# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:34:49 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 3-bromo-6-(4-nitro-1H-pyrazol-3-yl)pyrazolo[1,5-a]pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1c[nH]nc1C2=CN3NC(=O)C(=C3N=C2)Br
#
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
 NY2  NY2  3-bromo-6-(4-nitro-1H-pyrazol-3-yl)pyrazolo[1,5-a]pyrimidin-2(1H)-one  ligand  24  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NY2
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
 NY2  O01  O   O      0  -0.391  -4.9408  -2.1990   0.8509
 NY2  N02  N   N      1   0.345  -3.9025  -1.6109   0.6433
 NY2  O03  O   O     -1  -0.393  -2.8093  -2.0289   0.9569
 NY2  C04  C   CR5    0  -0.028  -3.9767  -0.3488   0.0102
 NY2  C05  C   CR15   0   0.060  -5.1533   0.3057  -0.2966
 NY2  N06  N   NR15   0  -0.406  -4.7741   1.4768  -0.7875
 NY2  N07  N   N      0  -0.250  -3.4549   1.6412  -0.8389
 NY2  C08  C   CR5    0   0.253  -2.9322   0.5350  -0.3516
 NY2  C09  C   CR6    0  -0.124  -1.4815   0.3974  -0.2501
 NY2  C10  C   CR16   0  -0.025  -0.7802  -0.7335  -0.7341
 NY2  N11  N   N      0  -0.419   0.5178  -0.8599  -0.7013
 NY2  C12  C   CR56   0   0.677   1.2294   0.1428  -0.1732
 NY2  C13  C   CR5    0  -0.545   2.5752   0.3243   0.0245
 NY2  BR   BR  BR     0  -0.014   3.9185  -0.8695  -0.4009
 NY2  C15  C   CR5    0   0.599   2.7910   1.6037   0.6334
 NY2  O16  O   O      0  -0.486   3.8071   2.1700   1.0019
 NY2  N17  N   NR15   0  -0.509   1.5161   2.1478   0.7347
 NY2  N18  N   N      0  -0.332   0.5899   1.2795   0.2894
 NY2  C19  C   CR16   0   0.123  -0.7342   1.4284   0.2577
 NY2  H1   H   HCR5   0   0.337  -6.1865   0.0214  -0.1886
 NY2  H2   H   HNR5   0   0.448  -5.3804   2.2118  -1.1210
 NY2  H3   H   HCR6   0   0.287  -1.3304  -1.5492  -1.1864
 NY2  H5   H   HNR5   0   0.445   1.2397   2.9811   1.2347
 NY2  H6   H   HCR6   0   0.349  -1.1478   2.3494   0.6441

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
 NY2  O01  N02  double    1.211  0.020  1.211
 NY2  N02  C04  single    1.414  0.020  1.414
 NY2  N02  O03  single    1.212  0.020  1.212
 NY2  C05  C04  aromatic  1.381  0.020  1.381
 NY2  C05  N06  aromatic  1.325  0.020  1.325
 NY2  C04  C08  aromatic  1.415  0.020  1.415
 NY2  N06  N07  aromatic  1.330  0.020  1.330
 NY2  C08  N07  aromatic  1.317  0.020  1.317
 NY2  C08  C09  single    1.461  0.020  1.461
 NY2  C10  C09  single    1.416  0.020  1.416
 NY2  C10  N11  double    1.305  0.020  1.305
 NY2  C09  C19  double    1.371  0.020  1.371
 NY2  N11  C12  single    1.338  0.020  1.338
 NY2  C19  N18  single    1.333  0.020  1.333
 NY2  C12  N18  single    1.384  0.020  1.384
 NY2  C12  C13  double    1.372  0.020  1.372
 NY2  N18  N17  single    1.345  0.020  1.345
 NY2  C13  BR   single    1.847  0.020  1.847
 NY2  C13  C15  single    1.433  0.020  1.433
 NY2  N17  C15  single    1.390  0.020  1.390
 NY2  C15  O16  double    1.220  0.020  1.220
 NY2  C05  H1   single    0.930  0.020  1.080
 NY2  N06  H2   single    0.860  0.020  1.020
 NY2  C10  H3   single    0.930  0.020  1.080
 NY2  N17  H5   single    0.860  0.020  1.020
 NY2  C19  H6   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
 NY2  C04  N02  O03  118.11  3.000
 NY2  O03  N02  O01  124.16  3.000
 NY2  C04  N02  O01  117.72  3.000
 NY2  C08  C04  C05  106.03  3.000
 NY2  C08  C04  N02  129.28  3.000
 NY2  C05  C04  N02  124.56  3.000
 NY2  H1   C05  N06  123.02  3.000
 NY2  H1   C05  C04  132.07  3.000
 NY2  N06  C05  C04  104.91  3.000
 NY2  H2   N06  N07  119.52  3.000
 NY2  H2   N06  C05  126.44  3.000
 NY2  N07  N06  C05  114.03  3.000
 NY2  C08  N07  N06  105.99  3.000
 NY2  C09  C08  N07  119.93  3.000
 NY2  C09  C08  C04  131.02  3.000
 NY2  N07  C08  C04  109.04  3.000
 NY2  C19  C09  C10  117.21  3.000
 NY2  C19  C09  C08  119.76  3.000
 NY2  C10  C09  C08  122.91  3.000
 NY2  H3   C10  N11  116.30  3.000
 NY2  H3   C10  C09  119.52  3.000
 NY2  N11  C10  C09  124.17  3.000
 NY2  C12  N11  C10  117.80  3.000
 NY2  N18  C12  C13  107.24  3.000
 NY2  C13  C12  N11  132.64  3.000
 NY2  N18  C12  N11  120.12  3.000
 NY2  C15  C13  BR   124.43  3.000
 NY2  C15  C13  C12  109.08  3.000
 NY2  BR   C13  C12  126.49  3.000
 NY2  N17  C15  O16  124.07  3.000
 NY2  O16  C15  C13  131.91  3.000
 NY2  N17  C15  C13  104.02  3.000
 NY2  H5   N17  N18  120.52  3.000
 NY2  H5   N17  C15  127.58  3.000
 NY2  N18  N17  C15  110.77  3.000
 NY2  C19  N18  N17  128.29  3.000
 NY2  N17  N18  C12  108.83  3.000
 NY2  C19  N18  C12  122.88  3.000
 NY2  H6   C19  N18  117.83  3.000
 NY2  H6   C19  C09  124.37  3.000
 NY2  N18  C19  C09  117.80  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
 NY2  CONST_01  N07  N06  C05  C04    0.00   0.0  0
 NY2  CONST_02  N06  N07  C08  C04    0.00   0.0  0
 NY2  CONST_03  N07  C08  C04  C05    0.00   0.0  0
 NY2  CONST_04  C08  N07  N06  C05    0.00   0.0  0
 NY2  CONST_05  C08  C04  C05  N06    0.00   0.0  0
 NY2  CONST_06  C09  C08  C04  C05  180.00   0.0  0
 NY2  CONST_07  C09  C08  N07  N06  180.00   0.0  0
 NY2  CONST_08  N18  C12  N11  C10    0.00   0.0  0
 NY2  CONST_09  C13  C12  N11  C10  180.00   0.0  0
 NY2  CONST_10  C19  N18  C12  N11    0.00   0.0  0
 NY2  CONST_11  N17  N18  C12  N11  180.00   0.0  0
 NY2  CONST_12  C19  N18  C12  C13  180.00   0.0  0
 NY2  CONST_13  N17  N18  C12  C13    0.00   0.0  0
 NY2  CONST_14  N18  N17  C15  C13    0.00   0.0  0
 NY2  CONST_15  N06  C05  C04  N02  180.00   0.0  0
 NY2  CONST_16  N07  C08  C04  N02  180.00   0.0  0
 NY2  CONST_17  C09  C08  C04  N02    0.00   0.0  0
 NY2  CONST_18  N18  N17  C15  O16  180.00   0.0  0
 NY2  CONST_19  H2   N06  C05  C04  180.00   0.0  0
 NY2  CONST_20  H1   C05  N06  N07  180.00   0.0  0
 NY2  CONST_21  H5   N17  C15  C13  180.00   0.0  0
 NY2  CONST_22  C05  C04  N02  O01    0.00   0.0  0
 NY2  CONST_23  C08  C04  N02  O01  180.00   0.0  0
 NY2  CONST_24  C05  C04  N02  O03  180.00   0.0  0
 NY2  CONST_25  C08  C04  N02  O03    0.00   0.0  0
 NY2  Var_01    C10  C09  C08  C04   50.55  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
 NY2  plan-1  N02  0.020
 NY2  plan-1  C04  0.020
 NY2  plan-1  C05  0.020
 NY2  plan-1  N06  0.020
 NY2  plan-1  N07  0.020
 NY2  plan-1  C08  0.020
 NY2  plan-1  C09  0.020
 NY2  plan-1  H1   0.020
 NY2  plan-1  H2   0.020
 NY2  plan-2  C08  0.020
 NY2  plan-2  C09  0.020
 NY2  plan-2  C10  0.020
 NY2  plan-2  N11  0.020
 NY2  plan-2  C12  0.020
 NY2  plan-2  C13  0.020
 NY2  plan-2  BR   0.020
 NY2  plan-2  C15  0.020
 NY2  plan-2  O16  0.020
 NY2  plan-2  N17  0.020
 NY2  plan-2  N18  0.020
 NY2  plan-2  C19  0.020
 NY2  plan-2  H3   0.020
 NY2  plan-2  H5   0.020
 NY2  plan-2  H6   0.020
 NY2  plan-3  O01  0.020
 NY2  plan-3  N02  0.020
 NY2  plan-3  O03  0.020
 NY2  plan-3  C04  0.020

