# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 11 02:05:31 2020
#   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  54  35  .  2021-08-15  2021-08-15  
;
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  -0.570  -0.0064  -2.2648   1.4932
 NEF  C3   C  CH1    0  -0.126   3.1789  -1.5107   0.8944
 NEF  C4   C  CH1    0  -0.312  -0.5382  -1.8796   0.1091
 NEF  C6   C  C1     0  -0.142  -1.6747  -0.9302   0.2943
 NEF  C7   C  CH2    0  -0.670   5.6160   0.7869  -0.8407
 NEF  C8   C  CR5    0  -0.115   6.0685   2.1618  -0.4914
 NEF  C11  C  CR15   0  -0.470   6.1798   4.5785   0.0513
 NEF  C13  C  CH1    0  -0.261   2.3921  -2.6156   0.1756
 NEF  C14  C  CR6    0   0.154  -4.0626  -0.3370   0.3282
 NEF  C15  C  CH1    0  -0.181   0.5678  -1.2441  -0.7632
 NEF  C16  C  C      0   0.432  -0.0309  -0.8709  -2.1378
 NEF  C17  C  CR16   0  -0.321  -3.9778   0.5999   1.3658
 NEF  S19  S  S2     0  -0.014   1.3223  -3.4965   1.3911
 NEF  C1   C  C1     0   0.172   4.0414  -2.1510   1.9755
 NEF  O2   O  O      0  -0.373   5.0166  -2.8101   1.7273
 NEF  N4   N  NH1    0  -0.644   3.9844  -0.8227  -0.0788
 NEF  C5   C  C      0   0.574   4.8755   0.1051   0.2968
 NEF  O6   O  O      0  -0.480   5.0990   0.3504   1.4725
 NEF  C9   C  CR15   0  -0.241   7.3296   2.5855  -0.2018
 NEF  C10  C  CR15   0  -0.182   7.3962   3.9726   0.1089
 NEF  S12  S  S2     0   0.208   4.9486   3.4675  -0.3862
 NEF  N14  N  NH1    0  -0.584   1.7150  -2.1090  -0.9680
 NEF  O17  O  O      0  -0.603  -0.0648  -1.7881  -2.9816
 NEF  O18  O  OC    -1  -0.594  -0.4489   0.2918  -2.2663
 NEF  C12  C  C1     0  -0.273  -2.9508  -1.2534   0.0789
 NEF  C18  C  CR16   0  -0.230  -5.0080   1.4639   1.6677
 NEF  C19  C  CR6    0   0.251  -6.1893   1.3818   0.9431
 NEF  C20  C  CR16   0  -0.293  -6.3431   0.4581  -0.0714
 NEF  C21  C  CR6    0   0.210  -5.2763  -0.3676  -0.3722
 NEF  N22  N  N      1   0.323  -5.4670  -1.2696  -1.5016
 NEF  N23  N  N      1   0.329  -7.2932   2.2719   1.2574
 NEF  O24  O  O     -1  -0.366  -6.5648  -1.7493  -1.6537
 NEF  O25  O  O      0  -0.356  -4.5283  -1.4590  -2.2350
 NEF  O26  O  O     -1  -0.372  -8.3151   2.1521   0.6244
 NEF  O27  O  O      0  -0.370  -7.1311   3.0796   2.1401
 NEF  H1   H  HCH2   0   0.270   0.3353  -1.3809   2.0376
 NEF  H2   H  HCH2   0   0.297  -0.7932  -2.7286   2.0891
 NEF  H3   H  HCH1   0   0.277   2.4923  -0.8135   1.3877
 NEF  H4   H  HCH1   0   0.254  -0.8961  -2.7876  -0.3879
 NEF  H5   H  H      0   0.265  -1.4134   0.0677   0.6362
 NEF  H7   H  HCH2   0   0.290   5.0066   0.7868  -1.7473
 NEF  H8   H  HCH2   0   0.310   6.4954   0.1765  -1.0658
 NEF  H9   H  HCR5   0   0.294   5.9405   5.6145   0.2345
 NEF  H10  H  HCH1   0   0.308   3.1015  -3.3734  -0.1642
 NEF  H11  H  HCH1   0   0.226   0.8997  -0.3267  -0.2648
 NEF  H12  H  HCR6   0   0.289  -3.0824   0.6300   1.9705
 NEF  H13  H  H      0   0.212   3.6892  -1.9982   3.0070
 NEF  H14  H  HNH1   0   0.405   3.7054  -0.9201  -1.0455
 NEF  H15  H  HCR5   0   0.263   8.1854   1.9244  -0.2102
 NEF  H16  H  HCR5   0   0.265   8.3091   4.4924   0.3620
 NEF  H17  H  HNH1   0   0.361   1.4770  -2.8446  -1.6209
 NEF  H20  H  H      0   0.262  -3.1830  -2.2426  -0.2952
 NEF  H22  H  HCR6   0   0.313  -4.8912   2.1735   2.4735
 NEF  H23  H  HCR6   0   0.329  -7.2625   0.3991  -0.6356

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    1.208  0.020  1.208
 NEF  N23  O27  double    1.207  0.020  1.207
 NEF  N23  C19  single    1.452  0.020  1.452
 NEF  C18  C19  aromatic  1.388  0.020  1.388
 NEF  C18  C17  aromatic  1.378  0.020  1.378
 NEF  C19  C20  aromatic  1.381  0.020  1.381
 NEF  C17  C14  aromatic  1.401  0.020  1.401
 NEF  S12  C11  aromatic  1.715  0.020  1.715
 NEF  S12  C8   aromatic  1.723  0.020  1.723
 NEF  C11  C10  aromatic  1.360  0.020  1.360
 NEF  C20  C21  aromatic  1.382  0.020  1.382
 NEF  C14  C21  aromatic  1.402  0.020  1.402
 NEF  C14  C12  single    1.462  0.020  1.462
 NEF  C8   C7   single    1.489  0.020  1.489
 NEF  C8   C9   aromatic  1.362  0.020  1.362
 NEF  C6   C12  double    1.334  0.020  1.334
 NEF  C6   C4   single    1.492  0.020  1.492
 NEF  C7   C5   single    1.519  0.020  1.519
 NEF  O17  C16  deloc     1.247  0.020  1.247
 NEF  C10  C9   aromatic  1.423  0.020  1.423
 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    1.532  0.020  1.532
 NEF  C16  C15  single    1.545  0.020  1.545
 NEF  C16  O18  deloc     1.242  0.020  1.242
 NEF  N4   C5   single    1.340  0.020  1.340
 NEF  N4   C3   single    1.438  0.020  1.438
 NEF  C15  N14  single    1.451  0.020  1.451
 NEF  C5   O6   double    1.222  0.020  1.222
 NEF  C1   C3   single    1.524  0.020  1.524
 NEF  C2   S19  single    1.815  0.020  1.815
 NEF  N22  O25  double    1.206  0.020  1.206
 NEF  N22  O24  single    1.208  0.020  1.208
 NEF  C3   C13  single    1.535  0.020  1.535
 NEF  N14  C13  single    1.422  0.020  1.422
 NEF  C13  S19  single    1.843  0.020  1.843
 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    0.860  0.020  1.020
 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  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   107.30  3.000
 NEF  H2   C2   S19  105.69  3.000
 NEF  H1   C2   S19  110.37  3.000
 NEF  H2   C2   C4   110.50  3.000
 NEF  H1   C2   C4   110.80  3.000
 NEF  S19  C2   C4   111.96  3.000
 NEF  H3   C3   N4   110.55  3.000
 NEF  H3   C3   C1   107.61  3.000
 NEF  N4   C3   C1   111.35  3.000
 NEF  H3   C3   C13  110.34  3.000
 NEF  C1   C3   C13  108.65  3.000
 NEF  N4   C3   C13  108.33  3.000
 NEF  H4   C4   C15  108.58  3.000
 NEF  H4   C4   C6   109.56  3.000
 NEF  C15  C4   C6   110.70  3.000
 NEF  H4   C4   C2   108.36  3.000
 NEF  C15  C4   C2   111.41  3.000
 NEF  C6   C4   C2   108.19  3.000
 NEF  H5   C6   C12  120.23  3.000
 NEF  H5   C6   C4   116.11  3.000
 NEF  C12  C6   C4   123.66  3.000
 NEF  H8   C7   H7   106.12  3.000
 NEF  H8   C7   C5   107.20  3.000
 NEF  H7   C7   C5   110.46  3.000
 NEF  H8   C7   C8   108.61  3.000
 NEF  H7   C7   C8   111.36  3.000
 NEF  C5   C7   C8   112.76  3.000
 NEF  S12  C8   C9   110.67  3.000
 NEF  C9   C8   C7   128.22  3.000
 NEF  S12  C8   C7   121.10  3.000
 NEF  H9   C11  S12  120.40  3.000
 NEF  H9   C11  C10  128.24  3.000
 NEF  S12  C11  C10  111.36  3.000
 NEF  H10  C13  N14  107.83  3.000
 NEF  H10  C13  S19  104.51  3.000
 NEF  N14  C13  S19  115.10  3.000
 NEF  H10  C13  C3   108.19  3.000
 NEF  S19  C13  C3   109.43  3.000
 NEF  N14  C13  C3   111.35  3.000
 NEF  C21  C14  C12  124.02  3.000
 NEF  C12  C14  C17  119.97  3.000
 NEF  C21  C14  C17  115.93  3.000
 NEF  H11  C15  N14  108.89  3.000
 NEF  H11  C15  C16  108.66  3.000
 NEF  N14  C15  C16  108.95  3.000
 NEF  H11  C15  C4   107.72  3.000
 NEF  N14  C15  C4   113.60  3.000
 NEF  C16  C15  C4   108.92  3.000
 NEF  O18  C16  O17  127.55  3.000
 NEF  O18  C16  C15  116.65  3.000
 NEF  O17  C16  C15  115.78  3.000
 NEF  H12  C17  C18  118.64  3.000
 NEF  H12  C17  C14  118.90  3.000
 NEF  C18  C17  C14  122.44  3.000
 NEF  C13  S19  C2    97.92  3.000
 NEF  H13  C1   O2   121.92  3.000
 NEF  H13  C1   C3   115.18  3.000
 NEF  O2   C1   C3   122.86  3.000
 NEF  H14  N4   C5   121.21  3.000
 NEF  H14  N4   C3   116.51  3.000
 NEF  C5   N4   C3   120.92  3.000
 NEF  O6   C5   N4   122.03  3.000
 NEF  O6   C5   C7   122.78  3.000
 NEF  N4   C5   C7   115.15  3.000
 NEF  H15  C9   C10  124.09  3.000
 NEF  H15  C9   C8   122.76  3.000
 NEF  C10  C9   C8   113.16  3.000
 NEF  H16  C10  C9   124.03  3.000
 NEF  H16  C10  C11  123.44  3.000
 NEF  C9   C10  C11  112.53  3.000
 NEF  C11  S12  C8    92.29  3.000
 NEF  H17  N14  C15  109.78  3.000
 NEF  H17  N14  C13  111.83  3.000
 NEF  C15  N14  C13  118.37  3.000
 NEF  H20  C12  C14  117.93  3.000
 NEF  H20  C12  C6   118.84  3.000
 NEF  C14  C12  C6   123.23  3.000
 NEF  H22  C18  C19  121.35  3.000
 NEF  H22  C18  C17  119.64  3.000
 NEF  C19  C18  C17  118.99  3.000
 NEF  N23  C19  C20  118.97  3.000
 NEF  C20  C19  C18  121.19  3.000
 NEF  N23  C19  C18  119.84  3.000
 NEF  H23  C20  C21  120.70  3.000
 NEF  H23  C20  C19  121.01  3.000
 NEF  C21  C20  C19  118.27  3.000
 NEF  N22  C21  C20  115.93  3.000
 NEF  N22  C21  C14  120.92  3.000
 NEF  C20  C21  C14  123.13  3.000
 NEF  O25  N22  O24  124.64  3.000
 NEF  O24  N22  C21  117.53  3.000
 NEF  O25  N22  C21  117.80  3.000
 NEF  O27  N23  O26  124.26  3.000
 NEF  O27  N23  C19  117.78  3.000
 NEF  O26  N23  C19  117.96  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  180.00   0.0  0
 NEF  CONST_29  O27  N23  C19  C18    0.00   0.0  0
 NEF  CONST_30  O26  N23  C19  C20    0.00   0.0  0
 NEF  CONST_31  O27  N23  C19  C20  180.00   0.0  0
 NEF  CONST_34  C7   C5   N4   C3   180.00   0.0  0
 NEF  CONST_35  O6   C5   N4   C3     0.00   0.0  0
 NEF  CONST_36  H14  N4   C5   C7     0.00   0.0  0
 NEF  Var_01    H1   C2   S19  C13  -71.96  30.0  1
 NEF  Var_02    C14  C12  C6   C4   176.79   0.0  2
 NEF  Var_03    C17  C14  C12  C6   -32.17  30.0  2
 NEF  Var_04    S12  C8   C7   C5   -73.65  30.0  2
 NEF  Var_05    N4   C5   C7   C8   152.84  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-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

