# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 01:11:49 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-{[(3-fluorophenyl)methyl]sulfanyl}-2-(oxetan-3-yl)-5-phenyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(CSC2=Nc3nn(cc3C(=O)N2c4ccccc4)C5COC5)c1
#
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
 A5Y  A5Y  6-{[(3-fluorophenyl)methyl]sulfanyl}-2-(oxetan-3-yl)-5-phenyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  46  29  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A5Y
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
 A5Y  N2   N  NR6   0  -0.650  -0.6557   1.4244   0.0472
 A5Y  C7   C  CR15  0   0.060  -4.0873   0.0225   0.0496
 A5Y  C6   C  CR56  0  -0.357  -2.7540   0.3792   0.0369
 A5Y  C5   C  CR56  0   0.427  -2.0593  -0.8329  -0.1303
 A5Y  C3   C  CR6   0   0.341  -0.0707   0.1821  -0.1136
 A5Y  C1   C  CR6   0   0.540  -2.0458   1.6196   0.1340
 A5Y  C21  C  CR16  0  -0.417   6.3142  -1.9062  -0.5182
 A5Y  C20  C  CR6   0   0.543   5.6239  -1.9073   0.6789
 A5Y  C19  C  CR16  0  -0.436   4.2489  -1.8017   0.7412
 A5Y  C18  C  CR6   0   0.105   3.5278  -1.6967  -0.4450
 A5Y  C17  C  CH2   0  -0.620   2.0349  -1.5629  -0.3985
 A5Y  C15  C  CR16  0  -0.228   0.6450   3.0121   1.3560
 A5Y  N4   N  N     0  -0.452  -0.7028  -0.9314  -0.2033
 A5Y  C10  C  CR6   0   0.223   0.1706   2.5895   0.1233
 A5Y  C14  C  CR16  0  -0.263   1.4522   4.1383   1.4232
 A5Y  C13  C  CR16  0  -0.238   1.7753   4.8333   0.2649
 A5Y  C12  C  CR16  0  -0.263   1.2906   4.4047  -0.9642
 A5Y  C11  C  CR16  0  -0.230   0.4843   3.2786  -1.0386
 A5Y  O25  O  O     0  -0.434  -2.5133   2.7298   0.2702
 A5Y  N8   N  NR5   0  -0.284  -4.1066  -1.3056  -0.1065
 A5Y  C26  C  C     0  -0.206  -5.2610  -2.1660  -0.1207
 A5Y  C28  C  C     0  -0.128  -6.1604  -2.1890   1.1223
 A5Y  O29  O  O     0  -0.503  -7.3102  -1.8549   0.3385
 A5Y  C27  C  C     0  -0.138  -6.5209  -1.6750  -0.8414
 A5Y  N9   N  N     0  -0.307  -2.8869  -1.8549  -0.2144
 A5Y  S16  S  S2    0   0.092   1.6815   0.2142  -0.1960
 A5Y  C23  C  CR16  0  -0.295   4.2025  -1.6883  -1.6619
 A5Y  C22  C  CR16  0  -0.224   5.5859  -1.7958  -1.6943
 A5Y  H1   H  HCR5  0   0.324  -4.9817   0.6151   0.1558
 A5Y  H2   H  HCR6  0   0.283   7.3928  -1.9910  -0.5328
 A5Y  H3   H  HCR6  0   0.280   3.7436  -1.8076   1.6996
 A5Y  H4   H  HCH2  0   0.308   1.5691  -1.9150  -1.3172
 A5Y  H5   H  HCH2  0   0.307   1.6062  -2.1055   0.4426
 A5Y  H6   H  HCR6  0   0.272   0.3883   2.4635   2.2530
 A5Y  H7   H  HCR6  0   0.268   1.8271   4.4724   2.3813
 A5Y  H8   H  HCR6  0   0.266   2.4055   5.7110   0.3202
 A5Y  H9   H  HCR6  0   0.267   1.5388   4.9469  -1.8669
 A5Y  H10  H  HCR6  0   0.272   0.1055   2.9336  -1.9921
 A5Y  H11  H  H     0   0.314  -4.9181  -3.1457  -0.4411
 A5Y  H12  H  H     0   0.245  -6.2519  -3.1584   1.6160
 A5Y  H13  H  H     0   0.232  -5.9193  -1.4266   1.8689
 A5Y  H14  H  H     0   0.233  -6.4869  -0.6335  -1.1739
 A5Y  H15  H  H     0   0.249  -6.8520  -2.2989  -1.6739
 A5Y  H16  H  HCR6  0   0.263   3.6439  -1.6021  -2.5855
 A5Y  H17  H  HCR6  0   0.272   6.1056  -1.7953  -2.6431
 A5Y  F24  F  F     0  -0.315   6.3138  -2.0181   1.8252

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
 A5Y  C22  C21  aromatic  1.388  0.020  1.388
 A5Y  C22  C23  aromatic  1.388  0.020  1.388
 A5Y  C21  C20  aromatic  1.382  0.020  1.382
 A5Y  C23  C18  aromatic  1.391  0.020  1.391
 A5Y  C20  F24  single    1.342  0.020  1.342
 A5Y  C20  C19  aromatic  1.380  0.020  1.380
 A5Y  C18  C19  aromatic  1.392  0.020  1.392
 A5Y  C18  C17  single    1.500  0.020  1.500
 A5Y  C17  S16  single    1.823  0.020  1.823
 A5Y  C27  O29  single    1.431  0.020  1.431
 A5Y  C27  C26  single    1.532  0.020  1.532
 A5Y  O29  C28  single    1.431  0.020  1.431
 A5Y  N9   C5   aromatic  1.318  0.020  1.318
 A5Y  N9   N8   aromatic  1.342  0.020  1.342
 A5Y  N4   C5   single    1.362  0.020  1.362
 A5Y  N4   C3   double    1.284  0.020  1.284
 A5Y  S16  C3   single    1.754  0.020  1.754
 A5Y  C26  N8   single    1.440  0.020  1.440
 A5Y  C26  C28  single    1.534  0.020  1.534
 A5Y  C5   C6   aromatic  1.407  0.020  1.407
 A5Y  C3   N2   single    1.383  0.020  1.383
 A5Y  N8   C7   aromatic  1.337  0.020  1.337
 A5Y  C6   C7   aromatic  1.380  0.020  1.380
 A5Y  C6   C1   single    1.432  0.020  1.432
 A5Y  N2   C1   single    1.406  0.020  1.406
 A5Y  N2   C10  single    1.430  0.020  1.430
 A5Y  C15  C10  aromatic  1.387  0.020  1.387
 A5Y  C15  C14  aromatic  1.387  0.020  1.387
 A5Y  C1   O25  double    1.212  0.020  1.212
 A5Y  C10  C11  aromatic  1.387  0.020  1.387
 A5Y  C14  C13  aromatic  1.389  0.020  1.389
 A5Y  C11  C12  aromatic  1.387  0.020  1.387
 A5Y  C13  C12  aromatic  1.389  0.020  1.389
 A5Y  C7   H1   single    0.930  0.020  1.080
 A5Y  C21  H2   single    0.930  0.020  1.080
 A5Y  C19  H3   single    0.930  0.020  1.080
 A5Y  C17  H4   single    0.970  0.020  1.090
 A5Y  C17  H5   single    0.970  0.020  1.090
 A5Y  C15  H6   single    0.930  0.020  1.080
 A5Y  C14  H7   single    0.930  0.020  1.080
 A5Y  C13  H8   single    0.930  0.020  1.080
 A5Y  C12  H9   single    0.930  0.020  1.080
 A5Y  C11  H10  single    0.930  0.020  1.080
 A5Y  C26  H11  single    0.970  0.020  1.090
 A5Y  C28  H12  single    0.970  0.020  1.090
 A5Y  C28  H13  single    0.970  0.020  1.090
 A5Y  C27  H14  single    0.970  0.020  1.090
 A5Y  C27  H15  single    0.970  0.020  1.090
 A5Y  C23  H16  single    0.930  0.020  1.080
 A5Y  C22  H17  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
 A5Y  C10  N2   C1   117.04  3.000
 A5Y  C10  N2   C3   119.58  3.000
 A5Y  C1   N2   C3   123.37  3.000
 A5Y  H1   C7   N8   123.05  3.000
 A5Y  H1   C7   C6   131.32  3.000
 A5Y  N8   C7   C6   105.64  3.000
 A5Y  C1   C6   C5   120.68  3.000
 A5Y  C1   C6   C7   134.52  3.000
 A5Y  C5   C6   C7   104.80  3.000
 A5Y  N9   C5   N4   124.47  3.000
 A5Y  N4   C5   C6   124.08  3.000
 A5Y  N9   C5   C6   111.45  3.000
 A5Y  S16  C3   N4   120.29  3.000
 A5Y  S16  C3   N2   114.30  3.000
 A5Y  N4   C3   N2   125.40  3.000
 A5Y  O25  C1   C6   127.61  3.000
 A5Y  O25  C1   N2   121.01  3.000
 A5Y  C6   C1   N2   111.38  3.000
 A5Y  H2   C21  C22  121.19  3.000
 A5Y  H2   C21  C20  120.64  3.000
 A5Y  C22  C21  C20  118.17  3.000
 A5Y  F24  C20  C19  118.67  3.000
 A5Y  C19  C20  C21  122.45  3.000
 A5Y  F24  C20  C21  118.88  3.000
 A5Y  H3   C19  C18  120.84  3.000
 A5Y  H3   C19  C20  120.27  3.000
 A5Y  C18  C19  C20  118.90  3.000
 A5Y  C23  C18  C17  120.61  3.000
 A5Y  C17  C18  C19  119.73  3.000
 A5Y  C23  C18  C19  119.64  3.000
 A5Y  H5   C17  H4   108.80  3.000
 A5Y  H5   C17  S16  108.88  3.000
 A5Y  H4   C17  S16  109.03  3.000
 A5Y  H5   C17  C18  111.81  3.000
 A5Y  H4   C17  C18  111.77  3.000
 A5Y  S16  C17  C18  106.46  3.000
 A5Y  H6   C15  C14  120.62  3.000
 A5Y  H6   C15  C10  120.07  3.000
 A5Y  C14  C15  C10  119.31  3.000
 A5Y  C3   N4   C5   115.08  3.000
 A5Y  C11  C10  C15  121.06  3.000
 A5Y  C11  C10  N2   119.40  3.000
 A5Y  C15  C10  N2   119.54  3.000
 A5Y  H7   C14  C13  120.23  3.000
 A5Y  H7   C14  C15  119.69  3.000
 A5Y  C13  C14  C15  120.08  3.000
 A5Y  H8   C13  C12  119.92  3.000
 A5Y  H8   C13  C14  119.92  3.000
 A5Y  C12  C13  C14  120.16  3.000
 A5Y  H9   C12  C11  119.70  3.000
 A5Y  H9   C12  C13  120.24  3.000
 A5Y  C11  C12  C13  120.05  3.000
 A5Y  H10  C11  C12  120.63  3.000
 A5Y  H10  C11  C10  120.03  3.000
 A5Y  C12  C11  C10  119.34  3.000
 A5Y  N9   N8   C26  118.90  3.000
 A5Y  C26  N8   C7   127.31  3.000
 A5Y  N9   N8   C7   113.75  3.000
 A5Y  H11  C26  C27  114.19  3.000
 A5Y  H11  C26  C28  114.23  3.000
 A5Y  C27  C26  C28   84.48  3.000
 A5Y  H11  C26  N8   106.78  3.000
 A5Y  C28  C26  N8   118.10  3.000
 A5Y  C27  C26  N8   118.19  3.000
 A5Y  H13  C28  H12  109.19  3.000
 A5Y  H13  C28  O29  112.84  3.000
 A5Y  H12  C28  O29  112.81  3.000
 A5Y  H13  C28  C26  114.40  3.000
 A5Y  H12  C28  C26  115.39  3.000
 A5Y  O29  C28  C26   91.36  3.000
 A5Y  C27  O29  C28   92.17  3.000
 A5Y  H15  C27  H14  108.77  3.000
 A5Y  H15  C27  O29  112.93  3.000
 A5Y  H14  C27  O29  112.80  3.000
 A5Y  H15  C27  C26  115.15  3.000
 A5Y  H14  C27  C26  114.99  3.000
 A5Y  O29  C27  C26   91.46  3.000
 A5Y  N8   N9   C5   104.38  3.000
 A5Y  C17  S16  C3   100.42  3.000
 A5Y  H16  C23  C22  120.02  3.000
 A5Y  H16  C23  C18  119.76  3.000
 A5Y  C22  C23  C18  120.21  3.000
 A5Y  H17  C22  C23  119.96  3.000
 A5Y  H17  C22  C21  119.41  3.000
 A5Y  C23  C22  C21  120.63  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
 A5Y  CONST_01  C5   N9   N8   C7      0.00   0.0  0
 A5Y  CONST_02  N9   C5   C6   C7      0.00   0.0  0
 A5Y  CONST_03  N8   N9   C5   C6      0.00   0.0  0
 A5Y  CONST_04  N9   N8   C7   C6      0.00   0.0  0
 A5Y  CONST_05  N8   C7   C6   C5      0.00   0.0  0
 A5Y  CONST_06  C18  C23  C22  C21     0.00   0.0  0
 A5Y  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 A5Y  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 A5Y  CONST_09  C23  C18  C19  C20     0.00   0.0  0
 A5Y  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 A5Y  CONST_11  C22  C23  C18  C19     0.00   0.0  0
 A5Y  CONST_12  C12  C11  C10  C15     0.00   0.0  0
 A5Y  CONST_13  C12  C13  C14  C15     0.00   0.0  0
 A5Y  CONST_14  C13  C14  C15  C10     0.00   0.0  0
 A5Y  CONST_15  C13  C12  C11  C10     0.00   0.0  0
 A5Y  CONST_16  C11  C10  C15  C14     0.00   0.0  0
 A5Y  CONST_17  C11  C12  C13  C14     0.00   0.0  0
 A5Y  CONST_18  C14  C15  C10  N2    180.00   0.0  0
 A5Y  CONST_19  C12  C11  C10  N2    180.00   0.0  0
 A5Y  CONST_20  C26  N8   C7   C6    180.00   0.0  0
 A5Y  CONST_21  C26  N8   N9   C5    180.00   0.0  0
 A5Y  CONST_22  C5   N4   C3   N2      0.00   0.0  0
 A5Y  CONST_23  C3   N2   C1   C6      0.00   0.0  0
 A5Y  CONST_24  C10  N2   C1   C6    180.00   0.0  0
 A5Y  CONST_25  N4   C3   N2   C1      0.00   0.0  0
 A5Y  CONST_26  C10  N2   C3   N4    180.00   0.0  0
 A5Y  CONST_27  C17  C18  C19  C20   180.00   0.0  0
 A5Y  CONST_28  F24  C20  C19  C18   180.00   0.0  0
 A5Y  CONST_29  C22  C23  C18  C17   180.00   0.0  0
 A5Y  CONST_30  F24  C20  C21  C22   180.00   0.0  0
 A5Y  CONST_31  S16  C3   N4   C5    180.00   0.0  0
 A5Y  CONST_32  O25  C1   N2   C3    180.00   0.0  0
 A5Y  CONST_33  S16  C3   N2   C1    180.00   0.0  0
 A5Y  CONST_34  S16  C3   N2   C10     0.00   0.0  0
 A5Y  CONST_35  O25  C1   N2   C10     0.00   0.0  0
 A5Y  CONST_36  H6   C15  C10  N2      0.00   0.0  0
 A5Y  CONST_37  H10  C11  C10  N2      0.00   0.0  0
 A5Y  CONST_38  H1   C7   C6   C5    180.00   0.0  0
 A5Y  CONST_39  H16  C23  C22  C21   180.00   0.0  0
 A5Y  CONST_40  H3   C19  C20  C21   180.00   0.0  0
 A5Y  CONST_41  H17  C22  C21  C20   180.00   0.0  0
 A5Y  CONST_42  H2   C21  C20  C19   180.00   0.0  0
 A5Y  CONST_43  H8   C13  C14  C15   180.00   0.0  0
 A5Y  CONST_44  H7   C14  C15  C10   180.00   0.0  0
 A5Y  CONST_45  H9   C12  C11  C10   180.00   0.0  0
 A5Y  Var_01    C15  C10  N2   C3    -89.17  30.0  2
 A5Y  Var_02    H14  C27  O29  C28  -112.27  30.0  1
 A5Y  Var_03    H12  C28  O29  C27  -124.07  30.0  1
 A5Y  Var_04    C18  C17  S16  C3   -178.39  30.0  2
 A5Y  Var_05    S16  C17  C18  C19    85.78  30.0  2
 A5Y  Var_06    N4   C3   S16  C17    -0.24  30.0  3

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
 A5Y  chir_01  C26  C27  N8  C28  negativ

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
 A5Y  plan-1  N2   0.020
 A5Y  plan-1  C15  0.020
 A5Y  plan-1  C10  0.020
 A5Y  plan-1  C14  0.020
 A5Y  plan-1  C13  0.020
 A5Y  plan-1  C12  0.020
 A5Y  plan-1  C11  0.020
 A5Y  plan-1  H6   0.020
 A5Y  plan-1  H7   0.020
 A5Y  plan-1  H8   0.020
 A5Y  plan-1  H9   0.020
 A5Y  plan-1  H10  0.020
 A5Y  plan-2  C21  0.020
 A5Y  plan-2  C20  0.020
 A5Y  plan-2  C19  0.020
 A5Y  plan-2  C18  0.020
 A5Y  plan-2  C17  0.020
 A5Y  plan-2  C23  0.020
 A5Y  plan-2  C22  0.020
 A5Y  plan-2  H2   0.020
 A5Y  plan-2  H3   0.020
 A5Y  plan-2  H16  0.020
 A5Y  plan-2  H17  0.020
 A5Y  plan-2  F24  0.020
 A5Y  plan-3  N2   0.020
 A5Y  plan-3  C7   0.020
 A5Y  plan-3  C6   0.020
 A5Y  plan-3  C5   0.020
 A5Y  plan-3  C3   0.020
 A5Y  plan-3  C1   0.020
 A5Y  plan-3  N4   0.020
 A5Y  plan-3  C10  0.020
 A5Y  plan-3  O25  0.020
 A5Y  plan-3  N8   0.020
 A5Y  plan-3  C26  0.020
 A5Y  plan-3  N9   0.020
 A5Y  plan-3  S16  0.020
 A5Y  plan-3  H1   0.020

