# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:42:44 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  37  23  .  2021-08-03  2021-08-03  
;
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  OH1   0  -0.578  -0.4523   3.1530  -1.4561
 0A4  S1    S  S2    0   0.016  -3.1714   1.7071  -0.5526
 0A4  C2    C  CH2   0  -0.638  -4.5290   0.8873   0.3306
 0A4  C3    C  C     0   0.125  -4.4661  -0.5817   0.0629
 0A4  C3'   C  C2    0  -0.535  -5.5111  -1.2559  -0.4177
 0A4  C4    C  C     0   0.161  -3.1568  -1.2133   0.3044
 0A4  C4'   C  C     0   0.499  -3.1002  -2.7054   0.5415
 0A4  O4A   O  OH1   0  -0.569  -2.0216  -3.2511   0.0196
 0A4  O4B   O  O     0  -0.417  -3.9376  -3.2970   1.1708
 0A4  N5    N  N     0  -0.344  -2.0438  -0.6213   0.4254
 0A4  C6    C  CH1   0  -0.274  -1.8604   0.7916   0.3206
 0A4  C7    C  CH1   0  -0.128  -0.5171   1.0500  -0.3876
 0A4  C8    C  C     0   0.529  -0.2186   2.5438  -0.3073
 0A4  O9    O  O     0  -0.428   0.1205   3.0961   0.7051
 0A4  N10   N  NH1   0  -0.657   0.5050   0.3047   0.2935
 0A4  C11   C  C     0   0.579   1.8034   0.4609  -0.0215
 0A4  O12   O  O     0  -0.473   2.1802   1.3055  -0.8154
 0A4  C13   C  CH2   0  -0.674   2.7408  -0.4863   0.7085
 0A4  C14   C  CR5   0  -0.117   4.1741  -0.2876   0.3631
 0A4  C15   C  CR15  0  -0.237   5.1590   0.2260   1.1523
 0A4  C16   C  CR15  0  -0.184   6.4262   0.2710   0.5073
 0A4  C17   C  CR15  0  -0.471   6.3797  -0.2104  -0.7643
 0A4  S19   S  S2    0   0.208   4.7966  -0.7183  -1.1831
 0A4  H2C1  H  HCH2  0   0.304  -4.4446   1.1066   1.3970
 0A4  H2C2  H  HCH2  0   0.312  -5.4606   1.3184  -0.0320
 0A4  H6    H  HCH1  0   0.322  -1.7812   1.1770   1.3439
 0A4  H3'1  H  H     0   0.272  -6.4433  -0.7450  -0.6203
 0A4  H3'2  H  H     0   0.268  -5.4874  -2.3135  -0.6365
 0A4  H4A   H  HOH1  0   0.492  -1.9904  -4.1968   0.2333
 0A4  H7    H  HCH1  0   0.302  -0.6051   0.7432  -1.4348
 0A4  H10   H  HNH1  0   0.413   0.2064  -0.5019   0.8230
 0A4  H131  H  HCH2  0   0.309   2.6123  -0.3387   1.7837
 0A4  H132  H  HCH2  0   0.302   2.4242  -1.5145   0.5079
 0A4  H151  H  HCR5  0   0.263   4.9829   0.5588   2.1662
 0A4  H16   H  HCR5  0   0.265   7.3286   0.6413   0.9721
 0A4  H17   H  HCR5  0   0.294   7.1867  -0.2947  -1.4754
 0A4  H14   H  HOH1  0   0.487  -0.3242   4.1096  -1.3616

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    single    1.321  0.020  1.321
 0A4  S1   C2    single    1.815  0.020  1.815
 0A4  S1   C6    single    1.822  0.020  1.822
 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    1.333  0.020  1.333
 0A4  C3   C4    single    1.474  0.020  1.474
 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    1.512  0.020  1.512
 0A4  C4   N5    double    1.266  0.020  1.266
 0A4  C4'  O4A   single    1.317  0.020  1.317
 0A4  C4'  O4B   double    1.203  0.020  1.203
 0A4  O4A  H4A   single    0.850  0.020  0.980
 0A4  N5   C6    single    1.429  0.020  1.429
 0A4  C6   C7    single    1.540  0.020  1.540
 0A4  C6   H6    single    0.970  0.020  1.090
 0A4  C7   C8    single    1.525  0.020  1.525
 0A4  C7   N10   single    1.437  0.020  1.437
 0A4  C7   H7    single    0.970  0.020  1.090
 0A4  C8   O9    double    1.202  0.020  1.202
 0A4  N10  C11   single    1.345  0.020  1.345
 0A4  N10  H10   single    0.860  0.020  1.020
 0A4  C11  O12   double    1.219  0.020  1.219
 0A4  C11  C13   single    1.519  0.020  1.519
 0A4  C13  C14   single    1.488  0.020  1.488
 0A4  C13  H131  single    0.970  0.020  1.090
 0A4  C13  H132  single    0.970  0.020  1.090
 0A4  C14  C15   aromatic  1.363  0.020  1.363
 0A4  C14  S19   aromatic  1.722  0.020  1.722
 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  1.715  0.020  1.715
 0A4  C17  H17   single    0.930  0.020  1.080
 0A4  OG   H14   single    0.850  0.020  0.980

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  H14   OG   C8    110.29  3.000
 0A4  C6    S1   C2     94.48  3.000
 0A4  H2C2  C2   H2C1  108.17  3.000
 0A4  H2C2  C2   C3    111.45  3.000
 0A4  H2C1  C2   C3    111.66  3.000
 0A4  H2C2  C2   S1    107.40  3.000
 0A4  H2C1  C2   S1    109.06  3.000
 0A4  C3    C2   S1    108.98  3.000
 0A4  C4    C3   C3'   122.60  3.000
 0A4  C4    C3   C2    115.43  3.000
 0A4  C3'   C3   C2    121.91  3.000
 0A4  H3'2  C3'  H3'1  116.31  3.000
 0A4  H3'2  C3'  C3    123.43  3.000
 0A4  H3'1  C3'  C3    120.26  3.000
 0A4  N5    C4   C4'   114.42  3.000
 0A4  N5    C4   C3    126.59  3.000
 0A4  C4'   C4   C3    118.82  3.000
 0A4  O4B   C4'  O4A   125.01  3.000
 0A4  O4B   C4'  C4    122.77  3.000
 0A4  O4A   C4'  C4    112.19  3.000
 0A4  H4A   O4A  C4'   110.07  3.000
 0A4  C6    N5   C4    124.62  3.000
 0A4  H6    C6   C7    107.89  3.000
 0A4  H6    C6   N5    106.77  3.000
 0A4  C7    C6   N5    108.16  3.000
 0A4  H6    C6   S1    108.82  3.000
 0A4  C7    C6   S1    108.83  3.000
 0A4  N5    C6   S1    116.09  3.000
 0A4  H7    C7   N10   111.42  3.000
 0A4  H7    C7   C8    109.91  3.000
 0A4  N10   C7   C8    110.11  3.000
 0A4  H7    C7   C6    108.83  3.000
 0A4  N10   C7   C6    108.38  3.000
 0A4  C8    C7   C6    108.11  3.000
 0A4  O9    C8   C7    123.33  3.000
 0A4  O9    C8   OG    124.78  3.000
 0A4  C7    C8   OG    111.78  3.000
 0A4  H10   N10  C11   120.05  3.000
 0A4  H10   N10  C7    116.91  3.000
 0A4  C11   N10  C7    121.03  3.000
 0A4  C13   C11  O12   123.65  3.000
 0A4  C13   C11  N10   114.24  3.000
 0A4  O12   C11  N10   122.10  3.000
 0A4  H132  C13  H131  105.86  3.000
 0A4  H132  C13  C14   111.20  3.000
 0A4  H131  C13  C14   108.88  3.000
 0A4  H132  C13  C11   108.61  3.000
 0A4  H131  C13  C11   108.42  3.000
 0A4  C14   C13  C11   113.55  3.000
 0A4  S19   C14  C15   110.68  3.000
 0A4  S19   C14  C13   121.57  3.000
 0A4  C15   C14  C13   127.76  3.000
 0A4  H151  C15  C16   124.07  3.000
 0A4  H151  C15  C14   122.77  3.000
 0A4  C16   C15  C14   113.16  3.000
 0A4  H16   C16  C17   123.49  3.000
 0A4  H16   C16  C15   124.05  3.000
 0A4  C17   C16  C15   112.47  3.000
 0A4  H17   C17  S19   120.43  3.000
 0A4  H17   C17  C16   128.18  3.000
 0A4  S19   C17  C16   111.39  3.000
 0A4  C17   S19  C14    92.31  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  H4A   O4A  C4'  C4    180.00   0.0  0
 0A4  CONST_12  O12   C11  N10  C7      0.00   0.0  0
 0A4  CONST_13  C13   C11  N10  C7    180.00   0.0  0
 0A4  CONST_14  H10   N10  C11  O12   180.00   0.0  0
 0A4  CONST_15  H14   OG   C8   C7    180.00   0.0  0
 0A4  Var_01    C4    C3   C2   S1     51.57  30.0  1
 0A4  Var_02    N5    C4   C3   C2    -16.43  30.0  1
 0A4  Var_03    O4A   C4'  C4   C3    144.26  30.0  2
 0A4  Var_04    C15   C14  C13  C11   109.72  30.0  2
 0A4  Var_05    H3'1  C3'  C3   C2     -0.43  30.0  2
 0A4  Var_06    C14   C13  C11  N10  -179.19  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-3  H4A   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
 0A4  plan-4  H14   0.020

