# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 04:53:40 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: ~{N}-[(2~{R})-2-fluoranyl-3-methyl-3-oxidanyl-butyl]-6-[(6-fluoranylpyrazolo[1,5-a]pyrimidin-5-yl)amino]-4-(propan-2-ylamino)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Nc1cc(Nc2nc3ccnn3cc2F)ncc1C(=O)NC[C@@H](F)C(C)(C)O
#
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
 EXF  EXF  ~{N}-[(2~{R})-2-fluoranyl-3-methyl-3-oxidanyl-butyl]-6-[(6-fluoranylpyrazolo[1,5-a]pyrimidin-5-yl)amino]-4-(propan-2-ylamino)pyridine-3-carboxamide  ligand  56  31  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EXF
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
 EXF  C13  C  CH3   0  -0.671  16.3800  -10.6916  12.8315
 EXF  C18  C  CH3   0  -0.653  16.6701   -5.0034   4.6850
 EXF  C17  C  CH3   0  -0.666  17.3739   -4.5499   7.0597
 EXF  C16  C  CH1   0  -0.106  17.5171   -5.4785   5.8630
 EXF  C15  C  CR6   0   0.519  17.5081   -7.9518   5.6353
 EXF  C19  C  CR16  0  -0.499  18.3707   -7.9189   4.5247
 EXF  C11  C  CH1   0   0.218  16.2653  -10.7271  10.3278
 EXF  C12  C  CT    0   0.139  15.5214  -11.0622  11.6215
 EXF  C9   C  C     0   0.561  16.1721   -9.3818   7.2508
 EXF  C10  C  CH2   0  -0.340  15.4401  -10.8759   9.0581
 EXF  F1   F  F     0  -0.376  16.7271   -9.4121  10.3791
 EXF  C14  C  CH3   0  -0.692  15.2196  -12.5613  11.6559
 EXF  O    O  OH1   0  -0.678  14.3219  -10.3092  11.6103
 EXF  C8   C  CR6   0  -0.237  17.0536   -9.2316   6.0679
 EXF  C7   C  CR16  0  -0.102  17.4415  -10.3290   5.3116
 EXF  N4   N  N     0  -0.481  18.2282  -10.2974   4.2524
 EXF  C6   C  CR6   0   0.476  18.6974   -9.1003   3.8857
 EXF  N3   N  NH1   0  -0.757  19.5299   -9.1875   2.7811
 EXF  C5   C  CR6   0   0.441  20.2195   -8.2249   2.1159
 EXF  C    C  CR6   0   0.333  21.0118   -8.6387   0.9913
 EXF  F    F  F     0  -0.292  21.0270   -9.9334   0.6572
 EXF  N2   N  N     0  -0.510  20.1787   -6.9704   2.4679
 EXF  C4   C  CR56  0   0.622  20.8892   -6.0739   1.7652
 EXF  N    N  N     0  -0.372  21.6568   -6.4488   0.6836
 EXF  C1   C  CR16  0  -0.075  21.7239   -7.7430   0.2840
 EXF  C3   C  CR15  0  -0.572  21.0574   -4.7041   1.8796
 EXF  C2   C  CR15  0  -0.015  21.9285   -4.3766   0.8359
 EXF  N1   N  N     0  -0.311  22.2932   -5.4246   0.1109
 EXF  H1   H  HCH3  0   0.233  15.8826  -11.0052  13.7517
 EXF  H2   H  HCH3  0   0.227  17.3484  -11.1929  12.7999
 EXF  H3   H  HCH3  0   0.242  16.5532   -9.6182  12.8930
 EXF  H4   H  HCH3  0   0.231  17.0012   -4.0202   4.3483
 EXF  H5   H  HCH3  0   0.235  16.7351   -5.6868   3.8378
 EXF  H6   H  HCH3  0   0.225  15.6207   -4.9266   4.9749
 EXF  H7   H  HCH3  0   0.241  18.0077   -4.8691   7.8873
 EXF  H8   H  HCH3  0   0.241  17.6596   -3.5352   6.7846
 EXF  H9   H  HCH3  0   0.227  16.3406   -4.5206   7.4120
 EXF  H10  H  HCH1  0   0.238  18.5697   -5.4761   5.5671
 EXF  H11  H  HCR6  0   0.311  18.7682   -6.9902   4.1565
 EXF  H12  H  HCH1  0   0.217  17.1479  -11.3731  10.2699
 EXF  H13  H  HNH1  0   0.405  16.9339  -11.2315   7.6280
 EXF  H14  H  HCH2  0   0.266  14.5720  -10.2214   9.0832
 EXF  H15  H  HCH2  0   0.267  15.0774  -11.9005   8.9737
 EXF  H16  H  HCH3  0   0.243  14.7378  -12.8217  12.6004
 EXF  H17  H  HCH3  0   0.243  14.5525  -12.8676  10.8501
 EXF  H18  H  HCH3  0   0.234  16.1317  -13.1549  11.5850
 EXF  H19  H  HOH1  0   0.450  13.8217  -10.5309  12.4024
 EXF  H20  H  HCR6  0   0.262  17.0652  -11.3149   5.5659
 EXF  H21  H  HNH1  0   0.399  16.4291   -6.9209   6.9646
 EXF  H22  H  HNH1  0   0.417  19.6193  -10.1340   2.4404
 EXF  H23  H  HCR6  0   0.344  22.3365   -7.9880  -0.5721
 EXF  H24  H  HCR5  0   0.270  20.6146   -4.0507   2.6115
 EXF  H25  H  HCR5  0   0.274  22.3112   -3.3994   0.5832
 EXF  N5   N  NH1   0  -0.649  16.2198  -10.5694   7.8829
 EXF  N6   N  NH1   0  -0.689  17.1640   -6.8250   6.2776
 EXF  O1   O  O     0  -0.509  15.4292   -8.4734   7.6209

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
 EXF  N1   C2   aromatic  1.325  0.020  1.325
 EXF  N1   N    aromatic  1.335  0.020  1.335
 EXF  C2   C3   aromatic  1.398  0.020  1.398
 EXF  C1   N    aromatic  1.356  0.020  1.356
 EXF  C1   C    aromatic  1.345  0.020  1.345
 EXF  N    C4   aromatic  1.378  0.020  1.378
 EXF  C3   C4   aromatic  1.385  0.020  1.385
 EXF  F    C    single    1.337  0.020  1.337
 EXF  C    C5   aromatic  1.437  0.020  1.437
 EXF  C4   N2   aromatic  1.342  0.020  1.342
 EXF  C5   N2   aromatic  1.304  0.020  1.304
 EXF  C5   N3   single    1.358  0.020  1.358
 EXF  N3   C6   single    1.386  0.020  1.386
 EXF  C6   N4   aromatic  1.337  0.020  1.337
 EXF  C6   C19  aromatic  1.382  0.020  1.382
 EXF  N4   C7   aromatic  1.320  0.020  1.320
 EXF  C19  C15  aromatic  1.407  0.020  1.407
 EXF  C18  C16  single    1.527  0.020  1.527
 EXF  C7   C8   aromatic  1.388  0.020  1.388
 EXF  C15  C8   aromatic  1.425  0.020  1.425
 EXF  C15  N6   single    1.342  0.020  1.342
 EXF  C16  N6   single    1.452  0.020  1.452
 EXF  C16  C17  single    1.521  0.020  1.521
 EXF  C8   C9   single    1.483  0.020  1.483
 EXF  C9   O1   double    1.230  0.020  1.230
 EXF  C9   N5   single    1.346  0.020  1.346
 EXF  N5   C10  single    1.443  0.020  1.443
 EXF  C10  C11  single    1.522  0.020  1.522
 EXF  C11  F1   single    1.395  0.020  1.395
 EXF  C11  C12  single    1.529  0.020  1.529
 EXF  O    C12  single    1.416  0.020  1.416
 EXF  C14  C12  single    1.530  0.020  1.530
 EXF  C12  C13  single    1.529  0.020  1.529
 EXF  C13  H1   single    0.970  0.020  1.090
 EXF  C13  H2   single    0.970  0.020  1.090
 EXF  C13  H3   single    0.970  0.020  1.090
 EXF  C18  H4   single    0.970  0.020  1.090
 EXF  C18  H5   single    0.970  0.020  1.090
 EXF  C18  H6   single    0.970  0.020  1.090
 EXF  C17  H7   single    0.970  0.020  1.090
 EXF  C17  H8   single    0.970  0.020  1.090
 EXF  C17  H9   single    0.970  0.020  1.090
 EXF  C16  H10  single    0.970  0.020  1.090
 EXF  C19  H11  single    0.930  0.020  1.080
 EXF  C11  H12  single    0.970  0.020  1.090
 EXF  N5   H13  single    0.860  0.020  1.020
 EXF  C10  H14  single    0.970  0.020  1.090
 EXF  C10  H15  single    0.970  0.020  1.090
 EXF  C14  H16  single    0.970  0.020  1.090
 EXF  C14  H17  single    0.970  0.020  1.090
 EXF  C14  H18  single    0.970  0.020  1.090
 EXF  O    H19  single    0.850  0.020  0.980
 EXF  C7   H20  single    0.930  0.020  1.080
 EXF  N6   H21  single    0.860  0.020  1.020
 EXF  N3   H22  single    0.860  0.020  1.020
 EXF  C1   H23  single    0.930  0.020  1.080
 EXF  C3   H24  single    0.930  0.020  1.080
 EXF  C2   H25  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
 EXF  H3   C13  H2   108.26  3.000
 EXF  H3   C13  H1   107.94  3.000
 EXF  H2   C13  H1   107.27  3.000
 EXF  H3   C13  C12  111.89  3.000
 EXF  H2   C13  C12  111.35  3.000
 EXF  H1   C13  C12  109.96  3.000
 EXF  H6   C18  H5   107.93  3.000
 EXF  H6   C18  H4   108.09  3.000
 EXF  H5   C18  H4   107.87  3.000
 EXF  H6   C18  C16  110.51  3.000
 EXF  H5   C18  C16  111.80  3.000
 EXF  H4   C18  C16  110.51  3.000
 EXF  H9   C17  H8   107.73  3.000
 EXF  H9   C17  H7   108.24  3.000
 EXF  H8   C17  H7   108.18  3.000
 EXF  H9   C17  C16  111.05  3.000
 EXF  H8   C17  C16  110.20  3.000
 EXF  H7   C17  C16  111.32  3.000
 EXF  H10  C16  N6   108.26  3.000
 EXF  H10  C16  C17  107.59  3.000
 EXF  N6   C16  C17  108.57  3.000
 EXF  H10  C16  C18  108.94  3.000
 EXF  C17  C16  C18  111.39  3.000
 EXF  N6   C16  C18  111.95  3.000
 EXF  N6   C15  C8   121.80  3.000
 EXF  N6   C15  C19  121.03  3.000
 EXF  C8   C15  C19  117.14  3.000
 EXF  H11  C19  C6   119.50  3.000
 EXF  H11  C19  C15  121.15  3.000
 EXF  C6   C19  C15  119.34  3.000
 EXF  H12  C11  F1   106.93  3.000
 EXF  H12  C11  C10  109.59  3.000
 EXF  F1   C11  C10  107.61  3.000
 EXF  H12  C11  C12  107.91  3.000
 EXF  F1   C11  C12  109.66  3.000
 EXF  C10  C11  C12  114.87  3.000
 EXF  O    C12  C14  110.74  3.000
 EXF  C14  C12  C11  109.25  3.000
 EXF  O    C12  C11  106.79  3.000
 EXF  C14  C12  C13  109.30  3.000
 EXF  O    C12  C13  110.66  3.000
 EXF  C11  C12  C13  110.06  3.000
 EXF  C8   C9   N5   116.29  3.000
 EXF  N5   C9   O1   122.10  3.000
 EXF  C8   C9   O1   121.61  3.000
 EXF  H15  C10  H14  107.57  3.000
 EXF  H15  C10  N5   108.44  3.000
 EXF  H14  C10  N5   108.80  3.000
 EXF  H15  C10  C11  109.69  3.000
 EXF  H14  C10  C11  110.78  3.000
 EXF  N5   C10  C11  111.45  3.000
 EXF  H18  C14  H17  108.11  3.000
 EXF  H18  C14  H16  107.19  3.000
 EXF  H17  C14  H16  107.60  3.000
 EXF  H18  C14  C12  111.54  3.000
 EXF  H17  C14  C12  112.31  3.000
 EXF  H16  C14  C12  109.90  3.000
 EXF  H19  O    C12  108.14  3.000
 EXF  C7   C8   C9   121.38  3.000
 EXF  C9   C8   C15  121.50  3.000
 EXF  C7   C8   C15  117.09  3.000
 EXF  H20  C7   N4   114.61  3.000
 EXF  H20  C7   C8   119.57  3.000
 EXF  N4   C7   C8   125.80  3.000
 EXF  C6   N4   C7   116.80  3.000
 EXF  N3   C6   N4   111.91  3.000
 EXF  N4   C6   C19  123.74  3.000
 EXF  N3   C6   C19  124.35  3.000
 EXF  H22  N3   C5   117.01  3.000
 EXF  H22  N3   C6   112.40  3.000
 EXF  C5   N3   C6   130.60  3.000
 EXF  N2   C5   C    120.38  3.000
 EXF  N2   C5   N3   122.27  3.000
 EXF  C    C5   N3   117.34  3.000
 EXF  C1   C    F    120.48  3.000
 EXF  F    C    C5   118.74  3.000
 EXF  C1   C    C5   120.78  3.000
 EXF  C4   N2   C5   119.00  3.000
 EXF  C3   C4   N    105.44  3.000
 EXF  C3   C4   N2   132.97  3.000
 EXF  N    C4   N2   121.59  3.000
 EXF  N1   N    C1   125.61  3.000
 EXF  C1   N    C4   121.22  3.000
 EXF  N1   N    C4   113.17  3.000
 EXF  H23  C1   N    118.53  3.000
 EXF  H23  C1   C    124.44  3.000
 EXF  N    C1   C    117.02  3.000
 EXF  H24  C3   C2   128.43  3.000
 EXF  H24  C3   C4   127.35  3.000
 EXF  C2   C3   C4   104.22  3.000
 EXF  H25  C2   N1   119.34  3.000
 EXF  H25  C2   C3   127.42  3.000
 EXF  N1   C2   C3   113.23  3.000
 EXF  C2   N1   N    103.93  3.000
 EXF  H13  N5   C10  116.73  3.000
 EXF  H13  N5   C9   119.11  3.000
 EXF  C10  N5   C9   123.41  3.000
 EXF  H21  N6   C15  115.61  3.000
 EXF  H21  N6   C16  117.31  3.000
 EXF  C15  N6   C16  125.42  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
 EXF  CONST_01  N4   C6   C19  C15     0.00   0.0  0
 EXF  CONST_02  N4   C7   C8   C15     0.00   0.0  0
 EXF  CONST_03  C7   N4   C6   C19     0.00   0.0  0
 EXF  CONST_04  C7   C8   C15  C19     0.00   0.0  0
 EXF  CONST_05  C6   N4   C7   C8      0.00   0.0  0
 EXF  CONST_06  C6   C19  C15  C8      0.00   0.0  0
 EXF  CONST_07  N    C1   C    C5      0.00   0.0  0
 EXF  CONST_08  N    C4   N2   C5      0.00   0.0  0
 EXF  CONST_09  C3   C4   N2   C5    180.00   0.0  0
 EXF  CONST_10  N1   N    C1   C     180.00   0.0  0
 EXF  CONST_11  C4   N    C1   C       0.00   0.0  0
 EXF  CONST_12  C4   N2   C5   C       0.00   0.0  0
 EXF  CONST_13  N1   N    C4   N2    180.00   0.0  0
 EXF  CONST_14  C1   N    C4   N2      0.00   0.0  0
 EXF  CONST_15  C2   C3   C4   N2    180.00   0.0  0
 EXF  CONST_16  C1   C    C5   N2      0.00   0.0  0
 EXF  CONST_17  C2   N1   N    C4      0.00   0.0  0
 EXF  CONST_18  N1   C2   C3   C4      0.00   0.0  0
 EXF  CONST_19  C3   C2   N1   N       0.00   0.0  0
 EXF  CONST_20  C2   C3   C4   N       0.00   0.0  0
 EXF  CONST_21  C2   N1   N    C1    180.00   0.0  0
 EXF  CONST_22  C3   C4   N    C1    180.00   0.0  0
 EXF  CONST_23  N1   N    C4   C3      0.00   0.0  0
 EXF  CONST_24  N3   C6   C19  C15   180.00   0.0  0
 EXF  CONST_25  C9   C8   C15  C19   180.00   0.0  0
 EXF  CONST_26  N4   C7   C8   C9    180.00   0.0  0
 EXF  CONST_27  N3   C6   N4   C7    180.00   0.0  0
 EXF  CONST_28  N6   C15  C8   C7    180.00   0.0  0
 EXF  CONST_29  C6   C19  C15  N6    180.00   0.0  0
 EXF  CONST_30  C1   C    C5   N3    180.00   0.0  0
 EXF  CONST_31  C4   N2   C5   N3    180.00   0.0  0
 EXF  CONST_32  N    C1   C    F     180.00   0.0  0
 EXF  CONST_33  N2   C5   C    F     180.00   0.0  0
 EXF  CONST_34  H20  C7   C8   C15   180.00   0.0  0
 EXF  CONST_35  H11  C19  C15  C8    180.00   0.0  0
 EXF  CONST_36  H23  C1   C    C5    180.00   0.0  0
 EXF  CONST_37  H24  C3   C4   N2      0.00   0.0  0
 EXF  CONST_38  H25  C2   C3   C4    180.00   0.0  0
 EXF  CONST_39  C19  C15  N6   C16     0.00   0.0  0
 EXF  CONST_40  C8   C15  N6   C16   180.00   0.0  0
 EXF  CONST_41  H21  N6   C15  C19   180.00   0.0  0
 EXF  CONST_42  C8   C9   N5   C10   180.00   0.0  0
 EXF  CONST_43  H13  N5   C9   C8      0.00   0.0  0
 EXF  CONST_44  C10  N5   C9   O1      0.00   0.0  0
 EXF  Var_01    C5   N3   C6   C19     2.16  30.0  2
 EXF  Var_02    C    C5   N3   C6    179.82  30.0  1
 EXF  Var_03    O1   C9   C8   C15    25.94  30.0  2
 EXF  Var_04    C15  N6   C16  C18    76.04  30.0  3
 EXF  Var_05    C9   N5   C10  C11   -99.14  30.0  2
 EXF  Var_06    H16  C14  C12  C13    56.38  30.0  3
 EXF  Var_07    H7   C17  C16  C18  -177.87  30.0  3
 EXF  Var_08    H4   C18  C16  C17    62.22  30.0  3
 EXF  Var_09    H1   C13  C12  C11  -175.43  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
 EXF  chir_01  C11  C10  F1  C12  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
 EXF  plan-1  C15  0.020
 EXF  plan-1  C19  0.020
 EXF  plan-1  C9   0.020
 EXF  plan-1  C8   0.020
 EXF  plan-1  C7   0.020
 EXF  plan-1  N4   0.020
 EXF  plan-1  C6   0.020
 EXF  plan-1  N3   0.020
 EXF  plan-1  H11  0.020
 EXF  plan-1  H20  0.020
 EXF  plan-1  N6   0.020
 EXF  plan-2  N3   0.020
 EXF  plan-2  C5   0.020
 EXF  plan-2  C    0.020
 EXF  plan-2  F    0.020
 EXF  plan-2  N2   0.020
 EXF  plan-2  C4   0.020
 EXF  plan-2  N    0.020
 EXF  plan-2  C1   0.020
 EXF  plan-2  C3   0.020
 EXF  plan-2  C2   0.020
 EXF  plan-2  N1   0.020
 EXF  plan-2  H23  0.020
 EXF  plan-2  H24  0.020
 EXF  plan-2  H25  0.020
 EXF  plan-3  C9   0.020
 EXF  plan-3  C10  0.020
 EXF  plan-3  C8   0.020
 EXF  plan-3  H13  0.020
 EXF  plan-3  N5   0.020
 EXF  plan-3  O1   0.020
 EXF  plan-4  C16  0.020
 EXF  plan-4  C15  0.020
 EXF  plan-4  H21  0.020
 EXF  plan-4  N6   0.020

