# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:19:52 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 3-cyclopropyl-5-phenyl-N-(pyridin-3-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC1c2cnn3c(NCc4cccnc4)cc(nc23)c5ccccc5
#
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
 SCZ  SCZ  3-cyclopropyl-5-phenyl-N-(pyridin-3-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amine  ligand  45  26  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SCZ
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
 SCZ  C01   C  CR5   0  -0.164   2.0742   2.4757   0.0595
 SCZ  C02   C  CR56  0   0.569   1.6425   1.1536   0.0306
 SCZ  N03   N  N     0  -0.441   0.2657   1.2169  -0.0282
 SCZ  N04   N  N     0  -0.325  -0.2038   2.4653  -0.0403
 SCZ  C05   C  CR15  0  -0.079   0.8873   3.2179   0.0132
 SCZ  N06   N  N     0  -0.485   2.3019  -0.0091   0.0607
 SCZ  C07   C  CR6   0   0.249   1.5796  -1.1099   0.0186
 SCZ  C08   C  CR16  0  -0.511   0.1714  -1.1082  -0.0647
 SCZ  C09   C  CR6   0   0.719  -0.5074   0.0972  -0.0801
 SCZ  N10   N  NH1   0  -0.672  -1.8266   0.2688  -0.1409
 SCZ  C11   C  CR6   0   0.056   2.3241  -2.3893   0.0467
 SCZ  C12   C  CH2   0  -0.343  -2.7593  -0.8384  -0.2036
 SCZ  C13   C  CR6   0  -0.035  -4.1655  -0.3227  -0.1262
 SCZ  C14   C  CR16  0  -0.076  -4.8056  -0.1911   1.1013
 SCZ  N15   N  N     0  -0.401  -6.0357   0.2826   1.2454
 SCZ  C16   C  CR16  0  -0.063  -6.6897   0.6536   0.1505
 SCZ  C17   C  CR16  0  -0.319  -6.1493   0.5653  -1.1238
 SCZ  C18   C  CR16  0  -0.165  -4.8631   0.0689  -1.2619
 SCZ  C19   C  CR16  0  -0.318   1.7185  -3.5806   0.4481
 SCZ  C20   C  CR16  0  -0.238   2.4368  -4.7673   0.4711
 SCZ  C21   C  CR16  0  -0.260   3.7713  -4.7835   0.0900
 SCZ  C22   C  CR16  0  -0.240   4.3852  -3.6020  -0.3075
 SCZ  C23   C  CR16  0  -0.287   3.6698  -2.4155  -0.3252
 SCZ  C24   C  CH1   0  -0.364   3.4729   2.9309   0.1117
 SCZ  C25   C  CH2   0  -0.474   3.9702   4.0064  -0.8183
 SCZ  C26   C  CH2   0  -0.480   3.8222   4.2922   0.6415
 SCZ  H05   H  HCR5  0   0.269   0.7832   4.2934   0.0181
 SCZ  H08   H  HCR6  0   0.287  -0.3880  -2.0272  -0.1444
 SCZ  HN10  H  HNH1  0   0.418  -2.1762   1.2145  -0.1877
 SCZ  H121  H  HCH2  0   0.271  -2.6163  -1.4049  -1.1287
 SCZ  H122  H  HCH2  0   0.270  -2.5699  -1.5256   0.6257
 SCZ  H14   H  HCR6  0   0.265  -4.2934  -0.4918   2.0103
 SCZ  H16   H  HCR6  0   0.269  -7.6940   1.0365   0.2925
 SCZ  H17   H  HCR6  0   0.276  -6.7252   0.8750  -1.9849
 SCZ  H18   H  HCR6  0   0.276  -4.4100  -0.0201  -2.2418
 SCZ  H19   H  HCR6  0   0.252   0.6850  -3.5916   0.7682
 SCZ  H20   H  HCR6  0   0.261   1.9518  -5.6802   0.7911
 SCZ  H21   H  HCR6  0   0.260   4.3306  -5.7100   0.1027
 SCZ  H22   H  HCR6  0   0.259   5.4255  -3.6056  -0.6060
 SCZ  H23   H  HCR6  0   0.256   4.1517  -1.4977  -0.6341
 SCZ  H24   H  HCH1  0   0.255   4.1817   2.1401   0.3305
 SCZ  H251  H  HCH2  0   0.253   4.9684   3.9023  -1.2243
 SCZ  H252  H  HCH2  0   0.247   3.2536   4.4499  -1.4990
 SCZ  H261  H  HCH2  0   0.249   3.0094   4.9370   0.9539
 SCZ  H262  H  HCH2  0   0.255   4.7176   4.3878   1.2422

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
 SCZ  N15  C16   aromatic  1.328  0.020  1.328
 SCZ  N15  C14   aromatic  1.326  0.020  1.326
 SCZ  C16  C17   aromatic  1.387  0.020  1.387
 SCZ  C14  C13   aromatic  1.391  0.020  1.391
 SCZ  C17  C18   aromatic  1.386  0.020  1.386
 SCZ  C13  C18   aromatic  1.389  0.020  1.389
 SCZ  C13  C12   single    1.500  0.020  1.500
 SCZ  N10  C12   single    1.449  0.020  1.449
 SCZ  N10  C09   single    1.332  0.020  1.332
 SCZ  N04  C05   aromatic  1.327  0.020  1.327
 SCZ  N04  N03   aromatic  1.334  0.020  1.334
 SCZ  C05  C01   aromatic  1.401  0.020  1.401
 SCZ  C09  N03   aromatic  1.362  0.020  1.362
 SCZ  C09  C08   aromatic  1.383  0.020  1.383
 SCZ  N03  C02   aromatic  1.379  0.020  1.379
 SCZ  C01  C02   aromatic  1.391  0.020  1.391
 SCZ  C01  C24   single    1.472  0.020  1.472
 SCZ  C08  C07   aromatic  1.411  0.020  1.411
 SCZ  C02  N06   aromatic  1.337  0.020  1.337
 SCZ  C24  C25   single    1.506  0.020  1.506
 SCZ  C24  C26   single    1.502  0.020  1.502
 SCZ  C07  N06   aromatic  1.317  0.020  1.317
 SCZ  C07  C11   single    1.480  0.020  1.480
 SCZ  C25  C26   single    1.495  0.020  1.495
 SCZ  C11  C23   aromatic  1.396  0.020  1.396
 SCZ  C11  C19   aromatic  1.395  0.020  1.395
 SCZ  C23  C22   aromatic  1.386  0.020  1.386
 SCZ  C19  C20   aromatic  1.387  0.020  1.387
 SCZ  C22  C21   aromatic  1.390  0.020  1.390
 SCZ  C20  C21   aromatic  1.388  0.020  1.388
 SCZ  C05  H05   single    0.930  0.020  1.080
 SCZ  C08  H08   single    0.930  0.020  1.080
 SCZ  N10  HN10  single    0.860  0.020  1.020
 SCZ  C12  H121  single    0.970  0.020  1.090
 SCZ  C12  H122  single    0.970  0.020  1.090
 SCZ  C14  H14   single    0.930  0.020  1.080
 SCZ  C16  H16   single    0.930  0.020  1.080
 SCZ  C17  H17   single    0.930  0.020  1.080
 SCZ  C18  H18   single    0.930  0.020  1.080
 SCZ  C19  H19   single    0.930  0.020  1.080
 SCZ  C20  H20   single    0.930  0.020  1.080
 SCZ  C21  H21   single    0.930  0.020  1.080
 SCZ  C22  H22   single    0.930  0.020  1.080
 SCZ  C23  H23   single    0.930  0.020  1.080
 SCZ  C24  H24   single    0.970  0.020  1.090
 SCZ  C25  H251  single    0.970  0.020  1.090
 SCZ  C25  H252  single    0.970  0.020  1.090
 SCZ  C26  H261  single    0.970  0.020  1.090
 SCZ  C26  H262  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
 SCZ  C24   C01  C05   129.98  3.000
 SCZ  C24   C01  C02   126.13  3.000
 SCZ  C05   C01  C02   103.88  3.000
 SCZ  N06   C02  N03   122.22  3.000
 SCZ  N06   C02  C01   132.29  3.000
 SCZ  N03   C02  C01   105.49  3.000
 SCZ  C09   N03  N04   124.71  3.000
 SCZ  C09   N03  C02   122.04  3.000
 SCZ  N04   N03  C02   113.25  3.000
 SCZ  C05   N04  N03   103.95  3.000
 SCZ  H05   C05  N04   119.05  3.000
 SCZ  H05   C05  C01   127.51  3.000
 SCZ  N04   C05  C01   113.43  3.000
 SCZ  C07   N06  C02   117.10  3.000
 SCZ  C11   C07  C08   120.28  3.000
 SCZ  C11   C07  N06   116.47  3.000
 SCZ  C08   C07  N06   123.25  3.000
 SCZ  H08   C08  C09   119.15  3.000
 SCZ  H08   C08  C07   121.39  3.000
 SCZ  C09   C08  C07   119.44  3.000
 SCZ  N10   C09  C08   126.79  3.000
 SCZ  C08   C09  N03   115.94  3.000
 SCZ  N10   C09  N03   117.27  3.000
 SCZ  HN10  N10  C12   119.41  3.000
 SCZ  HN10  N10  C09   117.77  3.000
 SCZ  C12   N10  C09   122.76  3.000
 SCZ  C23   C11  C19   118.61  3.000
 SCZ  C19   C11  C07   121.67  3.000
 SCZ  C23   C11  C07   119.72  3.000
 SCZ  H122  C12  H121  107.05  3.000
 SCZ  H122  C12  C13   109.84  3.000
 SCZ  H121  C12  C13   110.13  3.000
 SCZ  H122  C12  N10   109.63  3.000
 SCZ  H121  C12  N10   110.37  3.000
 SCZ  C13   C12  N10   109.79  3.000
 SCZ  C18   C13  C14   117.64  3.000
 SCZ  C18   C13  C12   121.71  3.000
 SCZ  C14   C13  C12   120.64  3.000
 SCZ  H14   C14  N15   116.46  3.000
 SCZ  H14   C14  C13   119.71  3.000
 SCZ  N15   C14  C13   123.83  3.000
 SCZ  C16   N15  C14   117.84  3.000
 SCZ  H16   C16  C17   120.24  3.000
 SCZ  H16   C16  N15   116.54  3.000
 SCZ  C17   C16  N15   123.21  3.000
 SCZ  H17   C17  C18   121.18  3.000
 SCZ  H17   C17  C16   120.40  3.000
 SCZ  C18   C17  C16   118.43  3.000
 SCZ  H18   C18  C17   120.52  3.000
 SCZ  H18   C18  C13   120.42  3.000
 SCZ  C17   C18  C13   119.06  3.000
 SCZ  H19   C19  C20   118.74  3.000
 SCZ  H19   C19  C11   120.55  3.000
 SCZ  C20   C19  C11   120.69  3.000
 SCZ  H20   C20  C21   120.15  3.000
 SCZ  H20   C20  C19   119.64  3.000
 SCZ  C21   C20  C19   120.21  3.000
 SCZ  H21   C21  C22   120.19  3.000
 SCZ  H21   C21  C20   120.24  3.000
 SCZ  C22   C21  C20   119.56  3.000
 SCZ  H22   C22  C23   119.71  3.000
 SCZ  H22   C22  C21   120.05  3.000
 SCZ  C23   C22  C21   120.24  3.000
 SCZ  H23   C23  C22   120.02  3.000
 SCZ  H23   C23  C11   119.30  3.000
 SCZ  C22   C23  C11   120.68  3.000
 SCZ  H24   C24  C26   115.97  3.000
 SCZ  H24   C24  C25   115.44  3.000
 SCZ  C26   C24  C25    59.60  3.000
 SCZ  H24   C24  C01   113.75  3.000
 SCZ  C26   C24  C01   120.92  3.000
 SCZ  C25   C24  C01   120.84  3.000
 SCZ  H252  C25  H251  114.43  3.000
 SCZ  H252  C25  C26   118.02  3.000
 SCZ  H251  C25  C26   118.42  3.000
 SCZ  H252  C25  C24   117.51  3.000
 SCZ  H251  C25  C24   117.86  3.000
 SCZ  C26   C25  C24    60.06  3.000
 SCZ  H262  C26  H261  114.08  3.000
 SCZ  H262  C26  C25   118.48  3.000
 SCZ  H261  C26  C25   118.01  3.000
 SCZ  H262  C26  C24   117.92  3.000
 SCZ  H261  C26  C24   117.82  3.000
 SCZ  C25   C26  C24    60.35  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
 SCZ  CONST_01  N03   N04  C05  C01    0.00   0.0  0
 SCZ  CONST_02  N04   N03  C02  C01    0.00   0.0  0
 SCZ  CONST_03  C09   N03  C02  C01  180.00   0.0  0
 SCZ  CONST_04  C07   N06  C02  C01  180.00   0.0  0
 SCZ  CONST_05  C05   N04  N03  C02    0.00   0.0  0
 SCZ  CONST_06  C08   C09  N03  C02    0.00   0.0  0
 SCZ  CONST_07  N04   C05  C01  C02    0.00   0.0  0
 SCZ  CONST_08  C08   C07  N06  C02    0.00   0.0  0
 SCZ  CONST_09  C11   C07  N06  C02  180.00   0.0  0
 SCZ  CONST_10  C07   C08  C09  N03    0.00   0.0  0
 SCZ  CONST_11  C05   C01  C02  N03    0.00   0.0  0
 SCZ  CONST_12  C07   N06  C02  N03    0.00   0.0  0
 SCZ  CONST_13  C08   C09  N03  N04  180.00   0.0  0
 SCZ  CONST_14  N06   C02  N03  N04  180.00   0.0  0
 SCZ  CONST_15  C09   N03  N04  C05  180.00   0.0  0
 SCZ  CONST_16  N06   C02  C01  C05  180.00   0.0  0
 SCZ  CONST_17  C09   N03  C02  N06    0.00   0.0  0
 SCZ  CONST_18  C09   C08  C07  N06    0.00   0.0  0
 SCZ  CONST_21  C22   C23  C11  C07  180.00   0.0  0
 SCZ  CONST_22  C20   C19  C11  C07  180.00   0.0  0
 SCZ  CONST_25  C11   C07  C08  C09  180.00   0.0  0
 SCZ  CONST_26  C21   C22  C23  C11    0.00   0.0  0
 SCZ  CONST_27  C21   C20  C19  C11    0.00   0.0  0
 SCZ  CONST_28  C16   N15  C14  C13    0.00   0.0  0
 SCZ  CONST_29  C16   C17  C18  C13    0.00   0.0  0
 SCZ  CONST_30  C17   C16  N15  C14    0.00   0.0  0
 SCZ  CONST_31  C17   C18  C13  C14    0.00   0.0  0
 SCZ  CONST_32  C18   C17  C16  N15    0.00   0.0  0
 SCZ  CONST_33  C18   C13  C14  N15    0.00   0.0  0
 SCZ  CONST_34  C22   C23  C11  C19    0.00   0.0  0
 SCZ  CONST_35  C22   C21  C20  C19    0.00   0.0  0
 SCZ  CONST_36  C23   C11  C19  C20    0.00   0.0  0
 SCZ  CONST_37  C23   C22  C21  C20    0.00   0.0  0
 SCZ  CONST_38  C24   C01  C02  N03  180.00   0.0  0
 SCZ  CONST_39  C24   C01  C05  N04  180.00   0.0  0
 SCZ  CONST_40  C24   C01  C02  N06    0.00   0.0  0
 SCZ  CONST_41  N10   C09  N03  C02  180.00   0.0  0
 SCZ  CONST_42  N10   C09  N03  N04    0.00   0.0  0
 SCZ  CONST_43  N10   C09  C08  C07  180.00   0.0  0
 SCZ  CONST_44  N15   C14  C13  C12  180.00   0.0  0
 SCZ  CONST_45  C17   C18  C13  C12  180.00   0.0  0
 SCZ  CONST_46  H05   C05  C01  C02  180.00   0.0  0
 SCZ  CONST_47  H08   C08  C09  N03  180.00   0.0  0
 SCZ  CONST_48  H23   C23  C11  C07    0.00   0.0  0
 SCZ  CONST_49  H19   C19  C11  C07    0.00   0.0  0
 SCZ  CONST_50  H22   C22  C23  C11  180.00   0.0  0
 SCZ  CONST_51  H20   C20  C19  C11  180.00   0.0  0
 SCZ  CONST_52  H17   C17  C18  C13  180.00   0.0  0
 SCZ  CONST_53  H16   C16  N15  C14  180.00   0.0  0
 SCZ  CONST_54  H18   C18  C13  C14  180.00   0.0  0
 SCZ  CONST_55  H14   C14  N15  C16  180.00   0.0  0
 SCZ  CONST_56  H21   C21  C20  C19  180.00   0.0  0
 SCZ  CONST_57  C12   N10  C09  N03  180.00   0.0  0
 SCZ  CONST_58  C12   N10  C09  C08    0.00   0.0  0
 SCZ  CONST_59  HN10  N10  C09  N03    0.00   0.0  0
 SCZ  Var_01    C26   C25  C24  C01  110.10  30.0  1
 SCZ  Var_02    C25   C24  C01  C02  132.21  30.0  2
 SCZ  Var_03    C13   C12  N10  C09  174.44  30.0  3
 SCZ  Var_04    C14   C13  C12  N10  -90.94  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
 SCZ  chir_01  C24  C01  C25  C26  both

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
 SCZ  plan-1  C07   0.020
 SCZ  plan-1  C11   0.020
 SCZ  plan-1  C19   0.020
 SCZ  plan-1  C20   0.020
 SCZ  plan-1  C21   0.020
 SCZ  plan-1  C22   0.020
 SCZ  plan-1  C23   0.020
 SCZ  plan-1  H19   0.020
 SCZ  plan-1  H20   0.020
 SCZ  plan-1  H21   0.020
 SCZ  plan-1  H22   0.020
 SCZ  plan-1  H23   0.020
 SCZ  plan-2  C12   0.020
 SCZ  plan-2  C13   0.020
 SCZ  plan-2  C14   0.020
 SCZ  plan-2  N15   0.020
 SCZ  plan-2  C16   0.020
 SCZ  plan-2  C17   0.020
 SCZ  plan-2  C18   0.020
 SCZ  plan-2  H14   0.020
 SCZ  plan-2  H16   0.020
 SCZ  plan-2  H17   0.020
 SCZ  plan-2  H18   0.020
 SCZ  plan-3  C01   0.020
 SCZ  plan-3  C02   0.020
 SCZ  plan-3  N03   0.020
 SCZ  plan-3  N04   0.020
 SCZ  plan-3  C05   0.020
 SCZ  plan-3  N06   0.020
 SCZ  plan-3  C07   0.020
 SCZ  plan-3  C08   0.020
 SCZ  plan-3  C09   0.020
 SCZ  plan-3  N10   0.020
 SCZ  plan-3  C11   0.020
 SCZ  plan-3  C24   0.020
 SCZ  plan-3  H05   0.020
 SCZ  plan-3  H08   0.020
 SCZ  plan-4  C09   0.020
 SCZ  plan-4  N10   0.020
 SCZ  plan-4  C12   0.020
 SCZ  plan-4  HN10  0.020

