# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 00:28:46 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-[[(2~{R})-oxolan-2-yl]methyl]-2-sulfanylidene-9~{H}-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=S)N(C[C@H]2CCCO2)c3[nH]cnc13
#
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
 UE8  UE8  "2-sulfanylidene-3-[(2R)-tetrahydro-2-furanylmethyl]-1,2,3,7-tetrahydro-6H-purin-6-one"
  ligand  29  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UE8
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
 UE8  C2   C  C     0   0.516  -4.3383  15.8838  19.1988
 UE8  N6   N  NT    0  -0.527  -3.6860  18.0759  17.4589
 UE8  C7   C  CH2   0  -0.375  -3.2966  19.1958  16.6036
 UE8  C8   C  CH1   0   0.071  -3.4901  18.8929  15.1289
 UE8  C10  C  CH2   0  -0.504  -3.0417  20.0626  14.2471
 UE8  C11  C  CH2   0  -0.485  -2.3474  19.3614  13.0842
 UE8  C12  C  CH2   0  -0.164  -1.7510  18.1488  13.7769
 UE8  C14  C  CR5   0   0.644  -2.7758  17.1230  17.8202
 UE8  C16  C  CR15  0   0.102  -0.9914  15.9132  18.1222
 UE8  C19  C  CR5   0  -0.055  -3.0269  16.0632  18.6584
 UE8  O1   O  O     0  -0.435  -4.7290  15.0231  19.9580
 UE8  N3   N  NH1   0  -0.698  -5.2071  16.8751  18.7272
 UE8  C4   C  C     0   0.391  -4.9632  17.9357  17.9097
 UE8  S5   S  S1    0  -0.335  -6.1982  18.9829  17.5120
 UE8  O13  O  O2    0  -0.502  -2.7122  17.7666  14.7509
 UE8  N15  N  NR15  0  -0.647  -1.4742  17.0225  17.4852
 UE8  N17  N  N     0  -0.422  -1.8966  15.3166  18.8352
 UE8  H1   H  HCH2  0   0.283  -2.2556  19.4438  16.8185
 UE8  H2   H  HCH2  0   0.294  -3.8945  20.0585  16.8913
 UE8  H3   H  HCH1  0   0.240  -4.5449  18.6549  14.9558
 UE8  H4   H  HCH2  0   0.244  -2.3327  20.7024  14.7803
 UE8  H5   H  HCH2  0   0.261  -3.8805  20.6853  13.9401
 UE8  H6   H  HCH2  0   0.250  -1.5924  19.9815  12.6023
 UE8  H7   H  HCH2  0   0.241  -3.0705  19.0568  12.3252
 UE8  H8   H  HCH2  0   0.232  -1.5782  17.3042  13.1082
 UE8  H9   H  HCH2  0   0.206  -0.7955  18.4053  14.2516
 UE8  H10  H  HCR5  0   0.298   0.0370  15.6074  18.0093
 UE8  H11  H  HNH1  0   0.432  -6.1655  16.8054  19.0474
 UE8  H12  H  HNR5  0   0.444  -0.9530  17.6033  16.8446

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
 UE8  C11  C12  single    1.519  0.020  1.519
 UE8  C11  C10  single    1.525  0.020  1.525
 UE8  C12  O13  single    1.421  0.020  1.421
 UE8  C10  C8   single    1.532  0.020  1.532
 UE8  O13  C8   single    1.420  0.020  1.420
 UE8  C8   C7   single    1.518  0.020  1.518
 UE8  C7   N6   single    1.462  0.020  1.462
 UE8  S5   C4   double    1.667  0.020  1.667
 UE8  N6   C4   single    1.362  0.020  1.362
 UE8  N6   C14  single    1.366  0.020  1.366
 UE8  N15  C14  aromatic  1.348  0.020  1.348
 UE8  N15  C16  aromatic  1.367  0.020  1.367
 UE8  C4   N3   single    1.361  0.020  1.361
 UE8  C14  C19  aromatic  1.374  0.020  1.374
 UE8  C16  N17  aromatic  1.298  0.020  1.298
 UE8  N3   C2   single    1.400  0.020  1.400
 UE8  C19  N17  aromatic  1.366  0.020  1.366
 UE8  C19  C2   single    1.430  0.020  1.430
 UE8  C2   O1   double    1.212  0.020  1.212
 UE8  C7   H1   single    0.970  0.020  1.090
 UE8  C7   H2   single    0.970  0.020  1.090
 UE8  C8   H3   single    0.970  0.020  1.090
 UE8  C10  H4   single    0.970  0.020  1.090
 UE8  C10  H5   single    0.970  0.020  1.090
 UE8  C11  H6   single    0.970  0.020  1.090
 UE8  C11  H7   single    0.970  0.020  1.090
 UE8  C12  H8   single    0.970  0.020  1.090
 UE8  C12  H9   single    0.970  0.020  1.090
 UE8  C16  H10  single    0.930  0.020  1.080
 UE8  N3   H11  single    0.860  0.020  1.020
 UE8  N15  H12  single    0.860  0.020  1.020

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
 UE8  N3   C2   O1   120.91  3.000
 UE8  O1   C2   C19  128.41  3.000
 UE8  N3   C2   C19  110.67  3.000
 UE8  C4   N6   C14  117.74  3.000
 UE8  C14  N6   C7   120.76  3.000
 UE8  C4   N6   C7   121.49  3.000
 UE8  H2   C7   H1   106.96  3.000
 UE8  H2   C7   C8   110.18  3.000
 UE8  H1   C7   C8   110.99  3.000
 UE8  H2   C7   N6   107.83  3.000
 UE8  H1   C7   N6   108.24  3.000
 UE8  C8   C7   N6   112.43  3.000
 UE8  H3   C8   O13  108.25  3.000
 UE8  H3   C8   C10  110.91  3.000
 UE8  O13  C8   C10  106.98  3.000
 UE8  H3   C8   C7   108.65  3.000
 UE8  O13  C8   C7   110.31  3.000
 UE8  C10  C8   C7   111.69  3.000
 UE8  H5   C10  H4   107.59  3.000
 UE8  H5   C10  C11  113.49  3.000
 UE8  H4   C10  C11  110.21  3.000
 UE8  H5   C10  C8   111.93  3.000
 UE8  H4   C10  C8   110.84  3.000
 UE8  C11  C10  C8   102.77  3.000
 UE8  H7   C11  H6   108.08  3.000
 UE8  H7   C11  C12  110.76  3.000
 UE8  H6   C11  C12  112.59  3.000
 UE8  H7   C11  C10  110.91  3.000
 UE8  H6   C11  C10  113.02  3.000
 UE8  C12  C11  C10  101.43  3.000
 UE8  H9   C12  H8   107.95  3.000
 UE8  H9   C12  O13  110.82  3.000
 UE8  H8   C12  O13  108.61  3.000
 UE8  H9   C12  C11  110.65  3.000
 UE8  H8   C12  C11  113.63  3.000
 UE8  O13  C12  C11  105.18  3.000
 UE8  N15  C14  C19  105.70  3.000
 UE8  C19  C14  N6   125.26  3.000
 UE8  N15  C14  N6   129.02  3.000
 UE8  H10  C16  N17  126.31  3.000
 UE8  H10  C16  N15  121.19  3.000
 UE8  N17  C16  N15  112.50  3.000
 UE8  N17  C19  C14  110.44  3.000
 UE8  N17  C19  C2   129.90  3.000
 UE8  C14  C19  C2   119.66  3.000
 UE8  H11  N3   C4   114.40  3.000
 UE8  H11  N3   C2   115.59  3.000
 UE8  C4   N3   C2   130.01  3.000
 UE8  S5   C4   N3   120.00  3.000
 UE8  N3   C4   N6   116.56  3.000
 UE8  S5   C4   N6   123.44  3.000
 UE8  C12  O13  C8   109.86  3.000
 UE8  H12  N15  C16  125.45  3.000
 UE8  H12  N15  C14  127.83  3.000
 UE8  C16  N15  C14  106.60  3.000
 UE8  C19  N17  C16  104.76  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
 UE8  CONST_01  N17  C16  N15  C14     0.00   0.0  0
 UE8  CONST_02  C16  N17  C19  C14     0.00   0.0  0
 UE8  CONST_03  C19  C14  N15  C16     0.00   0.0  0
 UE8  CONST_04  N15  C16  N17  C19     0.00   0.0  0
 UE8  CONST_05  N17  C19  C14  N15     0.00   0.0  0
 UE8  CONST_06  N6   C4   N3   C2      0.00   0.0  0
 UE8  CONST_07  N3   C4   N6   C14     0.00   0.0  0
 UE8  CONST_08  C4   N3   C2   C19     0.00   0.0  0
 UE8  CONST_09  S5   C4   N3   C2    180.00   0.0  0
 UE8  CONST_10  N3   C4   N6   C7    180.00   0.0  0
 UE8  CONST_11  S5   C4   N6   C14   180.00   0.0  0
 UE8  CONST_12  C4   N3   C2   O1    180.00   0.0  0
 UE8  CONST_13  H12  N15  C14  N6      0.00   0.0  0
 UE8  CONST_14  H10  C16  N15  C14   180.00   0.0  0
 UE8  CONST_15  H12  N15  C14  C19   180.00   0.0  0
 UE8  CONST_16  H10  C16  N17  C19   180.00   0.0  0
 UE8  CONST_17  H12  N15  C16  N17   180.00   0.0  0
 UE8  CONST_18  H11  N3   C4   N6    180.00   0.0  0
 UE8  CONST_19  H11  N3   C2   C19   180.00   0.0  0
 UE8  CONST_20  S5   C4   N6   C7      0.00   0.0  0
 UE8  CONST_21  H11  N3   C2   O1      0.00   0.0  0
 UE8  CONST_22  H11  N3   C4   S5      0.00   0.0  0
 UE8  Var_01    C12  C11  C10  C8    -33.06  30.0  1
 UE8  Var_02    C11  C12  O13  C8    -25.98  30.0  1
 UE8  Var_03    O13  C12  C11  C10    36.66  30.0  1
 UE8  Var_04    C4   N6   C7   C8    -88.70  30.0  3
 UE8  Var_05    C14  N6   C7   C8     90.54  30.0  3
 UE8  Var_06    H6   C11  C10  C8   -153.84  30.0  1
 UE8  Var_07    H7   C11  C10  C8     84.61  30.0  1
 UE8  Var_08    H8   C12  O13  C8   -147.95  30.0  1
 UE8  Var_09    H9   C12  O13  C8     93.63  30.0  1
 UE8  Var_10    H8   C12  C11  C10   155.31  30.0  1
 UE8  Var_11    H9   C12  C11  C10   -83.07  30.0  1
 UE8  Var_12    H4   C10  C11  C12    85.12  30.0  1
 UE8  Var_13    H5   C10  C11  C12  -154.13  30.0  1
 UE8  Var_14    H6   C11  C12  O13   157.74  30.0  1
 UE8  Var_15    H7   C11  C12  O13   -81.12  30.0  1
 UE8  Var_16    H1   C7   N6   C14   -32.42  30.0  2
 UE8  Var_17    H2   C7   N6   C14  -147.80  30.0  2
 UE8  Var_18    H1   C7   N6   C4    148.33  30.0  2
 UE8  Var_19    H2   C7   N6   C4     32.95  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
 UE8  chir_01  C8  C10  O13  C7  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
 UE8  plan-1  C2   0.020
 UE8  plan-1  N6   0.020
 UE8  plan-1  C7   0.020
 UE8  plan-1  C14  0.020
 UE8  plan-1  C16  0.020
 UE8  plan-1  C19  0.020
 UE8  plan-1  O1   0.020
 UE8  plan-1  N3   0.020
 UE8  plan-1  C4   0.020
 UE8  plan-1  S5   0.020
 UE8  plan-1  N15  0.020
 UE8  plan-1  N17  0.020
 UE8  plan-1  H10  0.020
 UE8  plan-1  H11  0.020
 UE8  plan-1  H12  0.020

