# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:12:56 2021
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{S},3~{S})-3-[bis(oxidanyl)-$l^{4}-sulfanyl]-3-methyl-4-(3-methyl-1,2,3-triazol-3-ium-1-yl)-2-[[(~{E})-3-oxidanylideneprop-1-enyl]amino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccn(C[C@@](C)([C@@H](N\C=C\C=O)C(O)=O)[SH](O)O)n1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 M9W  M9W  '(2~{S},3~{S})-3-[bis(oxidanyl)-$l^{4}-sulfanyl]-3-methyl-4-(3-methyl-1,2,3-triazol-3-ium-1-yl)-2-[[(~{E})-3-oxidanylideneprop-1-enyl]amino]butanoic acid'  ligand  40  21  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M9W
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
 M9W  C02  C  C1    0   0.105  -15.7726  12.7176  25.6104
 M9W  C09  C  C1    0  -0.509  -15.9250  14.1299  25.8088
 M9W  C10  C  C1    0   0.115  -14.9657  15.0020  25.3920
 M9W  C12  C  CH1   0  -0.226  -13.9394  17.2015  25.0963
 M9W  C13  C  C     0   0.574  -14.4201  18.2453  24.0958
 M9W  C16  C  CT    0  -0.363  -13.1475  17.8372  26.2744
 M9W  C17  C  CH3   0  -0.653  -12.6726  16.7138  27.1809
 M9W  C18  C  CH2   0  -0.273  -14.0607  18.8512  26.9745
 M9W  C23  C  CR15  0  -0.006  -13.7089  19.2983  30.5119
 M9W  C24  C  CR15  0  -0.020  -14.4770  18.8976  29.4545
 M9W  N11  N  NH1   0  -0.582  -15.0055  16.3302  25.5194
 M9W  N19  N  NR5   0  -0.209  -13.7118  19.1021  28.3707
 M9W  N20  N  N     0  -0.039  -12.5513  19.5884  28.6803
 M9W  N21  N  NR5   1  -0.201  -12.5498  19.7029  29.9706
 M9W  O01  O  O     0  -0.460  -14.8259  12.1531  25.0773
 M9W  O14  O  O     0  -0.417  -13.6874  18.7371  23.2767
 M9W  O15  O  OH1   0  -0.579  -15.6917  18.5601  24.2487
 M9W  S25  S  SH1   0   0.696  -11.6233  18.8060  25.3214
 M9W  H1   H  H     0   0.175  -16.6196  12.1206  25.9941
 M9W  H2   H  H     0   0.265  -16.8237  14.4833  26.2997
 M9W  H3   H  H     0   0.293  -14.0752  14.6165  24.9055
 M9W  H4   H  HCH1  0   0.317  -13.2306  16.5741  24.5464
 M9W  H5   H  HCH3  0   0.246  -12.0063  17.0573  27.9701
 M9W  H6   H  HCH3  0   0.252  -13.4960  16.1823  27.6638
 M9W  H7   H  HCH3  0   0.255  -12.1090  15.9774  26.6038
 M9W  H8   H  HCH2  0   0.327  -14.0669  19.8206  26.4694
 M9W  H9   H  HCH2  0   0.293  -15.0961  18.5163  27.0252
 M9W  H10  H  HCH3  0   0.300  -10.4933  19.7570  30.2861
 M9W  H11  H  HCH3  0   0.307  -11.3357  21.3188  30.4681
 M9W  H12  H  HCH3  0   0.295  -11.5010  20.0611  31.7146
 M9W  H13  H  HCR5  0   0.364  -13.9064  19.3186  31.5690
 M9W  H14  H  HCR5  0   0.367  -15.4754  18.4997  29.4089
 M9W  H15  H  HNH1  0   0.414  -15.8199  16.7354  25.9584
 M9W  H16  H  HOH1  0   0.496  -15.9553  19.2462  23.6151
 M9W  H17  H  HOH1  0   0.486  -11.2236  19.2183  27.4175
 M9W  H18  H  HOH1  0   0.429   -9.4228  18.8636  24.5351
 M9W  H19  H  HSH1  0   0.257  -11.3919  17.5891  24.7979
 M9W  O26  O  OH1   0  -0.729  -10.7011  18.8543  26.6778
 M9W  C22  C  CH3   0  -0.512  -11.3873  20.2501  30.6535
 M9W  O27  O  OH1   0  -0.850  -10.2147  19.4017  24.3999

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
 M9W  O14  C13  double    1.204  0.020  1.204
 M9W  O01  C02  double    1.224  0.020  1.224
 M9W  C13  O15  single    1.319  0.020  1.319
 M9W  C13  C12  single    1.524  0.020  1.524
 M9W  O27  S25  single    1.786  0.020  1.786
 M9W  C02  C09  single    1.434  0.020  1.434
 M9W  C12  N11  single    1.440  0.020  1.440
 M9W  C12  C16  single    1.555  0.020  1.555
 M9W  S25  C16  single    2.042  0.020  2.042
 M9W  S25  O26  single    1.641  0.020  1.641
 M9W  C10  C09  double    1.362  0.020  1.362
 M9W  C10  N11  single    1.335  0.020  1.335
 M9W  C16  C18  single    1.534  0.020  1.534
 M9W  C16  C17  single    1.520  0.020  1.520
 M9W  C18  N19  single    1.461  0.020  1.461
 M9W  N19  N20  aromatic  1.296  0.020  1.296
 M9W  N19  C24  aromatic  1.342  0.020  1.342
 M9W  N20  N21  aromatic  1.295  0.020  1.295
 M9W  C24  C23  aromatic  1.367  0.020  1.367
 M9W  N21  C23  aromatic  1.342  0.020  1.342
 M9W  N21  C22  single    1.455  0.020  1.455
 M9W  C02  H1   single    0.930  0.020  1.080
 M9W  C09  H2   single    0.930  0.020  1.080
 M9W  C10  H3   single    0.930  0.020  1.080
 M9W  C12  H4   single    0.970  0.020  1.090
 M9W  C17  H5   single    0.970  0.020  1.090
 M9W  C17  H6   single    0.970  0.020  1.090
 M9W  C17  H7   single    0.970  0.020  1.090
 M9W  C18  H8   single    0.970  0.020  1.090
 M9W  C18  H9   single    0.970  0.020  1.090
 M9W  C22  H10  single    0.970  0.020  1.090
 M9W  C22  H11  single    0.970  0.020  1.090
 M9W  C22  H12  single    0.970  0.020  1.090
 M9W  C23  H13  single    0.930  0.020  1.080
 M9W  C24  H14  single    0.930  0.020  1.080
 M9W  N11  H15  single    0.860  0.020  1.020
 M9W  O15  H16  single    0.850  0.020  0.980
 M9W  O26  H17  single    0.850  0.020  0.980
 M9W  O27  H18  single    0.850  0.020  0.980
 M9W  H19  S25  single    1.200  0.020  1.300

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
 M9W  H1   C02  O01  119.65  3.000
 M9W  H1   C02  C09  113.74  3.000
 M9W  O01  C02  C09  126.61  3.000
 M9W  H2   C09  C10  120.95  3.000
 M9W  H2   C09  C02  118.16  3.000
 M9W  C10  C09  C02  120.89  3.000
 M9W  H3   C10  N11  114.88  3.000
 M9W  H3   C10  C09  119.18  3.000
 M9W  N11  C10  C09  125.94  3.000
 M9W  H4   C12  N11  106.27  3.000
 M9W  H4   C12  C16  106.56  3.000
 M9W  N11  C12  C16  113.67  3.000
 M9W  H4   C12  C13  105.49  3.000
 M9W  C16  C12  C13  112.21  3.000
 M9W  N11  C12  C13  111.95  3.000
 M9W  O15  C13  O14  124.62  3.000
 M9W  O15  C13  C12  113.05  3.000
 M9W  O14  C13  C12  122.31  3.000
 M9W  S25  C16  C18  110.10  3.000
 M9W  C18  C16  C17  113.74  3.000
 M9W  S25  C16  C17  113.32  3.000
 M9W  C17  C16  C12  107.99  3.000
 M9W  C18  C16  C12  108.23  3.000
 M9W  S25  C16  C12  102.73  3.000
 M9W  H7   C17  H6   107.12  3.000
 M9W  H7   C17  H5   106.26  3.000
 M9W  H6   C17  H5   107.12  3.000
 M9W  H7   C17  C16  110.15  3.000
 M9W  H6   C17  C16  112.82  3.000
 M9W  H5   C17  C16  112.99  3.000
 M9W  H9   C18  H8   106.79  3.000
 M9W  H9   C18  N19  103.61  3.000
 M9W  H8   C18  N19  106.90  3.000
 M9W  H9   C18  C16  112.57  3.000
 M9W  H8   C18  C16  112.26  3.000
 M9W  N19  C18  C16  114.05  3.000
 M9W  H13  C23  N21  123.33  3.000
 M9W  H13  C23  C24  131.50  3.000
 M9W  N21  C23  C24  105.17  3.000
 M9W  H14  C24  N19  123.45  3.000
 M9W  H14  C24  C23  131.51  3.000
 M9W  N19  C24  C23  105.05  3.000
 M9W  H15  N11  C12  118.80  3.000
 M9W  H15  N11  C10  117.69  3.000
 M9W  C12  N11  C10  123.48  3.000
 M9W  N20  N19  C24  112.01  3.000
 M9W  C24  N19  C18  127.54  3.000
 M9W  N20  N19  C18  120.44  3.000
 M9W  N21  N20  N19  105.80  3.000
 M9W  N20  N21  C23  111.98  3.000
 M9W  C23  N21  C22  127.90  3.000
 M9W  N20  N21  C22  120.11  3.000
 M9W  H16  O15  C13  110.79  3.000
 M9W  H19  S25  O27   88.00  3.000
 M9W  H19  S25  O26  104.57  3.000
 M9W  O27  S25  O26   88.48  3.000
 M9W  H19  S25  C16   83.16  3.000
 M9W  O26  S25  C16   92.73  3.000
 M9W  O27  S25  C16  171.10  3.000
 M9W  H17  O26  S25  109.67  3.000
 M9W  H12  C22  H11  110.11  3.000
 M9W  H12  C22  H10  109.80  3.000
 M9W  H11  C22  H10  110.50  3.000
 M9W  H12  C22  N21  108.07  3.000
 M9W  H11  C22  N21  109.14  3.000
 M9W  H10  C22  N21  109.17  3.000
 M9W  H18  O27  S25  112.85  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
 M9W  CONST_01  N20  N19  C24  C23    0.00   0.0  0
 M9W  CONST_02  N19  N20  N21  C23    0.00   0.0  0
 M9W  CONST_03  N21  N20  N19  C24    0.00   0.0  0
 M9W  CONST_04  N20  N21  C23  C24    0.00   0.0  0
 M9W  CONST_05  N21  C23  C24  N19    0.00   0.0  0
 M9W  CONST_06  N21  N20  N19  C18  180.00   0.0  0
 M9W  CONST_07  C23  C24  N19  C18  180.00   0.0  0
 M9W  CONST_08  N19  N20  N21  C22  180.00   0.0  0
 M9W  CONST_09  C24  C23  N21  C22  180.00   0.0  0
 M9W  CONST_10  H13  C23  C24  N19  180.00   0.0  0
 M9W  CONST_11  H14  C24  N19  N20  180.00   0.0  0
 M9W  CONST_12  H16  O15  C13  C12  180.00   0.0  0
 M9W  Var_01    N20  N19  C18  C16   60.92  30.0  2
 M9W  Var_02    H10  C22  N21  C23  133.14  30.0  2
 M9W  Var_03    N11  C10  C09  C02  179.71   0.0  2
 M9W  Var_04    C12  N11  C10  C09  177.96  30.0  2
 M9W  Var_05    O01  C02  C09  C10   -0.02  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
 M9W  chir_01  C12  C13  N11  C16  positiv
 M9W  chir_02  C16  C17  C18  C12  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
 M9W  plan-1  C18  0.020
 M9W  plan-1  C23  0.020
 M9W  plan-1  C24  0.020
 M9W  plan-1  N19  0.020
 M9W  plan-1  N20  0.020
 M9W  plan-1  N21  0.020
 M9W  plan-1  H13  0.020
 M9W  plan-1  H14  0.020
 M9W  plan-1  C22  0.020
 M9W  plan-2  C12  0.020
 M9W  plan-2  C13  0.020
 M9W  plan-2  O14  0.020
 M9W  plan-2  O15  0.020
 M9W  plan-2  H16  0.020
 M9W  plan-3  C02  0.020
 M9W  plan-3  C09  0.020
 M9W  plan-3  O01  0.020
 M9W  plan-3  H1   0.020
 M9W  plan-4  C02  0.020
 M9W  plan-4  C09  0.020
 M9W  plan-4  C10  0.020
 M9W  plan-4  N11  0.020
 M9W  plan-4  H2   0.020
 M9W  plan-4  H3   0.020

