# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 12:37:35 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-oxo-2-[(2-oxo-2-phenylethyl)sulfanyl]-1,6-dihydropyrimidine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=CN=C(NC1=O)SCC(=O)c2ccccc2
#
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
 FIG  FIG  '6-oxo-2-[(2-oxo-2-phenylethyl)sulfanyl]-1,6-dihydropyrimidine-5-carboxylic acid'  ligand  30  20  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FIG
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
 FIG  C    C  CH2   0  -0.706   1.4124  -0.2472  -0.0233
 FIG  N    N  N     0  -0.436  -1.2853   0.5864  -0.0261
 FIG  O    O  O     0  -0.381   2.9193  -2.0651   0.0088
 FIG  S    S  S2    0   0.134   0.2261  -1.6114  -0.0159
 FIG  C1   C  C     0   0.391   2.7922  -0.8601  -0.0019
 FIG  N1   N  NR16  0  -0.685  -2.3813  -1.4610  -0.0009
 FIG  O1   O  OH1   0  -0.581  -6.0417   0.6054   0.1003
 FIG  C2   C  CR6   0   0.001   3.9546   0.0575   0.0056
 FIG  O2   O  O     0  -0.450  -4.9186   2.5218  -0.0391
 FIG  C3   C  CR16  0  -0.288   3.7980   1.4440  -0.0053
 FIG  O3   O  O     0  -0.436  -4.6187  -1.7204   0.0104
 FIG  C4   C  CR16  0  -0.237   4.9094   2.2725   0.0036
 FIG  C5   C  CR16  0  -0.241   6.1841   1.7230   0.0239
 FIG  C6   C  CR16  0  -0.240   6.3485   0.3423   0.0343
 FIG  C7   C  CR16  0  -0.256   5.2408  -0.4869   0.0252
 FIG  C8   C  CR6   0   0.396  -1.2640  -0.7160  -0.0147
 FIG  C9   C  CR16  0   0.010  -2.4980   1.1629  -0.0197
 FIG  C10  C  CR6   0  -0.347  -3.6976   0.5000  -0.0006
 FIG  C11  C  C     0   0.546  -4.9279   1.3125   0.0147
 FIG  C12  C  CR6   0   0.573  -3.6840  -0.9473   0.0049
 FIG  H    H  HCH2  0   0.334   1.2748   0.3681  -0.9137
 FIG  HA   H  HCH2  0   0.333   1.2572   0.3912   0.8472
 FIG  HN1  H  HNR6  0   0.439  -2.3127  -2.4732   0.0073
 FIG  HO1  H  HOH1  0   0.483  -6.8004   1.2086   0.1076
 FIG  H3   H  HCR6  0   0.271   2.8140   1.8939  -0.0214
 FIG  H4   H  HCR6  0   0.271   4.7794   3.3462  -0.0042
 FIG  H5   H  HCR6  0   0.272   7.0503   2.3714   0.0320
 FIG  H6   H  HCR6  0   0.268   7.3422  -0.0853   0.0497
 FIG  H7   H  HCR6  0   0.268   5.3718  -1.5606   0.0336
 FIG  H9   H  HCR6  0   0.298  -2.4907   2.2460  -0.0274

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
 FIG  C1   C    single    1.510  0.020  1.510
 FIG  C    S    single    1.808  0.020  1.808
 FIG  C    H    single    0.970  0.020  1.090
 FIG  C    HA   single    0.970  0.020  1.090
 FIG  C8   N    double    1.303  0.020  1.303
 FIG  N    C9   single    1.343  0.020  1.343
 FIG  O    C1   double    1.212  0.020  1.212
 FIG  S    C8   single    1.738  0.020  1.738
 FIG  C2   C1   single    1.481  0.020  1.481
 FIG  C8   N1   single    1.343  0.020  1.343
 FIG  N1   C12  single    1.400  0.020  1.400
 FIG  N1   HN1  single    0.860  0.020  1.020
 FIG  C11  O1   single    1.322  0.020  1.322
 FIG  O1   HO1  single    0.850  0.020  0.980
 FIG  C3   C2   aromatic  1.395  0.020  1.395
 FIG  C2   C7   aromatic  1.397  0.020  1.397
 FIG  C11  O2   double    1.211  0.020  1.211
 FIG  C4   C3   aromatic  1.386  0.020  1.386
 FIG  C3   H3   single    0.930  0.020  1.080
 FIG  C12  O3   double    1.213  0.020  1.213
 FIG  C4   C5   aromatic  1.388  0.020  1.388
 FIG  C4   H4   single    0.930  0.020  1.080
 FIG  C5   C6   aromatic  1.391  0.020  1.391
 FIG  C5   H5   single    0.930  0.020  1.080
 FIG  C6   C7   aromatic  1.384  0.020  1.384
 FIG  C6   H6   single    0.930  0.020  1.080
 FIG  C7   H7   single    0.930  0.020  1.080
 FIG  C9   C10  double    1.371  0.020  1.371
 FIG  C9   H9   single    0.930  0.020  1.080
 FIG  C12  C10  single    1.447  0.020  1.447
 FIG  C10  C11  single    1.475  0.020  1.475

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
 FIG  HA   C    H    107.65  3.000
 FIG  HA   C    C1   110.88  3.000
 FIG  H    C    C1   110.84  3.000
 FIG  HA   C    S    110.19  3.000
 FIG  H    C    S    110.25  3.000
 FIG  C1   C    S    107.05  3.000
 FIG  C9   N    C8   116.36  3.000
 FIG  C8   S    C    100.01  3.000
 FIG  C2   C1   O    122.26  3.000
 FIG  C2   C1   C    117.76  3.000
 FIG  O    C1   C    119.98  3.000
 FIG  HN1  N1   C12  115.40  3.000
 FIG  HN1  N1   C8   119.82  3.000
 FIG  C12  N1   C8   124.78  3.000
 FIG  HO1  O1   C11  109.10  3.000
 FIG  C7   C2   C3   119.39  3.000
 FIG  C7   C2   C1   118.77  3.000
 FIG  C3   C2   C1   121.84  3.000
 FIG  H3   C3   C4   118.73  3.000
 FIG  H3   C3   C2   121.01  3.000
 FIG  C4   C3   C2   120.26  3.000
 FIG  H4   C4   C5   120.22  3.000
 FIG  H4   C4   C3   119.80  3.000
 FIG  C5   C4   C3   119.98  3.000
 FIG  H5   C5   C6   120.02  3.000
 FIG  H5   C5   C4   119.87  3.000
 FIG  C6   C5   C4   120.12  3.000
 FIG  H6   C6   C7   119.90  3.000
 FIG  H6   C6   C5   120.08  3.000
 FIG  C7   C6   C5   120.02  3.000
 FIG  H7   C7   C6   119.86  3.000
 FIG  H7   C7   C2   119.90  3.000
 FIG  C6   C7   C2   120.24  3.000
 FIG  N1   C8   S    115.30  3.000
 FIG  N1   C8   N    122.76  3.000
 FIG  S    C8   N    121.94  3.000
 FIG  H9   C9   C10  119.32  3.000
 FIG  H9   C9   N    115.03  3.000
 FIG  C10  C9   N    125.65  3.000
 FIG  C12  C10  C11  123.97  3.000
 FIG  C11  C10  C9   117.64  3.000
 FIG  C12  C10  C9   118.39  3.000
 FIG  C10  C11  O2   122.93  3.000
 FIG  C10  C11  O1   114.14  3.000
 FIG  O2   C11  O1   122.93  3.000
 FIG  C10  C12  O3   129.06  3.000
 FIG  C10  C12  N1   112.06  3.000
 FIG  O3   C12  N1   118.88  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
 FIG  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 FIG  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 FIG  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 FIG  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 FIG  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 FIG  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 FIG  CONST_07  C12  N1   C8   N       0.00   0.0  0
 FIG  CONST_08  C9   N    C8   N1      0.00   0.0  0
 FIG  CONST_09  C10  C12  N1   C8      0.00   0.0  0
 FIG  CONST_10  C4   C3   C2   C1    180.00   0.0  0
 FIG  CONST_11  C6   C7   C2   C1    180.00   0.0  0
 FIG  CONST_12  C9   N    C8   S     180.00   0.0  0
 FIG  CONST_13  C12  N1   C8   S     180.00   0.0  0
 FIG  CONST_14  C8   N1   C12  O3    180.00   0.0  0
 FIG  CONST_15  H4   C4   C3   C2    180.00   0.0  0
 FIG  CONST_16  H6   C6   C7   C2    180.00   0.0  0
 FIG  CONST_17  H7   C7   C2   C3    180.00   0.0  0
 FIG  CONST_18  H5   C5   C4   C3    180.00   0.0  0
 FIG  CONST_19  H3   C3   C4   C5    180.00   0.0  0
 FIG  CONST_20  HN1  N1   C8   N     180.00   0.0  0
 FIG  CONST_21  HO1  O1   C11  C10   180.00   0.0  0
 FIG  Var_01    C3   C2   C1   C       0.05  30.0  2
 FIG  Var_02    N    C8   S    C       0.39  30.0  3
 FIG  Var_03    C9   C10  C11  O1   -176.79  30.0  2
 FIG  Var_04    C2   C1   C    S    -179.60  30.0  2

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
 FIG  plan-1  C1   0.020
 FIG  plan-1  C2   0.020
 FIG  plan-1  C3   0.020
 FIG  plan-1  C4   0.020
 FIG  plan-1  C5   0.020
 FIG  plan-1  C6   0.020
 FIG  plan-1  C7   0.020
 FIG  plan-1  H3   0.020
 FIG  plan-1  H4   0.020
 FIG  plan-1  H5   0.020
 FIG  plan-1  H6   0.020
 FIG  plan-1  H7   0.020
 FIG  plan-2  N    0.020
 FIG  plan-2  S    0.020
 FIG  plan-2  N1   0.020
 FIG  plan-2  O3   0.020
 FIG  plan-2  C8   0.020
 FIG  plan-2  C9   0.020
 FIG  plan-2  C10  0.020
 FIG  plan-2  C11  0.020
 FIG  plan-2  C12  0.020
 FIG  plan-2  HN1  0.020
 FIG  plan-2  H9   0.020
 FIG  plan-3  C    0.020
 FIG  plan-3  O    0.020
 FIG  plan-3  C1   0.020
 FIG  plan-3  C2   0.020
 FIG  plan-4  O1   0.020
 FIG  plan-4  O2   0.020
 FIG  plan-4  C10  0.020
 FIG  plan-4  C11  0.020
 FIG  plan-4  HO1  0.020

