# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:57:34 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 3-bromo-5-phenyl-N-(pyridin-3-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cnn2c(NCc3cccnc3)cc(nc12)c4ccccc4
#
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
 SCJ  SCJ  3-bromo-5-phenyl-N-(pyridin-3-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amine  ligand  38  24  .  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_SCJ
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
 SCJ  C01   C   CR5   0  -0.453   1.8686   2.0032   0.2834
 SCJ  C02   C   CR56  0   0.647   1.2947   0.7409   0.1912
 SCJ  N03   N   N     0  -0.443  -0.0536   0.9955   0.0903
 SCJ  N04   N   N     0  -0.317  -0.3599   2.2978   0.1099
 SCJ  C05   C   CR15  0   0.011   0.8074   2.9083   0.2261
 SCJ  N06   N   N     0  -0.477   1.8014  -0.4890   0.1927
 SCJ  C07   C   CR6   0   0.255   0.9398  -1.4832   0.0768
 SCJ  C08   C   CR16  0  -0.499  -0.4488  -1.2923  -0.0515
 SCJ  C09   C   CR6   0   0.729  -0.9669  -0.0085  -0.0363
 SCJ  N10   N   NH1   0  -0.668  -2.2472   0.3426  -0.1289
 SCJ  C11   C   CR6   0   0.054   1.5092  -2.8479   0.0601
 SCJ  C12   C   CH2   0  -0.347  -3.3103  -0.6190  -0.3453
 SCJ  C13   C   CR6   0  -0.026  -4.6431   0.0426  -0.1582
 SCJ  C14   C   CR16  0  -0.084  -5.4285   0.3855  -1.2515
 SCJ  N15   N   N     0  -0.401  -6.6096   0.9839  -1.1545
 SCJ  C16   C   CR16  0  -0.062  -7.0606   1.2704   0.0599
 SCJ  C17   C   CR16  0  -0.319  -6.3594   0.9744   1.2212
 SCJ  C18   C   CR16  0  -0.164  -5.1284   0.3518   1.1076
 SCJ  C19   C   CR16  0  -0.284   2.8340  -3.0372  -0.3378
 SCJ  C20   C   CR16  0  -0.240   3.3855  -4.3079  -0.3700
 SCJ  C21   C   CR16  0  -0.257   2.6264  -5.4093   0.0062
 SCJ  C22   C   CR16  0  -0.239   1.3121  -5.2300   0.4151
 SCJ  C23   C   CR16  0  -0.312   0.7561  -3.9592   0.4394
 SCJ  BR24  BR  BR    0  -0.038   3.6809   2.3575   0.4452
 SCJ  H05   H   HCR5  0   0.292   0.8556   3.9858   0.2663
 SCJ  H08   H   HCR6  0   0.292  -1.1134  -2.1290  -0.1967
 SCJ  HN10  H   HNH1  0   0.420  -2.4510   1.3247  -0.2477
 SCJ  H121  H   HCH2  0   0.272  -3.2407  -1.0548  -1.3468
 SCJ  H122  H   HCH2  0   0.275  -3.2021  -1.4358   0.3718
 SCJ  H14   H   HCR6  0   0.265  -5.0808   0.1602  -2.2551
 SCJ  H16   H   HCR6  0   0.269  -8.0270   1.7589   0.1163
 SCJ  H17   H   HCR6  0   0.276  -6.7740   1.2238   2.1879
 SCJ  H18   H   HCR6  0   0.276  -4.5545   0.1029   1.9921
 SCJ  H19   H   HCR6  0   0.258   3.4278  -2.1819  -0.6310
 SCJ  H20   H   HCR6  0   0.261   4.4107  -4.4403  -0.6904
 SCJ  H21   H   HCR6  0   0.262   3.0575  -6.4016  -0.0189
 SCJ  H22   H   HCR6  0   0.262   0.7170  -6.0811   0.7194
 SCJ  H23   H   HCR6  0   0.255  -0.2649  -3.8422   0.7788

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
 SCJ  C17  C16   aromatic  1.388  0.020  1.388
 SCJ  C17  C18   aromatic  1.384  0.020  1.384
 SCJ  C16  N15   aromatic  1.327  0.020  1.327
 SCJ  C18  C13   aromatic  1.390  0.020  1.390
 SCJ  N15  C14   aromatic  1.327  0.020  1.327
 SCJ  C13  C14   aromatic  1.389  0.020  1.389
 SCJ  C13  C12   single    1.500  0.020  1.500
 SCJ  N04  C05   aromatic  1.322  0.020  1.322
 SCJ  N04  N03   aromatic  1.338  0.020  1.338
 SCJ  N10  C12   single    1.450  0.020  1.450
 SCJ  N10  C09   single    1.331  0.020  1.331
 SCJ  C05  C01   aromatic  1.396  0.020  1.396
 SCJ  N03  C09   aromatic  1.363  0.020  1.363
 SCJ  N03  C02   aromatic  1.376  0.020  1.376
 SCJ  C09  C08   aromatic  1.385  0.020  1.385
 SCJ  C01  C02   aromatic  1.390  0.020  1.390
 SCJ  C01  BR24  single    1.854  0.020  1.854
 SCJ  C02  N06   aromatic  1.330  0.020  1.330
 SCJ  C08  C07   aromatic  1.407  0.020  1.407
 SCJ  N06  C07   aromatic  1.321  0.020  1.321
 SCJ  C07  C11   single    1.479  0.020  1.479
 SCJ  C23  C11   aromatic  1.395  0.020  1.395
 SCJ  C23  C22   aromatic  1.387  0.020  1.387
 SCJ  C11  C19   aromatic  1.396  0.020  1.396
 SCJ  C22  C21   aromatic  1.388  0.020  1.388
 SCJ  C19  C20   aromatic  1.386  0.020  1.386
 SCJ  C21  C20   aromatic  1.390  0.020  1.390
 SCJ  C05  H05   single    0.930  0.020  1.080
 SCJ  C08  H08   single    0.930  0.020  1.080
 SCJ  N10  HN10  single    0.860  0.020  1.020
 SCJ  C12  H121  single    0.970  0.020  1.090
 SCJ  C12  H122  single    0.970  0.020  1.090
 SCJ  C14  H14   single    0.930  0.020  1.080
 SCJ  C16  H16   single    0.930  0.020  1.080
 SCJ  C17  H17   single    0.930  0.020  1.080
 SCJ  C18  H18   single    0.930  0.020  1.080
 SCJ  C19  H19   single    0.930  0.020  1.080
 SCJ  C20  H20   single    0.930  0.020  1.080
 SCJ  C21  H21   single    0.930  0.020  1.080
 SCJ  C22  H22   single    0.930  0.020  1.080
 SCJ  C23  H23   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
 SCJ  BR24  C01  C05   128.53  3.000
 SCJ  BR24  C01  C02   125.67  3.000
 SCJ  C05   C01  C02   105.80  3.000
 SCJ  N06   C02  N03   122.99  3.000
 SCJ  N06   C02  C01   133.04  3.000
 SCJ  N03   C02  C01   103.97  3.000
 SCJ  C09   N03  N04   124.39  3.000
 SCJ  C09   N03  C02   121.81  3.000
 SCJ  N04   N03  C02   113.79  3.000
 SCJ  C05   N04  N03   104.39  3.000
 SCJ  H05   C05  N04   120.24  3.000
 SCJ  H05   C05  C01   127.72  3.000
 SCJ  N04   C05  C01   112.04  3.000
 SCJ  C07   N06  C02   116.58  3.000
 SCJ  C11   C07  C08   120.26  3.000
 SCJ  C11   C07  N06   116.39  3.000
 SCJ  C08   C07  N06   123.34  3.000
 SCJ  H08   C08  C09   119.36  3.000
 SCJ  H08   C08  C07   121.00  3.000
 SCJ  C09   C08  C07   119.60  3.000
 SCJ  N10   C09  C08   127.15  3.000
 SCJ  C08   C09  N03   115.67  3.000
 SCJ  N10   C09  N03   117.18  3.000
 SCJ  HN10  N10  C12   118.65  3.000
 SCJ  HN10  N10  C09   117.31  3.000
 SCJ  C12   N10  C09   122.74  3.000
 SCJ  C23   C11  C19   118.80  3.000
 SCJ  C19   C11  C07   119.59  3.000
 SCJ  C23   C11  C07   121.62  3.000
 SCJ  H122  C12  H121  107.26  3.000
 SCJ  H122  C12  C13   109.64  3.000
 SCJ  H121  C12  C13   110.27  3.000
 SCJ  H122  C12  N10   108.98  3.000
 SCJ  H121  C12  N10   110.74  3.000
 SCJ  C13   C12  N10   109.90  3.000
 SCJ  C18   C13  C14   117.66  3.000
 SCJ  C14   C13  C12   120.88  3.000
 SCJ  C18   C13  C12   121.46  3.000
 SCJ  H14   C14  N15   116.49  3.000
 SCJ  H14   C14  C13   119.67  3.000
 SCJ  N15   C14  C13   123.84  3.000
 SCJ  C16   N15  C14   117.81  3.000
 SCJ  H16   C16  C17   120.18  3.000
 SCJ  H16   C16  N15   116.60  3.000
 SCJ  C17   C16  N15   123.22  3.000
 SCJ  H17   C17  C18   121.21  3.000
 SCJ  H17   C17  C16   120.34  3.000
 SCJ  C18   C17  C16   118.45  3.000
 SCJ  H18   C18  C17   120.49  3.000
 SCJ  H18   C18  C13   120.49  3.000
 SCJ  C17   C18  C13   119.02  3.000
 SCJ  H19   C19  C20   120.02  3.000
 SCJ  H19   C19  C11   119.40  3.000
 SCJ  C20   C19  C11   120.58  3.000
 SCJ  H20   C20  C21   120.05  3.000
 SCJ  H20   C20  C19   119.75  3.000
 SCJ  C21   C20  C19   120.21  3.000
 SCJ  H21   C21  C22   120.16  3.000
 SCJ  H21   C21  C20   120.19  3.000
 SCJ  C22   C21  C20   119.65  3.000
 SCJ  H22   C22  C23   119.68  3.000
 SCJ  H22   C22  C21   120.13  3.000
 SCJ  C23   C22  C21   120.19  3.000
 SCJ  H23   C23  C22   118.85  3.000
 SCJ  H23   C23  C11   120.56  3.000
 SCJ  C22   C23  C11   120.57  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
 SCJ  CONST_01  N03   N04  C05  C01    0.00   0.0  0
 SCJ  CONST_02  N04   N03  C02  C01    0.00   0.0  0
 SCJ  CONST_03  C09   N03  C02  C01  180.00   0.0  0
 SCJ  CONST_04  C07   N06  C02  C01  180.00   0.0  0
 SCJ  CONST_05  C05   N04  N03  C02    0.00   0.0  0
 SCJ  CONST_06  C08   C09  N03  C02    0.00   0.0  0
 SCJ  CONST_07  N04   C05  C01  C02    0.00   0.0  0
 SCJ  CONST_08  C08   C07  N06  C02    0.00   0.0  0
 SCJ  CONST_09  C11   C07  N06  C02  180.00   0.0  0
 SCJ  CONST_10  C07   C08  C09  N03    0.00   0.0  0
 SCJ  CONST_11  C05   C01  C02  N03    0.00   0.0  0
 SCJ  CONST_12  C07   N06  C02  N03    0.00   0.0  0
 SCJ  CONST_13  C08   C09  N03  N04  180.00   0.0  0
 SCJ  CONST_14  N06   C02  N03  N04  180.00   0.0  0
 SCJ  CONST_15  C09   N03  N04  C05  180.00   0.0  0
 SCJ  CONST_16  N06   C02  C01  C05  180.00   0.0  0
 SCJ  CONST_17  C09   N03  C02  N06    0.00   0.0  0
 SCJ  CONST_18  C09   C08  C07  N06    0.00   0.0  0
 SCJ  CONST_21  C22   C23  C11  C07  180.00   0.0  0
 SCJ  CONST_22  C20   C19  C11  C07  180.00   0.0  0
 SCJ  CONST_25  C11   C07  C08  C09  180.00   0.0  0
 SCJ  CONST_26  C21   C22  C23  C11    0.00   0.0  0
 SCJ  CONST_27  C21   C20  C19  C11    0.00   0.0  0
 SCJ  CONST_28  C16   C17  C18  C13    0.00   0.0  0
 SCJ  CONST_29  C16   N15  C14  C13    0.00   0.0  0
 SCJ  CONST_30  C17   C16  N15  C14    0.00   0.0  0
 SCJ  CONST_31  C17   C18  C13  C14    0.00   0.0  0
 SCJ  CONST_32  C18   C17  C16  N15    0.00   0.0  0
 SCJ  CONST_33  C18   C13  C14  N15    0.00   0.0  0
 SCJ  CONST_34  C22   C23  C11  C19    0.00   0.0  0
 SCJ  CONST_35  C22   C21  C20  C19    0.00   0.0  0
 SCJ  CONST_36  C23   C11  C19  C20    0.00   0.0  0
 SCJ  CONST_37  C23   C22  C21  C20    0.00   0.0  0
 SCJ  CONST_38  N10   C09  N03  C02  180.00   0.0  0
 SCJ  CONST_39  BR24  C01  C02  N03  180.00   0.0  0
 SCJ  CONST_40  BR24  C01  C05  N04  180.00   0.0  0
 SCJ  CONST_41  N10   C09  N03  N04    0.00   0.0  0
 SCJ  CONST_42  BR24  C01  C02  N06    0.00   0.0  0
 SCJ  CONST_43  N10   C09  C08  C07  180.00   0.0  0
 SCJ  CONST_44  C17   C18  C13  C12  180.00   0.0  0
 SCJ  CONST_45  N15   C14  C13  C12  180.00   0.0  0
 SCJ  CONST_46  H05   C05  C01  C02  180.00   0.0  0
 SCJ  CONST_47  H08   C08  C09  N03  180.00   0.0  0
 SCJ  CONST_48  H23   C23  C11  C07    0.00   0.0  0
 SCJ  CONST_49  H19   C19  C11  C07    0.00   0.0  0
 SCJ  CONST_50  H22   C22  C23  C11  180.00   0.0  0
 SCJ  CONST_51  H20   C20  C19  C11  180.00   0.0  0
 SCJ  CONST_52  H17   C17  C18  C13  180.00   0.0  0
 SCJ  CONST_53  H16   C16  N15  C14  180.00   0.0  0
 SCJ  CONST_54  H18   C18  C13  C14  180.00   0.0  0
 SCJ  CONST_55  H14   C14  N15  C16  180.00   0.0  0
 SCJ  CONST_56  H21   C21  C20  C19  180.00   0.0  0
 SCJ  CONST_57  C12   N10  C09  N03  180.00   0.0  0
 SCJ  CONST_58  C12   N10  C09  C08    0.00   0.0  0
 SCJ  CONST_59  HN10  N10  C09  N03    0.00   0.0  0
 SCJ  Var_01    C13   C12  N10  C09  169.88  30.0  3
 SCJ  Var_02    C18   C13  C12  N10  -75.18  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
 SCJ  plan-1  C12   0.020
 SCJ  plan-1  C13   0.020
 SCJ  plan-1  C14   0.020
 SCJ  plan-1  N15   0.020
 SCJ  plan-1  C16   0.020
 SCJ  plan-1  C17   0.020
 SCJ  plan-1  C18   0.020
 SCJ  plan-1  H14   0.020
 SCJ  plan-1  H16   0.020
 SCJ  plan-1  H17   0.020
 SCJ  plan-1  H18   0.020
 SCJ  plan-2  C07   0.020
 SCJ  plan-2  C11   0.020
 SCJ  plan-2  C19   0.020
 SCJ  plan-2  C20   0.020
 SCJ  plan-2  C21   0.020
 SCJ  plan-2  C22   0.020
 SCJ  plan-2  C23   0.020
 SCJ  plan-2  H19   0.020
 SCJ  plan-2  H20   0.020
 SCJ  plan-2  H21   0.020
 SCJ  plan-2  H22   0.020
 SCJ  plan-2  H23   0.020
 SCJ  plan-3  C01   0.020
 SCJ  plan-3  C02   0.020
 SCJ  plan-3  N03   0.020
 SCJ  plan-3  N04   0.020
 SCJ  plan-3  C05   0.020
 SCJ  plan-3  N06   0.020
 SCJ  plan-3  C07   0.020
 SCJ  plan-3  C08   0.020
 SCJ  plan-3  C09   0.020
 SCJ  plan-3  N10   0.020
 SCJ  plan-3  C11   0.020
 SCJ  plan-3  BR24  0.020
 SCJ  plan-3  H05   0.020
 SCJ  plan-3  H08   0.020
 SCJ  plan-4  C09   0.020
 SCJ  plan-4  N10   0.020
 SCJ  plan-4  C12   0.020
 SCJ  plan-4  HN10  0.020

