# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:53:47 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCN(CC1)CCOc2ccc(cc2)c3cnc4n(c3)ncc4c5ccncc5
#
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
 TAK  TAK  6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine  ligand  55  30  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TAK
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
 TAK  C1   C  CH2   0  -0.279  -8.0947  -0.2282  -0.8689
 TAK  C2   C  CH2   0  -0.437  -8.5511  -1.6776  -0.9401
 TAK  C3   C  CH2   0  -0.441  -8.9161  -2.1964   0.4447
 TAK  C4   C  CH2   0  -0.434  -7.7572  -1.9641   1.4053
 TAK  C5   C  CH2   0  -0.286  -7.3250  -0.5056   1.3834
 TAK  N1   N  NT    0  -0.413  -6.9716  -0.0762   0.0409
 TAK  C6   C  CH2   0  -0.299  -6.4399   1.2707   0.0225
 TAK  C7   C  CH2   0  -0.203  -5.0041   1.3559   0.4914
 TAK  O1   O  O2    0  -0.462  -4.1978   0.6278  -0.4209
 TAK  C8   C  CR6   0   0.389  -2.8672   0.6189  -0.2523
 TAK  C9   C  CR16  0  -0.336  -2.1245  -0.0584  -1.2234
 TAK  C10  C  CR16  0  -0.289  -0.7484  -0.1140  -1.1386
 TAK  C11  C  CR16  0  -0.369  -2.1982   1.2285   0.8080
 TAK  C12  C  CR16  0  -0.295  -0.8145   1.1573   0.8835
 TAK  C13  C  CR6   0   0.066  -0.0636   0.4961  -0.0835
 TAK  C14  C  CR6   0  -0.093   1.4032   0.4456  -0.0096
 TAK  C15  C  CR16  0   0.065   2.1390   1.4956   0.4616
 TAK  C16  C  CR16  0  -0.056   2.1285  -0.7045  -0.4305
 TAK  N2   N  N     0  -0.424   3.4275  -0.8079  -0.4013
 TAK  C17  C  CR56  0   0.588   4.1246   0.2364   0.0617
 TAK  N3   N  N     0  -0.363   3.4812   1.3746   0.5005
 TAK  N4   N  N     0  -0.289   4.3249   2.3157   0.9267
 TAK  C18  C  CR15  0  -0.063   5.5216   1.7822   0.7639
 TAK  C19  C  CR5   0  -0.196   5.4898   0.4838   0.2271
 TAK  C20  C  CR6   0   0.207   6.6174  -0.3758  -0.0883
 TAK  C21  C  CR16  0  -0.407   7.9307   0.0401   0.1502
 TAK  C22  C  CR16  0  -0.065   8.9817  -0.7997  -0.1701
 TAK  N5   N  N     0  -0.416   8.8307  -2.0087  -0.7024
 TAK  C23  C  CR16  0  -0.060   7.5839  -2.4074  -0.9284
 TAK  C24  C  CR16  0  -0.423   6.4611  -1.6477  -0.6463
 TAK  H1   H  HCH2  0   0.233  -7.7869   0.1108  -1.8611
 TAK  H1A  H  HCH2  0   0.182  -8.9499   0.4047  -0.5683
 TAK  H2   H  HCH2  0   0.229  -9.4012  -1.7546  -1.6215
 TAK  H2A  H  HCH2  0   0.214  -7.7451  -2.2855  -1.3622
 TAK  H3   H  HCH2  0   0.210  -9.8000  -1.6614   0.8084
 TAK  H3A  H  HCH2  0   0.231  -9.1826  -3.2547   0.4055
 TAK  H4   H  HCH2  0   0.229  -8.0344  -2.2409   2.4249
 TAK  H4A  H  HCH2  0   0.215  -6.9086  -2.5940   1.1220
 TAK  H5   H  HCH2  0   0.185  -8.1370   0.1216   1.7956
 TAK  H5A  H  HCH2  0   0.235  -6.4660  -0.3734   2.0442
 TAK  H6   H  HCH2  0   0.241  -6.4877   1.6542  -0.9999
 TAK  H6A  H  HCH2  0   0.209  -7.0335   1.9670   0.6382
 TAK  H7   H  HCH2  0   0.236  -4.7002   2.4082   0.5180
 TAK  H7A  H  HCH2  0   0.229  -4.8868   0.9577   1.5053
 TAK  H9   H  HCR6  0   0.267  -2.6373  -0.5279  -2.0532
 TAK  H10  H  HCR6  0   0.261  -0.2019  -0.6230  -1.9229
 TAK  H11  H  HCR6  0   0.283  -2.7315   1.7523   1.5890
 TAK  H12  H  HCR6  0   0.262  -0.3224   1.6168   1.7317
 TAK  H15  H  HCR6  0   0.323   1.7304   2.4381   0.7981
 TAK  H16  H  HCR6  0   0.279   1.5843  -1.5698  -0.7923
 TAK  H18  H  HCR5  0   0.280   6.3916   2.3593   1.0398
 TAK  H21  H  HCR6  0   0.258   8.1501   1.0079   0.5805
 TAK  H22  H  HCR6  0   0.262   9.9998  -0.4742   0.0137
 TAK  H23  H  HCR6  0   0.261   7.4627  -3.3933  -1.3646
 TAK  H24  H  HCR6  0   0.270   5.4806  -2.0467  -0.8620

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
 TAK  C1   C2   single    1.521  0.020  1.521
 TAK  C1   N1   single    1.453  0.020  1.453
 TAK  C2   C3   single    1.523  0.020  1.523
 TAK  C3   C4   single    1.523  0.020  1.523
 TAK  C4   C5   single    1.521  0.020  1.521
 TAK  C5   N1   single    1.453  0.020  1.453
 TAK  N1   C6   single    1.448  0.020  1.448
 TAK  C6   C7   single    1.513  0.020  1.513
 TAK  C7   O1   single    1.419  0.020  1.419
 TAK  O1   C8   single    1.341  0.020  1.341
 TAK  C8   C9   aromatic  1.398  0.020  1.398
 TAK  C8   C11  aromatic  1.394  0.020  1.394
 TAK  C9   C10  aromatic  1.380  0.020  1.380
 TAK  C10  C13  aromatic  1.398  0.020  1.398
 TAK  C11  C12  aromatic  1.388  0.020  1.388
 TAK  C12  C13  aromatic  1.391  0.020  1.391
 TAK  C13  C14  single    1.469  0.020  1.469
 TAK  C14  C15  aromatic  1.366  0.020  1.366
 TAK  C14  C16  aromatic  1.423  0.020  1.423
 TAK  C15  N3   aromatic  1.348  0.020  1.348
 TAK  C16  N2   aromatic  1.303  0.020  1.303
 TAK  N2   C17  aromatic  1.338  0.020  1.338
 TAK  C17  N3   aromatic  1.379  0.020  1.379
 TAK  C17  C19  aromatic  1.397  0.020  1.397
 TAK  N3   N4   aromatic  1.334  0.020  1.334
 TAK  N4   C18  aromatic  1.320  0.020  1.320
 TAK  C18  C19  aromatic  1.405  0.020  1.405
 TAK  C19  C20  single    1.453  0.020  1.453
 TAK  C20  C21  aromatic  1.398  0.020  1.398
 TAK  C20  C24  aromatic  1.398  0.020  1.398
 TAK  C21  C22  aromatic  1.383  0.020  1.383
 TAK  C22  N5   aromatic  1.330  0.020  1.330
 TAK  N5   C23  aromatic  1.328  0.020  1.328
 TAK  C23  C24  aromatic  1.385  0.020  1.385
 TAK  C1   H1   single    0.970  0.020  1.090
 TAK  C1   H1A  single    0.970  0.020  1.090
 TAK  C2   H2   single    0.970  0.020  1.090
 TAK  C2   H2A  single    0.970  0.020  1.090
 TAK  C3   H3   single    0.970  0.020  1.090
 TAK  C3   H3A  single    0.970  0.020  1.090
 TAK  C4   H4   single    0.970  0.020  1.090
 TAK  C4   H4A  single    0.970  0.020  1.090
 TAK  C5   H5   single    0.970  0.020  1.090
 TAK  C5   H5A  single    0.970  0.020  1.090
 TAK  C6   H6   single    0.970  0.020  1.090
 TAK  C6   H6A  single    0.970  0.020  1.090
 TAK  C7   H7   single    0.970  0.020  1.090
 TAK  C7   H7A  single    0.970  0.020  1.090
 TAK  C9   H9   single    0.930  0.020  1.080
 TAK  C10  H10  single    0.930  0.020  1.080
 TAK  C11  H11  single    0.930  0.020  1.080
 TAK  C12  H12  single    0.930  0.020  1.080
 TAK  C15  H15  single    0.930  0.020  1.080
 TAK  C16  H16  single    0.930  0.020  1.080
 TAK  C18  H18  single    0.930  0.020  1.080
 TAK  C21  H21  single    0.930  0.020  1.080
 TAK  C22  H22  single    0.930  0.020  1.080
 TAK  C23  H23  single    0.930  0.020  1.080
 TAK  C24  H24  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
 TAK  H1A  C1   H1   106.69  3.000
 TAK  H1A  C1   N1   111.57  3.000
 TAK  H1   C1   N1   108.56  3.000
 TAK  H1A  C1   C2   109.03  3.000
 TAK  H1   C1   C2   109.73  3.000
 TAK  N1   C1   C2   111.15  3.000
 TAK  H2A  C2   H2   107.07  3.000
 TAK  H2A  C2   C3   109.76  3.000
 TAK  H2   C2   C3   110.89  3.000
 TAK  H2A  C2   C1   109.05  3.000
 TAK  H2   C2   C1   109.26  3.000
 TAK  C3   C2   C1   110.72  3.000
 TAK  H3A  C3   H3   106.76  3.000
 TAK  H3A  C3   C4   110.86  3.000
 TAK  H3   C3   C4   109.28  3.000
 TAK  H3A  C3   C2   110.85  3.000
 TAK  H3   C3   C2   109.20  3.000
 TAK  C4   C3   C2   109.82  3.000
 TAK  H4A  C4   H4   107.02  3.000
 TAK  H4A  C4   C5   109.14  3.000
 TAK  H4   C4   C5   109.18  3.000
 TAK  H4A  C4   C3   109.82  3.000
 TAK  H4   C4   C3   110.91  3.000
 TAK  C5   C4   C3   110.68  3.000
 TAK  H5A  C5   H5   106.47  3.000
 TAK  H5A  C5   N1   109.39  3.000
 TAK  H5   C5   N1   110.82  3.000
 TAK  H5A  C5   C4   109.32  3.000
 TAK  H5   C5   C4   109.26  3.000
 TAK  N1   C5   C4   111.45  3.000
 TAK  C6   N1   C5   112.08  3.000
 TAK  C6   N1   C1   111.90  3.000
 TAK  C5   N1   C1   111.07  3.000
 TAK  H6A  C6   H6   106.09  3.000
 TAK  H6A  C6   C7   107.60  3.000
 TAK  H6   C6   C7   108.16  3.000
 TAK  H6A  C6   N1   112.49  3.000
 TAK  H6   C6   N1   108.79  3.000
 TAK  C7   C6   N1   113.38  3.000
 TAK  H7A  C7   H7   107.27  3.000
 TAK  H7A  C7   O1   110.35  3.000
 TAK  H7   C7   O1   110.54  3.000
 TAK  H7A  C7   C6   111.59  3.000
 TAK  H7   C7   C6   108.96  3.000
 TAK  O1   C7   C6   108.13  3.000
 TAK  C8   O1   C7   119.11  3.000
 TAK  C11  C8   C9   119.03  3.000
 TAK  C11  C8   O1   124.67  3.000
 TAK  C9   C8   O1   116.30  3.000
 TAK  H9   C9   C10  120.13  3.000
 TAK  H9   C9   C8   119.41  3.000
 TAK  C10  C9   C8   120.45  3.000
 TAK  H10  C10  C13  120.29  3.000
 TAK  H10  C10  C9   118.54  3.000
 TAK  C13  C10  C9   121.15  3.000
 TAK  H11  C11  C12  118.52  3.000
 TAK  H11  C11  C8   121.64  3.000
 TAK  C12  C11  C8   119.84  3.000
 TAK  H12  C12  C13  120.05  3.000
 TAK  H12  C12  C11  118.29  3.000
 TAK  C13  C12  C11  121.65  3.000
 TAK  C14  C13  C12  121.34  3.000
 TAK  C14  C13  C10  120.79  3.000
 TAK  C12  C13  C10  117.87  3.000
 TAK  C16  C14  C15  116.66  3.000
 TAK  C16  C14  C13  121.44  3.000
 TAK  C15  C14  C13  121.91  3.000
 TAK  H15  C15  N3   116.46  3.000
 TAK  H15  C15  C14  125.03  3.000
 TAK  N3   C15  C14  118.50  3.000
 TAK  H16  C16  N2   116.39  3.000
 TAK  H16  C16  C14  119.19  3.000
 TAK  N2   C16  C14  124.42  3.000
 TAK  C17  N2   C16  117.71  3.000
 TAK  C19  C17  N3   105.78  3.000
 TAK  C19  C17  N2   133.48  3.000
 TAK  N3   C17  N2   120.74  3.000
 TAK  N4   N3   C17  112.89  3.000
 TAK  N4   N3   C15  125.14  3.000
 TAK  C17  N3   C15  121.96  3.000
 TAK  C18  N4   N3   104.40  3.000
 TAK  H18  C18  C19  127.56  3.000
 TAK  H18  C18  N4   118.87  3.000
 TAK  C19  C18  N4   113.57  3.000
 TAK  C20  C19  C18  127.74  3.000
 TAK  C20  C19  C17  128.90  3.000
 TAK  C18  C19  C17  103.35  3.000
 TAK  C24  C20  C21  116.35  3.000
 TAK  C24  C20  C19  122.57  3.000
 TAK  C21  C20  C19  121.07  3.000
 TAK  H21  C21  C22  118.78  3.000
 TAK  H21  C21  C20  121.64  3.000
 TAK  C22  C21  C20  119.58  3.000
 TAK  H22  C22  N5   116.58  3.000
 TAK  H22  C22  C21  119.46  3.000
 TAK  N5   C22  C21  123.96  3.000
 TAK  C23  N5   C22  116.59  3.000
 TAK  H23  C23  C24  119.34  3.000
 TAK  H23  C23  N5   116.49  3.000
 TAK  C24  C23  N5   124.18  3.000
 TAK  H24  C24  C23  119.51  3.000
 TAK  H24  C24  C20  121.15  3.000
 TAK  C23  C24  C20  119.33  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
 TAK  CONST_01  C13  C10  C9   C8      0.00   0.0  0
 TAK  CONST_02  C13  C12  C11  C8      0.00   0.0  0
 TAK  CONST_03  C12  C11  C8   C9      0.00   0.0  0
 TAK  CONST_04  C12  C13  C10  C9      0.00   0.0  0
 TAK  CONST_05  C14  C13  C10  C9    180.00   0.0  0
 TAK  CONST_06  C11  C8   C9   C10     0.00   0.0  0
 TAK  CONST_07  C11  C12  C13  C10     0.00   0.0  0
 TAK  CONST_10  C14  C13  C12  C11   180.00   0.0  0
 TAK  CONST_13  N3   C15  C14  C13   180.00   0.0  0
 TAK  CONST_14  N2   C16  C14  C13   180.00   0.0  0
 TAK  CONST_15  C17  N3   C15  C14     0.00   0.0  0
 TAK  CONST_16  N4   N3   C15  C14   180.00   0.0  0
 TAK  CONST_17  C17  N2   C16  C14     0.00   0.0  0
 TAK  CONST_18  N2   C16  C14  C15     0.00   0.0  0
 TAK  CONST_19  N2   C17  N3   C15     0.00   0.0  0
 TAK  CONST_20  C19  C17  N3   C15   180.00   0.0  0
 TAK  CONST_21  C18  N4   N3   C15   180.00   0.0  0
 TAK  CONST_22  N3   C15  C14  C16     0.00   0.0  0
 TAK  CONST_23  N3   C17  N2   C16     0.00   0.0  0
 TAK  CONST_24  C19  C17  N2   C16   180.00   0.0  0
 TAK  CONST_25  N4   N3   C17  N2    180.00   0.0  0
 TAK  CONST_26  C18  C19  C17  N2    180.00   0.0  0
 TAK  CONST_27  C20  C19  C17  N2      0.00   0.0  0
 TAK  CONST_28  C18  N4   N3   C17     0.00   0.0  0
 TAK  CONST_29  N4   C18  C19  C17     0.00   0.0  0
 TAK  CONST_30  C21  C20  C19  C17   180.00   0.0  0
 TAK  CONST_31  C24  C20  C19  C17     0.00   0.0  0
 TAK  CONST_32  C18  C19  C17  N3      0.00   0.0  0
 TAK  CONST_33  C20  C19  C17  N3    180.00   0.0  0
 TAK  CONST_34  C19  C18  N4   N3      0.00   0.0  0
 TAK  CONST_35  C19  C17  N3   N4      0.00   0.0  0
 TAK  CONST_36  C20  C19  C18  N4    180.00   0.0  0
 TAK  CONST_37  C21  C20  C19  C18     0.00   0.0  0
 TAK  CONST_38  C24  C20  C19  C18   180.00   0.0  0
 TAK  CONST_39  C22  C21  C20  C19   180.00   0.0  0
 TAK  CONST_40  C23  C24  C20  C19   180.00   0.0  0
 TAK  CONST_41  N5   C22  C21  C20     0.00   0.0  0
 TAK  CONST_42  N5   C23  C24  C20     0.00   0.0  0
 TAK  CONST_43  C23  C24  C20  C21     0.00   0.0  0
 TAK  CONST_44  C23  N5   C22  C21     0.00   0.0  0
 TAK  CONST_45  C24  C20  C21  C22     0.00   0.0  0
 TAK  CONST_46  C24  C23  N5   C22     0.00   0.0  0
 TAK  CONST_47  C10  C9   C8   O1    180.00   0.0  0
 TAK  CONST_48  C12  C11  C8   O1    180.00   0.0  0
 TAK  CONST_49  H10  C10  C9   C8    180.00   0.0  0
 TAK  CONST_50  H12  C12  C11  C8    180.00   0.0  0
 TAK  CONST_51  H11  C11  C8   C9    180.00   0.0  0
 TAK  CONST_52  H9   C9   C8   C11   180.00   0.0  0
 TAK  CONST_53  H15  C15  C14  C13     0.00   0.0  0
 TAK  CONST_54  H16  C16  C14  C13     0.00   0.0  0
 TAK  CONST_55  H18  C18  C19  C17   180.00   0.0  0
 TAK  CONST_56  H21  C21  C20  C19     0.00   0.0  0
 TAK  CONST_57  H24  C24  C20  C19     0.00   0.0  0
 TAK  CONST_58  H22  C22  C21  C20   180.00   0.0  0
 TAK  CONST_59  H23  C23  C24  C20   180.00   0.0  0
 TAK  Var_01    C4   C3   C2   C1    -53.53  30.0  1
 TAK  Var_02    C4   C5   N1   C1     59.39  30.0  1
 TAK  Var_03    C5   N1   C1   C2    -59.56  30.0  1
 TAK  Var_04    C5   C4   C3   C2     53.18  30.0  1
 TAK  Var_05    N1   C1   C2   C3     56.93  30.0  1
 TAK  Var_06    N1   C5   C4   C3    -56.41  30.0  1
 TAK  Var_07    C7   C6   N1   C1   -157.23  30.0  3
 TAK  Var_08    C9   C8   O1   C7   -176.79  30.0  2
 TAK  Var_09    O1   C7   C6   N1     63.88  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
 TAK  plan-1  O1   0.020
 TAK  plan-1  C8   0.020
 TAK  plan-1  C9   0.020
 TAK  plan-1  C10  0.020
 TAK  plan-1  C11  0.020
 TAK  plan-1  C12  0.020
 TAK  plan-1  C13  0.020
 TAK  plan-1  C14  0.020
 TAK  plan-1  H9   0.020
 TAK  plan-1  H10  0.020
 TAK  plan-1  H11  0.020
 TAK  plan-1  H12  0.020
 TAK  plan-2  C19  0.020
 TAK  plan-2  C20  0.020
 TAK  plan-2  C21  0.020
 TAK  plan-2  C22  0.020
 TAK  plan-2  N5   0.020
 TAK  plan-2  C23  0.020
 TAK  plan-2  C24  0.020
 TAK  plan-2  H21  0.020
 TAK  plan-2  H22  0.020
 TAK  plan-2  H23  0.020
 TAK  plan-2  H24  0.020
 TAK  plan-3  C13  0.020
 TAK  plan-3  C14  0.020
 TAK  plan-3  C15  0.020
 TAK  plan-3  C16  0.020
 TAK  plan-3  N2   0.020
 TAK  plan-3  C17  0.020
 TAK  plan-3  N3   0.020
 TAK  plan-3  N4   0.020
 TAK  plan-3  C18  0.020
 TAK  plan-3  C19  0.020
 TAK  plan-3  C20  0.020
 TAK  plan-3  H15  0.020
 TAK  plan-3  H16  0.020
 TAK  plan-3  H18  0.020

