# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 18:49:20 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(SCc3ccccc3F)nc2C(=O)N1
#
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
 5RU  5RU  2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one  ligand  30  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5RU
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
 5RU  C11  C  CR16  0  -0.256   5.4275   0.0829   1.5520
 5RU  C12  C  CR16  0  -0.246   6.1113   0.1276   0.3445
 5RU  C10  C  CR16  0  -0.263   4.0587  -0.1425   1.5612
 5RU  C13  C  CR16  0  -0.400   5.4297  -0.0487  -0.8519
 5RU  C9   C  CR6   0  -0.104   3.3512  -0.3292   0.3768
 5RU  C3   C  CR56  0  -0.084  -2.4200  -0.5436   0.0998
 5RU  C14  C  CR6   0   0.538   4.0674  -0.2687  -0.8103
 5RU  C4   C  CR56  0   0.481  -2.7762   0.7769  -0.0991
 5RU  C2   C  CR6   0   0.493  -3.4484  -1.5223   0.1897
 5RU  C18  C  CR6   0   0.689  -4.9543   0.4034  -0.1417
 5RU  C6   C  CR5   0   0.290  -0.6020   0.5322   0.0361
 5RU  C8   C  CH2   0  -0.613   1.8732  -0.5638   0.3845
 5RU  N17  N  N     0  -0.504  -4.0022   1.3006  -0.2221
 5RU  N5   N  NR15  0  -0.685  -1.5993   1.4556  -0.1386
 5RU  N20  N  NR16  0  -0.722  -4.7090  -0.9249   0.0505
 5RU  N16  N  N     0  -0.443  -1.0533  -0.6754   0.1820
 5RU  O1   O  O     0  -0.477  -3.3491  -2.7266   0.3610
 5RU  F15  F  F     0  -0.306   3.4042  -0.4350  -1.9652
 5RU  S7   S  S2    0   0.066   1.0663   1.0367   0.0477
 5RU  H1   H  HCR6  0   0.265   5.9580   0.2235   2.4838
 5RU  H2   H  HCR6  0   0.272   7.1793   0.2986   0.3276
 5RU  H3   H  HCR6  0   0.270   3.5228  -0.1820   2.5017
 5RU  H4   H  HCR6  0   0.282   5.9469  -0.0152  -1.8020
 5RU  H5   H  HCH2  0   0.307   1.5596  -1.2825  -0.3703
 5RU  H6   H  HCH2  0   0.307   1.5458  -0.9238   1.3583
 5RU  H7   H  HNR5  0   0.426  -1.4925   2.4514  -0.2629
 5RU  H8   H  HNR6  0   0.425  -5.4980  -1.5572   0.0944
 5RU  H10  H  HNH2  0   0.414  -6.9835   0.1609  -0.0090
 5RU  H11  H  HNH2  0   0.412  -6.4371   1.7590  -0.2682
 5RU  N19  N  NH2   0  -0.832  -6.2356   0.7735  -0.2861

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
 5RU  N19  C18  single    1.341  0.020  1.341
 5RU  N17  C18  double    1.311  0.020  1.311
 5RU  N17  C4   single    1.339  0.020  1.339
 5RU  C18  N20  single    1.364  0.020  1.364
 5RU  C4   N5   aromatic  1.359  0.020  1.359
 5RU  C4   C3   aromatic  1.382  0.020  1.382
 5RU  N5   C6   aromatic  1.370  0.020  1.370
 5RU  N20  C2   single    1.402  0.020  1.402
 5RU  C3   C2   single    1.422  0.020  1.422
 5RU  C3   N16  aromatic  1.376  0.020  1.376
 5RU  C2   O1   double    1.220  0.020  1.220
 5RU  C6   N16  aromatic  1.297  0.020  1.297
 5RU  C6   S7   single    1.743  0.020  1.743
 5RU  S7   C8   single    1.824  0.020  1.824
 5RU  C12  C11  aromatic  1.388  0.020  1.388
 5RU  C12  C13  aromatic  1.388  0.020  1.388
 5RU  C11  C10  aromatic  1.387  0.020  1.387
 5RU  C13  C14  aromatic  1.381  0.020  1.381
 5RU  C10  C9   aromatic  1.392  0.020  1.392
 5RU  C14  C9   aromatic  1.388  0.020  1.388
 5RU  C14  F15  single    1.342  0.020  1.342
 5RU  C9   C8   single    1.497  0.020  1.497
 5RU  C11  H1   single    0.930  0.020  1.080
 5RU  C12  H2   single    0.930  0.020  1.080
 5RU  C10  H3   single    0.930  0.020  1.080
 5RU  C13  H4   single    0.930  0.020  1.080
 5RU  C8   H5   single    0.970  0.020  1.090
 5RU  C8   H6   single    0.970  0.020  1.090
 5RU  N5   H7   single    0.860  0.020  1.020
 5RU  N20  H8   single    0.860  0.020  1.020
 5RU  N19  H10  single    0.890  0.020  1.040
 5RU  N19  H11  single    0.890  0.020  1.040

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
 5RU  H1   C11  C10  119.96  3.000
 5RU  H1   C11  C12  120.24  3.000
 5RU  C10  C11  C12  119.80  3.000
 5RU  H2   C12  C13  119.44  3.000
 5RU  H2   C12  C11  120.32  3.000
 5RU  C13  C12  C11  120.24  3.000
 5RU  H3   C10  C9   118.84  3.000
 5RU  H3   C10  C11  119.99  3.000
 5RU  C9   C10  C11  121.17  3.000
 5RU  H4   C13  C14  120.20  3.000
 5RU  H4   C13  C12  121.20  3.000
 5RU  C14  C13  C12  118.61  3.000
 5RU  C8   C9   C14  121.40  3.000
 5RU  C8   C9   C10  121.23  3.000
 5RU  C14  C9   C10  117.36  3.000
 5RU  N16  C3   C2   130.43  3.000
 5RU  N16  C3   C4   110.87  3.000
 5RU  C2   C3   C4   118.70  3.000
 5RU  F15  C14  C9   118.40  3.000
 5RU  F15  C14  C13  118.78  3.000
 5RU  C9   C14  C13  122.82  3.000
 5RU  N5   C4   N17  126.50  3.000
 5RU  N5   C4   C3   104.96  3.000
 5RU  N17  C4   C3   128.53  3.000
 5RU  O1   C2   N20  120.50  3.000
 5RU  O1   C2   C3   128.98  3.000
 5RU  N20  C2   C3   110.52  3.000
 5RU  N19  C18  N20  117.10  3.000
 5RU  N20  C18  N17  122.98  3.000
 5RU  N19  C18  N17  119.89  3.000
 5RU  S7   C6   N16  126.99  3.000
 5RU  S7   C6   N5   120.16  3.000
 5RU  N16  C6   N5   112.85  3.000
 5RU  H6   C8   H5   108.38  3.000
 5RU  H6   C8   S7   108.81  3.000
 5RU  H5   C8   S7   108.90  3.000
 5RU  H6   C8   C9   110.70  3.000
 5RU  H5   C8   C9   112.61  3.000
 5RU  S7   C8   C9   107.36  3.000
 5RU  C18  N17  C4   113.06  3.000
 5RU  H7   N5   C6   127.13  3.000
 5RU  H7   N5   C4   126.01  3.000
 5RU  C6   N5   C4   106.86  3.000
 5RU  H8   N20  C18  118.30  3.000
 5RU  H8   N20  C2   115.50  3.000
 5RU  C18  N20  C2   126.20  3.000
 5RU  C6   N16  C3   104.46  3.000
 5RU  C8   S7   C6    99.83  3.000
 5RU  H11  N19  H10  116.29  3.000
 5RU  H11  N19  C18  117.36  3.000
 5RU  H10  N19  C18  120.84  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
 5RU  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 5RU  CONST_02  C14  C9   C10  C11    0.00   0.0  0
 5RU  CONST_03  C9   C10  C11  C12    0.00   0.0  0
 5RU  CONST_04  C9   C14  C13  C12    0.00   0.0  0
 5RU  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 5RU  CONST_06  C13  C14  C9   C10    0.00   0.0  0
 5RU  CONST_07  C6   N5   C4   C3     0.00   0.0  0
 5RU  CONST_08  N5   C6   N16  C3     0.00   0.0  0
 5RU  CONST_09  N16  C6   N5   C4     0.00   0.0  0
 5RU  CONST_10  C6   N16  C3   C4     0.00   0.0  0
 5RU  CONST_11  N16  C3   C4   N5     0.00   0.0  0
 5RU  CONST_12  C18  N20  C2   C3     0.00   0.0  0
 5RU  CONST_13  N20  C18  N17  C4     0.00   0.0  0
 5RU  CONST_14  N17  C18  N20  C2     0.00   0.0  0
 5RU  CONST_15  C8   C9   C10  C11  180.00   0.0  0
 5RU  CONST_16  F15  C14  C13  C12  180.00   0.0  0
 5RU  CONST_17  F15  C14  C9   C10  180.00   0.0  0
 5RU  CONST_18  C8   C9   C14  C13  180.00   0.0  0
 5RU  CONST_19  S7   C6   N16  C3   180.00   0.0  0
 5RU  CONST_20  S7   C6   N5   C4   180.00   0.0  0
 5RU  CONST_21  N19  C18  N17  C4   180.00   0.0  0
 5RU  CONST_22  N19  C18  N20  C2   180.00   0.0  0
 5RU  CONST_23  O1   C2   N20  C18  180.00   0.0  0
 5RU  CONST_24  H4   C13  C12  C11  180.00   0.0  0
 5RU  CONST_25  H3   C10  C11  C12  180.00   0.0  0
 5RU  CONST_26  H2   C12  C11  C10  180.00   0.0  0
 5RU  CONST_27  H1   C11  C12  C13  180.00   0.0  0
 5RU  CONST_28  H7   N5   C4   C3   180.00   0.0  0
 5RU  CONST_29  H8   N20  C2   C3   180.00   0.0  0
 5RU  CONST_31  H11  N19  C18  N17    0.00   0.0  0
 5RU  Var_01    S7   C8   C9   C10   97.71  30.0  2
 5RU  Var_02    N5   C6   S7   C8   177.52  30.0  1

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
 5RU  plan-1  C11  0.020
 5RU  plan-1  C12  0.020
 5RU  plan-1  C10  0.020
 5RU  plan-1  C13  0.020
 5RU  plan-1  C9   0.020
 5RU  plan-1  C14  0.020
 5RU  plan-1  C8   0.020
 5RU  plan-1  F15  0.020
 5RU  plan-1  H1   0.020
 5RU  plan-1  H2   0.020
 5RU  plan-1  H3   0.020
 5RU  plan-1  H4   0.020
 5RU  plan-2  C3   0.020
 5RU  plan-2  C4   0.020
 5RU  plan-2  C2   0.020
 5RU  plan-2  C18  0.020
 5RU  plan-2  C6   0.020
 5RU  plan-2  N17  0.020
 5RU  plan-2  N5   0.020
 5RU  plan-2  N20  0.020
 5RU  plan-2  N16  0.020
 5RU  plan-2  O1   0.020
 5RU  plan-2  S7   0.020
 5RU  plan-2  H7   0.020
 5RU  plan-2  H8   0.020
 5RU  plan-2  H10  0.020
 5RU  plan-2  H11  0.020
 5RU  plan-2  N19  0.020

