK  N8   N9   aromatic  1.351  0.020  1.351
 1BK  C16  C11  aromatic  1.400  0.020  1.400
 1BK  C16  C15  aromatic  1.378  0.020  1.378
 1BK  C11  C12  aromatic  1.400  0.020  1.400
 1BK  C15  C14  aromatic  1.405  0.020  1.405
 1BK  N9   C10  aromatic  1.298  0.020  1.298
 1BK  C12  C10  aromatic  1.422  0.020  1.422
 1BK  C12  C13  aromatic  1.403  0.020  1.403
 1BK  C14  C13  aromatic  1.383  0.020  1.383
 1BK  C13  O24  single    1.339  0.020  1.339
 1BK  O24  C25  single    1.419  0.020  1.419
 1BK  C25  C26  single    1.516  0.020  1.516
 1BK  C26  C27  single    1.522  0.020  1.522
 1BK  C27  S28  single    1.791  0.020  1.791
 1BK  O30  S28  double    1.464  0.020  1.464
 1BK  S28  O31  double    1.464  0.020  1.464
 1BK  S28  C29  single    1.777  0.020  1.777
 1BK  N1   H1   single    0.890  0.020  1.040
 1BK  C4   H2   single    0.930  0.020  1.080
 1BK  C5   H3   single    0.930  0.020  1.080
 1BK  C10  H4   single    0.930  0.020  1.080
 1BK  C14  H5   single    0.930  0.020  1.080
 1BK  C15  H6   single    0.930  0.020  1.080
 1BK  C16  H7   single    0.930  0.020  1.080
 1BK  C17  H8   single    0.970  0.020  1.090
 1BK  C18  H9   single    0.970  0.020  1.090
 1BK  C18  H10  single    0.970  0.020  1.090
 1BK  C19  H11  single    0.970  0.020  1.090
 1BK  C19  H12  single    0.970  0.020  1.090
 1BK  C20  H13  single    0.970  0.020  1.090
 1BK  C21  H14  single    0.970  0.020  1.090
 1BK  C21  H15  single    0.970  0.020  1.090
 1BK  C22  H16  single    0.970  0.020  1.090
 1BK  C22  H17  single    0.970  0.020  1.090
 1BK  O23  H18  single    0.850  0.020  0.980
 1BK  C25  H19  single    0.970  0.020  1.090
 1BK  C25  H20  single    0.970  0.020  1.090
 1BK  C26  H21  single    0.970  0.020  1.090
 1BK  C26  H22  single    0.970  0.020  1.090
 1BK  C27  H23  single    0.970  0.020  1.090
 1BK  C27  H24  single    0.970  0.020  1.090
 1BK  C29  H25  single    0.970  0.020  1.090
 1BK  C29  H26  single    0.970  0.020  1.090
 1BK  C29  H27  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
 1BK  H1   N1   C17  117.25  3.000
 1BK  H1   N1   C2   115.38  3.000
 1BK  C17  N1   C2   124.35  3.000
 1BK  N7   C2   N3   125.25  3.000
 1BK  N7   C2   N1   116.05  3.000
 1BK  N3   C2   N1   118.70  3.000
 1BK  C4   N3   C2   115.81  3.000
 1BK  H2   C4   C5   119.57  3.000
 1BK  H2   C4   N3   116.21  3.000
 1BK  C5   C4   N3   124.22  3.000
 1BK  H3   C5   C6   123.25  3.000
 1BK  H3   C5   C4   122.06  3.000
 1BK  C6   C5   C4   114.69  3.000
 1BK  N8   C6   N7   116.40  3.000
 1BK  N8   C6   C5   120.87  3.000
 1BK  N7   C6   C5   122.73  3.000
 1BK  C6   N7   C2   117.30  3.000
 1BK  C11  N8   N9   111.56  3.000
 1BK  N9   N8   C6   118.95  3.000
 1BK  C11  N8   C6   129.47  3.000
 1BK  C10  N9   N8   107.16  3.000
 1BK  H4   C10  C12  128.57  3.000
 1BK  H4   C10  N9   120.45  3.000
 1BK  C12  C10  N9   110.98  3.000
 1BK  C16  C11  C12  121.57  3.000
 1BK  C12  C11  N8   105.11  3.000
 1BK  C16  C11  N8   133.32  3.000
 1BK  C13  C12  C11  121.05  3.000
 1BK  C13  C12  C10  133.76  3.000
 1BK  C11  C12  C10  105.19  3.000
 1BK  O24  C13  C14  126.02  3.000
 1BK  O24  C13  C12  116.17  3.000
 1BK  C14  C13  C12  117.81  3.000
 1BK  H5   C14  C15  118.48  3.000
 1BK  H5   C14  C13  121.54  3.000
 1BK  C15  C14  C13  119.98  3.000
 1BK  H6   C15  C16  118.67  3.000
 1BK  H6   C15  C14  117.85  3.000
 1BK  C16  C15  C14  123.48  3.000
 1BK  H7   C16  C15  121.63  3.000
 1BK  H7   C16  C11  122.26  3.000
 1BK  C15  C16  C11  116.10  3.000
 1BK  H8   C17  C22  108.53  3.000
 1BK  H8   C17  C18  108.43  3.000
 1BK  C22  C17  C18  110.61  3.000
 1BK  H8   C17  N1   107.88  3.000
 1BK  C18  C17  N1   109.23  3.000
 1BK  C22  C17  N1   112.06  3.000
 1BK  H10  C18  H9   106.78  3.000
 1BK  H10  C18  C19  110.04  3.000
 1BK  H9   C18  C19  109.42  3.000
 1BK  H10  C18  C17  109.86  3.000
 1BK  H9   C18  C17  109.17  3.000
 1BK  C19  C18  C17  111.45  3.000
 1BK  H12  C19  H11  107.09  3.000
 1BK  H12  C19  C20  109.01  3.000
 1BK  H11  C19  C20  110.18  3.000
 1BK  H12  C19  C18  109.59  3.000
 1BK  H11  C19  C18  109.66  3.000
 1BK  C20  C19  C18  111.22  3.000
 1BK  H13  C20  O23  110.35  3.000
 1BK  H13  C20  C21  107.88  3.000
 1BK  O23  C20  C21  112.38  3.000
 1BK  H13  C20  C19  107.94  3.000
 1BK  O23  C20  C19  108.05  3.000
 1BK  C21  C20  C19  110.16  3.000
 1BK  H15  C21  H14  106.97  3.000
 1BK  H15  C21  C22  109.88  3.000
 1BK  H14  C21  C22  109.80  3.000
 1BK  H15  C21  C20  109.03  3.000
 1BK  H14  C21  C20  110.26  3.000
 1BK  C22  C21  C20  110.83  3.000
 1BK  H17  C22  H16  107.00  3.000
 1BK  H17  C22  C21  109.72  3.000
 1BK  H16  C22  C21  110.17  3.000
 1BK  H17  C22  C17  108.77  3.000
 1BK  H16  C22  C17  109.97  3.000
 1BK  C21  C22  C17  111.12  3.000
 1BK  H18  O23  C20  108.14  3.000
 1BK  C25  O24  C13  118.56  3.000
 1BK  H20  C25  H19  107.80  3.000
 1BK  H20  C25  C26  110.44  3.000
 1BK  H19  C25  C26  110.49  3.000
 1BK  H20  C25  O24  110.34  3.000
 1BK  H19  C25  O24  110.28  3.000
 1BK  C26  C25  O24  107.51  3.000
 1BK  H22  C26  H21  108.11  3.000
 1BK  H22  C26  C27  110.05  3.000
 1BK  H21  C26  C27  110.03  3.000
 1BK  H22  C26  C25  109.63  3.000
 1BK  H21  C26  C25  109.59  3.000
 1BK  C27  C26  C25  109.42  3.000
 1BK  H24  C27  H23  108.55  3.000
 1BK  H24  C27  S28  107.03  3.000
 1BK  H23  C27  S28  107.09  3.000
 1BK  H24  C27  C26  111.81  3.000
 1BK  H23  C27  C26  111.82  3.000
 1BK  S28  C27  C26  110.32  3.000
 1BK  O31  S28  O30  117.80  3.000
 1BK  O31  S28  C29  108.73  3.000
 1BK  O30  S28  C29  108.71  3.000
 1BK  C29  S28  C27  103.83  3.000
 1BK  O31  S28  C27  108.40  3.000
 1BK  O30  S28  C27  108.48  3.000
 1BK  H27  C29  H26  109.94  3.000
 1BK  H27  C29  H25  110.58  3.000
 1BK  H26  C29  H25  110.02  3.000
 1BK  H27  C29  S28  109.55  3.000
 1BK  H26  C29  S28  107.19  3.000
 1BK  H25  C29  S28  109.49  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
 1BK  CONST_01  C5   C4   N3   C2     0.00   0.0  0
 1BK  CONST_02  C5   C6   N7   C2     0.00   0.0  0
 1BK  CONST_03  N8   C6   N7   C2   180.00   0.0  0
 1BK  CONST_04  C6   N7   C2   N3     0.00   0.0  0
 1BK  CONST_05  C6   C5   C4   N3     0.00   0.0  0
 1BK  CONST_06  N7   C2   N3   C4     0.00   0.0  0
 1BK  CONST_07  N7   C6   C5   C4     0.00   0.0  0
 1BK  CONST_08  N8   C6   C5   C4   180.00   0.0  0
 1BK  CONST_09  C11  N8   C6   C5   180.00   0.0  0
 1BK  CONST_10  N9   N8   C6   C5     0.00   0.0  0
 1BK  CONST_11  C16  C11  N8   C6     0.00   0.0  0
 1BK  CONST_12  C12  C11  N8   C6   180.00   0.0  0
 1BK  CONST_13  C10  N9   N8   C6   180.00   0.0  0
 1BK  CONST_14  C11  N8   C6   N7     0.00   0.0  0
 1BK  CONST_15  N9   N8   C6   N7   180.00   0.0  0
 1BK  CONST_16  C15  C16  C11  N8   180.00   0.0  0
 1BK  CONST_17  C10  C12  C11  N8     0.00   0.0  0
 1BK  CONST_18  C13  C12  C11  N8   180.00   0.0  0
 1BK  CONST_19  C12  C10  N9   N8     0.00   0.0  0
 1BK  CONST_20  C16  C11  N8   N9   180.00   0.0  0
 1BK  CONST_21  C12  C11  N8   N9     0.00   0.0  0
 1BK  CONST_22  C11  C12  C10  N9     0.00   0.0  0
 1BK  CONST_23  C13  C12  C10  N9   180.00   0.0  0
 1BK  CONST_24  C11  N8   N9   C10    0.00   0.0  0
 1BK  CONST_25  C16  C11  C12  C10  180.00   0.0  0
 1BK  CONST_26  C14  C13  C12  C10  180.00   0.0  0
 1BK  CONST_27  C14  C15  C16  C11    0.00   0.0  0
 1BK  CONST_28  C14  C13  C12  C11    0.00   0.0  0
 1BK  CONST_29  C15  C16  C11  C12    0.00   0.0  0
 1BK  CONST_30  C15  C14  C13  C12    0.00   0.0  0
 1BK  CONST_31  C16  C11  C12  C13    0.00   0.0  0
 1BK  CONST_32  C16  C15  C14  C13    0.00   0.0  0
 1BK  CONST_33  C4   N3   C2   N1   180.00   0.0  0
 1BK  CONST_34  C6   N7   C2   N1   180.00   0.0  0
 1BK  CONST_35  O24  C13  C12  C10    0.00   0.0  0
 1BK  CONST_36  O24  C13  C12  C11  180.00   0.0  0
 1BK  CONST_37  O24  C13  C14  C15  180.00   0.0  0
 1BK  CONST_38  C17  N1   C2   N3     0.00   0.0  0
 1BK  CONST_39  C17  N1   C2   N7   180.00   0.0  0
 1BK  CONST_40  H2   C4   N3   C2   180.00   0.0  0
 1BK  CONST_41  H3   C5   C4   N3   180.00   0.0  0
 1BK  CONST_42  H7   C16  C11  N8     0.00   0.0  0
 1BK  CONST_43  H4   C10  N9   N8   180.00   0.0  0
 1BK  CONST_44  H6   C15  C16  C11  180.00   0.0  0
 1BK  CONST_45  H5   C14  C13  C12  180.00   0.0  0
 1BK  CONST_46  H1   N1   C2   N3   180.00   0.0  0
 1BK  Var_01    C20  C21  C22  C17  -57.16  30.0  1
 1BK  Var_02    C20  C19  C18  C17   56.05  30.0  1
 1BK  Var_03    C26  C25  O24  C13  177.86  30.0  3
 1BK  Var_04    C27  C26  C25  O24  179.82  30.0  3
 1BK  Var_05    S28  C27  C26  C25  179.55  30.0  3
 1BK  Var_06    O30  S28  C27  C26  -65.05  30.0  3
 1BK  Var_07    H25  C29  S28  C27   61.80  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
 1BK  chir_01  C17  C22  N1   C18  positiv
 1BK  chir_02  C20  O23  C19  C21  positiv

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
 1BK  plan-1  N1   0.020
 1BK  plan-1  C2   0.020
 1BK  plan-1  N3   0.020
 1BK  plan-1  C4   0.020
 1BK  plan-1  C5   0.020
 1BK  plan-1  C6   0.020
 1BK  plan-1  N7   0.020
 1BK  plan-1  N8   0.020
 1BK  plan-1  H2   0.020
 1BK  plan-1  H3   0.020
 1BK  plan-2  C6   0.020
 1BK  plan-2  N8   0.020
 1BK  plan-2  N9   0.020
 1BK  plan-2  C10  0.020
 1BK  plan-2  C11  0.020
 1BK  plan-2  C12  0.020
 1BK  plan-2  C13  0.020
 1BK  plan-2  C14  0.020
 1BK  plan-2  C15  0.020
 1BK  plan-2  C16  0.020
 1BK  plan-2  O24  0.020
 1BK  plan-2  H4   0.020
 1BK  plan-2  H5   0.020
 1BK  plan-2  H6   0.020
 1BK  plan-2  H7   0.020
 1BK  plan-3  N1   0.020
 1BK  plan-3  C2   0.020
 1BK  plan-3  C17  0.020
 1BK  plan-3  H1   0.020

