# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 11:47:29 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-phenyl-2,5-dihydropyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=Nc2n[nH]c(c3ccccc3)c12
#
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
 QYB  QYB  3-phenyl-2,5-dihydropyrazolo[3,4-d]pyrimidin-4-one  ligand  24  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QYB
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
 QYB  C1   C  CR6   0   0.514  -21.6992  23.3237  -26.7696
 QYB  N1   N  NR16  0  -0.669  -22.4505  22.1800  -26.5205
 QYB  O1   O  O     0  -0.439  -20.5043  23.3558  -26.5472
 QYB  C2   C  CR16  0   0.145  -23.7847  22.0442  -26.7587
 QYB  N2   N  N     0  -0.440  -24.5516  22.9465  -27.2532
 QYB  C3   C  CR56  0   0.372  -23.9099  24.1188  -27.5388
 QYB  N3   N  NR15  0  -0.488  -23.5227  26.0588  -28.2056
 QYB  C4   C  CR56  0  -0.384  -22.5370  24.3647  -27.3019
 QYB  N4   N  N     0  -0.273  -24.5011  25.1617  -28.0878
 QYB  C5   C  CR5   0   0.462  -22.3233  25.6608  -27.7598
 QYB  C6   C  CR6   0   0.038  -21.1380  26.5135  -27.8225
 QYB  C7   C  CR16  0  -0.283  -20.2445  26.5604  -26.7524
 QYB  C8   C  CR16  0  -0.241  -19.1311  27.3835  -26.8105
 QYB  C9   C  CR16  0  -0.251  -18.8952  28.1646  -27.9347
 QYB  C10  C  CR16  0  -0.241  -19.7808  28.1216  -29.0028
 QYB  C11  C  CR16  0  -0.291  -20.8967  27.3006  -28.9493
 QYB  H1   H  HNR6  0   0.430  -21.9596  21.3818  -26.1391
 QYB  H2   H  HCR6  0   0.298  -24.1922  21.0755  -26.4963
 QYB  H3   H  HNR5  0   0.434  -23.7433  26.9712  -28.5802
 QYB  H4   H  HCR6  0   0.257  -20.4285  25.9663  -25.8684
 QYB  H5   H  HCR6  0   0.262  -18.4477  27.4170  -25.9723
 QYB  H6   H  HCR6  0   0.262  -18.0237  28.8047  -27.9777
 QYB  H7   H  HCR6  0   0.263  -19.6000  28.7230  -29.8839
 QYB  H8   H  HCR6  0   0.263  -21.5689  27.2611  -29.7978

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
 QYB  N3   N4   aromatic  1.333  0.020  1.333
 QYB  N3   C5   aromatic  1.340  0.020  1.340
 QYB  C10  C11  aromatic  1.386  0.020  1.386
 QYB  C10  C9   aromatic  1.388  0.020  1.388
 QYB  N4   C3   aromatic  1.318  0.020  1.318
 QYB  C11  C6   aromatic  1.395  0.020  1.395
 QYB  C9   C8   aromatic  1.389  0.020  1.389
 QYB  C5   C6   single    1.461  0.020  1.461
 QYB  C5   C4   aromatic  1.391  0.020  1.391
 QYB  C6   C7   aromatic  1.395  0.020  1.395
 QYB  C3   N2   single    1.367  0.020  1.367
 QYB  C3   C4   aromatic  1.415  0.020  1.415
 QYB  N2   C2   double    1.283  0.020  1.283
 QYB  C4   C1   single    1.438  0.020  1.438
 QYB  C8   C7   aromatic  1.386  0.020  1.386
 QYB  C2   N1   single    1.362  0.020  1.362
 QYB  C1   N1   single    1.391  0.020  1.391
 QYB  C1   O1   double    1.216  0.020  1.216
 QYB  N1   H1   single    0.860  0.020  1.020
 QYB  C2   H2   single    0.930  0.020  1.080
 QYB  N3   H3   single    0.860  0.020  1.020
 QYB  C7   H4   single    0.930  0.020  1.080
 QYB  C8   H5   single    0.930  0.020  1.080
 QYB  C9   H6   single    0.930  0.020  1.080
 QYB  C10  H7   single    0.930  0.020  1.080
 QYB  C11  H8   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
 QYB  C4   C1   O1   128.39  3.000
 QYB  O1   C1   N1   121.32  3.000
 QYB  C4   C1   N1   110.29  3.000
 QYB  H1   N1   C2   117.55  3.000
 QYB  H1   N1   C1   117.01  3.000
 QYB  C2   N1   C1   125.44  3.000
 QYB  H2   C2   N2   119.82  3.000
 QYB  H2   C2   N1   114.54  3.000
 QYB  N2   C2   N1   125.64  3.000
 QYB  C3   N2   C2   113.77  3.000
 QYB  N4   C3   C4   111.55  3.000
 QYB  C4   C3   N2   124.73  3.000
 QYB  N4   C3   N2   123.71  3.000
 QYB  H3   N3   C5   125.93  3.000
 QYB  H3   N3   N4   118.71  3.000
 QYB  C5   N3   N4   115.32  3.000
 QYB  C5   C4   C3   104.83  3.000
 QYB  C3   C4   C1   120.09  3.000
 QYB  C5   C4   C1   134.96  3.000
 QYB  N3   N4   C3   103.89  3.000
 QYB  C6   C5   C4   133.03  3.000
 QYB  C4   C5   N3   104.40  3.000
 QYB  C6   C5   N3   122.57  3.000
 QYB  C11  C6   C7   119.32  3.000
 QYB  C7   C6   C5   120.41  3.000
 QYB  C11  C6   C5   120.26  3.000
 QYB  H4   C7   C8   119.84  3.000
 QYB  H4   C7   C6   119.99  3.000
 QYB  C8   C7   C6   120.16  3.000
 QYB  H5   C8   C9   120.15  3.000
 QYB  H5   C8   C7   119.56  3.000
 QYB  C9   C8   C7   120.29  3.000
 QYB  H6   C9   C10  120.10  3.000
 QYB  H6   C9   C8   120.10  3.000
 QYB  C10  C9   C8   119.80  3.000
 QYB  H7   C10  C11  119.67  3.000
 QYB  H7   C10  C9   120.18  3.000
 QYB  C11  C10  C9   120.14  3.000
 QYB  H8   C11  C10  119.39  3.000
 QYB  H8   C11  C6   120.31  3.000
 QYB  C10  C11  C6   120.29  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
 QYB  CONST_01  C5   N3   N4   C3    0.00  0.0  0
 QYB  CONST_02  N3   C5   C4   C3    0.00  0.0  0
 QYB  CONST_03  C6   C5   C4   C3  180.00  0.0  0
 QYB  CONST_04  C4   C3   N4   N3    0.00  0.0  0
 QYB  CONST_07  N4   N3   C5   C4    0.00  0.0  0
 QYB  CONST_10  C6   C5   N3   N4  180.00  0.0  0
 QYB  CONST_11  C5   C4   C3   N4    0.00  0.0  0
 QYB  CONST_12  C10  C11  C6   C5  180.00  0.0  0
 QYB  CONST_13  C8   C7   C6   C5  180.00  0.0  0
 QYB  CONST_14  C9   C10  C11  C6    0.00  0.0  0
 QYB  CONST_15  C9   C8   C7   C6    0.00  0.0  0
 QYB  CONST_16  C10  C11  C6   C7    0.00  0.0  0
 QYB  CONST_17  C10  C9   C8   C7    0.00  0.0  0
 QYB  CONST_18  C11  C10  C9   C8    0.00  0.0  0
 QYB  CONST_19  C11  C6   C7   C8    0.00  0.0  0
 QYB  CONST_20  C6   C5   C4   C1    0.00  0.0  0
 QYB  CONST_21  N2   C2   N1   C1    0.00  0.0  0
 QYB  CONST_22  C3   N2   C2   N1    0.00  0.0  0
 QYB  CONST_23  C4   C1   N1   C2    0.00  0.0  0
 QYB  CONST_24  C2   N1   C1   O1  180.00  0.0  0
 QYB  CONST_25  H3   N3   N4   C3  180.00  0.0  0
 QYB  CONST_26  H8   C11  C6   C5    0.00  0.0  0
 QYB  CONST_27  H4   C7   C6   C5    0.00  0.0  0
 QYB  CONST_28  H7   C10  C11  C6  180.00  0.0  0
 QYB  CONST_29  H5   C8   C7   C6  180.00  0.0  0
 QYB  CONST_30  H6   C9   C8   C7  180.00  0.0  0
 QYB  CONST_31  H2   C2   N1   C1  180.00  0.0  0
 QYB  CONST_32  H1   N1   C2   N2  180.00  0.0  0

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
 QYB  plan-1  C5   0.020
 QYB  plan-1  C6   0.020
 QYB  plan-1  C7   0.020
 QYB  plan-1  C8   0.020
 QYB  plan-1  C9   0.020
 QYB  plan-1  C10  0.020
 QYB  plan-1  C11  0.020
 QYB  plan-1  H4   0.020
 QYB  plan-1  H5   0.020
 QYB  plan-1  H6   0.020
 QYB  plan-1  H7   0.020
 QYB  plan-1  H8   0.020
 QYB  plan-2  C1   0.020
 QYB  plan-2  N1   0.020
 QYB  plan-2  O1   0.020
 QYB  plan-2  C2   0.020
 QYB  plan-2  N2   0.020
 QYB  plan-2  C3   0.020
 QYB  plan-2  N3   0.020
 QYB  plan-2  C4   0.020
 QYB  plan-2  N4   0.020
 QYB  plan-2  C5   0.020
 QYB  plan-2  C6   0.020
 QYB  plan-2  H1   0.020
 QYB  plan-2  H2   0.020
 QYB  plan-2  H3   0.020

