# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 05:58:09 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: (2~{R},4~{R})-5-[(~{E})-2-(2,4-dinitrophenyl)ethenyl]-2-[(1~{R})-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-1,3-thiazinane-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1N[C@H](SC[C@H]1\C=C\c2ccc(cc2[N+]([O-])=O)[N+]([O-])=O)[C@H](NC(=O)Cc3sccc3)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
 NEF  NEF  '(2~{R},4~{R})-5-[(~{E})-2-(2,4-dinitrophenyl)ethenyl]-2-[(1~{R})-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-1,3-thiazinane-4-carboxylic acid'  ligand  55  35  .  2021-08-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NEF
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
 NEF  C2   C  CH2    0  -0.566  -3.7968   0.1236  17.5379
 NEF  C3   C  CH1    0  -0.169  -5.8655   3.0313  17.1633
 NEF  C4   C  CH1    0  -0.327  -2.5020   0.8360  17.1500
 NEF  C6   C  C1     0  -0.182  -1.7614   0.0256  16.1392
 NEF  C7   C  CH2    0  -0.646  -7.2397   0.4987  14.7100
 NEF  C8   C  CR5    0  -0.161  -6.0257  -0.2676  14.2888
 NEF  C11  C  CR15   0  -0.479  -3.8756  -1.0022  13.2902
 NEF  C13  C  CH1    0  -0.264  -4.6996   2.7222  18.1199
 NEF  C14  C  CR6    0   0.142   0.2324  -1.1164  15.2752
 NEF  C15  C  CH1    0  -0.163  -2.8353   2.2362  16.5887
 NEF  C16  C  C      0   0.559  -1.5962   2.8900  16.0079
 NEF  C17  C  CR16   0  -0.318  -0.4256  -2.1846  14.6584
 NEF  S19  S  S2     0   0.022  -4.7372   1.0228  18.8012
 NEF  C1   C  C1     0   0.187  -5.6302   4.4353  16.6502
 NEF  O2   O  O      0  -0.368  -5.6038   4.7298  15.4838
 NEF  N4   N  NH1    0  -0.634  -6.0659   2.1214  16.0716
 NEF  C5   C  C      0   0.559  -7.0717   1.2144  16.0452
 NEF  O6   O  O      0  -0.460  -7.7902   0.9835  16.9974
 NEF  C9   C  CR15   0  -0.212  -5.6789  -1.5379  14.6422
 NEF  C10  C  CR15   0  -0.186  -4.4487  -1.9606  14.0681
 NEF  S12  S  S2     0   0.201  -4.8341   0.4187  13.2477
 NEF  N14  N  NH1    0  -0.578  -3.4316   3.1257  17.5703
 NEF  O17  O  O      0  -0.424  -1.4199   3.0817  14.8339
 NEF  O18  O  OH1    0  -0.589  -0.7225   3.2083  16.9516
 NEF  C12  C  C1     0  -0.260  -0.4775  -0.3061  16.2675
 NEF  C18  C  CR16   0  -0.229   0.1990  -3.0025  13.7399
 NEF  C19  C  CR6    0   0.256   1.5350  -2.7784  13.4426
 NEF  C20  C  CR16   0  -0.293   2.2432  -1.7550  14.0415
 NEF  C21  C  CR6    0   0.218   1.5768  -0.9345  14.9318
 NEF  N22  N  N      1   0.327   2.3410   0.1782  15.4825
 NEF  N23  N  N      1   0.330   2.2145  -3.6410  12.4887
 NEF  O24  O  O     -1  -0.359   1.7571   1.2149  15.6836
 NEF  O25  O  O      0  -0.362   3.5177   0.0022  15.6844
 NEF  O26  O  O     -1  -0.367   1.5773  -4.5357  11.9886
 NEF  O27  O  O      0  -0.368   3.3762  -3.4149  12.2501
 NEF  H1   H  HCH2   0   0.278  -4.4107  -0.0629  16.6555
 NEF  H2   H  HCH2   0   0.299  -3.5711  -0.8438  17.9878
 NEF  H3   H  HCH1   0   0.312  -6.7753   3.0544  17.7717
 NEF  H4   H  HCH1   0   0.277  -1.8809   0.9541  18.0435
 NEF  H5   H  H      0   0.281  -2.3124  -0.2658  15.2482
 NEF  H7   H  HCH2   0   0.301  -7.5145   1.2368  13.9516
 NEF  H8   H  HCH2   0   0.300  -8.0800  -0.1872  14.8054
 NEF  H9   H  HCR5   0   0.303  -2.9572  -1.0564  12.7258
 NEF  H10  H  HCH1   0   0.320  -4.8646   3.3495  18.9984
 NEF  H11  H  HCH1   0   0.252  -3.5267   2.1134  15.7525
 NEF  H12  H  HCR6   0   0.290  -1.4493  -2.3941  14.9352
 NEF  H13  H  H      0   0.221  -5.4910   5.1875  17.4429
 NEF  H14  H  HNH1   0   0.387  -5.6666   2.3919  15.1849
 NEF  H15  H  HCR5   0   0.272  -6.2868  -2.1559  15.2886
 NEF  H16  H  HCR5   0   0.272  -4.0170  -2.9394  14.2226
 NEF  H17  H  HNH1   0   0.380  -2.7789   3.2946  18.3266
 NEF  H19  H  HOH1   0   0.488   0.0655   3.6178  16.5629
 NEF  H20  H  H      0   0.279   0.0700   0.0235  17.1426
 NEF  H22  H  HCR6   0   0.316  -0.3505  -3.8129  13.2841
 NEF  H23  H  HCR6   0   0.333   3.2830  -1.5822  13.8048

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
 NEF  O26  N23  single    1.207  0.020  1.207
 NEF  N23  O27  double    1.207  0.020  1.207
 NEF  N23  C19  single    1.455  0.020  1.455
 NEF  C18  C19  aromatic  1.387  0.020  1.387
 NEF  C18  C17  aromatic  1.379  0.020  1.379
 NEF  C19  C20  aromatic  1.381  0.020  1.381
 NEF  C17  C14  aromatic  1.398  0.020  1.398
 NEF  S12  C11  aromatic  1.715  0.020  1.715
 NEF  S12  C8   aromatic  1.725  0.020  1.725
 NEF  C11  C10  aromatic  1.361  0.020  1.361
 NEF  C20  C21  aromatic  1.382  0.020  1.382
 NEF  C14  C21  aromatic  1.399  0.020  1.399
 NEF  C14  C12  single    1.465  0.020  1.465
 NEF  C8   C7   single    1.496  0.020  1.496
 NEF  C8   C9   aromatic  1.363  0.020  1.363
 NEF  C6   C12  double    1.332  0.020  1.332
 NEF  C6   C4   single    1.492  0.020  1.492
 NEF  C7   C5   single    1.524  0.020  1.524
 NEF  O17  C16  double    1.203  0.020  1.203
 NEF  C10  C9   aromatic  1.422  0.020  1.422
 NEF  C21  N22  single    1.458  0.020  1.458
 NEF  O2   C1   double    1.203  0.020  1.203
 NEF  C4   C15  single    1.545  0.020  1.545
 NEF  C4   C2   single    1.528  0.020  1.528
 NEF  C16  C15  single    1.517  0.020  1.517
 NEF  C16  O18  single    1.325  0.020  1.325
 NEF  N4   C5   single    1.355  0.020  1.355
 NEF  N4   C3   single    1.435  0.020  1.435
 NEF  C15  N14  single    1.453  0.020  1.453
 NEF  C5   O6   double    1.215  0.020  1.215
 NEF  C1   C3   single    1.513  0.020  1.513
 NEF  C2   S19  single    1.813  0.020  1.813
 NEF  N22  O25  double    1.207  0.020  1.207
 NEF  N22  O24  single    1.207  0.020  1.207
 NEF  C3   C13  single    1.540  0.020  1.540
 NEF  N14  C13  single    1.440  0.020  1.440
 NEF  C13  S19  single    1.831  0.020  1.831
 NEF  C2   H1   single    0.970  0.020  1.090
 NEF  C2   H2   single    0.970  0.020  1.090
 NEF  C3   H3   single    0.970  0.020  1.090
 NEF  C4   H4   single    0.970  0.020  1.090
 NEF  C6   H5   single    0.930  0.020  1.080
 NEF  C7   H7   single    0.970  0.020  1.090
 NEF  C7   H8   single    0.970  0.020  1.090
 NEF  C11  H9   single    0.930  0.020  1.080
 NEF  C13  H10  single    0.970  0.020  1.090
 NEF  C15  H11  single    0.970  0.020  1.090
 NEF  C17  H12  single    0.930  0.020  1.080
 NEF  C1   H13  single    0.930  0.020  1.080
 NEF  N4   H14  single    0.890  0.020  1.040
 NEF  C9   H15  single    0.930  0.020  1.080
 NEF  C10  H16  single    0.930  0.020  1.080
 NEF  N14  H17  single    0.890  0.020  1.040
 NEF  O18  H19  single    0.850  0.020  0.980
 NEF  C12  H20  single    0.930  0.020  1.080
 NEF  C18  H22  single    0.930  0.020  1.080
 NEF  C20  H23  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
 NEF  H2   C2   H1   107.36  3.000
 NEF  H2   C2   S19  105.06  3.000
 NEF  H1   C2   S19  110.88  3.000
 NEF  H2   C2   C4   110.06  3.000
 NEF  H1   C2   C4   110.56  3.000
 NEF  S19  C2   C4   112.65  3.000
 NEF  H3   C3   N4   108.67  3.000
 NEF  H3   C3   C1   107.34  3.000
 NEF  N4   C3   C1   110.61  3.000
 NEF  H3   C3   C13  106.76  3.000
 NEF  C1   C3   C13  106.21  3.000
 NEF  N4   C3   C13  116.81  3.000
 NEF  H4   C4   C15  108.74  3.000
 NEF  H4   C4   C6   109.27  3.000
 NEF  C15  C4   C6   110.68  3.000
 NEF  H4   C4   C2   108.90  3.000
 NEF  C15  C4   C2   109.39  3.000
 NEF  C6   C4   C2   109.84  3.000
 NEF  H5   C6   C12  120.03  3.000
 NEF  H5   C6   C4   116.69  3.000
 NEF  C12  C6   C4   123.24  3.000
 NEF  H8   C7   H7   106.98  3.000
 NEF  H8   C7   C5   107.70  3.000
 NEF  H7   C7   C5   108.56  3.000
 NEF  H8   C7   C8   109.15  3.000
 NEF  H7   C7   C8   110.76  3.000
 NEF  C5   C7   C8   113.44  3.000
 NEF  S12  C8   C9   110.58  3.000
 NEF  C9   C8   C7   127.64  3.000
 NEF  S12  C8   C7   121.78  3.000
 NEF  H9   C11  S12  120.28  3.000
 NEF  H9   C11  C10  128.46  3.000
 NEF  S12  C11  C10  111.25  3.000
 NEF  H10  C13  N14  106.22  3.000
 NEF  H10  C13  S19  103.34  3.000
 NEF  N14  C13  S19  114.85  3.000
 NEF  H10  C13  C3   105.67  3.000
 NEF  S19  C13  C3   113.70  3.000
 NEF  N14  C13  C3   111.93  3.000
 NEF  C21  C14  C12  124.05  3.000
 NEF  C12  C14  C17  119.57  3.000
 NEF  C21  C14  C17  116.31  3.000
 NEF  H11  C15  N14  109.05  3.000
 NEF  H11  C15  C16  105.81  3.000
 NEF  N14  C15  C16  109.28  3.000
 NEF  H11  C15  C4   108.24  3.000
 NEF  N14  C15  C4   113.46  3.000
 NEF  C16  C15  C4   110.71  3.000
 NEF  O18  C16  O17  124.09  3.000
 NEF  O18  C16  C15  111.69  3.000
 NEF  O17  C16  C15  124.22  3.000
 NEF  H12  C17  C18  118.98  3.000
 NEF  H12  C17  C14  118.74  3.000
 NEF  C18  C17  C14  122.25  3.000
 NEF  C13  S19  C2   100.97  3.000
 NEF  H13  C1   O2   121.84  3.000
 NEF  H13  C1   C3   114.15  3.000
 NEF  O2   C1   C3   124.00  3.000
 NEF  H14  N4   C5   117.13  3.000
 NEF  H14  N4   C3   116.30  3.000
 NEF  C5   N4   C3   122.88  3.000
 NEF  O6   C5   N4   123.44  3.000
 NEF  O6   C5   C7   122.15  3.000
 NEF  N4   C5   C7   114.41  3.000
 NEF  H15  C9   C10  123.91  3.000
 NEF  H15  C9   C8   122.99  3.000
 NEF  C10  C9   C8   113.10  3.000
 NEF  H16  C10  C9   123.85  3.000
 NEF  H16  C10  C11  123.45  3.000
 NEF  C9   C10  C11  112.70  3.000
 NEF  C11  S12  C8    92.38  3.000
 NEF  H17  N14  C15  110.00  3.000
 NEF  H17  N14  C13  109.21  3.000
 NEF  C15  N14  C13  116.61  3.000
 NEF  H19  O18  C16  110.60  3.000
 NEF  H20  C12  C14  118.07  3.000
 NEF  H20  C12  C6   119.27  3.000
 NEF  C14  C12  C6   122.65  3.000
 NEF  H22  C18  C19  121.39  3.000
 NEF  H22  C18  C17  119.71  3.000
 NEF  C19  C18  C17  118.89  3.000
 NEF  N23  C19  C20  118.96  3.000
 NEF  C20  C19  C18  121.38  3.000
 NEF  N23  C19  C18  119.66  3.000
 NEF  H23  C20  C21  120.69  3.000
 NEF  H23  C20  C19  121.13  3.000
 NEF  C21  C20  C19  118.16  3.000
 NEF  N22  C21  C20  116.34  3.000
 NEF  N22  C21  C14  120.67  3.000
 NEF  C20  C21  C14  122.97  3.000
 NEF  O25  N22  O24  124.70  3.000
 NEF  O24  N22  C21  117.71  3.000
 NEF  O25  N22  C21  117.58  3.000
 NEF  O27  N23  O26  124.40  3.000
 NEF  O27  N23  C19  117.91  3.000
 NEF  O26  N23  C19  117.69  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
 NEF  CONST_01  C10  C11  S12  C8     0.00   0.0  0
 NEF  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 NEF  CONST_03  C9   C8   S12  C11    0.00   0.0  0
 NEF  CONST_04  C19  C18  C17  C14    0.00   0.0  0
 NEF  CONST_05  C19  C20  C21  C14    0.00   0.0  0
 NEF  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 NEF  CONST_07  C20  C21  C14  C17    0.00   0.0  0
 NEF  CONST_08  S12  C11  C10  C9     0.00   0.0  0
 NEF  CONST_09  S12  C8   C9   C10    0.00   0.0  0
 NEF  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 NEF  CONST_11  C21  C14  C17  C18    0.00   0.0  0
 NEF  CONST_12  C11  S12  C8   C7   180.00   0.0  0
 NEF  CONST_13  C10  C9   C8   C7   180.00   0.0  0
 NEF  CONST_14  N23  C19  C18  C17  180.00   0.0  0
 NEF  CONST_15  N22  C21  C14  C17  180.00   0.0  0
 NEF  CONST_16  C18  C17  C14  C12  180.00   0.0  0
 NEF  CONST_17  C20  C21  C14  C12  180.00   0.0  0
 NEF  CONST_18  N22  C21  C20  C19  180.00   0.0  0
 NEF  CONST_19  N23  C19  C20  C21  180.00   0.0  0
 NEF  CONST_20  H9   C11  S12  C8   180.00   0.0  0
 NEF  CONST_21  H16  C10  C9   C8   180.00   0.0  0
 NEF  CONST_22  H15  C9   C10  C11  180.00   0.0  0
 NEF  CONST_23  H22  C18  C17  C14  180.00   0.0  0
 NEF  CONST_24  H23  C20  C21  C14  180.00   0.0  0
 NEF  CONST_25  H12  C17  C18  C19  180.00   0.0  0
 NEF  CONST_28  O26  N23  C19  C18    0.00   0.0  0
 NEF  CONST_29  O27  N23  C19  C18  180.00   0.0  0
 NEF  CONST_30  O26  N23  C19  C20  180.00   0.0  0
 NEF  CONST_31  O27  N23  C19  C20    0.00   0.0  0
 NEF  CONST_34  H19  O18  C16  C15  180.00   0.0  0
 NEF  CONST_35  C7   C5   N4   C3   180.00   0.0  0
 NEF  CONST_36  O6   C5   N4   C3     0.00   0.0  0
 NEF  CONST_37  H14  N4   C5   C7     0.00   0.0  0
 NEF  Var_01    H1   C2   S19  C13  -77.50  30.0  1
 NEF  Var_02    C14  C12  C6   C4   179.22   0.0  2
 NEF  Var_03    C17  C14  C12  C6   -38.62  30.0  2
 NEF  Var_04    S12  C8   C7   C5   -94.13  30.0  1
 NEF  Var_05    N4   C5   C7   C8    59.95  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
 NEF  chir_01  C3   N4   C1   C13  positiv
 NEF  chir_02  C4   C6   C15  C2   negativ
 NEF  chir_03  C13  S19  N14  C3   negativ
 NEF  chir_04  C15  N14  C4   C16  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
 NEF  plan-1  C7   0.020
 NEF  plan-1  C8   0.020
 NEF  plan-1  C11  0.020
 NEF  plan-1  C9   0.020
 NEF  plan-1  C10  0.020
 NEF  plan-1  S12  0.020
 NEF  plan-1  H9   0.020
 NEF  plan-1  H15  0.020
 NEF  plan-1  H16  0.020
 NEF  plan-2  C3   0.020
 NEF  plan-2  C1   0.020
 NEF  plan-2  O2   0.020
 NEF  plan-2  H13  0.020
 NEF  plan-3  C14  0.020
 NEF  plan-3  C17  0.020
 NEF  plan-3  C12  0.020
 NEF  plan-3  C18  0.020
 NEF  plan-3  C19  0.020
 NEF  plan-3  C20  0.020
 NEF  plan-3  C21  0.020
 NEF  plan-3  N22  0.020
 NEF  plan-3  N23  0.020
 NEF  plan-3  H12  0.020
 NEF  plan-3  H22  0.020
 NEF  plan-3  H23  0.020
 NEF  plan-4  C21  0.020
 NEF  plan-4  N22  0.020
 NEF  plan-4  O24  0.020
 NEF  plan-4  O25  0.020
 NEF  plan-5  C19  0.020
 NEF  plan-5  N23  0.020
 NEF  plan-5  O26  0.020
 NEF  plan-5  O27  0.020
 NEF  plan-6  C3   0.020
 NEF  plan-6  C7   0.020
 NEF  plan-6  N4   0.020
 NEF  plan-6  C5   0.020
 NEF  plan-6  O6   0.020
 NEF  plan-6  H14  0.020
 NEF  plan-7  C15  0.020
 NEF  plan-7  C16  0.020
 NEF  plan-7  O17  0.020
 NEF  plan-7  O18  0.020
 NEF  plan-7  H19  0.020
 NEF  plan-8  C4   0.020
 NEF  plan-8  C6   0.020
 NEF  plan-8  C14  0.020
 NEF  plan-8  C12  0.020
 NEF  plan-8  H5   0.020
 NEF  plan-8  H20  0.020

