# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:16:58 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1,3-dimethyl-8-{[2-(pyrrolidin-1-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,9-tetrahydro-2H-purin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2[nH]c(SCCN3CCCC3)nc2C1=S
#
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
 M0S  M0S  1,3-dimethyl-8-{[2-(pyrrolidin-1-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,9-tetrahydro-2H-purin-2-one  ligand  40  21  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M0S
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
 M0S  C2   C  CR56  0   0.056   1.7359  -0.2870   0.0467
 M0S  C4   C  CR6   0   0.737   4.4919   0.1051  -0.0904
 M0S  C5   C  CH3   0  -0.524   4.8316  -2.2925   0.0733
 M0S  C6   C  CR5   0   0.305   0.1380   1.1043   0.0098
 M0S  C7   C  CH2   0  -0.562  -2.5055   0.4706   0.1390
 M0S  C8   C  CH2   0  -0.266  -3.9383   0.9877   0.1880
 M0S  C9   C  CH2   0  -0.277  -6.2203   0.3094   0.6178
 M0S  C11  C  CH2   0  -0.469  -6.3132  -1.6678  -0.7704
 M0S  C12  C  CH2   0  -0.283  -5.0317  -0.8518  -0.9797
 M0S  O    O  O     0  -0.473   5.6926   0.2590  -0.1680
 M0S  N    N  NR6   0  -0.579   3.6344   1.1851  -0.1118
 M0S  C    C  CH3   0  -0.562   4.1366   2.5448  -0.2404
 M0S  C1   C  CR56  0   0.662   2.3074   0.9557  -0.0507
 M0S  N3   N  NR15  0  -0.688   1.2967   1.8464  -0.0748
 M0S  N2   N  N     0  -0.422   0.3675  -0.1681   0.0832
 M0S  C3   C  CR6   0   0.162   2.5539  -1.4349   0.0926
 M0S  S    S  S1    0  -0.331   1.9578  -2.9791   0.2115
 M0S  N1   N  NR6   0  -0.564   3.9111  -1.1598   0.0279
 M0S  S1   S  S2    0   0.056  -1.4016   1.9072   0.0044
 M0S  N4   N  NT    0  -0.429  -4.8744  -0.1061   0.2602
 M0S  C10  C  CH2   0  -0.462  -7.0529  -0.9449   0.3745
 M0S  H1   H  HCH3  0   0.259   4.6673  -2.8639   0.9835
 M0S  H2   H  HCH3  0   0.259   4.6609  -2.9466  -0.7789
 M0S  H3   H  HCH3  0   0.274   5.8507  -1.9311   0.0525
 M0S  H4   H  HCH2  0   0.286  -2.2664  -0.0806   1.0471
 M0S  H5   H  HCH2  0   0.289  -2.3378  -0.1773  -0.7207
 M0S  H6   H  HCH2  0   0.252  -4.0599   1.6089   1.0787
 M0S  H7   H  HCH2  0   0.207  -4.1333   1.6365  -0.6837
 M0S  H9   H  HCH2  0   0.194  -6.5763   1.1347  -0.0218
 M0S  H10  H  HCH2  0   0.235  -6.9032  -1.7023  -1.6858
 M0S  H11  H  HCH2  0   0.237  -6.0847  -2.6980  -0.4981
 M0S  H12  H  HCH2  0   0.236  -4.1631  -1.4811  -1.1821
 M0S  H13  H  HCH2  0   0.196  -5.1471  -0.1696  -1.8388
 M0S  H14  H  HCH3  0   0.290   5.2154   2.5436  -0.1444
 M0S  H15  H  HCH3  0   0.275   3.8661   2.9570  -1.2117
 M0S  H16  H  HCH3  0   0.272   3.7185   3.1663   0.5492
 M0S  H17  H  HNR5  0   0.446   1.3660   2.8528  -0.1314
 M0S  H20  H  HCH2  0   0.234  -7.0734  -1.5653   1.2711
 M0S  H21  H  HCH2  0   0.235  -8.0848  -0.7020   0.1236
 M0S  H8   H  HCH2  0   0.236  -6.2580   0.6593   1.6516

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
 M0S  S1   C7   single    1.817  0.020  1.817
 M0S  S1   C6   single    1.736  0.020  1.736
 M0S  C7   C8   single    1.524  0.020  1.524
 M0S  C8   N4   single    1.442  0.020  1.442
 M0S  N3   C6   aromatic  1.379  0.020  1.379
 M0S  N3   C1   aromatic  1.347  0.020  1.347
 M0S  C6   N2   aromatic  1.295  0.020  1.295
 M0S  N4   C9   single    1.453  0.020  1.453
 M0S  N4   C12  single    1.455  0.020  1.455
 M0S  C    N    single    1.455  0.020  1.455
 M0S  C1   N    single    1.348  0.020  1.348
 M0S  C1   C2   aromatic  1.371  0.020  1.371
 M0S  N2   C2   aromatic  1.374  0.020  1.374
 M0S  C9   C10  single    1.525  0.020  1.525
 M0S  C12  C11  single    1.534  0.020  1.534
 M0S  N    C4   single    1.379  0.020  1.379
 M0S  C2   C3   single    1.410  0.020  1.410
 M0S  C10  C11  single    1.543  0.020  1.543
 M0S  C4   O    double    1.213  0.020  1.213
 M0S  C4   N1   single    1.397  0.020  1.397
 M0S  C3   N1   single    1.386  0.020  1.386
 M0S  C3   S    double    1.660  0.020  1.660
 M0S  N1   C5   single    1.460  0.020  1.460
 M0S  C5   H1   single    0.970  0.020  1.090
 M0S  C5   H2   single    0.970  0.020  1.090
 M0S  C5   H3   single    0.970  0.020  1.090
 M0S  C7   H4   single    0.970  0.020  1.090
 M0S  C7   H5   single    0.970  0.020  1.090
 M0S  C8   H6   single    0.970  0.020  1.090
 M0S  C8   H7   single    0.970  0.020  1.090
 M0S  C9   H8   single    0.970  0.020  1.090
 M0S  C9   H9   single    0.970  0.020  1.090
 M0S  C11  H10  single    0.970  0.020  1.090
 M0S  C11  H11  single    0.970  0.020  1.090
 M0S  C12  H12  single    0.970  0.020  1.090
 M0S  C12  H13  single    0.970  0.020  1.090
 M0S  C    H14  single    0.970  0.020  1.090
 M0S  C    H15  single    0.970  0.020  1.090
 M0S  C    H16  single    0.970  0.020  1.090
 M0S  N3   H17  single    0.860  0.020  1.020
 M0S  C10  H20  single    0.970  0.020  1.090
 M0S  C10  H21  single    0.970  0.020  1.090

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
 M0S  C3   C2   N2   130.33  3.000
 M0S  C3   C2   C1   119.88  3.000
 M0S  N2   C2   C1   109.79  3.000
 M0S  N1   C4   N    116.87  3.000
 M0S  N1   C4   O    122.14  3.000
 M0S  N    C4   O    121.00  3.000
 M0S  H3   C5   H2   109.50  3.000
 M0S  H3   C5   H1   109.52  3.000
 M0S  H2   C5   H1   108.43  3.000
 M0S  H3   C5   N1   109.53  3.000
 M0S  H2   C5   N1   110.07  3.000
 M0S  H1   C5   N1   109.78  3.000
 M0S  S1   C6   N2   127.71  3.000
 M0S  N2   C6   N3   112.55  3.000
 M0S  S1   C6   N3   119.74  3.000
 M0S  H5   C7   H4   108.86  3.000
 M0S  H5   C7   S1   108.56  3.000
 M0S  H4   C7   S1   109.18  3.000
 M0S  H5   C7   C8   111.83  3.000
 M0S  H4   C7   C8   110.57  3.000
 M0S  S1   C7   C8   107.78  3.000
 M0S  H7   C8   H6   106.85  3.000
 M0S  H7   C8   N4   111.76  3.000
 M0S  H6   C8   N4   108.56  3.000
 M0S  H7   C8   C7   109.88  3.000
 M0S  H6   C8   C7   108.89  3.000
 M0S  N4   C8   C7   110.77  3.000
 M0S  H9   C9   H8   107.34  3.000
 M0S  H9   C9   C10  110.28  3.000
 M0S  H8   C9   C10  113.31  3.000
 M0S  H9   C9   N4   111.72  3.000
 M0S  H8   C9   N4   110.89  3.000
 M0S  C10  C9   N4   103.37  3.000
 M0S  H11  C11  H10  107.07  3.000
 M0S  H11  C11  C10  110.97  3.000
 M0S  H10  C11  C10  112.25  3.000
 M0S  H11  C11  C12  111.22  3.000
 M0S  H10  C11  C12  110.78  3.000
 M0S  C10  C11  C12  104.63  3.000
 M0S  H13  C12  H12  107.18  3.000
 M0S  H13  C12  N4   110.98  3.000
 M0S  H12  C12  N4   111.56  3.000
 M0S  H13  C12  C11  110.36  3.000
 M0S  H12  C12  C11  112.54  3.000
 M0S  N4   C12  C11  104.28  3.000
 M0S  C1   N    C    120.19  3.000
 M0S  C1   N    C4   118.55  3.000
 M0S  C    N    C4   121.23  3.000
 M0S  H16  C    H15  109.60  3.000
 M0S  H16  C    H14  108.60  3.000
 M0S  H15  C    H14  109.08  3.000
 M0S  H16  C    N    109.69  3.000
 M0S  H15  C    N    110.28  3.000
 M0S  H14  C    N    109.57  3.000
 M0S  N3   C1   N    128.69  3.000
 M0S  N    C1   C2   124.59  3.000
 M0S  N3   C1   C2   106.72  3.000
 M0S  H17  N3   C1   127.44  3.000
 M0S  H17  N3   C6   126.68  3.000
 M0S  C1   N3   C6   105.87  3.000
 M0S  C6   N2   C2   105.07  3.000
 M0S  N1   C3   S    122.66  3.000
 M0S  S    C3   C2   123.46  3.000
 M0S  N1   C3   C2   113.88  3.000
 M0S  C3   N1   C5   117.50  3.000
 M0S  C5   N1   C4   116.29  3.000
 M0S  C3   N1   C4   126.21  3.000
 M0S  C7   S1   C6    99.95  3.000
 M0S  C12  N4   C9   104.84  3.000
 M0S  C12  N4   C8   114.60  3.000
 M0S  C9   N4   C8   113.37  3.000
 M0S  H21  C10  H20  107.37  3.000
 M0S  H21  C10  C11  112.82  3.000
 M0S  H20  C10  C11  110.64  3.000
 M0S  H21  C10  C9   111.74  3.000
 M0S  H20  C10  C9   110.30  3.000
 M0S  C11  C10  C9   104.00  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
 M0S  CONST_01  C6   N3   C1   C2      0.00   0.0  0
 M0S  CONST_02  N3   C6   N2   C2      0.00   0.0  0
 M0S  CONST_03  C1   C2   N2   C6      0.00   0.0  0
 M0S  CONST_04  N2   C6   N3   C1      0.00   0.0  0
 M0S  CONST_05  N2   C2   C1   N3      0.00   0.0  0
 M0S  CONST_06  C3   N1   C4   N       0.00   0.0  0
 M0S  CONST_07  N1   C4   N    C1      0.00   0.0  0
 M0S  CONST_08  S1   C6   N2   C2    180.00   0.0  0
 M0S  CONST_09  S1   C6   N3   C1    180.00   0.0  0
 M0S  CONST_10  N    C4   N1   C5    180.00   0.0  0
 M0S  CONST_11  C1   N    C4   O     180.00   0.0  0
 M0S  CONST_12  C3   N1   C4   O     180.00   0.0  0
 M0S  CONST_13  N1   C4   N    C     180.00   0.0  0
 M0S  CONST_14  H17  N3   C1   C2    180.00   0.0  0
 M0S  CONST_15  O    C4   N1   C5      0.00   0.0  0
 M0S  CONST_16  C    N    C4   O       0.00   0.0  0
 M0S  Var_01    C11  C12  N4   C9    -39.92  30.0  1
 M0S  Var_02    C12  C11  C10  C9      6.27  30.0  1
 M0S  Var_03    N4   C9   C10  C11   -30.12  30.0  1
 M0S  Var_04    C10  C9   N4   C12    44.09  30.0  1
 M0S  Var_05    C10  C11  C12  N4     19.72  30.0  1
 M0S  Var_06    N3   C6   S1   C7   -179.81  30.0  2
 M0S  Var_07    C9   N4   C8   C7    166.60  30.0  3
 M0S  Var_08    H14  C    N    C4     -9.28  30.0  3
 M0S  Var_09    H1   C5   N1   C4    123.03  30.0  3
 M0S  Var_10    C8   C7   S1   C6    178.50  30.0  3
 M0S  Var_11    N4   C8   C7   S1    178.50  30.0  3

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
 M0S  plan-1  C2   0.020
 M0S  plan-1  C4   0.020
 M0S  plan-1  C5   0.020
 M0S  plan-1  C6   0.020
 M0S  plan-1  O    0.020
 M0S  plan-1  N    0.020
 M0S  plan-1  C    0.020
 M0S  plan-1  C1   0.020
 M0S  plan-1  N3   0.020
 M0S  plan-1  N2   0.020
 M0S  plan-1  C3   0.020
 M0S  plan-1  S    0.020
 M0S  plan-1  N1   0.020
 M0S  plan-1  S1   0.020
 M0S  plan-1  H17  0.020

