# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:08:49 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@](NC(=O)Cc1sccc1)(C=O)[C@H]2SCC(=C)C(=N2)C(O)=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
 1S7  1S7  '(2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  39  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1S7
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
 1S7  C     C  CH3    0  -0.418   0.3348  -2.7425  -1.9456
 1S7  N     N  NH1    0  -0.673  -0.4648  -0.3291  -0.4455
 1S7  O     O  O2     0  -0.474   1.1244  -1.9690  -1.0559
 1S7  S     S  S2     0   0.221  -5.0407  -0.3853  -0.0546
 1S7  C1    C  CT     0   0.313   0.5032  -1.3062  -0.0137
 1S7  O1    O  O      0  -0.468  -2.3311  -1.5100   0.0116
 1S7  S1    S  S2     0   0.008   2.9064  -1.6944   1.2659
 1S7  N2    N  N      0  -0.400   2.0619   0.5393  -0.1189
 1S7  C3    C  CH2    0  -0.645  -2.5987   0.6088  -1.0709
 1S7  C4    C  CR5    0  -0.133  -3.9125   0.8680  -0.4131
 1S7  C5    C  CR15   0  -0.236  -4.4294   2.0882  -0.0907
 1S7  C6    C  CR15   0  -0.186  -5.7444   2.0163   0.4455
 1S7  C7    C  CR15   0  -0.476  -6.2051   0.7382   0.5132
 1S7  C8    C  CH1    0  -0.239   1.6177  -0.5259   0.7250
 1S7  C9    C  CH2    0  -0.636   3.9817  -0.3748   1.8924
 1S7  C10   C  C      0   0.111   4.3474   0.5320   0.7594
 1S7  C11   C  C2     0  -0.552   5.6062   0.9273   0.5644
 1S7  C13   C  C      0   0.157   3.2516   0.9897  -0.1225
 1S7  C14   C  C1     0   0.152  -0.1168  -2.2528   1.0228
 1S7  C15   C  C      0   0.361   3.5357   2.1222  -1.1034
 1S7  H     H  HCH3   0   0.232   0.5345  -3.8044  -1.8018
 1S7  HA    H  HCH3   0   0.226  -0.7368  -2.5831  -1.8310
 1S7  HB    H  HCH3   0   0.234   0.6039  -2.4710  -2.9666
 1S7  HN    H  HNH1   0   0.412  -0.0699   0.5270  -0.8150
 1S7  H3    H  HCH2   0   0.292  -2.0265   1.5367  -1.0941
 1S7  H3A   H  HCH2   0   0.311  -2.7492   0.3166  -2.1168
 1S7  H5    H  HCR5   0   0.262  -3.8883   3.0125  -0.2411
 1S7  H6    H  HCR5   0   0.263  -6.3135   2.8774   0.7652
 1S7  H7    H  HCR5   0   0.291  -7.1550   0.3924   0.8910
 1S7  H8    H  HCH1   0   0.307   1.1681  -0.0882   1.6246
 1S7  H9    H  HCH2   0   0.294   3.4590   0.1646   2.6861
 1S7  H9A   H  HCH2   0   0.301   4.8640  -0.8405   2.3282
 1S7  H11   H  H      0   0.262   6.4005   0.5963   1.2215
 1S7  H11A  H  H      0   0.259   5.8942   1.5782  -0.2497
 1S7  H14   H  H      0   0.219  -0.5490  -1.7417   1.8994
 1S7  O4    O  O      0  -0.358  -0.0118  -3.4469   0.9590
 1S7  C2    C  C      0   0.586  -1.7979  -0.5071  -0.4371
 1S7  O5    O  O      0  -0.585   3.2428   3.2603  -0.7062
 1S7  O6    O  OC    -1  -0.594   4.0193   1.7736  -2.1925

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
 1S7  O    C     single    1.419  0.020  1.419
 1S7  C    H     single    0.970  0.020  1.090
 1S7  C    HA    single    0.970  0.020  1.090
 1S7  C    HB    single    0.970  0.020  1.090
 1S7  C1   N     single    1.442  0.020  1.442
 1S7  N    C2    single    1.345  0.020  1.345
 1S7  N    HN    single    0.860  0.020  1.020
 1S7  C1   O     single    1.382  0.020  1.382
 1S7  C4   S     aromatic  1.724  0.020  1.724
 1S7  C7   S     aromatic  1.715  0.020  1.715
 1S7  C8   C1    single    1.548  0.020  1.548
 1S7  C14  C1    single    1.535  0.020  1.535
 1S7  O1   C2    double    1.221  0.020  1.221
 1S7  C9   S1    single    1.814  0.020  1.814
 1S7  S1   C8    single    1.822  0.020  1.822
 1S7  C2   C3    single    1.513  0.020  1.513
 1S7  C8   N2    single    1.430  0.020  1.430
 1S7  C13  N2    double    1.272  0.020  1.272
 1S7  C3   C4    single    1.492  0.020  1.492
 1S7  C3   H3    single    0.970  0.020  1.090
 1S7  C3   H3A   single    0.970  0.020  1.090
 1S7  C5   C4    aromatic  1.364  0.020  1.364
 1S7  O4   C14   double    1.200  0.020  1.200
 1S7  C5   C6    aromatic  1.422  0.020  1.422
 1S7  C5   H5    single    0.930  0.020  1.080
 1S7  C15  O5    deloc     1.241  0.020  1.241
 1S7  C6   C7    aromatic  1.360  0.020  1.360
 1S7  C6   H6    single    0.930  0.020  1.080
 1S7  C15  O6    deloc     1.242  0.020  1.242
 1S7  C7   H7    single    0.930  0.020  1.080
 1S7  C8   H8    single    0.970  0.020  1.090
 1S7  C9   C10   single    1.497  0.020  1.497
 1S7  C9   H9    single    0.970  0.020  1.090
 1S7  C9   H9A   single    0.970  0.020  1.090
 1S7  C11  C10   double    1.334  0.020  1.334
 1S7  C10  C13   single    1.479  0.020  1.479
 1S7  C11  H11   single    0.930  0.020  1.080
 1S7  C11  H11A  single    0.930  0.020  1.080
 1S7  C13  C15   single    1.525  0.020  1.525
 1S7  C14  H14   single    0.930  0.020  1.080

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
 1S7  HB    C    HA   107.75  3.000
 1S7  HB    C    H    108.72  3.000
 1S7  HA    C    H    107.99  3.000
 1S7  HB    C    O    108.31  3.000
 1S7  HA    C    O    113.69  3.000
 1S7  H     C    O    110.27  3.000
 1S7  HN    N    C2   120.05  3.000
 1S7  HN    N    C1   114.86  3.000
 1S7  C2    N    C1   125.03  3.000
 1S7  C1    O    C    118.95  3.000
 1S7  C7    S    C4    92.12  3.000
 1S7  C14   C1   C8   106.23  3.000
 1S7  C14   C1   O    113.26  3.000
 1S7  C8    C1   O    106.13  3.000
 1S7  C14   C1   N    110.43  3.000
 1S7  C8    C1   N    106.54  3.000
 1S7  O     C1   N    113.64  3.000
 1S7  C9    S1   C8    93.17  3.000
 1S7  C13   N2   C8   123.78  3.000
 1S7  H3A   C3   H3   106.18  3.000
 1S7  H3A   C3   C4   110.25  3.000
 1S7  H3    C3   C4   108.88  3.000
 1S7  H3A   C3   C2   106.01  3.000
 1S7  H3    C3   C2   111.03  3.000
 1S7  C4    C3   C2   114.18  3.000
 1S7  C5    C4   C3   126.40  3.000
 1S7  C5    C4   S    110.68  3.000
 1S7  C3    C4   S    122.79  3.000
 1S7  H5    C5   C6   123.94  3.000
 1S7  H5    C5   C4   122.83  3.000
 1S7  C6    C5   C4   113.23  3.000
 1S7  H6    C6   C7   123.76  3.000
 1S7  H6    C6   C5   123.94  3.000
 1S7  C7    C6   C5   112.30  3.000
 1S7  H7    C7   C6   128.06  3.000
 1S7  H7    C7   S    120.25  3.000
 1S7  C6    C7   S    111.66  3.000
 1S7  H8    C8   N2   108.31  3.000
 1S7  H8    C8   S1   107.60  3.000
 1S7  N2    C8   S1   115.68  3.000
 1S7  H8    C8   C1   107.30  3.000
 1S7  N2    C8   C1   108.51  3.000
 1S7  S1    C8   C1   109.13  3.000
 1S7  H9A   C9   H9   107.94  3.000
 1S7  H9A   C9   C10  111.36  3.000
 1S7  H9    C9   C10  111.57  3.000
 1S7  H9A   C9   S1   107.90  3.000
 1S7  H9    C9   S1   109.05  3.000
 1S7  C10   C9   S1   108.92  3.000
 1S7  C13   C10  C11  121.35  3.000
 1S7  C13   C10  C9   117.24  3.000
 1S7  C11   C10  C9   121.40  3.000
 1S7  H11A  C11  H11  116.46  3.000
 1S7  H11A  C11  C10  122.67  3.000
 1S7  H11   C11  C10  120.87  3.000
 1S7  C15   C13  C10  118.38  3.000
 1S7  C15   C13  N2   116.04  3.000
 1S7  C10   C13  N2   125.56  3.000
 1S7  H14   C14  O4   122.52  3.000
 1S7  H14   C14  C1   114.16  3.000
 1S7  O4    C14  C1   122.84  3.000
 1S7  C13   C15  O6   115.36  3.000
 1S7  C13   C15  O5   115.56  3.000
 1S7  O6    C15  O5   129.08  3.000
 1S7  C3    C2   O1   121.92  3.000
 1S7  C3    C2   N    115.12  3.000
 1S7  O1    C2   N    122.93  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
 1S7  CONST_01  C6   C5   C4   S      0.00   0.0  0
 1S7  CONST_02  C5   C6   C7   S      0.00   0.0  0
 1S7  CONST_03  C6   C7   S    C4     0.00   0.0  0
 1S7  CONST_04  C7   C6   C5   C4     0.00   0.0  0
 1S7  CONST_05  C7   S    C4   C5     0.00   0.0  0
 1S7  CONST_06  C7   S    C4   C3   180.00   0.0  0
 1S7  CONST_07  C6   C5   C4   C3   180.00   0.0  0
 1S7  CONST_08  H5   C5   C4   S    180.00   0.0  0
 1S7  CONST_09  H6   C6   C7   S    180.00   0.0  0
 1S7  CONST_10  H7   C7   S    C4   180.00   0.0  0
 1S7  CONST_11  O1   C2   N    C1     0.00   0.0  0
 1S7  CONST_12  C3   C2   N    C1   180.00   0.0  0
 1S7  CONST_13  HN   N    C2   O1   180.00   0.0  0
 1S7  Var_01    C13  C10  C9   S1    47.48  30.0  1
 1S7  Var_02    C9   C10  C13  N2   -10.34  30.0  1
 1S7  Var_03    C10  C9   S1   C8   -60.96  30.0  1
 1S7  Var_04    C10  C13  N2   C8    -2.21  30.0  1
 1S7  Var_05    C2   C3   C4   S    -49.42  30.0  1
 1S7  Var_06    O5   C15  C13  N2    83.89  30.0  2
 1S7  Var_07    H11  C11  C10  C9     0.31   0.0  2
 1S7  Var_08    C4   C3   C2   N   -145.25  30.0  3
 1S7  Var_09    H    C    O    C1  -110.11  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
 1S7  chir_01  C1  O   C8  C14  positiv
 1S7  chir_02  C8  S1  N2  C1   negativ

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
 1S7  plan-1  S     0.020
 1S7  plan-1  C3    0.020
 1S7  plan-1  C4    0.020
 1S7  plan-1  C5    0.020
 1S7  plan-1  C6    0.020
 1S7  plan-1  C7    0.020
 1S7  plan-1  H5    0.020
 1S7  plan-1  H6    0.020
 1S7  plan-1  H7    0.020
 1S7  plan-2  N     0.020
 1S7  plan-2  C1    0.020
 1S7  plan-2  O1    0.020
 1S7  plan-2  C3    0.020
 1S7  plan-2  HN    0.020
 1S7  plan-2  C2    0.020
 1S7  plan-3  C13   0.020
 1S7  plan-3  C15   0.020
 1S7  plan-3  O5    0.020
 1S7  plan-3  O6    0.020
 1S7  plan-4  C1    0.020
 1S7  plan-4  C14   0.020
 1S7  plan-4  H14   0.020
 1S7  plan-4  O4    0.020
 1S7  plan-5  C9    0.020
 1S7  plan-5  C10   0.020
 1S7  plan-5  C11   0.020
 1S7  plan-5  C13   0.020
 1S7  plan-5  H11   0.020
 1S7  plan-5  H11A  0.020

