# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:33:07 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)SC(=CN[C@H]1C(O)=O)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
 BIY  BIY  '(3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid'  ligand  23  14  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BIY
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
 BIY  O14   O  O      0  -0.621  -3.0657  -0.6984   1.3064
 BIY  C12   C  C      0   0.384  -2.8041  -0.0944   0.2418
 BIY  C3    C  C      0  -0.379  -1.3642  -0.0765  -0.1552
 BIY  C2    C  C1     0   0.033  -0.9058   0.5928  -1.2289
 BIY  N1    N  NH1    0  -0.605   0.3765   0.6437  -1.6729
 BIY  S4    S  S2     0  -0.002  -0.2691  -0.9314   0.9300
 BIY  C5    C  CT     0  -0.249   1.1903  -1.0905  -0.1644
 BIY  C11   C  CH3    0  -0.607   0.9058  -2.1465  -1.2313
 BIY  C10   C  CH3    0  -0.626   2.3368  -1.5730   0.7174
 BIY  C6    C  CH1    0  -0.141   1.4946   0.2650  -0.8427
 BIY  C7    C  C      0   0.410   1.9247   1.3784   0.1480
 BIY  O9    O  O      0  -0.583   1.0727   2.2225   0.4671
 BIY  O8    O  OC    -1  -0.618   3.1147   1.3338   0.5265
 BIY  OXT   O  OC    -1  -0.618  -3.6275   0.4968  -0.4923
 BIY  H1    H  HNH1   0   0.375   0.5694   1.3480  -2.3637
 BIY  H2    H  H      0   0.252  -1.6265   1.0977  -1.8610
 BIY  H6    H  HCH1   0   0.229   2.3398   0.0835  -1.5173
 BIY  H111  H  HCH3   0   0.239   0.0105  -1.9214  -1.8083
 BIY  H112  H  HCH3   0   0.217   1.7457  -2.2195  -1.9283
 BIY  H113  H  HCH3   0   0.223   0.7689  -3.1246  -0.7686
 BIY  H101  H  HCH3   0   0.221   2.1053  -2.5608   1.1202
 BIY  H102  H  HCH3   0   0.226   3.2539  -1.6590   0.1319
 BIY  H103  H  HCH3   0   0.237   2.5344  -0.9038   1.5503

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
 BIY  O14  C12   deloc   1.252  0.020  1.252
 BIY  C12  C3    single  1.494  0.020  1.494
 BIY  C3   C2    double  1.346  0.020  1.346
 BIY  C2   N1    single  1.358  0.020  1.358
 BIY  C3   S4    single  1.763  0.020  1.763
 BIY  S4   C5    single  1.831  0.020  1.831
 BIY  C5   C11   single  1.528  0.020  1.528
 BIY  C5   C10   single  1.525  0.020  1.525
 BIY  N1   C6    single  1.443  0.020  1.443
 BIY  C5   C6    single  1.546  0.020  1.546
 BIY  C6   C7    single  1.551  0.020  1.551
 BIY  C7   O9    deloc   1.241  0.020  1.241
 BIY  C7   O8    deloc   1.250  0.020  1.250
 BIY  C12  OXT   deloc   1.252  0.020  1.252
 BIY  N1   H1    single  0.890  0.020  1.040
 BIY  C2   H2    single  0.930  0.020  1.080
 BIY  C6   H6    single  0.970  0.020  1.090
 BIY  C11  H111  single  0.970  0.020  1.090
 BIY  C11  H112  single  0.970  0.020  1.090
 BIY  C11  H113  single  0.970  0.020  1.090
 BIY  C10  H101  single  0.970  0.020  1.090
 BIY  C10  H102  single  0.970  0.020  1.090
 BIY  C10  H103  single  0.970  0.020  1.090

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
 BIY  OXT   C12  C3    118.21  3.000
 BIY  OXT   C12  O14   126.11  3.000
 BIY  C3    C12  O14   115.67  3.000
 BIY  S4    C3   C2    121.38  3.000
 BIY  S4    C3   C12   115.43  3.000
 BIY  C2    C3   C12   123.12  3.000
 BIY  H2    C2   N1    114.82  3.000
 BIY  H2    C2   C3    118.08  3.000
 BIY  N1    C2   C3    126.96  3.000
 BIY  H1    N1   C6    115.50  3.000
 BIY  H1    N1   C2    115.61  3.000
 BIY  C6    N1   C2    122.25  3.000
 BIY  C5    S4   C3     99.75  3.000
 BIY  C6    C5   C10   112.53  3.000
 BIY  C6    C5   C11   109.65  3.000
 BIY  C10   C5   C11   108.97  3.000
 BIY  C6    C5   S4    110.06  3.000
 BIY  C10   C5   S4    106.33  3.000
 BIY  C11   C5   S4    109.21  3.000
 BIY  H113  C11  H112  107.87  3.000
 BIY  H113  C11  H111  107.88  3.000
 BIY  H112  C11  H111  107.91  3.000
 BIY  H113  C11  C5    110.30  3.000
 BIY  H112  C11  C5    110.37  3.000
 BIY  H111  C11  C5    112.35  3.000
 BIY  H103  C10  H102  107.87  3.000
 BIY  H103  C10  H101  108.25  3.000
 BIY  H102  C10  H101  107.75  3.000
 BIY  H103  C10  C5    112.65  3.000
 BIY  H102  C10  C5    110.28  3.000
 BIY  H101  C10  C5    109.90  3.000
 BIY  H6    C6   C7    107.34  3.000
 BIY  H6    C6   C5    106.05  3.000
 BIY  C7    C6   C5    113.81  3.000
 BIY  H6    C6   N1    106.66  3.000
 BIY  C7    C6   N1    113.19  3.000
 BIY  C5    C6   N1    109.27  3.000
 BIY  O8    C7   O9    126.88  3.000
 BIY  O8    C7   C6    115.59  3.000
 BIY  O9    C7   C6    117.52  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
 BIY  Var_01  C6    N1   C2   C3    -16.96  30.0  1
 BIY  Var_02  C6    C5   S4   C3     47.03  30.0  1
 BIY  Var_03  S4    C3   C2   N1      4.40  30.0  1
 BIY  Var_04  C2    C3   C12  O14  -176.11  30.0  2
 BIY  Var_05  H111  C11  C5   S4     56.52  30.0  3
 BIY  Var_06  H101  C10  C5   S4     63.22  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
 BIY  chir_01  C6  N1  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
 BIY  plan-1  C2   0.020
 BIY  plan-1  N1   0.020
 BIY  plan-1  C6   0.020
 BIY  plan-1  H1   0.020
 BIY  plan-2  O14  0.020
 BIY  plan-2  C12  0.020
 BIY  plan-2  C3   0.020
 BIY  plan-2  OXT  0.020
 BIY  plan-3  C6   0.020
 BIY  plan-3  C7   0.020
 BIY  plan-3  O9   0.020
 BIY  plan-3  O8   0.020

