# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 22:12:52 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc(Nc2n3nccc3nc(N[C@H]4CCCNC4)c2C)cc1
#
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
 PDY  PDY  N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine  ligand  53  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PDY
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
 PDY  C25   C  CH2   0  -0.454  -5.3673  -1.4284  -1.3157
 PDY  C26   C  CH2   0  -0.448  -6.7140  -0.8294  -1.7094
 PDY  C23   C  CH2   0  -0.314  -7.4063  -0.2141  -0.4965
 PDY  N12   N  NH1   0  -0.579  -6.5859   0.7535   0.2160
 PDY  C22   C  CH2   0  -0.307  -5.2948   0.2056   0.5888
 PDY  C15   C  CH1   0  -0.070  -4.5135  -0.3939  -0.5896
 PDY  N10   N  NH1   0  -0.693  -3.2717  -0.9971  -0.1577
 PDY  C4    C  CR6   0   0.521  -2.1445  -0.3032   0.1030
 PDY  C3    C  CR6   0  -0.168  -0.9973  -1.0233   0.5935
 PDY  C14   C  CH3   0  -0.762  -1.0613  -2.5114   0.7574
 PDY  N6    N  N     0  -0.528  -2.1377   0.9897  -0.1480
 PDY  C5    C  CR56  0   0.576  -1.0084   1.6588   0.1040
 PDY  C8    C  CR15  0  -0.595  -0.6728   3.0021   0.0009
 PDY  C11   C  CR15  0  -0.018   0.6322   3.0727   0.4984
 PDY  N7    N  N     0  -0.308   1.1094   1.9020   0.8846
 PDY  N2    N  N     0  -0.433   0.1081   1.0446   0.6258
 PDY  C1    C  CR6   0   0.587   0.1333  -0.3031   0.8731
 PDY  N9    N  NH1   0  -0.769   1.2738  -0.8145   1.4299
 PDY  C13   C  CR6   0   0.313   2.5583  -0.6523   0.8716
 PDY  C17   C  CR16  0  -0.305   3.6719  -0.8201   1.6912
 PDY  C20   C  CR16  0  -0.344   4.9496  -0.7046   1.1778
 PDY  C18   C  CR16  0  -0.263   2.7556  -0.3632  -0.4703
 PDY  C19   C  CR16  0  -0.386   4.0368  -0.2197  -0.9890
 PDY  C16   C  CR6   0   0.374   5.1479  -0.3916  -0.1680
 PDY  O21   O  O2    0  -0.475   6.4283  -0.2808  -0.5778
 PDY  C24   C  CH2   0  -0.187   6.6861  -0.0020  -1.9462
 PDY  C27   C  CH3   0  -0.682   8.1820   0.0792  -2.1355
 PDY  H25   H  HCH2  0   0.220  -5.5331  -2.2884  -0.6554
 PDY  H25A  H  HCH2  0   0.244  -4.8366  -1.8007  -2.1950
 PDY  H26   H  HCH2  0   0.218  -6.5648  -0.0577  -2.4717
 PDY  H26A  H  HCH2  0   0.232  -7.3500  -1.5958  -2.1589
 PDY  H23   H  HCH2  0   0.236  -8.3386   0.2708  -0.7929
 PDY  H23A  H  HCH2  0   0.214  -7.6771  -1.0116   0.2046
 PDY  HN12  H  HNH1  0   0.340  -6.4434   1.5655  -0.3740
 PDY  H22   H  HCH2  0   0.241  -4.6999   0.9869   1.0654
 PDY  H22A  H  HCH2  0   0.213  -5.4513  -0.5801   1.3370
 PDY  H15   H  HCH1  0   0.238  -4.2708   0.4138  -1.2860
 PDY  HN10  H  HNH1  0   0.404  -3.3250  -1.9488   0.1659
 PDY  H14   H  HCH3  0   0.257  -1.4445  -2.9898  -0.1463
 PDY  H14A  H  HCH3  0   0.252  -0.0837  -2.9504   0.9442
 PDY  H14B  H  HCH3  0   0.259  -1.7081  -2.8086   1.5864
 PDY  H8    H  HCR5  0   0.257  -1.2950   3.8021  -0.3630
 PDY  H11   H  HCR5  0   0.262   1.2500   3.9529   0.5991
 PDY  HN9   H  HNH1  0   0.408   1.1448  -1.6645   1.9558
 PDY  H17   H  HCR6  0   0.266   3.5375  -1.0421   2.7429
 PDY  H20   H  HCR6  0   0.262   5.8065  -0.8427   1.8254
 PDY  H18   H  HCR6  0   0.264   1.9115  -0.2548  -1.1401
 PDY  H19   H  HCR6  0   0.280   4.1413   0.0128  -2.0398
 PDY  H24   H  HCH2  0   0.222   6.2626  -0.7902  -2.5785
 PDY  H24A  H  HCH2  0   0.222   6.2129   0.9424  -2.2363
 PDY  H27   H  HCH3  0   0.235   8.6165   0.8755  -1.5310
 PDY  H27A  H  HCH3  0   0.234   8.6689  -0.8608  -1.8757
 PDY  H27B  H  HCH3  0   0.237   8.4027   0.2941  -3.1804

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
 PDY  C25  C26   single    1.526  0.020  1.526
 PDY  C25  C15   single    1.525  0.020  1.525
 PDY  C26  C23   single    1.526  0.020  1.526
 PDY  C23  N12   single    1.455  0.020  1.455
 PDY  N12  C22   single    1.451  0.020  1.451
 PDY  C22  C15   single    1.536  0.020  1.536
 PDY  C15  N10   single    1.446  0.020  1.446
 PDY  N10  C4    single    1.349  0.020  1.349
 PDY  C4   C3    aromatic  1.441  0.020  1.441
 PDY  C4   N6    aromatic  1.317  0.020  1.317
 PDY  C3   C14   single    1.498  0.020  1.498
 PDY  C3   C1    aromatic  1.369  0.020  1.369
 PDY  N6   C5    aromatic  1.337  0.020  1.337
 PDY  C5   C8    aromatic  1.388  0.020  1.388
 PDY  C5   N2    aromatic  1.377  0.020  1.377
 PDY  C8   C11   aromatic  1.398  0.020  1.398
 PDY  C11  N7    aromatic  1.322  0.020  1.322
 PDY  N7   N2    aromatic  1.343  0.020  1.343
 PDY  N2   C1    aromatic  1.370  0.020  1.370
 PDY  C1   N9    single    1.368  0.020  1.368
 PDY  N9   C13   single    1.410  0.020  1.410
 PDY  C13  C17   aromatic  1.393  0.020  1.393
 PDY  C13  C18   aromatic  1.387  0.020  1.387
 PDY  C17  C20   aromatic  1.382  0.020  1.382
 PDY  C20  C16   aromatic  1.396  0.020  1.396
 PDY  C18  C19   aromatic  1.390  0.020  1.390
 PDY  C19  C16   aromatic  1.392  0.020  1.392
 PDY  C16  O21   single    1.349  0.020  1.349
 PDY  O21  C24   single    1.420  0.020  1.420
 PDY  C24  C27   single    1.510  0.020  1.510
 PDY  C25  H25   single    0.970  0.020  1.090
 PDY  C25  H25A  single    0.970  0.020  1.090
 PDY  C26  H26   single    0.970  0.020  1.090
 PDY  C26  H26A  single    0.970  0.020  1.090
 PDY  C23  H23   single    0.970  0.020  1.090
 PDY  C23  H23A  single    0.970  0.020  1.090
 PDY  N12  HN12  single    0.890  0.020  1.040
 PDY  C22  H22   single    0.970  0.020  1.090
 PDY  C22  H22A  single    0.970  0.020  1.090
 PDY  C15  H15   single    0.970  0.020  1.090
 PDY  N10  HN10  single    0.860  0.020  1.020
 PDY  C14  H14   single    0.970  0.020  1.090
 PDY  C14  H14A  single    0.970  0.020  1.090
 PDY  C14  H14B  single    0.970  0.020  1.090
 PDY  C8   H8    single    0.930  0.020  1.080
 PDY  C11  H11   single    0.930  0.020  1.080
 PDY  N9   HN9   single    0.890  0.020  1.040
 PDY  C17  H17   single    0.930  0.020  1.080
 PDY  C20  H20   single    0.930  0.020  1.080
 PDY  C18  H18   single    0.930  0.020  1.080
 PDY  C19  H19   single    0.930  0.020  1.080
 PDY  C24  H24   single    0.970  0.020  1.090
 PDY  C24  H24A  single    0.970  0.020  1.090
 PDY  C27  H27   single    0.970  0.020  1.090
 PDY  C27  H27A  single    0.970  0.020  1.090
 PDY  C27  H27B  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
 PDY  H25A  C25  H25   106.90  3.000
 PDY  H25A  C25  C15   110.02  3.000
 PDY  H25   C25  C15   109.26  3.000
 PDY  H25A  C25  C26   110.79  3.000
 PDY  H25   C25  C26   109.26  3.000
 PDY  C15   C25  C26   110.53  3.000
 PDY  H26A  C26  H26   106.69  3.000
 PDY  H26A  C26  C23   110.23  3.000
 PDY  H26   C26  C23   109.33  3.000
 PDY  H26A  C26  C25   110.15  3.000
 PDY  H26   C26  C25   109.64  3.000
 PDY  C23   C26  C25   110.71  3.000
 PDY  H23A  C23  H23   106.61  3.000
 PDY  H23A  C23  N12   108.06  3.000
 PDY  H23   C23  N12   108.61  3.000
 PDY  H23A  C23  C26   109.10  3.000
 PDY  H23   C23  C26   110.52  3.000
 PDY  N12   C23  C26   113.67  3.000
 PDY  HN12  N12  C22   109.07  3.000
 PDY  HN12  N12  C23   109.09  3.000
 PDY  C22   N12  C23   112.11  3.000
 PDY  H22A  C22  H22   107.03  3.000
 PDY  H22A  C22  C15   108.45  3.000
 PDY  H22   C22  C15   109.71  3.000
 PDY  H22A  C22  N12   108.60  3.000
 PDY  H22   C22  N12   109.07  3.000
 PDY  C15   C22  N12   113.76  3.000
 PDY  H15   C15  N10   107.91  3.000
 PDY  H15   C15  C22   108.25  3.000
 PDY  N10   C15  C22   111.74  3.000
 PDY  H15   C15  C25   108.78  3.000
 PDY  N10   C15  C25   109.87  3.000
 PDY  C22   C15  C25   110.20  3.000
 PDY  HN10  N10  C4    117.93  3.000
 PDY  HN10  N10  C15   116.41  3.000
 PDY  C4    N10  C15   124.09  3.000
 PDY  N6    C4   C3    123.46  3.000
 PDY  N6    C4   N10   118.19  3.000
 PDY  C3    C4   N10   118.30  3.000
 PDY  C1    C3   C14   122.36  3.000
 PDY  C1    C3   C4    117.66  3.000
 PDY  C14   C3   C4    119.98  3.000
 PDY  H14B  C14  H14A  106.97  3.000
 PDY  H14B  C14  H14   107.51  3.000
 PDY  H14A  C14  H14   106.30  3.000
 PDY  H14B  C14  C3    112.23  3.000
 PDY  H14A  C14  C3    112.41  3.000
 PDY  H14   C14  C3    111.07  3.000
 PDY  C5    N6   C4    117.38  3.000
 PDY  N2    C5   C8    105.29  3.000
 PDY  N2    C5   N6    122.22  3.000
 PDY  C8    C5   N6    132.42  3.000
 PDY  H8    C8   C11   128.45  3.000
 PDY  H8    C8   C5    127.18  3.000
 PDY  C11   C8   C5    104.36  3.000
 PDY  H11   C11  N7    119.20  3.000
 PDY  H11   C11  C8    127.46  3.000
 PDY  N7    C11  C8    113.34  3.000
 PDY  N2    N7   C11   103.88  3.000
 PDY  C1    N2   N7    125.39  3.000
 PDY  C1    N2   C5    121.47  3.000
 PDY  N7    N2   C5    113.12  3.000
 PDY  N9    C1   N2    117.15  3.000
 PDY  N9    C1   C3    125.08  3.000
 PDY  N2    C1   C3    117.72  3.000
 PDY  HN9   N9   C13   114.84  3.000
 PDY  HN9   N9   C1    114.89  3.000
 PDY  C13   N9   C1    123.73  3.000
 PDY  C18   C13  C17   118.73  3.000
 PDY  C18   C13  N9    122.46  3.000
 PDY  C17   C13  N9    118.79  3.000
 PDY  H17   C17  C20   119.51  3.000
 PDY  H17   C17  C13   119.79  3.000
 PDY  C20   C17  C13   120.70  3.000
 PDY  H20   C20  C16   119.52  3.000
 PDY  H20   C20  C17   119.92  3.000
 PDY  C16   C20  C17   120.55  3.000
 PDY  H18   C18  C19   118.52  3.000
 PDY  H18   C18  C13   120.55  3.000
 PDY  C19   C18  C13   120.92  3.000
 PDY  H19   C19  C16   121.50  3.000
 PDY  H19   C19  C18   118.29  3.000
 PDY  C16   C19  C18   120.20  3.000
 PDY  O21   C16  C19   124.63  3.000
 PDY  O21   C16  C20   116.50  3.000
 PDY  C19   C16  C20   118.87  3.000
 PDY  C24   O21  C16   118.76  3.000
 PDY  H24A  C24  H24   107.48  3.000
 PDY  H24A  C24  C27   110.39  3.000
 PDY  H24   C24  C27   110.44  3.000
 PDY  H24A  C24  O21   110.25  3.000
 PDY  H24   C24  O21   110.17  3.000
 PDY  C27   C24  O21   108.13  3.000
 PDY  H27B  C27  H27A  107.95  3.000
 PDY  H27B  C27  H27   107.88  3.000
 PDY  H27A  C27  H27   108.65  3.000
 PDY  H27B  C27  C24   109.36  3.000
 PDY  H27A  C27  C24   111.48  3.000
 PDY  H27   C27  C24   111.39  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
 PDY  CONST_01  N2    C1   C3   C4     0.00   0.0  0
 PDY  CONST_02  C8    C5   N6   C4   180.00   0.0  0
 PDY  CONST_03  N2    C5   N6   C4     0.00   0.0  0
 PDY  CONST_04  C5    N6   C4   C3     0.00   0.0  0
 PDY  CONST_05  C5    N2   C1   C3     0.00   0.0  0
 PDY  CONST_06  N7    N2   C1   C3   180.00   0.0  0
 PDY  CONST_07  C1    C3   C4   N6     0.00   0.0  0
 PDY  CONST_08  C11   C8   C5   N6   180.00   0.0  0
 PDY  CONST_09  N7    N2   C5   N6   180.00   0.0  0
 PDY  CONST_10  C1    N2   C5   N6     0.00   0.0  0
 PDY  CONST_11  N7    C11  C8   C5     0.00   0.0  0
 PDY  CONST_12  C11   N7   N2   C5     0.00   0.0  0
 PDY  CONST_13  N7    N2   C5   C8     0.00   0.0  0
 PDY  CONST_14  C1    N2   C5   C8   180.00   0.0  0
 PDY  CONST_15  N2    N7   C11  C8     0.00   0.0  0
 PDY  CONST_16  N2    C5   C8   C11    0.00   0.0  0
 PDY  CONST_17  C1    N2   N7   C11  180.00   0.0  0
 PDY  CONST_18  C16   C20  C17  C13    0.00   0.0  0
 PDY  CONST_19  C16   C19  C18  C13    0.00   0.0  0
 PDY  CONST_20  C19   C18  C13  C17    0.00   0.0  0
 PDY  CONST_21  C19   C16  C20  C17    0.00   0.0  0
 PDY  CONST_22  C18   C13  C17  C20    0.00   0.0  0
 PDY  CONST_23  C18   C19  C16  C20    0.00   0.0  0
 PDY  CONST_24  C1    C3   C4   N10  180.00   0.0  0
 PDY  CONST_25  C5    N6   C4   N10  180.00   0.0  0
 PDY  CONST_26  N9    C1   C3   C4   180.00   0.0  0
 PDY  CONST_27  N6    C4   C3   C14  180.00   0.0  0
 PDY  CONST_28  N2    C1   C3   C14  180.00   0.0  0
 PDY  CONST_29  N9    C1   N2   C5   180.00   0.0  0
 PDY  CONST_30  N9    C1   N2   N7     0.00   0.0  0
 PDY  CONST_31  C20   C17  C13  N9   180.00   0.0  0
 PDY  CONST_32  C19   C18  C13  N9   180.00   0.0  0
 PDY  CONST_33  O21   C16  C20  C17  180.00   0.0  0
 PDY  CONST_34  O21   C16  C19  C18  180.00   0.0  0
 PDY  CONST_35  C3    C4   N10  C15  180.00   0.0  0
 PDY  CONST_36  N6    C4   N10  C15    0.00   0.0  0
 PDY  CONST_37  H8    C8   C5   N6     0.00   0.0  0
 PDY  CONST_38  H11   C11  C8   C5   180.00   0.0  0
 PDY  CONST_39  H20   C20  C17  C13  180.00   0.0  0
 PDY  CONST_40  H19   C19  C18  C13  180.00   0.0  0
 PDY  CONST_41  H18   C18  C13  C17  180.00   0.0  0
 PDY  CONST_42  H17   C17  C13  C18  180.00   0.0  0
 PDY  CONST_43  HN10  N10  C4   C3     0.00   0.0  0
 PDY  Var_01    N12   C23  C26  C25   53.88  30.0  1
 PDY  Var_02    C22   N12  C23  C26  -53.67  30.0  1
 PDY  Var_03    C15   C25  C26  C23  -53.43  30.0  1
 PDY  Var_04    C15   C22  N12  C23   53.86  30.0  1
 PDY  Var_05    C13   N9   C1   C3   127.33  30.0  2
 PDY  Var_06    C17   C13  N9   C1   159.67  30.0  2
 PDY  Var_07    H14   C14  C3   C4    49.78  30.0  2
 PDY  Var_08    C27   C24  O21  C16  179.63  30.0  3
 PDY  Var_09    H27   C27  C24  O21  -60.78  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
 PDY  chir_01  C15  C25  C22  N10  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
 PDY  plan-1  N9    0.020
 PDY  plan-1  C13   0.020
 PDY  plan-1  C17   0.020
 PDY  plan-1  C20   0.020
 PDY  plan-1  C18   0.020
 PDY  plan-1  C19   0.020
 PDY  plan-1  C16   0.020
 PDY  plan-1  O21   0.020
 PDY  plan-1  H17   0.020
 PDY  plan-1  H20   0.020
 PDY  plan-1  H18   0.020
 PDY  plan-1  H19   0.020
 PDY  plan-2  N10   0.020
 PDY  plan-2  C4    0.020
 PDY  plan-2  C3    0.020
 PDY  plan-2  C14   0.020
 PDY  plan-2  N6    0.020
 PDY  plan-2  C5    0.020
 PDY  plan-2  C8    0.020
 PDY  plan-2  C11   0.020
 PDY  plan-2  N7    0.020
 PDY  plan-2  N2    0.020
 PDY  plan-2  C1    0.020
 PDY  plan-2  N9    0.020
 PDY  plan-2  H8    0.020
 PDY  plan-2  H11   0.020
 PDY  plan-3  C15   0.020
 PDY  plan-3  N10   0.020
 PDY  plan-3  C4    0.020
 PDY  plan-3  HN10  0.020

