# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:44:03 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: N-[(2-aminopyrimidin-5-yl)methyl]-5-(2,6-difluorophenyl)-3-ethylpyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cnn2c(NCc3cnc(N)nc3)cc(nc12)c4c(F)cccc4F
#
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
 SCX  SCX  N-[(2-aminopyrimidin-5-yl)methyl]-5-(2,6-difluorophenyl)-3-ethylpyrazolo[1,5-a]pyrimidin-7-amine  ligand  45  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SCX
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
 SCX  C01   C  CR5   0  -0.220   1.6832   3.2709   0.2116
 SCX  C02   C  CR56  0   0.570   1.5238   1.8911   0.1557
 SCX  N03   N  N     0  -0.437   0.1611   1.6764   0.1013
 SCX  N04   N  N     0  -0.331  -0.5484   2.8063   0.1192
 SCX  C05   C  CR15  0  -0.049   0.3738   3.7594   0.1832
 SCX  N06   N  N     0  -0.454   2.4061   0.8837   0.1493
 SCX  C07   C  CR6   0   0.243   1.9030  -0.3271   0.0715
 SCX  C08   C  CR16  0  -0.471   0.5306  -0.6175   0.0007
 SCX  C09   C  CR6   0   0.710  -0.3785   0.4284   0.0227
 SCX  N10   N  NH1   0  -0.666  -1.7050   0.3330  -0.0225
 SCX  C11   C  CR6   0  -0.387   2.8768  -1.4439   0.0322
 SCX  C12   C  CH2   0  -0.348  -2.3942  -0.9359  -0.1753
 SCX  C13   C  CR6   0  -0.099  -3.8720  -0.7367  -0.0856
 SCX  C14   C  CR16  0  -0.022  -4.6804  -0.6162  -1.2075
 SCX  N15   N  N     0  -0.452  -5.9834  -0.4149  -1.1472
 SCX  C16   C  CR6   0   0.557  -6.5185  -0.3240   0.0766
 SCX  N17   N  N     0  -0.451  -5.8398  -0.4306   1.2274
 SCX  C18   C  CR16  0  -0.016  -4.5404  -0.6328   1.1288
 SCX  C19   C  CR6   0   0.561   2.9142  -2.4292   1.0090
 SCX  C20   C  CR16  0  -0.420   3.8234  -3.4682   0.9997
 SCX  C21   C  CR16  0  -0.228   4.7392  -3.5318  -0.0400
 SCX  C22   C  CR16  0  -0.423   4.7443  -2.5745  -1.0443
 SCX  C23   C  CR6   0   0.553   3.8178  -1.5528  -0.9838
 SCX  C24   C  CH2   0  -0.510   2.9741   4.0185   0.2454
 SCX  N25   N  NH2   0  -0.817  -7.8455  -0.1366   0.1585
 SCX  C26   C  CH3   0  -0.658   3.7272   3.9611  -1.0828
 SCX  F27   F  F     0  -0.297   2.0334  -2.3514   2.0139
 SCX  F28   F  F     0  -0.294   3.8061  -0.6375  -1.9574
 SCX  H05   H  HCR5  0   0.268   0.0657   4.7950   0.2108
 SCX  H08   H  HCR6  0   0.291   0.1869  -1.6359  -0.0938
 SCX  HN10  H  HNH1  0   0.416  -2.2343   1.1884  -0.1080
 SCX  H121  H  HCH2  0   0.269  -2.1339  -1.3947  -1.1343
 SCX  H122  H  HCH2  0   0.269  -2.0602  -1.6218   0.6075
 SCX  H14   H  HCR6  0   0.270  -4.2493  -0.6914  -2.2020
 SCX  H18   H  HCR6  0   0.271  -3.9935  -0.7229   2.0635
 SCX  H20   H  HCR6  0   0.287   3.8158  -4.2061   1.7900
 SCX  H21   H  HCR6  0   0.283   5.4583  -4.3384  -0.0685
 SCX  H22   H  HCR6  0   0.287   5.4501  -2.6213  -1.8622
 SCX  H241  H  HCH2  0   0.238   2.7787   5.0593   0.5121
 SCX  H242  H  HCH2  0   0.234   3.6122   3.6157   1.0361
 SCX  H251  H  HNH2  0   0.400  -8.3633   0.0961  -0.6706
 SCX  H252  H  HNH2  0   0.400  -8.2606   0.0841   1.0466
 SCX  H261  H  HCH3  0   0.227   4.6709   4.5048  -1.0198
 SCX  H262  H  HCH3  0   0.225   3.9517   2.9305  -1.3595
 SCX  H263  H  HCH3  0   0.222   3.1387   4.4035  -1.8874

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
 SCX  N25  C16   single    1.343  0.020  1.343
 SCX  N17  C16   aromatic  1.340  0.020  1.340
 SCX  N17  C18   aromatic  1.319  0.020  1.319
 SCX  C16  N15   aromatic  1.339  0.020  1.339
 SCX  C18  C13   aromatic  1.390  0.020  1.390
 SCX  N15  C14   aromatic  1.320  0.020  1.320
 SCX  C13  C14   aromatic  1.388  0.020  1.388
 SCX  C13  C12   single    1.494  0.020  1.494
 SCX  N04  C05   aromatic  1.328  0.020  1.328
 SCX  N04  N03   aromatic  1.334  0.020  1.334
 SCX  C05  C01   aromatic  1.398  0.020  1.398
 SCX  N10  C12   single    1.452  0.020  1.452
 SCX  N10  C09   single    1.331  0.020  1.331
 SCX  N03  C09   aromatic  1.362  0.020  1.362
 SCX  N03  C02   aromatic  1.381  0.020  1.381
 SCX  C09  C08   aromatic  1.386  0.020  1.386
 SCX  C01  C02   aromatic  1.390  0.020  1.390
 SCX  C01  C24   single    1.492  0.020  1.492
 SCX  C26  C24   single    1.528  0.020  1.528
 SCX  C02  N06   aromatic  1.339  0.020  1.339
 SCX  F28  C23   single    1.336  0.020  1.336
 SCX  C08  C07   aromatic  1.405  0.020  1.405
 SCX  N06  C07   aromatic  1.313  0.020  1.313
 SCX  C07  C11   single    1.482  0.020  1.482
 SCX  C23  C11   aromatic  1.389  0.020  1.389
 SCX  C23  C22   aromatic  1.381  0.020  1.381
 SCX  C11  C19   aromatic  1.388  0.020  1.388
 SCX  C22  C21   aromatic  1.387  0.020  1.387
 SCX  C19  F27   single    1.339  0.020  1.339
 SCX  C19  C20   aromatic  1.381  0.020  1.381
 SCX  C21  C20   aromatic  1.387  0.020  1.387
 SCX  C05  H05   single    0.930  0.020  1.080
 SCX  C08  H08   single    0.930  0.020  1.080
 SCX  N10  HN10  single    0.860  0.020  1.020
 SCX  C12  H121  single    0.970  0.020  1.090
 SCX  C12  H122  single    0.970  0.020  1.090
 SCX  C14  H14   single    0.930  0.020  1.080
 SCX  C18  H18   single    0.930  0.020  1.080
 SCX  C20  H20   single    0.930  0.020  1.080
 SCX  C21  H21   single    0.930  0.020  1.080
 SCX  C22  H22   single    0.930  0.020  1.080
 SCX  C24  H241  single    0.970  0.020  1.090
 SCX  C24  H242  single    0.970  0.020  1.090
 SCX  N25  H251  single    0.890  0.020  1.040
 SCX  N25  H252  single    0.890  0.020  1.040
 SCX  C26  H261  single    0.970  0.020  1.090
 SCX  C26  H262  single    0.970  0.020  1.090
 SCX  C26  H263  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
 SCX  C24   C01  C05   129.47  3.000
 SCX  C24   C01  C02   126.69  3.000
 SCX  C05   C01  C02   103.81  3.000
 SCX  N06   C02  N03   122.21  3.000
 SCX  N06   C02  C01   132.17  3.000
 SCX  N03   C02  C01   105.61  3.000
 SCX  C09   N03  N04   124.48  3.000
 SCX  C09   N03  C02   122.40  3.000
 SCX  N04   N03  C02   113.12  3.000
 SCX  C05   N04  N03   103.84  3.000
 SCX  H05   C05  N04   119.41  3.000
 SCX  H05   C05  C01   126.97  3.000
 SCX  N04   C05  C01   113.62  3.000
 SCX  C07   N06  C02   116.20  3.000
 SCX  C11   C07  C08   119.00  3.000
 SCX  C11   C07  N06   116.39  3.000
 SCX  C08   C07  N06   124.60  3.000
 SCX  H08   C08  C09   120.31  3.000
 SCX  H08   C08  C07   120.72  3.000
 SCX  C09   C08  C07   118.95  3.000
 SCX  N10   C09  C08   126.82  3.000
 SCX  C08   C09  N03   115.63  3.000
 SCX  N10   C09  N03   117.55  3.000
 SCX  HN10  N10  C12   118.86  3.000
 SCX  HN10  N10  C09   117.70  3.000
 SCX  C12   N10  C09   122.63  3.000
 SCX  C23   C11  C19   116.15  3.000
 SCX  C19   C11  C07   122.27  3.000
 SCX  C23   C11  C07   121.57  3.000
 SCX  H122  C12  H121  106.97  3.000
 SCX  H122  C12  C13   110.05  3.000
 SCX  H121  C12  C13   110.10  3.000
 SCX  H122  C12  N10   109.15  3.000
 SCX  H121  C12  N10   110.22  3.000
 SCX  C13   C12  N10   110.28  3.000
 SCX  C18   C13  C14   114.80  3.000
 SCX  C14   C13  C12   122.63  3.000
 SCX  C18   C13  C12   122.56  3.000
 SCX  H14   C14  N15   116.37  3.000
 SCX  H14   C14  C13   120.17  3.000
 SCX  N15   C14  C13   123.46  3.000
 SCX  C16   N15  C14   116.53  3.000
 SCX  N25   C16  N17   117.34  3.000
 SCX  N17   C16  N15   125.24  3.000
 SCX  N25   C16  N15   117.40  3.000
 SCX  C18   N17  C16   116.55  3.000
 SCX  H18   C18  N17   116.38  3.000
 SCX  H18   C18  C13   120.21  3.000
 SCX  N17   C18  C13   123.41  3.000
 SCX  F27   C19  C20   118.83  3.000
 SCX  C20   C19  C11   123.18  3.000
 SCX  F27   C19  C11   117.99  3.000
 SCX  H20   C20  C21   121.42  3.000
 SCX  H20   C20  C19   120.27  3.000
 SCX  C21   C20  C19   118.32  3.000
 SCX  H21   C21  C22   119.56  3.000
 SCX  H21   C21  C20   119.55  3.000
 SCX  C22   C21  C20   120.89  3.000
 SCX  H22   C22  C23   120.21  3.000
 SCX  H22   C22  C21   121.34  3.000
 SCX  C23   C22  C21   118.45  3.000
 SCX  F28   C23  C22   118.74  3.000
 SCX  C22   C23  C11   123.01  3.000
 SCX  F28   C23  C11   118.24  3.000
 SCX  H242  C24  H241  106.20  3.000
 SCX  H242  C24  C26   109.10  3.000
 SCX  H241  C24  C26   109.65  3.000
 SCX  H242  C24  C01   109.68  3.000
 SCX  H241  C24  C01   109.16  3.000
 SCX  C26   C24  C01   112.82  3.000
 SCX  H252  N25  H251  117.74  3.000
 SCX  H252  N25  C16   119.53  3.000
 SCX  H251  N25  C16   119.42  3.000
 SCX  H263  C26  H262  107.89  3.000
 SCX  H263  C26  H261  107.89  3.000
 SCX  H262  C26  H261  107.91  3.000
 SCX  H263  C26  C24   111.11  3.000
 SCX  H262  C26  C24   110.95  3.000
 SCX  H261  C26  C24   110.94  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
 SCX  CONST_01  N03   N04  C05  C01     0.00   0.0  0
 SCX  CONST_02  N04   N03  C02  C01     0.00   0.0  0
 SCX  CONST_03  C09   N03  C02  C01   180.00   0.0  0
 SCX  CONST_04  C07   N06  C02  C01   180.00   0.0  0
 SCX  CONST_05  C05   N04  N03  C02     0.00   0.0  0
 SCX  CONST_06  C08   C09  N03  C02     0.00   0.0  0
 SCX  CONST_07  N04   C05  C01  C02     0.00   0.0  0
 SCX  CONST_08  C08   C07  N06  C02     0.00   0.0  0
 SCX  CONST_09  C11   C07  N06  C02   180.00   0.0  0
 SCX  CONST_10  C07   C08  C09  N03     0.00   0.0  0
 SCX  CONST_11  C05   C01  C02  N03     0.00   0.0  0
 SCX  CONST_12  C07   N06  C02  N03     0.00   0.0  0
 SCX  CONST_13  C08   C09  N03  N04   180.00   0.0  0
 SCX  CONST_14  N06   C02  N03  N04   180.00   0.0  0
 SCX  CONST_15  C09   N03  N04  C05   180.00   0.0  0
 SCX  CONST_16  N06   C02  C01  C05   180.00   0.0  0
 SCX  CONST_17  C09   N03  C02  N06     0.00   0.0  0
 SCX  CONST_18  C09   C08  C07  N06     0.00   0.0  0
 SCX  CONST_21  C22   C23  C11  C07   180.00   0.0  0
 SCX  CONST_22  C20   C19  C11  C07   180.00   0.0  0
 SCX  CONST_25  C11   C07  C08  C09   180.00   0.0  0
 SCX  CONST_26  C21   C22  C23  C11     0.00   0.0  0
 SCX  CONST_27  C21   C20  C19  C11     0.00   0.0  0
 SCX  CONST_28  C16   N17  C18  C13     0.00   0.0  0
 SCX  CONST_29  C16   N15  C14  C13     0.00   0.0  0
 SCX  CONST_30  N17   C16  N15  C14     0.00   0.0  0
 SCX  CONST_31  N17   C18  C13  C14     0.00   0.0  0
 SCX  CONST_32  C18   N17  C16  N15     0.00   0.0  0
 SCX  CONST_33  C18   C13  C14  N15     0.00   0.0  0
 SCX  CONST_34  C22   C23  C11  C19     0.00   0.0  0
 SCX  CONST_35  C22   C21  C20  C19     0.00   0.0  0
 SCX  CONST_36  C23   C11  C19  C20     0.00   0.0  0
 SCX  CONST_37  C23   C22  C21  C20     0.00   0.0  0
 SCX  CONST_38  N10   C09  N03  C02   180.00   0.0  0
 SCX  CONST_39  C24   C01  C02  N03   180.00   0.0  0
 SCX  CONST_40  C24   C01  C05  N04   180.00   0.0  0
 SCX  CONST_41  N10   C09  N03  N04     0.00   0.0  0
 SCX  CONST_42  C24   C01  C02  N06     0.00   0.0  0
 SCX  CONST_43  N10   C09  C08  C07   180.00   0.0  0
 SCX  CONST_44  F28   C23  C11  C07     0.00   0.0  0
 SCX  CONST_45  F27   C19  C11  C07     0.00   0.0  0
 SCX  CONST_46  N17   C18  C13  C12   180.00   0.0  0
 SCX  CONST_47  N15   C14  C13  C12   180.00   0.0  0
 SCX  CONST_48  N25   C16  N15  C14   180.00   0.0  0
 SCX  CONST_49  N25   C16  N17  C18   180.00   0.0  0
 SCX  CONST_50  F28   C23  C11  C19   180.00   0.0  0
 SCX  CONST_51  F28   C23  C22  C21   180.00   0.0  0
 SCX  CONST_52  F27   C19  C20  C21   180.00   0.0  0
 SCX  CONST_53  F27   C19  C11  C23   180.00   0.0  0
 SCX  CONST_54  H05   C05  C01  C02   180.00   0.0  0
 SCX  CONST_55  H08   C08  C09  N03   180.00   0.0  0
 SCX  CONST_56  H22   C22  C23  C11   180.00   0.0  0
 SCX  CONST_57  H20   C20  C19  C11   180.00   0.0  0
 SCX  CONST_58  H18   C18  C13  C14   180.00   0.0  0
 SCX  CONST_59  H14   C14  N15  C16   180.00   0.0  0
 SCX  CONST_60  H21   C21  C20  C19   180.00   0.0  0
 SCX  CONST_61  C12   N10  C09  N03   180.00   0.0  0
 SCX  CONST_62  C12   N10  C09  C08     0.00   0.0  0
 SCX  CONST_63  HN10  N10  C09  N03     0.00   0.0  0
 SCX  CONST_64  H251  N25  C16  N15     0.00   0.0  0
 SCX  CONST_65  H252  N25  C16  N15   180.00   0.0  0
 SCX  Var_01    C26   C24  C01  C02    70.43  30.0  2
 SCX  Var_02    C13   C12  N10  C09   175.62  30.0  3
 SCX  Var_03    C18   C13  C12  N10   -81.60  30.0  2
 SCX  Var_04    H261  C26  C24  C01  -179.21  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
 SCX  plan-1  C12   0.020
 SCX  plan-1  C13   0.020
 SCX  plan-1  C14   0.020
 SCX  plan-1  N15   0.020
 SCX  plan-1  C16   0.020
 SCX  plan-1  N17   0.020
 SCX  plan-1  C18   0.020
 SCX  plan-1  N25   0.020
 SCX  plan-1  H14   0.020
 SCX  plan-1  H18   0.020
 SCX  plan-2  C07   0.020
 SCX  plan-2  C11   0.020
 SCX  plan-2  C19   0.020
 SCX  plan-2  C20   0.020
 SCX  plan-2  C21   0.020
 SCX  plan-2  C22   0.020
 SCX  plan-2  C23   0.020
 SCX  plan-2  F27   0.020
 SCX  plan-2  F28   0.020
 SCX  plan-2  H20   0.020
 SCX  plan-2  H21   0.020
 SCX  plan-2  H22   0.020
 SCX  plan-3  C01   0.020
 SCX  plan-3  C02   0.020
 SCX  plan-3  N03   0.020
 SCX  plan-3  N04   0.020
 SCX  plan-3  C05   0.020
 SCX  plan-3  N06   0.020
 SCX  plan-3  C07   0.020
 SCX  plan-3  C08   0.020
 SCX  plan-3  C09   0.020
 SCX  plan-3  N10   0.020
 SCX  plan-3  C11   0.020
 SCX  plan-3  C24   0.020
 SCX  plan-3  H05   0.020
 SCX  plan-3  H08   0.020
 SCX  plan-4  C09   0.020
 SCX  plan-4  N10   0.020
 SCX  plan-4  C12   0.020
 SCX  plan-4  HN10  0.020
 SCX  plan-5  C16   0.020
 SCX  plan-5  N25   0.020
 SCX  plan-5  H251  0.020
 SCX  plan-5  H252  0.020

