# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:08:22 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 6-{[(1R)-1-(3-hydroxyphenyl)ethyl]sulfanyl}-1-methyl-5-phenyl-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)c4cccc(O)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
 VM4  VM4  6-{[(1R)-1-(3-hydroxyphenyl)ethyl]sulfanyl}-1-methyl-5-phenyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  45  27  .  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_VM4
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
 VM4  O11  O  O     0  -0.444  37.3306  -15.0386  17.7120
 VM4  C1   C  CR6   0   0.544  37.3043  -15.7436  16.7247
 VM4  N2   N  NR6   0  -0.651  38.5016  -16.0452  16.0301
 VM4  C12  C  CR6   0   0.221  39.7088  -15.4804  16.5506
 VM4  C13  C  CR16  0  -0.229  40.1244  -14.2335  16.1086
 VM4  C14  C  CR16  0  -0.263  41.2980  -13.6916  16.6119
 VM4  C15  C  CR16  0  -0.238  42.0427  -14.3946  17.5501
 VM4  C16  C  CR16  0  -0.263  41.6150  -15.6413  17.9889
 VM4  C17  C  CR16  0  -0.228  40.4427  -16.1891  17.4894
 VM4  C3   C  CR6   0   0.363  38.5517  -16.8313  14.9051
 VM4  N4   N  N     0  -0.458  37.5242  -17.3850  14.3533
 VM4  C5   C  CR56  0   0.608  36.3568  -17.1328  14.9763
 VM4  N9   N  NR5   0  -0.359  35.1497  -17.5841  14.6126
 VM4  C10  C  CH3   0  -0.523  34.8190  -18.4156  13.4824
 VM4  N8   N  N     0  -0.259  34.1906  -17.1421  15.4453
 VM4  C7   C  CR15  0  -0.079  34.7863  -16.4061  16.3527
 VM4  C6   C  CR56  0  -0.321  36.1734  -16.3577  16.1126
 VM4  S18  S  S2    0   0.098  40.1495  -17.0303  14.2154
 VM4  C19  C  CH1   0  -0.470  39.8045  -18.1706  12.8155
 VM4  C26  C  CH3   0  -0.625  39.6326  -19.6044  13.2878
 VM4  C20  C  CR6   0   0.176  40.9463  -17.9772  11.8519
 VM4  C21  C  CR16  0  -0.339  40.7142  -17.3843  10.6167
 VM4  C22  C  CR16  0  -0.226  41.7677  -17.2056   9.7287
 VM4  C23  C  CR16  0  -0.348  43.0514  -17.6033  10.0598
 VM4  C24  C  CR6   0   0.378  43.2881  -18.1940  11.3004
 VM4  O24  O  OH1   0  -0.631  44.5512  -18.5642  11.5862
 VM4  C25  C  CR16  0  -0.425  42.2354  -18.3813  12.1912
 VM4  H1   H  HCR6  0   0.273  39.5356  -13.6951  15.3771
 VM4  H2   H  HCR6  0   0.268  41.6281  -12.7194  16.2715
 VM4  H3   H  HCR6  0   0.266  42.9578  -13.9699  17.9413
 VM4  H4   H  HCR6  0   0.268  42.1935  -16.1892  18.7205
 VM4  H5   H  HCR6  0   0.273  40.1019  -17.1617  17.8205
 VM4  H6   H  HCH3  0   0.264  34.2175  -17.8616  12.7641
 VM4  H7   H  HCH3  0   0.264  35.7400  -18.7342  13.0030
 VM4  H8   H  HCH3  0   0.265  34.2682  -19.2930  13.8139
 VM4  H9   H  HCR5  0   0.277  34.2192  -15.9368  17.1416
 VM4  H10  H  HCH1  0   0.314  38.8814  -17.8210  12.3536
 VM4  H11  H  HCH3  0   0.252  38.7941  -19.6863  13.9767
 VM4  H12  H  HCH3  0   0.246  39.4277  -20.2469  12.4301
 VM4  H13  H  HCH3  0   0.235  40.5260  -19.9784  13.7863
 VM4  H14  H  HCR6  0   0.256  39.7147  -17.0671  10.3481
 VM4  H15  H  HCR6  0   0.260  41.5851  -16.7487   8.7646
 VM4  H16  H  HCR6  0   0.266  43.8712  -17.4609   9.3669
 VM4  H17  H  HOH1  0   0.475  44.5951  -18.9682  12.4600
 VM4  H18  H  HCR6  0   0.271  42.4292  -18.8428  13.1549

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
 VM4  C22  C23  aromatic  1.384  0.020  1.384
 VM4  C22  C21  aromatic  1.389  0.020  1.389
 VM4  C23  C24  aromatic  1.394  0.020  1.394
 VM4  C21  C20  aromatic  1.390  0.020  1.390
 VM4  C24  O24  single    1.347  0.020  1.347
 VM4  C24  C25  aromatic  1.392  0.020  1.392
 VM4  C20  C25  aromatic  1.393  0.020  1.393
 VM4  C20  C19  single    1.507  0.020  1.507
 VM4  C19  C26  single    1.519  0.020  1.519
 VM4  C19  S18  single    1.838  0.020  1.838
 VM4  C10  N9   single    1.442  0.020  1.442
 VM4  S18  C3   single    1.752  0.020  1.752
 VM4  N4   C3   double    1.291  0.020  1.291
 VM4  N4   C5   single    1.347  0.020  1.347
 VM4  N9   C5   aromatic  1.339  0.020  1.339
 VM4  N9   N8   aromatic  1.345  0.020  1.345
 VM4  C3   N2   single    1.373  0.020  1.373
 VM4  C5   C6   aromatic  1.388  0.020  1.388
 VM4  N8   C7   aromatic  1.311  0.020  1.311
 VM4  N2   C12  single    1.431  0.020  1.431
 VM4  N2   C1   single    1.417  0.020  1.417
 VM4  C6   C7   aromatic  1.409  0.020  1.409
 VM4  C6   C1   single    1.425  0.020  1.425
 VM4  C13  C12  aromatic  1.387  0.020  1.387
 VM4  C13  C14  aromatic  1.387  0.020  1.387
 VM4  C12  C17  aromatic  1.386  0.020  1.386
 VM4  C1   O11  double    1.213  0.020  1.213
 VM4  C14  C15  aromatic  1.389  0.020  1.389
 VM4  C17  C16  aromatic  1.387  0.020  1.387
 VM4  C15  C16  aromatic  1.389  0.020  1.389
 VM4  C13  H1   single    0.930  0.020  1.080
 VM4  C14  H2   single    0.930  0.020  1.080
 VM4  C15  H3   single    0.930  0.020  1.080
 VM4  C16  H4   single    0.930  0.020  1.080
 VM4  C17  H5   single    0.930  0.020  1.080
 VM4  C10  H6   single    0.970  0.020  1.090
 VM4  C10  H7   single    0.970  0.020  1.090
 VM4  C10  H8   single    0.970  0.020  1.090
 VM4  C7   H9   single    0.930  0.020  1.080
 VM4  C19  H10  single    0.970  0.020  1.090
 VM4  C26  H11  single    0.970  0.020  1.090
 VM4  C26  H12  single    0.970  0.020  1.090
 VM4  C26  H13  single    0.970  0.020  1.090
 VM4  C21  H14  single    0.930  0.020  1.080
 VM4  C22  H15  single    0.930  0.020  1.080
 VM4  C23  H16  single    0.930  0.020  1.080
 VM4  O24  H17  single    0.850  0.020  0.980
 VM4  C25  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
 VM4  C6   C1   N2   111.61  3.000
 VM4  C6   C1   O11  128.10  3.000
 VM4  N2   C1   O11  120.28  3.000
 VM4  C3   N2   C12  119.55  3.000
 VM4  C12  N2   C1   116.79  3.000
 VM4  C3   N2   C1   123.66  3.000
 VM4  C17  C12  C13  121.13  3.000
 VM4  C17  C12  N2   119.41  3.000
 VM4  C13  C12  N2   119.46  3.000
 VM4  H1   C13  C14  120.74  3.000
 VM4  H1   C13  C12  119.98  3.000
 VM4  C14  C13  C12  119.28  3.000
 VM4  H2   C14  C15  120.26  3.000
 VM4  H2   C14  C13  119.67  3.000
 VM4  C15  C14  C13  120.07  3.000
 VM4  H3   C15  C16  119.90  3.000
 VM4  H3   C15  C14  119.93  3.000
 VM4  C16  C15  C14  120.17  3.000
 VM4  H4   C16  C17  119.70  3.000
 VM4  H4   C16  C15  120.23  3.000
 VM4  C17  C16  C15  120.06  3.000
 VM4  H5   C17  C16  120.72  3.000
 VM4  H5   C17  C12  119.99  3.000
 VM4  C16  C17  C12  119.29  3.000
 VM4  S18  C3   N4   120.60  3.000
 VM4  N4   C3   N2   124.51  3.000
 VM4  S18  C3   N2   114.89  3.000
 VM4  C5   N4   C3   114.32  3.000
 VM4  C6   C5   N9   106.95  3.000
 VM4  C6   C5   N4   126.71  3.000
 VM4  N9   C5   N4   126.34  3.000
 VM4  N8   N9   C10  120.75  3.000
 VM4  N8   N9   C5   111.35  3.000
 VM4  C10  N9   C5   127.89  3.000
 VM4  H8   C10  H7   109.11  3.000
 VM4  H8   C10  H6   109.38  3.000
 VM4  H7   C10  H6   109.06  3.000
 VM4  H8   C10  N9   110.03  3.000
 VM4  H7   C10  N9   108.71  3.000
 VM4  H6   C10  N9   110.53  3.000
 VM4  C7   N8   N9   106.79  3.000
 VM4  H9   C7   C6   128.85  3.000
 VM4  H9   C7   N8   120.75  3.000
 VM4  C6   C7   N8   110.41  3.000
 VM4  C7   C6   C5   104.51  3.000
 VM4  C7   C6   C1   136.31  3.000
 VM4  C5   C6   C1   119.18  3.000
 VM4  C19  S18  C3   101.48  3.000
 VM4  H10  C19  C20  109.25  3.000
 VM4  H10  C19  C26  109.80  3.000
 VM4  C20  C19  C26  113.94  3.000
 VM4  H10  C19  S18  106.43  3.000
 VM4  C26  C19  S18  111.71  3.000
 VM4  C20  C19  S18  105.38  3.000
 VM4  H13  C26  H12  108.15  3.000
 VM4  H13  C26  H11  108.45  3.000
 VM4  H12  C26  H11  107.97  3.000
 VM4  H13  C26  C19  111.94  3.000
 VM4  H12  C26  C19  109.42  3.000
 VM4  H11  C26  C19  110.78  3.000
 VM4  C25  C20  C21  119.67  3.000
 VM4  C25  C20  C19  120.55  3.000
 VM4  C21  C20  C19  119.78  3.000
 VM4  H14  C21  C22  120.25  3.000
 VM4  H14  C21  C20  119.99  3.000
 VM4  C22  C21  C20  119.76  3.000
 VM4  H15  C22  C23  119.39  3.000
 VM4  H15  C22  C21  119.72  3.000
 VM4  C23  C22  C21  120.89  3.000
 VM4  H16  C23  C24  119.78  3.000
 VM4  H16  C23  C22  120.75  3.000
 VM4  C24  C23  C22  119.47  3.000
 VM4  C25  C24  O24  122.45  3.000
 VM4  C25  C24  C23  119.88  3.000
 VM4  O24  C24  C23  117.67  3.000
 VM4  H17  O24  C24  110.51  3.000
 VM4  H18  C25  C24  119.36  3.000
 VM4  H18  C25  C20  120.31  3.000
 VM4  C24  C25  C20  120.33  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
 VM4  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 VM4  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 VM4  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 VM4  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 VM4  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 VM4  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 VM4  CONST_07  C7   N8   N9   C5      0.00   0.0  0
 VM4  CONST_08  N8   C7   C6   C5      0.00   0.0  0
 VM4  CONST_09  C7   C6   C5   N9      0.00   0.0  0
 VM4  CONST_10  C6   C7   N8   N9      0.00   0.0  0
 VM4  CONST_11  C6   C5   N9   N8      0.00   0.0  0
 VM4  CONST_12  C23  C22  C21  C20     0.00   0.0  0
 VM4  CONST_13  C23  C24  C25  C20     0.00   0.0  0
 VM4  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 VM4  CONST_15  C24  C25  C20  C21     0.00   0.0  0
 VM4  CONST_16  C25  C24  C23  C22     0.00   0.0  0
 VM4  CONST_17  C25  C20  C21  C22     0.00   0.0  0
 VM4  CONST_18  C14  C13  C12  N2    180.00   0.0  0
 VM4  CONST_19  C16  C17  C12  N2    180.00   0.0  0
 VM4  CONST_20  N4   C3   N2   C1      0.00   0.0  0
 VM4  CONST_21  C5   N4   C3   N2      0.00   0.0  0
 VM4  CONST_22  N4   C3   N2   C12   180.00   0.0  0
 VM4  CONST_23  C6   C1   N2   C12   180.00   0.0  0
 VM4  CONST_24  C6   C1   N2   C3      0.00   0.0  0
 VM4  CONST_25  C10  N9   C5   N4      0.00   0.0  0
 VM4  CONST_26  C6   C5   N9   C10   180.00   0.0  0
 VM4  CONST_27  C7   N8   N9   C10   180.00   0.0  0
 VM4  CONST_28  C22  C21  C20  C19   180.00   0.0  0
 VM4  CONST_29  C24  C25  C20  C19   180.00   0.0  0
 VM4  CONST_30  O24  C24  C25  C20   180.00   0.0  0
 VM4  CONST_31  O24  C24  C23  C22   180.00   0.0  0
 VM4  CONST_32  C3   N2   C1   O11   180.00   0.0  0
 VM4  CONST_33  C12  N2   C1   O11     0.00   0.0  0
 VM4  CONST_34  S18  C3   N2   C1    180.00   0.0  0
 VM4  CONST_35  S18  C3   N2   C12     0.00   0.0  0
 VM4  CONST_36  S18  C3   N4   C5    180.00   0.0  0
 VM4  CONST_37  H9   C7   C6   C1      0.00   0.0  0
 VM4  CONST_38  H1   C13  C12  N2      0.00   0.0  0
 VM4  CONST_39  H5   C17  C12  N2      0.00   0.0  0
 VM4  CONST_40  H2   C14  C13  C12   180.00   0.0  0
 VM4  CONST_41  H4   C16  C17  C12   180.00   0.0  0
 VM4  CONST_42  H3   C15  C14  C13   180.00   0.0  0
 VM4  CONST_43  H15  C22  C21  C20   180.00   0.0  0
 VM4  CONST_44  H16  C23  C22  C21   180.00   0.0  0
 VM4  CONST_45  H18  C25  C20  C21   180.00   0.0  0
 VM4  CONST_46  H14  C21  C22  C23   180.00   0.0  0
 VM4  Var_01    C13  C12  N2   C1    -89.74  30.0  2
 VM4  Var_02    H6   C10  N9   C5   -113.15  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
 VM4  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
 VM4  plan-1  N2   0.020
 VM4  plan-1  C12  0.020
 VM4  plan-1  C13  0.020
 VM4  plan-1  C14  0.020
 VM4  plan-1  C15  0.020
 VM4  plan-1  C16  0.020
 VM4  plan-1  C17  0.020
 VM4  plan-1  H1   0.020
 VM4  plan-1  H2   0.020
 VM4  plan-1  H3   0.020
 VM4  plan-1  H4   0.020
 VM4  plan-1  H5   0.020
 VM4  plan-2  C19  0.020
 VM4  plan-2  C20  0.020
 VM4  plan-2  C21  0.020
 VM4  plan-2  C22  0.020
 VM4  plan-2  C23  0.020
 VM4  plan-2  C24  0.020
 VM4  plan-2  O24  0.020
 VM4  plan-2  C25  0.020
 VM4  plan-2  H14  0.020
 VM4  plan-2  H15  0.020
 VM4  plan-2  H16  0.020
 VM4  plan-2  H18  0.020
 VM4  plan-3  O11  0.020
 VM4  plan-3  C1   0.020
 VM4  plan-3  N2   0.020
 VM4  plan-3  C12  0.020
 VM4  plan-3  C3   0.020
 VM4  plan-3  N4   0.020
 VM4  plan-3  C5   0.020
 VM4  plan-3  N9   0.020
 VM4  plan-3  C10  0.020
 VM4  plan-3  N8   0.020
 VM4  plan-3  C7   0.020
 VM4  plan-3  C6   0.020
 VM4  plan-3  S18  0.020
 VM4  plan-3  H9   0.020

