# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 13:49:19 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-(2-chlorophenyl)-6-[(2R)-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
 PDB  PDB  1-(2-chlorophenyl)-6-[(2R)-3,3,3-trifluoro-2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  36  24  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PDB
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
 PDB  C2   C   CR6   0  -0.058  -3.6962   1.0616   0.4926
 PDB  C3   C   CR16  0  -0.225  -4.3163   2.2970   0.4049
 PDB  C4   C   CR16  0  -0.242  -4.1061   3.0879  -0.7160
 PDB  C5   C   CR16  0  -0.251  -3.2860   2.6512  -1.7461
 PDB  F5   F   F     0  -0.316   4.7077   2.1668   0.2672
 PDB  C6   C   CR16  0  -0.270  -2.6778   1.4081  -1.6618
 PDB  F6   F   F     0  -0.309   6.0462   0.4826   0.2231
 PDB  C7   C   CR6   0   0.339  -2.8833   0.6120  -0.5446
 PDB  F7   F   F     0  -0.312   4.8453   0.8543   1.9662
 PDB  N8   N   NR5   0  -0.477  -2.2426  -0.6420  -0.4516
 PDB  N9   N   N     0  -0.251  -2.9246  -1.8047  -0.5983
 PDB  C10  C   CR15  0  -0.069  -2.0501  -2.7630  -0.4355
 PDB  C11  C   CR56  0   0.729  -0.9509  -0.8804  -0.1921
 PDB  C12  C   CR56  0  -0.358  -0.7614  -2.2433  -0.1715
 PDB  N13  N   NR16  0  -0.718   0.0610  -0.0087   0.0208
 PDB  C14  C   CR6   0   0.534   1.2891  -0.5389   0.2691
 PDB  N15  N   N     0  -0.491   1.5380  -1.8037   0.3004
 PDB  C16  C   CR6   0   0.447   0.5580  -2.7674   0.0835
 PDB  O17  O   O     0  -0.455   0.8359  -3.9543   0.1166
 PDB  C18  C   CH2   0  -0.572   2.3693   0.4590   0.5652
 PDB  C19  C   CH1   0  -0.469   3.7360   0.0086   0.0460
 PDB  C20  C   CH3   0  -0.679   3.7779   0.0076  -1.4799
 PDB  C21  C   CT    0   1.034   4.8298   0.8779   0.6243
 PDB  CL1  CL  CL    0  -0.086  -3.9152   0.0846   1.8937
 PDB  H1   H   HCR6  0   0.293  -4.9501   2.6426   1.2097
 PDB  H2   H   HCR6  0   0.281  -4.5881   4.0541  -0.7781
 PDB  H3   H   HCR6  0   0.278  -3.1249   3.2723  -2.6161
 PDB  H4   H   HCR6  0   0.293  -2.0469   1.0454  -2.4632
 PDB  H5   H   HCR5  0   0.285  -2.3510  -3.7963  -0.5118
 PDB  H6   H   HNR6  0   0.443  -0.0729   0.9931   0.0001
 PDB  H7   H   HCH2  0   0.285   2.0997   1.4281   0.1405
 PDB  H8   H   HCH2  0   0.317   2.3780   0.5850   1.6521
 PDB  H9   H   HCH1  0   0.299   3.9244  -1.0058   0.4072
 PDB  H10  H   HCH3  0   0.255   3.0354  -0.6890  -1.8654
 PDB  H11  H   HCH3  0   0.241   3.5535   0.9920  -1.8919
 PDB  H12  H   HCH3  0   0.256   4.7448  -0.3143  -1.8631

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
 PDB  C4   C3   aromatic  1.388  0.020  1.388
 PDB  C4   C5   aromatic  1.387  0.020  1.387
 PDB  C3   C2   aromatic  1.385  0.020  1.385
 PDB  C5   C6   aromatic  1.386  0.020  1.386
 PDB  C20  C19  single    1.527  0.020  1.527
 PDB  C2   CL1  single    1.722  0.020  1.722
 PDB  C2   C7   aromatic  1.392  0.020  1.392
 PDB  C6   C7   aromatic  1.387  0.020  1.387
 PDB  C7   N8   single    1.411  0.020  1.411
 PDB  C19  C18  single    1.530  0.020  1.530
 PDB  C19  C21  single    1.512  0.020  1.512
 PDB  C18  C14  single    1.500  0.020  1.500
 PDB  F7   C21  single    1.342  0.020  1.342
 PDB  N13  C14  single    1.361  0.020  1.361
 PDB  N13  C11  single    1.352  0.020  1.352
 PDB  C21  F6   single    1.341  0.020  1.341
 PDB  C21  F5   single    1.343  0.020  1.343
 PDB  N8   C11  aromatic  1.339  0.020  1.339
 PDB  N8   N9   aromatic  1.356  0.020  1.356
 PDB  C14  N15  double    1.289  0.020  1.289
 PDB  C11  C12  aromatic  1.376  0.020  1.376
 PDB  N9   C10  aromatic  1.308  0.020  1.308
 PDB  N15  C16  single    1.391  0.020  1.391
 PDB  C12  C10  aromatic  1.414  0.020  1.414
 PDB  C12  C16  single    1.442  0.020  1.442
 PDB  C16  O17  double    1.219  0.020  1.219
 PDB  C3   H1   single    0.930  0.020  1.080
 PDB  C4   H2   single    0.930  0.020  1.080
 PDB  C5   H3   single    0.930  0.020  1.080
 PDB  C6   H4   single    0.930  0.020  1.080
 PDB  C10  H5   single    0.930  0.020  1.080
 PDB  N13  H6   single    0.860  0.020  1.020
 PDB  C18  H7   single    0.970  0.020  1.090
 PDB  C18  H8   single    0.970  0.020  1.090
 PDB  C19  H9   single    0.970  0.020  1.090
 PDB  C20  H10  single    0.970  0.020  1.090
 PDB  C20  H11  single    0.970  0.020  1.090
 PDB  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
 PDB  CL1  C2   C7   119.81  3.000
 PDB  C7   C2   C3   120.15  3.000
 PDB  CL1  C2   C3   120.04  3.000
 PDB  H1   C3   C4   120.52  3.000
 PDB  H1   C3   C2   120.03  3.000
 PDB  C4   C3   C2   119.45  3.000
 PDB  H2   C4   C5   120.13  3.000
 PDB  H2   C4   C3   119.21  3.000
 PDB  C5   C4   C3   120.66  3.000
 PDB  H3   C5   C6   119.92  3.000
 PDB  H3   C5   C4   120.32  3.000
 PDB  C6   C5   C4   119.76  3.000
 PDB  H4   C6   C7   119.36  3.000
 PDB  H4   C6   C5   120.73  3.000
 PDB  C7   C6   C5   119.91  3.000
 PDB  N8   C7   C6   119.72  3.000
 PDB  N8   C7   C2   120.19  3.000
 PDB  C6   C7   C2   120.07  3.000
 PDB  C11  N8   N9   110.71  3.000
 PDB  N9   N8   C7   121.77  3.000
 PDB  C11  N8   C7   127.51  3.000
 PDB  C10  N9   N8   106.17  3.000
 PDB  H5   C10  C12  128.26  3.000
 PDB  H5   C10  N9   120.43  3.000
 PDB  C12  C10  N9   111.31  3.000
 PDB  N13  C11  C12  122.20  3.000
 PDB  C12  C11  N8   108.18  3.000
 PDB  N13  C11  N8   129.61  3.000
 PDB  C16  C12  C11  119.24  3.000
 PDB  C16  C12  C10  137.13  3.000
 PDB  C11  C12  C10  103.63  3.000
 PDB  H6   N13  C14  120.63  3.000
 PDB  H6   N13  C11  122.44  3.000
 PDB  C14  N13  C11  116.93  3.000
 PDB  C18  C14  N15  120.58  3.000
 PDB  N15  C14  N13  124.12  3.000
 PDB  C18  C14  N13  115.27  3.000
 PDB  C16  N15  C14  122.66  3.000
 PDB  O17  C16  N15  120.62  3.000
 PDB  O17  C16  C12  124.54  3.000
 PDB  N15  C16  C12  114.84  3.000
 PDB  H8   C18  H7   106.63  3.000
 PDB  H8   C18  C19  111.34  3.000
 PDB  H7   C18  C19  110.48  3.000
 PDB  H8   C18  C14  106.16  3.000
 PDB  H7   C18  C14  109.62  3.000
 PDB  C19  C18  C14  112.36  3.000
 PDB  H9   C19  C21  106.41  3.000
 PDB  H9   C19  C20  108.96  3.000
 PDB  C21  C19  C20  111.28  3.000
 PDB  H9   C19  C18  108.36  3.000
 PDB  C21  C19  C18  110.31  3.000
 PDB  C20  C19  C18  111.35  3.000
 PDB  H12  C20  H11  108.47  3.000
 PDB  H12  C20  H10  106.98  3.000
 PDB  H11  C20  H10  107.67  3.000
 PDB  H12  C20  C19  112.11  3.000
 PDB  H11  C20  C19  111.80  3.000
 PDB  H10  C20  C19  109.61  3.000
 PDB  C19  C21  F7   112.37  3.000
 PDB  F7   C21  F6   106.48  3.000
 PDB  C19  C21  F6   111.86  3.000
 PDB  F6   C21  F5   106.61  3.000
 PDB  F7   C21  F5   106.49  3.000
 PDB  C19  C21  F5   112.60  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
 PDB  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 PDB  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 PDB  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 PDB  CONST_06  C6   C7   C2   C3      0.00   0.0  0
 PDB  CONST_07  N8   C7   C2   C3    180.00   0.0  0
 PDB  CONST_08  C7   C2   C3   C4      0.00   0.0  0
 PDB  CONST_09  C7   C6   C5   C4      0.00   0.0  0
 PDB  CONST_10  N8   C7   C6   C5    180.00   0.0  0
 PDB  CONST_13  C12  C11  N8   C7    180.00   0.0  0
 PDB  CONST_14  C10  N9   N8   C7    180.00   0.0  0
 PDB  CONST_15  C10  C12  C11  N8      0.00   0.0  0
 PDB  CONST_16  C12  C10  N9   N8      0.00   0.0  0
 PDB  CONST_17  C12  C11  N8   N9      0.00   0.0  0
 PDB  CONST_18  C11  C12  C10  N9      0.00   0.0  0
 PDB  CONST_19  C11  N8   N9   C10     0.00   0.0  0
 PDB  CONST_20  N13  C11  N8   C7      0.00   0.0  0
 PDB  CONST_21  N15  C14  N13  C11     0.00   0.0  0
 PDB  CONST_22  C16  N15  C14  N13     0.00   0.0  0
 PDB  CONST_23  CL1  C2   C3   C4    180.00   0.0  0
 PDB  CONST_24  CL1  C2   C7   C6    180.00   0.0  0
 PDB  CONST_25  CL1  C2   C7   N8      0.00   0.0  0
 PDB  CONST_26  C18  C14  N13  C11   180.00   0.0  0
 PDB  CONST_27  C18  C14  N15  C16   180.00   0.0  0
 PDB  CONST_28  H2   C4   C3   C2    180.00   0.0  0
 PDB  CONST_29  H4   C6   C7   C2    180.00   0.0  0
 PDB  CONST_30  H3   C5   C4   C3    180.00   0.0  0
 PDB  CONST_31  H1   C3   C4   C5    180.00   0.0  0
 PDB  CONST_32  H5   C10  N9   N8    180.00   0.0  0
 PDB  CONST_33  H6   N13  C14  N15   180.00   0.0  0
 PDB  Var_01    C19  C18  C14  N13  -146.43  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
 PDB  chir_01  C19  C20  C18  C21  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
 PDB  plan-1  C2   0.020
 PDB  plan-1  C3   0.020
 PDB  plan-1  C4   0.020
 PDB  plan-1  C5   0.020
 PDB  plan-1  C6   0.020
 PDB  plan-1  C7   0.020
 PDB  plan-1  N8   0.020
 PDB  plan-1  CL1  0.020
 PDB  plan-1  H1   0.020
 PDB  plan-1  H2   0.020
 PDB  plan-1  H3   0.020
 PDB  plan-1  H4   0.020
 PDB  plan-2  C7   0.020
 PDB  plan-2  N8   0.020
 PDB  plan-2  N9   0.020
 PDB  plan-2  C10  0.020
 PDB  plan-2  C11  0.020
 PDB  plan-2  C12  0.020
 PDB  plan-2  N13  0.020
 PDB  plan-2  C14  0.020
 PDB  plan-2  N15  0.020
 PDB  plan-2  C16  0.020
 PDB  plan-2  O17  0.020
 PDB  plan-2  C18  0.020
 PDB  plan-2  H5   0.020
 PDB  plan-2  H6   0.020

