# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:28:06 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (2R)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=N[C@H](SCC1=C)[C@H](NC(=O)Cc2sccc2)C=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
 CEO  CEO  '(2R)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  35  22  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CEO
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
 CEO  S1    S  S2     0   0.004  -1.8421   1.2115   1.2613
 CEO  C2    C  CH2    0  -0.636  -2.3903   0.6814   2.9082
 CEO  C3    C  C      0   0.115  -1.5778  -0.5049   3.3187
 CEO  C3'   C  C2     0  -0.552  -2.1454  -1.6254   3.7667
 CEO  C4    C  C      0   0.150  -0.1076  -0.3645   3.2203
 CEO  C4'   C  C      0   0.365   0.7678  -1.3676   3.9640
 CEO  O4A   O  OC    -1  -0.592   0.9577  -2.4423   3.3719
 CEO  O4B   O  O      0  -0.585   1.1959  -0.9955   5.0670
 CEO  N5    N  N      0  -0.389   0.5072   0.5545   2.5890
 CEO  C6    C  CH1    0  -0.270  -0.1324   1.5584   1.7929
 CEO  C7    C  CH1    0  -0.206   0.7310   1.7837   0.5501
 CEO  C8    C  C1     0   0.199   2.1035   2.2522   0.9950
 CEO  O9    O  O      0  -0.359   3.1347   1.8014   0.5764
 CEO  N10   N  NH1    0  -0.618   0.8004   0.6065  -0.2588
 CEO  C11   C  C      0   0.564   0.8659   0.6325  -1.6017
 CEO  O12   O  O      0  -0.475   0.7764   1.6550  -2.2589
 CEO  C13   C  CH2    0  -0.678   1.0743  -0.7283  -2.2477
 CEO  C14   C  CR5    0  -0.113   0.3852  -0.8443  -3.5626
 CEO  C15   C  CR15   0  -0.241   0.9354  -0.8250  -4.8078
 CEO  C16   C  CR15   0  -0.182  -0.0303  -0.9341  -5.8476
 CEO  C17   C  CR15   0  -0.470  -1.3005  -1.0314  -5.3712
 CEO  S19   S  S2     0   0.208  -1.3292  -0.9959  -3.6565
 CEO  HC21  H  HCH2   0   0.292  -2.2714   1.5110   3.6089
 CEO  HC22  H  HCH2   0   0.300  -3.4510   0.4417   2.8479
 CEO  H3'1  H  H      0   0.258  -1.5696  -2.4956   4.0486
 CEO  H3'2  H  H      0   0.259  -3.2216  -1.7093   3.8486
 CEO  HC6   H  HCH1   0   0.309  -0.1417   2.4945   2.3635
 CEO  HC7   H  HCH1   0   0.316   0.2956   2.6036  -0.0319
 CEO  HC8   H  H      0   0.204   2.0848   3.0820   1.7230
 CEO  H10   H  HNH1   0   0.404   0.9396  -0.2711   0.2196
 CEO  H131  H  HCH2   0   0.309   2.1496  -0.8463  -2.4079
 CEO  H132  H  HCH2   0   0.289   0.7765  -1.5318  -1.5702
 CEO  H15   H  HCR5   0   0.263   1.9999  -0.7353  -4.9761
 CEO  H16   H  HCR5   0   0.266   0.2118  -0.9408  -6.9007
 CEO  H17   H  HCR5   0   0.294  -2.2178  -1.1282  -5.9312

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
 CEO  S1   C2    single    1.815  0.020  1.815
 CEO  S1   C6    single    1.824  0.020  1.824
 CEO  C2   C3    single    1.495  0.020  1.495
 CEO  C2   HC21  single    0.970  0.020  1.090
 CEO  C2   HC22  single    0.970  0.020  1.090
 CEO  C3   C3'   double    1.334  0.020  1.334
 CEO  C3   C4    single    1.480  0.020  1.480
 CEO  C3'  H3'1  single    0.930  0.020  1.080
 CEO  C3'  H3'2  single    0.930  0.020  1.080
 CEO  C4   C4'   single    1.525  0.020  1.525
 CEO  C4   N5    double    1.273  0.020  1.273
 CEO  C4'  O4A   deloc     1.242  0.020  1.242
 CEO  C4'  O4B   deloc     1.240  0.020  1.240
 CEO  N5   C6    single    1.432  0.020  1.432
 CEO  C6   C7    single    1.530  0.020  1.530
 CEO  C6   HC6   single    0.970  0.020  1.090
 CEO  C7   C8    single    1.517  0.020  1.517
 CEO  C7   N10   single    1.430  0.020  1.430
 CEO  C7   HC7   single    0.970  0.020  1.090
 CEO  C8   O9    double    1.201  0.020  1.201
 CEO  C8   HC8   single    0.930  0.020  1.080
 CEO  N10  C11   single    1.345  0.020  1.345
 CEO  N10  H10   single    0.860  0.020  1.020
 CEO  C11  O12   double    1.219  0.020  1.219
 CEO  C11  C13   single    1.521  0.020  1.521
 CEO  C13  C14   single    1.489  0.020  1.489
 CEO  C13  H131  single    0.970  0.020  1.090
 CEO  C13  H132  single    0.970  0.020  1.090
 CEO  C14  C15   aromatic  1.361  0.020  1.361
 CEO  C14  S19   aromatic  1.724  0.020  1.724
 CEO  C15  C16   aromatic  1.423  0.020  1.423
 CEO  C15  H15   single    0.930  0.020  1.080
 CEO  C16  C17   aromatic  1.360  0.020  1.360
 CEO  C16  H16   single    0.930  0.020  1.080
 CEO  C17  S19   aromatic  1.715  0.020  1.715
 CEO  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
 CEO  C6    S1   C2     94.26  3.000
 CEO  HC22  C2   HC21  107.98  3.000
 CEO  HC22  C2   C3    111.70  3.000
 CEO  HC21  C2   C3    111.54  3.000
 CEO  HC22  C2   S1    107.96  3.000
 CEO  HC21  C2   S1    109.10  3.000
 CEO  C3    C2   S1    108.47  3.000
 CEO  C4    C3   C3'   121.66  3.000
 CEO  C4    C3   C2    116.50  3.000
 CEO  C3'   C3   C2    121.84  3.000
 CEO  H3'2  C3'  H3'1  116.58  3.000
 CEO  H3'2  C3'  C3    120.91  3.000
 CEO  H3'1  C3'  C3    122.50  3.000
 CEO  N5    C4   C4'   116.06  3.000
 CEO  N5    C4   C3    125.53  3.000
 CEO  C4'   C4   C3    118.38  3.000
 CEO  O4B   C4'  O4A   129.12  3.000
 CEO  O4B   C4'  C4    115.75  3.000
 CEO  O4A   C4'  C4    115.12  3.000
 CEO  C6    N5   C4    124.47  3.000
 CEO  HC6   C6   C7    107.57  3.000
 CEO  HC6   C6   N5    108.24  3.000
 CEO  C7    C6   N5    107.63  3.000
 CEO  HC6   C6   S1    107.83  3.000
 CEO  C7    C6   S1    108.68  3.000
 CEO  N5    C6   S1    116.58  3.000
 CEO  HC7   C7   N10   109.56  3.000
 CEO  HC7   C7   C8    106.51  3.000
 CEO  N10   C7   C8    112.10  3.000
 CEO  HC7   C7   C6    108.51  3.000
 CEO  N10   C7   C6    111.45  3.000
 CEO  C8    C7   C6    108.53  3.000
 CEO  HC8   C8   O9    121.77  3.000
 CEO  HC8   C8   C7    114.22  3.000
 CEO  O9    C8   C7    123.97  3.000
 CEO  H10   N10  C11   118.92  3.000
 CEO  H10   N10  C7    117.02  3.000
 CEO  C11   N10  C7    123.46  3.000
 CEO  C13   C11  O12   122.12  3.000
 CEO  C13   C11  N10   114.43  3.000
 CEO  O12   C11  N10   123.45  3.000
 CEO  H132  C13  H131  106.23  3.000
 CEO  H132  C13  C14   111.36  3.000
 CEO  H131  C13  C14   108.50  3.000
 CEO  H132  C13  C11   110.94  3.000
 CEO  H131  C13  C11   107.07  3.000
 CEO  C14   C13  C11   112.42  3.000
 CEO  S19   C14  C15   110.69  3.000
 CEO  S19   C14  C13   121.02  3.000
 CEO  C15   C14  C13   128.28  3.000
 CEO  H15   C15  C16   124.09  3.000
 CEO  H15   C15  C14   122.77  3.000
 CEO  C16   C15  C14   113.14  3.000
 CEO  H16   C16  C17   123.38  3.000
 CEO  H16   C16  C15   124.09  3.000
 CEO  C17   C16  C15   112.53  3.000
 CEO  H17   C17  S19   120.43  3.000
 CEO  H17   C17  C16   128.21  3.000
 CEO  S19   C17  C16   111.36  3.000
 CEO  C17   S19  C14    92.27  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
 CEO  CONST_01  C17   C16  C15  C14    0.00   0.0  0
 CEO  CONST_02  C16   C17  S19  C14    0.00   0.0  0
 CEO  CONST_03  C17   S19  C14  C15    0.00   0.0  0
 CEO  CONST_04  S19   C17  C16  C15    0.00   0.0  0
 CEO  CONST_05  S19   C14  C15  C16    0.00   0.0  0
 CEO  CONST_06  C16   C15  C14  C13  180.00   0.0  0
 CEO  CONST_07  C17   S19  C14  C13  180.00   0.0  0
 CEO  CONST_08  H16   C16  C15  C14  180.00   0.0  0
 CEO  CONST_09  H17   C17  S19  C14  180.00   0.0  0
 CEO  CONST_10  H15   C15  C16  C17  180.00   0.0  0
 CEO  CONST_11  O12   C11  N10  C7     0.00   0.0  0
 CEO  CONST_12  C13   C11  N10  C7   180.00   0.0  0
 CEO  CONST_13  H10   N10  C11  O12  180.00   0.0  0
 CEO  Var_01    C4    C3   C2   S1    51.41  30.0  1
 CEO  Var_02    N5    C4   C3   C2   -14.34  30.0  1
 CEO  Var_03    O4A   C4'  C4   C3    82.77  30.0  2
 CEO  Var_04    C15   C14  C13  C11  105.59  30.0  2
 CEO  Var_05    H3'1  C3'  C3   C2   178.82   0.0  2
 CEO  Var_06    C14   C13  C11  N10  146.28  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
 CEO  chir_01  C6  S1   N5  C7  negativ
 CEO  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
 CEO  plan-1  C13   0.020
 CEO  plan-1  C14   0.020
 CEO  plan-1  C15   0.020
 CEO  plan-1  C16   0.020
 CEO  plan-1  C17   0.020
 CEO  plan-1  S19   0.020
 CEO  plan-1  H15   0.020
 CEO  plan-1  H16   0.020
 CEO  plan-1  H17   0.020
 CEO  plan-2  C7    0.020
 CEO  plan-2  N10   0.020
 CEO  plan-2  C11   0.020
 CEO  plan-2  O12   0.020
 CEO  plan-2  C13   0.020
 CEO  plan-2  H10   0.020
 CEO  plan-3  C4    0.020
 CEO  plan-3  C4'   0.020
 CEO  plan-3  O4A   0.020
 CEO  plan-3  O4B   0.020
 CEO  plan-4  C2    0.020
 CEO  plan-4  C3    0.020
 CEO  plan-4  C3'   0.020
 CEO  plan-4  C4    0.020
 CEO  plan-4  H3'1  0.020
 CEO  plan-4  H3'2  0.020
 CEO  plan-5  C7    0.020
 CEO  plan-5  C8    0.020
 CEO  plan-5  O9    0.020
 CEO  plan-5  HC8   0.020

