# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 22:28:25 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-methyl-N-phenyl-5,6-dihydro-1,4-oxathiine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(SCCO1)C(=O)Nc2ccccc2
#
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
 CBE  CBE  2-methyl-N-phenyl-5,6-dihydro-1,4-oxathiine-3-carboxamide  ligand  29  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CBE
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
 CBE  C1    C  CH3   0  -0.729  83.6967  98.7943  107.6115
 CBE  C2    C  C     0   0.461  83.2572  97.8853  106.5059
 CBE  C3    C  C     0  -0.433  83.8722  96.7403  106.1346
 CBE  S4    S  S2    0   0.058  83.2082  95.6299  104.9214
 CBE  C5    C  CH2   0  -0.607  81.5124  96.2364  104.9251
 CBE  C6    C  CH2   0  -0.179  81.5299  97.7444  104.8270
 CBE  O7    O  O2    0  -0.451  82.1214  98.3502  105.9669
 CBE  C8    C  C     0   0.524  85.1702  96.3334  106.7265
 CBE  O9    O  O     0  -0.463  86.0205  97.1381  107.0688
 CBE  N10   N  NH1   0  -0.753  85.3347  94.9858  106.8360
 CBE  C11   C  CR6   0   0.375  86.4490  94.2931  107.3209
 CBE  C12   C  CR16  0  -0.344  86.2291  93.0074  107.8204
 CBE  C13   C  CR16  0  -0.245  87.2841  92.2397  108.2848
 CBE  C14   C  CR16  0  -0.273  88.5789  92.7414  108.2651
 CBE  C15   C  CR16  0  -0.248  88.7979  94.0176  107.7665
 CBE  C16   C  CR16  0  -0.306  87.7504  94.7966  107.2937
 CBE  H11   H  HCH3  0   0.261  84.2824  99.6268  107.2181
 CBE  H12A  H  HCH3  0   0.253  82.8164  99.2138  108.0982
 CBE  H13A  H  HCH3  0   0.258  84.2960  98.2902  108.3612
 CBE  H51   H  HCH2  0   0.295  80.9843  95.8991  105.8175
 CBE  H52   H  HCH2  0   0.305  81.0208  95.8141  104.0497
 CBE  H61   H  HCH2  0   0.266  80.5134  98.1349  104.7875
 CBE  H62   H  HCH2  0   0.252  82.0551  98.0597  103.9228
 CBE  H10   H  HNH1  0   0.410  84.5122  94.4186  106.6835
 CBE  H12   H  HCR6  0   0.268  85.2217  92.6085  107.8474
 CBE  H13   H  HCR6  0   0.259  87.0877  91.2466  108.6674
 CBE  H14   H  HCR6  0   0.255  89.4053  92.1450  108.6284
 CBE  H15   H  HCR6  0   0.258  89.8023  94.4201  107.7352
 CBE  H16   H  HCR6  0   0.272  87.9608  95.7784  106.9014

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
 CBE  C1   C2    single    1.497  0.020  1.497
 CBE  C1   H11   single    0.970  0.020  1.090
 CBE  C1   H12A  single    0.970  0.020  1.090
 CBE  C1   H13A  single    0.970  0.020  1.090
 CBE  C2   C3    double    1.352  0.020  1.352
 CBE  C2   O7    single    1.340  0.020  1.340
 CBE  C3   S4    single    1.774  0.020  1.774
 CBE  C3   C8    single    1.483  0.020  1.483
 CBE  S4   C5    single    1.801  0.020  1.801
 CBE  C5   C6    single    1.511  0.020  1.511
 CBE  C5   H51   single    0.970  0.020  1.090
 CBE  C5   H52   single    0.970  0.020  1.090
 CBE  C6   O7    single    1.420  0.020  1.420
 CBE  C6   H61   single    0.970  0.020  1.090
 CBE  C6   H62   single    0.970  0.020  1.090
 CBE  C8   O9    double    1.220  0.020  1.220
 CBE  C8   N10   single    1.362  0.020  1.362
 CBE  N10  C11   single    1.399  0.020  1.399
 CBE  N10  H10   single    0.860  0.020  1.020
 CBE  C11  C12   aromatic  1.397  0.020  1.397
 CBE  C11  C16   aromatic  1.396  0.020  1.396
 CBE  C12  C13   aromatic  1.385  0.020  1.385
 CBE  C12  H12   single    0.930  0.020  1.080
 CBE  C13  C14   aromatic  1.389  0.020  1.389
 CBE  C13  H13   single    0.930  0.020  1.080
 CBE  C14  C15   aromatic  1.388  0.020  1.388
 CBE  C14  H14   single    0.930  0.020  1.080
 CBE  C15  C16   aromatic  1.388  0.020  1.388
 CBE  C15  H15   single    0.930  0.020  1.080
 CBE  C16  H16   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
 CBE  H13A  C1   H12A  108.46  3.000
 CBE  H13A  C1   H11   107.90  3.000
 CBE  H12A  C1   H11   107.51  3.000
 CBE  H13A  C1   C2    113.00  3.000
 CBE  H12A  C1   C2    109.05  3.000
 CBE  H11   C1   C2    110.76  3.000
 CBE  O7    C2   C3    124.67  3.000
 CBE  O7    C2   C1    109.58  3.000
 CBE  C3    C2   C1    125.70  3.000
 CBE  C8    C3   S4    115.39  3.000
 CBE  C8    C3   C2    121.39  3.000
 CBE  S4    C3   C2    123.22  3.000
 CBE  C5    S4   C3     98.06  3.000
 CBE  H52   C5   H51   108.62  3.000
 CBE  H52   C5   C6    109.87  3.000
 CBE  H51   C5   C6    111.56  3.000
 CBE  H52   C5   S4    107.02  3.000
 CBE  H51   C5   S4    110.70  3.000
 CBE  C6    C5   S4    108.96  3.000
 CBE  H62   C6   H61   108.37  3.000
 CBE  H62   C6   O7    109.95  3.000
 CBE  H61   C6   O7    105.36  3.000
 CBE  H62   C6   C5    110.32  3.000
 CBE  H61   C6   C5    110.43  3.000
 CBE  O7    C6   C5    112.24  3.000
 CBE  C6    O7   C2    121.86  3.000
 CBE  N10   C8   O9    123.09  3.000
 CBE  N10   C8   C3    114.15  3.000
 CBE  O9    C8   C3    122.75  3.000
 CBE  H10   N10  C11   115.00  3.000
 CBE  H10   N10  C8    116.42  3.000
 CBE  C11   N10  C8    127.88  3.000
 CBE  C16   C11  C12   119.07  3.000
 CBE  C16   C11  N10   123.88  3.000
 CBE  C12   C11  N10   117.03  3.000
 CBE  H12   C12  C13   119.72  3.000
 CBE  H12   C12  C11   119.60  3.000
 CBE  C13   C12  C11   120.68  3.000
 CBE  H13   C13  C14   120.38  3.000
 CBE  H13   C13  C12   119.27  3.000
 CBE  C14   C13  C12   120.34  3.000
 CBE  H14   C14  C15   120.47  3.000
 CBE  H14   C14  C13   120.54  3.000
 CBE  C15   C14  C13   118.99  3.000
 CBE  H15   C15  C16   118.78  3.000
 CBE  H15   C15  C14   119.93  3.000
 CBE  C16   C15  C14   121.29  3.000
 CBE  H16   C16  C15   119.19  3.000
 CBE  H16   C16  C11   121.17  3.000
 CBE  C15   C16  C11   119.63  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
 CBE  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 CBE  CONST_02  C14  C15  C16  C11    0.00   0.0  0
 CBE  CONST_03  C15  C16  C11  C12    0.00   0.0  0
 CBE  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 CBE  CONST_05  C16  C11  C12  C13    0.00   0.0  0
 CBE  CONST_06  C16  C15  C14  C13    0.00   0.0  0
 CBE  CONST_07  C13  C12  C11  N10  180.00   0.0  0
 CBE  CONST_08  C15  C16  C11  N10  180.00   0.0  0
 CBE  CONST_09  H13  C13  C12  C11  180.00   0.0  0
 CBE  CONST_10  H15  C15  C16  C11  180.00   0.0  0
 CBE  CONST_11  H16  C16  C11  C12  180.00   0.0  0
 CBE  CONST_12  H14  C14  C13  C12  180.00   0.0  0
 CBE  CONST_13  H12  C12  C13  C14  180.00   0.0  0
 CBE  CONST_14  C11  N10  C8   C3   180.00   0.0  0
 CBE  CONST_17  H10  N10  C11  C12    0.00   0.0  0
 CBE  CONST_18  C11  N10  C8   O9     0.00   0.0  0
 CBE  Var_01    C5   C6   O7   C2    44.36  30.0  1
 CBE  Var_02    C6   C5   S4   C3    47.69  30.0  1
 CBE  Var_03    O7   C2   C3   S4    -3.38  30.0  1
 CBE  Var_04    O7   C6   C5   S4   -65.00  30.0  1
 CBE  Var_05    C8   C3   S4   C5   162.97  30.0  1
 CBE  Var_06    O9   C8   C3   C2   -33.24  30.0  2
 CBE  Var_07    H11  C1   C2   C3    97.27  30.0  3

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
 CBE  plan-1  N10  0.020
 CBE  plan-1  C11  0.020
 CBE  plan-1  C12  0.020
 CBE  plan-1  C13  0.020
 CBE  plan-1  C14  0.020
 CBE  plan-1  C15  0.020
 CBE  plan-1  C16  0.020
 CBE  plan-1  H12  0.020
 CBE  plan-1  H13  0.020
 CBE  plan-1  H14  0.020
 CBE  plan-1  H15  0.020
 CBE  plan-1  H16  0.020
 CBE  plan-2  C3   0.020
 CBE  plan-2  C8   0.020
 CBE  plan-2  O9   0.020
 CBE  plan-2  N10  0.020
 CBE  plan-2  C11  0.020
 CBE  plan-2  H10  0.020

