# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:19:25 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: 1,3-dimethyl-8-{[2-(morpholin-4-yl)-2-oxoethyl]sulfanyl}-6-sulfanylidene-1,3,6,7-tetrahydro-2H-purin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc([nH]c2C1=S)SCC(=O)N3CCOCC3
#
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
 WDM  WDM  1,3-dimethyl-8-{[2-(morpholin-4-yl)-2-oxoethyl]sulfanyl}-6-sulfanylidene-1,3,6,7-tetrahydro-2H-purin-2-one  ligand  40  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WDM
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
 WDM  C11   C  C     0   0.583  29.1017  -0.0855  -1.1570
 WDM  C01   C  CH3   0  -0.527  24.7622   6.2673   0.0561
 WDM  C03   C  CR6   0   0.727  23.7564   4.0976   0.5359
 WDM  C05   C  CH3   0  -0.538  22.7486   1.9019   1.0155
 WDM  C06   C  CR56  0   0.461  25.1459   2.2010   0.7850
 WDM  C08   C  CR5   0   0.319  26.7748   0.8744   0.8878
 WDM  C10   C  CH2   0  -0.775  29.2183  -0.2830   0.3524
 WDM  C13   C  CH2   0  -0.290  31.5449   0.2973  -1.0998
 WDM  C14   C  CH2   0  -0.224  32.6620   0.3648  -2.1314
 WDM  C16   C  CH2   0  -0.140  31.3341  -0.5318  -3.8613
 WDM  C17   C  CH2   0  -0.382  30.3010   0.3886  -3.2220
 WDM  C20   C  CR56  0   0.234  26.2633   2.9659   0.5664
 WDM  C21   C  CR6   0   0.194  26.2130   4.3395   0.3119
 WDM  N02   N  NR6   0  -0.565  24.9264   4.8404   0.3136
 WDM  N04   N  NR6   0  -0.583  23.9051   2.7508   0.7761
 WDM  N07   N  N     0  -0.467  25.4523   0.9096   0.9797
 WDM  N12   N  NT    0  -0.460  30.2625   0.1707  -1.7875
 WDM  N19   N  NR15  0  -0.659  27.3099   2.0809   0.6468
 WDM  O15   O  O2    0  -0.483  32.5142  -0.6552  -3.0862
 WDM  O18   O  O     0  -0.468  28.0231  -0.1544  -1.7208
 WDM  S09   S  S2    0   0.140  27.6347  -0.6084   1.1435
 WDM  S22   S  S1    0  -0.328  27.5689   5.2645   0.0393
 WDM  H013  H  HCH3  0   0.276  23.7114   6.5229   0.0814
 WDM  H011  H  HCH3  0   0.259  25.2926   6.8439   0.8109
 WDM  H012  H  HCH3  0   0.259  25.1725   6.5149  -0.9206
 WDM  H051  H  HCH3  0   0.277  21.8496   2.5049   0.9992
 WDM  H052  H  HCH3  0   0.264  22.6793   1.1374   0.2442
 WDM  H053  H  HCH3  0   0.264  22.8379   1.4202   1.9871
 WDM  H101  H  HCH2  0   0.350  29.8140  -1.1722   0.5767
 WDM  H102  H  HCH2  0   0.327  29.7359   0.5461   0.8396
 WDM  H132  H  HCH2  0   0.257  31.7113  -0.5653  -0.4517
 WDM  H131  H  HCH2  0   0.255  31.5782   1.1956  -0.4754
 WDM  H142  H  HCH2  0   0.264  33.6156   0.2097  -1.6264
 WDM  H141  H  HCH2  0   0.224  32.7044   1.3573  -2.5961
 WDM  H161  H  HCH2  0   0.225  30.9152  -1.5344  -3.9758
 WDM  H162  H  HCH2  0   0.216  31.5667  -0.1529  -4.8634
 WDM  H171  H  HCH2  0   0.263  30.5282   1.4382  -3.4261
 WDM  H172  H  HCH2  0   0.285  29.3233   0.1851  -3.6501
 WDM  H191  H  HNR5  0   0.434  28.2849   2.3335   0.5738
 WDM  O23   O  O     0  -0.470  22.6624   4.6215   0.5162

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
 WDM  C16  C17   single    1.524  0.020  1.524
 WDM  C16  O15   single    1.417  0.020  1.417
 WDM  C17  N12   single    1.451  0.020  1.451
 WDM  O15  C14   single    1.405  0.020  1.405
 WDM  O18  C11   double    1.219  0.020  1.219
 WDM  C14  C13   single    1.522  0.020  1.522
 WDM  N12  C11   single    1.346  0.020  1.346
 WDM  N12  C13   single    1.461  0.020  1.461
 WDM  C11  C10   single    1.527  0.020  1.527
 WDM  S22  C21   double    1.664  0.020  1.664
 WDM  C21  C20   single    1.398  0.020  1.398
 WDM  C21  N02   single    1.381  0.020  1.381
 WDM  C01  N02   single    1.459  0.020  1.459
 WDM  N19  C20   aromatic  1.373  0.020  1.373
 WDM  N19  C08   aromatic  1.342  0.020  1.342
 WDM  C10  S09   single    1.800  0.020  1.800
 WDM  C20  C06   aromatic  1.372  0.020  1.372
 WDM  N02  C03   single    1.404  0.020  1.404
 WDM  C08  S09   single    1.733  0.020  1.733
 WDM  C08  N07   aromatic  1.326  0.020  1.326
 WDM  C06  N07   aromatic  1.341  0.020  1.341
 WDM  C06  N04   single    1.357  0.020  1.357
 WDM  C03  N04   single    1.376  0.020  1.376
 WDM  C03  O23   double    1.213  0.020  1.213
 WDM  N04  C05   single    1.454  0.020  1.454
 WDM  C01  H013  single    0.970  0.020  1.090
 WDM  C01  H011  single    0.970  0.020  1.090
 WDM  C01  H012  single    0.970  0.020  1.090
 WDM  C05  H051  single    0.970  0.020  1.090
 WDM  C05  H052  single    0.970  0.020  1.090
 WDM  C05  H053  single    0.970  0.020  1.090
 WDM  C10  H101  single    0.970  0.020  1.090
 WDM  C10  H102  single    0.970  0.020  1.090
 WDM  C13  H132  single    0.970  0.020  1.090
 WDM  C13  H131  single    0.970  0.020  1.090
 WDM  C14  H142  single    0.970  0.020  1.090
 WDM  C14  H141  single    0.970  0.020  1.090
 WDM  C16  H161  single    0.970  0.020  1.090
 WDM  C16  H162  single    0.970  0.020  1.090
 WDM  C17  H171  single    0.970  0.020  1.090
 WDM  C17  H172  single    0.970  0.020  1.090
 WDM  N19  H191  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
 WDM  O18   C11  N12   123.87  3.000
 WDM  N12   C11  C10   114.97  3.000
 WDM  O18   C11  C10   121.17  3.000
 WDM  H012  C01  H011  108.57  3.000
 WDM  H012  C01  H013  109.48  3.000
 WDM  H011  C01  H013  109.40  3.000
 WDM  H012  C01  N02   109.79  3.000
 WDM  H011  C01  N02   109.94  3.000
 WDM  H013  C01  N02   109.64  3.000
 WDM  O23   C03  N04   121.53  3.000
 WDM  O23   C03  N02   121.38  3.000
 WDM  N04   C03  N02   117.10  3.000
 WDM  H053  C05  H052  109.10  3.000
 WDM  H053  C05  H051  109.15  3.000
 WDM  H052  C05  H051  109.13  3.000
 WDM  H053  C05  N04   109.88  3.000
 WDM  H052  C05  N04   110.13  3.000
 WDM  H051  C05  N04   109.43  3.000
 WDM  N07   C06  N04   126.85  3.000
 WDM  N04   C06  C20   121.19  3.000
 WDM  N07   C06  C20   111.95  3.000
 WDM  S09   C08  N19   126.73  3.000
 WDM  S09   C08  N07   120.48  3.000
 WDM  N19   C08  N07   112.72  3.000
 WDM  H102  C10  H101  105.52  3.000
 WDM  H102  C10  S09   110.99  3.000
 WDM  H101  C10  S09   104.01  3.000
 WDM  H102  C10  C11   112.28  3.000
 WDM  H101  C10  C11   110.46  3.000
 WDM  S09   C10  C11   113.00  3.000
 WDM  H131  C13  H132  107.77  3.000
 WDM  H131  C13  N12   111.50  3.000
 WDM  H132  C13  N12   110.18  3.000
 WDM  H131  C13  C14   109.14  3.000
 WDM  H132  C13  C14   109.00  3.000
 WDM  N12   C13  C14   109.22  3.000
 WDM  H141  C14  H142  106.93  3.000
 WDM  H141  C14  O15   111.90  3.000
 WDM  H142  C14  O15   107.67  3.000
 WDM  H141  C14  C13   110.84  3.000
 WDM  H142  C14  C13   108.77  3.000
 WDM  O15   C14  C13   110.56  3.000
 WDM  H162  C16  H161  107.62  3.000
 WDM  H162  C16  O15   110.69  3.000
 WDM  H161  C16  O15   107.26  3.000
 WDM  H162  C16  C17   108.58  3.000
 WDM  H161  C16  C17   109.77  3.000
 WDM  O15   C16  C17   112.80  3.000
 WDM  H172  C17  H171  107.05  3.000
 WDM  H172  C17  N12   109.72  3.000
 WDM  H171  C17  N12   109.52  3.000
 WDM  H172  C17  C16   109.36  3.000
 WDM  H171  C17  C16   111.14  3.000
 WDM  N12   C17  C16   110.00  3.000
 WDM  N19   C20  C21   132.19  3.000
 WDM  N19   C20  C06   104.61  3.000
 WDM  C21   C20  C06   123.20  3.000
 WDM  S22   C21  N02   123.91  3.000
 WDM  N02   C21  C20   112.94  3.000
 WDM  S22   C21  C20   123.14  3.000
 WDM  C21   N02  C03   125.81  3.000
 WDM  C03   N02  C01   116.85  3.000
 WDM  C21   N02  C01   117.34  3.000
 WDM  C06   N04  C05   119.30  3.000
 WDM  C05   N04  C03   120.93  3.000
 WDM  C06   N04  C03   119.76  3.000
 WDM  C08   N07  C06   104.08  3.000
 WDM  C17   N12  C13   115.40  3.000
 WDM  C13   N12  C11   123.59  3.000
 WDM  C17   N12  C11   120.97  3.000
 WDM  H191  N19  C20   124.78  3.000
 WDM  H191  N19  C08   128.54  3.000
 WDM  C20   N19  C08   106.63  3.000
 WDM  C16   O15  C14   113.33  3.000
 WDM  C10   S09  C08   102.53  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
 WDM  CONST_01  C08   N19  C20  C06     0.00   0.0  0
 WDM  CONST_02  N19   C08  N07  C06     0.00   0.0  0
 WDM  CONST_03  C20   C06  N07  C08     0.00   0.0  0
 WDM  CONST_04  N07   C08  N19  C20     0.00   0.0  0
 WDM  CONST_05  N19   C20  C06  N07     0.00   0.0  0
 WDM  CONST_06  N02   C03  N04  C06     0.00   0.0  0
 WDM  CONST_07  N04   C03  N02  C21     0.00   0.0  0
 WDM  CONST_08  S09   C08  N07  C06   180.00   0.0  0
 WDM  CONST_09  S09   C08  N19  C20   180.00   0.0  0
 WDM  CONST_10  N04   C03  N02  C01   180.00   0.0  0
 WDM  CONST_11  N02   C03  N04  C05   180.00   0.0  0
 WDM  CONST_12  O23   C03  N04  C06   180.00   0.0  0
 WDM  CONST_13  O23   C03  N02  C21   180.00   0.0  0
 WDM  CONST_14  H191  N19  C20  C06   180.00   0.0  0
 WDM  CONST_15  C17   N12  C11  C10   180.00   0.0  0
 WDM  CONST_16  C13   N12  C11  C10     0.00   0.0  0
 WDM  CONST_17  O18   C11  N12  C13   180.00   0.0  0
 WDM  CONST_18  O18   C11  N12  C17     0.00   0.0  0
 WDM  CONST_19  O23   C03  N02  C01     0.00   0.0  0
 WDM  CONST_20  O23   C03  N04  C05     0.00   0.0  0
 WDM  Var_01    C16   C17  N12  C13    54.58  30.0  1
 WDM  Var_02    C17   C16  O15  C14   -17.86  30.0  1
 WDM  Var_03    C17   N12  C13  C14   -11.05  30.0  1
 WDM  Var_04    O15   C16  C17  N12   -39.96  30.0  1
 WDM  Var_05    O15   C14  C13  N12   -48.07  30.0  1
 WDM  Var_06    H142  C14  O15  C16  -177.22  30.0  1
 WDM  Var_07    N19   C08  S09  C10   -22.61  30.0  1
 WDM  Var_08    H013  C01  N02  C03    -0.03  30.0  3
 WDM  Var_09    H051  C05  N04  C03    -1.80  30.0  3
 WDM  Var_10    S09   C10  C11  N12   179.52  30.0  3
 WDM  Var_11    H101  C10  S09  C08   175.14  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
 WDM  plan-1  C01   0.020
 WDM  plan-1  C03   0.020
 WDM  plan-1  C05   0.020
 WDM  plan-1  C06   0.020
 WDM  plan-1  C08   0.020
 WDM  plan-1  C20   0.020
 WDM  plan-1  C21   0.020
 WDM  plan-1  N02   0.020
 WDM  plan-1  N04   0.020
 WDM  plan-1  N07   0.020
 WDM  plan-1  N19   0.020
 WDM  plan-1  S09   0.020
 WDM  plan-1  S22   0.020
 WDM  plan-1  H191  0.020
 WDM  plan-1  O23   0.020
 WDM  plan-2  C11   0.020
 WDM  plan-2  C10   0.020
 WDM  plan-2  C13   0.020
 WDM  plan-2  C17   0.020
 WDM  plan-2  N12   0.020
 WDM  plan-2  O18   0.020

