# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 16:47:31 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: N-{[2-(1,3-dimethyl-2-oxo-6-sulfanylidene-1,2,3,6-tetrahydro-7H-purin-7-yl)ethyl]carbamoyl}methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2ncn(CCNC(=O)N[S](C)(=O)=O)c2C1=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
 WD7  WD7  N-{[2-(1,3-dimethyl-2-oxo-6-sulfanylidene-1,2,3,6-tetrahydro-7H-purin-7-yl)ethyl]carbamoyl}methanesulfonamide  ligand  39  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_WD7
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
 WD7  C20   C  CR56  0   0.252  26.6990   2.2625   0.7620
 WD7  C21   C  CR6   0   0.198  25.5502   1.5687   1.1839
 WD7  C01   C  CH3   0  -0.519  23.0806   1.6204   1.1606
 WD7  C03   C  CR6   0   0.742  24.2699   3.4170   0.1270
 WD7  C05   C  CH3   0  -0.541  25.4278   5.3076  -0.9403
 WD7  C06   C  CR56  0   0.458  26.6246   3.4619   0.0860
 WD7  C08   C  CR15  0   0.123  28.6650   3.0496   0.2714
 WD7  C10   C  CH2   0  -0.326  28.7528   0.8332   1.3294
 WD7  C11   C  CH2   0  -0.309  28.7199  -0.2720   0.2783
 WD7  C13   C  C     0   0.780  28.5548   0.6737  -1.9705
 WD7  C16   C  CH3   0  -0.800  27.8312   3.2595  -3.9142
 WD7  N02   N  NR6   0  -0.568  24.3761   2.2047   0.8210
 WD7  N04   N  NR6   0  -0.584  25.4378   4.0429  -0.2225
 WD7  N07   N  N     0  -0.462  27.8339   3.9533  -0.2145
 WD7  N09   N  NR5   0  -0.483  28.0560   2.0223   0.8763
 WD7  N12   N  NH1   0  -0.657  29.2942   0.1399  -0.9784
 WD7  N14   N  NC1   0  -0.849  29.3107   1.1417  -3.0388
 WD7  O17   O  OS    0  -0.640  27.6481   0.8430  -4.9465
 WD7  O18   O  OS    0  -0.657  29.7856   2.1098  -5.2545
 WD7  O19   O  O     0  -0.491  27.3403   0.7516  -1.9692
 WD7  O23   O  O     0  -0.474  23.1804   3.8792  -0.1399
 WD7  S15   S  S     0   1.359  28.6383   1.7677  -4.4328
 WD7  S22   S  S1    0  -0.307  25.5912   0.1363   2.0383
 WD7  H013  H  HCH3  0   0.266  23.2465   0.6878   1.6844
 WD7  H012  H  HCH3  0   0.259  22.5191   2.2944   1.8034
 WD7  H011  H  HCH3  0   0.260  22.5070   1.4250   0.2577
 WD7  H052  H  HCH3  0   0.275  24.4038   5.6203  -1.1024
 WD7  H053  H  HCH3  0   0.263  25.9470   6.0683  -0.3609
 WD7  H051  H  HCH3  0   0.265  25.9243   5.1942  -1.9025
 WD7  H081  H  HCR5  0   0.308  29.7417   3.1114   0.2119
 WD7  H102  H  HCH2  0   0.282  28.3065   0.4806   2.2550
 WD7  H101  H  HCH2  0   0.282  29.7810   1.1287   1.5373
 WD7  H111  H  HCH2  0   0.264  27.6977  -0.6112   0.1214
 WD7  H112  H  HCH2  0   0.278  29.2870  -1.1213   0.6593
 WD7  H162  H  HCH3  0   0.300  27.0259   3.0213  -3.2256
 WD7  H161  H  HCH3  0   0.295  28.5614   3.9108  -3.4402
 WD7  H163  H  HCH3  0   0.307  27.4295   3.7341  -4.8086
 WD7  H121  H  HNH1  0   0.410  30.2993   0.1323  -1.0545
 WD7  H141  H  HNC1  0   0.440  30.3198   1.2124  -2.9792

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
 WD7  O18  S15   double    1.452  0.020  1.452
 WD7  C16  S15   single    1.774  0.020  1.774
 WD7  S15  O17   double    1.449  0.020  1.449
 WD7  S15  N14   single    1.670  0.020  1.670
 WD7  N14  C13   single    1.390  0.020  1.390
 WD7  O19  C13   double    1.217  0.020  1.217
 WD7  C13  N12   single    1.348  0.020  1.348
 WD7  N12  C11   single    1.442  0.020  1.442
 WD7  C11  C10   single    1.526  0.020  1.526
 WD7  N07  C08   aromatic  1.320  0.020  1.320
 WD7  N07  C06   aromatic  1.339  0.020  1.339
 WD7  C08  N09   aromatic  1.339  0.020  1.339
 WD7  C05  N04   single    1.454  0.020  1.454
 WD7  C06  N04   single    1.357  0.020  1.357
 WD7  C06  C20   aromatic  1.379  0.020  1.379
 WD7  N04  C03   single    1.370  0.020  1.370
 WD7  N09  C20   aromatic  1.383  0.020  1.383
 WD7  N09  C10   single    1.451  0.020  1.451
 WD7  C20  C21   single    1.407  0.020  1.407
 WD7  C03  O23   double    1.213  0.020  1.213
 WD7  C03  N02   single    1.401  0.020  1.401
 WD7  C21  N02   single    1.384  0.020  1.384
 WD7  C21  S22   double    1.668  0.020  1.668
 WD7  N02  C01   single    1.461  0.020  1.461
 WD7  C01  H013  single    0.970  0.020  1.090
 WD7  C01  H012  single    0.970  0.020  1.090
 WD7  C01  H011  single    0.970  0.020  1.090
 WD7  C05  H052  single    0.970  0.020  1.090
 WD7  C05  H053  single    0.970  0.020  1.090
 WD7  C05  H051  single    0.970  0.020  1.090
 WD7  C08  H081  single    0.930  0.020  1.080
 WD7  C10  H102  single    0.970  0.020  1.090
 WD7  C10  H101  single    0.970  0.020  1.090
 WD7  C11  H111  single    0.970  0.020  1.090
 WD7  C11  H112  single    0.970  0.020  1.090
 WD7  C16  H162  single    0.970  0.020  1.090
 WD7  C16  H161  single    0.970  0.020  1.090
 WD7  C16  H163  single    0.970  0.020  1.090
 WD7  N12  H121  single    0.860  0.020  1.020
 WD7  N14  H141  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
 WD7  N09   C20  C06   104.16  3.000
 WD7  N09   C20  C21   133.70  3.000
 WD7  C06   C20  C21   122.14  3.000
 WD7  S22   C21  N02   123.35  3.000
 WD7  S22   C21  C20   123.84  3.000
 WD7  N02   C21  C20   112.80  3.000
 WD7  H011  C01  H012  109.25  3.000
 WD7  H011  C01  H013  109.14  3.000
 WD7  H012  C01  H013  109.09  3.000
 WD7  H011  C01  N02   110.28  3.000
 WD7  H012  C01  N02   110.33  3.000
 WD7  H013  C01  N02   108.73  3.000
 WD7  O23   C03  N04   122.35  3.000
 WD7  O23   C03  N02   120.45  3.000
 WD7  N04   C03  N02   117.20  3.000
 WD7  H051  C05  H053  109.02  3.000
 WD7  H051  C05  H052  109.21  3.000
 WD7  H053  C05  H052  109.21  3.000
 WD7  H051  C05  N04   110.03  3.000
 WD7  H053  C05  N04   110.00  3.000
 WD7  H052  C05  N04   109.36  3.000
 WD7  N07   C06  N04   125.56  3.000
 WD7  N04   C06  C20   122.08  3.000
 WD7  N07   C06  C20   112.36  3.000
 WD7  H081  C08  N09   121.49  3.000
 WD7  H081  C08  N07   124.61  3.000
 WD7  N09   C08  N07   113.90  3.000
 WD7  H101  C10  H102  108.25  3.000
 WD7  H101  C10  N09   106.89  3.000
 WD7  H102  C10  N09   109.56  3.000
 WD7  H101  C10  C11   110.38  3.000
 WD7  H102  C10  C11   110.06  3.000
 WD7  N09   C10  C11   111.61  3.000
 WD7  H112  C11  H111  107.23  3.000
 WD7  H112  C11  N12   108.67  3.000
 WD7  H111  C11  N12   109.72  3.000
 WD7  H112  C11  C10   108.21  3.000
 WD7  H111  C11  C10   110.21  3.000
 WD7  N12   C11  C10   112.64  3.000
 WD7  O19   C13  N14   121.47  3.000
 WD7  O19   C13  N12   124.90  3.000
 WD7  N14   C13  N12   113.63  3.000
 WD7  H163  C16  H161  110.16  3.000
 WD7  H163  C16  H162  110.04  3.000
 WD7  H161  C16  H162  110.67  3.000
 WD7  H163  C16  S15   107.11  3.000
 WD7  H161  C16  S15   109.01  3.000
 WD7  H162  C16  S15   109.77  3.000
 WD7  C03   N02  C01   113.20  3.000
 WD7  C01   N02  C21   120.50  3.000
 WD7  C03   N02  C21   126.30  3.000
 WD7  C06   N04  C05   119.38  3.000
 WD7  C06   N04  C03   119.46  3.000
 WD7  C05   N04  C03   121.15  3.000
 WD7  C08   N07  C06   103.57  3.000
 WD7  C10   N09  C08   123.47  3.000
 WD7  C10   N09  C20   129.76  3.000
 WD7  C08   N09  C20   106.01  3.000
 WD7  H121  N12  C13   119.64  3.000
 WD7  H121  N12  C11   117.44  3.000
 WD7  C13   N12  C11   122.43  3.000
 WD7  H141  N14  S15   115.09  3.000
 WD7  H141  N14  C13   121.32  3.000
 WD7  S15   N14  C13   123.30  3.000
 WD7  O18   S15  O17   119.32  3.000
 WD7  O17   S15  N14   109.39  3.000
 WD7  O18   S15  N14   104.04  3.000
 WD7  N14   S15  C16   104.74  3.000
 WD7  O17   S15  C16   109.24  3.000
 WD7  O18   S15  C16   109.08  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
 WD7  CONST_01  C08   N07  C06  C20     0.00   0.0  0
 WD7  CONST_02  N07   C08  N09  C20     0.00   0.0  0
 WD7  CONST_03  N09   C08  N07  C06     0.00   0.0  0
 WD7  CONST_04  C08   N09  C20  C06     0.00   0.0  0
 WD7  CONST_05  N09   C20  C06  N07     0.00   0.0  0
 WD7  CONST_06  N04   C03  N02  C21     0.00   0.0  0
 WD7  CONST_07  N02   C03  N04  C06     0.00   0.0  0
 WD7  CONST_08  C10   N09  C20  C21     0.00   0.0  0
 WD7  CONST_09  C10   N09  C20  C06   180.00   0.0  0
 WD7  CONST_10  N07   C08  N09  C10   180.00   0.0  0
 WD7  CONST_11  O23   C03  N02  C21   180.00   0.0  0
 WD7  CONST_12  N04   C03  N02  C01   180.00   0.0  0
 WD7  CONST_13  N02   C03  N04  C05   180.00   0.0  0
 WD7  CONST_14  O23   C03  N04  C06   180.00   0.0  0
 WD7  CONST_15  H081  C08  N09  C20   180.00   0.0  0
 WD7  CONST_16  O23   C03  N02  C01     0.00   0.0  0
 WD7  CONST_17  O23   C03  N04  C05     0.00   0.0  0
 WD7  CONST_18  O19   C13  N12  C11     0.00   0.0  0
 WD7  CONST_19  S15   N14  C13  O19     0.00   0.0  0
 WD7  CONST_20  N14   C13  N12  C11   180.00   0.0  0
 WD7  CONST_21  S15   N14  C13  N12   180.00   0.0  0
 WD7  CONST_22  H141  N14  C13  O19   180.00   0.0  0
 WD7  CONST_23  H121  N12  C13  O19   180.00   0.0  0
 WD7  Var_01    C11   C10  N09  C20    74.77  30.0  2
 WD7  Var_02    H013  C01  N02  C21    -0.60  30.0  3
 WD7  Var_03    H052  C05  N04  C03     0.99  30.0  3
 WD7  Var_04    N12   C11  C10  N09    57.83  30.0  2
 WD7  Var_05    C13   N12  C11  C10   -91.89  30.0  1
 WD7  Var_06    O18   S15  N14  C13  -179.53  30.0  2
 WD7  Var_07    H162  C16  S15  N14   -63.99  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
 WD7  plan-1  C20   0.020
 WD7  plan-1  C21   0.020
 WD7  plan-1  C01   0.020
 WD7  plan-1  C03   0.020
 WD7  plan-1  C05   0.020
 WD7  plan-1  C06   0.020
 WD7  plan-1  C08   0.020
 WD7  plan-1  C10   0.020
 WD7  plan-1  N02   0.020
 WD7  plan-1  N04   0.020
 WD7  plan-1  N07   0.020
 WD7  plan-1  N09   0.020
 WD7  plan-1  O23   0.020
 WD7  plan-1  S22   0.020
 WD7  plan-1  H081  0.020
 WD7  plan-2  C11   0.020
 WD7  plan-2  C13   0.020
 WD7  plan-2  N12   0.020
 WD7  plan-2  N14   0.020
 WD7  plan-2  O19   0.020
 WD7  plan-2  S15   0.020
 WD7  plan-2  H121  0.020
 WD7  plan-2  H141  0.020

