# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:51:31 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: 5-[4-(hydroxymethyl)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(CO)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
 VMJ  VMJ  5-[4-(hydroxymethyl)phenyl]-1-methyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  48  28  .  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_VMJ
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
 VMJ  O11  O  O     0  -0.444  14.8720  146.5828  17.5008
 VMJ  C1   C  CR6   0   0.542  15.6446  146.5417  16.5659
 VMJ  N2   N  NR6   0  -0.652  15.9741  147.7237  15.8581
 VMJ  C12  C  CR6   0   0.208  15.3607  148.9361  16.3040
 VMJ  C13  C  CR16  0  -0.215  14.1353  149.3206  15.7805
 VMJ  C14  C  CR16  0  -0.300  13.5504  150.4975  16.2151
 VMJ  C15  C  CR6   0   0.057  14.1777  151.3016  17.1648
 VMJ  C27  C  CH2   0  -0.183  13.5302  152.5962  17.5725
 VMJ  O27  O  OH1   0  -0.665  14.0358  153.0245  18.8099
 VMJ  C16  C  CR16  0  -0.306  15.4045  150.8971  17.6824
 VMJ  C17  C  CR16  0  -0.212  15.9942  149.7160  17.2564
 VMJ  C3   C  CR6   0   0.358  16.8346  147.7565  14.7877
 VMJ  N4   N  N     0  -0.456  17.4408  146.7240  14.3036
 VMJ  C5   C  CR56  0   0.612  17.1655  145.5726  14.9457
 VMJ  N9   N  NR5   0  -0.354  17.6653  144.3678  14.6480
 VMJ  C10  C  CH3   0  -0.527  18.5982  144.0488  13.5936
 VMJ  N8   N  N     0  -0.258  17.1907  143.4227  15.4800
 VMJ  C7   C  CR15  0  -0.087  16.3812  144.0269  16.3171
 VMJ  C6   C  CR56  0  -0.319  16.3190  145.4052  16.0316
 VMJ  S18  S  S2    0   0.097  17.0561  149.3382  14.0693
 VMJ  C19  C  CH1   0  -0.466  18.2809  148.9751  12.7472
 VMJ  C26  C  CH3   0  -0.627  19.6852  148.8179  13.3059
 VMJ  C20  C  CR6   0   0.160  18.1435  150.1054  11.7603
 VMJ  C21  C  CR16  0  -0.309  17.6205  149.8619  10.4940
 VMJ  C22  C  CR16  0  -0.238  17.4856  150.8924   9.5730
 VMJ  C23  C  CR16  0  -0.265  17.8648  152.1835   9.9132
 VMJ  C24  C  CR16  0  -0.238  18.3831  152.4368  11.1770
 VMJ  C25  C  CR16  0  -0.291  18.5238  151.4045  12.0935
 VMJ  H1   H  HCR6  0   0.271  13.6418  148.7021  15.0420
 VMJ  H2   H  HCR6  0   0.261  12.5893  150.7904  15.8099
 VMJ  H3   H  HCH2  0   0.229  13.7180  153.3360  16.7831
 VMJ  H4   H  HCH2  0   0.217  12.4423  152.4525  17.6043
 VMJ  H5   H  HOH1  0   0.463  13.7609  153.9352  18.9476
 VMJ  H6   H  HCR6  0   0.262  15.9127  151.5000  18.4217
 VMJ  H7   H  HCR6  0   0.270  16.9497  149.4072  17.6611
 VMJ  H8   H  HCH3  0   0.272  18.8249  142.9892  13.6524
 VMJ  H9   H  HCH3  0   0.261  18.1681  144.2696  12.6186
 VMJ  H10  H  HCH3  0   0.261  19.5178  144.6184  13.7130
 VMJ  H11  H  HCR5  0   0.277  15.8725  143.4712  17.0894
 VMJ  H12  H  HCH1  0   0.311  17.9624  148.0431  12.2797
 VMJ  H13  H  HCH3  0   0.253  19.7327  147.9876  14.0075
 VMJ  H14  H  HCH3  0   0.246  20.3779  148.6088  12.4891
 VMJ  H15  H  HCH3  0   0.234  20.0240  149.7199  13.8140
 VMJ  H16  H  HCR6  0   0.258  17.3196  148.8566  10.2243
 VMJ  H17  H  HCR6  0   0.259  17.0817  150.6840   8.5908
 VMJ  H18  H  HCR6  0   0.259  17.7571  152.9892   9.1990
 VMJ  H19  H  HCR6  0   0.260  18.6780  153.4410  11.4519
 VMJ  H20  H  HCR6  0   0.258  18.9309  151.6218  13.0743

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
 VMJ  C22  C23  aromatic  1.388  0.020  1.388
 VMJ  C22  C21  aromatic  1.389  0.020  1.389
 VMJ  C23  C24  aromatic  1.389  0.020  1.389
 VMJ  C21  C20  aromatic  1.391  0.020  1.391
 VMJ  C24  C25  aromatic  1.388  0.020  1.388
 VMJ  C20  C25  aromatic  1.394  0.020  1.394
 VMJ  C20  C19  single    1.507  0.020  1.507
 VMJ  C19  C26  single    1.520  0.020  1.520
 VMJ  C19  S18  single    1.838  0.020  1.838
 VMJ  C10  N9   single    1.444  0.020  1.444
 VMJ  S18  C3   single    1.751  0.020  1.751
 VMJ  N4   C3   double    1.292  0.020  1.292
 VMJ  N4   C5   single    1.347  0.020  1.347
 VMJ  N9   C5   aromatic  1.338  0.020  1.338
 VMJ  N9   N8   aromatic  1.346  0.020  1.346
 VMJ  C3   N2   single    1.374  0.020  1.374
 VMJ  C5   C6   aromatic  1.387  0.020  1.387
 VMJ  N8   C7   aromatic  1.312  0.020  1.312
 VMJ  N2   C12  single    1.430  0.020  1.430
 VMJ  N2   C1   single    1.417  0.020  1.417
 VMJ  C6   C7   aromatic  1.409  0.020  1.409
 VMJ  C6   C1   single    1.425  0.020  1.425
 VMJ  C13  C12  aromatic  1.387  0.020  1.387
 VMJ  C13  C14  aromatic  1.384  0.020  1.384
 VMJ  C12  C17  aromatic  1.384  0.020  1.384
 VMJ  C14  C15  aromatic  1.393  0.020  1.393
 VMJ  C1   O11  double    1.214  0.020  1.214
 VMJ  C17  C16  aromatic  1.387  0.020  1.387
 VMJ  C15  C16  aromatic  1.392  0.020  1.392
 VMJ  C15  C27  single    1.504  0.020  1.504
 VMJ  C27  O27  single    1.404  0.020  1.404
 VMJ  C13  H1   single    0.930  0.020  1.080
 VMJ  C14  H2   single    0.930  0.020  1.080
 VMJ  C27  H3   single    0.970  0.020  1.090
 VMJ  C27  H4   single    0.970  0.020  1.090
 VMJ  O27  H5   single    0.850  0.020  0.980
 VMJ  C16  H6   single    0.930  0.020  1.080
 VMJ  C17  H7   single    0.930  0.020  1.080
 VMJ  C10  H8   single    0.970  0.020  1.090
 VMJ  C10  H9   single    0.970  0.020  1.090
 VMJ  C10  H10  single    0.970  0.020  1.090
 VMJ  C7   H11  single    0.930  0.020  1.080
 VMJ  C19  H12  single    0.970  0.020  1.090
 VMJ  C26  H13  single    0.970  0.020  1.090
 VMJ  C26  H14  single    0.970  0.020  1.090
 VMJ  C26  H15  single    0.970  0.020  1.090
 VMJ  C21  H16  single    0.930  0.020  1.080
 VMJ  C22  H17  single    0.930  0.020  1.080
 VMJ  C23  H18  single    0.930  0.020  1.080
 VMJ  C24  H19  single    0.930  0.020  1.080
 VMJ  C25  H20  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
 VMJ  C6   C1   N2   111.59  3.000
 VMJ  C6   C1   O11  128.10  3.000
 VMJ  N2   C1   O11  120.31  3.000
 VMJ  C3   N2   C12  119.43  3.000
 VMJ  C12  N2   C1   116.87  3.000
 VMJ  C3   N2   C1   123.70  3.000
 VMJ  C17  C12  C13  120.52  3.000
 VMJ  C17  C12  N2   119.72  3.000
 VMJ  C13  C12  N2   119.76  3.000
 VMJ  H1   C13  C14  120.49  3.000
 VMJ  H1   C13  C12  120.13  3.000
 VMJ  C14  C13  C12  119.37  3.000
 VMJ  H2   C14  C15  119.88  3.000
 VMJ  H2   C14  C13  119.16  3.000
 VMJ  C15  C14  C13  120.96  3.000
 VMJ  C16  C15  C27  121.93  3.000
 VMJ  C27  C15  C14  119.19  3.000
 VMJ  C16  C15  C14  118.85  3.000
 VMJ  H4   C27  H3   106.17  3.000
 VMJ  H4   C27  O27  111.80  3.000
 VMJ  H3   C27  O27  111.50  3.000
 VMJ  H4   C27  C15  108.77  3.000
 VMJ  H3   C27  C15  108.15  3.000
 VMJ  O27  C27  C15  110.28  3.000
 VMJ  H5   O27  C27  108.20  3.000
 VMJ  H6   C16  C17  119.01  3.000
 VMJ  H6   C16  C15  120.45  3.000
 VMJ  C17  C16  C15  120.53  3.000
 VMJ  H7   C17  C16  120.22  3.000
 VMJ  H7   C17  C12  120.02  3.000
 VMJ  C16  C17  C12  119.76  3.000
 VMJ  S18  C3   N4   120.59  3.000
 VMJ  N4   C3   N2   124.54  3.000
 VMJ  S18  C3   N2   114.86  3.000
 VMJ  C5   N4   C3   114.13  3.000
 VMJ  C6   C5   N9   107.07  3.000
 VMJ  C6   C5   N4   126.96  3.000
 VMJ  N9   C5   N4   125.97  3.000
 VMJ  N8   N9   C10  121.63  3.000
 VMJ  N8   N9   C5   111.29  3.000
 VMJ  C10  N9   C5   127.08  3.000
 VMJ  H10  C10  H9   109.03  3.000
 VMJ  H10  C10  H8   109.19  3.000
 VMJ  H9   C10  H8   109.22  3.000
 VMJ  H10  C10  N9   110.50  3.000
 VMJ  H9   C10  N9   110.74  3.000
 VMJ  H8   C10  N9   108.13  3.000
 VMJ  C7   N8   N9   106.78  3.000
 VMJ  H11  C7   C6   128.91  3.000
 VMJ  H11  C7   N8   120.70  3.000
 VMJ  C6   C7   N8   110.39  3.000
 VMJ  C7   C6   C5   104.47  3.000
 VMJ  C7   C6   C1   136.46  3.000
 VMJ  C5   C6   C1   119.07  3.000
 VMJ  C19  S18  C3   101.59  3.000
 VMJ  H12  C19  C20  109.50  3.000
 VMJ  H12  C19  C26  109.82  3.000
 VMJ  C20  C19  C26  113.75  3.000
 VMJ  H12  C19  S18  106.42  3.000
 VMJ  C26  C19  S18  111.82  3.000
 VMJ  C20  C19  S18  105.20  3.000
 VMJ  H15  C26  H14  108.08  3.000
 VMJ  H15  C26  H13  108.52  3.000
 VMJ  H14  C26  H13  107.99  3.000
 VMJ  H15  C26  C19  111.92  3.000
 VMJ  H14  C26  C19  109.34  3.000
 VMJ  H13  C26  C19  110.88  3.000
 VMJ  C25  C20  C21  118.89  3.000
 VMJ  C25  C20  C19  121.17  3.000
 VMJ  C21  C20  C19  119.94  3.000
 VMJ  H16  C21  C22  119.77  3.000
 VMJ  H16  C21  C20  119.55  3.000
 VMJ  C22  C21  C20  120.68  3.000
 VMJ  H17  C22  C23  120.23  3.000
 VMJ  H17  C22  C21  119.69  3.000
 VMJ  C23  C22  C21  120.08  3.000
 VMJ  H18  C23  C24  120.12  3.000
 VMJ  H18  C23  C22  120.24  3.000
 VMJ  C24  C23  C22  119.64  3.000
 VMJ  H19  C24  C25  119.66  3.000
 VMJ  H19  C24  C23  120.13  3.000
 VMJ  C25  C24  C23  120.20  3.000
 VMJ  H20  C25  C24  119.12  3.000
 VMJ  H20  C25  C20  120.37  3.000
 VMJ  C24  C25  C20  120.51  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
 VMJ  CONST_01  C15  C14  C13  C12    0.00   0.0  0
 VMJ  CONST_02  C15  C16  C17  C12    0.00   0.0  0
 VMJ  CONST_03  C16  C17  C12  C13    0.00   0.0  0
 VMJ  CONST_04  C16  C15  C14  C13    0.00   0.0  0
 VMJ  CONST_05  C17  C12  C13  C14    0.00   0.0  0
 VMJ  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 VMJ  CONST_07  C7   N8   N9   C5     0.00   0.0  0
 VMJ  CONST_08  N8   C7   C6   C5     0.00   0.0  0
 VMJ  CONST_09  C7   C6   C5   N9     0.00   0.0  0
 VMJ  CONST_10  C6   C7   N8   N9     0.00   0.0  0
 VMJ  CONST_11  C6   C5   N9   N8     0.00   0.0  0
 VMJ  CONST_12  C23  C22  C21  C20    0.00   0.0  0
 VMJ  CONST_13  C23  C24  C25  C20    0.00   0.0  0
 VMJ  CONST_14  C24  C23  C22  C21    0.00   0.0  0
 VMJ  CONST_15  C24  C25  C20  C21    0.00   0.0  0
 VMJ  CONST_16  C25  C24  C23  C22    0.00   0.0  0
 VMJ  CONST_17  C25  C20  C21  C22    0.00   0.0  0
 VMJ  CONST_18  C14  C13  C12  N2   180.00   0.0  0
 VMJ  CONST_19  C16  C17  C12  N2   180.00   0.0  0
 VMJ  CONST_20  N4   C3   N2   C1     0.00   0.0  0
 VMJ  CONST_21  C5   N4   C3   N2     0.00   0.0  0
 VMJ  CONST_22  N4   C3   N2   C12  180.00   0.0  0
 VMJ  CONST_23  C6   C1   N2   C12  180.00   0.0  0
 VMJ  CONST_24  C6   C1   N2   C3     0.00   0.0  0
 VMJ  CONST_25  C27  C15  C14  C13  180.00   0.0  0
 VMJ  CONST_26  C17  C16  C15  C27  180.00   0.0  0
 VMJ  CONST_27  C10  N9   C5   N4     0.00   0.0  0
 VMJ  CONST_28  C6   C5   N9   C10  180.00   0.0  0
 VMJ  CONST_29  C7   N8   N9   C10  180.00   0.0  0
 VMJ  CONST_30  C22  C21  C20  C19  180.00   0.0  0
 VMJ  CONST_31  C24  C25  C20  C19  180.00   0.0  0
 VMJ  CONST_32  C3   N2   C1   O11  180.00   0.0  0
 VMJ  CONST_33  C12  N2   C1   O11    0.00   0.0  0
 VMJ  CONST_34  S18  C3   N2   C1   180.00   0.0  0
 VMJ  CONST_35  S18  C3   N2   C12    0.00   0.0  0
 VMJ  CONST_36  S18  C3   N4   C5   180.00   0.0  0
 VMJ  CONST_37  H11  C7   C6   C1     0.00   0.0  0
 VMJ  CONST_38  H1   C13  C12  N2     0.00   0.0  0
 VMJ  CONST_39  H7   C17  C12  N2     0.00   0.0  0
 VMJ  CONST_40  H2   C14  C13  C12  180.00   0.0  0
 VMJ  CONST_41  H6   C16  C17  C12  180.00   0.0  0
 VMJ  CONST_42  H17  C22  C21  C20  180.00   0.0  0
 VMJ  CONST_43  H19  C24  C25  C20  180.00   0.0  0
 VMJ  CONST_44  H18  C23  C22  C21  180.00   0.0  0
 VMJ  CONST_45  H20  C25  C20  C21  180.00   0.0  0
 VMJ  CONST_46  H16  C21  C22  C23  180.00   0.0  0
 VMJ  Var_01    C13  C12  N2   C1   -89.27  30.0  2
 VMJ  Var_02    O27  C27  C15  C14  160.09  30.0  2
 VMJ  Var_03    H8   C10  N9   C5   177.87  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
 VMJ  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
 VMJ  plan-1  N2   0.020
 VMJ  plan-1  C12  0.020
 VMJ  plan-1  C13  0.020
 VMJ  plan-1  C14  0.020
 VMJ  plan-1  C15  0.020
 VMJ  plan-1  C27  0.020
 VMJ  plan-1  C16  0.020
 VMJ  plan-1  C17  0.020
 VMJ  plan-1  H1   0.020
 VMJ  plan-1  H2   0.020
 VMJ  plan-1  H6   0.020
 VMJ  plan-1  H7   0.020
 VMJ  plan-2  C19  0.020
 VMJ  plan-2  C20  0.020
 VMJ  plan-2  C21  0.020
 VMJ  plan-2  C22  0.020
 VMJ  plan-2  C23  0.020
 VMJ  plan-2  C24  0.020
 VMJ  plan-2  C25  0.020
 VMJ  plan-2  H16  0.020
 VMJ  plan-2  H17  0.020
 VMJ  plan-2  H18  0.020
 VMJ  plan-2  H19  0.020
 VMJ  plan-2  H20  0.020
 VMJ  plan-3  O11  0.020
 VMJ  plan-3  C1   0.020
 VMJ  plan-3  N2   0.020
 VMJ  plan-3  C12  0.020
 VMJ  plan-3  C3   0.020
 VMJ  plan-3  N4   0.020
 VMJ  plan-3  C5   0.020
 VMJ  plan-3  N9   0.020
 VMJ  plan-3  C10  0.020
 VMJ  plan-3  N8   0.020
 VMJ  plan-3  C7   0.020
 VMJ  plan-3  C6   0.020
 VMJ  plan-3  S18  0.020
 VMJ  plan-3  H11  0.020

