# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:11:30 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-methyl-5-phenyl-6-{[(1R)-1-(pyridin-2-yl)ethyl]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)c4ccccn4
#
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
 VMA  VMA  1-methyl-5-phenyl-6-{[(1R)-1-(pyridin-2-yl)ethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  43  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_VMA
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
 VMA  C5   C  CR56  0   0.608  36.9080  -17.1203  14.9474
 VMA  C6   C  CR56  0  -0.322  36.7287  -16.4172  16.1300
 VMA  C21  C  CR16  0  -0.334  41.2019  -17.6899  10.3956
 VMA  C24  C  CR16  0  -0.074  43.7045  -17.5848  11.4337
 VMA  O11  O  O     0  -0.445  37.8928  -15.2049  17.8067
 VMA  C1   C  CR6   0   0.543  37.8623  -15.8436  16.7752
 VMA  C7   C  CR15  0  -0.079  35.3429  -16.4840  16.3739
 VMA  N8   N  N     0  -0.259  34.7441  -17.1643  15.4260
 VMA  N9   N  NR5   0  -0.359  35.7000  -17.5511  14.5623
 VMA  C10  C  CH3   0  -0.523  35.3664  -18.3184  13.3883
 VMA  N4   N  N     0  -0.459  38.0726  -17.3330  14.3056
 VMA  C3   C  CR6   0   0.363  39.1040  -16.8146  14.8850
 VMA  N2   N  NR6   0  -0.652  39.0564  -16.0988  16.0572
 VMA  C12  C  CR6   0   0.223  40.2633  -15.5614  16.6069
 VMA  C17  C  CR16  0  -0.228  41.0002  -16.3186  17.5045
 VMA  C16  C  CR16  0  -0.263  42.1710  -15.7953  18.0332
 VMA  C15  C  CR16  0  -0.238  42.5938  -14.5244  17.6647
 VMA  C14  C  CR16  0  -0.263  41.8460  -13.7730  16.7674
 VMA  C13  C  CR16  0  -0.229  40.6741  -14.2904  16.2351
 VMA  S18  S  S2    0   0.107  40.7066  -16.9857  14.1974
 VMA  C19  C  CH1   0  -0.450  40.3290  -18.0167  12.7310
 VMA  C26  C  CH3   0  -0.629  40.1950  -19.4861  13.1052
 VMA  C20  C  CR6   0   0.306  41.4550  -17.7930  11.7583
 VMA  N25  N  N     0  -0.421  42.6818  -17.7416  12.2647
 VMA  C23  C  CR16  0  -0.327  43.5566  -17.4802  10.0588
 VMA  C22  C  CR16  0  -0.147  42.2752  -17.5350   9.5319
 VMA  H2   H  HCR6  0   0.267  44.6899  -17.5386  11.8836
 VMA  H3   H  HCR5  0   0.277  34.7785  -16.0655  17.1929
 VMA  H4   H  HCH3  0   0.265  34.8160  -19.2123  13.6730
 VMA  H5   H  HCH3  0   0.263  34.7641  -17.7256  12.7024
 VMA  H6   H  HCH3  0   0.264  36.2864  -18.6114  12.8908
 VMA  H7   H  HCR6  0   0.272  40.6629  -17.3090  17.7817
 VMA  H8   H  HCR6  0   0.268  42.7515  -16.3807  18.7335
 VMA  H9   H  HCR6  0   0.266  43.5075  -14.1189  18.0787
 VMA  H10  H  HCR6  0   0.267  42.1722  -12.7820  16.4820
 VMA  H11  H  HCR6  0   0.273  40.0831  -13.7140  15.5351
 VMA  H12  H  HCH1  0   0.310  39.3937  -17.6522  12.3068
 VMA  H13  H  HCH3  0   0.252  39.3906  -19.6307  13.8243
 VMA  H14  H  HCH3  0   0.246  39.9594  -20.0730  12.2158
 VMA  H15  H  HCH3  0   0.238  41.1224  -19.8661  13.5324
 VMA  H16  H  HCR6  0   0.273  44.4223  -17.3541   9.4239
 VMA  H17  H  HCR6  0   0.277  42.1126  -17.4531   8.4654
 VMA  H1   H  HCR6  0   0.273  40.1873  -17.7307  10.0216

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
 VMA  C22  C23  aromatic  1.387  0.020  1.387
 VMA  C22  C21  aromatic  1.386  0.020  1.386
 VMA  C23  C24  aromatic  1.387  0.020  1.387
 VMA  C21  C20  aromatic  1.390  0.020  1.390
 VMA  C24  N25  aromatic  1.327  0.020  1.327
 VMA  C20  N25  aromatic  1.328  0.020  1.328
 VMA  C20  C19  single    1.505  0.020  1.505
 VMA  C19  C26  single    1.522  0.020  1.522
 VMA  C19  S18  single    1.832  0.020  1.832
 VMA  C10  N9   single    1.442  0.020  1.442
 VMA  S18  C3   single    1.752  0.020  1.752
 VMA  N4   C5   single    1.347  0.020  1.347
 VMA  N4   C3   double    1.292  0.020  1.292
 VMA  N9   C5   aromatic  1.339  0.020  1.339
 VMA  N9   N8   aromatic  1.345  0.020  1.345
 VMA  C5   C6   aromatic  1.387  0.020  1.387
 VMA  C3   N2   single    1.374  0.020  1.374
 VMA  N8   C7   aromatic  1.311  0.020  1.311
 VMA  C6   C7   aromatic  1.409  0.020  1.409
 VMA  C6   C1   single    1.425  0.020  1.425
 VMA  N2   C1   single    1.417  0.020  1.417
 VMA  N2   C12  single    1.431  0.020  1.431
 VMA  C13  C12  aromatic  1.386  0.020  1.386
 VMA  C13  C14  aromatic  1.387  0.020  1.387
 VMA  C1   O11  double    1.214  0.020  1.214
 VMA  C12  C17  aromatic  1.386  0.020  1.386
 VMA  C14  C15  aromatic  1.389  0.020  1.389
 VMA  C17  C16  aromatic  1.387  0.020  1.387
 VMA  C15  C16  aromatic  1.389  0.020  1.389
 VMA  C21  H1   single    0.930  0.020  1.080
 VMA  C24  H2   single    0.930  0.020  1.080
 VMA  C7   H3   single    0.930  0.020  1.080
 VMA  C10  H4   single    0.970  0.020  1.090
 VMA  C10  H5   single    0.970  0.020  1.090
 VMA  C10  H6   single    0.970  0.020  1.090
 VMA  C17  H7   single    0.930  0.020  1.080
 VMA  C16  H8   single    0.930  0.020  1.080
 VMA  C15  H9   single    0.930  0.020  1.080
 VMA  C14  H10  single    0.930  0.020  1.080
 VMA  C13  H11  single    0.930  0.020  1.080
 VMA  C19  H12  single    0.970  0.020  1.090
 VMA  C26  H13  single    0.970  0.020  1.090
 VMA  C26  H14  single    0.970  0.020  1.090
 VMA  C26  H15  single    0.970  0.020  1.090
 VMA  C23  H16  single    0.930  0.020  1.080
 VMA  C22  H17  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
 VMA  N4   C5   N9   126.32  3.000
 VMA  N9   C5   C6   106.95  3.000
 VMA  N4   C5   C6   126.73  3.000
 VMA  C7   C6   C1   136.33  3.000
 VMA  C1   C6   C5   119.15  3.000
 VMA  C7   C6   C5   104.52  3.000
 VMA  H1   C21  C22  120.99  3.000
 VMA  H1   C21  C20  120.45  3.000
 VMA  C22  C21  C20  118.56  3.000
 VMA  H2   C24  C23  120.34  3.000
 VMA  H2   C24  N25  116.46  3.000
 VMA  C23  C24  N25  123.20  3.000
 VMA  N2   C1   O11  120.29  3.000
 VMA  O11  C1   C6   128.07  3.000
 VMA  N2   C1   C6   111.63  3.000
 VMA  H3   C7   N8   120.73  3.000
 VMA  H3   C7   C6   128.86  3.000
 VMA  N8   C7   C6   110.41  3.000
 VMA  N9   N8   C7   106.78  3.000
 VMA  C10  N9   N8   120.76  3.000
 VMA  N8   N9   C5   111.34  3.000
 VMA  C10  N9   C5   127.89  3.000
 VMA  H6   C10  H5   109.08  3.000
 VMA  H6   C10  H4   109.08  3.000
 VMA  H5   C10  H4   109.42  3.000
 VMA  H6   C10  N9   108.70  3.000
 VMA  H5   C10  N9   110.57  3.000
 VMA  H4   C10  N9   109.96  3.000
 VMA  C3   N4   C5   114.42  3.000
 VMA  S18  C3   N2   114.66  3.000
 VMA  N2   C3   N4   124.34  3.000
 VMA  S18  C3   N4   121.00  3.000
 VMA  C12  N2   C3   119.61  3.000
 VMA  C12  N2   C1   116.65  3.000
 VMA  C3   N2   C1   123.73  3.000
 VMA  C13  C12  C17  121.12  3.000
 VMA  C17  C12  N2   119.47  3.000
 VMA  C13  C12  N2   119.42  3.000
 VMA  H7   C17  C16  120.71  3.000
 VMA  H7   C17  C12  119.99  3.000
 VMA  C16  C17  C12  119.30  3.000
 VMA  H8   C16  C15  120.23  3.000
 VMA  H8   C16  C17  119.70  3.000
 VMA  C15  C16  C17  120.06  3.000
 VMA  H9   C15  C14  119.94  3.000
 VMA  H9   C15  C16  119.90  3.000
 VMA  C14  C15  C16  120.16  3.000
 VMA  H10  C14  C13  119.68  3.000
 VMA  H10  C14  C15  120.25  3.000
 VMA  C13  C14  C15  120.06  3.000
 VMA  H11  C13  C14  120.72  3.000
 VMA  H11  C13  C12  119.99  3.000
 VMA  C14  C13  C12  119.30  3.000
 VMA  C19  S18  C3   100.40  3.000
 VMA  H12  C19  C20  109.93  3.000
 VMA  H12  C19  C26  110.06  3.000
 VMA  C20  C19  C26  111.61  3.000
 VMA  H12  C19  S18  107.47  3.000
 VMA  C26  C19  S18  111.38  3.000
 VMA  C20  C19  S18  106.24  3.000
 VMA  H15  C26  H14  108.40  3.000
 VMA  H15  C26  H13  108.89  3.000
 VMA  H14  C26  H13  107.90  3.000
 VMA  H15  C26  C19  110.99  3.000
 VMA  H14  C26  C19  109.74  3.000
 VMA  H13  C26  C19  110.83  3.000
 VMA  N25  C20  C19  116.78  3.000
 VMA  C19  C20  C21  120.57  3.000
 VMA  N25  C20  C21  122.62  3.000
 VMA  C20  N25  C24  118.53  3.000
 VMA  H16  C23  C22  121.43  3.000
 VMA  H16  C23  C24  120.38  3.000
 VMA  C22  C23  C24  118.19  3.000
 VMA  H17  C22  C23  120.70  3.000
 VMA  H17  C22  C21  120.41  3.000
 VMA  C23  C22  C21  118.89  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
 VMA  CONST_01  C7   N8   N9   C5     0.00   0.0  0
 VMA  CONST_02  N8   C7   C6   C5     0.00   0.0  0
 VMA  CONST_03  N8   N9   C5   C6     0.00   0.0  0
 VMA  CONST_04  N9   N8   C7   C6     0.00   0.0  0
 VMA  CONST_05  C24  C23  C22  C21    0.00   0.0  0
 VMA  CONST_06  C24  N25  C20  C21    0.00   0.0  0
 VMA  CONST_07  N9   C5   C6   C7     0.00   0.0  0
 VMA  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 VMA  CONST_09  C15  C16  C17  C12    0.00   0.0  0
 VMA  CONST_10  C14  C13  C12  C17    0.00   0.0  0
 VMA  CONST_11  C14  C15  C16  C17    0.00   0.0  0
 VMA  CONST_12  C13  C12  C17  C16    0.00   0.0  0
 VMA  CONST_13  C13  C14  C15  C16    0.00   0.0  0
 VMA  CONST_14  C23  C22  C21  C20    0.00   0.0  0
 VMA  CONST_15  C23  C24  N25  C20    0.00   0.0  0
 VMA  CONST_16  C22  C23  C24  N25    0.00   0.0  0
 VMA  CONST_17  C22  C21  C20  N25    0.00   0.0  0
 VMA  CONST_18  C14  C13  C12  N2   180.00   0.0  0
 VMA  CONST_19  C16  C17  C12  N2   180.00   0.0  0
 VMA  CONST_20  N2   C3   N4   C5     0.00   0.0  0
 VMA  CONST_21  C3   N2   C1   C6     0.00   0.0  0
 VMA  CONST_22  C12  N2   C1   C6   180.00   0.0  0
 VMA  CONST_23  N4   C3   N2   C1     0.00   0.0  0
 VMA  CONST_24  C12  N2   C3   N4   180.00   0.0  0
 VMA  CONST_25  C10  N9   C5   C6   180.00   0.0  0
 VMA  CONST_26  C19  C20  N25  C24  180.00   0.0  0
 VMA  CONST_27  C10  N9   N8   C7   180.00   0.0  0
 VMA  CONST_28  N4   C5   N9   C10    0.00   0.0  0
 VMA  CONST_29  C22  C21  C20  C19  180.00   0.0  0
 VMA  CONST_30  S18  C3   N4   C5   180.00   0.0  0
 VMA  CONST_31  C3   N2   C1   O11  180.00   0.0  0
 VMA  CONST_32  C12  N2   C1   O11    0.00   0.0  0
 VMA  CONST_33  S18  C3   N2   C1   180.00   0.0  0
 VMA  CONST_34  S18  C3   N2   C12    0.00   0.0  0
 VMA  CONST_35  H3   C7   C6   C5   180.00   0.0  0
 VMA  CONST_36  H16  C23  C22  C21  180.00   0.0  0
 VMA  CONST_37  H17  C22  C23  C24  180.00   0.0  0
 VMA  CONST_38  H11  C13  C12  N2     0.00   0.0  0
 VMA  CONST_39  H7   C17  C12  N2     0.00   0.0  0
 VMA  CONST_40  H10  C14  C13  C12  180.00   0.0  0
 VMA  CONST_41  H8   C16  C17  C12  180.00   0.0  0
 VMA  CONST_42  H9   C15  C16  C17  180.00   0.0  0
 VMA  CONST_43  H2   C24  N25  C20  180.00   0.0  0
 VMA  CONST_44  H1   C21  C20  N25  180.00   0.0  0
 VMA  Var_01    C13  C12  N2   C1   -90.02  30.0  2
 VMA  Var_02    H4   C10  N9   C5   126.00  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
 VMA  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
 VMA  plan-1  N2   0.020
 VMA  plan-1  C12  0.020
 VMA  plan-1  C17  0.020
 VMA  plan-1  C16  0.020
 VMA  plan-1  C15  0.020
 VMA  plan-1  C14  0.020
 VMA  plan-1  C13  0.020
 VMA  plan-1  H7   0.020
 VMA  plan-1  H8   0.020
 VMA  plan-1  H9   0.020
 VMA  plan-1  H10  0.020
 VMA  plan-1  H11  0.020
 VMA  plan-2  C21  0.020
 VMA  plan-2  C24  0.020
 VMA  plan-2  C19  0.020
 VMA  plan-2  C20  0.020
 VMA  plan-2  N25  0.020
 VMA  plan-2  C23  0.020
 VMA  plan-2  C22  0.020
 VMA  plan-2  H2   0.020
 VMA  plan-2  H16  0.020
 VMA  plan-2  H17  0.020
 VMA  plan-2  H1   0.020
 VMA  plan-3  C5   0.020
 VMA  plan-3  C6   0.020
 VMA  plan-3  O11  0.020
 VMA  plan-3  C1   0.020
 VMA  plan-3  C7   0.020
 VMA  plan-3  N8   0.020
 VMA  plan-3  N9   0.020
 VMA  plan-3  C10  0.020
 VMA  plan-3  N4   0.020
 VMA  plan-3  C3   0.020
 VMA  plan-3  N2   0.020
 VMA  plan-3  C12  0.020
 VMA  plan-3  S18  0.020
 VMA  plan-3  H3   0.020

