# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 09:45:52 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[5-(6-methoxy-1H-indazol-5-yl)-1H-pyrazol-4-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2[nH]ncc2cc1c3[nH]ncc3NC(=O)c4cnn5cccnc45
#
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
 KF4  KF4  N-[5-(6-methoxy-1H-indazol-5-yl)-1H-pyrazol-4-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  42  28  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KF4
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
 KF4  C4   C  CR56  0  -0.105  -4.4381  -0.5653  -0.5962
 KF4  C14  C  CR16  0  -0.043   5.7651  -0.2055   1.0781
 KF4  C5   C  CR16  0  -0.345  -3.7052   0.6089  -0.7914
 KF4  C6   C  CR6   0  -0.086  -2.5142   0.7829  -0.1189
 KF4  C11  C  CR5   0  -0.376   2.3914  -0.1572  -0.2327
 KF4  C7   C  CR5   0   0.422  -1.7357   2.0064  -0.3164
 KF4  C8   C  CR5   0   0.022  -0.4086   2.2140  -0.6475
 KF4  C9   C  CR15  0  -0.090  -0.2729   3.6068  -0.7616
 KF4  C10  C  C     0   0.498   1.6509   1.0965  -0.0746
 KF4  C12  C  CR15  0  -0.033   1.9816  -1.3834  -0.7795
 KF4  C13  C  CR56  0   0.627   3.6912  -0.4042   0.2122
 KF4  N1   N  NR15  0  -0.497  -2.2826   3.2375  -0.2733
 KF4  N2   N  NH1   0  -0.753   0.5524   1.2246  -0.8634
 KF4  C3   C  CR56  0   0.460  -3.9394  -1.5478   0.2721
 KF4  N3   N  N     0  -0.291   2.9048  -2.3220  -0.7035
 KF4  O1   O  O     0  -0.467   2.0039   1.9686   0.7021
 KF4  N5   N  N     0  -0.412   4.6164   0.3562   0.8064
 KF4  C15  C  CR16  0  -0.389   6.0720  -1.5524   0.7809
 KF4  C16  C  CR16  0   0.089   5.1231  -2.3106   0.1718
 KF4  N4   N  N     0  -0.359   3.9400  -1.7240  -0.1073
 KF4  N    N  N     0  -0.262  -1.4202   4.2136  -0.5238
 KF4  C1   C  CR6   0   0.370  -2.0418  -0.2252   0.7802
 KF4  O    O  O2    0  -0.458  -0.9000   0.0735   1.4140
 KF4  C    C  CH3   0  -0.444  -0.3287  -0.8814   2.2860
 KF4  C17  C  CR15  0  -0.128  -5.6548  -1.1132  -1.0848
 KF4  N6   N  N     0  -0.232  -5.8710  -2.2954  -0.5694
 KF4  N7   N  NR15  0  -0.555  -4.8381  -2.5540   0.2442
 KF4  C2   C  CR16  0  -0.437  -2.7384  -1.4003   0.9750
 KF4  H2   H  HCR6  0   0.267  -4.0569   1.3678  -1.4792
 KF4  H3   H  HCR5  0   0.265   0.6128   4.1728  -1.0065
 KF4  H4   H  HCR5  0   0.281   1.0268  -1.6307  -1.2203
 KF4  H5   H  HNR5  0   0.420  -3.2378   3.4616  -0.0411
 KF4  H6   H  HNH1  0   0.404   0.3034   0.4702  -1.4828
 KF4  H7   H  HCR6  0   0.302   7.0351  -1.9714   1.0272
 KF4  H8   H  HCR6  0   0.332   5.2385  -3.3467  -0.1107
 KF4  H9   H  HCH3  0   0.238  -0.9801  -1.0971   3.1367
 KF4  H10  H  HCH3  0   0.230  -0.0972  -1.8161   1.7695
 KF4  H11  H  HCH3  0   0.264   0.5977  -0.4451   2.6501
 KF4  H12  H  HCR5  0   0.269  -6.3551  -0.6784  -1.7819
 KF4  H13  H  HNR5  0   0.417  -4.8066  -3.4248   0.7485
 KF4  H14  H  HCR6  0   0.295  -2.3934  -2.1740   1.6465
 KF4  H1   H  HCR6  0   0.286   6.5117   0.4163   1.5579

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
 KF4  C    O    single    1.414  0.020  1.414
 KF4  O    C1   single    1.340  0.020  1.340
 KF4  C2   C1   aromatic  1.380  0.020  1.380
 KF4  C2   C3   aromatic  1.399  0.020  1.399
 KF4  N7   C3   aromatic  1.349  0.020  1.349
 KF4  N7   N6   aromatic  1.340  0.020  1.340
 KF4  C1   C6   aromatic  1.431  0.020  1.431
 KF4  C3   C4   aromatic  1.403  0.020  1.403
 KF4  C15  C14  aromatic  1.413  0.020  1.413
 KF4  C15  C16  aromatic  1.359  0.020  1.359
 KF4  C14  N5   aromatic  1.307  0.020  1.307
 KF4  C16  N4   aromatic  1.350  0.020  1.350
 KF4  N6   C17  aromatic  1.308  0.020  1.308
 KF4  N5   C13  aromatic  1.337  0.020  1.337
 KF4  C6   C7   single    1.463  0.020  1.463
 KF4  C6   C5   aromatic  1.379  0.020  1.379
 KF4  C4   C17  aromatic  1.421  0.020  1.421
 KF4  C4   C5   aromatic  1.398  0.020  1.398
 KF4  N4   C13  aromatic  1.380  0.020  1.380
 KF4  N4   N3   aromatic  1.336  0.020  1.336
 KF4  C13  C11  aromatic  1.396  0.020  1.396
 KF4  C7   N1   aromatic  1.348  0.020  1.348
 KF4  C7   C8   aromatic  1.384  0.020  1.384
 KF4  N1   N    aromatic  1.326  0.020  1.326
 KF4  N2   C8   single    1.396  0.020  1.396
 KF4  N2   C10  single    1.358  0.020  1.358
 KF4  C8   C9   aromatic  1.404  0.020  1.404
 KF4  N3   C12  aromatic  1.319  0.020  1.319
 KF4  C11  C10  single    1.465  0.020  1.465
 KF4  C11  C12  aromatic  1.404  0.020  1.404
 KF4  N    C9   aromatic  1.319  0.020  1.319
 KF4  C10  O1   double    1.220  0.020  1.220
 KF4  C14  H1   single    0.930  0.020  1.080
 KF4  C5   H2   single    0.930  0.020  1.080
 KF4  C9   H3   single    0.930  0.020  1.080
 KF4  C12  H4   single    0.930  0.020  1.080
 KF4  N1   H5   single    0.860  0.020  1.020
 KF4  N2   H6   single    0.860  0.020  1.020
 KF4  C15  H7   single    0.930  0.020  1.080
 KF4  C16  H8   single    0.930  0.020  1.080
 KF4  C    H9   single    0.970  0.020  1.090
 KF4  C    H10  single    0.970  0.020  1.090
 KF4  C    H11  single    0.970  0.020  1.090
 KF4  C17  H12  single    0.930  0.020  1.080
 KF4  N7   H13  single    0.860  0.020  1.020
 KF4  C2   H14  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
 KF4  C17  C4   C3   104.31  3.000
 KF4  C17  C4   C5   136.45  3.000
 KF4  C3   C4   C5   119.23  3.000
 KF4  H1   C14  C15  119.37  3.000
 KF4  H1   C14  N5   116.80  3.000
 KF4  C15  C14  N5   123.83  3.000
 KF4  H2   C5   C6   120.12  3.000
 KF4  H2   C5   C4   120.47  3.000
 KF4  C6   C5   C4   119.39  3.000
 KF4  C1   C6   C7   119.88  3.000
 KF4  C7   C6   C5   119.95  3.000
 KF4  C1   C6   C5   120.18  3.000
 KF4  C13  C11  C12  103.97  3.000
 KF4  C12  C11  C10  129.96  3.000
 KF4  C13  C11  C10  126.01  3.000
 KF4  N1   C7   C8   105.06  3.000
 KF4  C8   C7   C6   131.92  3.000
 KF4  N1   C7   C6   122.92  3.000
 KF4  N2   C8   C9   128.61  3.000
 KF4  C9   C8   C7   105.13  3.000
 KF4  N2   C8   C7   126.22  3.000
 KF4  H3   C9   N    120.89  3.000
 KF4  H3   C9   C8   128.16  3.000
 KF4  N    C9   C8   110.95  3.000
 KF4  O1   C10  N2   122.43  3.000
 KF4  O1   C10  C11  122.30  3.000
 KF4  N2   C10  C11  115.27  3.000
 KF4  H4   C12  N3   118.64  3.000
 KF4  H4   C12  C11  128.09  3.000
 KF4  N3   C12  C11  113.26  3.000
 KF4  N4   C13  N5   121.46  3.000
 KF4  N4   C13  C11  105.26  3.000
 KF4  N5   C13  C11  133.27  3.000
 KF4  H5   N1   N    119.73  3.000
 KF4  H5   N1   C7   126.50  3.000
 KF4  N    N1   C7   113.72  3.000
 KF4  H6   N2   C10  119.10  3.000
 KF4  H6   N2   C8   117.10  3.000
 KF4  C10  N2   C8   122.26  3.000
 KF4  C2   C3   N7   131.35  3.000
 KF4  N7   C3   C4   105.82  3.000
 KF4  C2   C3   C4   122.83  3.000
 KF4  N4   N3   C12  104.45  3.000
 KF4  C13  N5   C14  117.14  3.000
 KF4  H7   C15  C16  120.61  3.000
 KF4  H7   C15  C14  121.07  3.000
 KF4  C16  C15  C14  118.32  3.000
 KF4  H8   C16  N4   117.17  3.000
 KF4  H8   C16  C15  125.30  3.000
 KF4  N4   C16  C15  117.54  3.000
 KF4  C16  N4   N3   125.23  3.000
 KF4  N3   N4   C13  113.05  3.000
 KF4  C16  N4   C13  121.71  3.000
 KF4  N1   N    C9   105.13  3.000
 KF4  C2   C1   O    123.60  3.000
 KF4  C2   C1   C6   121.47  3.000
 KF4  O    C1   C6   114.93  3.000
 KF4  C    O    C1   119.06  3.000
 KF4  H11  C    H10  108.73  3.000
 KF4  H11  C    H9   109.06  3.000
 KF4  H10  C    H9   108.98  3.000
 KF4  H11  C    O    106.26  3.000
 KF4  H10  C    O    111.83  3.000
 KF4  H9   C    O    111.87  3.000
 KF4  H12  C17  N6   120.76  3.000
 KF4  H12  C17  C4   128.47  3.000
 KF4  N6   C17  C4   110.77  3.000
 KF4  N7   N6   C17  106.64  3.000
 KF4  H13  N7   N6   119.67  3.000
 KF4  H13  N7   C3   127.87  3.000
 KF4  N6   N7   C3   112.46  3.000
 KF4  H14  C2   C1   122.43  3.000
 KF4  H14  C2   C3   120.69  3.000
 KF4  C1   C2   C3   116.88  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
 KF4  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 KF4  CONST_02  N6   N7   C3   C4     0.00   0.0  0
 KF4  CONST_03  N7   N6   C17  C4     0.00   0.0  0
 KF4  CONST_04  C1   C6   C5   C4     0.00   0.0  0
 KF4  CONST_05  C7   C6   C5   C4   180.00   0.0  0
 KF4  CONST_06  N4   C16  C15  C14    0.00   0.0  0
 KF4  CONST_07  N4   C13  N5   C14    0.00   0.0  0
 KF4  CONST_08  C11  C13  N5   C14  180.00   0.0  0
 KF4  CONST_09  C2   C1   C6   C5     0.00   0.0  0
 KF4  CONST_12  C2   C3   C4   C5     0.00   0.0  0
 KF4  CONST_13  N7   C3   C4   C5   180.00   0.0  0
 KF4  CONST_14  N6   C17  C4   C5   180.00   0.0  0
 KF4  CONST_15  C3   C2   C1   C6     0.00   0.0  0
 KF4  CONST_16  N    N1   C7   C6   180.00   0.0  0
 KF4  CONST_17  C9   C8   C7   C6   180.00   0.0  0
 KF4  CONST_18  C3   C4   C5   C6     0.00   0.0  0
 KF4  CONST_19  C17  C4   C5   C6   180.00   0.0  0
 KF4  CONST_20  C16  N4   C13  C11  180.00   0.0  0
 KF4  CONST_21  N3   N4   C13  C11    0.00   0.0  0
 KF4  CONST_22  N4   N3   C12  C11    0.00   0.0  0
 KF4  CONST_23  C2   C1   C6   C7   180.00   0.0  0
 KF4  CONST_24  C9   N    N1   C7     0.00   0.0  0
 KF4  CONST_25  N    C9   C8   C7     0.00   0.0  0
 KF4  CONST_27  N    N1   C7   C8     0.00   0.0  0
 KF4  CONST_28  N1   N    C9   C8     0.00   0.0  0
 KF4  CONST_29  N1   C7   C8   C9     0.00   0.0  0
 KF4  CONST_30  C16  N4   N3   C12  180.00   0.0  0
 KF4  CONST_31  C13  N4   N3   C12    0.00   0.0  0
 KF4  CONST_32  N5   C13  C11  C12  180.00   0.0  0
 KF4  CONST_33  N4   C13  C11  C12    0.00   0.0  0
 KF4  CONST_34  C15  C14  N5   C13    0.00   0.0  0
 KF4  CONST_35  C15  C16  N4   C13    0.00   0.0  0
 KF4  CONST_36  N3   C12  C11  C13    0.00   0.0  0
 KF4  CONST_38  C17  N6   N7   C3     0.00   0.0  0
 KF4  CONST_39  N6   C17  C4   C3     0.00   0.0  0
 KF4  CONST_40  C15  C16  N4   N3   180.00   0.0  0
 KF4  CONST_41  N5   C13  N4   N3   180.00   0.0  0
 KF4  CONST_42  C16  C15  C14  N5     0.00   0.0  0
 KF4  CONST_43  C16  N4   C13  N5     0.00   0.0  0
 KF4  CONST_44  N7   C3   C2   C1   180.00   0.0  0
 KF4  CONST_45  C2   C3   C4   C17  180.00   0.0  0
 KF4  CONST_46  N7   C3   C4   C17    0.00   0.0  0
 KF4  CONST_47  C2   C3   N7   N6   180.00   0.0  0
 KF4  CONST_48  O    C1   C6   C5   180.00   0.0  0
 KF4  CONST_49  N2   C8   C7   C6     0.00   0.0  0
 KF4  CONST_50  O    C1   C6   C7     0.00   0.0  0
 KF4  CONST_51  N5   C13  C11  C10    0.00   0.0  0
 KF4  CONST_52  N4   C13  C11  C10  180.00   0.0  0
 KF4  CONST_53  N3   C12  C11  C10  180.00   0.0  0
 KF4  CONST_54  N2   C8   C7   N1   180.00   0.0  0
 KF4  CONST_55  N    C9   C8   N2   180.00   0.0  0
 KF4  CONST_56  O    C1   C2   C3   180.00   0.0  0
 KF4  CONST_57  H14  C2   C3   C4   180.00   0.0  0
 KF4  CONST_58  H13  N7   C3   C4   180.00   0.0  0
 KF4  CONST_59  H8   C16  C15  C14  180.00   0.0  0
 KF4  CONST_60  H12  C17  C4   C5     0.00   0.0  0
 KF4  CONST_61  H5   N1   C7   C6     0.00   0.0  0
 KF4  CONST_62  H2   C5   C6   C7     0.00   0.0  0
 KF4  CONST_63  H3   C9   C8   C7   180.00   0.0  0
 KF4  CONST_64  H1   C14  N5   C13  180.00   0.0  0
 KF4  CONST_65  H4   C12  C11  C13  180.00   0.0  0
 KF4  CONST_66  H7   C15  C14  N5   180.00   0.0  0
 KF4  CONST_67  C8   N2   C10  C11  180.00   0.0  0
 KF4  CONST_71  O1   C10  N2   C8     0.00   0.0  0
 KF4  Var_01    N2   C10  C11  C12  -19.34  30.0  2
 KF4  Var_02    C2   C1   O    C      3.14  30.0  2
 KF4  Var_03    H9   C    O    C1   -63.29  30.0  3

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
 KF4  plan-1  C6   0.020
 KF4  plan-1  C7   0.020
 KF4  plan-1  C8   0.020
 KF4  plan-1  C9   0.020
 KF4  plan-1  N1   0.020
 KF4  plan-1  N2   0.020
 KF4  plan-1  N    0.020
 KF4  plan-1  H3   0.020
 KF4  plan-1  H5   0.020
 KF4  plan-2  C14  0.020
 KF4  plan-2  C11  0.020
 KF4  plan-2  C10  0.020
 KF4  plan-2  C12  0.020
 KF4  plan-2  C13  0.020
 KF4  plan-2  N3   0.020
 KF4  plan-2  N5   0.020
 KF4  plan-2  C15  0.020
 KF4  plan-2  C16  0.020
 KF4  plan-2  N4   0.020
 KF4  plan-2  H4   0.020
 KF4  plan-2  H7   0.020
 KF4  plan-2  H8   0.020
 KF4  plan-2  H1   0.020
 KF4  plan-3  C4   0.020
 KF4  plan-3  C5   0.020
 KF4  plan-3  C6   0.020
 KF4  plan-3  C7   0.020
 KF4  plan-3  C3   0.020
 KF4  plan-3  C1   0.020
 KF4  plan-3  O    0.020
 KF4  plan-3  C17  0.020
 KF4  plan-3  N6   0.020
 KF4  plan-3  N7   0.020
 KF4  plan-3  C2   0.020
 KF4  plan-3  H2   0.020
 KF4  plan-3  H12  0.020
 KF4  plan-3  H13  0.020
 KF4  plan-3  H14  0.020
 KF4  plan-4  C11  0.020
 KF4  plan-4  C8   0.020
 KF4  plan-4  C10  0.020
 KF4  plan-4  N2   0.020
 KF4  plan-4  O1   0.020
 KF4  plan-4  H6   0.020

