# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:45:20 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2R)-2-{[1-(3-chlorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](SC1=Nc2n(ncc2C(=O)N1)c3cccc(Cl)c3)C(N)=O
#
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
 DUK  DUK  (2R)-2-{[1-(3-chlorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}propanamide  ligand  35  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DUK
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
 DUK  O1   O   O     0  -0.472   3.5306  -3.4754  -0.0221
 DUK  C13  C   C     0   0.576   2.3201  -3.3361  -0.0975
 DUK  N4   N   NH2   0  -0.791   1.4704  -4.3001  -0.4613
 DUK  C11  C   CH1   0  -0.531   1.6538  -2.0188   0.2693
 DUK  C12  C   CH3   0  -0.636   1.0179  -2.0997   1.6523
 DUK  S    S   S2    0   0.123   2.9854  -0.7769   0.1785
 DUK  C6   C   CR6   0   0.384   2.0326   0.6790   0.0288
 DUK  N1   N   N     0  -0.472   0.7399   0.6376   0.0435
 DUK  C9   C   CR56  0   0.623   0.1454   1.8340  -0.1011
 DUK  N3   N   NR5   0  -0.494  -1.1861   2.0742  -0.1053
 DUK  N2   N   N     0  -0.250  -1.4376   3.3950  -0.2483
 DUK  C10  C   CR15  0  -0.046  -0.2792   3.9931  -0.3399
 DUK  C8   C   CR56  0  -0.345   0.7734   3.0586  -0.2532
 DUK  C7   C   CR6   0   0.532   2.2038   3.1069  -0.2676
 DUK  O    O   O     0  -0.443   2.9208   4.0790  -0.3906
 DUK  N    N   NR16  0  -0.717   2.7504   1.8246  -0.1141
 DUK  C2   C   CR6   0   0.353  -2.2436   1.1682   0.1047
 DUK  C    C   CR16  0  -0.254  -2.0777  -0.1785  -0.2005
 DUK  C4   C   CR16  0  -0.293  -3.4465   1.6271   0.6315
 DUK  C5   C   CR16  0  -0.254  -4.4736   0.7263   0.8628
 DUK  C3   C   CR16  0  -0.223  -4.3192  -0.6271   0.5967
 DUK  C1   C   CR6   0  -0.035  -3.1132  -1.0558   0.0685
 DUK  CL   CL  CL    0  -0.119  -2.8696  -2.7384  -0.2712
 DUK  H1   H   HNH2  0   0.412   1.8059  -5.2304  -0.6535
 DUK  H2   H   HNH2  0   0.405   0.4780  -4.1480  -0.5224
 DUK  H3   H   HCH1  0   0.327   0.9039  -1.7549  -0.4781
 DUK  H4   H   HCH3  0   0.250   1.7412  -2.4279   2.3977
 DUK  H5   H   HCH3  0   0.266   0.6219  -1.1323   1.9506
 DUK  H6   H   HCH3  0   0.245   0.1864  -2.8065   1.6444
 DUK  H7   H   HCR5  0   0.288  -0.2245   5.0629  -0.4689
 DUK  H8   H   HNR6  0   0.437   3.7626   1.7727  -0.1237
 DUK  H9   H   HCR6  0   0.307  -1.1597  -0.5440  -0.6314
 DUK  H10  H   HCR6  0   0.284  -3.5791   2.6738   0.8633
 DUK  H11  H   HCR6  0   0.277  -5.4080   1.0832   1.2739
 DUK  H12  H   HCR6  0   0.285  -5.1181  -1.3267   0.7989

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
 DUK  O    C7   double    1.214  0.020  1.214
 DUK  C10  C8   aromatic  1.410  0.020  1.410
 DUK  C10  N2   aromatic  1.307  0.020  1.307
 DUK  C7   C8   single    1.431  0.020  1.431
 DUK  C7   N    single    1.402  0.020  1.402
 DUK  C8   C9   aromatic  1.385  0.020  1.385
 DUK  N2   N3   aromatic  1.352  0.020  1.352
 DUK  N    C6   single    1.359  0.020  1.359
 DUK  C9   N3   aromatic  1.353  0.020  1.353
 DUK  C9   N1   single    1.344  0.020  1.344
 DUK  N3   C2   single    1.408  0.020  1.408
 DUK  C6   N1   double    1.293  0.020  1.293
 DUK  C6   S    single    1.746  0.020  1.746
 DUK  C    C2   aromatic  1.391  0.020  1.391
 DUK  C    C1   aromatic  1.384  0.020  1.384
 DUK  C2   C4   aromatic  1.391  0.020  1.391
 DUK  S    C11  single    1.823  0.020  1.823
 DUK  CL   C1   single    1.734  0.020  1.734
 DUK  C1   C3   aromatic  1.385  0.020  1.385
 DUK  C4   C5   aromatic  1.386  0.020  1.386
 DUK  C11  C12  single    1.524  0.020  1.524
 DUK  C11  C13  single    1.521  0.020  1.521
 DUK  C3   C5   aromatic  1.388  0.020  1.388
 DUK  C13  N4   single    1.336  0.020  1.336
 DUK  C13  O1   double    1.221  0.020  1.221
 DUK  N4   H1   single    0.860  0.020  1.020
 DUK  N4   H2   single    0.860  0.020  1.020
 DUK  C11  H3   single    0.970  0.020  1.090
 DUK  C12  H4   single    0.970  0.020  1.090
 DUK  C12  H5   single    0.970  0.020  1.090
 DUK  C12  H6   single    0.970  0.020  1.090
 DUK  C10  H7   single    0.930  0.020  1.080
 DUK  N    H8   single    0.860  0.020  1.020
 DUK  C    H9   single    0.930  0.020  1.080
 DUK  C4   H10  single    0.930  0.020  1.080
 DUK  C5   H11  single    0.930  0.020  1.080
 DUK  C3   H12  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
 DUK  C11  C13  N4   114.33  3.000
 DUK  N4   C13  O1   124.43  3.000
 DUK  C11  C13  O1   121.22  3.000
 DUK  H2   N4   H1   117.17  3.000
 DUK  H2   N4   C13  122.35  3.000
 DUK  H1   N4   C13  120.44  3.000
 DUK  H3   C11  S    107.64  3.000
 DUK  H3   C11  C12  110.34  3.000
 DUK  S    C11  C12  112.71  3.000
 DUK  H3   C11  C13  110.20  3.000
 DUK  C12  C11  C13  110.83  3.000
 DUK  S    C11  C13  104.95  3.000
 DUK  H6   C12  H5   107.51  3.000
 DUK  H6   C12  H4   108.40  3.000
 DUK  H5   C12  H4   108.79  3.000
 DUK  H6   C12  C11  110.22  3.000
 DUK  H5   C12  C11  110.72  3.000
 DUK  H4   C12  C11  111.09  3.000
 DUK  C6   S    C11  100.00  3.000
 DUK  N    C6   N1   123.78  3.000
 DUK  N1   C6   S    121.17  3.000
 DUK  N    C6   S    115.05  3.000
 DUK  C9   N1   C6   114.36  3.000
 DUK  C8   C9   N3   106.79  3.000
 DUK  N3   C9   N1   126.43  3.000
 DUK  C8   C9   N1   126.77  3.000
 DUK  C2   N3   N2   120.30  3.000
 DUK  C2   N3   C9   128.63  3.000
 DUK  N2   N3   C9   110.91  3.000
 DUK  C10  N2   N3   106.84  3.000
 DUK  H7   C10  C8   128.80  3.000
 DUK  H7   C10  N2   120.47  3.000
 DUK  C8   C10  N2   110.73  3.000
 DUK  C7   C8   C10  136.30  3.000
 DUK  C7   C8   C9   118.96  3.000
 DUK  C10  C8   C9   104.74  3.000
 DUK  N    C7   O    120.87  3.000
 DUK  N    C7   C8   110.95  3.000
 DUK  O    C7   C8   128.18  3.000
 DUK  H8   N    C7   115.78  3.000
 DUK  H8   N    C6   119.03  3.000
 DUK  C7   N    C6   125.19  3.000
 DUK  C4   C2   C    120.38  3.000
 DUK  C4   C2   N3   119.58  3.000
 DUK  C    C2   N3   120.04  3.000
 DUK  H9   C    C1   120.01  3.000
 DUK  H9   C    C2   121.18  3.000
 DUK  C1   C    C2   118.82  3.000
 DUK  H10  C4   C5   120.21  3.000
 DUK  H10  C4   C2   120.47  3.000
 DUK  C5   C4   C2   119.32  3.000
 DUK  H11  C5   C3   119.40  3.000
 DUK  H11  C5   C4   119.30  3.000
 DUK  C3   C5   C4   121.30  3.000
 DUK  H12  C3   C1   120.98  3.000
 DUK  H12  C3   C5   120.86  3.000
 DUK  C1   C3   C5   118.16  3.000
 DUK  CL   C1   C3   119.84  3.000
 DUK  C3   C1   C    121.99  3.000
 DUK  CL   C1   C    118.18  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
 DUK  CONST_01  N2   C10  C8   C9      0.00   0.0  0
 DUK  CONST_02  C10  N2   N3   C9      0.00   0.0  0
 DUK  CONST_05  C8   C10  N2   N3      0.00   0.0  0
 DUK  CONST_06  C10  C8   C9   N3      0.00   0.0  0
 DUK  CONST_07  C1   C    C2   N3    180.00   0.0  0
 DUK  CONST_08  C5   C4   C2   N3    180.00   0.0  0
 DUK  CONST_09  C8   C9   N3   N2      0.00   0.0  0
 DUK  CONST_12  C2   N3   N2   C10   180.00   0.0  0
 DUK  CONST_13  C2   N3   C9   C8    180.00   0.0  0
 DUK  CONST_14  C3   C1   C    C2      0.00   0.0  0
 DUK  CONST_15  C3   C5   C4   C2      0.00   0.0  0
 DUK  CONST_16  C5   C4   C2   C       0.00   0.0  0
 DUK  CONST_17  C5   C3   C1   C       0.00   0.0  0
 DUK  CONST_18  C1   C    C2   C4      0.00   0.0  0
 DUK  CONST_19  C1   C3   C5   C4      0.00   0.0  0
 DUK  CONST_20  C2   N3   C9   N1      0.00   0.0  0
 DUK  CONST_21  C8   C7   N    C6      0.00   0.0  0
 DUK  CONST_22  C7   N    C6   N1      0.00   0.0  0
 DUK  CONST_23  N    C6   N1   C9      0.00   0.0  0
 DUK  CONST_24  CL   C1   C    C2    180.00   0.0  0
 DUK  CONST_25  CL   C1   C3   C5    180.00   0.0  0
 DUK  CONST_26  C7   N    C6   S     180.00   0.0  0
 DUK  CONST_27  C9   N1   C6   S     180.00   0.0  0
 DUK  CONST_28  O    C7   N    C6    180.00   0.0  0
 DUK  CONST_29  H7   C10  C8   C9    180.00   0.0  0
 DUK  CONST_30  H9   C    C2   N3      0.00   0.0  0
 DUK  CONST_31  H10  C4   C2   N3      0.00   0.0  0
 DUK  CONST_32  H11  C5   C4   C2    180.00   0.0  0
 DUK  CONST_33  H12  C3   C1   C     180.00   0.0  0
 DUK  CONST_34  H8   N    C6   N1    180.00   0.0  0
 DUK  CONST_35  H1   N4   C13  O1      0.00   0.0  0
 DUK  CONST_36  H2   N4   C13  O1    180.00   0.0  0
 DUK  Var_01    N    C6   S    C11  -177.67  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
 DUK  chir_01  C11  S  C12  C13  positiv

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
 DUK  plan-1  N3   0.020
 DUK  plan-1  C2   0.020
 DUK  plan-1  C    0.020
 DUK  plan-1  C4   0.020
 DUK  plan-1  C5   0.020
 DUK  plan-1  C3   0.020
 DUK  plan-1  C1   0.020
 DUK  plan-1  CL   0.020
 DUK  plan-1  H9   0.020
 DUK  plan-1  H10  0.020
 DUK  plan-1  H11  0.020
 DUK  plan-1  H12  0.020
 DUK  plan-2  S    0.020
 DUK  plan-2  C6   0.020
 DUK  plan-2  N1   0.020
 DUK  plan-2  C9   0.020
 DUK  plan-2  N3   0.020
 DUK  plan-2  N2   0.020
 DUK  plan-2  C10  0.020
 DUK  plan-2  C8   0.020
 DUK  plan-2  C7   0.020
 DUK  plan-2  O    0.020
 DUK  plan-2  N    0.020
 DUK  plan-2  C2   0.020
 DUK  plan-2  H7   0.020
 DUK  plan-2  H8   0.020
 DUK  plan-3  O1   0.020
 DUK  plan-3  C13  0.020
 DUK  plan-3  N4   0.020
 DUK  plan-3  C11  0.020
 DUK  plan-3  H1   0.020
 DUK  plan-3  H2   0.020

