# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:36:17 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 6-benzyl-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=Nc2n(ncc12)C3CCCC3)Cc4ccccc4
#
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
 WTC  WTC  6-benzyl-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  40  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WTC
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
 WTC  C1    C  CR56  0  -0.343  -1.3368   2.1525   0.0224
 WTC  C2    C  CR56  0   0.593  -0.8290   0.8581  -0.0013
 WTC  N3    N  NR5   0  -0.376  -1.8820   0.0284  -0.0008
 WTC  N4    N  N     0  -0.253  -3.0391   0.7069   0.0256
 WTC  C5    C  CR15  0  -0.071  -2.7339   1.9832   0.0397
 WTC  C6    C  CR6   0   0.516  -0.4234   3.2514   0.0219
 WTC  N7    N  NR16  0  -0.711   0.8954   2.7931  -0.0014
 WTC  C8    C  CR6   0   0.535   1.2941   1.4898  -0.0201
 WTC  N9    N  N     0  -0.447   0.4724   0.4932  -0.0207
 WTC  C10   C  CH1   0  -0.095  -1.8678  -1.4231  -0.0057
 WTC  C11   C  CH2   0  -0.455  -2.5785  -2.0052  -1.2492
 WTC  C12   C  CH2   0  -0.452  -3.5384  -3.0693  -0.7108
 WTC  C13   C  CH2   0  -0.441  -3.9292  -2.5363   0.6649
 WTC  C14   C  CH2   0  -0.454  -2.6011  -2.0220   1.2128
 WTC  O15   O  O     0  -0.459  -0.6762   4.4427   0.0390
 WTC  C16   C  CH2   0  -0.650   2.7800   1.2723  -0.0434
 WTC  C17   C  CR6   0   0.162   3.1725  -0.1747  -0.0050
 WTC  C18   C  CR16  0  -0.298   3.3699  -0.8189   1.2115
 WTC  C19   C  CR16  0  -0.243   3.7296  -2.1591   1.2515
 WTC  C20   C  CR16  0  -0.268   3.8950  -2.8709   0.0705
 WTC  C21   C  CR16  0  -0.243   3.7003  -2.2341  -1.1483
 WTC  C22   C  CR16  0  -0.297   3.3402  -0.8939  -1.1831
 WTC  H5    H  HCR5  0   0.276  -3.5079   2.7346   0.0606
 WTC  HN7   H  HNR6  0   0.431   1.6140   3.5063  -0.0008
 WTC  H10   H  HCH1  0   0.279  -0.8133  -1.6952   0.0089
 WTC  H11   H  HCH2  0   0.244  -3.1452  -1.2188  -1.7501
 WTC  H11A  H  HCH2  0   0.247  -1.8655  -2.4010  -1.9721
 WTC  H12   H  HCH2  0   0.237  -4.3905  -3.2288  -1.3725
 WTC  H12A  H  HCH2  0   0.224  -3.0249  -4.0287  -0.6037
 WTC  H13   H  HCH2  0   0.225  -4.6407  -1.7139   0.5599
 WTC  H13A  H  HCH2  0   0.234  -4.3871  -3.2916   1.3046
 WTC  H14   H  HCH2  0   0.241  -2.0130  -2.8621   1.5883
 WTC  H14A  H  HCH2  0   0.248  -2.7022  -1.3068   2.0293
 WTC  H16   H  HCH2  0   0.304   3.1783   1.7553  -0.9411
 WTC  H16A  H  HCH2  0   0.301   3.2156   1.8092   0.8048
 WTC  H18   H  HCR6  0   0.250   3.2446  -0.2675   2.1362
 WTC  H19   H  HCR6  0   0.254   3.8847  -2.6468   2.2054
 WTC  H20   H  HCR6  0   0.255   4.1802  -3.9147   0.0994
 WTC  H21   H  HCR6  0   0.254   3.8335  -2.7802  -2.0735
 WTC  H22   H  HCR6  0   0.249   3.1915  -0.4017  -2.1370

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
 WTC  C2   C1    aromatic  1.391  0.020  1.391
 WTC  C1   C5    aromatic  1.407  0.020  1.407
 WTC  C1   C6    single    1.429  0.020  1.429
 WTC  N9   C2    single    1.352  0.020  1.352
 WTC  N3   C2    aromatic  1.341  0.020  1.341
 WTC  C10  N3    single    1.452  0.020  1.452
 WTC  N3   N4    aromatic  1.342  0.020  1.342
 WTC  N4   C5    aromatic  1.312  0.020  1.312
 WTC  C5   H5    single    0.930  0.020  1.080
 WTC  N7   C6    single    1.396  0.020  1.396
 WTC  C6   O15   double    1.218  0.020  1.218
 WTC  C8   N7    single    1.363  0.020  1.363
 WTC  N7   HN7   single    0.860  0.020  1.020
 WTC  C16  C8    single    1.502  0.020  1.502
 WTC  N9   C8    double    1.292  0.020  1.292
 WTC  C11  C10   single    1.546  0.020  1.546
 WTC  C14  C10   single    1.543  0.020  1.543
 WTC  C10  H10   single    0.970  0.020  1.090
 WTC  C12  C11   single    1.531  0.020  1.531
 WTC  C11  H11   single    0.970  0.020  1.090
 WTC  C11  H11A  single    0.970  0.020  1.090
 WTC  C12  C13   single    1.526  0.020  1.526
 WTC  C12  H12   single    0.970  0.020  1.090
 WTC  C12  H12A  single    0.970  0.020  1.090
 WTC  C13  C14   single    1.526  0.020  1.526
 WTC  C13  H13   single    0.970  0.020  1.090
 WTC  C13  H13A  single    0.970  0.020  1.090
 WTC  C14  H14   single    0.970  0.020  1.090
 WTC  C14  H14A  single    0.970  0.020  1.090
 WTC  C17  C16   single    1.500  0.020  1.500
 WTC  C16  H16   single    0.970  0.020  1.090
 WTC  C16  H16A  single    0.970  0.020  1.090
 WTC  C18  C17   aromatic  1.391  0.020  1.391
 WTC  C17  C22   aromatic  1.390  0.020  1.390
 WTC  C19  C18   aromatic  1.388  0.020  1.388
 WTC  C18  H18   single    0.930  0.020  1.080
 WTC  C19  C20   aromatic  1.389  0.020  1.389
 WTC  C19  H19   single    0.930  0.020  1.080
 WTC  C20  C21   aromatic  1.389  0.020  1.389
 WTC  C20  H20   single    0.930  0.020  1.080
 WTC  C21  C22   aromatic  1.388  0.020  1.388
 WTC  C21  H21   single    0.930  0.020  1.080
 WTC  C22  H22   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
 WTC  C6    C1   C5   136.64  3.000
 WTC  C6    C1   C2   118.84  3.000
 WTC  C5    C1   C2   104.52  3.000
 WTC  N9    C2   N3   126.09  3.000
 WTC  N3    C2   C1   106.81  3.000
 WTC  N9    C2   C1   127.09  3.000
 WTC  C10   N3   N4   120.94  3.000
 WTC  N4    N3   C2   111.37  3.000
 WTC  C10   N3   C2   127.68  3.000
 WTC  C5    N4   N3   106.95  3.000
 WTC  H5    C5   N4   120.70  3.000
 WTC  H5    C5   C1   128.95  3.000
 WTC  N4    C5   C1   110.35  3.000
 WTC  O15   C6   N7   121.15  3.000
 WTC  O15   C6   C1   128.28  3.000
 WTC  N7    C6   C1   110.57  3.000
 WTC  HN7   N7   C8   117.78  3.000
 WTC  HN7   N7   C6   116.04  3.000
 WTC  C8    N7   C6   126.18  3.000
 WTC  C16   C8   N9   121.17  3.000
 WTC  N9    C8   N7   123.48  3.000
 WTC  C16   C8   N7   115.34  3.000
 WTC  C8    N9   C2   113.84  3.000
 WTC  H10   C10  C14  110.65  3.000
 WTC  H10   C10  C11  111.21  3.000
 WTC  C14   C10  C11  105.69  3.000
 WTC  H10   C10  N3   105.02  3.000
 WTC  C14   C10  N3   112.39  3.000
 WTC  C11   C10  N3   112.01  3.000
 WTC  H11A  C11  H11  107.28  3.000
 WTC  H11A  C11  C12  113.02  3.000
 WTC  H11   C11  C12  109.68  3.000
 WTC  H11A  C11  C10  111.69  3.000
 WTC  H11   C11  C10  109.67  3.000
 WTC  C12   C11  C10  105.49  3.000
 WTC  H12A  C12  H12  107.34  3.000
 WTC  H12A  C12  C13  109.78  3.000
 WTC  H12   C12  C13  113.45  3.000
 WTC  H12A  C12  C11  110.48  3.000
 WTC  H12   C12  C11  112.22  3.000
 WTC  C13   C12  C11  103.58  3.000
 WTC  H13A  C13  H13  107.71  3.000
 WTC  H13A  C13  C14  112.84  3.000
 WTC  H13   C13  C14  110.34  3.000
 WTC  H13A  C13  C12  113.23  3.000
 WTC  H13   C13  C12  110.06  3.000
 WTC  C14   C13  C12  102.62  3.000
 WTC  H14A  C14  H14  107.28  3.000
 WTC  H14A  C14  C13  114.16  3.000
 WTC  H14   C14  C13  109.44  3.000
 WTC  H14A  C14  C10  112.38  3.000
 WTC  H14   C14  C10  108.31  3.000
 WTC  C13   C14  C10  105.12  3.000
 WTC  H16A  C16  H16  105.93  3.000
 WTC  H16A  C16  C17  110.45  3.000
 WTC  H16   C16  C17  110.59  3.000
 WTC  H16A  C16  C8   108.10  3.000
 WTC  H16   C16  C8   107.99  3.000
 WTC  C17   C16  C8   113.47  3.000
 WTC  C22   C17  C18  118.98  3.000
 WTC  C22   C17  C16  120.59  3.000
 WTC  C18   C17  C16  120.43  3.000
 WTC  H18   C18  C19  119.77  3.000
 WTC  H18   C18  C17  119.62  3.000
 WTC  C19   C18  C17  120.61  3.000
 WTC  H19   C19  C20  120.09  3.000
 WTC  H19   C19  C18  119.83  3.000
 WTC  C20   C19  C18  120.08  3.000
 WTC  H20   C20  C21  120.16  3.000
 WTC  H20   C20  C19  120.19  3.000
 WTC  C21   C20  C19  119.64  3.000
 WTC  H21   C21  C22  119.83  3.000
 WTC  H21   C21  C20  120.10  3.000
 WTC  C22   C21  C20  120.07  3.000
 WTC  H22   C22  C21  119.75  3.000
 WTC  H22   C22  C17  119.63  3.000
 WTC  C21   C22  C17  120.62  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
 WTC  CONST_01  N4   N3   C2   C1     0.00   0.0  0
 WTC  CONST_02  N3   N4   C5   C1     0.00   0.0  0
 WTC  CONST_03  N4   C5   C1   C2     0.00   0.0  0
 WTC  CONST_04  C5   N4   N3   C2     0.00   0.0  0
 WTC  CONST_05  C5   C1   C2   N3     0.00   0.0  0
 WTC  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 WTC  CONST_07  C20  C21  C22  C17    0.00   0.0  0
 WTC  CONST_08  C21  C22  C17  C18    0.00   0.0  0
 WTC  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 WTC  CONST_10  C22  C17  C18  C19    0.00   0.0  0
 WTC  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 WTC  CONST_12  C10  N3   C2   C1   180.00   0.0  0
 WTC  CONST_13  C10  N3   N4   C5   180.00   0.0  0
 WTC  CONST_14  C10  N3   C2   N9     0.00   0.0  0
 WTC  CONST_15  C8   N7   C6   C1     0.00   0.0  0
 WTC  CONST_16  N7   C8   N9   C2     0.00   0.0  0
 WTC  CONST_17  N9   C8   N7   C6     0.00   0.0  0
 WTC  CONST_18  C19  C18  C17  C16  180.00   0.0  0
 WTC  CONST_19  C21  C22  C17  C16  180.00   0.0  0
 WTC  CONST_20  C16  C8   N9   C2   180.00   0.0  0
 WTC  CONST_21  C16  C8   N7   C6   180.00   0.0  0
 WTC  CONST_22  O15  C6   N7   C8   180.00   0.0  0
 WTC  CONST_23  H5   C5   C1   C2   180.00   0.0  0
 WTC  CONST_24  H19  C19  C18  C17  180.00   0.0  0
 WTC  CONST_25  H21  C21  C22  C17  180.00   0.0  0
 WTC  CONST_26  H22  C22  C17  C18  180.00   0.0  0
 WTC  CONST_27  H20  C20  C19  C18  180.00   0.0  0
 WTC  CONST_28  H18  C18  C19  C20  180.00   0.0  0
 WTC  CONST_29  HN7  N7   C6   C1   180.00   0.0  0
 WTC  Var_01    C13  C12  C11  C10   31.17  30.0  1
 WTC  Var_02    C12  C13  C14  C10   36.74  30.0  1
 WTC  Var_03    C14  C13  C12  C11  -41.99  30.0  1
 WTC  Var_04    C17  C16  C8   N7   177.57  30.0  2
 WTC  Var_05    C18  C17  C16  C8   -89.44  30.0  2

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
 WTC  chir_01  C10  N3  C11  C14  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
 WTC  plan-1  C16  0.020
 WTC  plan-1  C17  0.020
 WTC  plan-1  C18  0.020
 WTC  plan-1  C19  0.020
 WTC  plan-1  C20  0.020
 WTC  plan-1  C21  0.020
 WTC  plan-1  C22  0.020
 WTC  plan-1  H18  0.020
 WTC  plan-1  H19  0.020
 WTC  plan-1  H20  0.020
 WTC  plan-1  H21  0.020
 WTC  plan-1  H22  0.020
 WTC  plan-2  C1   0.020
 WTC  plan-2  C2   0.020
 WTC  plan-2  N3   0.020
 WTC  plan-2  N4   0.020
 WTC  plan-2  C5   0.020
 WTC  plan-2  C6   0.020
 WTC  plan-2  N7   0.020
 WTC  plan-2  C8   0.020
 WTC  plan-2  N9   0.020
 WTC  plan-2  C10  0.020
 WTC  plan-2  O15  0.020
 WTC  plan-2  C16  0.020
 WTC  plan-2  H5   0.020
 WTC  plan-2  HN7  0.020

