# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:04:40 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCNC(=O)C1=CN=C2SCCN2C1=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
 SJK  SJK  5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxamide  ligand  27  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SJK
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
 SJK  N1   N  NR5   0  -0.528  23.7549  -25.9941   4.0053
 SJK  N3   N  NH1   0  -0.629  21.5631  -26.6706   8.0888
 SJK  C4   C  C     0   0.601  23.7417  -25.7601   5.3815
 SJK  C5   C  CH2   0  -0.596  24.0994  -25.4574   1.7075
 SJK  C6   C  CH2   0  -0.264  24.6376  -25.2463   3.1139
 SJK  C8   C  CH2   0  -0.300  21.3001  -26.7106   9.5100
 SJK  C1   C  CR5   0   0.357  23.0698  -27.0068   3.4341
 SJK  N2   N  N     0  -0.449  22.3075  -27.8394   4.0671
 SJK  C2   C  C1    0  -0.042  22.2236  -27.6508   5.4028
 SJK  C3   C  C     0  -0.306  22.8756  -26.6725   6.0925
 SJK  S1   S  S2    0   0.123  23.3304  -27.1079   1.7182
 SJK  O1   O  O     0  -0.453  24.4036  -24.8563   5.8534
 SJK  O2   O  O     0  -0.475  23.8058  -26.4881   8.2672
 SJK  C9   C  CH2   0  -0.550  21.4879  -25.3737  10.2115
 SJK  S2   S  S2    0  -0.263  20.5133  -24.0919   9.3514
 SJK  H1   H  HNH1  0   0.412  20.7750  -26.6668   7.4625
 SJK  H2   H  HCH2  0   0.318  24.8935  -25.4331   0.9667
 SJK  H3   H  HCH2  0   0.312  23.3415  -24.7208   1.4477
 SJK  H4   H  HCH2  0   0.292  25.6532  -25.6297   3.2202
 SJK  H5   H  HCH2  0   0.298  24.6322  -24.1923   3.3789
 SJK  H6   H  HCH2  0   0.267  20.2732  -27.0502   9.6345
 SJK  H7   H  HCH2  0   0.267  21.9479  -27.4491   9.9861
 SJK  H8   H  H     0   0.291  21.5944  -28.3609   5.9282
 SJK  H9   H  HCH2  0   0.284  21.1363  -25.4646  11.2382
 SJK  H10  H  HCH2  0   0.272  22.5380  -25.0893  10.2316
 SJK  H11  H  HSH1  0   0.224  20.4070  -23.2401  10.3761
 SJK  C7   C  C     0   0.534  22.8033  -26.5895   7.5776

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
 SJK  S1  C5   single  1.821  0.020  1.821
 SJK  S1  C1   single  1.739  0.020  1.739
 SJK  C5  C6   single  1.521  0.020  1.521
 SJK  C6  N1   single  1.460  0.020  1.460
 SJK  C1  N1   single  1.350  0.020  1.350
 SJK  C1  N2   double  1.294  0.020  1.294
 SJK  N1  C4   single  1.396  0.020  1.396
 SJK  N2  C2   single  1.352  0.020  1.352
 SJK  C4  O1   double  1.216  0.020  1.216
 SJK  C4  C3   single  1.445  0.020  1.445
 SJK  C2  C3   double  1.363  0.020  1.363
 SJK  C3  C7   single  1.489  0.020  1.489
 SJK  C7  O2   double  1.221  0.020  1.221
 SJK  C7  N3   single  1.344  0.020  1.344
 SJK  N3  C8   single  1.446  0.020  1.446
 SJK  C8  C9   single  1.521  0.020  1.521
 SJK  C9  S2   single  1.826  0.020  1.826
 SJK  N3  H1   single  0.860  0.020  1.020
 SJK  C5  H2   single  0.970  0.020  1.090
 SJK  C5  H3   single  0.970  0.020  1.090
 SJK  C6  H4   single  0.970  0.020  1.090
 SJK  C6  H5   single  0.970  0.020  1.090
 SJK  C8  H6   single  0.970  0.020  1.090
 SJK  C8  H7   single  0.970  0.020  1.090
 SJK  C2  H8   single  0.930  0.020  1.080
 SJK  C9  H9   single  0.970  0.020  1.090
 SJK  C9  H10  single  0.970  0.020  1.090
 SJK  S2  H11  single  1.200  0.020  1.300

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
 SJK  C1   N1  C6  115.64  3.000
 SJK  C1   N1  C4  122.57  3.000
 SJK  C6   N1  C4  121.44  3.000
 SJK  H1   N3  C8  117.99  3.000
 SJK  H1   N3  C7  119.05  3.000
 SJK  C8   N3  C7  122.91  3.000
 SJK  O1   C4  C3  127.21  3.000
 SJK  C3   C4  N1  112.64  3.000
 SJK  O1   C4  N1  120.14  3.000
 SJK  H3   C5  H2  109.33  3.000
 SJK  H3   C5  S1  108.71  3.000
 SJK  H2   C5  S1  109.45  3.000
 SJK  H3   C5  C6  111.92  3.000
 SJK  H2   C5  C6  111.65  3.000
 SJK  S1   C5  C6  105.66  3.000
 SJK  H5   C6  H4  108.77  3.000
 SJK  H5   C6  C5  111.00  3.000
 SJK  H4   C6  C5  111.77  3.000
 SJK  H5   C6  N1  110.17  3.000
 SJK  H4   C6  N1  108.86  3.000
 SJK  C5   C6  N1  106.23  3.000
 SJK  H7   C8  H6  107.39  3.000
 SJK  H7   C8  C9  108.67  3.000
 SJK  H6   C8  C9  109.74  3.000
 SJK  H7   C8  N3  109.85  3.000
 SJK  H6   C8  N3  107.01  3.000
 SJK  C9   C8  N3  113.98  3.000
 SJK  S1   C1  N2  122.25  3.000
 SJK  N2   C1  N1  125.08  3.000
 SJK  S1   C1  N1  112.67  3.000
 SJK  C2   N2  C1  115.48  3.000
 SJK  H8   C2  C3  120.15  3.000
 SJK  H8   C2  N2  115.05  3.000
 SJK  C3   C2  N2  124.79  3.000
 SJK  C2   C3  C7  121.42  3.000
 SJK  C7   C3  C4  118.99  3.000
 SJK  C2   C3  C4  119.40  3.000
 SJK  C1   S1  C5   90.94  3.000
 SJK  H10  C9  H9  108.42  3.000
 SJK  H10  C9  S2  109.91  3.000
 SJK  H9   C9  S2  109.30  3.000
 SJK  H10  C9  C8  110.93  3.000
 SJK  H9   C9  C8  108.75  3.000
 SJK  S2   C9  C8  109.50  3.000
 SJK  H11  S2  C9   97.39  3.000
 SJK  O2   C7  C3  121.87  3.000
 SJK  O2   C7  N3  123.22  3.000
 SJK  C3   C7  N3  114.88  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
 SJK  CONST_01  C2  N2  C1  N1     0.00   0.0  0
 SJK  CONST_02  S1  C1  N1  C4   180.00   0.0  0
 SJK  CONST_03  N2  C1  N1  C4     0.00   0.0  0
 SJK  CONST_04  S1  C1  N1  C6     0.00   0.0  0
 SJK  CONST_05  N2  C1  N1  C6   180.00   0.0  0
 SJK  CONST_06  C3  C4  N1  C6   180.00   0.0  0
 SJK  CONST_07  C3  C4  N1  C1     0.00   0.0  0
 SJK  CONST_08  S1  C1  N2  C2   180.00   0.0  0
 SJK  CONST_09  O1  C4  N1  C6     0.00   0.0  0
 SJK  CONST_10  O1  C4  N1  C1   180.00   0.0  0
 SJK  CONST_11  C3  C7  N3  C8   180.00   0.0  0
 SJK  CONST_12  H1  N3  C7  C3     0.00   0.0  0
 SJK  CONST_13  O2  C7  N3  C8     0.00   0.0  0
 SJK  Var_01    S1  C5  C6  N1   -30.28  30.0  1
 SJK  Var_02    C5  C6  N1  C4  -163.61  30.0  1
 SJK  Var_03    N2  C1  S1  C5   167.64  30.0  1
 SJK  Var_04    C4  C3  C7  N3   136.38  30.0  2
 SJK  Var_05    S2  C9  C8  N3    52.76  30.0  3
 SJK  Var_06    C9  C8  N3  C7    73.92  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
 SJK  plan-1  N3  0.020
 SJK  plan-1  C8  0.020
 SJK  plan-1  C3  0.020
 SJK  plan-1  O2  0.020
 SJK  plan-1  H1  0.020
 SJK  plan-1  C7  0.020
 SJK  plan-2  N1  0.020
 SJK  plan-2  C4  0.020
 SJK  plan-2  C6  0.020
 SJK  plan-2  C1  0.020
 SJK  plan-2  N2  0.020
 SJK  plan-2  C2  0.020
 SJK  plan-2  C3  0.020
 SJK  plan-2  S1  0.020
 SJK  plan-2  O1  0.020
 SJK  plan-2  H8  0.020
 SJK  plan-2  C7  0.020

