# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:33:42 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (6~{R},7~{R})-7-[[(2~{Z})-2-(2-azanyl-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-3-[(1-methylpyrrolidin-1-ium-1-yl)methyl]-8-oxidanylidene-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO\N=C(/C(=O)N[C@H]1[C@H]2SCC(=C(N2C1=O)C(O)=O)C[N+]3(C)CCCC3)c4csc(N)n4
#
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
 9WT  9WT  '(6~{R},7~{R})-7-[[(2~{Z})-2-(2-azanyl-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-3-[(1-methylpyrrolidin-1-ium-1-yl)methyl]-8-oxidanylidene-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  56  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9WT
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
 9WT  S01  S  S2     0   0.068   0.1006   1.0052  -0.2891
 9WT  S02  S  S2     0   0.197  -4.4090   3.8835   0.4367
 9WT  O03  O  O      0  -0.399  -0.2858  -3.2560   0.7210
 9WT  O04  O  OC    -1  -0.570   3.2226  -2.5637   1.9745
 9WT  O05  O  O      0  -0.569   2.8135  -3.5246  -0.0035
 9WT  O06  O  O      0  -0.446  -3.5332  -0.9748  -2.2068
 9WT  O07  O  O2     0  -0.389  -5.4236  -1.9445   0.0909
 9WT  N08  N  NT     1  -0.387   5.1407   0.2775   0.0389
 9WT  N09  N  N      0  -0.503   0.9145  -1.5379  -0.3601
 9WT  N10  N  NH1    0  -0.611  -2.2621  -1.0203  -0.3266
 9WT  N11  N  N      0  -0.093  -5.4419  -0.6052   0.2907
 9WT  N12  N  N      0  -0.456  -3.1464   1.9537  -0.6791
 9WT  N13  N  NH2    0  -0.819  -2.0912   4.0198  -0.9688
 9WT  C14  C  CH2    0  -0.323   6.3791   0.5855   0.8315
 9WT  C15  C  CH2    0  -0.334   5.0777   1.4216  -0.9291
 9WT  C16  C  CH2    0  -0.422   3.9485   0.2028   0.9641
 9WT  C17  C  CH2    0  -0.490   7.3805   1.1070  -0.1893
 9WT  C18  C  CH2    0  -0.480   6.5243   1.6750  -1.3394
 9WT  C19  C  CH3    0  -0.561   5.3213  -1.0046  -0.6909
 9WT  C20  C  C      0   0.005   2.6369  -0.0715   0.2950
 9WT  C21  C  C      0  -0.190   0.1395  -0.5892  -1.1342
 9WT  C22  C  C      0  -0.273  -1.0842  -1.5247  -0.9422
 9WT  C23  C  C      0   0.211   2.1295  -1.3180   0.2677
 9WT  C24  C  CH2    0  -0.650   1.9188   1.1264  -0.2822
 9WT  C25  C  C      0   0.546  -0.1530  -2.3351  -0.0338
 9WT  C26  C  C      0   0.381   2.7863  -2.5952   0.8137
 9WT  C27  C  C      0   0.508  -3.3741  -0.7292  -1.0293
 9WT  C28  C  C      0   0.022  -4.4385  -0.0202  -0.2236
 9WT  C29  C  CR5    0   0.357  -4.2670   1.4242  -0.0989
 9WT  C30  C  CR15   0  -0.552  -5.0787   2.2992   0.5479
 9WT  C31  C  CR5    0   0.269  -3.0731   3.2313  -0.4787
 9WT  C32  C  CH3    0  -0.389  -6.5495  -2.5527   0.7025
 9WT  H2   H  HNH1   0   0.421  -2.2118  -0.7227   0.6365
 9WT  H3   H  HNH2   0   0.406  -1.9239   4.9106  -0.5312
 9WT  H4   H  HNH2   0   0.397  -1.2513   3.5296  -1.2395
 9WT  H5   H  HCH2   0   0.302   6.1147   1.3546   1.5571
 9WT  H6   H  HCH2   0   0.308   6.6954  -0.3070   1.3670
 9WT  H7   H  HCH2   0   0.305   4.4167   1.1679  -1.7542
 9WT  H8   H  HCH2   0   0.303   4.6649   2.2725  -0.3886
 9WT  H9   H  HCH2   0   0.322   4.1777  -0.5712   1.6916
 9WT  H10  H  HCH2   0   0.309   3.9190   1.1626   1.4817
 9WT  H11  H  HCH2   0   0.283   8.0120   1.8656   0.2683
 9WT  H12  H  HCH2   0   0.272   8.0343   0.3111  -0.5418
 9WT  H13  H  HCH2   0   0.272   6.7586   1.1852  -2.2828
 9WT  H14  H  HCH2   0   0.283   6.6836   2.7416  -1.4820
 9WT  H15  H  HCH3   0   0.290   5.4370  -1.8087   0.0308
 9WT  H16  H  HCH3   0   0.296   4.4560  -1.1900  -1.3200
 9WT  H17  H  HCH3   0   0.306   6.2102  -0.9504  -1.3131
 9WT  H19  H  H      0   0.320   0.4917  -0.4723  -2.1594
 9WT  H20  H  H      0   0.338  -1.3399  -2.0463  -1.8646
 9WT  H22  H  HCH2   0   0.297   2.2386   1.3423  -1.3045
 9WT  H23  H  HCH2   0   0.302   2.1502   2.0125   0.3114
 9WT  H24  H  HCR5   0   0.306  -5.9996   2.1109   1.0754
 9WT  H25  H  HCH3   0   0.245  -6.4624  -3.6172   0.4985
 9WT  H26  H  HCH3   0   0.228  -6.5531  -2.3940   1.7823
 9WT  H27  H  HCH3   0   0.228  -7.4844  -2.1820   0.2788

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
 9WT  O06  C27  double    1.213  0.020  1.213
 9WT  O03  C25  double    1.198  0.020  1.198
 9WT  C19  N08  single    1.486  0.020  1.486
 9WT  S02  C30  aromatic  1.724  0.020  1.724
 9WT  S02  C31  aromatic  1.746  0.020  1.746
 9WT  C18  C17  single    1.542  0.020  1.542
 9WT  C18  C15  single    1.525  0.020  1.525
 9WT  C30  C29  aromatic  1.358  0.020  1.358
 9WT  N13  C31  single    1.351  0.020  1.351
 9WT  C31  N12  aromatic  1.295  0.020  1.295
 9WT  C25  N09  single    1.372  0.020  1.372
 9WT  C25  C22  single    1.533  0.020  1.533
 9WT  C27  C28  single    1.512  0.020  1.512
 9WT  C27  N10  single    1.347  0.020  1.347
 9WT  C29  N12  aromatic  1.369  0.020  1.369
 9WT  C29  C28  single    1.460  0.020  1.460
 9WT  C17  C14  single    1.522  0.020  1.522
 9WT  C15  N08  single    1.500  0.020  1.500
 9WT  C23  N09  single    1.385  0.020  1.385
 9WT  C23  C20  double    1.346  0.020  1.346
 9WT  C23  C26  single    1.536  0.020  1.536
 9WT  N08  C14  single    1.502  0.020  1.502
 9WT  N08  C16  single    1.511  0.020  1.511
 9WT  C28  N11  double    1.270  0.020  1.270
 9WT  N09  C21  single    1.449  0.020  1.449
 9WT  C20  C24  single    1.511  0.020  1.511
 9WT  C20  C16  single    1.498  0.020  1.498
 9WT  C26  O05  deloc     1.238  0.020  1.238
 9WT  C26  O04  deloc     1.241  0.020  1.241
 9WT  C24  S01  single    1.822  0.020  1.822
 9WT  C22  N10  single    1.422  0.020  1.422
 9WT  C22  C21  single    1.552  0.020  1.552
 9WT  N11  O07  single    1.354  0.020  1.354
 9WT  S01  C21  single    1.805  0.020  1.805
 9WT  O07  C32  single    1.418  0.020  1.418
 9WT  N10  H2   single    0.860  0.020  1.020
 9WT  N13  H3   single    0.890  0.020  1.040
 9WT  N13  H4   single    0.890  0.020  1.040
 9WT  C14  H5   single    0.970  0.020  1.090
 9WT  C14  H6   single    0.970  0.020  1.090
 9WT  C15  H7   single    0.970  0.020  1.090
 9WT  C15  H8   single    0.970  0.020  1.090
 9WT  C16  H9   single    0.970  0.020  1.090
 9WT  C16  H10  single    0.970  0.020  1.090
 9WT  C17  H11  single    0.970  0.020  1.090
 9WT  C17  H12  single    0.970  0.020  1.090
 9WT  C18  H13  single    0.970  0.020  1.090
 9WT  C18  H14  single    0.970  0.020  1.090
 9WT  C19  H15  single    0.970  0.020  1.090
 9WT  C19  H16  single    0.970  0.020  1.090
 9WT  C19  H17  single    0.970  0.020  1.090
 9WT  C21  H19  single    0.970  0.020  1.090
 9WT  C22  H20  single    0.970  0.020  1.090
 9WT  C24  H22  single    0.970  0.020  1.090
 9WT  C24  H23  single    0.970  0.020  1.090
 9WT  C30  H24  single    0.930  0.020  1.080
 9WT  C32  H25  single    0.970  0.020  1.090
 9WT  C32  H26  single    0.970  0.020  1.090
 9WT  C32  H27  single    0.970  0.020  1.090

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
 9WT  C24  S01  C21   92.24  3.000
 9WT  C31  S02  C30   89.30  3.000
 9WT  C32  O07  N11  110.47  3.000
 9WT  C19  N08  C16  110.73  3.000
 9WT  C16  N08  C15  113.56  3.000
 9WT  C19  N08  C15  110.25  3.000
 9WT  C16  N08  C14  109.73  3.000
 9WT  C15  N08  C14  102.64  3.000
 9WT  C19  N08  C14  109.62  3.000
 9WT  C25  N09  C23  131.84  3.000
 9WT  C23  N09  C21  127.39  3.000
 9WT  C25  N09  C21   95.24  3.000
 9WT  H2   N10  C27  118.37  3.000
 9WT  H2   N10  C22  118.46  3.000
 9WT  C27  N10  C22  122.32  3.000
 9WT  C28  N11  O07  112.65  3.000
 9WT  C31  N12  C29  111.25  3.000
 9WT  H4   N13  H3   114.09  3.000
 9WT  H4   N13  C31  114.74  3.000
 9WT  H3   N13  C31  118.66  3.000
 9WT  H6   C14  H5   108.77  3.000
 9WT  H6   C14  C17  114.83  3.000
 9WT  H5   C14  C17  111.36  3.000
 9WT  H6   C14  N08  109.34  3.000
 9WT  H5   C14  N08  107.22  3.000
 9WT  C17  C14  N08  105.00  3.000
 9WT  H8   C15  H7   109.17  3.000
 9WT  H8   C15  C18  111.30  3.000
 9WT  H7   C15  C18  114.30  3.000
 9WT  H8   C15  N08  106.94  3.000
 9WT  H7   C15  N08  109.71  3.000
 9WT  C18  C15  N08  105.10  3.000
 9WT  H10  C16  H9   108.34  3.000
 9WT  H10  C16  C20  110.46  3.000
 9WT  H9   C16  C20  110.70  3.000
 9WT  H10  C16  N08  105.56  3.000
 9WT  H9   C16  N08  106.18  3.000
 9WT  C20  C16  N08  115.25  3.000
 9WT  H12  C17  H11  107.30  3.000
 9WT  H12  C17  C18  111.17  3.000
 9WT  H11  C17  C18  112.28  3.000
 9WT  H12  C17  C14  111.21  3.000
 9WT  H11  C17  C14  109.80  3.000
 9WT  C18  C17  C14  105.13  3.000
 9WT  H14  C18  H13  107.22  3.000
 9WT  H14  C18  C17  112.18  3.000
 9WT  H13  C18  C17  111.16  3.000
 9WT  H14  C18  C15  109.71  3.000
 9WT  H13  C18  C15  111.26  3.000
 9WT  C17  C18  C15  105.36  3.000
 9WT  H17  C19  H16  109.20  3.000
 9WT  H17  C19  H15  109.28  3.000
 9WT  H16  C19  H15  110.08  3.000
 9WT  H17  C19  N08  109.73  3.000
 9WT  H16  C19  N08  109.57  3.000
 9WT  H15  C19  N08  108.97  3.000
 9WT  C24  C20  C23  123.18  3.000
 9WT  C24  C20  C16  116.20  3.000
 9WT  C23  C20  C16  120.58  3.000
 9WT  H19  C21  C22  115.82  3.000
 9WT  H19  C21  N09  113.56  3.000
 9WT  C22  C21  N09   87.76  3.000
 9WT  H19  C21  S01  110.64  3.000
 9WT  C22  C21  S01  117.23  3.000
 9WT  N09  C21  S01  109.86  3.000
 9WT  H20  C22  C25  113.02  3.000
 9WT  H20  C22  C21  111.63  3.000
 9WT  C25  C22  C21   85.01  3.000
 9WT  H20  C22  N10  109.99  3.000
 9WT  C21  C22  N10  119.53  3.000
 9WT  C25  C22  N10  115.75  3.000
 9WT  C26  C23  C20  126.97  3.000
 9WT  C26  C23  N09  113.83  3.000
 9WT  C20  C23  N09  119.13  3.000
 9WT  H23  C24  H22  106.65  3.000
 9WT  H23  C24  C20  109.57  3.000
 9WT  H22  C24  C20  112.02  3.000
 9WT  H23  C24  S01  105.52  3.000
 9WT  H22  C24  S01  107.56  3.000
 9WT  C20  C24  S01  115.01  3.000
 9WT  C22  C25  N09   91.41  3.000
 9WT  C22  C25  O03  135.43  3.000
 9WT  N09  C25  O03  133.07  3.000
 9WT  C23  C26  O05  113.51  3.000
 9WT  O05  C26  O04  128.98  3.000
 9WT  C23  C26  O04  117.50  3.000
 9WT  C28  C27  N10  113.86  3.000
 9WT  N10  C27  O06  124.80  3.000
 9WT  C28  C27  O06  121.33  3.000
 9WT  C29  C28  C27  115.27  3.000
 9WT  C29  C28  N11  120.92  3.000
 9WT  C27  C28  N11  123.78  3.000
 9WT  C30  C29  C28  127.46  3.000
 9WT  C28  C29  N12  116.28  3.000
 9WT  C30  C29  N12  116.24  3.000
 9WT  H24  C30  C29  129.16  3.000
 9WT  H24  C30  S02  121.61  3.000
 9WT  C29  C30  S02  109.23  3.000
 9WT  N13  C31  N12  124.09  3.000
 9WT  N12  C31  S02  113.97  3.000
 9WT  N13  C31  S02  121.88  3.000
 9WT  H27  C32  H26  109.38  3.000
 9WT  H27  C32  H25  109.17  3.000
 9WT  H26  C32  H25  109.16  3.000
 9WT  H27  C32  O07  111.53  3.000
 9WT  H26  C32  O07  111.52  3.000
 9WT  H25  C32  O07  105.98  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
 9WT  CONST_01  N12  C29  C30  S02     0.00   0.0  0
 9WT  CONST_02  C29  N12  C31  S02     0.00   0.0  0
 9WT  CONST_03  C30  S02  C31  N12     0.00   0.0  0
 9WT  CONST_04  C31  S02  C30  C29     0.00   0.0  0
 9WT  CONST_05  C31  N12  C29  C30     0.00   0.0  0
 9WT  CONST_06  C22  C25  N09  C21     0.00   0.0  0
 9WT  CONST_08  C28  C29  C30  S02   180.00   0.0  0
 9WT  CONST_09  C30  S02  C31  N13   180.00   0.0  0
 9WT  CONST_10  C29  N12  C31  N13   180.00   0.0  0
 9WT  CONST_11  C31  N12  C29  C28   180.00   0.0  0
 9WT  CONST_13  C21  N09  C25  O03   180.00   0.0  0
 9WT  CONST_14  H24  C30  C29  N12   180.00   0.0  0
 9WT  CONST_17  C22  N10  C27  O06     0.00   0.0  0
 9WT  CONST_18  C28  C27  N10  C22   180.00   0.0  0
 9WT  CONST_19  H2   N10  C27  O06   180.00   0.0  0
 9WT  Var_01    C23  C20  C24  S01    28.10  30.0  1
 9WT  Var_02    C17  C18  C15  N08   -23.39  30.0  1
 9WT  Var_03    C18  C17  C14  N08    25.27  30.0  1
 9WT  Var_04    C24  C20  C23  N09     2.49  30.0  1
 9WT  Var_05    C15  C18  C17  C14    -1.17  30.0  1
 9WT  Var_06    C25  N09  C23  C20  -140.48  30.0  1
 9WT  Var_07    H22  C24  S01  C21    72.81  30.0  1
 9WT  Var_08    N09  C23  C26  O04  -132.68  30.0  3
 9WT  Var_09    C30  C29  C28  N11     0.79  30.0  2
 9WT  Var_10    C29  C28  N11  O07  -179.10   0.0  2
 9WT  Var_11    H25  C32  O07  N11   179.99  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
 9WT  chir_01  N08  C15  C14  C16  negativ
 9WT  chir_02  C21  S01  N09  C22  negativ
 9WT  chir_03  C22  N10  C21  C25  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
 9WT  plan-1  S02  0.020
 9WT  plan-1  N12  0.020
 9WT  plan-1  N13  0.020
 9WT  plan-1  C28  0.020
 9WT  plan-1  C29  0.020
 9WT  plan-1  C30  0.020
 9WT  plan-1  C31  0.020
 9WT  plan-1  H24  0.020
 9WT  plan-2  O07  0.020
 9WT  plan-2  N11  0.020
 9WT  plan-2  C27  0.020
 9WT  plan-2  C28  0.020
 9WT  plan-2  C29  0.020
 9WT  plan-3  O06  0.020
 9WT  plan-3  N10  0.020
 9WT  plan-3  C22  0.020
 9WT  plan-3  C27  0.020
 9WT  plan-3  C28  0.020
 9WT  plan-3  H2   0.020
 9WT  plan-4  N13  0.020
 9WT  plan-4  C31  0.020
 9WT  plan-4  H3   0.020
 9WT  plan-4  H4   0.020
 9WT  plan-5  O03  0.020
 9WT  plan-5  N09  0.020
 9WT  plan-5  C21  0.020
 9WT  plan-5  C22  0.020
 9WT  plan-5  C23  0.020
 9WT  plan-5  C25  0.020
 9WT  plan-6  O04  0.020
 9WT  plan-6  O05  0.020
 9WT  plan-6  C23  0.020
 9WT  plan-6  C26  0.020

