# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:32:16 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 5-(propan-2-yl)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C1C(=O)NC(=S)NC1=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
 56L  56L  5-(propan-2-yl)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione  ligand  22  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_56L
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
 56L  C10  C  CH3   0  -0.650  -3.3852  -0.5529  -0.1206
 56L  C9   C  CH1   0  -0.246  -2.1944   0.3501  -0.4159
 56L  C5   C  C     0   0.375   1.6185  -0.0872  -0.1233
 56L  C3   C  C     0   0.590  -0.4483  -1.0640   0.7511
 56L  C2   C  CH1   0  -0.550  -1.1123   0.2836   0.7090
 56L  C1   C  C     0   0.592  -0.1688   1.4451   0.5395
 56L  C11  C  CH3   0  -0.682  -1.6205   0.0717  -1.8002
 56L  O12  O  O     0  -0.400  -0.9842  -2.0567   1.1783
 56L  N4   N  NH1   0  -0.652   0.8249  -1.1330   0.2225
 56L  N6   N  NH1   0  -0.655   1.0929   1.1505   0.0713
 56L  O8   O  O     0  -0.405  -0.4946   2.5877   0.7492
 56L  H1   H  HCH3  0   0.236  -3.7803  -0.3833   0.8815
 56L  H2   H  HCH3  0   0.240  -4.1814  -0.3376  -0.8340
 56L  H3   H  HCH3  0   0.232  -3.1387  -1.6099  -0.2156
 56L  H4   H  HCH1  0   0.270  -2.5546   1.3816  -0.3903
 56L  H5   H  HCH1  0   0.347  -1.6252   0.4250   1.6640
 56L  H6   H  HCH3  0   0.256  -2.3951   0.2173  -2.5534
 56L  H7   H  HCH3  0   0.239  -0.7963   0.7374  -2.0616
 56L  H8   H  HCH3  0   0.234  -1.2714  -0.9583  -1.8971
 56L  H9   H  HNH1  0   0.437   1.2437  -2.0523   0.1483
 56L  H10  H  HNH1  0   0.438   1.7066   1.9317  -0.1278
 56L  S7   S  S1    0  -0.247   3.1389  -0.3036  -0.7161

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
 56L  C10  C9   single  1.523  0.020  1.523
 56L  C11  C9   single  1.524  0.020  1.524
 56L  C9   C2   single  1.562  0.020  1.562
 56L  O12  C3   double  1.206  0.020  1.206
 56L  C3   C2   single  1.503  0.020  1.503
 56L  C3   N4   single  1.380  0.020  1.380
 56L  C2   C1   single  1.506  0.020  1.506
 56L  N4   C5   single  1.358  0.020  1.358
 56L  C1   O8   double  1.206  0.020  1.206
 56L  C1   N6   single  1.378  0.020  1.378
 56L  C5   N6   single  1.359  0.020  1.359
 56L  C5   S7   double  1.646  0.020  1.646
 56L  C10  H1   single  0.970  0.020  1.090
 56L  C10  H2   single  0.970  0.020  1.090
 56L  C10  H3   single  0.970  0.020  1.090
 56L  C9   H4   single  0.970  0.020  1.090
 56L  C2   H5   single  0.970  0.020  1.090
 56L  C11  H6   single  0.970  0.020  1.090
 56L  C11  H7   single  0.970  0.020  1.090
 56L  C11  H8   single  0.970  0.020  1.090
 56L  N4   H9   single  0.860  0.020  1.020
 56L  N6   H10  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
 56L  H3   C10  H2   107.44  3.000
 56L  H3   C10  H1   108.24  3.000
 56L  H2   C10  H1   107.81  3.000
 56L  H3   C10  C9   112.42  3.000
 56L  H2   C10  C9   109.07  3.000
 56L  H1   C10  C9   111.67  3.000
 56L  H4   C9   C11  108.53  3.000
 56L  H4   C9   C2   104.57  3.000
 56L  C11  C9   C2   112.66  3.000
 56L  H4   C9   C10  107.30  3.000
 56L  C2   C9   C10  112.12  3.000
 56L  C11  C9   C10  111.23  3.000
 56L  N6   C5   S7   121.91  3.000
 56L  S7   C5   N4   122.03  3.000
 56L  N6   C5   N4   116.04  3.000
 56L  N4   C3   O12  120.28  3.000
 56L  N4   C3   C2   116.21  3.000
 56L  O12  C3   C2   123.47  3.000
 56L  H5   C2   C1   107.01  3.000
 56L  H5   C2   C3   107.38  3.000
 56L  C1   C2   C3   114.70  3.000
 56L  H5   C2   C9   107.37  3.000
 56L  C1   C2   C9   108.67  3.000
 56L  C3   C2   C9   111.37  3.000
 56L  O8   C1   N6   120.60  3.000
 56L  N6   C1   C2   116.56  3.000
 56L  O8   C1   C2   122.79  3.000
 56L  H8   C11  H7   108.23  3.000
 56L  H8   C11  H6   106.97  3.000
 56L  H7   C11  H6   106.84  3.000
 56L  H8   C11  C9   111.91  3.000
 56L  H7   C11  C9   112.99  3.000
 56L  H6   C11  C9   109.60  3.000
 56L  H9   N4   C3   117.05  3.000
 56L  H9   N4   C5   116.03  3.000
 56L  C3   N4   C5   126.75  3.000
 56L  H10  N6   C1   117.17  3.000
 56L  H10  N6   C5   116.10  3.000
 56L  C1   N6   C5   126.71  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
 56L  CONST_01  C2   C3   N4  C5     0.00   0.0  0
 56L  CONST_02  C2   C1   N6  C5     0.00   0.0  0
 56L  CONST_03  N6   C5   N4  C3     0.00   0.0  0
 56L  CONST_04  N4   C5   N6  C1     0.00   0.0  0
 56L  CONST_05  O12  C3   N4  C5   180.00   0.0  0
 56L  CONST_06  O8   C1   N6  C5   180.00   0.0  0
 56L  CONST_07  S7   C5   N4  C3   180.00   0.0  0
 56L  CONST_08  S7   C5   N6  C1   180.00   0.0  0
 56L  CONST_09  H9   N4   C3  C2   180.00   0.0  0
 56L  CONST_10  H10  N6   C1  C2   180.00   0.0  0
 56L  Var_01    H1   C10  C9  C2    50.89  30.0  3
 56L  Var_02    H6   C11  C9  C2  -175.01  30.0  3

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
 56L  chir_01  C2  C9  C3  C1  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
 56L  plan-1  C5   0.020
 56L  plan-1  C3   0.020
 56L  plan-1  C2   0.020
 56L  plan-1  C1   0.020
 56L  plan-1  O12  0.020
 56L  plan-1  N4   0.020
 56L  plan-1  N6   0.020
 56L  plan-1  O8   0.020
 56L  plan-1  H9   0.020
 56L  plan-1  H10  0.020
 56L  plan-1  S7   0.020

