# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 04:45:28 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  37  22  .  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_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  -0.015  -1.9893  -1.7496   0.6296
 CED  C2    C  CH2    0  -0.607  -3.4673  -2.0536  -0.3666
 CED  C3    C  C      0   0.013  -4.3692  -0.8594  -0.5373
 CED  C3'   C  CH3    0  -0.707  -5.7307  -1.2741  -1.0213
 CED  C4    C  C      0   0.110  -3.9682   0.4042  -0.3052
 CED  C4'   C  C      0   0.385  -4.8519   1.6510  -0.4304
 CED  O4A   O  O      0  -0.575  -6.0802   1.5258  -0.3059
 CED  O4B   O  OC    -1  -0.603  -4.2265   2.7143  -0.6326
 CED  N5    N  NH1    0  -0.654  -2.6795   0.7543   0.0961
 CED  C6    C  CH1    0  -0.215  -1.5958  -0.1403  -0.1340
 CED  C7    C  CH1    0  -0.213  -0.3194   0.4046   0.5099
 CED  C8    C  C1     0   0.186  -0.4735   0.4865   2.0194
 CED  O9    O  O      0  -0.362   0.3334   0.0446   2.7936
 CED  N10   N  NH1    0  -0.638   0.8201  -0.3694   0.1166
 CED  C11   C  C      0   0.570   2.0738   0.1234   0.1564
 CED  O12   O  O      0  -0.472   2.3223   1.2848   0.4230
 CED  C13   C  CH2    0  -0.679   3.1451  -0.8994  -0.1924
 CED  C14   C  CR5    0  -0.117   4.5273  -0.3512  -0.1506
 CED  C15   C  CR15   0  -0.238   5.5169  -0.6506   0.7371
 CED  C16   C  CR15   0  -0.185   6.7273   0.0534   0.4850
 CED  C17   C  CR15   0  -0.472   6.6341   0.8776  -0.5934
 CED  S19   S  S2     0   0.208   5.0762   0.8025  -1.3047
 CED  H21   H  HCH2   0   0.279  -3.1727  -2.4655  -1.3365
 CED  H22   H  HCH2   0   0.283  -4.0086  -2.8495   0.1528
 CED  H3'1  H  HCH3   0   0.217  -5.6257  -2.0739  -1.7595
 CED  H3'2  H  HCH3   0   0.224  -6.3369  -1.6842  -0.2078
 CED  H3'3  H  HCH3   0   0.248  -6.2900  -0.4642  -1.4750
 CED  HN5   H  HNH1   0   0.375  -2.4961   1.7192  -0.1564
 CED  H6    H  HCH1   0   0.289  -1.4064  -0.3209  -1.2011
 CED  H7    H  HCH1   0   0.315  -0.1949   1.4357   0.1550
 CED  H8    H  H      0   0.216  -1.3806   1.0113   2.3585
 CED  HN1   H  HNH1   0   0.407   0.6920  -1.3604  -0.0281
 CED  H131  H  HCH2   0   0.305   3.0759  -1.7316   0.5132
 CED  H132  H  HCH2   0   0.303   2.9143  -1.3204  -1.1758
 CED  H15   H  HCR5   0   0.262   5.3856  -1.3564   1.5458
 CED  H16   H  HCR5   0   0.265   7.6234  -0.0520   1.0796
 CED  H17   H  HCR5   0   0.293   7.3923   1.5260  -1.0045

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    1.808  0.020  1.808
 CED  S1   C6    single    1.824  0.020  1.824
 CED  C2   C3    single    1.506  0.020  1.506
 CED  C2   H21   single    0.970  0.020  1.090
 CED  C2   H22   single    0.970  0.020  1.090
 CED  C3   C3'   single    1.503  0.020  1.503
 CED  C3   C4    double    1.346  0.020  1.346
 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    1.533  0.020  1.533
 CED  C4   N5    single    1.394  0.020  1.394
 CED  C4'  O4A   deloc     1.241  0.020  1.241
 CED  C4'  O4B   deloc     1.250  0.020  1.250
 CED  N5   C6    single    1.424  0.020  1.424
 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    1.520  0.020  1.520
 CED  C7   N10   single    1.433  0.020  1.433
 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    1.348  0.020  1.348
 CED  N10  HN1   single    0.860  0.020  1.020
 CED  C11  O12   double    1.217  0.020  1.217
 CED  C11  C13   single    1.522  0.020  1.522
 CED  C13  C14   single    1.488  0.020  1.488
 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  1.361  0.020  1.361
 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     95.40  3.000
 CED  H22   C2   H21   106.28  3.000
 CED  H22   C2   C3    109.54  3.000
 CED  H21   C2   C3    111.06  3.000
 CED  H22   C2   S1    105.38  3.000
 CED  H21   C2   S1    109.36  3.000
 CED  C3    C2   S1    114.75  3.000
 CED  C4    C3   C3'   125.76  3.000
 CED  C4    C3   C2    123.12  3.000
 CED  C3'   C3   C2    111.11  3.000
 CED  H3'3  C3'  H3'2  107.78  3.000
 CED  H3'3  C3'  H3'1  108.28  3.000
 CED  H3'2  C3'  H3'1  106.31  3.000
 CED  H3'3  C3'  C3    113.33  3.000
 CED  H3'2  C3'  C3    111.45  3.000
 CED  H3'1  C3'  C3    109.40  3.000
 CED  N5    C4   C4'   110.61  3.000
 CED  N5    C4   C3    124.11  3.000
 CED  C4'   C4   C3    125.28  3.000
 CED  O4B   C4'  O4A   126.67  3.000
 CED  O4B   C4'  C4    114.62  3.000
 CED  O4A   C4'  C4    118.70  3.000
 CED  HN5   N5   C6    114.83  3.000
 CED  HN5   N5   C4    109.54  3.000
 CED  C6    N5   C4    119.94  3.000
 CED  H6    C6   C7    108.87  3.000
 CED  H6    C6   N5    113.04  3.000
 CED  C7    C6   N5    110.07  3.000
 CED  H6    C6   S1    107.38  3.000
 CED  C7    C6   S1    108.54  3.000
 CED  N5    C6   S1    108.81  3.000
 CED  H7    C7   N10   109.19  3.000
 CED  H7    C7   C8    106.38  3.000
 CED  N10   C7   C8    112.49  3.000
 CED  H7    C7   C6    107.04  3.000
 CED  N10   C7   C6    110.83  3.000
 CED  C8    C7   C6    110.65  3.000
 CED  H8    C8   O9    121.97  3.000
 CED  H8    C8   C7    114.52  3.000
 CED  O9    C8   C7    123.49  3.000
 CED  HN1   N10  C11   118.76  3.000
 CED  HN1   N10  C7    117.95  3.000
 CED  C11   N10  C7    122.30  3.000
 CED  C13   C11  O12   123.22  3.000
 CED  C13   C11  N10   113.73  3.000
 CED  O12   C11  N10   123.04  3.000
 CED  H132  C13  H131  105.89  3.000
 CED  H132  C13  C14   111.28  3.000
 CED  H131  C13  C14   108.74  3.000
 CED  H132  C13  C11   108.42  3.000
 CED  H131  C13  C11   108.61  3.000
 CED  C14   C13  C11   113.58  3.000
 CED  S19   C14  C15   110.63  3.000
 CED  S19   C14  C13   121.63  3.000
 CED  C15   C14  C13   127.74  3.000
 CED  H15   C15  C16   123.97  3.000
 CED  H15   C15  C14   122.85  3.000
 CED  C16   C15  C14   113.18  3.000
 CED  H16   C16  C17   123.50  3.000
 CED  H16   C16  C15   124.04  3.000
 CED  C17   C16  C15   112.46  3.000
 CED  H17   C17  S19   120.45  3.000
 CED  H17   C17  C16   128.17  3.000
 CED  S19   C17  C16   111.38  3.000
 CED  C17   S19  C14    92.35  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  O12   C11  N10  C7     0.00   0.0  0
 CED  CONST_12  C13   C11  N10  C7   180.00   0.0  0
 CED  CONST_13  HN1   N10  C11  O12  180.00   0.0  0
 CED  Var_01    C4    C3   C2   S1    17.56  30.0  1
 CED  Var_02    N5    C4   C3   C2     1.02  30.0  1
 CED  Var_03    C6    N5   C4   C3    20.78  30.0  1
 CED  Var_04    O4A   C4'  C4   C3    24.84  30.0  2
 CED  Var_05    C15   C14  C13  C11  111.43  30.0  2
 CED  Var_06    H3'1  C3'  C3   C2   -39.34  30.0  3
 CED  Var_07    C14   C13  C11  N10  179.86  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-5  C7   0.020
 CED  plan-5  C8   0.020
 CED  plan-5  O9   0.020
 CED  plan-5  H8   0.020

