# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 16:32:13 2022
#   Inital geometry file: a 162 line input string
#   Ligand name: (2~{R})-2-[(1~{R})-1-[[(2~{Z})-2-(2-azanyl-1,3-thiazol-4-yl)-2-(2-methyl-1-oxidanyl-1-oxidanylidene-propan-2-yl)oxyimino-ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5-(pyridin-1-ium-1-ylmethyl)-3,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O\N=C(/C(=O)N[C@@H]([C@@H]1NC(=C(CS1)C[n+]2ccccc2)C(O)=O)C(O)=O)c3csc(N)n3)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
 RYE  RYE  '(2~{R})-2-[(1~{R})-1-[[(2~{Z})-2-(2-azanyl-1,3-thiazol-4-yl)-2-(2-methyl-1-oxidanyl-1-oxidanylidene-propan-2-yl)oxyimino-ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5-(pyridin-1-ium-1-ylmethyl)-3,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid'  ligand  60  38  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RYE
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
 RYE  C     C  C      0   0.432  36.0257  -69.4037  31.8632
 RYE  S1    S  S2     0  -0.012  34.8326  -73.3516  31.3387
 RYE  C2    C  CH2    0  -0.625  34.5959  -74.2400  32.9056
 RYE  C3    C  C      0   0.003  35.8083  -74.1763  33.7938
 RYE  C4    C  C      0   0.184  36.6449  -73.1085  33.7942
 RYE  N5    N  NH1    0  -0.662  36.4472  -72.0097  33.0170
 RYE  C6    C  CH1    0  -0.217  35.3287  -71.7893  32.1572
 RYE  CA    C  CH1    0  -0.217  35.6463  -70.7232  31.1174
 RYE  N10   N  NH1    0  -0.599  36.6776  -71.2009  30.2310
 RYE  C11   C  C      0   0.469  36.9892  -70.5651  29.1020
 RYE  O12   O  O      0  -0.471  36.4068  -69.5815  28.6732
 RYE  C13   C  C      0   0.044  38.1633  -71.1512  28.3556
 RYE  C14   C  CR5    0   0.327  39.4615  -70.5158  28.5463
 RYE  C15   C  CR15   0  -0.602  39.7249  -69.6693  29.5769
 RYE  N16   N  N      0  -0.080  38.0470  -72.1360  27.5590
 RYE  S16   S  S2     0   0.181  41.3682  -69.1580  29.4965
 RYE  C17   C  CR5    0   0.265  41.5711  -70.1435  28.0660
 RYE  O17   O  O2     0  -0.413  36.7731  -72.5841  27.4890
 RYE  C18   C  CT     0   0.118  36.6936  -73.8699  26.8573
 RYE  N18   N  NH2    0  -0.819  42.7429  -70.1528  27.3927
 RYE  C19   C  CH3    0  -0.679  35.2110  -74.2179  26.9380
 RYE  N19   N  N      0  -0.446  40.5064  -70.7830  27.6993
 RYE  C20   C  CH3    0  -0.658  37.1401  -73.7684  25.4048
 RYE  C21   C  C      0   0.404  37.4909  -74.9329  27.6690
 RYE  O2A   O  O      0  -0.598  37.7789  -75.9722  27.0454
 RYE  O2B   O  OC    -1  -0.593  37.7174  -74.6799  28.8651
 RYE  C3'   C  CH2    0  -0.441  36.0317  -75.3930  34.6234
 RYE  C4'   C  C      0   0.409  37.9367  -72.9637  34.6263
 RYE  O4A   O  O      0  -0.571  38.7723  -72.1765  34.1521
 RYE  O4B   O  OC    -1  -0.562  38.0256  -73.6025  35.6907
 RYE  N6    N  N      1  -0.399  35.0471  -75.4613  35.7501
 RYE  C26   C  C1     0   0.085  35.1363  -74.5481  36.7275
 RYE  C25   C  C1     0  -0.349  34.2363  -74.5505  37.7671
 RYE  C24   C  C1     0  -0.097  33.2272  -75.5035  37.7900
 RYE  C23   C  C1     0  -0.347  33.1536  -76.4348  36.7669
 RYE  C22   C  C1     0   0.079  34.0860  -76.3900  35.7536
 RYE  OB    O  O      0  -0.580  35.0652  -68.8129  32.3803
 RYE  OA    O  OC    -1  -0.573  37.2321  -69.1026  31.9068
 RYE  H2A   H  HCH2   0   0.280  33.6957  -73.8521  33.3911
 RYE  H2    H  HCH2   0   0.281  34.3776  -75.2747  32.6304
 RYE  HN5   H  HNH1   0   0.385  37.2537  -71.4027  32.9433
 RYE  H6    H  HCH1   0   0.293  34.4572  -71.4513  32.7250
 RYE  HA    H  HCH1   0   0.271  34.7331  -70.5440  30.5447
 RYE  HN10  H  HNH1   0   0.400  37.2309  -71.9994  30.5050
 RYE  H15   H  HCR5   0   0.314  39.0678  -69.3504  30.3741
 RYE  HN18  H  HNH2   0   0.406  43.5867  -69.9064  27.8831
 RYE  H8    H  HNH2   0   0.400  42.8564  -70.8925  26.7174
 RYE  H19A  H  HCH3   0   0.231  35.0373  -75.1991  26.4985
 RYE  H19   H  HCH3   0   0.231  34.8655  -74.2459  27.9730
 RYE  H19B  H  HCH3   0   0.230  34.6030  -73.4936  26.3918
 RYE  H20   H  HCH3   0   0.226  36.9584  -74.7071  24.8863
 RYE  H20B  H  HCH3   0   0.215  36.5791  -72.9882  24.8861
 RYE  H20A  H  HCH3   0   0.228  38.2022  -73.5404  25.3157
 RYE  H3'A  H  HCH2   0   0.290  35.8786  -76.3043  34.0440
 RYE  H3'   H  HCH2   0   0.312  37.0175  -75.4254  35.0719
 RYE  H26   H  H      0   0.350  35.9525  -73.8435  36.6412
 RYE  H25   H  H      0   0.309  34.3330  -73.8106  38.5477
 RYE  H24   H  H      0   0.309  32.5078  -75.5188  38.5970
 RYE  H23   H  H      0   0.311  32.3847  -77.1925  36.7427
 RYE  H22   H  H      0   0.343  34.0809  -77.0866  34.9281

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
 RYE  C    CA    single    1.562  0.020  1.562
 RYE  C    OB    deloc     1.241  0.020  1.241
 RYE  C    OA    deloc     1.244  0.020  1.244
 RYE  S1   C2    single    1.817  0.020  1.817
 RYE  S1   C6    single    1.832  0.020  1.832
 RYE  C2   C3    single    1.504  0.020  1.504
 RYE  C3   C4    double    1.357  0.020  1.357
 RYE  C3   C3'   single    1.489  0.020  1.489
 RYE  C4   N5    single    1.360  0.020  1.360
 RYE  C4   C4'   single    1.543  0.020  1.543
 RYE  N5   C6    single    1.428  0.020  1.428
 RYE  C6   CA    single    1.523  0.020  1.523
 RYE  CA   N10   single    1.441  0.020  1.441
 RYE  N10  C11   single    1.333  0.020  1.333
 RYE  C11  O12   double    1.221  0.020  1.221
 RYE  C11  C13   single    1.510  0.020  1.510
 RYE  C13  C14   single    1.458  0.020  1.458
 RYE  C13  N16   double    1.272  0.020  1.272
 RYE  C14  C15   aromatic  1.359  0.020  1.359
 RYE  C14  N19   aromatic  1.371  0.020  1.371
 RYE  C15  S16   aromatic  1.723  0.020  1.723
 RYE  N16  O17   single    1.352  0.020  1.352
 RYE  S16  C17   aromatic  1.749  0.020  1.749
 RYE  C17  N18   single    1.351  0.020  1.351
 RYE  C17  N19   aromatic  1.295  0.020  1.295
 RYE  O17  C18   single    1.435  0.020  1.435
 RYE  C18  C19   single    1.525  0.020  1.525
 RYE  C18  C20   single    1.523  0.020  1.523
 RYE  C18  C21   single    1.557  0.020  1.557
 RYE  C21  O2A   deloc     1.246  0.020  1.246
 RYE  C21  O2B   deloc     1.243  0.020  1.243
 RYE  C3'  N6    single    1.498  0.020  1.498
 RYE  C4'  O4A   deloc     1.242  0.020  1.242
 RYE  C4'  O4B   deloc     1.245  0.020  1.245
 RYE  N6   C26   aromatic  1.341  0.020  1.341
 RYE  N6   C22   aromatic  1.336  0.020  1.336
 RYE  C26  C25   aromatic  1.375  0.020  1.375
 RYE  C25  C24   aromatic  1.388  0.020  1.388
 RYE  C24  C23   aromatic  1.385  0.020  1.385
 RYE  C23  C22   aromatic  1.378  0.020  1.378
 RYE  C2   H2A   single    0.970  0.020  1.090
 RYE  C2   H2    single    0.970  0.020  1.090
 RYE  N5   HN5   single    0.860  0.020  1.020
 RYE  C6   H6    single    0.970  0.020  1.090
 RYE  CA   HA    single    0.970  0.020  1.090
 RYE  N10  HN10  single    0.860  0.020  1.020
 RYE  C15  H15   single    0.930  0.020  1.080
 RYE  N18  HN18  single    0.890  0.020  1.040
 RYE  N18  H8    single    0.890  0.020  1.040
 RYE  C19  H19A  single    0.970  0.020  1.090
 RYE  C19  H19   single    0.970  0.020  1.090
 RYE  C19  H19B  single    0.970  0.020  1.090
 RYE  C20  H20   single    0.970  0.020  1.090
 RYE  C20  H20B  single    0.970  0.020  1.090
 RYE  C20  H20A  single    0.970  0.020  1.090
 RYE  C3'  H3'A  single    0.970  0.020  1.090
 RYE  C3'  H3'   single    0.970  0.020  1.090
 RYE  C26  H26   single    0.930  0.020  1.080
 RYE  C25  H25   single    0.930  0.020  1.080
 RYE  C24  H24   single    0.930  0.020  1.080
 RYE  C23  H23   single    0.930  0.020  1.080
 RYE  C22  H22   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
 RYE  OA    C    OB    128.38  3.000
 RYE  OA    C    CA    117.16  3.000
 RYE  OB    C    CA    114.40  3.000
 RYE  C6    S1   C2     93.84  3.000
 RYE  H2    C2   H2A   106.44  3.000
 RYE  H2    C2   C3    110.48  3.000
 RYE  H2A   C2   C3    112.72  3.000
 RYE  H2    C2   S1    105.77  3.000
 RYE  H2A   C2   S1    108.46  3.000
 RYE  C3    C2   S1    112.56  3.000
 RYE  C3'   C3   C4    123.40  3.000
 RYE  C3'   C3   C2    114.53  3.000
 RYE  C4    C3   C2    122.04  3.000
 RYE  C4'   C4   N5    110.72  3.000
 RYE  C4'   C4   C3    126.16  3.000
 RYE  N5    C4   C3    123.10  3.000
 RYE  HN5   N5   C6    119.19  3.000
 RYE  HN5   N5   C4    114.23  3.000
 RYE  C6    N5   C4    125.63  3.000
 RYE  H6    C6   CA    107.72  3.000
 RYE  H6    C6   N5    111.06  3.000
 RYE  CA    C6   N5    110.84  3.000
 RYE  H6    C6   S1    106.24  3.000
 RYE  CA    C6   S1    110.39  3.000
 RYE  N5    C6   S1    110.46  3.000
 RYE  HA    CA   N10   109.27  3.000
 RYE  HA    CA   C6    107.36  3.000
 RYE  N10   CA   C6    109.70  3.000
 RYE  HA    CA   C     108.34  3.000
 RYE  N10   CA   C     113.56  3.000
 RYE  C6    CA   C     108.42  3.000
 RYE  HN10  N10  C11   118.64  3.000
 RYE  HN10  N10  CA    119.17  3.000
 RYE  C11   N10  CA    122.02  3.000
 RYE  C13   C11  O12   120.67  3.000
 RYE  C13   C11  N10   114.55  3.000
 RYE  O12   C11  N10   124.78  3.000
 RYE  N16   C13  C14   120.05  3.000
 RYE  N16   C13  C11   122.62  3.000
 RYE  C14   C13  C11   117.30  3.000
 RYE  N19   C14  C15   116.23  3.000
 RYE  N19   C14  C13   120.85  3.000
 RYE  C15   C14  C13   122.89  3.000
 RYE  H15   C15  S16   121.77  3.000
 RYE  H15   C15  C14   128.68  3.000
 RYE  S16   C15  C14   109.53  3.000
 RYE  O17   N16  C13   112.03  3.000
 RYE  C17   S16  C15    88.94  3.000
 RYE  N19   C17  N18   124.63  3.000
 RYE  N19   C17  S16   114.49  3.000
 RYE  N18   C17  S16   120.80  3.000
 RYE  C18   O17  N16   111.84  3.000
 RYE  C21   C18  C20   113.11  3.000
 RYE  C21   C18  C19   108.33  3.000
 RYE  C20   C18  C19   110.53  3.000
 RYE  C21   C18  O17   110.73  3.000
 RYE  C20   C18  O17   110.12  3.000
 RYE  C19   C18  O17   103.59  3.000
 RYE  H8    N18  HN18  114.31  3.000
 RYE  H8    N18  C17   115.88  3.000
 RYE  HN18  N18  C17   118.84  3.000
 RYE  H19B  C19  H19   108.37  3.000
 RYE  H19B  C19  H19A  107.87  3.000
 RYE  H19   C19  H19A  108.00  3.000
 RYE  H19B  C19  C18   111.31  3.000
 RYE  H19   C19  C18   111.33  3.000
 RYE  H19A  C19  C18   109.83  3.000
 RYE  C17   N19  C14   110.81  3.000
 RYE  H20A  C20  H20B  108.19  3.000
 RYE  H20A  C20  H20   107.72  3.000
 RYE  H20B  C20  H20   107.72  3.000
 RYE  H20A  C20  C18   112.19  3.000
 RYE  H20B  C20  C18   110.49  3.000
 RYE  H20   C20  C18   110.38  3.000
 RYE  O2B   C21  O2A   127.53  3.000
 RYE  O2B   C21  C18   117.12  3.000
 RYE  O2A   C21  C18   115.28  3.000
 RYE  H3'   C3'  H3'A  108.82  3.000
 RYE  H3'   C3'  N6    106.58  3.000
 RYE  H3'A  C3'  N6    105.62  3.000
 RYE  H3'   C3'  C3    113.04  3.000
 RYE  H3'A  C3'  C3    111.44  3.000
 RYE  N6    C3'  C3    110.96  3.000
 RYE  O4B   C4'  O4A   127.14  3.000
 RYE  O4B   C4'  C4    118.21  3.000
 RYE  O4A   C4'  C4    114.62  3.000
 RYE  C22   N6   C26   121.29  3.000
 RYE  C22   N6   C3'   120.42  3.000
 RYE  C26   N6   C3'   118.27  3.000
 RYE  H26   C26  C25   123.74  3.000
 RYE  H26   C26  N6    115.83  3.000
 RYE  C25   C26  N6    120.43  3.000
 RYE  H25   C25  C24   121.57  3.000
 RYE  H25   C25  C26   119.12  3.000
 RYE  C24   C25  C26   119.30  3.000
 RYE  H24   C24  C23   120.41  3.000
 RYE  H24   C24  C25   120.38  3.000
 RYE  C23   C24  C25   119.21  3.000
 RYE  H23   C23  C22   119.23  3.000
 RYE  H23   C23  C24   121.74  3.000
 RYE  C22   C23  C24   119.03  3.000
 RYE  H22   C22  C23   122.54  3.000
 RYE  H22   C22  N6    116.71  3.000
 RYE  C23   C22  N6    120.75  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
 RYE  CONST_01  C17   S16  C15  C14     0.00   0.0  0
 RYE  CONST_02  S16   C17  N19  C14     0.00   0.0  0
 RYE  CONST_03  C17   N19  C14  C15     0.00   0.0  0
 RYE  CONST_04  N19   C17  S16  C15     0.00   0.0  0
 RYE  CONST_05  N19   C14  C15  S16     0.00   0.0  0
 RYE  CONST_06  C24   C25  C26  N6      0.00   0.0  0
 RYE  CONST_07  C24   C23  C22  N6      0.00   0.0  0
 RYE  CONST_08  C23   C22  N6   C26     0.00   0.0  0
 RYE  CONST_09  C23   C24  C25  C26     0.00   0.0  0
 RYE  CONST_10  C22   N6   C26  C25     0.00   0.0  0
 RYE  CONST_11  C22   C23  C24  C25     0.00   0.0  0
 RYE  CONST_12  S16   C15  C14  C13   180.00   0.0  0
 RYE  CONST_13  C17   N19  C14  C13   180.00   0.0  0
 RYE  CONST_14  N18   C17  N19  C14   180.00   0.0  0
 RYE  CONST_15  N18   C17  S16  C15   180.00   0.0  0
 RYE  CONST_16  C25   C26  N6   C3'   180.00   0.0  0
 RYE  CONST_17  C23   C22  N6   C3'   180.00   0.0  0
 RYE  CONST_18  H15   C15  S16  C17   180.00   0.0  0
 RYE  CONST_19  H25   C25  C26  N6    180.00   0.0  0
 RYE  CONST_20  H23   C23  C22  N6    180.00   0.0  0
 RYE  CONST_21  H22   C22  N6   C26   180.00   0.0  0
 RYE  CONST_22  H24   C24  C25  C26   180.00   0.0  0
 RYE  CONST_23  H26   C26  C25  C24   180.00   0.0  0
 RYE  CONST_25  H8    N18  C17  S16   180.00   0.0  0
 RYE  CONST_26  O12   C11  N10  CA      0.00   0.0  0
 RYE  CONST_27  C13   C11  N10  CA    180.00   0.0  0
 RYE  CONST_28  HN10  N10  C11  O12   180.00   0.0  0
 RYE  Var_01    C4    C3   C2   S1     31.36  30.0  1
 RYE  Var_02    N5    C4   C3   C2      1.12  30.0  1
 RYE  Var_03    C6    N5   C4   C3      3.21  30.0  1
 RYE  Var_04    N6    C3'  C3   C2    -73.87  30.0  3
 RYE  Var_05    C26   N6   C3'  C3    -67.87  30.0  2
 RYE  Var_06    O4A   C4'  C4   C3    155.50  30.0  2
 RYE  Var_07    C15   C14  C13  C11    16.62  30.0  2
 RYE  Var_08    C14   C13  C11  N10   -98.16  30.0  2
 RYE  Var_09    C19   C18  O17  N16   177.40  30.0  3
 RYE  Var_10    O2A   C21  C18  O17  -161.94  30.0  3
 RYE  Var_11    H19A  C19  C18  O17  -178.86  30.0  3
 RYE  Var_12    H20   C20  C18  O17  -172.55  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
 RYE  chir_01  C6  S1   N5  CA  negativ
 RYE  chir_02  CA  N10  C6  C   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
 RYE  plan-1  C13   0.020
 RYE  plan-1  C14   0.020
 RYE  plan-1  C15   0.020
 RYE  plan-1  S16   0.020
 RYE  plan-1  C17   0.020
 RYE  plan-1  N18   0.020
 RYE  plan-1  N19   0.020
 RYE  plan-1  H15   0.020
 RYE  plan-2  C4    0.020
 RYE  plan-2  C4'   0.020
 RYE  plan-2  O4A   0.020
 RYE  plan-2  O4B   0.020
 RYE  plan-3  C11   0.020
 RYE  plan-3  C13   0.020
 RYE  plan-3  C14   0.020
 RYE  plan-3  N16   0.020
 RYE  plan-3  O17   0.020
 RYE  plan-4  C3'   0.020
 RYE  plan-4  N6    0.020
 RYE  plan-4  C26   0.020
 RYE  plan-4  C25   0.020
 RYE  plan-4  C24   0.020
 RYE  plan-4  C23   0.020
 RYE  plan-4  C22   0.020
 RYE  plan-4  H26   0.020
 RYE  plan-4  H25   0.020
 RYE  plan-4  H24   0.020
 RYE  plan-4  H23   0.020
 RYE  plan-4  H22   0.020
 RYE  plan-5  C17   0.020
 RYE  plan-5  N18   0.020
 RYE  plan-5  HN18  0.020
 RYE  plan-5  H8    0.020
 RYE  plan-6  CA    0.020
 RYE  plan-6  N10   0.020
 RYE  plan-6  C11   0.020
 RYE  plan-6  O12   0.020
 RYE  plan-6  C13   0.020
 RYE  plan-6  HN10  0.020
 RYE  plan-7  C4    0.020
 RYE  plan-7  N5    0.020
 RYE  plan-7  C6    0.020
 RYE  plan-7  HN5   0.020
 RYE  plan-8  C     0.020
 RYE  plan-8  CA    0.020
 RYE  plan-8  OB    0.020
 RYE  plan-8  OA    0.020
 RYE  plan-9  C18   0.020
 RYE  plan-9  C21   0.020
 RYE  plan-9  O2A   0.020
 RYE  plan-9  O2B   0.020

