# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 16:09:08 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  55  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 PERFECT
;

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  -0.608   0.7370  -0.1654  -0.6864
 2U3  CA   C  CH1    0  -0.129   1.7746   0.8378  -0.8043
 2U3  C    C  CH2    0  -0.141   1.8276   1.3216  -2.2500
 2U3  O    O  OH1    0  -0.668   1.9550   0.2225  -3.1238
 2U3  C2   C  CT     0   0.079   3.1130   0.3452  -0.1814
 2U3  N3   N  N      0  -0.453   0.2037  -2.5141   1.5762
 2U3  C4   C  CR5    0   0.358  -0.8477  -2.5397   0.6994
 2U3  C5   C  CR15   0  -0.546  -1.4247  -3.7503   0.4884
 2U3  S6   S  S2     0   0.197  -0.6279  -4.9375   1.4474
 2U3  C7   C  CR5    0   0.274   0.4409  -3.6959   2.0527
 2U3  N8   N  NH2    0  -0.818   1.3787  -3.9737   2.9835
 2U3  C9   C  C      0   0.030  -1.2359  -1.2842   0.0619
 2U3  C10  C  C      0   0.521  -0.2794  -0.1165   0.1770
 2U3  N11  N  N      0  -0.106  -2.3658  -1.2046  -0.5133
 2U3  O12  O  O      0  -0.467  -0.4726   0.7492   1.0125
 2U3  C13  C  CH3    0  -0.679   2.8823   0.0223   1.2989
 2U3  C14  C  CH3    0  -0.643   3.6807  -0.8841  -0.8819
 2U3  O15  O  OC2    0  -0.525   5.2604   1.1995   0.2450
 2U3  S16  S  S      0   1.576   6.5229   1.5966  -0.7595
 2U3  O17  O  OS     0  -0.745   7.6346   1.2049   0.1064
 2U3  O18  O  OS     0  -0.727   6.3754   0.7910  -1.9697
 2U3  O19  O  OS    -1  -0.745   6.3985   3.0377  -0.9837
 2U3  O20  O  O2     0  -0.382  -2.5467  -0.0006  -1.1364
 2U3  C21  C  CH2    0  -0.204  -3.8911   0.1492  -1.5138
 2U3  C22  C  CR6    0   0.353  -4.7501   0.5830  -0.3519
 2U3  N23  N  NR6    0  -0.222  -6.0800   0.6166  -0.5514
 2U3  C24  C  CR16   0  -0.094  -6.9732   0.9806   0.4129
 2U3  C25  C  CR6    0   0.153  -6.5238   1.3552   1.6332
 2U3  C26  C  CR6    0   0.370  -5.1033   1.3723   1.9356
 2U3  C27  C  CR16   0  -0.546  -4.2541   0.9617   0.8661
 2U3  O28  O  OH1    0  -0.524  -6.5812   0.2032  -1.7461
 2U3  O29  O  O      0  -0.529  -4.7283   1.7274   3.0659
 2U3  O30  O  OH1    0  -0.629  -7.3681   1.7270   2.6052
 2U3  H1   H  HNH1   0   0.408   0.7452  -0.9112  -1.3655
 2U3  H2   H  HCH1   0   0.269   1.4511   1.6999  -0.2133
 2U3  H3   H  HCH2   0   0.214   0.8967   1.8687  -2.4419
 2U3  H4   H  HCH2   0   0.216   2.6532   2.0305  -2.3598
 2U3  H5   H  HOH1   0   0.461   1.7931   0.5308  -4.0196
 2U3  H6   H  HNH1   0   0.357   3.6597   2.2684   0.1804
 2U3  H7   H  HCR5   0   0.307  -2.2378  -4.0085  -0.1704
 2U3  H8   H  HNH2   0   0.403   2.0774  -3.2616   3.1273
 2U3  H9   H  HNH2   0   0.408   1.7286  -4.9147   3.0541
 2U3  H10  H  HCH3   0   0.253   2.1835  -0.8044   1.4221
 2U3  H11  H  HCH3   0   0.236   3.8185  -0.2670   1.7772
 2U3  H12  H  HCH3   0   0.220   2.4793   0.8840   1.8361
 2U3  H13  H  HCH3   0   0.245   3.9814  -0.6720  -1.9033
 2U3  H14  H  HCH3   0   0.227   4.5498  -1.2561  -0.3407
 2U3  H15  H  HCH3   0   0.214   2.9436  -1.6874  -0.8941
 2U3  H16  H  HCH2   0   0.291  -3.9004   0.9157  -2.2916
 2U3  H17  H  HCH2   0   0.272  -4.2677  -0.7784  -1.9517
 2U3  H18  H  HCR6   0   0.325  -8.0179   0.9521   0.1380
 2U3  H19  H  HCR6   0   0.278  -3.1859   0.9582   1.0331
 2U3  H20  H  HOH1   0   0.497  -6.6916   0.9974  -2.2913
 2U3  H21  H  HOH1   0   0.464  -6.8180   1.9428   3.3761
 2U3  N1   N  NH1    0  -0.342   4.0209   1.4847  -0.3588

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    1.350  0.020  1.350
 2U3  C7   N3   aromatic  1.296  0.020  1.296
 2U3  C7   S6   aromatic  1.746  0.020  1.746
 2U3  N3   C4   aromatic  1.369  0.020  1.369
 2U3  O28  N23  single    1.360  0.020  1.360
 2U3  N23  C24  single    1.364  0.020  1.364
 2U3  N23  C22  single    1.345  0.020  1.345
 2U3  C24  C25  double    1.353  0.020  1.353
 2U3  C21  C22  single    1.509  0.020  1.509
 2U3  C21  O20  single    1.404  0.020  1.404
 2U3  S6   C5   aromatic  1.722  0.020  1.722
 2U3  C22  C27  double    1.369  0.020  1.369
 2U3  C25  O30  single    1.340  0.020  1.340
 2U3  C25  C26  single    1.452  0.020  1.452
 2U3  N11  O20  single    1.368  0.020  1.368
 2U3  N11  C9   double    1.270  0.020  1.270
 2U3  C27  C26  single    1.426  0.020  1.426
 2U3  C4   C9   single    1.461  0.020  1.461
 2U3  C4   C5   aromatic  1.358  0.020  1.358
 2U3  C26  O29  double    1.243  0.020  1.243
 2U3  C9   C10  single    1.514  0.020  1.514
 2U3  O18  S16  deloc     1.461  0.020  1.461
 2U3  O    C    single    1.410  0.020  1.410
 2U3  N    C10  single    1.335  0.020  1.335
 2U3  N    CA   single    1.448  0.020  1.448
 2U3  C10  O12  double    1.219  0.020  1.219
 2U3  S16  O15  single    1.661  0.020  1.661
 2U3  S16  O17  deloc     1.463  0.020  1.463
 2U3  S16  O19  deloc     1.464  0.020  1.464
 2U3  O15  N1   single    1.408  0.020  1.408
 2U3  C14  C2   single    1.525  0.020  1.525
 2U3  C    CA   single    1.525  0.020  1.525
 2U3  CA   C2   single    1.556  0.020  1.556
 2U3  C2   N1   single    1.468  0.020  1.468
 2U3  C2   C13  single    1.533  0.020  1.533
 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

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  117.96  3.000
 2U3  H1   N    CA   116.85  3.000
 2U3  C10  N    CA   124.96  3.000
 2U3  H2   CA   C2   106.71  3.000
 2U3  H2   CA   C    105.80  3.000
 2U3  C2   CA   C    116.74  3.000
 2U3  H2   CA   N    106.86  3.000
 2U3  C2   CA   N    111.37  3.000
 2U3  C    CA   N    108.77  3.000
 2U3  H4   C    H3   107.45  3.000
 2U3  H4   C    O    112.01  3.000
 2U3  H3   C    O    110.93  3.000
 2U3  H4   C    CA   109.08  3.000
 2U3  H3   C    CA   107.13  3.000
 2U3  O    C    CA   110.08  3.000
 2U3  H5   O    C    108.20  3.000
 2U3  C14  C2   C13  109.26  3.000
 2U3  C13  C2   N1   111.93  3.000
 2U3  C14  C2   N1   109.88  3.000
 2U3  C13  C2   CA   108.90  3.000
 2U3  N1   C2   CA   103.76  3.000
 2U3  C14  C2   CA   113.05  3.000
 2U3  C7   N3   C4   111.03  3.000
 2U3  C9   C4   C5   125.85  3.000
 2U3  C5   C4   N3   116.27  3.000
 2U3  C9   C4   N3   117.87  3.000
 2U3  H7   C5   S6   121.63  3.000
 2U3  H7   C5   C4   128.99  3.000
 2U3  S6   C5   C4   109.36  3.000
 2U3  C7   S6   C5    89.20  3.000
 2U3  N8   C7   S6   121.18  3.000
 2U3  S6   C7   N3   114.13  3.000
 2U3  N8   C7   N3   124.62  3.000
 2U3  H9   N8   H8   114.17  3.000
 2U3  H9   N8   C7   118.83  3.000
 2U3  H8   N8   C7   115.75  3.000
 2U3  N11  C9   C10  123.23  3.000
 2U3  C10  C9   C4   117.51  3.000
 2U3  N11  C9   C4   119.20  3.000
 2U3  O12  C10  C9   120.00  3.000
 2U3  O12  C10  N    126.19  3.000
 2U3  C9   C10  N    113.81  3.000
 2U3  O20  N11  C9   112.28  3.000
 2U3  H12  C13  H11  108.08  3.000
 2U3  H12  C13  H10  107.84  3.000
 2U3  H11  C13  H10  107.45  3.000
 2U3  H12  C13  C2   111.36  3.000
 2U3  H11  C13  C2   110.51  3.000
 2U3  H10  C13  C2   111.44  3.000
 2U3  H15  C14  H14  107.06  3.000
 2U3  H15  C14  H13  108.70  3.000
 2U3  H14  C14  H13  108.25  3.000
 2U3  H15  C14  C2   110.33  3.000
 2U3  H14  C14  C2   110.13  3.000
 2U3  H13  C14  C2   112.20  3.000
 2U3  S16  O15  N1   111.17  3.000
 2U3  O19  S16  O18  114.04  3.000
 2U3  O19  S16  O17  114.77  3.000
 2U3  O18  S16  O17  114.79  3.000
 2U3  O19  S16  O15  105.27  3.000
 2U3  O17  S16  O15   98.95  3.000
 2U3  O18  S16  O15  106.99  3.000
 2U3  C21  O20  N11  110.06  3.000
 2U3  H17  C21  H16  107.91  3.000
 2U3  H17  C21  C22  110.89  3.000
 2U3  H16  C21  C22  109.99  3.000
 2U3  H17  C21  O20  110.31  3.000
 2U3  H16  C21  O20  105.93  3.000
 2U3  C22  C21  O20  111.64  3.000
 2U3  C27  C22  N23  118.91  3.000
 2U3  C27  C22  C21  123.96  3.000
 2U3  N23  C22  C21  117.12  3.000
 2U3  O28  N23  C24  117.45  3.000
 2U3  C24  N23  C22  123.32  3.000
 2U3  O28  N23  C22  119.14  3.000
 2U3  H18  C24  C25  123.90  3.000
 2U3  H18  C24  N23  116.50  3.000
 2U3  C25  C24  N23  119.60  3.000
 2U3  O30  C25  C26  117.51  3.000
 2U3  C26  C25  C24  121.05  3.000
 2U3  O30  C25  C24  121.44  3.000
 2U3  O29  C26  C27  125.78  3.000
 2U3  O29  C26  C25  119.20  3.000
 2U3  C27  C26  C25  115.02  3.000
 2U3  H19  C27  C26  118.26  3.000
 2U3  H19  C27  C22  119.65  3.000
 2U3  C26  C27  C22  122.09  3.000
 2U3  H20  O28  N23  106.68  3.000
 2U3  H21  O30  C25  106.29  3.000
 2U3  H6   N1   O15  103.96  3.000
 2U3  H6   N1   C2   108.32  3.000
 2U3  O15  N1   C2   109.60  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   -164.51  30.0  2
 2U3  Var_02    N23  C22  C21  O20  -172.81  30.0  3
 2U3  Var_03    C4   C9   C10  N      80.21  30.0  1
 2U3  Var_04    C22  C21  O20  N11    80.18  30.0  1
 2U3  Var_05    O15  N1   C2   CA    176.29  30.0  3
 2U3  Var_06    O18  S16  O15  N1    -60.59  30.0  3
 2U3  Var_07    H13  C14  C2   CA     65.88  30.0  3
 2U3  Var_08    H10  C13  C2   CA     64.10  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

