# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:39:52 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 1-{2-[(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)sulfanyl]ethyl}piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc([nH]c2C1=O)SCCN3CCC(CC3)C(O)=O
#
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
 WDG  WDG  '1-{2-[(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)sulfanyl]ethyl}piperidine-4-carboxylic acid'  ligand  45  25  .  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_WDG
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
 WDG  C10   C  CH2    0  -0.605  29.3535  -0.4157  -0.1656
 WDG  N12   N  NR6    0  -0.416  31.4289  -1.4754  -0.9501
 WDG  C13   C  C      0  -0.281  32.0817  -2.7641  -1.1257
 WDG  C15   C  CR16   0  -0.392  34.2174  -1.6425  -1.8308
 WDG  C20   C  C      0  -0.287  32.3979  -0.4643  -0.5555
 WDG  C22   C  CR56   0   0.127  26.2071   2.6258   0.1494
 WDG  C03   C  CR6    0   0.718  24.0317   3.9780   1.2065
 WDG  C06   C  CR56   0   0.447  25.4853   2.1095   1.1883
 WDG  C08   C  CR5    0   0.331  27.0202   0.7168   0.8129
 WDG  C11   C  CH2    0  -0.255  30.3323  -1.5763  -0.0125
 WDG  C14   C  C      0  -0.417  33.1763  -2.7014  -2.1772
 WDG  C16   C  C      0   0.427  35.3670  -1.5476  -2.8604
 WDG  C19   C  C      0  -0.415  33.5053  -0.3172  -1.5872
 WDG  C23   C  CR6    0   0.555  25.8999   3.8730  -0.4521
 WDG  N02   N  NR6    0  -0.603  24.7906   4.4807   0.1503
 WDG  N04   N  NR6    0  -0.590  24.4081   2.7561   1.7149
 WDG  N07   N  N      0  -0.479  25.9794   0.9307   1.6041
 WDG  N21   N  NR15   0  -0.661  27.2020   1.7016  -0.0799
 WDG  O17   O  OC    -1  -0.605  35.6387  -2.5849  -3.4989
 WDG  O18   O  O      0  -0.605  35.9536  -0.4498  -2.9522
 WDG  O24   O  O      0  -0.464  26.4901   4.4025  -1.3767
 WDG  S09   S  S2     0   0.085  27.9774  -0.7174   0.9847
 WDG  H101  H  HCH2   0   0.293  29.8149   0.5393   0.0865
 WDG  H102  H  HCH2   0   0.289  28.9803  -0.3789  -1.1896
 WDG  H132  H  H      0   0.230  31.3253  -3.4972  -1.4176
 WDG  H131  H  H      0   0.181  32.5179  -3.1197  -0.1743
 WDG  H151  H  HCR6   0   0.211  34.6793  -1.9425  -0.8764
 WDG  H201  H  H      0   0.183  32.8431  -0.7160   0.4247
 WDG  H202  H  H      0   0.232  31.8922   0.4956  -0.4310
 WDG  H012  H  HCH3   0   0.269  23.5675   6.1691   0.1453
 WDG  H013  H  HCH3   0   0.253  25.2421   6.4787  -0.3188
 WDG  H011  H  HCH3   0   0.253  24.1412   5.6792  -1.4510
 WDG  H051  H  HCH3   0   0.273  22.8624   2.7851   3.1086
 WDG  H052  H  HCH3   0   0.258  23.2935   1.1754   2.5182
 WDG  H053  H  HCH3   0   0.258  24.3483   2.0098   3.6719
 WDG  H111  H  HCH2   0   0.250  29.7942  -2.5062  -0.2137
 WDG  H112  H  HCH2   0   0.212  30.6811  -1.6322   1.0321
 WDG  H141  H  H      0   0.203  32.7270  -2.4729  -3.1494
 WDG  H142  H  H      0   0.219  33.6373  -3.6858  -2.2630
 WDG  H191  H  H      0   0.220  34.2083   0.4429  -1.2453
 WDG  H192  H  H      0   0.203  33.0717   0.0475  -2.5244
 WDG  H211  H  HNR5   0   0.442  27.9098   1.7617  -0.7970
 WDG  C01   C  CH3    0  -0.530  24.4143   5.7774  -0.4021
 WDG  C05   C  CH3    0  -0.536  23.6866   2.1450   2.8184
 WDG  O25   O  O      0  -0.480  23.0822   4.5887   1.6571

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
 WDG  O18  C16   deloc     1.248  0.020  1.248
 WDG  O17  C16   deloc     1.248  0.020  1.248
 WDG  C16  C15   single    1.546  0.020  1.546
 WDG  C19  C15   single    1.524  0.020  1.524
 WDG  C19  C20   single    1.521  0.020  1.521
 WDG  C15  C14   single    1.525  0.020  1.525
 WDG  C14  C13   single    1.519  0.020  1.519
 WDG  C20  N12   single    1.455  0.020  1.455
 WDG  N12  C13   single    1.455  0.020  1.455
 WDG  N12  C11   single    1.446  0.020  1.446
 WDG  C10  C11   single    1.526  0.020  1.526
 WDG  C10  S09   single    1.819  0.020  1.819
 WDG  O24  C23   double    1.218  0.020  1.218
 WDG  C23  C22   single    1.418  0.020  1.418
 WDG  C23  N02   single    1.401  0.020  1.401
 WDG  N21  C22   aromatic  1.377  0.020  1.377
 WDG  N21  C08   aromatic  1.342  0.020  1.342
 WDG  C01  N02   single    1.459  0.020  1.459
 WDG  C22  C06   aromatic  1.366  0.020  1.366
 WDG  S09  C08   single    1.733  0.020  1.733
 WDG  N02  C03   single    1.394  0.020  1.394
 WDG  C08  N07   aromatic  1.325  0.020  1.325
 WDG  C06  N07   aromatic  1.344  0.020  1.344
 WDG  C06  N04   single    1.362  0.020  1.362
 WDG  C03  N04   single    1.376  0.020  1.376
 WDG  C03  O25   double    1.215  0.020  1.215
 WDG  N04  C05   single    1.453  0.020  1.453
 WDG  C10  H101  single    0.970  0.020  1.090
 WDG  C10  H102  single    0.970  0.020  1.090
 WDG  C13  H132  single    0.970  0.020  1.090
 WDG  C13  H131  single    0.970  0.020  1.090
 WDG  C15  H151  single    0.970  0.020  1.090
 WDG  C20  H201  single    0.970  0.020  1.090
 WDG  C20  H202  single    0.970  0.020  1.090
 WDG  C01  H012  single    0.970  0.020  1.090
 WDG  C01  H013  single    0.970  0.020  1.090
 WDG  C01  H011  single    0.970  0.020  1.090
 WDG  C05  H051  single    0.970  0.020  1.090
 WDG  C05  H052  single    0.970  0.020  1.090
 WDG  C05  H053  single    0.970  0.020  1.090
 WDG  C11  H111  single    0.970  0.020  1.090
 WDG  C11  H112  single    0.970  0.020  1.090
 WDG  C14  H141  single    0.970  0.020  1.090
 WDG  C14  H142  single    0.970  0.020  1.090
 WDG  C19  H191  single    0.970  0.020  1.090
 WDG  C19  H192  single    0.970  0.020  1.090
 WDG  N21  H211  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
 WDG  H102  C10  H101  109.42  3.000
 WDG  H102  C10  S09   109.91  3.000
 WDG  H101  C10  S09   108.61  3.000
 WDG  H102  C10  C11   109.84  3.000
 WDG  H101  C10  C11   111.82  3.000
 WDG  S09   C10  C11   107.20  3.000
 WDG  C11   N12  C20   112.19  3.000
 WDG  C11   N12  C13   110.89  3.000
 WDG  C20   N12  C13   110.45  3.000
 WDG  H131  C13  H132  106.69  3.000
 WDG  H131  C13  C14   108.95  3.000
 WDG  H132  C13  C14   109.97  3.000
 WDG  H131  C13  N12   110.98  3.000
 WDG  H132  C13  N12   108.40  3.000
 WDG  C14   C13  N12   111.73  3.000
 WDG  H151  C15  C19   107.11  3.000
 WDG  H151  C15  C16   106.37  3.000
 WDG  C19   C15  C16   113.61  3.000
 WDG  H151  C15  C14   107.09  3.000
 WDG  C19   C15  C14   108.73  3.000
 WDG  C16   C15  C14   113.52  3.000
 WDG  H202  C20  H201  106.59  3.000
 WDG  H202  C20  C19   109.24  3.000
 WDG  H201  C20  C19   109.29  3.000
 WDG  H202  C20  N12   109.47  3.000
 WDG  H201  C20  N12   110.51  3.000
 WDG  C19   C20  N12   111.61  3.000
 WDG  N21   C22  C23   132.53  3.000
 WDG  N21   C22  C06   104.75  3.000
 WDG  C23   C22  C06   122.71  3.000
 WDG  O25   C03  N04   121.53  3.000
 WDG  O25   C03  N02   121.66  3.000
 WDG  N04   C03  N02   116.82  3.000
 WDG  N07   C06  N04   125.97  3.000
 WDG  N04   C06  C22   122.16  3.000
 WDG  N07   C06  C22   111.86  3.000
 WDG  S09   C08  N21   126.77  3.000
 WDG  S09   C08  N07   120.56  3.000
 WDG  N21   C08  N07   112.67  3.000
 WDG  H112  C11  H111  106.68  3.000
 WDG  H112  C11  N12   112.20  3.000
 WDG  H111  C11  N12   108.26  3.000
 WDG  H112  C11  C10   109.66  3.000
 WDG  H111  C11  C10   108.23  3.000
 WDG  N12   C11  C10   111.60  3.000
 WDG  H142  C14  H141  106.97  3.000
 WDG  H142  C14  C15   110.86  3.000
 WDG  H141  C14  C15   109.69  3.000
 WDG  H142  C14  C13   108.77  3.000
 WDG  H141  C14  C13   109.12  3.000
 WDG  C15   C14  C13   111.31  3.000
 WDG  O18   C16  O17   126.24  3.000
 WDG  O17   C16  C15   116.84  3.000
 WDG  O18   C16  C15   116.90  3.000
 WDG  H192  C19  H191  106.95  3.000
 WDG  H192  C19  C20   108.93  3.000
 WDG  H191  C19  C20   108.92  3.000
 WDG  H192  C19  C15   109.74  3.000
 WDG  H191  C19  C15   110.80  3.000
 WDG  C20   C19  C15   111.38  3.000
 WDG  O24   C23  N02   121.43  3.000
 WDG  N02   C23  C22   111.75  3.000
 WDG  O24   C23  C22   126.82  3.000
 WDG  C23   N02  C03   126.89  3.000
 WDG  C03   N02  C01   117.83  3.000
 WDG  C23   N02  C01   115.28  3.000
 WDG  C06   N04  C05   119.12  3.000
 WDG  C05   N04  C03   121.21  3.000
 WDG  C06   N04  C03   119.67  3.000
 WDG  C08   N07  C06   104.22  3.000
 WDG  H211  N21  C08   127.70  3.000
 WDG  H211  N21  C22   125.80  3.000
 WDG  C08   N21  C22   106.49  3.000
 WDG  C08   S09  C10   102.59  3.000
 WDG  H011  C01  H013  108.84  3.000
 WDG  H011  C01  H012  108.90  3.000
 WDG  H013  C01  H012  108.87  3.000
 WDG  H011  C01  N02   110.45  3.000
 WDG  H013  C01  N02   110.35  3.000
 WDG  H012  C01  N02   109.40  3.000
 WDG  H053  C05  H052  108.98  3.000
 WDG  H053  C05  H051  109.02  3.000
 WDG  H052  C05  H051  108.99  3.000
 WDG  H053  C05  N04   110.24  3.000
 WDG  H052  C05  N04   110.15  3.000
 WDG  H051  C05  N04   109.44  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
 WDG  CONST_01  N07   C08  N21  C22    0.00   0.0  0
 WDG  CONST_02  C08   N07  C06  C22    0.00   0.0  0
 WDG  CONST_03  C08   N21  C22  C06    0.00   0.0  0
 WDG  CONST_04  N21   C08  N07  C06    0.00   0.0  0
 WDG  CONST_05  N21   C22  C06  N07    0.00   0.0  0
 WDG  CONST_06  N02   C03  N04  C06    0.00   0.0  0
 WDG  CONST_07  N04   C03  N02  C23    0.00   0.0  0
 WDG  CONST_08  S09   C08  N21  C22  180.00   0.0  0
 WDG  CONST_09  S09   C08  N07  C06  180.00   0.0  0
 WDG  CONST_10  N04   C03  N02  C01  180.00   0.0  0
 WDG  CONST_11  N02   C03  N04  C05  180.00   0.0  0
 WDG  CONST_12  O25   C03  N04  C06  180.00   0.0  0
 WDG  CONST_13  O25   C03  N02  C23  180.00   0.0  0
 WDG  CONST_14  H211  N21  C22  C06  180.00   0.0  0
 WDG  CONST_15  O25   C03  N02  C01    0.00   0.0  0
 WDG  CONST_16  O25   C03  N04  C05    0.00   0.0  0
 WDG  Var_01    C15   C19  C20  N12  -57.06  30.0  1
 WDG  Var_02    C15   C14  C13  N12   57.06  30.0  1
 WDG  Var_03    C19   C20  N12  C13   58.78  30.0  1
 WDG  Var_04    C14   C13  N12  C20  -58.86  30.0  1
 WDG  Var_05    C20   N12  C11  C10   75.66  30.0  2
 WDG  Var_06    N21   C08  S09  C10    7.16  30.0  2
 WDG  Var_07    H012  C01  N02  C03    1.17  30.0  3
 WDG  Var_08    H051  C05  N04  C03    1.05  30.0  3
 WDG  Var_09    S09   C10  C11  N12  176.37  30.0  2
 WDG  Var_10    C11   C10  S09  C08  175.42  30.0  1

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
 WDG  chir_01  C15  C16  C19  C14  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
 WDG  plan-1  C22   0.020
 WDG  plan-1  C03   0.020
 WDG  plan-1  C06   0.020
 WDG  plan-1  C08   0.020
 WDG  plan-1  C23   0.020
 WDG  plan-1  N02   0.020
 WDG  plan-1  N04   0.020
 WDG  plan-1  N07   0.020
 WDG  plan-1  N21   0.020
 WDG  plan-1  O24   0.020
 WDG  plan-1  S09   0.020
 WDG  plan-1  H211  0.020
 WDG  plan-1  C01   0.020
 WDG  plan-1  C05   0.020
 WDG  plan-1  O25   0.020
 WDG  plan-2  C15   0.020
 WDG  plan-2  C16   0.020
 WDG  plan-2  O17   0.020
 WDG  plan-2  O18   0.020

