# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 23:50:45 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2R)-5-methyl-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N[C@H](SC1)[C@H](NC(=O)Cc2sccc2)C=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
 CED  CED  '(2R)-5-methyl-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  38  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CED
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
 CED  S1    S  S2    0   0.010  -1.9785  -1.7650   0.6240
 CED  C2    C  CH2   0  -0.625  -3.4479  -2.0425  -0.3866
 CED  C3    C  C     0   0.067  -4.3653  -0.8583  -0.4999
 CED  C3'   C  CH3   0  -0.710  -5.7469  -1.2563  -0.9404
 CED  C4    C  C     0   0.167  -3.9537   0.3993  -0.2382
 CED  C4'   C  C     0   0.511  -4.9119   1.5395  -0.2756
 CED  O4A   O  O     0  -0.426  -6.1139   1.4438  -0.2779
 CED  O4B   O  OH1   0  -0.607  -4.2861   2.7123  -0.2947
 CED  N5    N  NH1   0  -0.672  -2.6565   0.7580   0.1428
 CED  C6    C  CH1   0  -0.222  -1.5775  -0.1478  -0.1055
 CED  C7    C  CH1   0  -0.219  -0.3014   0.3833   0.5511
 CED  C8    C  C1    0   0.186  -0.4508   0.4288   2.0639
 CED  O9    O  O     0  -0.358   0.3594  -0.0333   2.8216
 CED  N10   N  NH1   0  -0.639   0.8386  -0.3772   0.1353
 CED  C11   C  C     0   0.571   2.0889   0.1272   0.1790
 CED  O12   O  O     0  -0.470   2.3251   1.2861   0.4651
 CED  C13   C  CH2   0  -0.679   3.1691  -0.8773  -0.1914
 CED  C14   C  CR5   0  -0.117   4.5462  -0.3182  -0.1324
 CED  C15   C  CR15  0  -0.238   5.5374  -0.6366   0.7469
 CED  C16   C  CR15  0  -0.185   6.7417   0.0855   0.5189
 CED  C17   C  CR15  0  -0.471   6.6429   0.9423  -0.5332
 CED  S19   S  S2    0   0.208   5.0866   0.8760  -1.2492
 CED  H21   H  HCH2  0   0.301  -3.1571  -2.3979  -1.3791
 CED  H22   H  HCH2  0   0.305  -3.9841  -2.8657   0.0913
 CED  H3'1  H  HCH3  0   0.242  -5.7019  -2.2405  -1.4088
 CED  H3'2  H  HCH3  0   0.250  -6.4357  -1.3350  -0.0973
 CED  H3'3  H  HCH3  0   0.249  -6.1859  -0.5718  -1.6613
 CED  HO4   H  HOH1  0   0.492  -4.9301   3.4361  -0.2889
 CED  HN5   H  HNH1  0   0.396  -2.4200   1.7106  -0.0955
 CED  H6    H  HCH1  0   0.305  -1.3907  -0.3015  -1.1762
 CED  H7    H  HCH1  0   0.320  -0.1769   1.4229   0.2215
 CED  H8    H  H     0   0.219  -1.3551   0.9467   2.4207
 CED  HN1   H  HNH1  0   0.409   0.7196  -1.3677  -0.0200
 CED  H131  H  HCH2  0   0.306   3.1057  -1.7266   0.4941
 CED  H132  H  HCH2  0   0.304   2.9438  -1.2771  -1.1850
 CED  H15   H  HCR5  0   0.262   5.4113  -1.3682   1.5332
 CED  H16   H  HCR5  0   0.265   7.6376  -0.0298   1.1120
 CED  H17   H  HCR5  0   0.293   7.3963   1.6095  -0.9224

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
 CED  S1   C2    single    1.805  0.020  1.805
 CED  S1   C6    single    1.819  0.020  1.819
 CED  C2   C3    single    1.502  0.020  1.502
 CED  C2   H21   single    0.970  0.020  1.090
 CED  C2   H22   single    0.970  0.020  1.090
 CED  C3   C3'   single    1.504  0.020  1.504
 CED  C3   C4    double    1.349  0.020  1.349
 CED  C3'  H3'1  single    0.970  0.020  1.090
 CED  C3'  H3'2  single    0.970  0.020  1.090
 CED  C3'  H3'3  single    0.970  0.020  1.090
 CED  C4   C4'   single    1.490  0.020  1.490
 CED  C4   N5    single    1.399  0.020  1.399
 CED  C4'  O4A   double    1.206  0.020  1.206
 CED  C4'  O4B   single    1.329  0.020  1.329
 CED  O4B  HO4   single    0.850  0.020  0.980
 CED  N5   C6    single    1.431  0.020  1.431
 CED  N5   HN5   single    0.890  0.020  1.040
 CED  C6   C7    single    1.530  0.020  1.530
 CED  C6   H6    single    0.970  0.020  1.090
 CED  C7   C8    single    1.521  0.020  1.521
 CED  C7   N10   single    1.432  0.020  1.432
 CED  C7   H7    single    0.970  0.020  1.090
 CED  C8   O9    double    1.202  0.020  1.202
 CED  C8   H8    single    0.930  0.020  1.080
 CED  N10  C11   single    1.349  0.020  1.349
 CED  N10  HN1   single    0.860  0.020  1.020
 CED  C11  O12   double    1.217  0.020  1.217
 CED  C11  C13   single    1.521  0.020  1.521
 CED  C13  C14   single    1.487  0.020  1.487
 CED  C13  H131  single    0.970  0.020  1.090
 CED  C13  H132  single    0.970  0.020  1.090
 CED  C14  C15   aromatic  1.363  0.020  1.363
 CED  C14  S19   aromatic  1.722  0.020  1.722
 CED  C15  C16   aromatic  1.423  0.020  1.423
 CED  C15  H15   single    0.930  0.020  1.080
 CED  C16  C17   aromatic  1.360  0.020  1.360
 CED  C16  H16   single    0.930  0.020  1.080
 CED  C17  S19   aromatic  1.714  0.020  1.714
 CED  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
 CED  C6    S1   C2     95.26  3.000
 CED  H22   C2   H21   106.42  3.000
 CED  H22   C2   C3    109.10  3.000
 CED  H21   C2   C3    110.49  3.000
 CED  H22   C2   S1    105.70  3.000
 CED  H21   C2   S1    109.98  3.000
 CED  C3    C2   S1    114.72  3.000
 CED  C4    C3   C3'   125.73  3.000
 CED  C4    C3   C2    122.28  3.000
 CED  C3'   C3   C2    111.99  3.000
 CED  H3'3  C3'  H3'2  107.63  3.000
 CED  H3'3  C3'  H3'1  107.46  3.000
 CED  H3'2  C3'  H3'1  107.02  3.000
 CED  H3'3  C3'  C3    113.50  3.000
 CED  H3'2  C3'  C3    111.87  3.000
 CED  H3'1  C3'  C3    109.07  3.000
 CED  N5    C4   C4'   114.02  3.000
 CED  N5    C4   C3    125.09  3.000
 CED  C4'   C4   C3    120.83  3.000
 CED  O4B   C4'  O4A   122.64  3.000
 CED  O4B   C4'  C4    111.88  3.000
 CED  O4A   C4'  C4    125.48  3.000
 CED  HO4   O4B  C4'   110.24  3.000
 CED  HN5   N5   C6    112.32  3.000
 CED  HN5   N5   C4    113.24  3.000
 CED  C6    N5   C4    119.33  3.000
 CED  H6    C6   C7    108.98  3.000
 CED  H6    C6   N5    112.72  3.000
 CED  C7    C6   N5    109.55  3.000
 CED  H6    C6   S1    107.72  3.000
 CED  C7    C6   S1    108.69  3.000
 CED  N5    C6   S1    109.09  3.000
 CED  H7    C7   N10   109.00  3.000
 CED  H7    C7   C8    106.35  3.000
 CED  N10   C7   C8    112.51  3.000
 CED  H7    C7   C6    107.13  3.000
 CED  N10   C7   C6    110.79  3.000
 CED  C8    C7   C6    110.81  3.000
 CED  H8    C8   O9    122.01  3.000
 CED  H8    C8   C7    114.64  3.000
 CED  O9    C8   C7    123.33  3.000
 CED  HN1   N10  C11   118.75  3.000
 CED  HN1   N10  C7    118.15  3.000
 CED  C11   N10  C7    122.00  3.000
 CED  C13   C11  O12   123.26  3.000
 CED  C13   C11  N10   113.79  3.000
 CED  O12   C11  N10   122.93  3.000
 CED  H132  C13  H131  105.88  3.000
 CED  H132  C13  C14   111.34  3.000
 CED  H131  C13  C14   108.71  3.000
 CED  H132  C13  C11   108.43  3.000
 CED  H131  C13  C11   108.61  3.000
 CED  C14   C13  C11   113.55  3.000
 CED  S19   C14  C15   110.63  3.000
 CED  S19   C14  C13   121.70  3.000
 CED  C15   C14  C13   127.67  3.000
 CED  H15   C15  C16   123.96  3.000
 CED  H15   C15  C14   122.85  3.000
 CED  C16   C15  C14   113.19  3.000
 CED  H16   C16  C17   123.50  3.000
 CED  H16   C16  C15   124.04  3.000
 CED  C17   C16  C15   112.47  3.000
 CED  H17   C17  S19   120.47  3.000
 CED  H17   C17  C16   128.15  3.000
 CED  S19   C17  C16   111.38  3.000
 CED  C17   S19  C14    92.34  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
 CED  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 CED  CONST_02  C16   C17  S19  C14     0.00   0.0  0
 CED  CONST_03  C17   S19  C14  C15     0.00   0.0  0
 CED  CONST_04  S19   C17  C16  C15     0.00   0.0  0
 CED  CONST_05  S19   C14  C15  C16     0.00   0.0  0
 CED  CONST_06  C16   C15  C14  C13   180.00   0.0  0
 CED  CONST_07  C17   S19  C14  C13   180.00   0.0  0
 CED  CONST_08  H16   C16  C15  C14   180.00   0.0  0
 CED  CONST_09  H17   C17  S19  C14   180.00   0.0  0
 CED  CONST_10  H15   C15  C16  C17   180.00   0.0  0
 CED  CONST_11  HO4   O4B  C4'  C4    180.00   0.0  0
 CED  CONST_12  O12   C11  N10  C7      0.00   0.0  0
 CED  CONST_13  C13   C11  N10  C7    180.00   0.0  0
 CED  CONST_14  HN1   N10  C11  O12   180.00   0.0  0
 CED  Var_01    C4    C3   C2   S1     19.55  30.0  1
 CED  Var_02    N5    C4   C3   C2      0.90  30.0  1
 CED  Var_03    C6    N5   C4   C3     18.74  30.0  1
 CED  Var_04    O4A   C4'  C4   C3     14.83  30.0  2
 CED  Var_05    C15   C14  C13  C11   111.81  30.0  2
 CED  Var_06    H3'1  C3'  C3   C2    -19.45  30.0  3
 CED  Var_07    C14   C13  C11  N10  -179.61  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
 CED  chir_01  C6  S1   N5  C7  negativ
 CED  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
 CED  plan-1  C13  0.020
 CED  plan-1  C14  0.020
 CED  plan-1  C15  0.020
 CED  plan-1  C16  0.020
 CED  plan-1  C17  0.020
 CED  plan-1  S19  0.020
 CED  plan-1  H15  0.020
 CED  plan-1  H16  0.020
 CED  plan-1  H17  0.020
 CED  plan-2  C7   0.020
 CED  plan-2  N10  0.020
 CED  plan-2  C11  0.020
 CED  plan-2  O12  0.020
 CED  plan-2  C13  0.020
 CED  plan-2  HN1  0.020
 CED  plan-3  C4   0.020
 CED  plan-3  N5   0.020
 CED  plan-3  C6   0.020
 CED  plan-3  HN5  0.020
 CED  plan-4  C4   0.020
 CED  plan-4  C4'  0.020
 CED  plan-4  O4A  0.020
 CED  plan-4  O4B  0.020
 CED  plan-4  HO4  0.020
 CED  plan-5  C7   0.020
 CED  plan-5  C8   0.020
 CED  plan-5  O9   0.020
 CED  plan-5  H8   0.020

