# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:25:23 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-bromo-5-(2-methylphenyl)-N-[(1-oxidopyridin-3-yl)methyl]pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2cc(NCc3ccc[n+]([O-])c3)n4ncc(Br)c4n2
#
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
 5SC  5SC  3-bromo-5-(2-methylphenyl)-N-[(1-oxidopyridin-3-yl)methyl]pyrazolo[1,5-a]pyrimidin-7-amine  ligand  42  26  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5SC
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
 5SC  C01   C   CR5    0  -0.452   2.0611   2.2105  -0.3382
 5SC  C02   C   CR56   0   0.640   1.5416   0.9245  -0.2539
 5SC  N03   N   N      0  -0.440   0.1811   1.1197  -0.1842
 5SC  N04   N   N      0  -0.317  -0.1816   2.4070  -0.2183
 5SC  C05   C   CR15   0   0.011   0.9601   3.0680  -0.3110
 5SC  N06   N   N      0  -0.462   2.1036  -0.2827  -0.2283
 5SC  C07   C   CR6    0   0.195   1.2801  -1.3102  -0.1314
 5SC  C08   C   CR16   0  -0.473  -0.1184  -1.1822  -0.0759
 5SC  C09   C   CR6    0   0.726  -0.6921   0.0768  -0.1059
 5SC  N10   N   NH1    0  -0.672  -1.9916   0.3706  -0.0844
 5SC  C11   C   CR6    0   0.022   1.9053  -2.6539  -0.1374
 5SC  C12   C   CH2    0  -0.347  -3.0123  -0.6406   0.0951
 5SC  C13   C   CR6    0  -0.057  -4.3625  -0.0524  -0.1972
 5SC  C14   C   CR16   0  -0.024  -5.2342   0.1846   0.8437
 5SC  N15   N   NR6    1  -0.018  -6.4616   0.7221   0.6406
 5SC  C16   C   CR16   0  -0.011  -6.8371   1.0381  -0.6201
 5SC  C17   C   CR16   0  -0.346  -5.9957   0.8224  -1.6894
 5SC  C18   C   CR16   0  -0.160  -4.7408   0.2732  -1.4948
 5SC  C19   C   CR6    0   0.080   1.5731  -3.6507   0.7916
 5SC  C20   C   CR16   0  -0.291   2.2220  -4.8815   0.6927
 5SC  C21   C   CR16   0  -0.243   3.1649  -5.1344  -0.2910
 5SC  C22   C   CR16   0  -0.262   3.4963  -4.1387  -1.1994
 5SC  C23   C   CR16   0  -0.278   2.8741  -2.9054  -1.1104
 5SC  BR24  BR  BR     0  -0.037   3.8594   2.6442  -0.4592
 5SC  C25   C   CH3    0  -0.755   0.5834  -3.4447   1.9053
 5SC  O26   O   O     -1  -0.582  -7.2421   0.9260   1.6218
 5SC  H05   H   HCR5   0   0.293   0.9616   4.1463  -0.3560
 5SC  H08   H   HCR6   0   0.293  -0.7481  -2.0562  -0.0270
 5SC  HN10  H   HNH1   0   0.422  -2.2436   1.3415   0.0356
 5SC  H121  H   HCH2   0   0.284  -2.8251  -1.4641  -0.5972
 5SC  H122  H   HCH2   0   0.277  -2.9840  -1.0524   1.1081
 5SC  H14   H   HCR6   0   0.312  -4.9944  -0.0409   1.8729
 5SC  H16   H   HCR6   0   0.315  -7.8247   1.4626  -0.7195
 5SC  H17   H   HCR6   0   0.296  -6.3441   1.0881  -2.6771
 5SC  H18   H   HCR6   0   0.282  -4.0752   0.0963  -2.3287
 5SC  H20   H   HCR6   0   0.252   1.9876  -5.6554   1.4138
 5SC  H21   H   HCR6   0   0.258   3.6454  -6.1030  -0.3408
 5SC  H22   H   HCR6   0   0.257   4.2351  -4.3181  -1.9694
 5SC  H23   H   HCR6   0   0.254   3.1296  -2.1222  -1.8123
 5SC  H251  H   HCH3   0   0.251  -0.4411  -3.6307   1.5762
 5SC  H252  H   HCH3   0   0.257   0.7863  -4.1348   2.7233
 5SC  H253  H   HCH3   0   0.251   0.6145  -2.4326   2.3064

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
 5SC  O26  N15   single    1.270  0.020  1.270
 5SC  N15  C16   aromatic  1.353  0.020  1.353
 5SC  N15  C14   aromatic  1.355  0.020  1.355
 5SC  C16  C17   aromatic  1.378  0.020  1.378
 5SC  C14  C13   aromatic  1.378  0.020  1.378
 5SC  C17  C18   aromatic  1.384  0.020  1.384
 5SC  C13  C18   aromatic  1.390  0.020  1.390
 5SC  C13  C12   single    1.502  0.020  1.502
 5SC  N04  C05   aromatic  1.323  0.020  1.323
 5SC  N04  N03   aromatic  1.338  0.020  1.338
 5SC  N10  C12   single    1.448  0.020  1.448
 5SC  N10  C09   single    1.333  0.020  1.333
 5SC  C05  C01   aromatic  1.396  0.020  1.396
 5SC  N03  C09   aromatic  1.362  0.020  1.362
 5SC  N03  C02   aromatic  1.376  0.020  1.376
 5SC  C09  C08   aromatic  1.384  0.020  1.384
 5SC  C01  C02   aromatic  1.390  0.020  1.390
 5SC  C01  BR24  single    1.854  0.020  1.854
 5SC  C02  N06   aromatic  1.332  0.020  1.332
 5SC  C08  C07   aromatic  1.406  0.020  1.406
 5SC  C07  N06   aromatic  1.320  0.020  1.320
 5SC  C07  C11   single    1.482  0.020  1.482
 5SC  C23  C22   aromatic  1.384  0.020  1.384
 5SC  C23  C11   aromatic  1.396  0.020  1.396
 5SC  C22  C21   aromatic  1.388  0.020  1.388
 5SC  C11  C19   aromatic  1.403  0.020  1.403
 5SC  C21  C20   aromatic  1.386  0.020  1.386
 5SC  C19  C20   aromatic  1.395  0.020  1.395
 5SC  C19  C25   single    1.504  0.020  1.504
 5SC  C05  H05   single    0.930  0.020  1.080
 5SC  C08  H08   single    0.930  0.020  1.080
 5SC  N10  HN10  single    0.860  0.020  1.020
 5SC  C12  H121  single    0.970  0.020  1.090
 5SC  C12  H122  single    0.970  0.020  1.090
 5SC  C14  H14   single    0.930  0.020  1.080
 5SC  C16  H16   single    0.930  0.020  1.080
 5SC  C17  H17   single    0.930  0.020  1.080
 5SC  C18  H18   single    0.930  0.020  1.080
 5SC  C20  H20   single    0.930  0.020  1.080
 5SC  C21  H21   single    0.930  0.020  1.080
 5SC  C22  H22   single    0.930  0.020  1.080
 5SC  C23  H23   single    0.930  0.020  1.080
 5SC  C25  H251  single    0.970  0.020  1.090
 5SC  C25  H252  single    0.970  0.020  1.090
 5SC  C25  H253  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
 5SC  BR24  C01  C05   128.51  3.000
 5SC  BR24  C01  C02   125.67  3.000
 5SC  C05   C01  C02   105.81  3.000
 5SC  N06   C02  N03   123.01  3.000
 5SC  N06   C02  C01   133.02  3.000
 5SC  N03   C02  C01   103.97  3.000
 5SC  C09   N03  N04   124.35  3.000
 5SC  C09   N03  C02   121.86  3.000
 5SC  N04   N03  C02   113.78  3.000
 5SC  C05   N04  N03   104.40  3.000
 5SC  H05   C05  N04   120.23  3.000
 5SC  H05   C05  C01   127.73  3.000
 5SC  N04   C05  C01   112.04  3.000
 5SC  C07   N06  C02   116.33  3.000
 5SC  C11   C07  C08   120.16  3.000
 5SC  C11   C07  N06   116.24  3.000
 5SC  C08   C07  N06   123.55  3.000
 5SC  H08   C08  C09   119.75  3.000
 5SC  H08   C08  C07   120.60  3.000
 5SC  C09   C08  C07   119.63  3.000
 5SC  N10   C09  C08   127.19  3.000
 5SC  C08   C09  N03   115.60  3.000
 5SC  N10   C09  N03   117.20  3.000
 5SC  HN10  N10  C12   118.72  3.000
 5SC  HN10  N10  C09   117.20  3.000
 5SC  C12   N10  C09   122.38  3.000
 5SC  C23   C11  C19   119.87  3.000
 5SC  C19   C11  C07   122.81  3.000
 5SC  C23   C11  C07   117.32  3.000
 5SC  H122  C12  H121  107.39  3.000
 5SC  H122  C12  C13   110.55  3.000
 5SC  H121  C12  C13   109.04  3.000
 5SC  H122  C12  N10   111.06  3.000
 5SC  H121  C12  N10   109.10  3.000
 5SC  C13   C12  N10   109.65  3.000
 5SC  C18   C13  C14   119.51  3.000
 5SC  C18   C13  C12   121.21  3.000
 5SC  C14   C13  C12   119.28  3.000
 5SC  H14   C14  N15   115.24  3.000
 5SC  H14   C14  C13   122.90  3.000
 5SC  N15   C14  C13   121.85  3.000
 5SC  O26   N15  C16   120.78  3.000
 5SC  C16   N15  C14   118.93  3.000
 5SC  O26   N15  C14   120.29  3.000
 5SC  H16   C16  C17   123.29  3.000
 5SC  H16   C16  N15   115.57  3.000
 5SC  C17   C16  N15   121.15  3.000
 5SC  H17   C17  C18   121.24  3.000
 5SC  H17   C17  C16   118.30  3.000
 5SC  C18   C17  C16   120.46  3.000
 5SC  H18   C18  C17   120.97  3.000
 5SC  H18   C18  C13   120.92  3.000
 5SC  C17   C18  C13   118.10  3.000
 5SC  C25   C19  C20   118.65  3.000
 5SC  C25   C19  C11   123.29  3.000
 5SC  C20   C19  C11   118.03  3.000
 5SC  H20   C20  C21   119.29  3.000
 5SC  H20   C20  C19   118.84  3.000
 5SC  C21   C20  C19   121.86  3.000
 5SC  H21   C21  C22   120.39  3.000
 5SC  H21   C21  C20   119.86  3.000
 5SC  C22   C21  C20   119.74  3.000
 5SC  H22   C22  C23   120.03  3.000
 5SC  H22   C22  C21   120.65  3.000
 5SC  C23   C22  C21   119.32  3.000
 5SC  H23   C23  C22   119.80  3.000
 5SC  H23   C23  C11   119.04  3.000
 5SC  C22   C23  C11   121.16  3.000
 5SC  H253  C25  H252  107.86  3.000
 5SC  H253  C25  H251  107.22  3.000
 5SC  H252  C25  H251  107.05  3.000
 5SC  H253  C25  C19   112.41  3.000
 5SC  H252  C25  C19   110.29  3.000
 5SC  H251  C25  C19   111.77  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
 5SC  CONST_01  N03   N04  C05  C01     0.00   0.0  0
 5SC  CONST_02  N04   N03  C02  C01     0.00   0.0  0
 5SC  CONST_03  C09   N03  C02  C01   180.00   0.0  0
 5SC  CONST_04  C07   N06  C02  C01   180.00   0.0  0
 5SC  CONST_05  C05   N04  N03  C02     0.00   0.0  0
 5SC  CONST_06  C08   C09  N03  C02     0.00   0.0  0
 5SC  CONST_07  N04   C05  C01  C02     0.00   0.0  0
 5SC  CONST_08  C08   C07  N06  C02     0.00   0.0  0
 5SC  CONST_09  C11   C07  N06  C02   180.00   0.0  0
 5SC  CONST_10  C07   C08  C09  N03     0.00   0.0  0
 5SC  CONST_11  C05   C01  C02  N03     0.00   0.0  0
 5SC  CONST_12  C07   N06  C02  N03     0.00   0.0  0
 5SC  CONST_13  C08   C09  N03  N04   180.00   0.0  0
 5SC  CONST_14  N06   C02  N03  N04   180.00   0.0  0
 5SC  CONST_15  C09   N03  N04  C05   180.00   0.0  0
 5SC  CONST_16  N06   C02  C01  C05   180.00   0.0  0
 5SC  CONST_17  C09   N03  C02  N06     0.00   0.0  0
 5SC  CONST_18  C09   C08  C07  N06     0.00   0.0  0
 5SC  CONST_21  C22   C23  C11  C07   180.00   0.0  0
 5SC  CONST_22  C20   C19  C11  C07   180.00   0.0  0
 5SC  CONST_25  C11   C07  C08  C09   180.00   0.0  0
 5SC  CONST_26  C21   C22  C23  C11     0.00   0.0  0
 5SC  CONST_27  C21   C20  C19  C11     0.00   0.0  0
 5SC  CONST_28  C16   N15  C14  C13     0.00   0.0  0
 5SC  CONST_29  C16   C17  C18  C13     0.00   0.0  0
 5SC  CONST_30  C17   C16  N15  C14     0.00   0.0  0
 5SC  CONST_31  C17   C18  C13  C14     0.00   0.0  0
 5SC  CONST_32  C18   C17  C16  N15     0.00   0.0  0
 5SC  CONST_33  C18   C13  C14  N15     0.00   0.0  0
 5SC  CONST_34  C22   C23  C11  C19     0.00   0.0  0
 5SC  CONST_35  C22   C21  C20  C19     0.00   0.0  0
 5SC  CONST_36  C23   C22  C21  C20     0.00   0.0  0
 5SC  CONST_37  C23   C11  C19  C20     0.00   0.0  0
 5SC  CONST_38  N10   C09  N03  C02   180.00   0.0  0
 5SC  CONST_39  BR24  C01  C02  N03   180.00   0.0  0
 5SC  CONST_40  BR24  C01  C05  N04   180.00   0.0  0
 5SC  CONST_41  N10   C09  N03  N04     0.00   0.0  0
 5SC  CONST_42  BR24  C01  C02  N06     0.00   0.0  0
 5SC  CONST_43  N10   C09  C08  C07   180.00   0.0  0
 5SC  CONST_44  C25   C19  C11  C07     0.00   0.0  0
 5SC  CONST_45  N15   C14  C13  C12   180.00   0.0  0
 5SC  CONST_46  C17   C18  C13  C12   180.00   0.0  0
 5SC  CONST_47  O26   N15  C14  C13   180.00   0.0  0
 5SC  CONST_48  O26   N15  C16  C17   180.00   0.0  0
 5SC  CONST_49  C25   C19  C20  C21   180.00   0.0  0
 5SC  CONST_50  C25   C19  C11  C23   180.00   0.0  0
 5SC  CONST_51  H05   C05  C01  C02   180.00   0.0  0
 5SC  CONST_52  H08   C08  C09  N03   180.00   0.0  0
 5SC  CONST_53  H23   C23  C11  C07     0.00   0.0  0
 5SC  CONST_54  H22   C22  C23  C11   180.00   0.0  0
 5SC  CONST_55  H20   C20  C19  C11   180.00   0.0  0
 5SC  CONST_56  H17   C17  C18  C13   180.00   0.0  0
 5SC  CONST_57  H16   C16  N15  C14   180.00   0.0  0
 5SC  CONST_58  H18   C18  C13  C14   180.00   0.0  0
 5SC  CONST_59  H14   C14  N15  C16   180.00   0.0  0
 5SC  CONST_60  H21   C21  C20  C19   180.00   0.0  0
 5SC  CONST_61  C12   N10  C09  N03   180.00   0.0  0
 5SC  CONST_62  C12   N10  C09  C08     0.00   0.0  0
 5SC  CONST_63  HN10  N10  C09  N03     0.00   0.0  0
 5SC  Var_01    C13   C12  N10  C09  -168.79  30.0  3
 5SC  Var_02    C14   C13  C12  N10  -108.08  30.0  2
 5SC  Var_03    H251  C25  C19  C11    85.57  30.0  2

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
 5SC  plan-1  C12   0.020
 5SC  plan-1  C13   0.020
 5SC  plan-1  C14   0.020
 5SC  plan-1  N15   0.020
 5SC  plan-1  C16   0.020
 5SC  plan-1  C17   0.020
 5SC  plan-1  C18   0.020
 5SC  plan-1  O26   0.020
 5SC  plan-1  H14   0.020
 5SC  plan-1  H16   0.020
 5SC  plan-1  H17   0.020
 5SC  plan-1  H18   0.020
 5SC  plan-2  C07   0.020
 5SC  plan-2  C11   0.020
 5SC  plan-2  C19   0.020
 5SC  plan-2  C20   0.020
 5SC  plan-2  C21   0.020
 5SC  plan-2  C22   0.020
 5SC  plan-2  C23   0.020
 5SC  plan-2  C25   0.020
 5SC  plan-2  H20   0.020
 5SC  plan-2  H21   0.020
 5SC  plan-2  H22   0.020
 5SC  plan-2  H23   0.020
 5SC  plan-3  C01   0.020
 5SC  plan-3  C02   0.020
 5SC  plan-3  N03   0.020
 5SC  plan-3  N04   0.020
 5SC  plan-3  C05   0.020
 5SC  plan-3  N06   0.020
 5SC  plan-3  C07   0.020
 5SC  plan-3  C08   0.020
 5SC  plan-3  C09   0.020
 5SC  plan-3  N10   0.020
 5SC  plan-3  C11   0.020
 5SC  plan-3  BR24  0.020
 5SC  plan-3  H05   0.020
 5SC  plan-3  H08   0.020
 5SC  plan-4  C09   0.020
 5SC  plan-4  N10   0.020
 5SC  plan-4  C12   0.020
 5SC  plan-4  HN10  0.020

