# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 14:36:34 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}-N-{(2S)-1-hydroxy-3-methyl-3-[(sulfooxy)amino]butan-2-yl}ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(NO[S](O)(=O)=O)[C@@H](CO)NC(=O)C(=N/OCC1=CC(=O)C(=CN1O)O)\c2csc(N)n2
#
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
 2U3  2U3  (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)methoxy]imino}-N-{(2S)-1-hydroxy-3-methyl-3-[(sulfooxy)amino]butan-2-yl}ethanamide  ligand  56  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2U3
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
 2U3  N    N  NH1   0  -0.612   0.2793  -0.3053   0.5708
 2U3  CA   C  CH1   0  -0.114   1.1580   0.8215   0.7801
 2U3  C    C  CH2   0  -0.177   0.6117   2.0039  -0.0330
 2U3  O    O  OH1   0  -0.712   0.2974   1.6192  -1.3470
 2U3  C2   C  CT    0   0.067   2.6452   0.4462   0.5133
 2U3  N3   N  N     0  -0.454   0.6878  -3.3825   0.1327
 2U3  C4   C  CR5   0   0.355  -0.6576  -3.3355   0.3852
 2U3  C5   C  CR15  0  -0.546  -1.3703  -4.4419   0.0511
 2U3  S6   S  S2    0   0.200  -0.3153  -5.6154  -0.6351
 2U3  C7   C  CR5   0   0.275   1.0200  -4.5135  -0.4073
 2U3  N8   N  NH2   0  -0.818   2.2633  -4.8251  -0.8280
 2U3  C9   C  C     0   0.035  -1.2003  -2.1198   0.9870
 2U3  C10  C  C     0   0.512  -0.2269  -1.0918   1.5265
 2U3  N11  N  N     0  -0.108  -2.4618  -1.9734   1.0565
 2U3  O12  O  O     0  -0.460   0.0093  -1.0206   2.7179
 2U3  C13  C  CH3   0  -0.677   3.0497  -0.7527   1.3742
 2U3  C14  C  CH3   0  -0.656   2.9185   0.1334  -0.9520
 2U3  O15  O  OC2   0  -0.472   4.7638   1.4822   0.7893
 2U3  S16  S  S     0   1.661   5.4104   2.6909  -0.0524
 2U3  O17  O  OS    0  -0.624   6.8229   2.4941   0.1030
 2U3  O18  O  OS    0  -0.615   4.8024   2.7961  -1.3508
 2U3  O19  O  OS    0  -0.700   5.0398   3.9552   0.8233
 2U3  O20  O  O2    0  -0.384  -2.8198  -0.8356   1.7286
 2U3  C21  C  CH2   0  -0.196  -4.1466  -0.4804   1.4303
 2U3  C22  C  CR6   0   0.361  -4.2026   0.4272   0.2267
 2U3  N23  N  NR6   0  -0.218  -5.4079   0.7235  -0.2836
 2U3  C24  C  CR16  0  -0.086  -5.5872   1.5791  -1.3270
 2U3  C25  C  CR6   0   0.173  -4.5126   2.1572  -1.9193
 2U3  C26  C  CR6   0   0.403  -3.1760   1.8872  -1.4396
 2U3  C27  C  CR16  0  -0.534  -3.0939   0.9946  -0.3406
 2U3  O28  O  OH1   0  -0.520  -6.5192   0.2388   0.3305
 2U3  O29  O  O     0  -0.563  -2.2028   2.4462  -1.9977
 2U3  O30  O  OH1   0  -0.624  -4.6649   2.9941  -2.9531
 2U3  H1   H  HNH1  0   0.407   0.0328  -0.4976  -0.3895
 2U3  H2   H  HCH1  0   0.271   1.0800   1.0989   1.8362
 2U3  H3   H  HCH2  0   0.222  -0.2746   2.3720   0.4969
 2U3  H4   H  HCH2  0   0.223   1.3481   2.8134  -0.0206
 2U3  H5   H  HOH1  0   0.468  -0.6007   1.9385  -1.5743
 2U3  H6   H  HNH1  0   0.391   3.2456   1.7936   1.9251
 2U3  H7   H  HCR5  0   0.308  -2.4232  -4.6343   0.1776
 2U3  H8   H  HNH2  0   0.402   3.0071  -4.2410  -0.4804
 2U3  H9   H  HNH2  0   0.409   2.5133  -5.7927  -0.9444
 2U3  H10  H  HCH3  0   0.255   2.5311  -1.6537   1.0477
 2U3  H11  H  HCH3  0   0.244   4.1199  -0.9438   1.2857
 2U3  H12  H  HCH3  0   0.230   2.8174  -0.5892   2.4281
 2U3  H13  H  HCH3  0   0.250   2.7444   0.9852  -1.6040
 2U3  H14  H  HCH3  0   0.235   3.9472  -0.2004  -1.0885
 2U3  H15  H  HCH3  0   0.232   2.2788  -0.6873  -1.2769
 2U3  H16  H  HCH2  0   0.272  -4.7555  -1.3753   1.2845
 2U3  H17  H  HCH2  0   0.295  -4.5307   0.0509   2.3037
 2U3  H18  H  HCR6  0   0.332  -6.6071   1.7531  -1.6387
 2U3  H19  H  HCR6  0   0.270  -2.1228   0.7692   0.0722
 2U3  H20  H  HOH1  0   0.500  -6.7777  -0.5615  -0.1528
 2U3  H21  H  HOH1  0   0.470  -3.7803   3.2891  -3.2196
 2U3  H22  H  H     0   0.511   4.1463   4.2910   0.6366
 2U3  N1   N  NH1   0  -0.368   3.3592   1.6684   0.9216

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
 2U3  N8   C7   single    1.349  0.020  1.349
 2U3  C7   N3   aromatic  1.297  0.020  1.297
 2U3  C7   S6   aromatic  1.746  0.020  1.746
 2U3  N3   C4   aromatic  1.370  0.020  1.370
 2U3  O28  N23  single    1.359  0.020  1.359
 2U3  N23  C24  single    1.361  0.020  1.361
 2U3  N23  C22  single    1.342  0.020  1.342
 2U3  C24  C25  double    1.356  0.020  1.356
 2U3  C21  C22  single    1.508  0.020  1.508
 2U3  C21  O20  single    1.406  0.020  1.406
 2U3  S6   C5   aromatic  1.721  0.020  1.721
 2U3  C22  C27  double    1.369  0.020  1.369
 2U3  C25  O30  single    1.339  0.020  1.339
 2U3  C25  C26  single    1.446  0.020  1.446
 2U3  N11  O20  single    1.369  0.020  1.369
 2U3  N11  C9   double    1.272  0.020  1.272
 2U3  C27  C26  single    1.418  0.020  1.418
 2U3  C4   C9   single    1.461  0.020  1.461
 2U3  C4   C5   aromatic  1.358  0.020  1.358
 2U3  C26  O29  double    1.253  0.020  1.253
 2U3  C9   C10  single    1.515  0.020  1.515
 2U3  O18  S16  double    1.437  0.020  1.437
 2U3  O    C    single    1.405  0.020  1.405
 2U3  N    C10  single    1.337  0.020  1.337
 2U3  N    CA   single    1.444  0.020  1.444
 2U3  C10  O12  double    1.217  0.020  1.217
 2U3  S16  O15  single    1.609  0.020  1.609
 2U3  S16  O17  double    1.435  0.020  1.435
 2U3  S16  O19  single    1.582  0.020  1.582
 2U3  O15  N1   single    1.423  0.020  1.423
 2U3  C14  C2   single    1.523  0.020  1.523
 2U3  C    CA   single    1.535  0.020  1.535
 2U3  CA   C2   single    1.557  0.020  1.557
 2U3  C2   N1   single    1.473  0.020  1.473
 2U3  C2   C13  single    1.530  0.020  1.530
 2U3  N    H1   single    0.860  0.020  1.020
 2U3  CA   H2   single    0.970  0.020  1.090
 2U3  C    H3   single    0.970  0.020  1.090
 2U3  C    H4   single    0.970  0.020  1.090
 2U3  O    H5   single    0.850  0.020  0.980
 2U3  N1   H6   single    0.890  0.020  1.040
 2U3  C5   H7   single    0.930  0.020  1.080
 2U3  N8   H8   single    0.890  0.020  1.040
 2U3  N8   H9   single    0.890  0.020  1.040
 2U3  C13  H10  single    0.970  0.020  1.090
 2U3  C13  H11  single    0.970  0.020  1.090
 2U3  C13  H12  single    0.970  0.020  1.090
 2U3  C14  H13  single    0.970  0.020  1.090
 2U3  C14  H14  single    0.970  0.020  1.090
 2U3  C14  H15  single    0.970  0.020  1.090
 2U3  C21  H16  single    0.970  0.020  1.090
 2U3  C21  H17  single    0.970  0.020  1.090
 2U3  C24  H18  single    0.930  0.020  1.080
 2U3  C27  H19  single    0.930  0.020  1.080
 2U3  O28  H20  single    0.850  0.020  0.980
 2U3  O30  H21  single    0.850  0.020  0.980
 2U3  O19  H22  single    0.850  0.020  0.980

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
 2U3  H1   N    C10  118.37  3.000
 2U3  H1   N    CA   115.79  3.000
 2U3  C10  N    CA   125.85  3.000
 2U3  H2   CA   C2   107.12  3.000
 2U3  H2   CA   C    106.88  3.000
 2U3  C2   CA   C    115.77  3.000
 2U3  H2   CA   N    107.11  3.000
 2U3  C2   CA   N    111.61  3.000
 2U3  C    CA   N    107.92  3.000
 2U3  H4   C    H3   106.87  3.000
 2U3  H4   C    O    111.33  3.000
 2U3  H3   C    O    111.29  3.000
 2U3  H4   C    CA   108.92  3.000
 2U3  H3   C    CA   106.87  3.000
 2U3  O    C    CA   111.35  3.000
 2U3  H5   O    C    109.43  3.000
 2U3  C14  C2   C13  109.44  3.000
 2U3  C13  C2   N1   111.47  3.000
 2U3  C14  C2   N1   110.49  3.000
 2U3  C13  C2   CA   110.18  3.000
 2U3  N1   C2   CA   102.44  3.000
 2U3  C14  C2   CA   112.69  3.000
 2U3  C7   N3   C4   111.00  3.000
 2U3  C9   C4   C5   125.76  3.000
 2U3  C5   C4   N3   116.25  3.000
 2U3  C9   C4   N3   117.99  3.000
 2U3  H7   C5   S6   121.60  3.000
 2U3  H7   C5   C4   129.00  3.000
 2U3  S6   C5   C4   109.39  3.000
 2U3  C7   S6   C5    89.22  3.000
 2U3  N8   C7   S6   121.22  3.000
 2U3  S6   C7   N3   114.14  3.000
 2U3  N8   C7   N3   124.57  3.000
 2U3  H9   N8   H8   114.46  3.000
 2U3  H9   N8   C7   119.16  3.000
 2U3  H8   N8   C7   116.03  3.000
 2U3  N11  C9   C10  122.66  3.000
 2U3  C10  C9   C4   118.20  3.000
 2U3  N11  C9   C4   119.12  3.000
 2U3  O12  C10  C9   120.88  3.000
 2U3  O12  C10  N    126.29  3.000
 2U3  C9   C10  N    112.82  3.000
 2U3  O20  N11  C9   112.45  3.000
 2U3  H12  C13  H11  108.26  3.000
 2U3  H12  C13  H10  108.17  3.000
 2U3  H11  C13  H10  107.33  3.000
 2U3  H12  C13  C2   111.69  3.000
 2U3  H11  C13  C2   110.54  3.000
 2U3  H10  C13  C2   110.70  3.000
 2U3  H15  C14  H14  106.61  3.000
 2U3  H15  C14  H13  108.50  3.000
 2U3  H14  C14  H13  108.43  3.000
 2U3  H15  C14  C2   109.63  3.000
 2U3  H14  C14  C2   110.65  3.000
 2U3  H13  C14  C2   112.80  3.000
 2U3  S16  O15  N1   110.31  3.000
 2U3  O19  S16  O18  110.02  3.000
 2U3  O19  S16  O17  106.28  3.000
 2U3  O18  S16  O17  121.62  3.000
 2U3  O19  S16  O15  102.51  3.000
 2U3  O17  S16  O15  103.65  3.000
 2U3  O18  S16  O15  110.95  3.000
 2U3  H22  O19  S16  112.63  3.000
 2U3  C21  O20  N11  110.65  3.000
 2U3  H17  C21  H16  108.02  3.000
 2U3  H17  C21  C22  109.42  3.000
 2U3  H16  C21  C22  111.46  3.000
 2U3  H17  C21  O20  106.57  3.000
 2U3  H16  C21  O20  110.33  3.000
 2U3  C22  C21  O20  110.88  3.000
 2U3  C27  C22  N23  118.58  3.000
 2U3  C27  C22  C21  123.38  3.000
 2U3  N23  C22  C21  118.01  3.000
 2U3  O28  N23  C24  117.57  3.000
 2U3  C24  N23  C22  123.27  3.000
 2U3  O28  N23  C22  118.94  3.000
 2U3  H18  C24  C25  123.58  3.000
 2U3  H18  C24  N23  116.53  3.000
 2U3  C25  C24  N23  119.89  3.000
 2U3  O30  C25  C26  118.57  3.000
 2U3  C26  C25  C24  120.53  3.000
 2U3  O30  C25  C24  120.90  3.000
 2U3  O29  C26  C27  125.51  3.000
 2U3  O29  C26  C25  119.13  3.000
 2U3  C27  C26  C25  115.36  3.000
 2U3  H19  C27  C26  118.69  3.000
 2U3  H19  C27  C22  118.94  3.000
 2U3  C26  C27  C22  122.36  3.000
 2U3  H20  O28  N23  106.69  3.000
 2U3  H21  O30  C25  107.37  3.000
 2U3  H6   N1   O15  102.59  3.000
 2U3  H6   N1   C2   108.74  3.000
 2U3  O15  N1   C2   110.13  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
 2U3  CONST_01  C5   S6   C7   N3     0.00   0.0  0
 2U3  CONST_02  S6   C5   C4   N3     0.00   0.0  0
 2U3  CONST_03  S6   C7   N3   C4     0.00   0.0  0
 2U3  CONST_04  C7   S6   C5   C4     0.00   0.0  0
 2U3  CONST_05  C7   N3   C4   C5     0.00   0.0  0
 2U3  CONST_06  N8   C7   N3   C4   180.00   0.0  0
 2U3  CONST_07  N8   C7   S6   C5   180.00   0.0  0
 2U3  CONST_08  C9   C4   C5   S6   180.00   0.0  0
 2U3  CONST_09  C9   C4   N3   C7   180.00   0.0  0
 2U3  CONST_10  H7   C5   C4   N3   180.00   0.0  0
 2U3  CONST_13  C9   C10  N    CA   180.00   0.0  0
 2U3  CONST_14  O12  C10  N    CA     0.00   0.0  0
 2U3  CONST_15  H1   N    C10  C9     0.00   0.0  0
 2U3  Var_01    N11  C9   C4   N3   170.08  30.0  2
 2U3  Var_02    N23  C22  C21  O20  172.04  30.0  3
 2U3  Var_03    C4   C9   C10  N     80.87  30.0  2
 2U3  Var_04    C22  C21  O20  N11  -89.50  30.0  1
 2U3  Var_05    O15  N1   C2   CA   177.79  30.0  3
 2U3  Var_06    O18  S16  O15  N1   -57.76  30.0  1
 2U3  Var_07    H13  C14  C2   CA    62.81  30.0  3
 2U3  Var_08    H10  C13  C2   CA    68.22  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
 2U3  chir_01  CA  N  C  C2  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
 2U3  plan-1  N3   0.020
 2U3  plan-1  C4   0.020
 2U3  plan-1  C5   0.020
 2U3  plan-1  S6   0.020
 2U3  plan-1  C7   0.020
 2U3  plan-1  N8   0.020
 2U3  plan-1  C9   0.020
 2U3  plan-1  H7   0.020
 2U3  plan-2  C4   0.020
 2U3  plan-2  C9   0.020
 2U3  plan-2  C10  0.020
 2U3  plan-2  N11  0.020
 2U3  plan-2  O20  0.020
 2U3  plan-3  C21  0.020
 2U3  plan-3  C22  0.020
 2U3  plan-3  N23  0.020
 2U3  plan-3  C24  0.020
 2U3  plan-3  C25  0.020
 2U3  plan-3  C26  0.020
 2U3  plan-3  C27  0.020
 2U3  plan-3  O28  0.020
 2U3  plan-3  O29  0.020
 2U3  plan-3  O30  0.020
 2U3  plan-3  H18  0.020
 2U3  plan-3  H19  0.020
 2U3  plan-4  N    0.020
 2U3  plan-4  CA   0.020
 2U3  plan-4  C9   0.020
 2U3  plan-4  C10  0.020
 2U3  plan-4  O12  0.020
 2U3  plan-4  H1   0.020
 2U3  plan-5  C7   0.020
 2U3  plan-5  N8   0.020
 2U3  plan-5  H8   0.020
 2U3  plan-5  H9   0.020

