# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:54:23 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 3-(1-methyl-1H-pyrazol-4-yl)-N-(3-methyl-1,2-thiazol-5-yl)-5-[(3R)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cnn3c(Nc4snc(C)c4)cc(nc23)[C@@H]5CCCNC5
#
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
 MI5  MI5  3-(1-methyl-1H-pyrazol-4-yl)-N-(3-methyl-1,2-thiazol-5-yl)-5-[(3R)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidin-7-amine  ligand  50  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MI5
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
 MI5  C01   C  CR5   0  -0.214   0.9812   1.9247   0.0175
 MI5  C02   C  CR56  0   0.548   0.6605   0.5837   0.2176
 MI5  N03   N  N     0  -0.414  -0.6902   0.5711   0.5222
 MI5  N04   N  N     0  -0.318  -1.2256   1.7889   0.5559
 MI5  C05   C  CR15  0  -0.069  -0.2268   2.5989   0.2416
 MI5  N06   N  N     0  -0.460   1.3966  -0.5298   0.1963
 MI5  C07   C  CR6   0   0.316   0.7941  -1.6574   0.4947
 MI5  C08   C  CR16  0  -0.487  -0.5837  -1.7242   0.8023
 MI5  C09   C  CR6   0   0.686  -1.3423  -0.5807   0.8027
 MI5  N10   N  NH1   0  -0.739  -2.6670  -0.5667   1.1354
 MI5  C11   C  CH1   0  -0.354   1.5829  -2.9308   0.4209
 MI5  C12   C  CR5   0  -0.134   2.2761   2.4710  -0.3288
 MI5  C13   C  CH2   0  -0.288   1.5063  -3.4989  -1.0138
 MI5  N14   N  NH1   0  -0.577   2.2422  -4.7333  -1.1920
 MI5  C15   C  CH2   0  -0.313   3.6294  -4.6174  -0.7670
 MI5  C16   C  CH2   0  -0.449   3.7908  -4.0946   0.6573
 MI5  C17   C  CH2   0  -0.421   3.0464  -2.7748   0.8318
 MI5  C18   C  CR15  0  -0.138   3.4877   1.7865  -0.5586
 MI5  N19   N  N     0  -0.279   4.4659   2.6219  -0.8576
 MI5  N20   N  NR5   0  -0.265   3.9210   3.8316  -0.8281
 MI5  C21   C  CR15  0  -0.003   2.6145   3.7982  -0.5164
 MI5  C22   C  CH3   0  -0.506   4.7248   4.9982  -1.1020
 MI5  C23   C  CR5   0   0.100  -3.7428   0.0982   0.5685
 MI5  S24   S  S2    0   0.379  -3.7946   1.6287  -0.2376
 MI5  N25   N  N     0  -0.563  -5.4234   1.5396  -0.5421
 MI5  C26   C  CR5   0   0.280  -5.9331   0.4459  -0.0430
 MI5  C27   C  CR15  0  -0.372  -5.0097  -0.4185   0.5978
 MI5  C28   C  CH3   0  -0.726  -7.3899   0.1487  -0.1781
 MI5  H05   H  HCR5  0   0.274  -0.4059   3.6628   0.1920
 MI5  H08   H  HCR6  0   0.294  -1.0504  -2.6753   1.0171
 MI5  HN10  H  HNH1  0   0.436  -2.9539  -1.4458   1.5445
 MI5  H11   H  HCH1  0   0.246   1.1063  -3.6617   1.0851
 MI5  H13   H  HCH2  0   0.244   0.4641  -3.6675  -1.2955
 MI5  H13A  H  HCH2  0   0.222   1.9064  -2.7485  -1.7048
 MI5  HN14  H  HNH1  0   0.341   1.7926  -5.4669  -0.6561
 MI5  H15   H  HCH2  0   0.235   4.1085  -5.5923  -0.8775
 MI5  H15A  H  HCH2  0   0.215   4.1387  -3.9376  -1.4592
 MI5  H16   H  HCH2  0   0.215   3.4041  -4.8372   1.3636
 MI5  H16A  H  HCH2  0   0.229   4.8508  -3.9625   0.8882
 MI5  H17   H  HCH2  0   0.230   3.5152  -2.0043   0.2137
 MI5  H17A  H  HCH2  0   0.235   3.1134  -2.4299   1.8664
 MI5  H18   H  HCR5  0   0.259   3.6632   0.7228  -0.5131
 MI5  H21   H  HCR5  0   0.286   2.0259   4.6992  -0.4482
 MI5  H22   H  HCH3  0   0.260   5.1733   4.9247  -2.0907
 MI5  H22A  H  HCH3  0   0.258   4.0908   5.8793  -1.0675
 MI5  H22B  H  HCH3  0   0.260   5.5133   5.1014  -0.3588
 MI5  H27   H  HCR5  0   0.282  -5.2665  -1.3714   1.0394
 MI5  H28   H  HCH3  0   0.255  -7.5476  -0.7264  -0.8105
 MI5  H28A  H  HCH3  0   0.253  -7.8343  -0.0712   0.7930
 MI5  H28B  H  HCH3  0   0.252  -7.9197   0.9903  -0.6194

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
 MI5  C05  C01   aromatic  1.401  0.020  1.401
 MI5  C01  C02   aromatic  1.393  0.020  1.393
 MI5  C01  C12   single    1.447  0.020  1.447
 MI5  N03  C02   aromatic  1.385  0.020  1.385
 MI5  C02  N06   aromatic  1.335  0.020  1.335
 MI5  N04  N03   aromatic  1.331  0.020  1.331
 MI5  N03  C09   aromatic  1.353  0.020  1.353
 MI5  N04  C05   aromatic  1.324  0.020  1.324
 MI5  C05  H05   single    0.930  0.020  1.080
 MI5  N06  C07   aromatic  1.313  0.020  1.313
 MI5  C08  C07   aromatic  1.413  0.020  1.413
 MI5  C07  C11   single    1.500  0.020  1.500
 MI5  C09  C08   aromatic  1.372  0.020  1.372
 MI5  C08  H08   single    0.930  0.020  1.080
 MI5  N10  C09   single    1.366  0.020  1.366
 MI5  C23  N10   single    1.386  0.020  1.386
 MI5  N10  HN10  single    0.890  0.020  1.040
 MI5  C17  C11   single    1.528  0.020  1.528
 MI5  C11  C13   single    1.545  0.020  1.545
 MI5  C11  H11   single    0.970  0.020  1.090
 MI5  C12  C18   aromatic  1.410  0.020  1.410
 MI5  C12  C21   aromatic  1.382  0.020  1.382
 MI5  C13  N14   single    1.448  0.020  1.448
 MI5  C13  H13   single    0.970  0.020  1.090
 MI5  C13  H13A  single    0.970  0.020  1.090
 MI5  C15  N14   single    1.455  0.020  1.455
 MI5  N14  HN14  single    0.890  0.020  1.040
 MI5  C16  C15   single    1.526  0.020  1.526
 MI5  C15  H15   single    0.970  0.020  1.090
 MI5  C15  H15A  single    0.970  0.020  1.090
 MI5  C17  C16   single    1.525  0.020  1.525
 MI5  C16  H16   single    0.970  0.020  1.090
 MI5  C16  H16A  single    0.970  0.020  1.090
 MI5  C17  H17   single    0.970  0.020  1.090
 MI5  C17  H17A  single    0.970  0.020  1.090
 MI5  C18  N19   aromatic  1.321  0.020  1.321
 MI5  C18  H18   single    0.930  0.020  1.080
 MI5  N19  N20   aromatic  1.327  0.020  1.327
 MI5  C21  N20   aromatic  1.344  0.020  1.344
 MI5  N20  C22   single    1.443  0.020  1.443
 MI5  C21  H21   single    0.930  0.020  1.080
 MI5  C22  H22   single    0.970  0.020  1.090
 MI5  C22  H22A  single    0.970  0.020  1.090
 MI5  C22  H22B  single    0.970  0.020  1.090
 MI5  C27  C23   aromatic  1.369  0.020  1.369
 MI5  C23  S24   aromatic  1.731  0.020  1.731
 MI5  N25  S24   aromatic  1.659  0.020  1.659
 MI5  C26  N25   aromatic  1.306  0.020  1.306
 MI5  C28  C26   single    1.493  0.020  1.493
 MI5  C26  C27   aromatic  1.418  0.020  1.418
 MI5  C27  H27   single    0.930  0.020  1.080
 MI5  C28  H28   single    0.970  0.020  1.090
 MI5  C28  H28A  single    0.970  0.020  1.090
 MI5  C28  H28B  single    0.970  0.020  1.090

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
 MI5  C12   C01  C05   128.89  3.000
 MI5  C12   C01  C02   127.12  3.000
 MI5  C05   C01  C02   103.98  3.000
 MI5  N06   C02  N03   122.26  3.000
 MI5  N06   C02  C01   132.34  3.000
 MI5  N03   C02  C01   105.36  3.000
 MI5  C09   N03  N04   125.44  3.000
 MI5  C09   N03  C02   121.57  3.000
 MI5  N04   N03  C02   112.94  3.000
 MI5  C05   N04  N03   104.49  3.000
 MI5  H05   C05  N04   119.24  3.000
 MI5  H05   C05  C01   127.56  3.000
 MI5  N04   C05  C01   113.20  3.000
 MI5  C07   N06  C02   117.37  3.000
 MI5  C11   C07  C08   118.90  3.000
 MI5  C11   C07  N06   118.47  3.000
 MI5  C08   C07  N06   122.51  3.000
 MI5  H08   C08  C09   119.63  3.000
 MI5  H08   C08  C07   120.38  3.000
 MI5  C09   C08  C07   119.97  3.000
 MI5  N10   C09  C08   123.01  3.000
 MI5  N10   C09  N03   120.61  3.000
 MI5  C08   C09  N03   116.29  3.000
 MI5  HN10  N10  C23   111.24  3.000
 MI5  HN10  N10  C09   111.40  3.000
 MI5  C23   N10  C09   131.15  3.000
 MI5  H11   C11  C17   108.75  3.000
 MI5  H11   C11  C13   107.21  3.000
 MI5  C17   C11  C13   109.56  3.000
 MI5  H11   C11  C07   107.91  3.000
 MI5  C13   C11  C07   109.38  3.000
 MI5  C17   C11  C07   113.82  3.000
 MI5  C21   C12  C18   103.51  3.000
 MI5  C21   C12  C01   127.86  3.000
 MI5  C18   C12  C01   128.63  3.000
 MI5  H13A  C13  H13   106.94  3.000
 MI5  H13A  C13  N14   108.70  3.000
 MI5  H13   C13  N14   108.75  3.000
 MI5  H13A  C13  C11   108.40  3.000
 MI5  H13   C13  C11   110.09  3.000
 MI5  N14   C13  C11   113.73  3.000
 MI5  HN14  N14  C15   109.03  3.000
 MI5  HN14  N14  C13   109.06  3.000
 MI5  C15   N14  C13   112.37  3.000
 MI5  H15A  C15  H15   106.62  3.000
 MI5  H15A  C15  C16   109.14  3.000
 MI5  H15   C15  C16   110.73  3.000
 MI5  H15A  C15  N14   107.94  3.000
 MI5  H15   C15  N14   108.52  3.000
 MI5  C16   C15  N14   113.62  3.000
 MI5  H16A  C16  H16   106.74  3.000
 MI5  H16A  C16  C17   110.16  3.000
 MI5  H16   C16  C17   109.91  3.000
 MI5  H16A  C16  C15   109.95  3.000
 MI5  H16   C16  C15   109.41  3.000
 MI5  C17   C16  C15   110.59  3.000
 MI5  H17A  C17  H17   106.65  3.000
 MI5  H17A  C17  C16   110.58  3.000
 MI5  H17   C17  C16   109.63  3.000
 MI5  H17A  C17  C11   110.21  3.000
 MI5  H17   C17  C11   109.30  3.000
 MI5  C16   C17  C11   110.38  3.000
 MI5  H18   C18  N19   120.84  3.000
 MI5  H18   C18  C12   127.68  3.000
 MI5  N19   C18  C12   111.48  3.000
 MI5  N20   N19  C18   105.51  3.000
 MI5  C22   N20  C21   127.29  3.000
 MI5  C22   N20  N19   120.27  3.000
 MI5  C21   N20  N19   112.44  3.000
 MI5  H21   C21  N20   121.65  3.000
 MI5  H21   C21  C12   131.30  3.000
 MI5  N20   C21  C12   107.06  3.000
 MI5  H22B  C22  H22A  108.92  3.000
 MI5  H22B  C22  H22   109.16  3.000
 MI5  H22A  C22  H22   108.92  3.000
 MI5  H22B  C22  N20   110.53  3.000
 MI5  H22A  C22  N20   108.95  3.000
 MI5  H22   C22  N20   110.33  3.000
 MI5  C27   C23  S24   108.43  3.000
 MI5  S24   C23  N10   129.65  3.000
 MI5  C27   C23  N10   121.92  3.000
 MI5  N25   S24  C23    93.86  3.000
 MI5  C26   N25  S24   110.98  3.000
 MI5  C28   C26  C27   123.72  3.000
 MI5  C27   C26  N25   115.41  3.000
 MI5  C28   C26  N25   120.86  3.000
 MI5  H27   C27  C26   124.55  3.000
 MI5  H27   C27  C23   124.15  3.000
 MI5  C26   C27  C23   111.29  3.000
 MI5  H28B  C28  H28A  108.59  3.000
 MI5  H28B  C28  H28   108.36  3.000
 MI5  H28A  C28  H28   107.19  3.000
 MI5  H28B  C28  C26   110.97  3.000
 MI5  H28A  C28  C26   110.93  3.000
 MI5  H28   C28  C26   110.68  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
 MI5  CONST_01  N03  N04  C05  C01    0.00   0.0  0
 MI5  CONST_02  N04  N03  C02  C01    0.00   0.0  0
 MI5  CONST_03  C09  N03  C02  C01  180.00   0.0  0
 MI5  CONST_04  C07  N06  C02  C01  180.00   0.0  0
 MI5  CONST_05  N19  C18  C12  C01  180.00   0.0  0
 MI5  CONST_06  N20  C21  C12  C01  180.00   0.0  0
 MI5  CONST_07  N04  C05  C01  C02    0.00   0.0  0
 MI5  CONST_08  C18  C12  C01  C02    0.00   0.0  0
 MI5  CONST_09  C21  C12  C01  C02  180.00   0.0  0
 MI5  CONST_10  C05  N04  N03  C02    0.00   0.0  0
 MI5  CONST_11  C08  C09  N03  C02    0.00   0.0  0
 MI5  CONST_12  C08  C07  N06  C02    0.00   0.0  0
 MI5  CONST_13  C05  C01  C02  N03    0.00   0.0  0
 MI5  CONST_14  C12  C01  C02  N03  180.00   0.0  0
 MI5  CONST_15  C07  N06  C02  N03    0.00   0.0  0
 MI5  CONST_16  C07  C08  C09  N03    0.00   0.0  0
 MI5  CONST_17  N06  C02  N03  N04  180.00   0.0  0
 MI5  CONST_18  C08  C09  N03  N04  180.00   0.0  0
 MI5  CONST_19  C12  C01  C05  N04  180.00   0.0  0
 MI5  CONST_20  N06  C02  C01  C05  180.00   0.0  0
 MI5  CONST_21  C18  C12  C01  C05  180.00   0.0  0
 MI5  CONST_22  C21  C12  C01  C05    0.00   0.0  0
 MI5  CONST_23  C09  N03  N04  C05  180.00   0.0  0
 MI5  CONST_24  C12  C01  C02  N06    0.00   0.0  0
 MI5  CONST_25  C09  N03  C02  N06    0.00   0.0  0
 MI5  CONST_26  C09  C08  C07  N06    0.00   0.0  0
 MI5  CONST_27  N20  N19  C18  C12    0.00   0.0  0
 MI5  CONST_28  N19  N20  C21  C12    0.00   0.0  0
 MI5  CONST_29  N20  C21  C12  C18    0.00   0.0  0
 MI5  CONST_30  C21  N20  N19  C18    0.00   0.0  0
 MI5  CONST_31  C21  C12  C18  N19    0.00   0.0  0
 MI5  CONST_32  N25  C26  C27  C23    0.00   0.0  0
 MI5  CONST_33  C26  N25  S24  C23    0.00   0.0  0
 MI5  CONST_34  C26  C27  C23  S24    0.00   0.0  0
 MI5  CONST_35  C27  C26  N25  S24    0.00   0.0  0
 MI5  CONST_36  C27  C23  S24  N25    0.00   0.0  0
 MI5  CONST_37  C11  C07  N06  C02  180.00   0.0  0
 MI5  CONST_38  C11  C07  C08  C09  180.00   0.0  0
 MI5  CONST_39  N10  C09  N03  C02  180.00   0.0  0
 MI5  CONST_40  N10  C09  N03  N04    0.00   0.0  0
 MI5  CONST_41  N10  C09  C08  C07  180.00   0.0  0
 MI5  CONST_42  C26  C27  C23  N10  180.00   0.0  0
 MI5  CONST_43  N25  S24  C23  N10  180.00   0.0  0
 MI5  CONST_44  C22  N20  C21  C12  180.00   0.0  0
 MI5  CONST_45  C22  N20  N19  C18  180.00   0.0  0
 MI5  CONST_46  C28  C26  C27  C23  180.00   0.0  0
 MI5  CONST_47  C28  C26  N25  S24  180.00   0.0  0
 MI5  CONST_48  H18  C18  C12  C01    0.00   0.0  0
 MI5  CONST_49  H21  C21  C12  C01    0.00   0.0  0
 MI5  CONST_50  H05  C05  C01  C02  180.00   0.0  0
 MI5  CONST_51  H08  C08  C09  N03  180.00   0.0  0
 MI5  CONST_52  H27  C27  C23  S24  180.00   0.0  0
 MI5  Var_01    C15  C16  C17  C11   54.48  30.0  1
 MI5  Var_02    C15  N14  C13  C11  -53.72  30.0  1
 MI5  Var_03    C16  C15  N14  C13   53.36  30.0  1
 MI5  Var_04    C17  C16  C15  N14  -54.03  30.0  1
 MI5  Var_05    C23  N10  C09  N03   45.50  30.0  2
 MI5  Var_06    C27  C23  N10  C09  149.60  30.0  1
 MI5  Var_07    H22  C22  N20  N19   58.26  30.0  2
 MI5  Var_08    H28  C28  C26  N25  113.91  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
 MI5  chir_01  C11  C07  C17  C13  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
 MI5  plan-1  C01  0.020
 MI5  plan-1  C12  0.020
 MI5  plan-1  C18  0.020
 MI5  plan-1  N19  0.020
 MI5  plan-1  N20  0.020
 MI5  plan-1  C21  0.020
 MI5  plan-1  C22  0.020
 MI5  plan-1  H18  0.020
 MI5  plan-1  H21  0.020
 MI5  plan-2  N10  0.020
 MI5  plan-2  C23  0.020
 MI5  plan-2  S24  0.020
 MI5  plan-2  N25  0.020
 MI5  plan-2  C26  0.020
 MI5  plan-2  C27  0.020
 MI5  plan-2  C28  0.020
 MI5  plan-2  H27  0.020
 MI5  plan-3  C01  0.020
 MI5  plan-3  C02  0.020
 MI5  plan-3  N03  0.020
 MI5  plan-3  N04  0.020
 MI5  plan-3  C05  0.020
 MI5  plan-3  N06  0.020
 MI5  plan-3  C07  0.020
 MI5  plan-3  C08  0.020
 MI5  plan-3  C09  0.020
 MI5  plan-3  N10  0.020
 MI5  plan-3  C11  0.020
 MI5  plan-3  C12  0.020
 MI5  plan-3  H05  0.020
 MI5  plan-3  H08  0.020

