# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 01:36:56 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: [(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSC1=NC(=CC(=O)N1)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
 7IA  7IA  '[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetic acid'  ligand  27  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7IA
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
 7IA  C    C  CH2    0  -0.687  -2.5012   0.9385  -0.1227
 7IA  N    N  NR16   0  -0.688  -0.4245  -2.4991   0.0589
 7IA  O    O  O      0  -0.592  -4.8212   0.4570  -0.1889
 7IA  S    S  S2     0   0.062  -2.4721  -0.8695  -0.0616
 7IA  C1   C  C      0   0.448  -3.9781   1.3721  -0.1914
 7IA  N1   N  N      0  -0.468   0.1240  -0.2419  -0.0240
 7IA  O1   O  OC    -1  -0.599  -4.1688   2.5968  -0.2417
 7IA  C2   C  CR6    0   0.355  -0.7573  -1.1885  -0.0041
 7IA  C3   C  CR6    0   0.558   0.8876  -2.9527   0.1269
 7IA  C4   C  CR16   0  -0.509   1.8492  -1.8901   0.1171
 7IA  C5   C  CR6    0   0.299   1.4397  -0.5910   0.0295
 7IA  C6   C  CR6    0   0.058   2.3913   0.5397   0.0026
 7IA  C7   C  CR16   0  -0.282   1.9415   1.8326   0.2764
 7IA  C8   C  CR16   0  -0.239   2.8233   2.9029   0.2722
 7IA  C9   C  CR16   0  -0.257   4.1659   2.7016  -0.0177
 7IA  C10  C  CR16   0  -0.237   4.6213   1.4208  -0.3045
 7IA  C11  C  CR16   0  -0.318   3.7423   0.3497  -0.2949
 7IA  H    H  HCH2   0   0.288  -2.0135   1.3460   0.7634
 7IA  HA   H  HCH2   0   0.288  -1.9467   1.2891  -0.9936
 7IA  HN   H  HNR6   0   0.427  -1.1526  -3.2037   0.0672
 7IA  H4   H  HCR6   0   0.273   2.8915  -2.1621   0.1946
 7IA  H7   H  HCR6   0   0.265   0.8962   1.9977   0.4976
 7IA  H8   H  HCR6   0   0.260   2.4588   3.8971   0.4943
 7IA  H9   H  HCR6   0   0.262   4.8536   3.5370  -0.0259
 7IA  H10  H  HCR6   0   0.262   5.6638   1.2548  -0.5422
 7IA  H11  H  HCR6   0   0.257   4.1178  -0.6347  -0.5410
 7IA  O2   O  O      0  -0.486   1.1249  -4.1498   0.1905

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
 7IA  C1   C    single    1.541  0.020  1.541
 7IA  S    C    single    1.809  0.020  1.809
 7IA  C    H    single    0.970  0.020  1.090
 7IA  C    HA   single    0.970  0.020  1.090
 7IA  C3   N    single    1.390  0.020  1.390
 7IA  N    C2   single    1.354  0.020  1.354
 7IA  N    HN   single    0.860  0.020  1.020
 7IA  O    C1   deloc     1.244  0.020  1.244
 7IA  C2   S    single    1.745  0.020  1.745
 7IA  O1   C1   deloc     1.240  0.020  1.240
 7IA  C5   N1   single    1.362  0.020  1.362
 7IA  N1   C2   double    1.294  0.020  1.294
 7IA  O2   C3   double    1.222  0.020  1.222
 7IA  C4   C3   single    1.433  0.020  1.433
 7IA  C4   C5   double    1.365  0.020  1.365
 7IA  C4   H4   single    0.930  0.020  1.080
 7IA  C6   C5   single    1.478  0.020  1.478
 7IA  C11  C6   aromatic  1.396  0.020  1.396
 7IA  C6   C7   aromatic  1.396  0.020  1.396
 7IA  C8   C7   aromatic  1.387  0.020  1.387
 7IA  C7   H7   single    0.930  0.020  1.080
 7IA  C9   C8   aromatic  1.388  0.020  1.388
 7IA  C8   H8   single    0.930  0.020  1.080
 7IA  C10  C9   aromatic  1.389  0.020  1.389
 7IA  C9   H9   single    0.930  0.020  1.080
 7IA  C10  C11  aromatic  1.386  0.020  1.386
 7IA  C10  H10  single    0.930  0.020  1.080
 7IA  C11  H11  single    0.930  0.020  1.080

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
 7IA  HA   C    H    107.54  3.000
 7IA  HA   C    C1   111.18  3.000
 7IA  H    C    C1   111.08  3.000
 7IA  HA   C    S    109.89  3.000
 7IA  H    C    S    109.81  3.000
 7IA  C1   C    S    107.35  3.000
 7IA  HN   N    C3   116.81  3.000
 7IA  HN   N    C2   119.80  3.000
 7IA  C3   N    C2   123.39  3.000
 7IA  C2   S    C    101.51  3.000
 7IA  O1   C1   O    128.46  3.000
 7IA  O1   C1   C    115.28  3.000
 7IA  O    C1   C    116.26  3.000
 7IA  C5   N1   C2   118.02  3.000
 7IA  N1   C2   S    122.35  3.000
 7IA  N1   C2   N    122.81  3.000
 7IA  S    C2   N    114.84  3.000
 7IA  C4   C3   O2   126.61  3.000
 7IA  C4   C3   N    113.03  3.000
 7IA  O2   C3   N    120.36  3.000
 7IA  H4   C4   C5   122.27  3.000
 7IA  H4   C4   C3   117.41  3.000
 7IA  C5   C4   C3   120.32  3.000
 7IA  C6   C5   C4   122.42  3.000
 7IA  C6   C5   N1   115.15  3.000
 7IA  C4   C5   N1   122.42  3.000
 7IA  C11  C6   C7   118.65  3.000
 7IA  C7   C6   C5   119.84  3.000
 7IA  C11  C6   C5   121.51  3.000
 7IA  H7   C7   C8   119.84  3.000
 7IA  H7   C7   C6   119.54  3.000
 7IA  C8   C7   C6   120.62  3.000
 7IA  H8   C8   C9   120.13  3.000
 7IA  H8   C8   C7   119.63  3.000
 7IA  C9   C8   C7   120.25  3.000
 7IA  H9   C9   C10  120.12  3.000
 7IA  H9   C9   C8   120.29  3.000
 7IA  C10  C9   C8   119.59  3.000
 7IA  H10  C10  C11  119.61  3.000
 7IA  H10  C10  C9   120.17  3.000
 7IA  C11  C10  C9   120.22  3.000
 7IA  H11  C11  C10  118.79  3.000
 7IA  H11  C11  C6   120.53  3.000
 7IA  C10  C11  C6   120.67  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
 7IA  CONST_01  C9   C10  C11  C6     0.00   0.0  0
 7IA  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 7IA  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 7IA  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 7IA  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 7IA  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 7IA  CONST_07  C10  C11  C6   C5   180.00   0.0  0
 7IA  CONST_08  C8   C7   C6   C5   180.00   0.0  0
 7IA  CONST_09  C5   N1   C2   N      0.00   0.0  0
 7IA  CONST_10  C3   N    C2   N1     0.00   0.0  0
 7IA  CONST_11  C4   C3   N    C2     0.00   0.0  0
 7IA  CONST_12  C3   N    C2   S    180.00   0.0  0
 7IA  CONST_13  C5   N1   C2   S    180.00   0.0  0
 7IA  CONST_14  O2   C3   N    C2   180.00   0.0  0
 7IA  CONST_15  H11  C11  C6   C5     0.00   0.0  0
 7IA  CONST_16  H7   C7   C6   C5     0.00   0.0  0
 7IA  CONST_17  H10  C10  C11  C6   180.00   0.0  0
 7IA  CONST_18  H8   C8   C7   C6   180.00   0.0  0
 7IA  CONST_19  H9   C9   C8   C7   180.00   0.0  0
 7IA  CONST_20  HN   N    C2   N1   180.00   0.0  0
 7IA  Var_01    C11  C6   C5   N1  -163.21  30.0  2
 7IA  Var_02    N    C2   S    C    179.52  30.0  3
 7IA  Var_03    H    C    S    C2   -59.67  30.0  3
 7IA  Var_04    S    C    C1   O      0.16  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
 7IA  plan-1  N    0.020
 7IA  plan-1  S    0.020
 7IA  plan-1  N1   0.020
 7IA  plan-1  C2   0.020
 7IA  plan-1  C3   0.020
 7IA  plan-1  C4   0.020
 7IA  plan-1  C5   0.020
 7IA  plan-1  C6   0.020
 7IA  plan-1  HN   0.020
 7IA  plan-1  H4   0.020
 7IA  plan-1  O2   0.020
 7IA  plan-2  C5   0.020
 7IA  plan-2  C6   0.020
 7IA  plan-2  C7   0.020
 7IA  plan-2  C8   0.020
 7IA  plan-2  C9   0.020
 7IA  plan-2  C10  0.020
 7IA  plan-2  C11  0.020
 7IA  plan-2  H7   0.020
 7IA  plan-2  H8   0.020
 7IA  plan-2  H9   0.020
 7IA  plan-2  H10  0.020
 7IA  plan-2  H11  0.020
 7IA  plan-3  C    0.020
 7IA  plan-3  O    0.020
 7IA  plan-3  C1   0.020
 7IA  plan-3  O1   0.020

