# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 10:34:58 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC1=CC(=O)NC(=S)N1
#
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
 3CJ  3CJ  6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one  ligand  21  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3CJ
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
 3CJ  C7   C  CH3   0  -0.666   4.4705  -0.8001   0.3202
 3CJ  C6   C  CH2   0  -0.429   3.0054  -0.4989   0.5949
 3CJ  C5   C  CH2   0  -0.519   2.2940   0.0240  -0.6590
 3CJ  C2   C  CR6   0   0.448   0.8593   0.3433  -0.4038
 3CJ  C3   C  CR16  0  -0.528   0.3617   1.5956  -0.3338
 3CJ  N1   N  NR16  0  -0.653   0.0302  -0.7264  -0.1933
 3CJ  C1   C  CR6   0   0.361  -1.2860  -0.6272   0.0970
 3CJ  S1   S  S1    0  -0.336  -2.2441  -1.9614   0.3481
 3CJ  N2   N  NR16  0  -0.666  -1.7558   0.6377   0.1635
 3CJ  C4   C  CR6   0   0.578  -1.0306   1.8129  -0.0385
 3CJ  O1   O  O     0  -0.458  -1.5862   2.8911   0.0461
 3CJ  H1   H  HCH3  0   0.238   4.9717  -1.1527   1.2216
 3CJ  H2   H  HCH3  0   0.226   4.5812  -1.5709  -0.4441
 3CJ  H3   H  HCH3  0   0.226   4.9991   0.0898  -0.0250
 3CJ  H4   H  HCH2  0   0.232   2.5084  -1.4017   0.9586
 3CJ  H5   H  HCH2  0   0.240   2.9202   0.2457   1.3895
 3CJ  H6   H  HCH2  0   0.274   2.7925   0.9255  -1.0157
 3CJ  H7   H  HCH2  0   0.273   2.3621  -0.7188  -1.4596
 3CJ  H8   H  HCR6  0   0.292   0.9997   2.4511  -0.4969
 3CJ  H10  H  HNR6  0   0.432  -2.7414   0.7388   0.3719
 3CJ  H9   H  HNR6  0   0.437   0.4012  -1.6637  -0.2684

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
 3CJ  S1  C1   double  1.662  0.020  1.662
 3CJ  C1  N1   single  1.352  0.020  1.352
 3CJ  C1  N2   single  1.351  0.020  1.351
 3CJ  N1  C2   single  1.370  0.020  1.370
 3CJ  N2  C4   single  1.396  0.020  1.396
 3CJ  C2  C5   single  1.492  0.020  1.492
 3CJ  C2  C3   double  1.349  0.020  1.349
 3CJ  C5  C6   single  1.534  0.020  1.534
 3CJ  C4  C3   single  1.440  0.020  1.440
 3CJ  C4  O1   double  1.216  0.020  1.216
 3CJ  C7  C6   single  1.521  0.020  1.521
 3CJ  C7  H1   single  0.970  0.020  1.090
 3CJ  C7  H2   single  0.970  0.020  1.090
 3CJ  C7  H3   single  0.970  0.020  1.090
 3CJ  C6  H4   single  0.970  0.020  1.090
 3CJ  C6  H5   single  0.970  0.020  1.090
 3CJ  C5  H6   single  0.970  0.020  1.090
 3CJ  C5  H7   single  0.970  0.020  1.090
 3CJ  C3  H8   single  0.930  0.020  1.080
 3CJ  N2  H10  single  0.860  0.020  1.020
 3CJ  N1  H9   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
 3CJ  H3   C7  H2  107.78  3.000
 3CJ  H3   C7  H1  107.62  3.000
 3CJ  H2   C7  H1  107.71  3.000
 3CJ  H3   C7  C6  111.24  3.000
 3CJ  H2   C7  C6  111.36  3.000
 3CJ  H1   C7  C6  110.96  3.000
 3CJ  H5   C6  H4  106.60  3.000
 3CJ  H5   C6  C5  109.04  3.000
 3CJ  H4   C6  C5  110.05  3.000
 3CJ  H5   C6  C7  109.97  3.000
 3CJ  H4   C6  C7  109.55  3.000
 3CJ  C5   C6  C7  111.51  3.000
 3CJ  H7   C5  H6  107.07  3.000
 3CJ  H7   C5  C2  109.29  3.000
 3CJ  H6   C5  C2  108.58  3.000
 3CJ  H7   C5  C6  109.75  3.000
 3CJ  H6   C5  C6  109.72  3.000
 3CJ  C2   C5  C6  112.28  3.000
 3CJ  N1   C2  C3  119.58  3.000
 3CJ  C3   C2  C5  124.20  3.000
 3CJ  N1   C2  C5  116.19  3.000
 3CJ  H8   C3  C4  118.88  3.000
 3CJ  H8   C3  C2  120.64  3.000
 3CJ  C4   C3  C2  120.48  3.000
 3CJ  H9   N1  C1  116.19  3.000
 3CJ  H9   N1  C2  119.38  3.000
 3CJ  C1   N1  C2  124.42  3.000
 3CJ  N2   C1  S1  122.95  3.000
 3CJ  N2   C1  N1  114.70  3.000
 3CJ  S1   C1  N1  122.35  3.000
 3CJ  H10  N2  C4  116.84  3.000
 3CJ  H10  N2  C1  116.24  3.000
 3CJ  C4   N2  C1  126.92  3.000
 3CJ  O1   C4  N2  119.95  3.000
 3CJ  O1   C4  C3  126.16  3.000
 3CJ  N2   C4  C3  113.90  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
 3CJ  CONST_01  N2   C1  N1  C2     0.00   0.0  0
 3CJ  CONST_02  C1   N2  C4  C3     0.00   0.0  0
 3CJ  CONST_03  C4   N2  C1  N1     0.00   0.0  0
 3CJ  CONST_04  S1   C1  N1  C2   180.00   0.0  0
 3CJ  CONST_05  O1   C4  N2  C1   180.00   0.0  0
 3CJ  CONST_06  C4   N2  C1  S1   180.00   0.0  0
 3CJ  CONST_07  H10  N2  C4  C3   180.00   0.0  0
 3CJ  CONST_08  H9   N1  C1  N2   180.00   0.0  0
 3CJ  Var_01    N1   C2  C5  C6   -70.40  30.0  2
 3CJ  Var_02    C2   C5  C6  C7  -179.20  30.0  1
 3CJ  Var_03    H1   C7  C6  C5   178.91  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
 3CJ  plan-1  C5   0.020
 3CJ  plan-1  C2   0.020
 3CJ  plan-1  C3   0.020
 3CJ  plan-1  N1   0.020
 3CJ  plan-1  C1   0.020
 3CJ  plan-1  S1   0.020
 3CJ  plan-1  N2   0.020
 3CJ  plan-1  C4   0.020
 3CJ  plan-1  O1   0.020
 3CJ  plan-1  H8   0.020
 3CJ  plan-1  H10  0.020
 3CJ  plan-1  H9   0.020

