# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:33:44 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: methyl ~{N}-[4-aminocarbonyl-1-[(3~{R},4~{R})-4-(cyanomethyl)-1-[(4-ethenyl-2-fluoranyl-5-oxidanyl-phenyl)methyl]-3-fluoranyl-piperidin-4-yl]pyrazol-3-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1nn(cc1C(N)=O)[C@]2(CCN(C[C@H]2F)Cc3cc(O)c(C=C)cc3F)CC#N
#
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
 KHH  KHH  'methyl ~{N}-[4-aminocarbonyl-1-[(3~{R},4~{R})-4-(cyanomethyl)-1-[(4-ethenyl-2-fluoranyl-5-oxidanyl-phenyl)methyl]-3-fluoranyl-piperidin-4-yl]pyrazol-3-yl]carbamate'  ligand  58  34  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KHH
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
 KHH  C7   C  CH2   0  -0.334  39.5869  21.5755  237.6123
 KHH  C9   C  CH2   0  -0.480  39.1973  20.9499  241.2885
 KHH  C10  C  CT    0   0.005  40.5375  21.4682  241.8077
 KHH  C11  C  CH2   0  -0.554  41.6086  20.3592  241.8192
 KHH  C12  C  CSP   0   0.136  41.2906  19.3269  242.7903
 KHH  C16  C  CR5   0   0.564  41.1171  22.8010  244.9717
 KHH  C18  C  CH3   0  -0.418  45.1192  24.3098  247.0886
 KHH  C19  C  CH1   0   0.252  41.0245  22.6120  240.9040
 KHH  C13  C  CR15  0   0.093  39.3153  22.0967  243.9215
 KHH  C14  C  CR5   0  -0.372  39.7150  22.6406  245.1259
 KHH  C6   C  CR6   0  -0.112  38.1747  21.3476  237.1525
 KHH  C5   C  CR6   0   0.537  37.2090  22.3393  237.2477
 KHH  C4   C  CR16  0  -0.473  35.9108  22.1431  236.8379
 KHH  C3   C  CR6   0   0.003  35.5083  20.9158  236.3068
 KHH  C2   C  C1    0  -0.210  34.1280  20.6846  235.8668
 KHH  C1   C  C2    0  -0.531  33.0622  21.3740  236.2721
 KHH  C21  C  CR16  0  -0.411  37.7785  20.1303  236.6169
 KHH  C22  C  CR6   0   0.341  36.4722  19.9054  236.1923
 KHH  F1   F  F     0  -0.311  37.5585  23.5470  237.7251
 KHH  N1   N  NT    0  -0.402  39.6659  21.7828  239.0451
 KHH  C8   C  CH2   0  -0.291  39.2654  20.6176  239.8053
 KHH  N2   N  NS    0  -0.257  41.0350  18.5123  243.5608
 KHH  N3   N  NR5   0  -0.306  40.4079  21.9668  243.1702
 KHH  N4   N  NH2   0  -0.819  37.6116  22.7589  246.2636
 KHH  O1   O  O     0  -0.505  39.4775  23.4731  247.3051
 KHH  C17  C  C     0   0.729  43.2817  23.5107  245.8618
 KHH  O2   O  O     0  -0.477  43.9755  23.2575  244.9078
 KHH  O3   O  O2    0  -0.477  43.7247  24.0294  247.0063
 KHH  N6   N  N     0  -0.301  41.5213  22.3930  243.7923
 KHH  F2   F  F     0  -0.364  40.1933  23.7001  241.1253
 KHH  C20  C  CH2   0  -0.358  40.9802  22.2366  239.4385
 KHH  O4   O  OH1   0  -0.627  36.0867  18.7181  235.6814
 KHH  H1   H  HCH2  0   0.226  40.2072  20.7267  237.2813
 KHH  H2   H  HCH2  0   0.262  39.9933  22.4627  237.1193
 KHH  H3   H  HCH2  0   0.274  38.4276  21.7116  241.4230
 KHH  H4   H  HCH2  0   0.276  38.8819  20.0668  241.8488
 KHH  H5   H  HCH2  0   0.332  41.7023  19.8877  240.8409
 KHH  H6   H  HCH2  0   0.341  42.5870  20.7712  242.0715
 KHH  H7   H  HCH3  0   0.252  45.2789  24.7235  248.0800
 KHH  H8   H  HCH3  0   0.238  45.7189  23.4068  246.9762
 KHH  H9   H  HCH3  0   0.238  45.4264  25.0411  246.3415
 KHH  H10  H  HCH1  0   0.248  42.0401  22.9057  241.1816
 KHH  H11  H  HCR5  0   0.315  38.3386  21.7998  243.5790
 KHH  H12  H  HCR6  0   0.272  35.2049  22.9610  236.9087
 KHH  H13  H  H     0   0.254  33.9767  19.8818  235.1549
 KHH  H14  H  H     0   0.250  32.0794  21.1504  235.8808
 KHH  H15  H  H     0   0.245  33.1193  22.1700  237.0041
 KHH  H16  H  HCR6  0   0.277  38.5096  19.3324  236.5363
 KHH  H18  H  HCH2  0   0.270  38.2702  20.3026  239.4906
 KHH  H19  H  HCH2  0   0.209  39.9351  19.7588  239.6251
 KHH  H20  H  HNH2  0   0.409  37.0291  23.0213  247.0418
 KHH  H21  H  HNH2  0   0.412  37.1465  22.4092  245.4445
 KHH  H22  H  HNH1  0   0.423  41.4504  23.5805  246.7982
 KHH  H23  H  HCH2  0   0.222  41.7662  21.4851  239.2484
 KHH  H24  H  HCH2  0   0.274  41.2549  23.1157  238.8507
 KHH  H25  H  HOH1  0   0.478  36.8433  18.1271  235.5976
 KHH  N5   N  NH1   0  -0.757  41.9374  23.3173  245.9488
 KHH  C15  C  C     0   0.496  38.9301  22.9905  246.3121

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
 KHH  C1   C2   double    1.332  0.020  1.332
 KHH  C2   C3   single    1.467  0.020  1.467
 KHH  C3   C4   aromatic  1.397  0.020  1.397
 KHH  C3   C22  aromatic  1.401  0.020  1.401
 KHH  O4   C22  single    1.349  0.020  1.349
 KHH  C4   C5   aromatic  1.375  0.020  1.375
 KHH  C22  C21  aromatic  1.392  0.020  1.392
 KHH  C5   F1   single    1.345  0.020  1.345
 KHH  C5   C6   aromatic  1.388  0.020  1.388
 KHH  C21  C6   aromatic  1.388  0.020  1.388
 KHH  C6   C7   single    1.503  0.020  1.503
 KHH  C7   N1   single    1.450  0.020  1.450
 KHH  N1   C20  single    1.445  0.020  1.445
 KHH  N1   C8   single    1.448  0.020  1.448
 KHH  C20  C19  single    1.513  0.020  1.513
 KHH  C8   C9   single    1.521  0.020  1.521
 KHH  C19  F2   single    1.387  0.020  1.387
 KHH  C19  C10  single    1.537  0.020  1.537
 KHH  C9   C10  single    1.528  0.020  1.528
 KHH  C11  C10  single    1.542  0.020  1.542
 KHH  C11  C12  single    1.452  0.020  1.452
 KHH  C10  N3   single    1.457  0.020  1.457
 KHH  C12  N2   triple    1.150  0.020  1.150
 KHH  N3   N6   aromatic  1.345  0.020  1.345
 KHH  N3   C13  aromatic  1.332  0.020  1.332
 KHH  N6   C16  aromatic  1.312  0.020  1.312
 KHH  C13  C14  aromatic  1.381  0.020  1.381
 KHH  O2   C17  double    1.206  0.020  1.206
 KHH  C16  C14  aromatic  1.420  0.020  1.420
 KHH  C16  N5   single    1.376  0.020  1.376
 KHH  C14  C15  single    1.465  0.020  1.465
 KHH  C17  N5   single    1.361  0.020  1.361
 KHH  C17  O3   single    1.332  0.020  1.332
 KHH  C18  O3   single    1.425  0.020  1.425
 KHH  C15  N4   single    1.340  0.020  1.340
 KHH  C15  O1   double    1.232  0.020  1.232
 KHH  C7   H1   single    0.970  0.020  1.090
 KHH  C7   H2   single    0.970  0.020  1.090
 KHH  C9   H3   single    0.970  0.020  1.090
 KHH  C9   H4   single    0.970  0.020  1.090
 KHH  C11  H5   single    0.970  0.020  1.090
 KHH  C11  H6   single    0.970  0.020  1.090
 KHH  C18  H7   single    0.970  0.020  1.090
 KHH  C18  H8   single    0.970  0.020  1.090
 KHH  C18  H9   single    0.970  0.020  1.090
 KHH  C19  H10  single    0.970  0.020  1.090
 KHH  C13  H11  single    0.930  0.020  1.080
 KHH  C4   H12  single    0.930  0.020  1.080
 KHH  C2   H13  single    0.930  0.020  1.080
 KHH  C1   H14  single    0.930  0.020  1.080
 KHH  C1   H15  single    0.930  0.020  1.080
 KHH  C21  H16  single    0.930  0.020  1.080
 KHH  C8   H18  single    0.970  0.020  1.090
 KHH  C8   H19  single    0.970  0.020  1.090
 KHH  N4   H20  single    0.860  0.020  1.020
 KHH  N4   H21  single    0.860  0.020  1.020
 KHH  N5   H22  single    0.860  0.020  1.020
 KHH  C20  H23  single    0.970  0.020  1.090
 KHH  C20  H24  single    0.970  0.020  1.090
 KHH  O4   H25  single    0.850  0.020  0.980

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
 KHH  H2   C7   H1   106.28  3.000
 KHH  H2   C7   N1   108.02  3.000
 KHH  H1   C7   N1   112.09  3.000
 KHH  H2   C7   C6   109.55  3.000
 KHH  H1   C7   C6   108.68  3.000
 KHH  N1   C7   C6   112.05  3.000
 KHH  H4   C9   H3   107.30  3.000
 KHH  H4   C9   C8   109.66  3.000
 KHH  H3   C9   C8   107.71  3.000
 KHH  H4   C9   C10  110.68  3.000
 KHH  H3   C9   C10  109.88  3.000
 KHH  C8   C9   C10  111.48  3.000
 KHH  N3   C10  C19  108.87  3.000
 KHH  N3   C10  C11  107.52  3.000
 KHH  C19  C10  C11  108.64  3.000
 KHH  N3   C10  C9   110.85  3.000
 KHH  C11  C10  C9   111.58  3.000
 KHH  C19  C10  C9   109.30  3.000
 KHH  H6   C11  H5   107.08  3.000
 KHH  H6   C11  C12  108.07  3.000
 KHH  H5   C11  C12  108.15  3.000
 KHH  H6   C11  C10  110.67  3.000
 KHH  H5   C11  C10  111.35  3.000
 KHH  C12  C11  C10  111.36  3.000
 KHH  N2   C12  C11  180.00  3.000
 KHH  N6   C16  N5   124.84  3.000
 KHH  N5   C16  C14  123.64  3.000
 KHH  N6   C16  C14  111.52  3.000
 KHH  H9   C18  H8   109.28  3.000
 KHH  H9   C18  H7   109.19  3.000
 KHH  H8   C18  H7   109.20  3.000
 KHH  H9   C18  O3   111.61  3.000
 KHH  H8   C18  O3   111.69  3.000
 KHH  H7   C18  O3   105.77  3.000
 KHH  H10  C19  C20  109.86  3.000
 KHH  H10  C19  F2   107.79  3.000
 KHH  C20  C19  F2   109.36  3.000
 KHH  H10  C19  C10  110.19  3.000
 KHH  F2   C19  C10  107.47  3.000
 KHH  C20  C19  C10  112.05  3.000
 KHH  H11  C13  N3   122.52  3.000
 KHH  H11  C13  C14  130.44  3.000
 KHH  N3   C13  C14  107.03  3.000
 KHH  C13  C14  C16  103.63  3.000
 KHH  C16  C14  C15  126.17  3.000
 KHH  C13  C14  C15  130.20  3.000
 KHH  C21  C6   C5   117.05  3.000
 KHH  C21  C6   C7   121.30  3.000
 KHH  C5   C6   C7   121.65  3.000
 KHH  F1   C5   C4   118.63  3.000
 KHH  F1   C5   C6   119.03  3.000
 KHH  C4   C5   C6   122.31  3.000
 KHH  H12  C4   C3   120.05  3.000
 KHH  H12  C4   C5   119.22  3.000
 KHH  C3   C4   C5   120.71  3.000
 KHH  C22  C3   C2   120.61  3.000
 KHH  C22  C3   C4   117.81  3.000
 KHH  C2   C3   C4   121.58  3.000
 KHH  H13  C2   C1   118.13  3.000
 KHH  H13  C2   C3   116.43  3.000
 KHH  C1   C2   C3   125.44  3.000
 KHH  H15  C1   H14  116.39  3.000
 KHH  H15  C1   C2   122.94  3.000
 KHH  H14  C1   C2   120.66  3.000
 KHH  H16  C21  C22  119.40  3.000
 KHH  H16  C21  C6   118.77  3.000
 KHH  C22  C21  C6   121.83  3.000
 KHH  O4   C22  C21  121.74  3.000
 KHH  C21  C22  C3   120.28  3.000
 KHH  O4   C22  C3   117.97  3.000
 KHH  C20  N1   C8   111.19  3.000
 KHH  C8   N1   C7   112.88  3.000
 KHH  C20  N1   C7   111.32  3.000
 KHH  H19  C8   H18  106.37  3.000
 KHH  H19  C8   N1   111.88  3.000
 KHH  H18  C8   N1   109.49  3.000
 KHH  H19  C8   C9   110.86  3.000
 KHH  H18  C8   C9   107.68  3.000
 KHH  N1   C8   C9   110.40  3.000
 KHH  N6   N3   C13  112.78  3.000
 KHH  C13  N3   C10  129.33  3.000
 KHH  N6   N3   C10  117.87  3.000
 KHH  H21  N4   H20  116.93  3.000
 KHH  H21  N4   C15  123.05  3.000
 KHH  H20  N4   C15  119.76  3.000
 KHH  O3   C17  O2   124.73  3.000
 KHH  O3   C17  N5   109.20  3.000
 KHH  O2   C17  N5   126.08  3.000
 KHH  C17  O3   C18  116.85  3.000
 KHH  N3   N6   C16  105.03  3.000
 KHH  H24  C20  H23  106.02  3.000
 KHH  H24  C20  N1   109.56  3.000
 KHH  H23  C20  N1   112.76  3.000
 KHH  H24  C20  C19  108.31  3.000
 KHH  H23  C20  C19  108.35  3.000
 KHH  N1   C20  C19  111.60  3.000
 KHH  H25  O4   C22  110.39  3.000
 KHH  H22  N5   C17  119.42  3.000
 KHH  H22  N5   C16  113.95  3.000
 KHH  C17  N5   C16  126.63  3.000
 KHH  O1   C15  N4   122.28  3.000
 KHH  O1   C15  C14  120.54  3.000
 KHH  N4   C15  C14  117.18  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
 KHH  CONST_01  C13  N3   N6   C16     0.00   0.0  0
 KHH  CONST_02  N3   C13  C14  C16     0.00   0.0  0
 KHH  CONST_03  N6   C16  C14  C13     0.00   0.0  0
 KHH  CONST_04  N6   N3   C13  C14     0.00   0.0  0
 KHH  CONST_05  N3   N6   C16  C14     0.00   0.0  0
 KHH  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 KHH  CONST_07  C3   C22  C21  C6      0.00   0.0  0
 KHH  CONST_08  C22  C3   C4   C5      0.00   0.0  0
 KHH  CONST_09  C22  C21  C6   C5      0.00   0.0  0
 KHH  CONST_10  C21  C22  C3   C4      0.00   0.0  0
 KHH  CONST_11  C21  C6   C5   C4      0.00   0.0  0
 KHH  CONST_12  C16  N6   N3   C10   180.00   0.0  0
 KHH  CONST_13  C14  C13  N3   C10   180.00   0.0  0
 KHH  CONST_14  C4   C5   C6   C7    180.00   0.0  0
 KHH  CONST_15  C22  C21  C6   C7    180.00   0.0  0
 KHH  CONST_16  N3   C13  C14  C15   180.00   0.0  0
 KHH  CONST_17  N6   C16  C14  C15   180.00   0.0  0
 KHH  CONST_18  N5   C16  C14  C13   180.00   0.0  0
 KHH  CONST_19  O4   C22  C21  C6    180.00   0.0  0
 KHH  CONST_20  C2   C3   C4   C5    180.00   0.0  0
 KHH  CONST_21  O4   C22  C3   C4    180.00   0.0  0
 KHH  CONST_22  F1   C5   C4   C3    180.00   0.0  0
 KHH  CONST_23  C21  C22  C3   C2    180.00   0.0  0
 KHH  CONST_24  F1   C5   C6   C21   180.00   0.0  0
 KHH  CONST_25  N5   C16  N6   N3    180.00   0.0  0
 KHH  CONST_26  H11  C13  N3   C10     0.00   0.0  0
 KHH  CONST_27  H12  C4   C5   C6    180.00   0.0  0
 KHH  CONST_28  H16  C21  C6   C5    180.00   0.0  0
 KHH  CONST_29  C17  N5   C16  C14   180.00   0.0  0
 KHH  CONST_30  N6   C16  N5   C17     0.00   0.0  0
 KHH  CONST_31  H22  N5   C16  C14     0.00   0.0  0
 KHH  CONST_32  O2   C17  N5   C16     0.00   0.0  0
 KHH  CONST_33  O3   C17  N5   C16   180.00   0.0  0
 KHH  CONST_34  H20  N4   C15  C14   180.00   0.0  0
 KHH  CONST_35  H21  N4   C15  C14     0.00   0.0  0
 KHH  Var_01    C20  N1   C8   C9     61.33  30.0  1
 KHH  Var_02    N1   C8   C9   C10   -57.79  30.0  1
 KHH  Var_03    C8   N1   C20  C19   -59.97  30.0  1
 KHH  Var_04    N1   C7   C6   C5     65.36  30.0  2
 KHH  Var_05    N4   C15  C14  C16  -179.85  30.0  2
 KHH  Var_06    C1   C2   C3   C4    -22.01  30.0  1
 KHH  Var_07    H14  C1   C2   C3    178.73   0.0  2
 KHH  Var_08    H5   C11  C12  N2   -130.49  30.0  2
 KHH  Var_09    H7   C18  O3   C17   179.78  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
 KHH  chir_01  C10  C9  C19  N3   negativ
 KHH  chir_02  C19  F2  C10  C20  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
 KHH  plan-1  C10  0.020
 KHH  plan-1  C16  0.020
 KHH  plan-1  C13  0.020
 KHH  plan-1  C14  0.020
 KHH  plan-1  N3   0.020
 KHH  plan-1  N6   0.020
 KHH  plan-1  H11  0.020
 KHH  plan-1  N5   0.020
 KHH  plan-1  C15  0.020
 KHH  plan-2  C7   0.020
 KHH  plan-2  C6   0.020
 KHH  plan-2  C5   0.020
 KHH  plan-2  C4   0.020
 KHH  plan-2  C3   0.020
 KHH  plan-2  C2   0.020
 KHH  plan-2  C21  0.020
 KHH  plan-2  C22  0.020
 KHH  plan-2  F1   0.020
 KHH  plan-2  O4   0.020
 KHH  plan-2  H12  0.020
 KHH  plan-2  H16  0.020
 KHH  plan-3  C14  0.020
 KHH  plan-3  N4   0.020
 KHH  plan-3  O1   0.020
 KHH  plan-3  H20  0.020
 KHH  plan-3  H21  0.020
 KHH  plan-3  C15  0.020
 KHH  plan-4  C16  0.020
 KHH  plan-4  C17  0.020
 KHH  plan-4  H22  0.020
 KHH  plan-4  N5   0.020
 KHH  plan-5  C3   0.020
 KHH  plan-5  C2   0.020
 KHH  plan-5  C1   0.020
 KHH  plan-5  H13  0.020
 KHH  plan-5  H14  0.020
 KHH  plan-5  H15  0.020
 KHH  plan-6  C17  0.020
 KHH  plan-6  O2   0.020
 KHH  plan-6  O3   0.020
 KHH  plan-6  N5   0.020

