# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 21:26:46 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-(2-chlorophenyl)-6-[(2S)-3,3,3-trifluoro-2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC1=NC(=O)c2cnn(c2N1)c3ccccc3Cl)C(F)(F)F
#
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
 BYE  BYE  1-(2-chlorophenyl)-6-[(2S)-3,3,3-trifluoro-2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  36  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYE
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
 BYE  C2   C   CR6   0  -0.060  -3.6271   0.8900   0.7666
 BYE  C3   C   CR16  0  -0.224  -4.2816   2.0954   0.9579
 BYE  C4   C   CR16  0  -0.243  -4.2110   3.0739  -0.0239
 BYE  C5   C   CR16  0  -0.251  -3.4926   2.8542  -1.1903
 BYE  F5   F   F     0  -0.309   6.0444   0.4470   0.5773
 BYE  C6   C   CR16  0  -0.271  -2.8520   1.6401  -1.3861
 BYE  F6   F   F     0  -0.316   4.6697   2.0394   1.0233
 BYE  C7   C   CR6   0   0.341  -2.9190   0.6569  -0.4095
 BYE  F7   F   F     0  -0.312   5.0171   1.4551  -1.0189
 BYE  N8   N   NR5   0  -0.477  -2.2490  -0.5699  -0.6024
 BYE  N9   N   N     0  -0.251  -2.9237  -1.7169  -0.8632
 BYE  C10  C   CR15  0  -0.068  -2.0182  -2.6508  -0.9929
 BYE  C11  C   CR56  0   0.730  -0.9295  -0.7945  -0.5659
 BYE  C12  C   CR56  0  -0.359  -0.7150  -2.1319  -0.8102
 BYE  N13  N   NR16  0  -0.717   0.0861   0.0673  -0.3341
 BYE  C14  C   CR6   0   0.539   1.3491  -0.4399  -0.3808
 BYE  N15  N   N     0  -0.495   1.6214  -1.6788  -0.6097
 BYE  C16  C   CR6   0   0.448   0.6355  -2.6359  -0.8306
 BYE  O17  O   O     0  -0.455   0.9363  -3.8005  -1.0325
 BYE  C18  C   CH2   0  -0.573   2.4403   0.5715  -0.1943
 BYE  C19  C   CH1   0  -0.467   3.7429  -0.0358   0.3237
 BYE  C20  C   CH3   0  -0.681   3.5936  -0.5447   1.7556
 BYE  C21  C   CT    0   1.034   4.8640   0.9764   0.2261
 BYE  CL1  CL  CL    0  -0.086  -3.6721  -0.3188   1.9927
 BYE  H1   H   HCR6  0   0.292  -4.8361   2.2716   1.8693
 BYE  H2   H   HCR6  0   0.281  -4.7192   4.0158   0.1326
 BYE  H3   H   HCR6  0   0.279  -3.4370   3.6200  -1.9509
 BYE  H4   H   HCR6  0   0.293  -2.3051   1.4448  -2.2997
 BYE  H5   H   HCR5  0   0.286  -2.3076  -3.6665  -1.2130
 BYE  H6   H   HNR6  0   0.443  -0.0698   1.0464  -0.1356
 BYE  H7   H   HCH2  0   0.317   2.5839   1.0423  -1.1721
 BYE  H8   H   HCH2  0   0.286   2.0921   1.3586   0.4792
 BYE  H9   H   HCH1  0   0.296   4.0236  -0.8684  -0.3270
 BYE  H10  H   HCH3  0   0.254   4.5245  -0.9561   2.1426
 BYE  H11  H   HCH3  0   0.239   3.2596   0.2458   2.4283
 BYE  H12  H   HCH3  0   0.257   2.8549  -1.3432   1.7880

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
 BYE  C4   C3   aromatic  1.388  0.020  1.388
 BYE  C4   C5   aromatic  1.387  0.020  1.387
 BYE  F6   C21  single    1.343  0.020  1.343
 BYE  C3   C2   aromatic  1.385  0.020  1.385
 BYE  F7   C21  single    1.343  0.020  1.343
 BYE  C5   C6   aromatic  1.387  0.020  1.387
 BYE  C21  F5   single    1.341  0.020  1.341
 BYE  C21  C19  single    1.514  0.020  1.514
 BYE  C2   CL1  single    1.722  0.020  1.722
 BYE  C2   C7   aromatic  1.393  0.020  1.393
 BYE  C6   C7   aromatic  1.387  0.020  1.387
 BYE  C19  C18  single    1.528  0.020  1.528
 BYE  C19  C20  single    1.527  0.020  1.527
 BYE  C7   N8   single    1.411  0.020  1.411
 BYE  C18  C14  single    1.500  0.020  1.500
 BYE  N13  C14  single    1.362  0.020  1.362
 BYE  N13  C11  single    1.352  0.020  1.352
 BYE  C14  N15  double    1.289  0.020  1.289
 BYE  N8   C11  aromatic  1.339  0.020  1.339
 BYE  N8   N9   aromatic  1.356  0.020  1.356
 BYE  C11  C12  aromatic  1.376  0.020  1.376
 BYE  N9   C10  aromatic  1.307  0.020  1.307
 BYE  N15  C16  single    1.392  0.020  1.392
 BYE  C12  C10  aromatic  1.415  0.020  1.415
 BYE  C12  C16  single    1.442  0.020  1.442
 BYE  C16  O17  double    1.220  0.020  1.220
 BYE  C3   H1   single    0.930  0.020  1.080
 BYE  C4   H2   single    0.930  0.020  1.080
 BYE  C5   H3   single    0.930  0.020  1.080
 BYE  C6   H4   single    0.930  0.020  1.080
 BYE  C10  H5   single    0.930  0.020  1.080
 BYE  N13  H6   single    0.860  0.020  1.020
 BYE  C18  H7   single    0.970  0.020  1.090
 BYE  C18  H8   single    0.970  0.020  1.090
 BYE  C19  H9   single    0.970  0.020  1.090
 BYE  C20  H10  single    0.970  0.020  1.090
 BYE  C20  H11  single    0.970  0.020  1.090
 BYE  C20  H12  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
 BYE  CL1  C2   C7   119.81  3.000
 BYE  C7   C2   C3   120.18  3.000
 BYE  CL1  C2   C3   120.01  3.000
 BYE  H1   C3   C4   120.49  3.000
 BYE  H1   C3   C2   120.04  3.000
 BYE  C4   C3   C2   119.47  3.000
 BYE  H2   C4   C5   120.19  3.000
 BYE  H2   C4   C3   119.19  3.000
 BYE  C5   C4   C3   120.62  3.000
 BYE  H3   C5   C6   119.81  3.000
 BYE  H3   C5   C4   120.41  3.000
 BYE  C6   C5   C4   119.78  3.000
 BYE  H4   C6   C7   119.37  3.000
 BYE  H4   C6   C5   120.70  3.000
 BYE  C7   C6   C5   119.92  3.000
 BYE  N8   C7   C6   119.80  3.000
 BYE  N8   C7   C2   120.16  3.000
 BYE  C6   C7   C2   120.03  3.000
 BYE  C11  N8   N9   110.72  3.000
 BYE  N9   N8   C7   121.70  3.000
 BYE  C11  N8   C7   127.59  3.000
 BYE  C10  N9   N8   106.18  3.000
 BYE  H5   C10  C12  128.23  3.000
 BYE  H5   C10  N9   120.46  3.000
 BYE  C12  C10  N9   111.31  3.000
 BYE  N13  C11  C12  122.19  3.000
 BYE  C12  C11  N8   108.16  3.000
 BYE  N13  C11  N8   129.65  3.000
 BYE  C16  C12  C11  119.22  3.000
 BYE  C16  C12  C10  137.14  3.000
 BYE  C11  C12  C10  103.64  3.000
 BYE  H6   N13  C14  120.69  3.000
 BYE  H6   N13  C11  122.35  3.000
 BYE  C14  N13  C11  116.96  3.000
 BYE  C18  C14  N15  121.11  3.000
 BYE  N15  C14  N13  124.05  3.000
 BYE  C18  C14  N13  114.80  3.000
 BYE  C16  N15  C14  122.65  3.000
 BYE  O17  C16  N15  120.54  3.000
 BYE  O17  C16  C12  124.56  3.000
 BYE  N15  C16  C12  114.90  3.000
 BYE  H8   C18  H7   106.41  3.000
 BYE  H8   C18  C19  110.43  3.000
 BYE  H7   C18  C19  111.23  3.000
 BYE  H8   C18  C14  109.30  3.000
 BYE  H7   C18  C14  105.93  3.000
 BYE  C19  C18  C14  113.24  3.000
 BYE  H9   C19  C21  106.31  3.000
 BYE  H9   C19  C20  109.23  3.000
 BYE  C21  C19  C20  110.84  3.000
 BYE  H9   C19  C18  108.65  3.000
 BYE  C20  C19  C18  111.54  3.000
 BYE  C21  C19  C18  110.11  3.000
 BYE  H12  C20  H11  107.80  3.000
 BYE  H12  C20  H10  107.01  3.000
 BYE  H11  C20  H10  108.45  3.000
 BYE  H12  C20  C19  109.81  3.000
 BYE  H11  C20  C19  111.52  3.000
 BYE  H10  C20  C19  112.06  3.000
 BYE  C19  C21  F7   112.50  3.000
 BYE  C19  C21  F6   112.58  3.000
 BYE  F7   C21  F6   106.55  3.000
 BYE  C19  C21  F5   111.79  3.000
 BYE  F7   C21  F5   106.46  3.000
 BYE  F6   C21  F5   106.52  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
 BYE  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 BYE  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 BYE  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 BYE  CONST_06  C6   C7   C2   C3     0.00   0.0  0
 BYE  CONST_07  N8   C7   C2   C3   180.00   0.0  0
 BYE  CONST_08  C7   C2   C3   C4     0.00   0.0  0
 BYE  CONST_09  C7   C6   C5   C4     0.00   0.0  0
 BYE  CONST_10  N8   C7   C6   C5   180.00   0.0  0
 BYE  CONST_13  C12  C11  N8   C7   180.00   0.0  0
 BYE  CONST_14  C10  N9   N8   C7   180.00   0.0  0
 BYE  CONST_15  C10  C12  C11  N8     0.00   0.0  0
 BYE  CONST_16  C12  C10  N9   N8     0.00   0.0  0
 BYE  CONST_17  C12  C11  N8   N9     0.00   0.0  0
 BYE  CONST_18  C11  C12  C10  N9     0.00   0.0  0
 BYE  CONST_19  C11  N8   N9   C10    0.00   0.0  0
 BYE  CONST_20  N13  C11  N8   C7     0.00   0.0  0
 BYE  CONST_21  N15  C14  N13  C11    0.00   0.0  0
 BYE  CONST_22  C16  N15  C14  N13    0.00   0.0  0
 BYE  CONST_23  CL1  C2   C3   C4   180.00   0.0  0
 BYE  CONST_24  CL1  C2   C7   C6   180.00   0.0  0
 BYE  CONST_25  CL1  C2   C7   N8     0.00   0.0  0
 BYE  CONST_26  C18  C14  N13  C11  180.00   0.0  0
 BYE  CONST_27  C18  C14  N15  C16  180.00   0.0  0
 BYE  CONST_28  H2   C4   C3   C2   180.00   0.0  0
 BYE  CONST_29  H4   C6   C7   C2   180.00   0.0  0
 BYE  CONST_30  H3   C5   C4   C3   180.00   0.0  0
 BYE  CONST_31  H1   C3   C4   C5   180.00   0.0  0
 BYE  CONST_32  H5   C10  N9   N8   180.00   0.0  0
 BYE  CONST_33  H6   N13  C14  N15  180.00   0.0  0
 BYE  Var_01    C19  C18  C14  N13  155.95  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BYE  chir_01  C19  C21  C18  C20  positiv

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
 BYE  plan-1  C2   0.020
 BYE  plan-1  C3   0.020
 BYE  plan-1  C4   0.020
 BYE  plan-1  C5   0.020
 BYE  plan-1  C6   0.020
 BYE  plan-1  C7   0.020
 BYE  plan-1  N8   0.020
 BYE  plan-1  CL1  0.020
 BYE  plan-1  H1   0.020
 BYE  plan-1  H2   0.020
 BYE  plan-1  H3   0.020
 BYE  plan-1  H4   0.020
 BYE  plan-2  C7   0.020
 BYE  plan-2  N8   0.020
 BYE  plan-2  N9   0.020
 BYE  plan-2  C10  0.020
 BYE  plan-2  C11  0.020
 BYE  plan-2  C12  0.020
 BYE  plan-2  N13  0.020
 BYE  plan-2  C14  0.020
 BYE  plan-2  N15  0.020
 BYE  plan-2  C16  0.020
 BYE  plan-2  O17  0.020
 BYE  plan-2  C18  0.020
 BYE  plan-2  H5   0.020
 BYE  plan-2  H6   0.020

