# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 29 05:16:13 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](NC(=O)[C@@H](c1ccccc1)[S](O)(=O)=O)[C@@H]2NC(=C(CS2)C[n+]3ccccc3)C(O)=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
 3LU  3LU  1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium  ligand  53  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_3LU
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
 3LU  S1   S  S      0   1.415   3.6598  -1.6331  -0.5848
 3LU  C1   C  CR16   0  -0.300   7.2155   1.4465  -1.5800
 3LU  C2   C  CR16   0  -0.267   7.8067   1.4661  -0.3251
 3LU  C3   C  CR16   0  -0.238   7.0663   1.0789   0.7860
 3LU  C4   C  CR6    0   0.109   5.1444   0.6544  -0.6117
 3LU  C5   C  CH1    0  -0.702   3.7354   0.1862  -0.8035
 3LU  C6   C  C      0   0.609   2.7181   0.9450   0.0542
 3LU  C7   C  CH1    0  -0.189  -0.9288   0.9745  -0.1128
 3LU  C9   C  CH2    0  -0.599  -2.7529  -0.5018  -1.2839
 3LU  C10  C  C      0  -0.001  -3.6658   0.6002  -0.8138
 3LU  C11  C  CR16   0  -0.215   5.8942   1.0400  -1.7176
 3LU  N1   N  NH1    0  -0.587   1.4426   0.5708  -0.1046
 3LU  O1   O  OS    -1  -0.838   3.8351  -1.8786   0.8530
 3LU  N3   N  NH1    0  -0.642  -1.9850   1.7578   0.4233
 3LU  O2   O  OS     0  -0.690   2.3222  -2.0165  -1.0925
 3LU  S2   S  S2     0  -0.037  -1.3822  -0.8161  -0.1475
 3LU  O3   O  OS     0  -0.642   4.7539  -2.1535  -1.4195
 3LU  O4   O  O      0  -0.586   3.0573   1.8895   0.7499
 3LU  C12  C  CR16   0  -0.273   5.7472   0.6753   0.6455
 3LU  O7   O  O      0  -0.346  -3.7103   3.6356   1.1131
 3LU  O8   O  OC    -1  -0.725  -5.4392   2.2712   0.7948
 3LU  C13  C  CH1    0  -0.153   0.3832   1.2034   0.6362
 3LU  C14  C  C      0   0.354   0.2846   0.7496   2.1206
 3LU  C15  C  C      0   0.272  -3.2847   1.5752   0.0485
 3LU  H1   H  HCR6   0   0.239   7.7806   1.7432  -2.4543
 3LU  H2   H  HCR6   0   0.245   8.8365   1.7794  -0.2103
 3LU  H3   H  HCR6   0   0.254   7.5204   1.0906   1.7688
 3LU  H4   H  HCH1   0   0.298   3.4439   0.3373  -1.8485
 3LU  H5   H  HCH1   0   0.287  -0.7782   1.2392  -1.1649
 3LU  H6   H  HCH2   0   0.245  -3.3066  -1.4440  -1.3470
 3LU  H7   H  HCH2   0   0.276  -2.3614  -0.3155  -2.2889
 3LU  H9   H  HCR6   0   0.249   5.4412   1.0235  -2.7020
 3LU  H10  H  HNH1   0   0.379   1.2669  -0.3345  -0.5286
 3LU  H11  H  HCR6   0   0.272   5.1889   0.3730   1.5205
 3LU  H14  H  HCH1   0   0.312   0.5539   2.2840   0.6212
 3LU  H15  H  HCH2   0   0.348  -4.9505   0.3622  -2.5000
 3LU  N2   N  N      1  -0.372  -5.8213  -0.6242  -0.9058
 3LU  H17  H  HCH2   0   0.315  -5.6124   1.4312  -1.2621
 3LU  C19  C  C1     0   0.146  -5.9618  -0.7777   0.4174
 3LU  C17  C  C1     0  -0.347  -6.6875  -1.8330   0.9247
 3LU  C20  C  C1     0  -0.121  -7.2707  -2.7405   0.0543
 3LU  C21  C  C1     0  -0.263  -7.1177  -2.5579  -1.3121
 3LU  C22  C  C1     0   0.079  -6.3823  -1.4851  -1.7655
 3LU  H16  H  H      0   0.352  -5.4969  -0.0189   1.0313
 3LU  H18  H  H      0   0.271  -6.7883  -1.9340   1.9948
 3LU  H19  H  H      0   0.249  -7.8403  -3.5765   0.4344
 3LU  H20  H  H      0   0.263  -7.5543  -3.2389  -2.0271
 3LU  H21  H  H      0   0.308  -6.2285  -1.2923  -2.8173
 3LU  H22  H  HNH1   0   0.371  -1.8182   2.1081   1.3601
 3LU  O5   O  OC    -1  -0.684  -0.4600   1.4658   2.8296
 3LU  C8   C  C      0   0.279  -4.2383   2.5940   0.6985
 3LU  O6   O  O      0  -0.456   0.9227  -0.2505   2.4576
 3LU  C16  C  CH2    0  -0.524  -5.0239   0.5328  -1.4250

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
 3LU  O6   C14  deloc     1.233  0.020  1.233
 3LU  C14  O5   deloc     1.253  0.020  1.253
 3LU  C14  C13  single    1.555  0.020  1.555
 3LU  C7   C13  single    1.528  0.020  1.528
 3LU  C7   N3   single    1.420  0.020  1.420
 3LU  C7   S2   single    1.847  0.020  1.847
 3LU  C13  N1   single    1.439  0.020  1.439
 3LU  N3   C15  single    1.365  0.020  1.365
 3LU  S2   C9   single    1.808  0.020  1.808
 3LU  C9   C10  single    1.506  0.020  1.506
 3LU  O7   C8   deloc     1.239  0.020  1.239
 3LU  C15  C8   single    1.539  0.020  1.539
 3LU  C15  C10  double    1.356  0.020  1.356
 3LU  N1   C6   single    1.339  0.020  1.339
 3LU  C8   O8   deloc     1.247  0.020  1.247
 3LU  C10  C16  single    1.491  0.020  1.491
 3LU  O4   C6   double    1.221  0.020  1.221
 3LU  C6   C5   single    1.532  0.020  1.532
 3LU  O3   S1   deloc     1.471  0.020  1.471
 3LU  C5   S1   single    1.834  0.020  1.834
 3LU  C5   C4   single    1.497  0.020  1.497
 3LU  S1   O2   deloc     1.481  0.020  1.481
 3LU  S1   O1   deloc     1.469  0.020  1.469
 3LU  C4   C11  aromatic  1.391  0.020  1.391
 3LU  C4   C12  aromatic  1.394  0.020  1.394
 3LU  C11  C1   aromatic  1.389  0.020  1.389
 3LU  C12  C3   aromatic  1.387  0.020  1.387
 3LU  C1   C2   aromatic  1.387  0.020  1.387
 3LU  C3   C2   aromatic  1.390  0.020  1.390
 3LU  C1   H1   single    0.930  0.020  1.080
 3LU  C2   H2   single    0.930  0.020  1.080
 3LU  C3   H3   single    0.930  0.020  1.080
 3LU  C5   H4   single    0.970  0.020  1.090
 3LU  C7   H5   single    0.970  0.020  1.090
 3LU  C9   H6   single    0.970  0.020  1.090
 3LU  C9   H7   single    0.970  0.020  1.090
 3LU  C11  H9   single    0.930  0.020  1.080
 3LU  N1   H10  single    0.860  0.020  1.020
 3LU  C12  H11  single    0.930  0.020  1.080
 3LU  C13  H14  single    0.970  0.020  1.090
 3LU  C16  H15  single    0.970  0.020  1.090
 3LU  C16  N2   single    1.498  0.020  1.498
 3LU  C16  H17  single    0.970  0.020  1.090
 3LU  N2   C19  aromatic  1.339  0.020  1.339
 3LU  C19  C17  aromatic  1.378  0.020  1.378
 3LU  C17  C20  aromatic  1.386  0.020  1.386
 3LU  C20  C21  aromatic  1.387  0.020  1.387
 3LU  C21  C22  aromatic  1.377  0.020  1.377
 3LU  C22  N2   aromatic  1.340  0.020  1.340
 3LU  C19  H16  single    0.930  0.020  1.080
 3LU  C17  H18  single    0.930  0.020  1.080
 3LU  C20  H19  single    0.930  0.020  1.080
 3LU  C21  H20  single    0.930  0.020  1.080
 3LU  C22  H21  single    0.930  0.020  1.080
 3LU  N3   H22  single    0.890  0.020  1.040

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
 3LU  O3   S1   O2   112.68  3.000
 3LU  O2   S1   O1   113.57  3.000
 3LU  O3   S1   O1   114.04  3.000
 3LU  O1   S1   C5   106.11  3.000
 3LU  O2   S1   C5   104.66  3.000
 3LU  O3   S1   C5   104.63  3.000
 3LU  H1   C1   C11  119.78  3.000
 3LU  H1   C1   C2   120.28  3.000
 3LU  C11  C1   C2   119.94  3.000
 3LU  H2   C2   C3   120.16  3.000
 3LU  H2   C2   C1   120.36  3.000
 3LU  C3   C2   C1   119.47  3.000
 3LU  H3   C3   C12  119.61  3.000
 3LU  H3   C3   C2   119.94  3.000
 3LU  C12  C3   C2   120.45  3.000
 3LU  C12  C4   C11  118.67  3.000
 3LU  C12  C4   C5   121.81  3.000
 3LU  C11  C4   C5   119.49  3.000
 3LU  H4   C5   C6   106.80  3.000
 3LU  H4   C5   C4   109.24  3.000
 3LU  C6   C5   C4   113.47  3.000
 3LU  H4   C5   S1   103.87  3.000
 3LU  C4   C5   S1   109.50  3.000
 3LU  C6   C5   S1   113.41  3.000
 3LU  O4   C6   N1   123.26  3.000
 3LU  O4   C6   C5   121.18  3.000
 3LU  N1   C6   C5   115.33  3.000
 3LU  H5   C7   C13  108.46  3.000
 3LU  H5   C7   S2   104.47  3.000
 3LU  C13  C7   S2   111.41  3.000
 3LU  H5   C7   N3   109.37  3.000
 3LU  S2   C7   N3   111.05  3.000
 3LU  C13  C7   N3   111.78  3.000
 3LU  H7   C9   H6   105.93  3.000
 3LU  H7   C9   S2   109.61  3.000
 3LU  H6   C9   S2   105.67  3.000
 3LU  H7   C9   C10  112.26  3.000
 3LU  H6   C9   C10  109.94  3.000
 3LU  S2   C9   C10  112.99  3.000
 3LU  C16  C10  C15  123.31  3.000
 3LU  C16  C10  C9   113.02  3.000
 3LU  C15  C10  C9   123.65  3.000
 3LU  H9   C11  C4   119.52  3.000
 3LU  H9   C11  C1   119.47  3.000
 3LU  C4   C11  C1   121.01  3.000
 3LU  H10  N1   C13  118.66  3.000
 3LU  H10  N1   C6   117.63  3.000
 3LU  C13  N1   C6   121.16  3.000
 3LU  H22  N3   C15  117.16  3.000
 3LU  H22  N3   C7   114.65  3.000
 3LU  C15  N3   C7   122.06  3.000
 3LU  C9   S2   C7    91.68  3.000
 3LU  H11  C12  C4   120.15  3.000
 3LU  H11  C12  C3   119.39  3.000
 3LU  C4   C12  C3   120.46  3.000
 3LU  H14  C13  C14  108.13  3.000
 3LU  H14  C13  N1   108.19  3.000
 3LU  C14  C13  N1   114.19  3.000
 3LU  H14  C13  C7   105.96  3.000
 3LU  N1   C13  C7   108.30  3.000
 3LU  C14  C13  C7   111.70  3.000
 3LU  C13  C14  O6   117.69  3.000
 3LU  C13  C14  O5   114.26  3.000
 3LU  O6   C14  O5   128.05  3.000
 3LU  N3   C15  C10  122.57  3.000
 3LU  C10  C15  C8   124.76  3.000
 3LU  N3   C15  C8   112.67  3.000
 3LU  C22  N2   C19  121.09  3.000
 3LU  C22  N2   C16  119.78  3.000
 3LU  C19  N2   C16  119.13  3.000
 3LU  H16  C19  C17  123.72  3.000
 3LU  H16  C19  N2   115.81  3.000
 3LU  C17  C19  N2   120.45  3.000
 3LU  H18  C17  C20  121.47  3.000
 3LU  H18  C17  C19  119.06  3.000
 3LU  C20  C17  C19  119.47  3.000
 3LU  H19  C20  C21  120.43  3.000
 3LU  H19  C20  C17  120.49  3.000
 3LU  C21  C20  C17  119.08  3.000
 3LU  H20  C21  C22  119.29  3.000
 3LU  H20  C21  C20  121.66  3.000
 3LU  C22  C21  C20  119.06  3.000
 3LU  H21  C22  C21  122.38  3.000
 3LU  H21  C22  N2   116.77  3.000
 3LU  C21  C22  N2   120.85  3.000
 3LU  C15  C8   O8   117.24  3.000
 3LU  O8   C8   O7   127.01  3.000
 3LU  C15  C8   O7   115.70  3.000
 3LU  H17  C16  N2   107.36  3.000
 3LU  H17  C16  H15  108.28  3.000
 3LU  N2   C16  H15  104.87  3.000
 3LU  H17  C16  C10  113.24  3.000
 3LU  N2   C16  C10  112.19  3.000
 3LU  H15  C16  C10  110.47  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
 3LU  CONST_01  C12  C4   C11  C1      0.00   0.0  0
 3LU  CONST_02  C12  C3   C2   C1      0.00   0.0  0
 3LU  CONST_03  C4   C11  C1   C2      0.00   0.0  0
 3LU  CONST_04  C4   C12  C3   C2      0.00   0.0  0
 3LU  CONST_05  C11  C4   C12  C3      0.00   0.0  0
 3LU  CONST_06  C11  C1   C2   C3      0.00   0.0  0
 3LU  CONST_07  C20  C17  C19  N2      0.00   0.0  0
 3LU  CONST_08  C20  C21  C22  N2      0.00   0.0  0
 3LU  CONST_09  C21  C22  N2   C19     0.00   0.0  0
 3LU  CONST_10  C21  C20  C17  C19     0.00   0.0  0
 3LU  CONST_11  C22  N2   C19  C17     0.00   0.0  0
 3LU  CONST_12  C22  C21  C20  C17     0.00   0.0  0
 3LU  CONST_13  C5   C4   C11  C1    180.00   0.0  0
 3LU  CONST_14  C5   C4   C12  C3    180.00   0.0  0
 3LU  CONST_15  C17  C19  N2   C16   180.00   0.0  0
 3LU  CONST_16  C21  C22  N2   C16   180.00   0.0  0
 3LU  CONST_17  H3   C3   C2   C1    180.00   0.0  0
 3LU  CONST_18  H9   C11  C1   C2    180.00   0.0  0
 3LU  CONST_19  H11  C12  C3   C2    180.00   0.0  0
 3LU  CONST_20  H1   C1   C2   C3    180.00   0.0  0
 3LU  CONST_21  H2   C2   C1   C11   180.00   0.0  0
 3LU  CONST_22  H18  C17  C19  N2    180.00   0.0  0
 3LU  CONST_23  H20  C21  C22  N2    180.00   0.0  0
 3LU  CONST_24  H21  C22  N2   C19   180.00   0.0  0
 3LU  CONST_25  H19  C20  C17  C19   180.00   0.0  0
 3LU  CONST_26  H16  C19  C17  C20   180.00   0.0  0
 3LU  CONST_27  C13  N1   C6   C5    180.00   0.0  0
 3LU  CONST_28  C13  N1   C6   O4      0.00   0.0  0
 3LU  Var_01    C10  C15  N3   C7      2.92  30.0  1
 3LU  Var_02    C10  C9   S2   C7    -51.11  30.0  1
 3LU  Var_03    N3   C15  C10  C9      9.56  30.0  1
 3LU  Var_04    C15  C10  C9   S2     23.27  30.0  1
 3LU  Var_05    N2   C16  C10  C9     70.68  30.0  3
 3LU  Var_06    C19  N2   C16  C10    52.88  30.0  2
 3LU  Var_07    O7   C8   C15  C10  -158.65  30.0  2

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
 3LU  chir_01  C5   C6  S1  C4   positiv
 3LU  chir_02  C7   S2  N3  C13  negativ
 3LU  chir_03  C13  N1  C7  C14  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
 3LU  plan-1  C1   0.020
 3LU  plan-1  C2   0.020
 3LU  plan-1  C3   0.020
 3LU  plan-1  C4   0.020
 3LU  plan-1  C5   0.020
 3LU  plan-1  C11  0.020
 3LU  plan-1  C12  0.020
 3LU  plan-1  H1   0.020
 3LU  plan-1  H2   0.020
 3LU  plan-1  H3   0.020
 3LU  plan-1  H9   0.020
 3LU  plan-1  H11  0.020
 3LU  plan-2  N2   0.020
 3LU  plan-2  C19  0.020
 3LU  plan-2  C17  0.020
 3LU  plan-2  C20  0.020
 3LU  plan-2  C21  0.020
 3LU  plan-2  C22  0.020
 3LU  plan-2  H16  0.020
 3LU  plan-2  H18  0.020
 3LU  plan-2  H19  0.020
 3LU  plan-2  H20  0.020
 3LU  plan-2  H21  0.020
 3LU  plan-2  C16  0.020
 3LU  plan-3  C5   0.020
 3LU  plan-3  C6   0.020
 3LU  plan-3  N1   0.020
 3LU  plan-3  O4   0.020
 3LU  plan-3  C13  0.020
 3LU  plan-3  H10  0.020
 3LU  plan-4  C7   0.020
 3LU  plan-4  N3   0.020
 3LU  plan-4  C15  0.020
 3LU  plan-4  H22  0.020
 3LU  plan-5  C13  0.020
 3LU  plan-5  C14  0.020
 3LU  plan-5  O5   0.020
 3LU  plan-5  O6   0.020
 3LU  plan-6  O7   0.020
 3LU  plan-6  O8   0.020
 3LU  plan-6  C15  0.020
 3LU  plan-6  C8   0.020

