# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 21:26:49 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)CC(=O)N(CC)C1=S
#
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
 1U6  1U6  1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione  ligand  25  13  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1U6
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
 1U6  C01  C  CH3   0  -0.659   3.1428  -1.0479   0.8074
 1U6  C02  C  CH2   0  -0.319   2.4113  -0.6989  -0.4743
 1U6  N03  N  NT    0  -0.538   1.1584   0.0371  -0.2310
 1U6  C04  C  C     0   0.603   1.2667   1.4153  -0.1705
 1U6  O05  O  O     0  -0.427   2.3365   1.9684  -0.2617
 1U6  C06  C  CH2   0  -0.705   0.0074   2.1942  -0.0175
 1U6  C07  C  C     0   0.602  -1.2610   1.4304   0.1365
 1U6  O08  O  O     0  -0.426  -2.3257   1.9954   0.2113
 1U6  N09  N  NT    0  -0.538  -1.1670   0.0522   0.2201
 1U6  C10  C  CH2   0  -0.320  -2.4282  -0.6672   0.4688
 1U6  C11  C  CH3   0  -0.658  -3.1523  -1.0362  -0.8117
 1U6  C12  C  C     0   0.438  -0.0073  -0.6582   0.0028
 1U6  S13  S  S1    0  -0.253  -0.0148  -2.3137   0.0209
 1U6  H1   H  HCH3  0   0.236   3.4473  -0.1540   1.3505
 1U6  H2   H  HCH3  0   0.234   2.5273  -1.6625   1.4627
 1U6  H3   H  HCH3  0   0.242   4.0426  -1.6129   0.5640
 1U6  H4   H  HCH2  0   0.273   3.0311  -0.0751  -1.1120
 1U6  H5   H  HCH2  0   0.270   2.1622  -1.5933  -1.0360
 1U6  H6   H  HCH2  0   0.345   0.1098   2.8538   0.8487
 1U6  H7   H  HCH2  0   0.345  -0.0875   2.8553  -0.8832
 1U6  H8   H  HCH2  0   0.270  -2.1923  -1.5517   1.0517
 1U6  H9   H  HCH2  0   0.273  -3.0474  -0.0244   1.0879
 1U6  H10  H  HCH3  0   0.235  -3.4439  -0.1508  -1.3756
 1U6  H11  H  HCH3  0   0.234  -2.5365  -1.6696  -1.4486
 1U6  H12  H  HCH3  0   0.242  -4.0592  -1.5880  -0.5648

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
 1U6  C11  C10  single  1.517  0.020  1.517
 1U6  C10  N09  single  1.473  0.020  1.473
 1U6  O08  C07  double  1.208  0.020  1.208
 1U6  N09  C07  single  1.384  0.020  1.384
 1U6  N09  C12  single  1.377  0.020  1.377
 1U6  C07  C06  single  1.489  0.020  1.489
 1U6  S13  C12  double  1.656  0.020  1.656
 1U6  C12  N03  single  1.377  0.020  1.377
 1U6  C06  C04  single  1.489  0.020  1.489
 1U6  N03  C04  single  1.384  0.020  1.384
 1U6  N03  C02  single  1.473  0.020  1.473
 1U6  C04  O05  double  1.208  0.020  1.208
 1U6  C01  C02  single  1.517  0.020  1.517
 1U6  C01  H1   single  0.970  0.020  1.090
 1U6  C01  H2   single  0.970  0.020  1.090
 1U6  C01  H3   single  0.970  0.020  1.090
 1U6  C02  H4   single  0.970  0.020  1.090
 1U6  C02  H5   single  0.970  0.020  1.090
 1U6  C06  H6   single  0.970  0.020  1.090
 1U6  C06  H7   single  0.970  0.020  1.090
 1U6  C10  H8   single  0.970  0.020  1.090
 1U6  C10  H9   single  0.970  0.020  1.090
 1U6  C11  H10  single  0.970  0.020  1.090
 1U6  C11  H11  single  0.970  0.020  1.090
 1U6  C11  H12  single  0.970  0.020  1.090

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
 1U6  H3   C01  H2   107.97  3.000
 1U6  H3   C01  H1   107.82  3.000
 1U6  H2   C01  H1   108.73  3.000
 1U6  H3   C01  C02  109.19  3.000
 1U6  H2   C01  C02  111.46  3.000
 1U6  H1   C01  C02  111.55  3.000
 1U6  H5   C02  H4   107.48  3.000
 1U6  H5   C02  N03  107.58  3.000
 1U6  H4   C02  N03  107.18  3.000
 1U6  H5   C02  C01  111.01  3.000
 1U6  H4   C02  C01  110.67  3.000
 1U6  N03  C02  C01  112.68  3.000
 1U6  C12  N03  C04  124.16  3.000
 1U6  C04  N03  C02  115.99  3.000
 1U6  C12  N03  C02  119.71  3.000
 1U6  C06  C04  O05  121.16  3.000
 1U6  O05  C04  N03  121.47  3.000
 1U6  C06  C04  N03  117.35  3.000
 1U6  H7   C06  H6   105.70  3.000
 1U6  H7   C06  C07  108.55  3.000
 1U6  H6   C06  C07  107.90  3.000
 1U6  H7   C06  C04  107.96  3.000
 1U6  H6   C06  C04  108.53  3.000
 1U6  C07  C06  C04  117.58  3.000
 1U6  N09  C07  O08  121.48  3.000
 1U6  N09  C07  C06  117.34  3.000
 1U6  O08  C07  C06  121.17  3.000
 1U6  C12  N09  C10  119.71  3.000
 1U6  C12  N09  C07  124.15  3.000
 1U6  C10  N09  C07  116.00  3.000
 1U6  H9   C10  H8   107.46  3.000
 1U6  H9   C10  C11  110.67  3.000
 1U6  H8   C10  C11  111.04  3.000
 1U6  H9   C10  N09  107.17  3.000
 1U6  H8   C10  N09  107.61  3.000
 1U6  C11  C10  N09  112.65  3.000
 1U6  H12  C11  H11  107.97  3.000
 1U6  H12  C11  H10  107.82  3.000
 1U6  H11  C11  H10  108.74  3.000
 1U6  H12  C11  C10  109.22  3.000
 1U6  H11  C11  C10  111.43  3.000
 1U6  H10  C11  C10  111.54  3.000
 1U6  S13  C12  N09  120.68  3.000
 1U6  S13  C12  N03  120.69  3.000
 1U6  N09  C12  N03  118.63  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
 1U6  CONST_01  C07  N09  C12  N03    0.00   0.0  0
 1U6  CONST_02  N09  C12  N03  C04    0.00   0.0  0
 1U6  CONST_03  C12  N09  C07  C06    0.00   0.0  0
 1U6  CONST_04  C12  N03  C04  C06    0.00   0.0  0
 1U6  CONST_05  N09  C12  N03  C02  180.00   0.0  0
 1U6  CONST_06  C06  C04  N03  C02  180.00   0.0  0
 1U6  CONST_07  C10  N09  C12  N03  180.00   0.0  0
 1U6  CONST_08  S13  C12  N03  C04  180.00   0.0  0
 1U6  CONST_09  C12  N03  C04  O05  180.00   0.0  0
 1U6  CONST_10  C10  N09  C07  C06  180.00   0.0  0
 1U6  CONST_11  S13  C12  N09  C07  180.00   0.0  0
 1U6  CONST_12  C12  N09  C07  O08  180.00   0.0  0
 1U6  CONST_13  S13  C12  N03  C02    0.00   0.0  0
 1U6  CONST_14  O05  C04  N03  C02    0.00   0.0  0
 1U6  CONST_15  C10  N09  C07  O08    0.00   0.0  0
 1U6  CONST_16  S13  C12  N09  C10    0.00   0.0  0
 1U6  Var_01    H6   C06  C04  N03  126.14  30.0  1
 1U6  Var_02    C12  N03  C02  C01  -86.96  30.0  2
 1U6  Var_03    C11  C10  N09  C07   89.31  30.0  2
 1U6  Var_04    H1   C01  C02  N03  -62.51  30.0  3
 1U6  Var_05    H10  C11  C10  N09  -62.49  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
 1U6  plan-1  C02  0.020
 1U6  plan-1  N03  0.020
 1U6  plan-1  C04  0.020
 1U6  plan-1  O05  0.020
 1U6  plan-1  C06  0.020
 1U6  plan-1  C07  0.020
 1U6  plan-1  O08  0.020
 1U6  plan-1  N09  0.020
 1U6  plan-1  C10  0.020
 1U6  plan-1  C12  0.020
 1U6  plan-1  S13  0.020

