# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 10:01:40 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-[(2S)-4-(5-fluoropyrimidin-2-yl)-1-({4-[5-(2,2,2-trifluoroethoxy)pyrimidin-2-yl]piperazin-1-yl}sulfonyl)butan-2-yl]-N-hydroxyformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON(C=O)[C@@H](CCc1ncc(F)cn1)C[S](=O)(=O)N2CCN(CC2)c3ncc(OCC(F)(F)F)cn3
#
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
 AZ4  AZ4  N-[(2S)-4-(5-fluoropyrimidin-2-yl)-1-({4-[5-(2,2,2-trifluoroethoxy)pyrimidin-2-yl]piperazin-1-yl}sulfonyl)butan-2-yl]-N-hydroxyformamide  ligand  59  36  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AZ4
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
 AZ4  C1   C  C1    0   0.268    4.5396   2.9616   0.6436
 AZ4  C2   C  CH1   0  -0.100    4.1192   0.9570  -0.7687
 AZ4  C3   C  CH2   0  -0.433    4.9013  -0.1122  -0.0047
 AZ4  O4   O  OS    0  -0.661    1.9118   1.9299  -2.7556
 AZ4  O5   O  O2    0  -0.477   -7.2908  -1.7818   0.3480
 AZ4  N6   N  N     0  -0.450   -4.2493  -0.8586  -1.2853
 AZ4  C7   C  CR6   0   0.399    8.2952  -3.1778   1.6677
 AZ4  C8   C  CR16  0  -0.159    8.3274  -1.8946   2.1706
 AZ4  C9   C  CH2   0  -0.649    2.6246   0.8148  -0.4721
 AZ4  C10  C  CH2   0  -0.312   -0.5088   1.6089   0.2221
 AZ4  C11  C  CH2   0  -0.289   -2.0228   1.6512   0.1308
 AZ4  C12  C  CH2   0  -0.289   -1.9287   0.4247  -1.9654
 AZ4  C13  C  CH2   0  -0.311   -0.4156   0.3777  -1.8695
 AZ4  C14  C  CR6   0   0.642   -3.7342  -0.0225  -0.3766
 AZ4  C15  C  CR16  0  -0.082   -5.4084  -1.4167  -1.0109
 AZ4  C16  C  CR6   0   0.240   -6.1004  -1.1646   0.1694
 AZ4  C19  C  CR16  0  -0.115   -5.4875  -0.2882   1.0501
 AZ4  N1   N  NT    0  -0.184    4.6265   2.3008  -0.5280
 AZ4  O2   O  O     0  -0.472    4.2054   2.4512   1.6949
 AZ4  C4   C  CH2   0  -0.503    6.3965  -0.0778  -0.3225
 AZ4  C5   C  CR6   0   0.356    7.1089  -1.1892   0.3853
 AZ4  N2   N  N     0  -0.387    7.0378  -2.4018  -0.1565
 AZ4  C6   C  CR16  0  -0.158    7.6294  -3.4003   0.4795
 AZ4  N3   N  N     0  -0.388    7.7306  -0.9035   1.5241
 AZ4  S1   S  S     0   1.377    1.6180   2.0247  -1.3337
 AZ4  O3   O  OS    0  -0.653    1.7607   3.3081  -0.6634
 AZ4  N4   N  N     0  -0.577    0.0517   1.5455  -1.1270
 AZ4  N5   N  NT    0  -0.516   -2.5188   0.5355  -0.6479
 AZ4  C17  C  CH2   0  -0.372   -7.9998  -1.4943   1.5235
 AZ4  C18  C  CT    0   0.987   -9.3176  -2.2253   1.4181
 AZ4  F2   F  F     0  -0.305   -9.1534  -3.5451   1.2870
 AZ4  F3   F  F     0  -0.307  -10.0489  -2.0156   2.5172
 AZ4  F4   F  F     0  -0.305  -10.0367  -1.8140   0.3691
 AZ4  N7   N  N     0  -0.459   -4.3210   0.2789   0.7782
 AZ4  H1   H  H     0   0.225    4.8299   4.0168   0.5445
 AZ4  H2   H  HCH1  0   0.304    4.2710   0.7774  -1.8340
 AZ4  H3   H  HCH2  0   0.260    4.7410  -0.0074   1.0689
 AZ4  H4   H  HCH2  0   0.260    4.4951  -1.0842  -0.2951
 AZ4  H5   H  HCR6  0   0.300    8.8377  -1.6643   3.0998
 AZ4  H6   H  HCH2  0   0.319    2.2897  -0.1710  -0.8019
 AZ4  H7   H  HCH2  0   0.309    2.4094   0.9106   0.5923
 AZ4  H8   H  HCH2  0   0.281   -0.1669   2.5107   0.7254
 AZ4  H9   H  HCH2  0   0.246   -0.1980   0.7409   0.8156
 AZ4  H10  H  HCH2  0   0.278   -2.4327   1.6100   1.1357
 AZ4  H11  H  HCH2  0   0.238   -2.3309   2.6019  -0.3218
 AZ4  H12  H  HCH2  0   0.238   -2.2276   1.2715  -2.5957
 AZ4  H13  H  HCH2  0   0.278   -2.2738  -0.4854  -2.4470
 AZ4  H14  H  HCH2  0   0.243   -0.1066  -0.5529  -1.3782
 AZ4  H15  H  HCH2  0   0.281   -0.0068   0.3872  -2.8770
 AZ4  H16  H  HCR6  0   0.282   -5.8232  -2.0929  -1.7525
 AZ4  H17  H  HCR6  0   0.289   -5.9326  -0.0222   2.0031
 AZ4  H18  H  HOH1  0   0.479    5.7421   2.9515  -1.9001
 AZ4  H19  H  HCH2  0   0.260    6.5435  -0.1838  -1.3994
 AZ4  H20  H  HCH2  0   0.259    6.8298   0.8741  -0.0145
 AZ4  H21  H  HCR6  0   0.299    7.5752  -4.3909   0.0405
 AZ4  H22  H  HCH2  0   0.275   -7.4712  -1.8388   2.4194
 AZ4  H23  H  HCH2  0   0.274   -8.2005  -0.4228   1.6348
 AZ4  F1   F  F     0  -0.290    8.8934  -4.1809   2.3115
 AZ4  O1   O  OH1   0  -0.543    4.8206   3.0826  -1.6393

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
 AZ4  F3   C18  single    1.337  0.020  1.337
 AZ4  F4   C18  single    1.337  0.020  1.337
 AZ4  C18  F2   single    1.336  0.020  1.336
 AZ4  C18  C17  single    1.511  0.020  1.511
 AZ4  C17  O5   single    1.403  0.020  1.403
 AZ4  O5   C16  single    1.353  0.020  1.353
 AZ4  C16  C15  aromatic  1.391  0.020  1.391
 AZ4  C16  C19  aromatic  1.385  0.020  1.385
 AZ4  C15  N6   aromatic  1.315  0.020  1.315
 AZ4  C19  N7   aromatic  1.325  0.020  1.325
 AZ4  N6   C14  aromatic  1.338  0.020  1.338
 AZ4  N7   C14  aromatic  1.330  0.020  1.330
 AZ4  C14  N5   single    1.365  0.020  1.365
 AZ4  N5   C11  single    1.448  0.020  1.448
 AZ4  N5   C12  single    1.448  0.020  1.448
 AZ4  C11  C10  single    1.517  0.020  1.517
 AZ4  C12  C13  single    1.517  0.020  1.517
 AZ4  F1   C7   single    1.334  0.020  1.334
 AZ4  C10  N4   single    1.462  0.020  1.462
 AZ4  O2   C1   double    1.215  0.020  1.215
 AZ4  O1   N1   single    1.373  0.020  1.373
 AZ4  C7   C6   aromatic  1.380  0.020  1.380
 AZ4  C7   C8   aromatic  1.379  0.020  1.379
 AZ4  C6   N2   aromatic  1.323  0.020  1.323
 AZ4  C13  N4   single    1.461  0.020  1.461
 AZ4  N4   S1   single    1.651  0.020  1.651
 AZ4  C1   N1   single    1.348  0.020  1.348
 AZ4  C8   N3   aromatic  1.325  0.020  1.325
 AZ4  N1   C2   single    1.456  0.020  1.456
 AZ4  N2   C5   aromatic  1.330  0.020  1.330
 AZ4  N3   C5   aromatic  1.328  0.020  1.328
 AZ4  C5   C4   single    1.498  0.020  1.498
 AZ4  S1   C9   single    1.794  0.020  1.794
 AZ4  S1   O4   double    1.455  0.020  1.455
 AZ4  S1   O3   double    1.455  0.020  1.455
 AZ4  C9   C2   single    1.530  0.020  1.530
 AZ4  C2   C3   single    1.529  0.020  1.529
 AZ4  C3   C4   single    1.529  0.020  1.529
 AZ4  C1   H1   single    0.930  0.020  1.080
 AZ4  C2   H2   single    0.970  0.020  1.090
 AZ4  C3   H3   single    0.970  0.020  1.090
 AZ4  C3   H4   single    0.970  0.020  1.090
 AZ4  C8   H5   single    0.930  0.020  1.080
 AZ4  C9   H6   single    0.970  0.020  1.090
 AZ4  C9   H7   single    0.970  0.020  1.090
 AZ4  C10  H8   single    0.970  0.020  1.090
 AZ4  C10  H9   single    0.970  0.020  1.090
 AZ4  C11  H10  single    0.970  0.020  1.090
 AZ4  C11  H11  single    0.970  0.020  1.090
 AZ4  C12  H12  single    0.970  0.020  1.090
 AZ4  C12  H13  single    0.970  0.020  1.090
 AZ4  C13  H14  single    0.970  0.020  1.090
 AZ4  C13  H15  single    0.970  0.020  1.090
 AZ4  C15  H16  single    0.930  0.020  1.080
 AZ4  C19  H17  single    0.930  0.020  1.080
 AZ4  O1   H18  single    0.850  0.020  0.980
 AZ4  C4   H19  single    0.970  0.020  1.090
 AZ4  C4   H20  single    0.970  0.020  1.090
 AZ4  C6   H21  single    0.930  0.020  1.080
 AZ4  C17  H22  single    0.970  0.020  1.090
 AZ4  C17  H23  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
 AZ4  H1   C1   O2   123.63  3.000
 AZ4  H1   C1   N1   112.04  3.000
 AZ4  O2   C1   N1   124.31  3.000
 AZ4  H2   C2   N1   105.36  3.000
 AZ4  H2   C2   C9   108.05  3.000
 AZ4  N1   C2   C9   113.20  3.000
 AZ4  H2   C2   C3   107.55  3.000
 AZ4  C9   C2   C3   109.73  3.000
 AZ4  N1   C2   C3   112.60  3.000
 AZ4  H4   C3   H3   107.01  3.000
 AZ4  H4   C3   C4   109.16  3.000
 AZ4  H3   C3   C4   110.25  3.000
 AZ4  H4   C3   C2   107.40  3.000
 AZ4  H3   C3   C2   110.46  3.000
 AZ4  C4   C3   C2   112.37  3.000
 AZ4  C17  O5   C16  117.51  3.000
 AZ4  C15  N6   C14  117.57  3.000
 AZ4  F1   C7   C6   120.72  3.000
 AZ4  C6   C7   C8   118.38  3.000
 AZ4  F1   C7   C8   120.90  3.000
 AZ4  H5   C8   N3   118.10  3.000
 AZ4  H5   C8   C7   121.40  3.000
 AZ4  N3   C8   C7   120.50  3.000
 AZ4  H7   C9   H6   108.27  3.000
 AZ4  H7   C9   S1   107.39  3.000
 AZ4  H6   C9   S1   106.96  3.000
 AZ4  H7   C9   C2   111.95  3.000
 AZ4  H6   C9   C2   108.96  3.000
 AZ4  S1   C9   C2   113.09  3.000
 AZ4  H9   C10  H8   108.47  3.000
 AZ4  H9   C10  N4   110.88  3.000
 AZ4  H8   C10  N4   110.02  3.000
 AZ4  H9   C10  C11  109.72  3.000
 AZ4  H8   C10  C11  108.56  3.000
 AZ4  N4   C10  C11  109.15  3.000
 AZ4  H11  C11  H10  107.97  3.000
 AZ4  H11  C11  N5   110.46  3.000
 AZ4  H10  C11  N5   109.81  3.000
 AZ4  H11  C11  C10  109.22  3.000
 AZ4  H10  C11  C10  108.66  3.000
 AZ4  N5   C11  C10  110.65  3.000
 AZ4  H13  C12  H12  107.79  3.000
 AZ4  H13  C12  N5   109.76  3.000
 AZ4  H12  C12  N5   110.66  3.000
 AZ4  H13  C12  C13  108.60  3.000
 AZ4  H12  C12  C13  109.39  3.000
 AZ4  N5   C12  C13  110.57  3.000
 AZ4  H15  C13  H14  108.45  3.000
 AZ4  H15  C13  N4   110.10  3.000
 AZ4  H14  C13  N4   111.13  3.000
 AZ4  H15  C13  C12  108.43  3.000
 AZ4  H14  C13  C12  109.62  3.000
 AZ4  N4   C13  C12  109.06  3.000
 AZ4  N7   C14  N5   118.22  3.000
 AZ4  N5   C14  N6   117.61  3.000
 AZ4  N7   C14  N6   124.16  3.000
 AZ4  H16  C15  C16  120.15  3.000
 AZ4  H16  C15  N6   117.28  3.000
 AZ4  C16  C15  N6   122.57  3.000
 AZ4  C19  C16  C15  115.72  3.000
 AZ4  C19  C16  O5   126.44  3.000
 AZ4  C15  C16  O5   117.84  3.000
 AZ4  H17  C19  N7   115.87  3.000
 AZ4  H17  C19  C16  122.14  3.000
 AZ4  N7   C19  C16  121.98  3.000
 AZ4  O1   N1   C2   116.17  3.000
 AZ4  C2   N1   C1   125.00  3.000
 AZ4  O1   N1   C1   115.70  3.000
 AZ4  H20  C4   H19  108.05  3.000
 AZ4  H20  C4   C5   108.98  3.000
 AZ4  H19  C4   C5   109.26  3.000
 AZ4  H20  C4   C3   110.46  3.000
 AZ4  H19  C4   C3   109.54  3.000
 AZ4  C5   C4   C3   110.50  3.000
 AZ4  N3   C5   N2   124.77  3.000
 AZ4  N3   C5   C4   117.90  3.000
 AZ4  N2   C5   C4   117.29  3.000
 AZ4  C6   N2   C5   117.92  3.000
 AZ4  H21  C6   N2   118.17  3.000
 AZ4  H21  C6   C7   121.31  3.000
 AZ4  N2   C6   C7   120.52  3.000
 AZ4  C5   N3   C8   117.91  3.000
 AZ4  N4   S1   O3   106.95  3.000
 AZ4  O3   S1   C9   108.58  3.000
 AZ4  N4   S1   C9   106.04  3.000
 AZ4  O3   S1   O4   119.20  3.000
 AZ4  C9   S1   O4   108.18  3.000
 AZ4  N4   S1   O4   107.16  3.000
 AZ4  S1   N4   C13  118.16  3.000
 AZ4  S1   N4   C10  117.81  3.000
 AZ4  C13  N4   C10  112.39  3.000
 AZ4  C14  N5   C12  120.84  3.000
 AZ4  C12  N5   C11  114.12  3.000
 AZ4  C14  N5   C11  120.88  3.000
 AZ4  H23  C17  H22  108.22  3.000
 AZ4  H23  C17  C18  108.69  3.000
 AZ4  H22  C17  C18  109.01  3.000
 AZ4  H23  C17  O5   112.22  3.000
 AZ4  H22  C17  O5   112.15  3.000
 AZ4  C18  C17  O5   106.46  3.000
 AZ4  F4   C18  F3   107.62  3.000
 AZ4  F4   C18  F2   107.04  3.000
 AZ4  F3   C18  F2   107.62  3.000
 AZ4  F2   C18  C17  112.18  3.000
 AZ4  F4   C18  C17  112.04  3.000
 AZ4  F3   C18  C17  110.12  3.000
 AZ4  C19  N7   C14  118.01  3.000
 AZ4  H18  O1   N1   106.02  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
 AZ4  CONST_01  C19  C16  C15  N6      0.00   0.0  0
 AZ4  CONST_02  C19  N7   C14  N6      0.00   0.0  0
 AZ4  CONST_03  C5   N2   C6   C7      0.00   0.0  0
 AZ4  CONST_04  C5   N3   C8   C7      0.00   0.0  0
 AZ4  CONST_05  N2   C6   C7   C8      0.00   0.0  0
 AZ4  CONST_06  N2   C5   N3   C8      0.00   0.0  0
 AZ4  CONST_07  C16  C15  N6   C14     0.00   0.0  0
 AZ4  CONST_08  C16  C19  N7   C14     0.00   0.0  0
 AZ4  CONST_09  N7   C19  C16  C15     0.00   0.0  0
 AZ4  CONST_10  N7   C14  N6   C15     0.00   0.0  0
 AZ4  CONST_11  N3   C8   C7   C6      0.00   0.0  0
 AZ4  CONST_12  N3   C5   N2   C6      0.00   0.0  0
 AZ4  CONST_13  N5   C14  N6   C15   180.00   0.0  0
 AZ4  CONST_14  N5   C14  N7   C19   180.00   0.0  0
 AZ4  CONST_15  N6   C15  C16  O5    180.00   0.0  0
 AZ4  CONST_16  N7   C19  C16  O5    180.00   0.0  0
 AZ4  CONST_17  C4   C5   N3   C8    180.00   0.0  0
 AZ4  CONST_18  C6   N2   C5   C4    180.00   0.0  0
 AZ4  CONST_19  F1   C7   C6   N2    180.00   0.0  0
 AZ4  CONST_20  N3   C8   C7   F1    180.00   0.0  0
 AZ4  CONST_21  H21  C6   C7   C8    180.00   0.0  0
 AZ4  CONST_22  H16  C15  N6   C14   180.00   0.0  0
 AZ4  CONST_23  H17  C19  N7   C14   180.00   0.0  0
 AZ4  CONST_24  H5   C8   N3   C5    180.00   0.0  0
 AZ4  CONST_25  O2   C1   N1   C2      0.00   0.0  0
 AZ4  CONST_26  O2   C1   N1   O1    180.00   0.0  0
 AZ4  Var_01    C11  N5   C14  N6    166.87  30.0  2
 AZ4  Var_02    C14  N5   C11  C10   148.44  30.0  1
 AZ4  Var_03    C12  C13  N4   C10    59.03  30.0  1
 AZ4  Var_04    C13  C12  N5   C11    54.57  30.0  1
 AZ4  Var_05    C13  N4   C10  C11   -58.79  30.0  1
 AZ4  Var_06    N5   C11  C10  N4     54.46  30.0  1
 AZ4  Var_07    N5   C12  C13  N4    -54.97  30.0  1
 AZ4  Var_08    N2   C5   C4   C3     79.71  30.0  1
 AZ4  Var_09    C10  N4   S1   O4   -177.30  30.0  2
 AZ4  Var_10    N4   S1   C9   C2    169.55  30.0  2
 AZ4  Var_11    C5   C4   C3   C2   -176.75  30.0  3
 AZ4  Var_12    C18  C17  O5   C16   175.87  30.0  1
 AZ4  Var_13    F3   C18  C17  O5    179.12  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
 AZ4  chir_01  C2  N1  C9  C3  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
 AZ4  plan-1  C7   0.020
 AZ4  plan-1  C8   0.020
 AZ4  plan-1  C4   0.020
 AZ4  plan-1  C5   0.020
 AZ4  plan-1  N2   0.020
 AZ4  plan-1  C6   0.020
 AZ4  plan-1  N3   0.020
 AZ4  plan-1  H5   0.020
 AZ4  plan-1  H21  0.020
 AZ4  plan-1  F1   0.020
 AZ4  plan-2  O5   0.020
 AZ4  plan-2  N6   0.020
 AZ4  plan-2  C14  0.020
 AZ4  plan-2  C15  0.020
 AZ4  plan-2  C16  0.020
 AZ4  plan-2  C19  0.020
 AZ4  plan-2  N5   0.020
 AZ4  plan-2  N7   0.020
 AZ4  plan-2  H16  0.020
 AZ4  plan-2  H17  0.020
 AZ4  plan-3  C1   0.020
 AZ4  plan-3  C2   0.020
 AZ4  plan-3  N1   0.020
 AZ4  plan-3  O2   0.020
 AZ4  plan-3  H1   0.020
 AZ4  plan-3  O1   0.020

