# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 13:07:45 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: {[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](SCC(O)=O)C(=O)N1CCNC1=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
 W8A  W8A  '{[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid'  ligand  26  15  .  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_W8A
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
 W8A  C01   C  CH3    0  -0.652  -44.2098  -28.1402  1.3300
 W8A  C02   C  CH1    0  -0.509  -44.6732  -29.5016  1.8436
 W8A  C04   C  CH2    0  -0.703  -44.8000  -32.2664  1.4206
 W8A  C05   C  C      0   0.427  -44.0247  -32.6472  2.7087
 W8A  C08   C  C      0   0.600  -46.1611  -29.4437  2.1459
 W8A  C11   C  CH2    0  -0.300  -47.9944  -29.3095  3.7667
 W8A  C12   C  CH2    0  -0.285  -47.9967  -29.3833  5.2919
 W8A  C14   C  CR5    0   0.718  -45.8201  -28.9299  4.5817
 W8A  N10   N  NR5    0  -0.574  -46.5687  -29.3016  3.4512
 W8A  N13   N  NR15   0  -0.657  -46.6902  -28.8580  5.6069
 W8A  O06   O  O      0  -0.607  -44.5289  -33.6047  3.3258
 W8A  O07   O  OC    -1  -0.583  -42.9988  -32.0102  2.9952
 W8A  O09   O  O      0  -0.439  -47.0018  -29.5252  1.2751
 W8A  S03   S  S2     0  -0.004  -44.3180  -30.7455  0.5719
 W8A  H013  H  HCH3   0   0.251  -44.3832  -27.3690  2.0801
 W8A  H012  H  HCH3   0   0.250  -43.1423  -28.1622  1.1141
 W8A  H011  H  HCH3   0   0.237  -44.7387  -27.8566  0.4201
 W8A  H021  H  HCH1   0   0.307  -44.1018  -29.7719  2.7242
 W8A  H041  H  HCH2   0   0.258  -45.8736  -32.2524  1.6225
 W8A  H042  H  HCH2   0   0.278  -44.6510  -33.0591  0.6811
 W8A  H112  H  HCH2   0   0.273  -48.4945  -30.1614  3.3130
 W8A  H122  H  HCH2   0   0.265  -48.7900  -28.7793  5.7280
 W8A  H121  H  HCH2   0   0.253  -48.1107  -30.4111  5.6455
 W8A  H131  H  HNR5   0   0.410  -46.3524  -28.7636  6.5512
 W8A  O15   O  O      0  -0.479  -44.6319  -28.6895  4.6211
 W8A  H111  H  HCH2   0   0.265  -48.4700  -28.3954  3.4062

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
 W8A  S03  C04   single  1.807  0.020  1.807
 W8A  S03  C02   single  1.814  0.020  1.814
 W8A  C01  C02   single  1.527  0.020  1.527
 W8A  O09  C08   double  1.213  0.020  1.213
 W8A  C04  C05   single  1.551  0.020  1.551
 W8A  C02  C08   single  1.519  0.020  1.519
 W8A  C08  N10   single  1.375  0.020  1.375
 W8A  C05  O06   deloc   1.246  0.020  1.246
 W8A  C05  O07   deloc   1.241  0.020  1.241
 W8A  N10  C11   single  1.460  0.020  1.460
 W8A  N10  C14   single  1.406  0.020  1.406
 W8A  C11  C12   single  1.527  0.020  1.527
 W8A  O15  C14   double  1.213  0.020  1.213
 W8A  C14  N13   single  1.347  0.020  1.347
 W8A  C12  N13   single  1.443  0.020  1.443
 W8A  C01  H013  single  0.970  0.020  1.090
 W8A  C01  H012  single  0.970  0.020  1.090
 W8A  C01  H011  single  0.970  0.020  1.090
 W8A  C02  H021  single  0.970  0.020  1.090
 W8A  C04  H041  single  0.970  0.020  1.090
 W8A  C04  H042  single  0.970  0.020  1.090
 W8A  C11  H111  single  0.970  0.020  1.090
 W8A  C11  H112  single  0.970  0.020  1.090
 W8A  C12  H122  single  0.970  0.020  1.090
 W8A  C12  H121  single  0.970  0.020  1.090
 W8A  N13  H131  single  0.890  0.020  1.040

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
 W8A  H011  C01  H012  108.38  3.000
 W8A  H011  C01  H013  108.26  3.000
 W8A  H012  C01  H013  107.86  3.000
 W8A  H011  C01  C02   111.44  3.000
 W8A  H012  C01  C02   110.24  3.000
 W8A  H013  C01  C02   110.56  3.000
 W8A  H021  C02  S03   107.17  3.000
 W8A  H021  C02  C08   111.35  3.000
 W8A  S03   C02  C08   110.94  3.000
 W8A  H021  C02  C01   109.61  3.000
 W8A  C08   C02  C01   109.28  3.000
 W8A  S03   C02  C01   108.43  3.000
 W8A  H042  C04  H041  105.54  3.000
 W8A  H042  C04  S03   104.83  3.000
 W8A  H041  C04  S03   109.76  3.000
 W8A  H042  C04  C05   108.38  3.000
 W8A  H041  C04  C05   109.93  3.000
 W8A  S03   C04  C05   117.61  3.000
 W8A  O07   C05  O06   127.93  3.000
 W8A  O07   C05  C04   118.61  3.000
 W8A  O06   C05  C04   113.44  3.000
 W8A  O09   C08  N10   118.88  3.000
 W8A  N10   C08  C02   118.89  3.000
 W8A  O09   C08  C02   122.22  3.000
 W8A  H112  C11  H111  108.54  3.000
 W8A  H112  C11  N10   111.30  3.000
 W8A  H111  C11  N10   110.46  3.000
 W8A  H112  C11  C12   112.23  3.000
 W8A  H111  C11  C12   111.69  3.000
 W8A  N10   C11  C12   102.56  3.000
 W8A  H121  C12  H122  108.44  3.000
 W8A  H121  C12  N13   111.49  3.000
 W8A  H122  C12  N13   111.75  3.000
 W8A  H121  C12  C11   111.63  3.000
 W8A  H122  C12  C11   112.00  3.000
 W8A  N13   C12  C11   101.48  3.000
 W8A  O15   C14  N13   126.71  3.000
 W8A  N13   C14  N10   106.40  3.000
 W8A  O15   C14  N10   126.88  3.000
 W8A  C14   N10  C11   110.34  3.000
 W8A  C14   N10  C08   129.27  3.000
 W8A  C11   N10  C08   119.60  3.000
 W8A  H131  N13  C14   120.13  3.000
 W8A  H131  N13  C12   122.84  3.000
 W8A  C14   N13  C12   113.54  3.000
 W8A  C04   S03  C02   101.28  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
 W8A  CONST_01  N13   C14  N10  C11     0.00   0.0  0
 W8A  CONST_04  N10   C14  N13  C12     0.00   0.0  0
 W8A  CONST_06  C12   C11  N10  C08   180.00   0.0  0
 W8A  CONST_07  N13   C14  N10  C08   180.00   0.0  0
 W8A  CONST_08  O15   C14  N10  C11   180.00   0.0  0
 W8A  CONST_09  O15   C14  N13  C12   180.00   0.0  0
 W8A  CONST_10  H131  N13  C12  C11   180.00   0.0  0
 W8A  CONST_11  C11   N10  C08  C02   180.00   0.0  0
 W8A  CONST_12  C14   N10  C08  C02     0.00   0.0  0
 W8A  CONST_13  O09   C08  N10  C11     0.00   0.0  0
 W8A  CONST_14  O09   C08  N10  C14   180.00   0.0  0
 W8A  CONST_15  O15   C14  N10  C08     0.00   0.0  0
 W8A  Var_01    H111  C11  N10  C14   100.14  30.0  1
 W8A  Var_02    H122  C12  N13  C14  -140.58  30.0  1
 W8A  Var_03    C05   C04  S03  C02   -62.10  30.0  3
 W8A  Var_04    S03   C04  C05  O06   171.06  30.0  2

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
 W8A  chir_01  C02  S03  C01  C08  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
 W8A  plan-1  C02   0.020
 W8A  plan-1  C08   0.020
 W8A  plan-1  C11   0.020
 W8A  plan-1  C12   0.020
 W8A  plan-1  C14   0.020
 W8A  plan-1  N10   0.020
 W8A  plan-1  N13   0.020
 W8A  plan-1  O09   0.020
 W8A  plan-1  H131  0.020
 W8A  plan-1  O15   0.020
 W8A  plan-2  C04   0.020
 W8A  plan-2  C05   0.020
 W8A  plan-2  O06   0.020
 W8A  plan-2  O07   0.020

