# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 15:50:10 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[C@H](C)CN1C(=S)NC(=O)c2nc[nH]c12
#
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
 0KY  0KY  3-[(2R)-2-ethoxypropyl]-2-thioxo-1,2,3,9-tetrahydro-6H-purin-6-one  ligand  31  17  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0KY
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
 0KY  S    S  S1    0  -0.336   1.0161   2.0142  -1.9514
 0KY  C9   C  CR6   0   0.402  -0.1294   1.1817  -1.0769
 0KY  N2   N  NR16  0  -0.699  -1.1444   1.8669  -0.4782
 0KY  N1   N  NR6   0  -0.523  -0.1503  -0.1734  -0.9300
 0KY  C5   C  CH2   0  -0.365   0.9346  -1.0246  -1.4009
 0KY  C3   C  CH1   0   0.049   1.8658  -1.4414  -0.2639
 0KY  O1   O  O2    0  -0.476   2.2151  -0.2750   0.4325
 0KY  C2   C  CH2   0  -0.149   2.6118  -0.4866   1.7703
 0KY  C1   C  CH3   0  -0.684   2.9262   0.8511   2.4001
 0KY  C4   C  CH3   0  -0.679   3.0711  -2.1778  -0.8303
 0KY  C6   C  CR56  0   0.641  -1.1771  -0.7177  -0.2164
 0KY  N4   N  NR15  0  -0.655  -1.4225  -2.0188   0.0420
 0KY  C10  C  CR15  0   0.107  -2.5767  -2.0595   0.7761
 0KY  N3   N  N     0  -0.423  -3.0673  -0.8785   0.9931
 0KY  C7   C  CR56  0  -0.052  -2.2006  -0.0207   0.3771
 0KY  C8   C  CR6   0   0.519  -2.2322   1.4043   0.2686
 0KY  O2   O  O     0  -0.444  -3.0504   2.1760   0.7235
 0KY  H1   H  HNR6  0   0.432  -1.1051   2.8692  -0.6151
 0KY  H2   H  HCH2  0   0.288   0.5111  -1.9022  -1.8917
 0KY  H3   H  HCH2  0   0.291   1.4805  -0.4660  -2.1581
 0KY  H4   H  HCH1  0   0.207   1.3312  -2.1298   0.4097
 0KY  H5   H  HCH2  0   0.201   1.8094  -0.9880   2.3282
 0KY  H6   H  HCH2  0   0.202   3.4908  -1.1414   1.8239
 0KY  H7   H  HCH3  0   0.228   3.7547   1.3446   1.8910
 0KY  H8   H  HCH3  0   0.229   2.0602   1.5125   2.3703
 0KY  H9   H  HCH3  0   0.229   3.2096   0.7119   3.4430
 0KY  H10  H  HCH3  0   0.237   2.7564  -3.0585  -1.3913
 0KY  H11  H  HCH3  0   0.234   3.6432  -1.5321  -1.4980
 0KY  H12  H  HCH3  0   0.245   3.7318  -2.5180  -0.0330
 0KY  H13  H  HNR5  0   0.444  -0.8847  -2.8257  -0.2384
 0KY  H14  H  HCR5  0   0.302  -2.9907  -2.9970   1.1115

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
 0KY  O2   C8   double    1.213  0.020  1.213
 0KY  C8   C7   single    1.429  0.020  1.429
 0KY  C8   N2   single    1.398  0.020  1.398
 0KY  N3   C7   aromatic  1.366  0.020  1.366
 0KY  N3   C10  aromatic  1.297  0.020  1.297
 0KY  C7   C6   aromatic  1.373  0.020  1.373
 0KY  N2   C9   single    1.363  0.020  1.363
 0KY  C10  N4   aromatic  1.368  0.020  1.368
 0KY  C6   N4   aromatic  1.349  0.020  1.349
 0KY  C6   N1   single    1.364  0.020  1.364
 0KY  C9   N1   single    1.363  0.020  1.363
 0KY  C9   S    double    1.664  0.020  1.664
 0KY  N1   C5   single    1.457  0.020  1.457
 0KY  C4   C3   single    1.522  0.020  1.522
 0KY  C3   C5   single    1.528  0.020  1.528
 0KY  C3   O1   single    1.403  0.020  1.403
 0KY  O1   C2   single    1.411  0.020  1.411
 0KY  C1   C2   single    1.512  0.020  1.512
 0KY  N2   H1   single    0.860  0.020  1.020
 0KY  C5   H2   single    0.970  0.020  1.090
 0KY  C5   H3   single    0.970  0.020  1.090
 0KY  C3   H4   single    0.970  0.020  1.090
 0KY  C2   H5   single    0.970  0.020  1.090
 0KY  C2   H6   single    0.970  0.020  1.090
 0KY  C1   H7   single    0.970  0.020  1.090
 0KY  C1   H8   single    0.970  0.020  1.090
 0KY  C1   H9   single    0.970  0.020  1.090
 0KY  C4   H10  single    0.970  0.020  1.090
 0KY  C4   H11  single    0.970  0.020  1.090
 0KY  C4   H12  single    0.970  0.020  1.090
 0KY  N4   H13  single    0.860  0.020  1.020
 0KY  C10  H14  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
 0KY  N1   C9   N2   116.16  3.000
 0KY  N1   C9   S    124.36  3.000
 0KY  N2   C9   S    119.46  3.000
 0KY  H1   N2   C8   115.47  3.000
 0KY  H1   N2   C9   114.17  3.000
 0KY  C8   N2   C9   130.36  3.000
 0KY  C6   N1   C5   119.77  3.000
 0KY  C5   N1   C9   122.30  3.000
 0KY  C6   N1   C9   117.69  3.000
 0KY  H3   C5   H2   107.14  3.000
 0KY  H3   C5   C3   110.63  3.000
 0KY  H2   C5   C3   110.60  3.000
 0KY  H3   C5   N1   107.37  3.000
 0KY  H2   C5   N1   109.04  3.000
 0KY  C3   C5   N1   111.88  3.000
 0KY  H4   C3   C4   108.03  3.000
 0KY  H4   C3   O1   109.69  3.000
 0KY  C4   C3   O1   112.95  3.000
 0KY  H4   C3   C5   109.26  3.000
 0KY  O1   C3   C5   107.12  3.000
 0KY  C4   C3   C5   109.75  3.000
 0KY  C2   O1   C3   114.58  3.000
 0KY  H6   C2   H5   106.73  3.000
 0KY  H6   C2   C1   109.94  3.000
 0KY  H5   C2   C1   110.14  3.000
 0KY  H6   C2   O1   111.16  3.000
 0KY  H5   C2   O1   110.16  3.000
 0KY  C1   C2   O1   108.71  3.000
 0KY  H9   C1   H8   108.08  3.000
 0KY  H9   C1   H7   107.89  3.000
 0KY  H8   C1   H7   108.44  3.000
 0KY  H9   C1   C2   109.86  3.000
 0KY  H8   C1   C2   111.12  3.000
 0KY  H7   C1   C2   111.34  3.000
 0KY  H12  C4   H11  108.34  3.000
 0KY  H12  C4   H10  107.40  3.000
 0KY  H11  C4   H10  108.33  3.000
 0KY  H12  C4   C3   111.04  3.000
 0KY  H11  C4   C3   110.90  3.000
 0KY  H10  C4   C3   110.72  3.000
 0KY  C7   C6   N4   105.74  3.000
 0KY  N4   C6   N1   128.47  3.000
 0KY  C7   C6   N1   125.78  3.000
 0KY  H13  N4   C10  125.07  3.000
 0KY  H13  N4   C6   128.38  3.000
 0KY  C10  N4   C6   106.55  3.000
 0KY  H14  C10  N3   126.47  3.000
 0KY  H14  C10  N4   121.10  3.000
 0KY  N3   C10  N4   112.43  3.000
 0KY  C7   N3   C10  104.85  3.000
 0KY  C8   C7   N3   130.26  3.000
 0KY  N3   C7   C6   110.42  3.000
 0KY  C8   C7   C6   119.32  3.000
 0KY  O2   C8   C7   128.35  3.000
 0KY  C7   C8   N2   110.68  3.000
 0KY  O2   C8   N2   120.96  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
 0KY  CONST_01  C10  N3   C7   C6      0.00   0.0  0
 0KY  CONST_02  N3   C10  N4   C6      0.00   0.0  0
 0KY  CONST_03  C7   N3   C10  N4      0.00   0.0  0
 0KY  CONST_04  N3   C7   C6   N4      0.00   0.0  0
 0KY  CONST_05  C7   C6   N4   C10     0.00   0.0  0
 0KY  CONST_06  C7   C8   N2   C9      0.00   0.0  0
 0KY  CONST_07  C6   N1   C9   N2      0.00   0.0  0
 0KY  CONST_08  C8   N2   C9   N1      0.00   0.0  0
 0KY  CONST_09  C8   N2   C9   S     180.00   0.0  0
 0KY  CONST_10  C6   N1   C9   S     180.00   0.0  0
 0KY  CONST_11  O2   C8   N2   C9    180.00   0.0  0
 0KY  CONST_12  C5   N1   C9   N2    180.00   0.0  0
 0KY  CONST_13  H13  N4   C6   N1      0.00   0.0  0
 0KY  CONST_14  H14  C10  N4   C6    180.00   0.0  0
 0KY  CONST_15  H1   N2   C9   N1    180.00   0.0  0
 0KY  CONST_16  C5   N1   C9   S       0.00   0.0  0
 0KY  Var_01    C3   C5   N1   C9    100.50  30.0  3
 0KY  Var_02    C1   C2   O1   C3   -178.74  30.0  3
 0KY  Var_03    H7   C1   C2   O1    -62.04  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
 0KY  chir_01  C3  C4  C5  O1  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
 0KY  plan-1  S    0.020
 0KY  plan-1  C9   0.020
 0KY  plan-1  N2   0.020
 0KY  plan-1  N1   0.020
 0KY  plan-1  C5   0.020
 0KY  plan-1  C6   0.020
 0KY  plan-1  N4   0.020
 0KY  plan-1  C10  0.020
 0KY  plan-1  N3   0.020
 0KY  plan-1  C7   0.020
 0KY  plan-1  C8   0.020
 0KY  plan-1  O2   0.020
 0KY  plan-1  H1   0.020
 0KY  plan-1  H13  0.020
 0KY  plan-1  H14  0.020

