# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:59:52 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: 5-[4-(2-hydroxyethyl)phenyl]-1-methyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](SC1=Nc2n(C)ncc2C(=O)N1c3ccc(CCO)cc3)c4ccccc4
#
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
 VMG  VMG  5-[4-(2-hydroxyethyl)phenyl]-1-methyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  51  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VMG
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
 VMG  O11  O  O     0  -0.444  37.0451  -14.9926  17.5621
 VMG  C1   C  CR6   0   0.543  37.0627  -15.7300  16.5985
 VMG  C6   C  CR56  0  -0.322  35.9645  -16.4012  15.9861
 VMG  C7   C  CR15  0  -0.079  34.5759  -16.4911  16.2044
 VMG  N8   N  N     0  -0.259  34.0220  -17.2751  15.3108
 VMG  N9   N  NR5   0  -0.359  35.0106  -17.7079  14.5081
 VMG  C10  C  CH3   0  -0.523  34.7289  -18.5827  13.3976
 VMG  C5   C  CR56  0   0.608  36.1949  -17.2041  14.8782
 VMG  N4   N  N     0  -0.459  37.3812  -17.4349  14.2837
 VMG  C3   C  CR6   0   0.361  38.3794  -16.8319  14.8382
 VMG  S18  S  S2    0   0.097  39.9962  -17.0006  14.1854
 VMG  C19  C  CH1   0  -0.468  39.7160  -18.1913  12.8126
 VMG  C20  C  CR6   0   0.162  40.8702  -17.9872  11.8661
 VMG  C25  C  CR16  0  -0.292  42.1694  -18.3428  12.2243
 VMG  C24  C  CR16  0  -0.238  43.2230  -18.1411  11.3439
 VMG  C23  C  CR16  0  -0.265  42.9911  -17.5860  10.0918
 VMG  C22  C  CR16  0  -0.238  41.6999  -17.2300   9.7271
 VMG  C21  C  CR16  0  -0.309  40.6481  -17.4258  10.6122
 VMG  C26  C  CH3   0  -0.625  39.5847  -19.6158  13.3244
 VMG  N2   N  NR6   0  -0.651  38.2828  -16.0142  15.9373
 VMG  C12  C  CR6   0   0.205  39.4631  -15.4035  16.4668
 VMG  C17  C  CR16  0  -0.215  40.1774  -16.0467  17.4649
 VMG  C16  C  CR16  0  -0.312  41.3238  -15.4558  17.9715
 VMG  C15  C  CR6   0   0.152  41.7731  -14.2301  17.4859
 VMG  C14  C  CR16  0  -0.315  41.0374  -13.6014  16.4835
 VMG  C13  C  CR16  0  -0.213  39.8845  -14.1781  15.9746
 VMG  C27  C  CH2   0  -0.546  43.0009  -13.5767  18.0529
 VMG  C28  C  CH2   0  -0.148  42.6715  -12.5539  19.1303
 VMG  O28  O  OH1   0  -0.666  42.0299  -13.2069  20.2007
 VMG  H1   H  HCR5  0   0.277  33.9788  -16.0188  16.9692
 VMG  H2   H  HCH3  0   0.265  34.1949  -19.4646  13.7441
 VMG  H3   H  HCH3  0   0.263  34.1292  -18.0681  12.6491
 VMG  H4   H  HCH3  0   0.264  35.6690  -18.8899  12.9486
 VMG  H5   H  HCH1  0   0.312  38.7895  -17.8867  12.3260
 VMG  H6   H  HCR6  0   0.258  42.3702  -18.7772  13.1968
 VMG  H7   H  HCR6  0   0.260  44.2272  -18.4174  11.6378
 VMG  H8   H  HCR6  0   0.259  43.8133  -17.4315   9.4053
 VMG  H9   H  HCR6  0   0.259  41.5085  -16.7965   8.7541
 VMG  H10  H  HCR6  0   0.258  39.6427  -17.1433  10.3239
 VMG  H11  H  HCH3  0   0.252  38.7401  -19.7056  14.0048
 VMG  H12  H  HCH3  0   0.246  39.4140  -20.2899  12.4836
 VMG  H13  H  HCH3  0   0.234  40.4832  -19.9448  13.8451
 VMG  H14  H  HCR6  0   0.268  39.8413  -17.0048  17.8406
 VMG  H15  H  HCR6  0   0.254  41.8826  -15.9619  18.7484
 VMG  H16  H  HCR6  0   0.257  41.3691  -12.6478  16.0898
 VMG  H17  H  HCR6  0   0.269  39.3191  -13.6838  15.1950
 VMG  H18  H  HCH2  0   0.251  43.6728  -14.3324  18.4664
 VMG  H19  H  HCH2  0   0.206  43.6040  -12.0716  19.4504
 VMG  H20  H  HOH1  0   0.454  41.7519  -12.5395  20.8340
 VMG  H21  H  HCH2  0   0.256  43.5521  -13.0623  17.2629
 VMG  H22  H  HCH2  0   0.200  42.0385  -11.7676  18.6988

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
 VMG  C22  C23  aromatic  1.388  0.020  1.388
 VMG  C22  C21  aromatic  1.388  0.020  1.388
 VMG  C23  C24  aromatic  1.389  0.020  1.389
 VMG  C21  C20  aromatic  1.392  0.020  1.392
 VMG  C24  C25  aromatic  1.388  0.020  1.388
 VMG  C20  C25  aromatic  1.394  0.020  1.394
 VMG  C20  C19  single    1.507  0.020  1.507
 VMG  C19  C26  single    1.519  0.020  1.519
 VMG  C19  S18  single    1.839  0.020  1.839
 VMG  C10  N9   single    1.442  0.020  1.442
 VMG  S18  C3   single    1.752  0.020  1.752
 VMG  N4   C5   single    1.347  0.020  1.347
 VMG  N4   C3   double    1.291  0.020  1.291
 VMG  N9   C5   aromatic  1.339  0.020  1.339
 VMG  N9   N8   aromatic  1.345  0.020  1.345
 VMG  C5   C6   aromatic  1.388  0.020  1.388
 VMG  C3   N2   single    1.373  0.020  1.373
 VMG  N8   C7   aromatic  1.311  0.020  1.311
 VMG  C6   C7   aromatic  1.409  0.020  1.409
 VMG  C6   C1   single    1.425  0.020  1.425
 VMG  N2   C1   single    1.417  0.020  1.417
 VMG  N2   C12  single    1.431  0.020  1.431
 VMG  C1   O11  double    1.214  0.020  1.214
 VMG  C13  C12  aromatic  1.386  0.020  1.386
 VMG  C13  C14  aromatic  1.386  0.020  1.386
 VMG  C12  C17  aromatic  1.386  0.020  1.386
 VMG  C14  C15  aromatic  1.393  0.020  1.393
 VMG  C17  C16  aromatic  1.386  0.020  1.386
 VMG  C15  C16  aromatic  1.393  0.020  1.393
 VMG  C15  C27  single    1.502  0.020  1.502
 VMG  C27  C28  single    1.522  0.020  1.522
 VMG  C28  O28  single    1.408  0.020  1.408
 VMG  C7   H1   single    0.930  0.020  1.080
 VMG  C10  H2   single    0.970  0.020  1.090
 VMG  C10  H3   single    0.970  0.020  1.090
 VMG  C10  H4   single    0.970  0.020  1.090
 VMG  C19  H5   single    0.970  0.020  1.090
 VMG  C25  H6   single    0.930  0.020  1.080
 VMG  C24  H7   single    0.930  0.020  1.080
 VMG  C23  H8   single    0.930  0.020  1.080
 VMG  C22  H9   single    0.930  0.020  1.080
 VMG  C21  H10  single    0.930  0.020  1.080
 VMG  C26  H11  single    0.970  0.020  1.090
 VMG  C26  H12  single    0.970  0.020  1.090
 VMG  C26  H13  single    0.970  0.020  1.090
 VMG  C17  H14  single    0.930  0.020  1.080
 VMG  C16  H15  single    0.930  0.020  1.080
 VMG  C14  H16  single    0.930  0.020  1.080
 VMG  C13  H17  single    0.930  0.020  1.080
 VMG  C27  H18  single    0.970  0.020  1.090
 VMG  C28  H19  single    0.970  0.020  1.090
 VMG  O28  H20  single    0.850  0.020  0.980
 VMG  C27  H21  single    0.970  0.020  1.090
 VMG  C28  H22  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
 VMG  N2   C1   C6   111.63  3.000
 VMG  N2   C1   O11  120.33  3.000
 VMG  C6   C1   O11  128.04  3.000
 VMG  C5   C6   C7   104.51  3.000
 VMG  C7   C6   C1   136.31  3.000
 VMG  C5   C6   C1   119.19  3.000
 VMG  H1   C7   N8   120.72  3.000
 VMG  H1   C7   C6   128.86  3.000
 VMG  N8   C7   C6   110.42  3.000
 VMG  N9   N8   C7   106.78  3.000
 VMG  C5   N9   C10  127.88  3.000
 VMG  C5   N9   N8   111.35  3.000
 VMG  C10  N9   N8   120.76  3.000
 VMG  H4   C10  H3   109.05  3.000
 VMG  H4   C10  H2   109.11  3.000
 VMG  H3   C10  H2   109.38  3.000
 VMG  H4   C10  N9   108.72  3.000
 VMG  H3   C10  N9   110.52  3.000
 VMG  H2   C10  N9   110.03  3.000
 VMG  N4   C5   N9   126.33  3.000
 VMG  N9   C5   C6   106.95  3.000
 VMG  N4   C5   C6   126.72  3.000
 VMG  C3   N4   C5   114.28  3.000
 VMG  N2   C3   S18  114.87  3.000
 VMG  N2   C3   N4   124.57  3.000
 VMG  S18  C3   N4   120.56  3.000
 VMG  C19  S18  C3   101.53  3.000
 VMG  H5   C19  C26  109.81  3.000
 VMG  H5   C19  C20  109.45  3.000
 VMG  C26  C19  C20  113.88  3.000
 VMG  H5   C19  S18  106.37  3.000
 VMG  C26  C19  S18  111.64  3.000
 VMG  C20  C19  S18  105.34  3.000
 VMG  C21  C20  C25  118.90  3.000
 VMG  C25  C20  C19  121.20  3.000
 VMG  C21  C20  C19  119.90  3.000
 VMG  H6   C25  C24  119.14  3.000
 VMG  H6   C25  C20  120.36  3.000
 VMG  C24  C25  C20  120.50  3.000
 VMG  H7   C24  C23  120.11  3.000
 VMG  H7   C24  C25  119.68  3.000
 VMG  C23  C24  C25  120.21  3.000
 VMG  H8   C23  C22  120.23  3.000
 VMG  H8   C23  C24  120.13  3.000
 VMG  C22  C23  C24  119.64  3.000
 VMG  H9   C22  C21  119.71  3.000
 VMG  H9   C22  C23  120.23  3.000
 VMG  C21  C22  C23  120.06  3.000
 VMG  H10  C21  C22  119.77  3.000
 VMG  H10  C21  C20  119.54  3.000
 VMG  C22  C21  C20  120.69  3.000
 VMG  H13  C26  H12  108.11  3.000
 VMG  H13  C26  H11  108.44  3.000
 VMG  H12  C26  H11  108.02  3.000
 VMG  H13  C26  C19  111.90  3.000
 VMG  H12  C26  C19  109.46  3.000
 VMG  H11  C26  C19  110.80  3.000
 VMG  C12  N2   C3   119.50  3.000
 VMG  C12  N2   C1   116.89  3.000
 VMG  C3   N2   C1   123.62  3.000
 VMG  C13  C12  C17  120.63  3.000
 VMG  C17  C12  N2   119.59  3.000
 VMG  C13  C12  N2   119.79  3.000
 VMG  H14  C17  C16  120.49  3.000
 VMG  H14  C17  C12  120.05  3.000
 VMG  C16  C17  C12  119.46  3.000
 VMG  H15  C16  C15  119.67  3.000
 VMG  H15  C16  C17  119.34  3.000
 VMG  C15  C16  C17  120.98  3.000
 VMG  C27  C15  C14  120.46  3.000
 VMG  C27  C15  C16  121.00  3.000
 VMG  C14  C15  C16  118.52  3.000
 VMG  H16  C14  C13  119.17  3.000
 VMG  H16  C14  C15  119.79  3.000
 VMG  C13  C14  C15  121.04  3.000
 VMG  H17  C13  C14  120.59  3.000
 VMG  H17  C13  C12  120.04  3.000
 VMG  C14  C13  C12  119.36  3.000
 VMG  H21  C27  H18  106.81  3.000
 VMG  H21  C27  C28  107.75  3.000
 VMG  H18  C27  C28  109.28  3.000
 VMG  H21  C27  C15  110.15  3.000
 VMG  H18  C27  C15  110.16  3.000
 VMG  C28  C27  C15  112.51  3.000
 VMG  H22  C28  H19  106.85  3.000
 VMG  H22  C28  O28  111.60  3.000
 VMG  H19  C28  O28  111.66  3.000
 VMG  H22  C28  C27  109.15  3.000
 VMG  H19  C28  C27  108.54  3.000
 VMG  O28  C28  C27  108.97  3.000
 VMG  H20  O28  C28  108.09  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
 VMG  CONST_01  N8   N9   C5   C6     0.00   0.0  0
 VMG  CONST_02  N9   N8   C7   C6     0.00   0.0  0
 VMG  CONST_03  C5   N9   N8   C7     0.00   0.0  0
 VMG  CONST_04  N9   C5   C6   C7     0.00   0.0  0
 VMG  CONST_05  C5   C6   C7   N8     0.00   0.0  0
 VMG  CONST_06  C23  C22  C21  C20    0.00   0.0  0
 VMG  CONST_07  C23  C24  C25  C20    0.00   0.0  0
 VMG  CONST_08  C22  C23  C24  C25    0.00   0.0  0
 VMG  CONST_09  C22  C21  C20  C25    0.00   0.0  0
 VMG  CONST_10  C21  C22  C23  C24    0.00   0.0  0
 VMG  CONST_11  C21  C20  C25  C24    0.00   0.0  0
 VMG  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 VMG  CONST_13  C15  C16  C17  C12    0.00   0.0  0
 VMG  CONST_14  C14  C13  C12  C17    0.00   0.0  0
 VMG  CONST_15  C14  C15  C16  C17    0.00   0.0  0
 VMG  CONST_16  C13  C12  C17  C16    0.00   0.0  0
 VMG  CONST_17  C13  C14  C15  C16    0.00   0.0  0
 VMG  CONST_18  C14  C13  C12  N2   180.00   0.0  0
 VMG  CONST_19  C16  C17  C12  N2   180.00   0.0  0
 VMG  CONST_20  N4   C3   N2   C1     0.00   0.0  0
 VMG  CONST_21  C3   N2   C1   C6     0.00   0.0  0
 VMG  CONST_22  C12  N2   C1   C6   180.00   0.0  0
 VMG  CONST_23  N2   C3   N4   C5     0.00   0.0  0
 VMG  CONST_24  C12  N2   C3   N4   180.00   0.0  0
 VMG  CONST_25  C10  N9   C5   C6   180.00   0.0  0
 VMG  CONST_26  C10  N9   N8   C7   180.00   0.0  0
 VMG  CONST_27  N4   C5   N9   C10    0.00   0.0  0
 VMG  CONST_28  C22  C21  C20  C19  180.00   0.0  0
 VMG  CONST_29  C24  C25  C20  C19  180.00   0.0  0
 VMG  CONST_30  C27  C15  C16  C17  180.00   0.0  0
 VMG  CONST_31  C27  C15  C14  C13  180.00   0.0  0
 VMG  CONST_32  C3   N2   C1   O11  180.00   0.0  0
 VMG  CONST_33  C12  N2   C1   O11    0.00   0.0  0
 VMG  CONST_34  S18  C3   N2   C1   180.00   0.0  0
 VMG  CONST_35  S18  C3   N4   C5   180.00   0.0  0
 VMG  CONST_36  C12  N2   C3   S18    0.00   0.0  0
 VMG  CONST_37  H1   C7   C6   C1     0.00   0.0  0
 VMG  CONST_38  H9   C22  C21  C20  180.00   0.0  0
 VMG  CONST_39  H7   C24  C25  C20  180.00   0.0  0
 VMG  CONST_40  H8   C23  C24  C25  180.00   0.0  0
 VMG  CONST_41  H10  C21  C20  C25  180.00   0.0  0
 VMG  CONST_42  H6   C25  C24  C23  180.00   0.0  0
 VMG  CONST_43  H17  C13  C12  N2     0.00   0.0  0
 VMG  CONST_44  H14  C17  C12  N2     0.00   0.0  0
 VMG  CONST_45  H16  C14  C13  C12  180.00   0.0  0
 VMG  CONST_46  H15  C16  C17  C12  180.00   0.0  0
 VMG  Var_01    C13  C12  N2   C1   -91.89  30.0  2
 VMG  Var_02    N2   C3   S18  C19  177.80  30.0  3
 VMG  Var_03    C28  C27  C15  C16  -95.63  30.0  2
 VMG  Var_04    H2   C10  N9   N8   -54.81  30.0  2
 VMG  Var_05    O28  C28  C27  C15   61.90  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
 VMG  chir_01  C19  C20  C26  S18  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
 VMG  plan-1  C19  0.020
 VMG  plan-1  C20  0.020
 VMG  plan-1  C25  0.020
 VMG  plan-1  C24  0.020
 VMG  plan-1  C23  0.020
 VMG  plan-1  C22  0.020
 VMG  plan-1  C21  0.020
 VMG  plan-1  H6   0.020
 VMG  plan-1  H7   0.020
 VMG  plan-1  H8   0.020
 VMG  plan-1  H9   0.020
 VMG  plan-1  H10  0.020
 VMG  plan-2  N2   0.020
 VMG  plan-2  C12  0.020
 VMG  plan-2  C17  0.020
 VMG  plan-2  C16  0.020
 VMG  plan-2  C15  0.020
 VMG  plan-2  C14  0.020
 VMG  plan-2  C13  0.020
 VMG  plan-2  C27  0.020
 VMG  plan-2  H14  0.020
 VMG  plan-2  H15  0.020
 VMG  plan-2  H16  0.020
 VMG  plan-2  H17  0.020
 VMG  plan-3  O11  0.020
 VMG  plan-3  C1   0.020
 VMG  plan-3  C6   0.020
 VMG  plan-3  C7   0.020
 VMG  plan-3  N8   0.020
 VMG  plan-3  N9   0.020
 VMG  plan-3  C10  0.020
 VMG  plan-3  C5   0.020
 VMG  plan-3  N4   0.020
 VMG  plan-3  C3   0.020
 VMG  plan-3  S18  0.020
 VMG  plan-3  N2   0.020
 VMG  plan-3  C12  0.020
 VMG  plan-3  H1   0.020

