# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:28:58 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 6-{[(3-fluorophenyl)methyl]sulfanyl}-5-(2-methylphenyl)-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1N2C(=O)c3c[nH]nc3N=C2SCc4cccc(F)c4
#
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
 M39  M39  6-{[(3-fluorophenyl)methyl]sulfanyl}-5-(2-methylphenyl)-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  41  26  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M39
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
 M39  O10  O  O     0  -0.438  -4.1145  -0.6760  -0.3291
 M39  C9   C  CR6   0   0.546  -3.2335   0.1539  -0.2478
 M39  C3   C  CR56  0  -0.316  -3.3734   1.5771  -0.1964
 M39  C4   C  CR15  0   0.031  -4.4461   2.4495  -0.2220
 M39  N5   N  NR15  0  -0.408  -3.9073   3.6638  -0.1375
 M39  N1   N  N     0  -0.293  -2.5733   3.6824  -0.0569
 M39  C2   C  CR56  0   0.398  -2.2392   2.4070  -0.0923
 M39  N6   N  N     0  -0.452  -0.9587   1.9446  -0.0344
 M39  N8   N  NR6   0  -0.641  -1.8831  -0.2321  -0.1862
 M39  C19  C  CR6   0   0.178  -1.6007  -1.6346  -0.2318
 M39  C20  C  CR16  0  -0.215  -1.3674  -2.2246  -1.4645
 M39  C21  C  CR16  0  -0.284  -1.0838  -3.5795  -1.5351
 M39  C22  C  CR16  0  -0.224  -1.0435  -4.3278  -0.3673
 M39  C23  C  CR16  0  -0.322  -1.2856  -3.7252   0.8595
 M39  C24  C  CR6   0   0.131  -1.5722  -2.3664   0.9552
 M39  C25  C  CH3   0  -0.733  -1.8312  -1.7181   2.2809
 M39  C7   C  CR6   0   0.334  -0.8395   0.6680  -0.0824
 M39  S11  S  S2    0   0.091   0.7467  -0.0795  -0.0060
 M39  C12  C  CH2   0  -0.620   1.7976   1.3932   0.2163
 M39  C13  C  CR6   0   0.103   3.2045   0.8907   0.3470
 M39  C18  C  CR16  0  -0.437   3.9626   0.6424  -0.7939
 M39  C17  C  CR6   0   0.542   5.2467   0.1560  -0.6495
 M39  F26  F  F     0  -0.315   5.9744  -0.0755  -1.7536
 M39  C14  C  CR16  0  -0.294   3.7489   0.6364   1.6022
 M39  C15  C  CR16  0  -0.225   5.0426   0.1478   1.7172
 M39  C16  C  CR16  0  -0.416   5.8086  -0.0999   0.5865
 M39  H1   H  HCR5  0   0.310  -5.5098   2.2932  -0.2903
 M39  H2   H  HNR5  0   0.439  -4.4112   4.5381  -0.1301
 M39  H3   H  HCR6  0   0.269  -1.4051  -1.6200  -2.3618
 M39  H4   H  HCR6  0   0.264  -0.8974  -4.0451  -2.4934
 M39  H5   H  HCR6  0   0.264  -0.8243  -5.3866  -0.4094
 M39  H6   H  HCR6  0   0.259  -1.2515  -4.3212   1.7631
 M39  H7   H  HCH3  0   0.254  -2.8293  -1.2801   2.3261
 M39  H8   H  HCH3  0   0.259  -1.7535  -2.4458   3.0865
 M39  H9   H  HCH3  0   0.248  -1.1148  -0.9208   2.4860
 M39  H10  H  HCH2  0   0.307   1.6763   2.0509  -0.6429
 M39  H11  H  HCH2  0   0.307   1.4766   1.9233   1.1110
 M39  H12  H  HCR6  0   0.281   3.5592   0.8306  -1.7814
 M39  H13  H  HCR6  0   0.263   3.1621   0.8245   2.4923
 M39  H14  H  HCR6  0   0.272   5.4622  -0.0435   2.6957
 M39  H15  H  HCR6  0   0.283   6.8180  -0.4817   0.6649

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
 M39  F26  C17  single    1.342  0.020  1.342
 M39  C16  C17  aromatic  1.382  0.020  1.382
 M39  C16  C15  aromatic  1.388  0.020  1.388
 M39  C17  C18  aromatic  1.381  0.020  1.381
 M39  C15  C14  aromatic  1.388  0.020  1.388
 M39  C18  C13  aromatic  1.392  0.020  1.392
 M39  C14  C13  aromatic  1.392  0.020  1.392
 M39  C13  C12  single    1.500  0.020  1.500
 M39  C12  S11  single    1.823  0.020  1.823
 M39  N1   N5   aromatic  1.337  0.020  1.337
 M39  N1   C2   aromatic  1.319  0.020  1.319
 M39  N6   C2   single    1.363  0.020  1.363
 M39  N6   C7   double    1.283  0.020  1.283
 M39  N5   C4   aromatic  1.331  0.020  1.331
 M39  C2   C3   aromatic  1.409  0.020  1.409
 M39  S11  C7   single    1.755  0.020  1.755
 M39  C7   N8   single    1.382  0.020  1.382
 M39  C4   C3   aromatic  1.383  0.020  1.383
 M39  C3   C9   single    1.431  0.020  1.431
 M39  N8   C9   single    1.406  0.020  1.406
 M39  N8   C19  single    1.431  0.020  1.431
 M39  C9   O10  double    1.213  0.020  1.213
 M39  C19  C20  aromatic  1.386  0.020  1.386
 M39  C19  C24  aromatic  1.395  0.020  1.395
 M39  C20  C21  aromatic  1.386  0.020  1.386
 M39  C25  C24  single    1.498  0.020  1.498
 M39  C24  C23  aromatic  1.392  0.020  1.392
 M39  C21  C22  aromatic  1.388  0.020  1.388
 M39  C23  C22  aromatic  1.388  0.020  1.388
 M39  C4   H1   single    0.930  0.020  1.080
 M39  N5   H2   single    0.860  0.020  1.020
 M39  C20  H3   single    0.930  0.020  1.080
 M39  C21  H4   single    0.930  0.020  1.080
 M39  C22  H5   single    0.930  0.020  1.080
 M39  C23  H6   single    0.930  0.020  1.080
 M39  C25  H7   single    0.970  0.020  1.090
 M39  C25  H8   single    0.970  0.020  1.090
 M39  C25  H9   single    0.970  0.020  1.090
 M39  C12  H10  single    0.970  0.020  1.090
 M39  C12  H11  single    0.970  0.020  1.090
 M39  C18  H12  single    0.930  0.020  1.080
 M39  C14  H13  single    0.930  0.020  1.080
 M39  C15  H14  single    0.930  0.020  1.080
 M39  C16  H15  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
 M39  N8   C9   C3   111.43  3.000
 M39  N8   C9   O10  120.85  3.000
 M39  C3   C9   O10  127.72  3.000
 M39  C2   C3   C4   104.72  3.000
 M39  C4   C3   C9   134.64  3.000
 M39  C2   C3   C9   120.64  3.000
 M39  H1   C4   N5   122.41  3.000
 M39  H1   C4   C3   132.50  3.000
 M39  N5   C4   C3   105.09  3.000
 M39  H2   N5   N1   119.06  3.000
 M39  H2   N5   C4   126.06  3.000
 M39  N1   N5   C4   114.87  3.000
 M39  C2   N1   N5   103.75  3.000
 M39  N6   C2   N1   124.40  3.000
 M39  N6   C2   C3   124.03  3.000
 M39  N1   C2   C3   111.57  3.000
 M39  C7   N6   C2   115.04  3.000
 M39  C7   N8   C19  119.45  3.000
 M39  C19  N8   C9   117.20  3.000
 M39  C7   N8   C9   123.35  3.000
 M39  C24  C19  C20  122.01  3.000
 M39  C24  C19  N8   119.41  3.000
 M39  C20  C19  N8   118.59  3.000
 M39  H3   C20  C21  120.72  3.000
 M39  H3   C20  C19  119.56  3.000
 M39  C21  C20  C19  119.72  3.000
 M39  H4   C21  C22  120.57  3.000
 M39  H4   C21  C20  120.08  3.000
 M39  C22  C21  C20  119.35  3.000
 M39  H5   C22  C23  119.63  3.000
 M39  H5   C22  C21  120.05  3.000
 M39  C23  C22  C21  120.31  3.000
 M39  H6   C23  C24  119.10  3.000
 M39  H6   C23  C22  119.54  3.000
 M39  C24  C23  C22  121.36  3.000
 M39  C25  C24  C23  121.25  3.000
 M39  C23  C24  C19  117.25  3.000
 M39  C25  C24  C19  121.50  3.000
 M39  H9   C25  H8   107.60  3.000
 M39  H9   C25  H7   107.43  3.000
 M39  H8   C25  H7   107.64  3.000
 M39  H9   C25  C24  111.65  3.000
 M39  H8   C25  C24  110.69  3.000
 M39  H7   C25  C24  111.63  3.000
 M39  S11  C7   N8   114.10  3.000
 M39  N8   C7   N6   125.50  3.000
 M39  S11  C7   N6   120.40  3.000
 M39  C12  S11  C7   100.50  3.000
 M39  H11  C12  H10  108.76  3.000
 M39  H11  C12  C13  111.61  3.000
 M39  H10  C12  C13  112.07  3.000
 M39  H11  C12  S11  108.89  3.000
 M39  H10  C12  S11  109.12  3.000
 M39  C13  C12  S11  106.31  3.000
 M39  C14  C13  C18  119.58  3.000
 M39  C14  C13  C12  120.45  3.000
 M39  C18  C13  C12  119.95  3.000
 M39  H12  C18  C17  120.19  3.000
 M39  H12  C18  C13  120.89  3.000
 M39  C17  C18  C13  118.92  3.000
 M39  C16  C17  F26  118.91  3.000
 M39  C16  C17  C18  122.48  3.000
 M39  F26  C17  C18  118.61  3.000
 M39  H13  C14  C15  119.89  3.000
 M39  H13  C14  C13  119.86  3.000
 M39  C15  C14  C13  120.25  3.000
 M39  H14  C15  C16  119.43  3.000
 M39  H14  C15  C14  119.92  3.000
 M39  C16  C15  C14  120.65  3.000
 M39  H15  C16  C15  121.25  3.000
 M39  H15  C16  C17  120.63  3.000
 M39  C15  C16  C17  118.12  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
 M39  CONST_01  N5   N1   C2   C3     0.00   0.0  0
 M39  CONST_02  N1   N5   C4   C3     0.00   0.0  0
 M39  CONST_03  C2   N1   N5   C4     0.00   0.0  0
 M39  CONST_04  N1   C2   C3   C4     0.00   0.0  0
 M39  CONST_05  C2   C3   C4   N5     0.00   0.0  0
 M39  CONST_06  C22  C21  C20  C19    0.00   0.0  0
 M39  CONST_07  C22  C23  C24  C19    0.00   0.0  0
 M39  CONST_08  C23  C24  C19  C20    0.00   0.0  0
 M39  CONST_09  C23  C22  C21  C20    0.00   0.0  0
 M39  CONST_10  C24  C19  C20  C21    0.00   0.0  0
 M39  CONST_11  C24  C23  C22  C21    0.00   0.0  0
 M39  CONST_12  C16  C17  C18  C13    0.00   0.0  0
 M39  CONST_13  C16  C15  C14  C13    0.00   0.0  0
 M39  CONST_14  C15  C16  C17  C18    0.00   0.0  0
 M39  CONST_15  C15  C14  C13  C18    0.00   0.0  0
 M39  CONST_16  C14  C15  C16  C17    0.00   0.0  0
 M39  CONST_17  C14  C13  C18  C17    0.00   0.0  0
 M39  CONST_18  C21  C20  C19  N8   180.00   0.0  0
 M39  CONST_19  C23  C24  C19  N8   180.00   0.0  0
 M39  CONST_20  N6   C7   N8   C9     0.00   0.0  0
 M39  CONST_21  C7   N8   C9   C3     0.00   0.0  0
 M39  CONST_22  C19  N8   C9   C3   180.00   0.0  0
 M39  CONST_23  N8   C7   N6   C2     0.00   0.0  0
 M39  CONST_24  C19  N8   C7   N6   180.00   0.0  0
 M39  CONST_25  C25  C24  C19  N8     0.00   0.0  0
 M39  CONST_26  C25  C24  C19  C20  180.00   0.0  0
 M39  CONST_27  C25  C24  C23  C22  180.00   0.0  0
 M39  CONST_28  C17  C18  C13  C12  180.00   0.0  0
 M39  CONST_29  C15  C14  C13  C12  180.00   0.0  0
 M39  CONST_30  F26  C17  C18  C13  180.00   0.0  0
 M39  CONST_31  C15  C16  C17  F26  180.00   0.0  0
 M39  CONST_32  C7   N8   C9   O10  180.00   0.0  0
 M39  CONST_33  C19  N8   C9   O10    0.00   0.0  0
 M39  CONST_34  S11  C7   N8   C9   180.00   0.0  0
 M39  CONST_35  S11  C7   N6   C2   180.00   0.0  0
 M39  CONST_36  S11  C7   N8   C19    0.00   0.0  0
 M39  CONST_37  H1   C4   C3   C9     0.00   0.0  0
 M39  CONST_38  H2   N5   C4   C3   180.00   0.0  0
 M39  CONST_39  H3   C20  C19  N8     0.00   0.0  0
 M39  CONST_40  H4   C21  C20  C19  180.00   0.0  0
 M39  CONST_41  H6   C23  C24  C19  180.00   0.0  0
 M39  CONST_42  H5   C22  C21  C20  180.00   0.0  0
 M39  CONST_43  H14  C15  C14  C13  180.00   0.0  0
 M39  CONST_44  H15  C16  C17  C18  180.00   0.0  0
 M39  CONST_45  H13  C14  C13  C18  180.00   0.0  0
 M39  CONST_46  H12  C18  C13  C14  180.00   0.0  0
 M39  Var_01    C20  C19  N8   C9    91.53  30.0  2
 M39  Var_02    C13  C12  S11  C7   178.07  30.0  1
 M39  Var_03    C18  C13  C12  S11   85.15  30.0  2
 M39  Var_04    H7   C25  C24  C19   60.80  30.0  2

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
 M39  plan-1  N8   0.020
 M39  plan-1  C19  0.020
 M39  plan-1  C20  0.020
 M39  plan-1  C21  0.020
 M39  plan-1  C22  0.020
 M39  plan-1  C23  0.020
 M39  plan-1  C24  0.020
 M39  plan-1  C25  0.020
 M39  plan-1  H3   0.020
 M39  plan-1  H4   0.020
 M39  plan-1  H5   0.020
 M39  plan-1  H6   0.020
 M39  plan-2  C12  0.020
 M39  plan-2  C13  0.020
 M39  plan-2  C18  0.020
 M39  plan-2  C17  0.020
 M39  plan-2  F26  0.020
 M39  plan-2  C14  0.020
 M39  plan-2  C15  0.020
 M39  plan-2  C16  0.020
 M39  plan-2  H12  0.020
 M39  plan-2  H13  0.020
 M39  plan-2  H14  0.020
 M39  plan-2  H15  0.020
 M39  plan-3  O10  0.020
 M39  plan-3  C9   0.020
 M39  plan-3  C3   0.020
 M39  plan-3  C4   0.020
 M39  plan-3  N5   0.020
 M39  plan-3  N1   0.020
 M39  plan-3  C2   0.020
 M39  plan-3  N6   0.020
 M39  plan-3  N8   0.020
 M39  plan-3  C19  0.020
 M39  plan-3  C7   0.020
 M39  plan-3  S11  0.020
 M39  plan-3  H1   0.020
 M39  plan-3  H2   0.020

