# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 11:28:34 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 7-[[ethyl(phenyl)amino]methyl]-2-methyl-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC1=CC(=O)N2N=C(C)SC2=N1)c3ccccc3
#
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
 5YC  5YC  7-[[ethyl(phenyl)amino]methyl]-2-methyl-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one  ligand  37  21  .  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_5YC
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
 5YC  C4   C  CR16  0  -0.492   1.0245   2.1714   1.0378
 5YC  C14  C  CR16  0  -0.355  -4.0029  -0.1898  -0.8330
 5YC  C5   C  CR6   0   0.583   2.3992   1.9360   0.7124
 5YC  C6   C  CR56  0   0.348   1.5793  -0.2817   0.1656
 5YC  C11  C  CR16  0  -0.249  -3.5514  -2.2076   0.9959
 5YC  C7   C  CR5   0   0.118   3.7953  -1.0306  -0.4895
 5YC  C8   C  CH3   0  -0.724   4.9816  -1.7870  -0.9514
 5YC  C9   C  CR6   0   0.399  -2.9928  -0.0048   0.1294
 5YC  C10  C  CR16  0  -0.331  -2.7773  -1.0596   1.0349
 5YC  C12  C  CR16  0  -0.300  -4.5547  -2.3717   0.0498
 5YC  C13  C  CR16  0  -0.245  -4.7620  -1.3490  -0.8648
 5YC  N1   N  N     0  -0.417   2.5997   0.6147   0.2573
 5YC  N2   N  N     0  -0.450   0.3493  -0.0543   0.4679
 5YC  C3   C  CR6   0   0.293   0.0759   1.1997   0.9118
 5YC  N3   N  N     0  -0.176   3.8293   0.1901  -0.1106
 5YC  O    O  O     0  -0.454   3.3293   2.7127   0.7815
 5YC  S    S  S2    0   0.234   2.2171  -1.7789  -0.4272
 5YC  C2   C  CH2   0  -0.420  -1.3658   1.4719   1.2545
 5YC  N    N  NT    0  -0.504  -2.2765   1.1707   0.1822
 5YC  C1   C  CH2   0  -0.329  -2.2779   2.1017  -0.9322
 5YC  C    C  CH3   0  -0.660  -1.5369   1.6067  -2.1682
 5YC  H1   H  HCR6  0   0.284   0.7571   3.1608   1.3828
 5YC  H3   H  HCR6  0   0.247  -3.3495  -2.9936   1.7132
 5YC  H4   H  HCH3  0   0.282   5.1638  -2.6461  -0.3061
 5YC  H5   H  HCH3  0   0.281   4.8301  -2.1584  -1.9646
 5YC  H6   H  HCH3  0   0.283   5.8575  -1.1432  -0.9376
 5YC  H7   H  HCR6  0   0.250  -1.9791  -1.0075   1.7602
 5YC  H8   H  HCR6  0   0.243  -5.1495  -3.2747   0.0201
 5YC  H9   H  HCR6  0   0.248  -5.5310  -1.4442  -1.6214
 5YC  H11  H  HCH2  0   0.284  -1.6338   0.9091   2.1502
 5YC  H12  H  HCH2  0   0.282  -1.4724   2.5245   1.5269
 5YC  H13  H  HCH2  0   0.244  -3.3032   2.3736  -1.1966
 5YC  H14  H  HCH2  0   0.256  -1.8164   3.0250  -0.5807
 5YC  H15  H  HCH3  0   0.232  -1.5841   2.3587  -2.9562
 5YC  H16  H  HCH3  0   0.228  -0.4864   1.4130  -1.9519
 5YC  H17  H  HCH3  0   0.230  -1.9729   0.6875  -2.5593
 5YC  H2   H  HCR6  0   0.259  -4.2138   0.5765  -1.5654

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
 5YC  O    C5   double    1.214  0.020  1.214
 5YC  C8   C7   single    1.481  0.020  1.481
 5YC  N3   C7   double    1.279  0.020  1.279
 5YC  N3   N1   single    1.352  0.020  1.352
 5YC  C5   N1   single    1.412  0.020  1.412
 5YC  C5   C4   single    1.432  0.020  1.432
 5YC  C7   S    single    1.748  0.020  1.748
 5YC  N1   C6   single    1.361  0.020  1.361
 5YC  C    C1   single    1.524  0.020  1.524
 5YC  C4   C3   double    1.364  0.020  1.364
 5YC  C6   S    single    1.732  0.020  1.732
 5YC  C6   N2   double    1.287  0.020  1.287
 5YC  C3   N2   single    1.358  0.020  1.358
 5YC  C3   C2   single    1.507  0.020  1.507
 5YC  C1   N    single    1.452  0.020  1.452
 5YC  C2   N    single    1.439  0.020  1.439
 5YC  N    C9   single    1.378  0.020  1.378
 5YC  C9   C14  aromatic  1.407  0.020  1.407
 5YC  C9   C10  aromatic  1.407  0.020  1.407
 5YC  C14  C13  aromatic  1.386  0.020  1.386
 5YC  C10  C11  aromatic  1.385  0.020  1.385
 5YC  C13  C12  aromatic  1.388  0.020  1.388
 5YC  C11  C12  aromatic  1.389  0.020  1.389
 5YC  C4   H1   single    0.930  0.020  1.080
 5YC  C14  H2   single    0.930  0.020  1.080
 5YC  C11  H3   single    0.930  0.020  1.080
 5YC  C8   H4   single    0.970  0.020  1.090
 5YC  C8   H5   single    0.970  0.020  1.090
 5YC  C8   H6   single    0.970  0.020  1.090
 5YC  C10  H7   single    0.930  0.020  1.080
 5YC  C12  H8   single    0.930  0.020  1.080
 5YC  C13  H9   single    0.930  0.020  1.080
 5YC  C2   H11  single    0.970  0.020  1.090
 5YC  C2   H12  single    0.970  0.020  1.090
 5YC  C1   H13  single    0.970  0.020  1.090
 5YC  C1   H14  single    0.970  0.020  1.090
 5YC  C    H15  single    0.970  0.020  1.090
 5YC  C    H16  single    0.970  0.020  1.090
 5YC  C    H17  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
 5YC  H1   C4   C3   120.62  3.000
 5YC  H1   C4   C5   117.41  3.000
 5YC  C3   C4   C5   121.98  3.000
 5YC  H2   C14  C13  118.07  3.000
 5YC  H2   C14  C9   120.68  3.000
 5YC  C13  C14  C9   121.25  3.000
 5YC  O    C5   N1   120.55  3.000
 5YC  N1   C5   C4   111.31  3.000
 5YC  O    C5   C4   128.13  3.000
 5YC  S    C6   N2   125.82  3.000
 5YC  N2   C6   N1   125.75  3.000
 5YC  S    C6   N1   108.43  3.000
 5YC  H3   C11  C12  120.00  3.000
 5YC  H3   C11  C10  118.60  3.000
 5YC  C12  C11  C10  121.39  3.000
 5YC  S    C7   N3   114.97  3.000
 5YC  S    C7   C8   121.05  3.000
 5YC  N3   C7   C8   123.97  3.000
 5YC  H6   C8   H5   109.01  3.000
 5YC  H6   C8   H4   108.94  3.000
 5YC  H5   C8   H4   107.77  3.000
 5YC  H6   C8   C7   109.81  3.000
 5YC  H5   C8   C7   110.65  3.000
 5YC  H4   C8   C7   110.60  3.000
 5YC  N    C9   C10  122.37  3.000
 5YC  C10  C9   C14  116.84  3.000
 5YC  N    C9   C14  120.77  3.000
 5YC  H7   C10  C9   120.63  3.000
 5YC  H7   C10  C11  118.17  3.000
 5YC  C9   C10  C11  121.17  3.000
 5YC  H8   C12  C13  121.00  3.000
 5YC  H8   C12  C11  120.97  3.000
 5YC  C13  C12  C11  118.03  3.000
 5YC  H9   C13  C12  120.12  3.000
 5YC  H9   C13  C14  118.59  3.000
 5YC  C12  C13  C14  121.29  3.000
 5YC  N3   N1   C6   117.17  3.000
 5YC  C6   N1   C5   122.11  3.000
 5YC  N3   N1   C5   120.72  3.000
 5YC  C3   N2   C6   115.62  3.000
 5YC  C2   C3   N2   115.71  3.000
 5YC  C2   C3   C4   121.06  3.000
 5YC  N2   C3   C4   123.23  3.000
 5YC  N1   N3   C7   110.88  3.000
 5YC  C7   S    C6    88.55  3.000
 5YC  H12  C2   H11  105.57  3.000
 5YC  H12  C2   N    109.01  3.000
 5YC  H11  C2   N    110.39  3.000
 5YC  H12  C2   C3   108.91  3.000
 5YC  H11  C2   C3   109.18  3.000
 5YC  N    C2   C3   113.47  3.000
 5YC  C1   N    C2   116.00  3.000
 5YC  C2   N    C9   122.44  3.000
 5YC  C1   N    C9   121.14  3.000
 5YC  H14  C1   H13  105.33  3.000
 5YC  H14  C1   C    109.31  3.000
 5YC  H13  C1   C    109.92  3.000
 5YC  H14  C1   N    107.16  3.000
 5YC  H13  C1   N    110.25  3.000
 5YC  C    C1   N    114.44  3.000
 5YC  H17  C    H16  107.87  3.000
 5YC  H17  C    H15  107.76  3.000
 5YC  H16  C    H15  107.92  3.000
 5YC  H17  C    C1   111.75  3.000
 5YC  H16  C    C1   111.44  3.000
 5YC  H15  C    C1   109.95  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
 5YC  CONST_01  C11  C10  C9   C14    0.00   0.0  0
 5YC  CONST_02  C11  C12  C13  C14    0.00   0.0  0
 5YC  CONST_03  C12  C13  C14  C9     0.00   0.0  0
 5YC  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 5YC  CONST_05  C13  C14  C9   C10    0.00   0.0  0
 5YC  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 5YC  CONST_07  N3   N1   C5   C4   180.00   0.0  0
 5YC  CONST_08  C6   N1   C5   C4     0.00   0.0  0
 5YC  CONST_09  S    C6   N1   C5   180.00   0.0  0
 5YC  CONST_10  N2   C6   N1   C5     0.00   0.0  0
 5YC  CONST_11  C3   N2   C6   N1     0.00   0.0  0
 5YC  CONST_12  N3   N1   C6   N2   180.00   0.0  0
 5YC  CONST_13  S    C6   N2   C3   180.00   0.0  0
 5YC  CONST_14  S    C6   N1   N3     0.00   0.0  0
 5YC  CONST_15  N    C9   C10  C11  180.00   0.0  0
 5YC  CONST_16  N    C9   C14  C13  180.00   0.0  0
 5YC  CONST_17  O    C5   N1   C6   180.00   0.0  0
 5YC  CONST_18  O    C5   N1   N3     0.00   0.0  0
 5YC  CONST_19  H7   C10  C9   C14  180.00   0.0  0
 5YC  CONST_20  H8   C12  C13  C14  180.00   0.0  0
 5YC  CONST_21  H9   C13  C12  C11  180.00   0.0  0
 5YC  CONST_22  H3   C11  C10  C9   180.00   0.0  0
 5YC  CONST_23  H2   C14  C9   C10  180.00   0.0  0
 5YC  CONST_25  C2   N    C9   C14  180.00   0.0  0
 5YC  CONST_27  C2   N    C9   C10    0.00   0.0  0
 5YC  Var_01    N    C2   C3   C4   125.19  30.0  3
 5YC  Var_02    C3   C2   N    C9    99.00  30.0  3
 5YC  Var_03    H4   C8   C7   N3   118.97  30.0  3
 5YC  Var_04    C    C1   N    C9   -69.78  30.0  2
 5YC  Var_05    H15  C    C1   N    179.97  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
 5YC  plan-1  C14  0.020
 5YC  plan-1  C11  0.020
 5YC  plan-1  C9   0.020
 5YC  plan-1  C10  0.020
 5YC  plan-1  C12  0.020
 5YC  plan-1  C13  0.020
 5YC  plan-1  N    0.020
 5YC  plan-1  H3   0.020
 5YC  plan-1  H7   0.020
 5YC  plan-1  H8   0.020
 5YC  plan-1  H9   0.020
 5YC  plan-1  H2   0.020
 5YC  plan-2  C4   0.020
 5YC  plan-2  C5   0.020
 5YC  plan-2  C6   0.020
 5YC  plan-2  C7   0.020
 5YC  plan-2  C8   0.020
 5YC  plan-2  N1   0.020
 5YC  plan-2  N2   0.020
 5YC  plan-2  C3   0.020
 5YC  plan-2  N3   0.020
 5YC  plan-2  O    0.020
 5YC  plan-2  S    0.020
 5YC  plan-2  C2   0.020
 5YC  plan-2  H1   0.020
 5YC  plan-3  C9   0.020
 5YC  plan-3  C2   0.020
 5YC  plan-3  N    0.020
 5YC  plan-3  C1   0.020

