# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 13:31:44 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-amino-N-{5-[(4S)-4-aminoazepan-1-yl]-1-methyl-1H-pyrazol-4-yl}-2-(2,6-difluorophenyl)-1,3-thiazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncc(NC(=O)c2nc(sc2N)c3c(F)cccc3F)c1N4CCC[C@H](N)CC4
#
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
 KUY  KUY  5-amino-N-{5-[(4S)-4-aminoazepan-1-yl]-1-methyl-1H-pyrazol-4-yl}-2-(2,6-difluorophenyl)-1,3-thiazole-4-carboxamide  ligand  54  31  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KUY
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
 KUY  N2   N  NR5   0  -0.294   4.9175  -1.5499  -0.0255
 KUY  C10  C  CR5   0   0.088  -0.9227  -1.9005  -0.0427
 KUY  C4   C  CR5   0   0.120   2.7686  -1.9492  -0.0696
 KUY  C1   C  CH3   0  -0.519   6.2115  -0.9185   0.0520
 KUY  C11  C  CR5   0   0.051  -2.1354  -2.5577   0.0873
 KUY  C13  C  CR5   0   0.051  -2.2204  -0.1126  -0.1076
 KUY  C15  C  CR6   0  -0.374  -2.5880   1.2972  -0.2220
 KUY  C16  C  CR6   0   0.557  -2.0471   2.1098  -1.2159
 KUY  C17  C  CR16  0  -0.430  -2.3215   3.4591  -1.3100
 KUY  C18  C  CR16  0  -0.224  -3.1839   4.0280  -0.3829
 KUY  C19  C  CR16  0  -0.416  -3.7612   3.2608   0.6182
 KUY  C20  C  CR6   0   0.560  -3.4522   1.9180   0.6736
 KUY  C25  C  CH2   0  -0.319   3.6439   1.2269   1.0765
 KUY  C26  C  CH2   0  -0.433   2.3492   1.8205   1.6218
 KUY  C27  C  CH1   0  -0.071   1.3722   2.3711   0.5769
 KUY  C29  C  CH2   0  -0.450   2.0471   3.0313  -0.6289
 KUY  C3   C  CR5   0   0.483   3.7071  -0.9336  -0.0767
 KUY  C31  C  CH2   0  -0.435   2.4598   2.0407  -1.7172
 KUY  C32  C  CH2   0  -0.304   3.6403   1.1401  -1.3833
 KUY  C5   C  CR15  0  -0.099   3.5095  -3.1374  -0.0074
 KUY  C8   C  C     0   0.523   0.3909  -2.5449  -0.0187
 KUY  F21  F  F     0  -0.294  -3.9899   1.1662   1.6400
 KUY  F22  F  F     0  -0.289  -1.2374   1.5568  -2.1200
 KUY  N14  N  N     0  -0.381  -1.0144  -0.5450  -0.1546
 KUY  N23  N  NH2   0  -0.819  -2.3812  -3.8729   0.1741
 KUY  N24  N  NT    0  -0.509   3.4703   0.4261  -0.1265
 KUY  N6   N  N     0  -0.285   4.8078  -2.8671   0.0236
 KUY  N7   N  NH1   0  -0.747   1.4135  -1.6742  -0.1253
 KUY  O9   O  O     0  -0.498   0.5371  -3.7601   0.0979
 KUY  S12  S  S2    0   0.232  -3.4088  -1.3850   0.0710
 KUY  H1   H  HCH3  0   0.259   6.6118  -0.9748   1.0637
 KUY  H2   H  HCH3  0   0.266   6.9012  -1.4048  -0.6336
 KUY  H3   H  HCH3  0   0.257   6.1167   0.1267  -0.2286
 KUY  H4   H  HCR6  0   0.294  -1.8781   4.0492  -2.1008
 KUY  H5   H  HCR6  0   0.289  -3.4107   5.0832  -0.4436
 KUY  H6   H  HCR6  0   0.293  -4.4323   3.6971   1.3452
 KUY  H7   H  HCH2  0   0.224   4.3539   2.0334   0.8589
 KUY  H8   H  HCH2  0   0.251   4.1133   0.6216   1.8547
 KUY  H9   H  HCH2  0   0.224   1.8249   1.0747   2.2276
 KUY  H10  H  HCH2  0   0.223   2.6180   2.6352   2.3015
 KUY  H28  H  HCH1  0   0.215   0.7848   1.5278   0.1853
 KUY  H11  H  HCH2  0   0.229   1.3321   3.7275  -1.0781
 KUY  H12  H  HCH2  0   0.220   2.8998   3.6416  -0.3115
 KUY  H13  H  HCH2  0   0.216   1.5950   1.4161  -1.9614
 KUY  H14  H  HCH2  0   0.230   2.7109   2.5888  -2.6296
 KUY  H15  H  HCH2  0   0.248   3.7699   0.4113  -2.1852
 KUY  H16  H  HCH2  0   0.213   4.5595   1.7429  -1.3523
 KUY  H17  H  HCR5  0   0.265   3.1643  -4.1574   0.0142
 KUY  H18  H  HNH2  0   0.413  -1.5898  -4.4737   0.3416
 KUY  H19  H  HNH2  0   0.411  -3.2727  -4.2044   0.5003
 KUY  H20  H  HNH2  0   0.334  -0.2770   3.5646   0.6445
 KUY  H21  H  HNH2  0   0.340   0.1019   2.9172   2.0709
 KUY  H23  H  HNH1  0   0.417   1.1801  -0.6919  -0.2008
 KUY  N34  N  NH2   0  -0.807   0.5081   3.3435   1.2459

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
 KUY  N23  C11  single    1.341  0.020  1.341
 KUY  O9   C8   double    1.229  0.020  1.229
 KUY  C11  C10  aromatic  1.385  0.020  1.385
 KUY  C11  S12  aromatic  1.731  0.020  1.731
 KUY  C5   N6   aromatic  1.327  0.020  1.327
 KUY  C5   C4   aromatic  1.402  0.020  1.402
 KUY  C8   C10  single    1.463  0.020  1.463
 KUY  C8   N7   single    1.347  0.020  1.347
 KUY  N6   N2   aromatic  1.323  0.020  1.323
 KUY  C10  N14  aromatic  1.363  0.020  1.363
 KUY  S12  C13  aromatic  1.750  0.020  1.750
 KUY  C4   N7   single    1.384  0.020  1.384
 KUY  C4   C3   aromatic  1.383  0.020  1.383
 KUY  N2   C3   aromatic  1.359  0.020  1.359
 KUY  N2   C1   single    1.442  0.020  1.442
 KUY  N14  C13  aromatic  1.282  0.020  1.282
 KUY  C13  C15  single    1.461  0.020  1.461
 KUY  C3   N24  single    1.381  0.020  1.381
 KUY  F21  C20  single    1.337  0.020  1.337
 KUY  N24  C25  single    1.456  0.020  1.456
 KUY  N24  C32  single    1.455  0.020  1.455
 KUY  C15  C20  aromatic  1.391  0.020  1.391
 KUY  C15  C16  aromatic  1.393  0.020  1.393
 KUY  C20  C19  aromatic  1.379  0.020  1.379
 KUY  C25  C26  single    1.525  0.020  1.525
 KUY  C32  C31  single    1.522  0.020  1.522
 KUY  F22  C16  single    1.334  0.020  1.334
 KUY  C16  C17  aromatic  1.380  0.020  1.380
 KUY  C19  C18  aromatic  1.387  0.020  1.387
 KUY  C31  C29  single    1.528  0.020  1.528
 KUY  C26  C27  single    1.533  0.020  1.533
 KUY  C27  C29  single    1.531  0.020  1.531
 KUY  C27  N34  single    1.463  0.020  1.463
 KUY  C17  C18  aromatic  1.388  0.020  1.388
 KUY  C1   H1   single    0.970  0.020  1.090
 KUY  C1   H2   single    0.970  0.020  1.090
 KUY  C1   H3   single    0.970  0.020  1.090
 KUY  C17  H4   single    0.930  0.020  1.080
 KUY  C18  H5   single    0.930  0.020  1.080
 KUY  C19  H6   single    0.930  0.020  1.080
 KUY  C25  H7   single    0.970  0.020  1.090
 KUY  C25  H8   single    0.970  0.020  1.090
 KUY  C26  H9   single    0.970  0.020  1.090
 KUY  C26  H10  single    0.970  0.020  1.090
 KUY  C27  H28  single    0.970  0.020  1.090
 KUY  C29  H11  single    0.970  0.020  1.090
 KUY  C29  H12  single    0.970  0.020  1.090
 KUY  C31  H13  single    0.970  0.020  1.090
 KUY  C31  H14  single    0.970  0.020  1.090
 KUY  C32  H15  single    0.970  0.020  1.090
 KUY  C32  H16  single    0.970  0.020  1.090
 KUY  C5   H17  single    0.930  0.020  1.080
 KUY  N23  H18  single    0.890  0.020  1.040
 KUY  N23  H19  single    0.890  0.020  1.040
 KUY  N34  H20  single    0.890  0.020  1.040
 KUY  N34  H21  single    0.890  0.020  1.040
 KUY  N7   H23  single    0.860  0.020  1.020

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
 KUY  N6   N2   C3   112.28  3.000
 KUY  C3   N2   C1   127.06  3.000
 KUY  N6   N2   C1   120.57  3.000
 KUY  N14  C10  C8   119.98  3.000
 KUY  N14  C10  C11  114.86  3.000
 KUY  C8   C10  C11  125.12  3.000
 KUY  N7   C4   C5   133.46  3.000
 KUY  N7   C4   C3   121.23  3.000
 KUY  C5   C4   C3   105.31  3.000
 KUY  H3   C1   H2   108.83  3.000
 KUY  H3   C1   H1   108.76  3.000
 KUY  H2   C1   H1   109.23  3.000
 KUY  H3   C1   N2   109.21  3.000
 KUY  H2   C1   N2   109.85  3.000
 KUY  H1   C1   N2   110.92  3.000
 KUY  S12  C11  N23  122.02  3.000
 KUY  S12  C11  C10  108.77  3.000
 KUY  N23  C11  C10  129.19  3.000
 KUY  S12  C13  N14  113.40  3.000
 KUY  N14  C13  C15  124.00  3.000
 KUY  S12  C13  C15  122.58  3.000
 KUY  C20  C15  C16  116.12  3.000
 KUY  C16  C15  C13  121.39  3.000
 KUY  C20  C15  C13  122.45  3.000
 KUY  F22  C16  C17  118.68  3.000
 KUY  C17  C16  C15  122.80  3.000
 KUY  F22  C16  C15  118.52  3.000
 KUY  H4   C17  C18  121.29  3.000
 KUY  H4   C17  C16  120.11  3.000
 KUY  C18  C17  C16  118.60  3.000
 KUY  H5   C18  C19  119.54  3.000
 KUY  H5   C18  C17  119.53  3.000
 KUY  C19  C18  C17  120.93  3.000
 KUY  H6   C19  C20  120.33  3.000
 KUY  H6   C19  C18  121.35  3.000
 KUY  C20  C19  C18  118.31  3.000
 KUY  F21  C20  C19  119.10  3.000
 KUY  C19  C20  C15  123.23  3.000
 KUY  F21  C20  C15  117.66  3.000
 KUY  H8   C25  H7   105.71  3.000
 KUY  H8   C25  N24  109.60  3.000
 KUY  H7   C25  N24  108.54  3.000
 KUY  H8   C25  C26  109.01  3.000
 KUY  H7   C25  C26  109.54  3.000
 KUY  N24  C25  C26  114.10  3.000
 KUY  H10  C26  H9   106.33  3.000
 KUY  H10  C26  C27  108.20  3.000
 KUY  H9   C26  C27  108.46  3.000
 KUY  H10  C26  C25  107.66  3.000
 KUY  H9   C26  C25  109.84  3.000
 KUY  C27  C26  C25  115.92  3.000
 KUY  H28  C27  N34  110.92  3.000
 KUY  H28  C27  C29  106.59  3.000
 KUY  N34  C27  C29  109.50  3.000
 KUY  H28  C27  C26  107.92  3.000
 KUY  N34  C27  C26  107.67  3.000
 KUY  C29  C27  C26  114.25  3.000
 KUY  H12  C29  H11  105.84  3.000
 KUY  H12  C29  C31  110.92  3.000
 KUY  H11  C29  C31  107.24  3.000
 KUY  H12  C29  C27  110.80  3.000
 KUY  H11  C29  C27  108.03  3.000
 KUY  C31  C29  C27  113.60  3.000
 KUY  N24  C3   C4   127.36  3.000
 KUY  N24  C3   N2   126.90  3.000
 KUY  C4   C3   N2   105.73  3.000
 KUY  H14  C31  H13  106.34  3.000
 KUY  H14  C31  C32  107.55  3.000
 KUY  H13  C31  C32  108.92  3.000
 KUY  H14  C31  C29  109.34  3.000
 KUY  H13  C31  C29  108.38  3.000
 KUY  C32  C31  C29  115.90  3.000
 KUY  H16  C32  H15  106.71  3.000
 KUY  H16  C32  N24  110.01  3.000
 KUY  H15  C32  N24  108.71  3.000
 KUY  H16  C32  C31  109.28  3.000
 KUY  H15  C32  C31  109.03  3.000
 KUY  N24  C32  C31  112.90  3.000
 KUY  H17  C5   N6   120.41  3.000
 KUY  H17  C5   C4   129.37  3.000
 KUY  N6   C5   C4   110.22  3.000
 KUY  O9   C8   N7   123.78  3.000
 KUY  N7   C8   C10  113.30  3.000
 KUY  O9   C8   C10  122.93  3.000
 KUY  C13  N14  C10  113.31  3.000
 KUY  H19  N23  H18  116.48  3.000
 KUY  H19  N23  C11  120.46  3.000
 KUY  H18  N23  C11  116.85  3.000
 KUY  C32  N24  C3   119.61  3.000
 KUY  C32  N24  C25  115.46  3.000
 KUY  C3   N24  C25  119.43  3.000
 KUY  C5   N6   N2   106.46  3.000
 KUY  H23  N7   C8   117.25  3.000
 KUY  H23  N7   C4   114.93  3.000
 KUY  C8   N7   C4   127.71  3.000
 KUY  C13  S12  C11   89.65  3.000
 KUY  H21  N34  H20  105.33  3.000
 KUY  H21  N34  C27  109.23  3.000
 KUY  H20  N34  C27  109.35  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
 KUY  CONST_01  C4   C5   N6   N2     0.00   0.0  0
 KUY  CONST_02  C5   C4   C3   N2     0.00   0.0  0
 KUY  CONST_03  C13  S12  C11  C10    0.00   0.0  0
 KUY  CONST_04  S12  C13  N14  C10    0.00   0.0  0
 KUY  CONST_05  C15  C13  N14  C10  180.00   0.0  0
 KUY  CONST_06  N6   N2   C3   C4     0.00   0.0  0
 KUY  CONST_07  C13  N14  C10  C11    0.00   0.0  0
 KUY  CONST_08  N14  C13  S12  C11    0.00   0.0  0
 KUY  CONST_09  C15  C13  S12  C11  180.00   0.0  0
 KUY  CONST_10  C19  C20  C15  C13  180.00   0.0  0
 KUY  CONST_11  C17  C16  C15  C13  180.00   0.0  0
 KUY  CONST_12  C18  C19  C20  C15    0.00   0.0  0
 KUY  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 KUY  CONST_16  C19  C20  C15  C16    0.00   0.0  0
 KUY  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 KUY  CONST_18  C20  C15  C16  C17    0.00   0.0  0
 KUY  CONST_19  C20  C19  C18  C17    0.00   0.0  0
 KUY  CONST_22  N6   C5   C4   C3     0.00   0.0  0
 KUY  CONST_23  C5   N6   N2   C3     0.00   0.0  0
 KUY  CONST_24  S12  C11  C10  N14    0.00   0.0  0
 KUY  CONST_25  N24  C3   C4   C5   180.00   0.0  0
 KUY  CONST_26  N6   N2   C3   N24  180.00   0.0  0
 KUY  CONST_27  N7   C4   C3   N2   180.00   0.0  0
 KUY  CONST_28  C1   N2   C3   C4   180.00   0.0  0
 KUY  CONST_29  C5   N6   N2   C1   180.00   0.0  0
 KUY  CONST_30  N24  C3   N2   C1     0.00   0.0  0
 KUY  CONST_31  N23  C11  S12  C13  180.00   0.0  0
 KUY  CONST_32  C8   C10  N14  C13  180.00   0.0  0
 KUY  CONST_33  F21  C20  C15  C13    0.00   0.0  0
 KUY  CONST_34  F22  C16  C15  C13    0.00   0.0  0
 KUY  CONST_35  F21  C20  C15  C16  180.00   0.0  0
 KUY  CONST_36  F21  C20  C19  C18  180.00   0.0  0
 KUY  CONST_37  F22  C16  C17  C18  180.00   0.0  0
 KUY  CONST_38  F22  C16  C15  C20  180.00   0.0  0
 KUY  CONST_39  S12  C11  C10  C8   180.00   0.0  0
 KUY  CONST_40  N23  C11  C10  N14  180.00   0.0  0
 KUY  CONST_41  N7   C4   C3   N24    0.00   0.0  0
 KUY  CONST_42  N7   C4   C5   N6   180.00   0.0  0
 KUY  CONST_43  H17  C5   N6   N2   180.00   0.0  0
 KUY  CONST_44  H6   C19  C20  C15  180.00   0.0  0
 KUY  CONST_45  H4   C17  C16  C15  180.00   0.0  0
 KUY  CONST_46  H5   C18  C17  C16  180.00   0.0  0
 KUY  CONST_47  C4   N7   C8   C10  180.00   0.0  0
 KUY  CONST_48  C8   N7   C4   C3   180.00   0.0  0
 KUY  CONST_49  C8   N7   C4   C5     0.00   0.0  0
 KUY  CONST_50  H18  N23  C11  C10    0.00   0.0  0
 KUY  CONST_52  H23  N7   C4   C3     0.00   0.0  0
 KUY  CONST_53  O9   C8   N7   C4     0.00   0.0  0
 KUY  Var_01    O9   C8   C10  C11    1.38  30.0  1
 KUY  Var_02    H1   C1   N2   C3   103.22  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
 KUY  chir_01  C27  C26  C29  N34  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
 KUY  plan-1  C10  0.020
 KUY  plan-1  C11  0.020
 KUY  plan-1  C13  0.020
 KUY  plan-1  C15  0.020
 KUY  plan-1  C8   0.020
 KUY  plan-1  N14  0.020
 KUY  plan-1  N23  0.020
 KUY  plan-1  S12  0.020
 KUY  plan-2  N2   0.020
 KUY  plan-2  C4   0.020
 KUY  plan-2  C1   0.020
 KUY  plan-2  C3   0.020
 KUY  plan-2  C5   0.020
 KUY  plan-2  N24  0.020
 KUY  plan-2  N6   0.020
 KUY  plan-2  N7   0.020
 KUY  plan-2  H17  0.020
 KUY  plan-3  C13  0.020
 KUY  plan-3  C15  0.020
 KUY  plan-3  C16  0.020
 KUY  plan-3  C17  0.020
 KUY  plan-3  C18  0.020
 KUY  plan-3  C19  0.020
 KUY  plan-3  C20  0.020
 KUY  plan-3  F21  0.020
 KUY  plan-3  F22  0.020
 KUY  plan-3  H4   0.020
 KUY  plan-3  H5   0.020
 KUY  plan-3  H6   0.020
 KUY  plan-4  C10  0.020
 KUY  plan-4  C4   0.020
 KUY  plan-4  C8   0.020
 KUY  plan-4  N7   0.020
 KUY  plan-4  O9   0.020
 KUY  plan-4  H23  0.020
 KUY  plan-5  C11  0.020
 KUY  plan-5  N23  0.020
 KUY  plan-5  H18  0.020
 KUY  plan-5  H19  0.020

