# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:39:02 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-methyl-5-phenyl-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)N1c3ccccc3)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
 VLY  VLY  1-methyl-5-phenyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  44  26  .  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_VLY
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
 VLY  C1   C  CR6   0   0.544  37.4470  -15.7247  16.7597
 VLY  N2   N  NR6   0  -0.651  38.6092  -16.0582  16.0215
 VLY  C3   C  CR6   0   0.362  38.5987  -16.8589  14.9057
 VLY  N4   N  N     0  -0.458  37.5385  -17.3944  14.3994
 VLY  C5   C  CR56  0   0.608  36.4020  -17.1088  15.0636
 VLY  C6   C  CR56  0  -0.321  36.2800  -16.3188  16.1978
 VLY  C7   C  CR15  0  -0.079  34.9025  -16.3346  16.4922
 VLY  C12  C  CR6   0   0.221  39.8474  -15.5131  16.4869
 VLY  C13  C  CR16  0  -0.229  40.2712  -14.2812  16.0116
 VLY  C14  C  CR16  0  -0.263  41.4751  -13.7583  16.4604
 VLY  C15  C  CR16  0  -0.238  42.2417  -14.4650  17.3780
 VLY  C16  C  CR16  0  -0.263  41.8056  -15.6964  17.8506
 VLY  C17  C  CR16  0  -0.228  40.6030  -16.2252  17.4057
 VLY  C19  C  CH1   0  -0.466  39.7475  -18.2585  12.7913
 VLY  O11  O  O     0  -0.444  37.5277  -15.0130  17.7393
 VLY  N8   N  N     0  -0.259  34.2560  -17.0661  15.6165
 VLY  N9   N  NR5   0  -0.359  35.1722  -17.5367  14.7516
 VLY  S18  S  S2    0   0.098  40.1645  -17.1058  14.1610
 VLY  C26  C  CH3   0  -0.626  39.5380  -19.6780  13.2915
 VLY  C20  C  CR6   0   0.159  40.8773  -18.1240  11.8031
 VLY  C25  C  CR16  0  -0.291  42.1617  -18.5704  12.1098
 VLY  C24  C  CR16  0  -0.237  43.1926  -18.4346  11.1909
 VLY  C23  C  CR16  0  -0.265  42.9524  -17.8549   9.9515
 VLY  C22  C  CR16  0  -0.238  41.6758  -17.4087   9.6382
 VLY  C21  C  CR16  0  -0.308  40.6469  -17.5394  10.5614
 VLY  H1   H  HCR5  0   0.277  34.3766  -15.8456  17.2975
 VLY  H2   H  HCH3  0   0.263  34.1721  -17.8116  12.9380
 VLY  H3   H  HCH3  0   0.264  35.6761  -18.7245  13.1405
 VLY  H4   H  HCH3  0   0.265  34.2166  -19.2296  14.0065
 VLY  H5   H  HCR6  0   0.273  39.6652  -13.7405  15.2962
 VLY  H6   H  HCR6  0   0.268  41.8119  -12.7981  16.0934
 VLY  H7   H  HCR6  0   0.266  43.1805  -14.0553  17.7265
 VLY  H8   H  HCR6  0   0.268  42.4012  -16.2466  18.5665
 VLY  H9   H  HCR6  0   0.273  40.2555  -17.1857  17.7639
 VLY  H10  H  HCH1  0   0.311  38.8268  -17.8852  12.3422
 VLY  H11  H  HCH3  0   0.253  38.7102  -19.7236  13.9962
 VLY  H12  H  HCH3  0   0.246  39.2965  -20.3266  12.4478
 VLY  H13  H  HCH3  0   0.235  40.4283  -20.0729  13.7789
 VLY  H14  H  HCR6  0   0.258  42.3690  -19.0250  13.0717
 VLY  H15  H  HCR6  0   0.260  44.1855  -18.7825  11.4446
 VLY  H16  H  HCR6  0   0.259  43.7568  -17.7512   9.2352
 VLY  H17  H  HCR6  0   0.259  41.4781  -16.9560   8.6752
 VLY  H18  H  HCR6  0   0.258  39.6528  -17.1877  10.3125
 VLY  C10  C  CH3   0  -0.523  34.7806  -18.3729  13.6447

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
 VLY  C22  C23  aromatic  1.388  0.020  1.388
 VLY  C22  C21  aromatic  1.389  0.020  1.389
 VLY  C23  C24  aromatic  1.389  0.020  1.389
 VLY  C21  C20  aromatic  1.392  0.020  1.392
 VLY  C24  C25  aromatic  1.388  0.020  1.388
 VLY  C20  C25  aromatic  1.394  0.020  1.394
 VLY  C20  C19  single    1.507  0.020  1.507
 VLY  C19  C26  single    1.520  0.020  1.520
 VLY  C19  S18  single    1.838  0.020  1.838
 VLY  C10  N9   single    1.442  0.020  1.442
 VLY  S18  C3   single    1.751  0.020  1.751
 VLY  N4   C3   double    1.291  0.020  1.291
 VLY  N4   C5   single    1.347  0.020  1.347
 VLY  N9   C5   aromatic  1.339  0.020  1.339
 VLY  N9   N8   aromatic  1.345  0.020  1.345
 VLY  C3   N2   single    1.373  0.020  1.373
 VLY  C5   C6   aromatic  1.388  0.020  1.388
 VLY  N8   C7   aromatic  1.312  0.020  1.312
 VLY  N2   C12  single    1.431  0.020  1.431
 VLY  N2   C1   single    1.417  0.020  1.417
 VLY  C6   C7   aromatic  1.409  0.020  1.409
 VLY  C6   C1   single    1.425  0.020  1.425
 VLY  C13  C12  aromatic  1.387  0.020  1.387
 VLY  C13  C14  aromatic  1.387  0.020  1.387
 VLY  C12  C17  aromatic  1.386  0.020  1.386
 VLY  C1   O11  double    1.214  0.020  1.214
 VLY  C14  C15  aromatic  1.389  0.020  1.389
 VLY  C17  C16  aromatic  1.387  0.020  1.387
 VLY  C15  C16  aromatic  1.389  0.020  1.389
 VLY  C7   H1   single    0.930  0.020  1.080
 VLY  C10  H2   single    0.970  0.020  1.090
 VLY  C10  H3   single    0.970  0.020  1.090
 VLY  C10  H4   single    0.970  0.020  1.090
 VLY  C13  H5   single    0.930  0.020  1.080
 VLY  C14  H6   single    0.930  0.020  1.080
 VLY  C15  H7   single    0.930  0.020  1.080
 VLY  C16  H8   single    0.930  0.020  1.080
 VLY  C17  H9   single    0.930  0.020  1.080
 VLY  C19  H10  single    0.970  0.020  1.090
 VLY  C26  H11  single    0.970  0.020  1.090
 VLY  C26  H12  single    0.970  0.020  1.090
 VLY  C26  H13  single    0.970  0.020  1.090
 VLY  C25  H14  single    0.930  0.020  1.080
 VLY  C24  H15  single    0.930  0.020  1.080
 VLY  C23  H16  single    0.930  0.020  1.080
 VLY  C22  H17  single    0.930  0.020  1.080
 VLY  C21  H18  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
 VLY  O11  C1   C6   128.11  3.000
 VLY  O11  C1   N2   120.28  3.000
 VLY  C6   C1   N2   111.61  3.000
 VLY  C12  N2   C3   119.54  3.000
 VLY  C12  N2   C1   116.80  3.000
 VLY  C3   N2   C1   123.67  3.000
 VLY  S18  C3   N4   120.60  3.000
 VLY  N4   C3   N2   124.51  3.000
 VLY  S18  C3   N2   114.88  3.000
 VLY  C5   N4   C3   114.30  3.000
 VLY  N9   C5   C6   106.96  3.000
 VLY  C6   C5   N4   126.73  3.000
 VLY  N9   C5   N4   126.32  3.000
 VLY  C7   C6   C5   104.50  3.000
 VLY  C7   C6   C1   136.31  3.000
 VLY  C5   C6   C1   119.18  3.000
 VLY  H1   C7   N8   120.72  3.000
 VLY  H1   C7   C6   128.87  3.000
 VLY  N8   C7   C6   110.41  3.000
 VLY  C17  C12  C13  121.12  3.000
 VLY  C17  C12  N2   119.44  3.000
 VLY  C13  C12  N2   119.43  3.000
 VLY  H5   C13  C14  120.76  3.000
 VLY  H5   C13  C12  119.95  3.000
 VLY  C14  C13  C12  119.29  3.000
 VLY  H6   C14  C15  120.26  3.000
 VLY  H6   C14  C13  119.68  3.000
 VLY  C15  C14  C13  120.06  3.000
 VLY  H7   C15  C16  119.90  3.000
 VLY  H7   C15  C14  119.93  3.000
 VLY  C16  C15  C14  120.17  3.000
 VLY  H8   C16  C17  119.72  3.000
 VLY  H8   C16  C15  120.21  3.000
 VLY  C17  C16  C15  120.07  3.000
 VLY  H9   C17  C16  120.70  3.000
 VLY  H9   C17  C12  120.01  3.000
 VLY  C16  C17  C12  119.29  3.000
 VLY  H10  C19  C20  109.41  3.000
 VLY  H10  C19  C26  109.82  3.000
 VLY  C20  C19  C26  113.74  3.000
 VLY  H10  C19  S18  106.49  3.000
 VLY  C26  C19  S18  111.83  3.000
 VLY  C20  C19  S18  105.22  3.000
 VLY  N9   N8   C7   106.78  3.000
 VLY  N8   N9   C10  120.78  3.000
 VLY  N8   N9   C5   111.35  3.000
 VLY  C10  N9   C5   127.87  3.000
 VLY  C19  S18  C3   101.68  3.000
 VLY  H13  C26  H12  108.15  3.000
 VLY  H13  C26  H11  108.48  3.000
 VLY  H12  C26  H11  107.91  3.000
 VLY  H13  C26  C19  111.92  3.000
 VLY  H12  C26  C19  109.34  3.000
 VLY  H11  C26  C19  110.93  3.000
 VLY  C21  C20  C25  118.90  3.000
 VLY  C25  C20  C19  121.19  3.000
 VLY  C21  C20  C19  119.90  3.000
 VLY  H14  C25  C24  119.11  3.000
 VLY  H14  C25  C20  120.38  3.000
 VLY  C24  C25  C20  120.50  3.000
 VLY  H15  C24  C23  120.13  3.000
 VLY  H15  C24  C25  119.67  3.000
 VLY  C23  C24  C25  120.21  3.000
 VLY  H16  C23  C22  120.22  3.000
 VLY  H16  C23  C24  120.14  3.000
 VLY  C22  C23  C24  119.64  3.000
 VLY  H17  C22  C21  119.71  3.000
 VLY  H17  C22  C23  120.22  3.000
 VLY  C21  C22  C23  120.07  3.000
 VLY  H18  C21  C22  119.77  3.000
 VLY  H18  C21  C20  119.55  3.000
 VLY  C22  C21  C20  120.68  3.000
 VLY  H4   C10  H3   109.09  3.000
 VLY  H4   C10  H2   109.41  3.000
 VLY  H3   C10  H2   109.06  3.000
 VLY  H4   C10  N9   110.02  3.000
 VLY  H3   C10  N9   108.68  3.000
 VLY  H2   C10  N9   110.56  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
 VLY  CONST_01  C7   N8   N9   C5      0.00   0.0  0
 VLY  CONST_02  N8   C7   C6   C5      0.00   0.0  0
 VLY  CONST_03  N8   N9   C5   C6      0.00   0.0  0
 VLY  CONST_04  N9   N8   C7   C6      0.00   0.0  0
 VLY  CONST_05  N9   C5   C6   C7      0.00   0.0  0
 VLY  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 VLY  CONST_07  C15  C16  C17  C12     0.00   0.0  0
 VLY  CONST_08  C16  C17  C12  C13     0.00   0.0  0
 VLY  CONST_09  C16  C15  C14  C13     0.00   0.0  0
 VLY  CONST_10  C17  C12  C13  C14     0.00   0.0  0
 VLY  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 VLY  CONST_12  C23  C22  C21  C20     0.00   0.0  0
 VLY  CONST_13  C23  C24  C25  C20     0.00   0.0  0
 VLY  CONST_14  C22  C23  C24  C25     0.00   0.0  0
 VLY  CONST_15  C22  C21  C20  C25     0.00   0.0  0
 VLY  CONST_16  C21  C22  C23  C24     0.00   0.0  0
 VLY  CONST_17  C21  C20  C25  C24     0.00   0.0  0
 VLY  CONST_18  C14  C13  C12  N2    180.00   0.0  0
 VLY  CONST_19  C16  C17  C12  N2    180.00   0.0  0
 VLY  CONST_20  N4   C3   N2   C1      0.00   0.0  0
 VLY  CONST_21  C5   N4   C3   N2      0.00   0.0  0
 VLY  CONST_22  C6   C1   N2   C3      0.00   0.0  0
 VLY  CONST_23  C12  N2   C3   N4    180.00   0.0  0
 VLY  CONST_24  C12  N2   C1   C6    180.00   0.0  0
 VLY  CONST_25  C10  N9   C5   N4      0.00   0.0  0
 VLY  CONST_26  C10  N9   C5   C6    180.00   0.0  0
 VLY  CONST_27  C10  N9   N8   C7    180.00   0.0  0
 VLY  CONST_28  C22  C21  C20  C19   180.00   0.0  0
 VLY  CONST_29  C24  C25  C20  C19   180.00   0.0  0
 VLY  CONST_30  S18  C3   N2   C1    180.00   0.0  0
 VLY  CONST_31  O11  C1   N2   C3    180.00   0.0  0
 VLY  CONST_32  S18  C3   N4   C5    180.00   0.0  0
 VLY  CONST_33  S18  C3   N2   C12     0.00   0.0  0
 VLY  CONST_34  O11  C1   N2   C12     0.00   0.0  0
 VLY  CONST_35  H1   C7   C6   C1      0.00   0.0  0
 VLY  CONST_36  H5   C13  C12  N2      0.00   0.0  0
 VLY  CONST_37  H9   C17  C12  N2      0.00   0.0  0
 VLY  CONST_38  H6   C14  C13  C12   180.00   0.0  0
 VLY  CONST_39  H8   C16  C17  C12   180.00   0.0  0
 VLY  CONST_40  H7   C15  C14  C13   180.00   0.0  0
 VLY  CONST_41  H17  C22  C21  C20   180.00   0.0  0
 VLY  CONST_42  H15  C24  C25  C20   180.00   0.0  0
 VLY  CONST_43  H16  C23  C24  C25   180.00   0.0  0
 VLY  CONST_44  H18  C21  C20  C25   180.00   0.0  0
 VLY  CONST_45  H14  C25  C24  C23   180.00   0.0  0
 VLY  Var_01    C13  C12  N2   C1    -89.90  30.0  2
 VLY  Var_02    H2   C10  N9   C5   -112.63  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
 VLY  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
 VLY  plan-1  N2   0.020
 VLY  plan-1  C12  0.020
 VLY  plan-1  C13  0.020
 VLY  plan-1  C14  0.020
 VLY  plan-1  C15  0.020
 VLY  plan-1  C16  0.020
 VLY  plan-1  C17  0.020
 VLY  plan-1  H5   0.020
 VLY  plan-1  H6   0.020
 VLY  plan-1  H7   0.020
 VLY  plan-1  H8   0.020
 VLY  plan-1  H9   0.020
 VLY  plan-2  C19  0.020
 VLY  plan-2  C20  0.020
 VLY  plan-2  C25  0.020
 VLY  plan-2  C24  0.020
 VLY  plan-2  C23  0.020
 VLY  plan-2  C22  0.020
 VLY  plan-2  C21  0.020
 VLY  plan-2  H14  0.020
 VLY  plan-2  H15  0.020
 VLY  plan-2  H16  0.020
 VLY  plan-2  H17  0.020
 VLY  plan-2  H18  0.020
 VLY  plan-3  C1   0.020
 VLY  plan-3  N2   0.020
 VLY  plan-3  C3   0.020
 VLY  plan-3  N4   0.020
 VLY  plan-3  C5   0.020
 VLY  plan-3  C6   0.020
 VLY  plan-3  C7   0.020
 VLY  plan-3  C12  0.020
 VLY  plan-3  O11  0.020
 VLY  plan-3  N8   0.020
 VLY  plan-3  N9   0.020
 VLY  plan-3  S18  0.020
 VLY  plan-3  H1   0.020
 VLY  plan-3  C10  0.020

