# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:28:40 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (2R)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](NC(=O)Cc1sccc1)[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
 0A4  0A4  '(2R)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  35  23  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0A4
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
 0A4  OG    O  OC    -1  -0.596  -0.6934   3.5202  -1.0737
 0A4  S1    S  S2     0  -0.011  -3.1795   1.6939  -0.5879
 0A4  C2    C  CH2    0  -0.638  -4.5164   0.6522   0.0583
 0A4  C3    C  C      0   0.111  -4.2276  -0.7754  -0.2748
 0A4  C3'   C  C2     0  -0.560  -5.1277  -1.5595  -0.8695
 0A4  C4    C  C      0   0.139  -2.8929  -1.2726   0.1250
 0A4  C4'   C  C      0   0.366  -2.6776  -2.7793   0.2239
 0A4  O4A   O  OC    -1  -0.598  -2.4931  -3.3631  -0.8578
 0A4  O4B   O  O      0  -0.587  -2.7014  -3.2560   1.3693
 0A4  N5    N  N      0  -0.391  -1.9032  -0.5440   0.4504
 0A4  C6    C  CH1    0  -0.263  -1.8660   0.8859   0.3947
 0A4  C7    C  CH1    0  -0.125  -0.5085   1.3381  -0.1631
 0A4  C8    C  C      0   0.406  -0.4159   2.8829  -0.0421
 0A4  O9    O  O      0  -0.600  -0.1416   3.3322   1.0827
 0A4  N10   N  NH1    0  -0.645   0.5178   0.6579   0.5887
 0A4  C11   C  C      0   0.557   1.8185   0.9100   0.4133
 0A4  O12   O  O      0  -0.490   2.2445   1.7537  -0.3608
 0A4  C13   C  CH2    0  -0.670   2.7534   0.0787   1.2836
 0A4  C14   C  CR5    0  -0.114   4.0071  -0.2946   0.5710
 0A4  C15   C  CR15   0  -0.241   5.2413   0.2700   0.6800
 0A4  C16   C  CR15   0  -0.183   6.2057  -0.3208  -0.1840
 0A4  C17   C  CR15   0  -0.472   5.6843  -1.3242  -0.9398
 0A4  S19   S  S2     0   0.206   4.0188  -1.5583  -0.6018
 0A4  H2C1  H  HCH2   0   0.285  -4.5992   0.8012   1.1378
 0A4  H2C2  H  HCH2   0   0.294  -5.4471   0.9887  -0.3970
 0A4  H6    H  HCH1   0   0.282  -1.9443   1.2526   1.4255
 0A4  H3'1  H  H      0   0.254  -6.1075  -1.1809  -1.1311
 0A4  H3'2  H  H      0   0.254  -4.9168  -2.5868  -1.1310
 0A4  H7    H  HCH1   0   0.236  -0.4568   1.0486  -1.2189
 0A4  H10   H  HNH1   0   0.393   0.2384  -0.1652   1.1018
 0A4  H131  H  HCH2   0   0.300   3.0171   0.6899   2.1511
 0A4  H132  H  HCH2   0   0.282   2.2434  -0.8041   1.6739
 0A4  H151  H  HCR5   0   0.261   5.4543   1.0850   1.3585
 0A4  H16   H  HCR5   0   0.264   7.2398  -0.0119  -0.2373
 0A4  H17   H  HCR5   0   0.293   6.1870  -1.9409  -1.6687

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
 0A4  OG   C8    deloc     1.244  0.020  1.244
 0A4  S1   C2    single    1.814  0.020  1.814
 0A4  S1   C6    single    1.829  0.020  1.829
 0A4  C2   C3    single    1.494  0.020  1.494
 0A4  C2   H2C1  single    0.970  0.020  1.090
 0A4  C2   H2C2  single    0.970  0.020  1.090
 0A4  C3   C3'   double    1.334  0.020  1.334
 0A4  C3   C4    single    1.479  0.020  1.479
 0A4  C3'  H3'1  single    0.930  0.020  1.080
 0A4  C3'  H3'2  single    0.930  0.020  1.080
 0A4  C4   C4'   single    1.525  0.020  1.525
 0A4  C4   N5    double    1.271  0.020  1.271
 0A4  C4'  O4A   deloc     1.243  0.020  1.243
 0A4  C4'  O4B   deloc     1.241  0.020  1.241
 0A4  N5   C6    single    1.432  0.020  1.432
 0A4  C6   C7    single    1.536  0.020  1.536
 0A4  C6   H6    single    0.970  0.020  1.090
 0A4  C7   C8    single    1.552  0.020  1.552
 0A4  C7   N10   single    1.443  0.020  1.443
 0A4  C7   H7    single    0.970  0.020  1.090
 0A4  C8   O9    deloc     1.242  0.020  1.242
 0A4  N10  C11   single    1.336  0.020  1.336
 0A4  N10  H10   single    0.860  0.020  1.020
 0A4  C11  O12   double    1.222  0.020  1.222
 0A4  C11  C13   single    1.524  0.020  1.524
 0A4  C13  C14   single    1.490  0.020  1.490
 0A4  C13  H131  single    0.970  0.020  1.090
 0A4  C13  H132  single    0.970  0.020  1.090
 0A4  C14  C15   aromatic  1.362  0.020  1.362
 0A4  C14  S19   aromatic  1.724  0.020  1.724
 0A4  C15  C16   aromatic  1.423  0.020  1.423
 0A4  C15  H151  single    0.930  0.020  1.080
 0A4  C16  C17   aromatic  1.360  0.020  1.360
 0A4  C16  H16   single    0.930  0.020  1.080
 0A4  C17  S19   aromatic  1.716  0.020  1.716
 0A4  C17  H17   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
 0A4  C6    S1   C2     94.83  3.000
 0A4  H2C2  C2   H2C1  107.82  3.000
 0A4  H2C2  C2   C3    111.54  3.000
 0A4  H2C1  C2   C3    111.42  3.000
 0A4  H2C2  C2   S1    107.65  3.000
 0A4  H2C1  C2   S1    109.23  3.000
 0A4  C3    C2   S1    109.08  3.000
 0A4  C4    C3   C3'   122.13  3.000
 0A4  C4    C3   C2    115.81  3.000
 0A4  C3'   C3   C2    122.05  3.000
 0A4  H3'2  C3'  H3'1  116.78  3.000
 0A4  H3'2  C3'  C3    122.35  3.000
 0A4  H3'1  C3'  C3    120.87  3.000
 0A4  N5    C4   C4'   116.08  3.000
 0A4  N5    C4   C3    125.37  3.000
 0A4  C4'   C4   C3    118.48  3.000
 0A4  O4B   C4'  O4A   128.74  3.000
 0A4  O4B   C4'  C4    115.89  3.000
 0A4  O4A   C4'  C4    115.37  3.000
 0A4  C6    N5   C4    125.65  3.000
 0A4  H6    C6   C7    107.82  3.000
 0A4  H6    C6   N5    107.19  3.000
 0A4  C7    C6   N5    109.34  3.000
 0A4  H6    C6   S1    107.82  3.000
 0A4  C7    C6   S1    108.04  3.000
 0A4  N5    C6   S1    116.33  3.000
 0A4  H7    C7   N10   110.12  3.000
 0A4  H7    C7   C8    109.58  3.000
 0A4  N10   C7   C8    112.72  3.000
 0A4  H7    C7   C6    108.29  3.000
 0A4  N10   C7   C6    107.50  3.000
 0A4  C8    C7   C6    108.51  3.000
 0A4  O9    C8   C7    116.35  3.000
 0A4  O9    C8   OG    127.95  3.000
 0A4  C7    C8   OG    115.59  3.000
 0A4  H10   N10  C11   119.34  3.000
 0A4  H10   N10  C7    116.90  3.000
 0A4  C11   N10  C7    122.35  3.000
 0A4  C13   C11  O12   121.65  3.000
 0A4  C13   C11  N10   114.79  3.000
 0A4  O12   C11  N10   123.55  3.000
 0A4  H132  C13  H131  106.32  3.000
 0A4  H132  C13  C14   111.19  3.000
 0A4  H131  C13  C14   108.46  3.000
 0A4  H132  C13  C11   111.02  3.000
 0A4  H131  C13  C11   107.23  3.000
 0A4  C14   C13  C11   112.32  3.000
 0A4  S19   C14  C15   110.62  3.000
 0A4  S19   C14  C13   120.99  3.000
 0A4  C15   C14  C13   128.37  3.000
 0A4  H151  C15  C16   124.06  3.000
 0A4  H151  C15  C14   122.76  3.000
 0A4  C16   C15  C14   113.17  3.000
 0A4  H16   C16  C17   123.39  3.000
 0A4  H16   C16  C15   124.04  3.000
 0A4  C17   C16  C15   112.57  3.000
 0A4  H17   C17  S19   120.49  3.000
 0A4  H17   C17  C16   128.20  3.000
 0A4  S19   C17  C16   111.30  3.000
 0A4  C17   S19  C14    92.33  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
 0A4  CONST_01  C17   C16  C15  C14    0.00   0.0  0
 0A4  CONST_02  C16   C17  S19  C14    0.00   0.0  0
 0A4  CONST_03  C17   S19  C14  C15    0.00   0.0  0
 0A4  CONST_04  S19   C17  C16  C15    0.00   0.0  0
 0A4  CONST_05  S19   C14  C15  C16    0.00   0.0  0
 0A4  CONST_06  C16   C15  C14  C13  180.00   0.0  0
 0A4  CONST_07  C17   S19  C14  C13  180.00   0.0  0
 0A4  CONST_08  H16   C16  C15  C14  180.00   0.0  0
 0A4  CONST_09  H17   C17  S19  C14  180.00   0.0  0
 0A4  CONST_10  H151  C15  C16  C17  180.00   0.0  0
 0A4  CONST_11  O12   C11  N10  C7     0.00   0.0  0
 0A4  CONST_12  C13   C11  N10  C7   180.00   0.0  0
 0A4  CONST_13  H10   N10  C11  O12  180.00   0.0  0
 0A4  Var_01    C4    C3   C2   S1    52.50  30.0  1
 0A4  Var_02    N5    C4   C3   C2   -15.86  30.0  1
 0A4  Var_03    O4A   C4'  C4   C3    79.28  30.0  2
 0A4  Var_04    C15   C14  C13  C11  101.12  30.0  2
 0A4  Var_05    H3'1  C3'  C3   C2    -0.07  30.0  2
 0A4  Var_06    C14   C13  C11  N10  143.53  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
 0A4  chir_01  C6  S1   N5  C7  negativ
 0A4  chir_02  C7  N10  C6  C8  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
 0A4  plan-1  C13   0.020
 0A4  plan-1  C14   0.020
 0A4  plan-1  C15   0.020
 0A4  plan-1  C16   0.020
 0A4  plan-1  C17   0.020
 0A4  plan-1  S19   0.020
 0A4  plan-1  H151  0.020
 0A4  plan-1  H16   0.020
 0A4  plan-1  H17   0.020
 0A4  plan-2  C7    0.020
 0A4  plan-2  N10   0.020
 0A4  plan-2  C11   0.020
 0A4  plan-2  O12   0.020
 0A4  plan-2  C13   0.020
 0A4  plan-2  H10   0.020
 0A4  plan-3  C4    0.020
 0A4  plan-3  C4'   0.020
 0A4  plan-3  O4A   0.020
 0A4  plan-3  O4B   0.020
 0A4  plan-4  OG    0.020
 0A4  plan-4  C7    0.020
 0A4  plan-4  C8    0.020
 0A4  plan-4  O9    0.020

