# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:17:46 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: N'-acetyl-2-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NNC(=O)C[C@@H]1CC[S](=O)(=O)C1
#
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
 J5P  J5P  N'-acetyl-2-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetohydrazide  ligand  29  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J5P
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
 J5P  C    C  CH3   0  -0.778   4.8677  -1.6870   0.1558
 J5P  O    O  O     0  -0.467   2.5310  -1.5173   0.6654
 J5P  C1   C  C     0   0.527   3.5481  -0.9758   0.2771
 J5P  C2   C  C     0   0.545   1.5441   0.9508  -1.0999
 J5P  C3   C  CH2   0  -0.565   0.2696   1.7315  -0.8833
 J5P  C4   C  CH1   0  -0.271  -0.9153   0.7893  -0.7013
 J5P  C5   C  CH2   0  -0.447  -2.2445   1.5398  -0.5701
 J5P  C6   C  CH2   0  -0.612  -3.2943   0.4965  -0.2215
 J5P  S    S  S     0   1.228  -2.4639  -0.6027   0.9521
 J5P  O2   O  OS    0  -0.689  -2.8001  -0.2086   2.3205
 J5P  C7   C  CH2   0  -0.616  -0.7799  -0.0639   0.5603
 J5P  O1   O  O     0  -0.461   1.7286   0.2484  -2.0740
 J5P  N1   N  NH1   0  -0.489   2.4554   1.0846  -0.1051
 J5P  N    N  NH1   0  -0.489   3.5859   0.3336  -0.0821
 J5P  H1   H  HCH3  0   0.272   5.0862  -2.2050   1.0884
 J5P  H2   H  HCH3  0   0.276   4.7952  -2.4391  -0.6298
 J5P  H3   H  HCH3  0   0.255   5.6989  -1.0249  -0.0789
 J5P  H4   H  HCH2  0   0.266   0.3440   2.4010  -0.0229
 J5P  H5   H  HCH2  0   0.293   0.1018   2.3554  -1.7640
 J5P  H6   H  HCH1  0   0.280  -0.9772   0.1280  -1.5708
 J5P  H7   H  HCH2  0   0.260  -2.1758   2.2943   0.2175
 J5P  H8   H  HCH2  0   0.285  -2.5053   2.0494  -1.4973
 J5P  H9   H  HCH2  0   0.317  -4.1922   0.8905   0.2516
 J5P  H10  H  HCH2  0   0.305  -3.5705  -0.0998  -1.0912
 J5P  H11  H  HCH2  0   0.324  -0.1399  -0.9380   0.4495
 J5P  H12  H  HCH2  0   0.299  -0.4304   0.5299   1.4068
 J5P  H13  H  HNH1  0   0.418   2.2411   1.6168   0.7249
 J5P  H14  H  HNH1  0   0.419   4.4199   0.7454  -0.4715
 J5P  O3   O  OS    0  -0.686  -2.6613  -2.0010   0.5717

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
 J5P  O   C1   double  1.216  0.020  1.216
 J5P  C   C1   single  1.504  0.020  1.504
 J5P  C1  N    single  1.358  0.020  1.358
 J5P  N   N1   single  1.357  0.020  1.357
 J5P  N1  C2   single  1.356  0.020  1.356
 J5P  C2  O1   double  1.215  0.020  1.215
 J5P  C2  C3   single  1.510  0.020  1.510
 J5P  C3  C4   single  1.525  0.020  1.525
 J5P  O2  S    double  1.463  0.020  1.463
 J5P  C4  C5   single  1.532  0.020  1.532
 J5P  C4  C7   single  1.529  0.020  1.529
 J5P  C5  C6   single  1.521  0.020  1.521
 J5P  C7  S    single  1.811  0.020  1.811
 J5P  S   C6   single  1.810  0.020  1.810
 J5P  S   O3   double  1.462  0.020  1.462
 J5P  C   H1   single  0.970  0.020  1.090
 J5P  C   H2   single  0.970  0.020  1.090
 J5P  C   H3   single  0.970  0.020  1.090
 J5P  C3  H4   single  0.970  0.020  1.090
 J5P  C3  H5   single  0.970  0.020  1.090
 J5P  C4  H6   single  0.970  0.020  1.090
 J5P  C5  H7   single  0.970  0.020  1.090
 J5P  C5  H8   single  0.970  0.020  1.090
 J5P  C6  H9   single  0.970  0.020  1.090
 J5P  C6  H10  single  0.970  0.020  1.090
 J5P  C7  H11  single  0.970  0.020  1.090
 J5P  C7  H12  single  0.970  0.020  1.090
 J5P  N1  H13  single  0.860  0.020  1.020
 J5P  N   H14  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
 J5P  H3   C   H2   108.37  3.000
 J5P  H3   C   H1   108.71  3.000
 J5P  H2   C   H1   107.60  3.000
 J5P  H3   C   C1   113.57  3.000
 J5P  H2   C   C1   109.03  3.000
 J5P  H1   C   C1   109.39  3.000
 J5P  N    C1  O    122.49  3.000
 J5P  N    C1  C    114.21  3.000
 J5P  O    C1  C    123.30  3.000
 J5P  N1   C2  O1   122.91  3.000
 J5P  O1   C2  C3   122.82  3.000
 J5P  N1   C2  C3   114.27  3.000
 J5P  H5   C3  H4   107.18  3.000
 J5P  H5   C3  C4   109.26  3.000
 J5P  H4   C3  C4   109.73  3.000
 J5P  H5   C3  C2   108.01  3.000
 J5P  H4   C3  C2   111.85  3.000
 J5P  C4   C3  C2   110.70  3.000
 J5P  H6   C4  C7   108.87  3.000
 J5P  H6   C4  C5   108.37  3.000
 J5P  C7   C4  C5   106.23  3.000
 J5P  H6   C4  C3   108.82  3.000
 J5P  C7   C4  C3   111.99  3.000
 J5P  C5   C4  C3   112.44  3.000
 J5P  H8   C5  H7   107.78  3.000
 J5P  H8   C5  C6   110.53  3.000
 J5P  H7   C5  C6   110.60  3.000
 J5P  H8   C5  C4   111.34  3.000
 J5P  H7   C5  C4   110.21  3.000
 J5P  C6   C5  C4   106.41  3.000
 J5P  H10  C6  H9   109.61  3.000
 J5P  H10  C6  S    107.54  3.000
 J5P  H9   C6  S    108.45  3.000
 J5P  H10  C6  C5   111.55  3.000
 J5P  H9   C6  C5   114.88  3.000
 J5P  S    C6  C5   104.40  3.000
 J5P  C7   S   O2   109.62  3.000
 J5P  C7   S   O3   110.71  3.000
 J5P  O2   S   O3   118.02  3.000
 J5P  O3   S   C6   110.50  3.000
 J5P  C7   S   C6    96.06  3.000
 J5P  O2   S   C6   109.72  3.000
 J5P  H12  C7  H11  109.11  3.000
 J5P  H12  C7  S    106.97  3.000
 J5P  H11  C7  S    109.25  3.000
 J5P  H12  C7  C4   111.39  3.000
 J5P  H11  C7  C4   114.58  3.000
 J5P  S    C7  C4   105.20  3.000
 J5P  H13  N1  N    117.05  3.000
 J5P  H13  N1  C2   120.86  3.000
 J5P  N    N1  C2   121.17  3.000
 J5P  H14  N   N1   117.15  3.000
 J5P  H14  N   C1   121.26  3.000
 J5P  N1   N   C1   120.97  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
 J5P  CONST_01  N1   N   C1  C    180.00   0.0  0
 J5P  CONST_02  N1   N   C1  O      0.00   0.0  0
 J5P  CONST_03  N    N1  C2  C3   180.00   0.0  0
 J5P  CONST_04  N    N1  C2  O1     0.00   0.0  0
 J5P  CONST_05  H14  N   C1  C      0.00   0.0  0
 J5P  CONST_06  H13  N1  C2  C3     0.00   0.0  0
 J5P  Var_01    S    C6  C5  C4    40.14  30.0  1
 J5P  Var_02    C6   S   C7  C4   -10.90  30.0  1
 J5P  Var_03    C7   S   C6  C5   -16.81  30.0  1
 J5P  Var_04    N1   C2  C3  C4  -114.27  30.0  1
 J5P  Var_05    C2   N1  N   C1   -75.29  30.0  2
 J5P  Var_06    H1   C   C1  O    -50.66  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
 J5P  chir_01  C4  C3  C5  C7  positiv

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
 J5P  plan-1  C    0.020
 J5P  plan-1  O    0.020
 J5P  plan-1  C1   0.020
 J5P  plan-1  N1   0.020
 J5P  plan-1  N    0.020
 J5P  plan-1  H14  0.020
 J5P  plan-2  C2   0.020
 J5P  plan-2  C3   0.020
 J5P  plan-2  O1   0.020
 J5P  plan-2  N1   0.020
 J5P  plan-2  N    0.020
 J5P  plan-2  H13  0.020

