# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 18:31:15 2021
#   Inital geometry file: a 177 line input string
#   Ligand name: (6R,7S,10Z)-10-(2-amino-1,3-thiazol-4-yl)-1-(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)-7-formyl-13,13-dimethyl-3,9-dioxo-6-(sulfoamino)-12-oxa-2,4,8,11-tetraazatetradec-10-en-14-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O/N=C(C(=O)N[C@H](C=O)[C@@H](CNC(=O)NCC1=CC(=O)C(=CN1O)O)N[S](O)(=O)=O)/c2csc(N)n2)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
 PFV  PFV  '(6R,7S,10Z)-10-(2-amino-1,3-thiazol-4-yl)-1-(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)-7-formyl-13,13-dimethyl-3,9-dioxo-6-(sulfoamino)-12-oxa-2,4,8,11-tetraazatetradec-10-en-14-oic acid'  ligand  68  42  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PFV
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
 PFV  C36  C  C     0   0.784   -1.9818  -1.2056  -17.8574
 PFV  C34  C  CH2   0  -0.378    0.2247  -0.2699  -17.4501
 PFV  C6   C  C     0   0.053   -7.3685  -0.8246  -15.1287
 PFV  C9   C  CR5   0   0.342   -8.2785  -1.3617  -14.1260
 PFV  O15  O  O2    0  -0.399   -5.9017   0.5900  -15.9101
 PFV  C18  C  CH3   0  -0.695   -4.2659   1.9977  -16.8187
 PFV  C16  C  CT    0   0.125   -5.1143   1.7267  -15.5787
 PFV  C19  C  CH3   0  -0.678   -4.2238   1.4508  -14.3734
 PFV  C26  C  CR16  0  -0.512   -0.4461   1.5895  -15.8805
 PFV  O37  O  O     0  -0.542   -2.2715  -1.1415  -16.6605
 PFV  N35  N  NH1   0  -0.660   -0.7484  -0.8832  -18.3169
 PFV  C27  C  CR6   0   0.402   -0.0876   1.1697  -17.1318
 PFV  N28  N  NR6   0  -0.214   -0.0313   2.0759  -18.1272
 PFV  O38  O  OH1   0  -0.526    0.2895   1.6700  -19.3847
 PFV  C29  C  CR16  0  -0.096   -0.3561   3.3882  -17.9591
 PFV  C30  C  CR6   0   0.153   -0.7146   3.8391  -16.7330
 PFV  O33  O  OH1   0  -0.630   -1.0437   5.1226  -16.5305
 PFV  C31  C  CR6   0   0.372   -0.7629   2.9478  -15.5891
 PFV  O32  O  O     0  -0.534   -1.0852   3.4035  -14.4774
 PFV  N4   N  NH1   0  -0.672   -2.8727  -1.6142  -18.7943
 PFV  C3   C  CH2   0  -0.307   -4.2659  -1.7975  -18.4865
 PFV  C2   C  CH1   0  -0.115   -4.6035  -3.2144  -18.0169
 PFV  N1   N  NC1   0  -0.786   -3.7996  -3.5648  -16.8400
 PFV  S22  S  S     0   1.569   -2.7871  -4.8507  -16.9219
 PFV  O25  O  OS    0  -0.643   -3.5182  -5.9336  -17.5442
 PFV  O24  O  OS    0  -0.704   -2.5526  -5.1338  -15.3747
 PFV  O23  O  OS    0  -0.632   -1.4676  -4.5224  -17.4082
 PFV  CA   C  CH1   0  -0.208   -6.0905  -3.3198  -17.6429
 PFV  C    C  C1    0   0.196   -6.4817  -4.7662  -17.4466
 PFV  O    O  O     0  -0.354   -6.9855  -5.1972  -16.4447
 PFV  N    N  NH1   0  -0.607   -6.3821  -2.5263  -16.4841
 PFV  C5   C  C     0   0.478   -7.2786  -1.5296  -16.4611
 PFV  O7   O  O     0  -0.444   -7.9813  -1.1948  -17.3948
 PFV  N8   N  N     0  -0.080   -6.7107   0.2338  -14.8772
 PFV  C17  C  C     0   0.542   -6.0578   2.9120  -15.3770
 PFV  O21  O  O     0  -0.430   -7.1890   2.9535  -15.7824
 PFV  O20  O  OH1   0  -0.586   -5.4589   3.9135  -14.7512
 PFV  N13  N  N     0  -0.442   -8.5654  -0.6387  -12.9994
 PFV  C12  C  CR5   0   0.270   -9.3689  -1.2948  -12.2236
 PFV  N14  N  NH2   0  -0.817   -9.8777  -0.8199  -11.0677
 PFV  S11  S  S2    0   0.195   -9.8368  -2.8683  -12.8276
 PFV  C10  C  CR15  0  -0.582   -8.8606  -2.5870  -14.2183
 PFV  H1   H  HCH2  0   0.283    0.2826  -0.8159  -16.5110
 PFV  H2   H  HCH2  0   0.296    1.2028  -0.3571  -17.9222
 PFV  H3   H  HCH3  0   0.250   -3.7208   2.9336  -16.7084
 PFV  H4   H  HCH3  0   0.269   -3.5319   1.2005  -16.9357
 PFV  H5   H  HCH3  0   0.254   -4.8758   2.0591  -17.7202
 PFV  H6   H  HCH3  0   0.247   -4.7927   1.3308  -13.4528
 PFV  H7   H  HCH3  0   0.248   -3.6593   0.5367  -14.5606
 PFV  H8   H  HCH3  0   0.252   -3.5009   2.2524  -14.2315
 PFV  H9   H  HCR6  0   0.272   -0.5072   0.8535  -15.0914
 PFV  H10  H  HNH1  0   0.401   -0.5985  -0.7991  -19.3089
 PFV  H11  H  HOH1  0   0.497    1.2410   1.8220  -19.4916
 PFV  H12  H  HCR6  0   0.324   -0.3060   4.0164  -18.8371
 PFV  H13  H  HOH1  0   0.463   -1.2489   5.2048  -15.5846
 PFV  H14  H  HNH1  0   0.405   -2.5874  -1.7021  -19.7559
 PFV  H15  H  HCH2  0   0.266   -4.5721  -1.0731  -17.7294
 PFV  H16  H  HCH2  0   0.284   -4.8467  -1.5846  -19.3836
 PFV  H17  H  HCH1  0   0.299   -4.4073  -3.9057  -18.8398
 PFV  H18  H  HNC1  0   0.432   -3.3370  -2.7513  -16.4189
 PFV  H19  H  HCH1  0   0.319   -6.6811  -2.9508  -18.4886
 PFV  H20  H  H     0   0.214   -6.2813  -5.4072  -18.3208
 PFV  H21  H  HNH1  0   0.416   -5.8806  -2.7461  -15.6355
 PFV  H22  H  HOH1  0   0.485   -6.0569   4.6738  -14.6894
 PFV  H23  H  HNH2  0   0.408  -10.2303  -1.4720  -10.3871
 PFV  H24  H  HNH2  0   0.405   -9.4050  -0.0219  -10.6732
 PFV  H25  H  HCR5  0   0.301   -8.7571  -3.3381  -14.9856
 PFV  H26  H  H     0   0.503   -3.3735  -5.3716  -14.9128

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
 PFV  O38  N28  single    1.360  0.020  1.360
 PFV  C29  N28  single    1.362  0.020  1.362
 PFV  C29  C30  double    1.355  0.020  1.355
 PFV  O33  C30  single    1.340  0.020  1.340
 PFV  N28  C27  single    1.347  0.020  1.347
 PFV  C30  C31  single    1.451  0.020  1.451
 PFV  N4   C3   single    1.439  0.020  1.439
 PFV  N4   C36  single    1.356  0.020  1.356
 PFV  N35  C36  single    1.355  0.020  1.355
 PFV  N35  C34  single    1.440  0.020  1.440
 PFV  C3   C2   single    1.530  0.020  1.530
 PFV  C27  C34  single    1.507  0.020  1.507
 PFV  C27  C26  double    1.368  0.020  1.368
 PFV  C31  O32  double    1.244  0.020  1.244
 PFV  C31  C26  single    1.425  0.020  1.425
 PFV  O23  S22  double    1.444  0.020  1.444
 PFV  C36  O37  double    1.233  0.020  1.233
 PFV  C2   CA   single    1.537  0.020  1.537
 PFV  C2   N1   single    1.468  0.020  1.468
 PFV  O7   C5   double    1.216  0.020  1.216
 PFV  CA   C    single    1.511  0.020  1.511
 PFV  CA   N    single    1.434  0.020  1.434
 PFV  C    O    double    1.201  0.020  1.201
 PFV  O25  S22  double    1.447  0.020  1.447
 PFV  S22  N1   single    1.639  0.020  1.639
 PFV  S22  O24  single    1.590  0.020  1.590
 PFV  C5   N    single    1.341  0.020  1.341
 PFV  C5   C6   single    1.510  0.020  1.510
 PFV  C10  C9   aromatic  1.360  0.020  1.360
 PFV  C10  S11  aromatic  1.722  0.020  1.722
 PFV  C6   C9   single    1.457  0.020  1.457
 PFV  C6   N8   double    1.271  0.020  1.271
 PFV  C18  C16  single    1.527  0.020  1.527
 PFV  O15  N8   single    1.359  0.020  1.359
 PFV  O15  C16  single    1.422  0.020  1.422
 PFV  O21  C17  double    1.202  0.020  1.202
 PFV  C9   N13  aromatic  1.369  0.020  1.369
 PFV  C16  C17  single    1.528  0.020  1.528
 PFV  C16  C19  single    1.524  0.020  1.524
 PFV  S11  C12  aromatic  1.749  0.020  1.749
 PFV  C17  O20  single    1.324  0.020  1.324
 PFV  N13  C12  aromatic  1.295  0.020  1.295
 PFV  C12  N14  single    1.349  0.020  1.349
 PFV  C34  H1   single    0.970  0.020  1.090
 PFV  C34  H2   single    0.970  0.020  1.090
 PFV  C18  H3   single    0.970  0.020  1.090
 PFV  C18  H4   single    0.970  0.020  1.090
 PFV  C18  H5   single    0.970  0.020  1.090
 PFV  C19  H6   single    0.970  0.020  1.090
 PFV  C19  H7   single    0.970  0.020  1.090
 PFV  C19  H8   single    0.970  0.020  1.090
 PFV  C26  H9   single    0.930  0.020  1.080
 PFV  N35  H10  single    0.860  0.020  1.020
 PFV  O38  H11  single    0.850  0.020  0.980
 PFV  C29  H12  single    0.930  0.020  1.080
 PFV  O33  H13  single    0.850  0.020  0.980
 PFV  N4   H14  single    0.860  0.020  1.020
 PFV  C3   H15  single    0.970  0.020  1.090
 PFV  C3   H16  single    0.970  0.020  1.090
 PFV  C2   H17  single    0.970  0.020  1.090
 PFV  N1   H18  single    0.890  0.020  1.040
 PFV  CA   H19  single    0.970  0.020  1.090
 PFV  C    H20  single    0.930  0.020  1.080
 PFV  N    H21  single    0.860  0.020  1.020
 PFV  O20  H22  single    0.850  0.020  0.980
 PFV  N14  H23  single    0.890  0.020  1.040
 PFV  N14  H24  single    0.890  0.020  1.040
 PFV  C10  H25  single    0.930  0.020  1.080
 PFV  O24  H26  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
 PFV  N4   C36  N35  115.81  3.000
 PFV  N35  C36  O37  122.04  3.000
 PFV  N4   C36  O37  122.14  3.000
 PFV  H2   C34  H1   106.63  3.000
 PFV  H2   C34  C27  110.73  3.000
 PFV  H1   C34  C27  107.95  3.000
 PFV  H2   C34  N35  108.16  3.000
 PFV  H1   C34  N35  109.98  3.000
 PFV  C27  C34  N35  113.20  3.000
 PFV  N8   C6   C5   122.17  3.000
 PFV  N8   C6   C9   119.61  3.000
 PFV  C5   C6   C9   118.19  3.000
 PFV  C10  C9   N13  116.24  3.000
 PFV  N13  C9   C6   120.17  3.000
 PFV  C10  C9   C6   123.57  3.000
 PFV  N8   O15  C16  111.22  3.000
 PFV  H5   C18  H4   109.22  3.000
 PFV  H5   C18  H3   108.39  3.000
 PFV  H4   C18  H3   107.60  3.000
 PFV  H5   C18  C16  111.77  3.000
 PFV  H4   C18  C16  109.37  3.000
 PFV  H3   C18  C16  110.40  3.000
 PFV  C17  C16  C19  113.38  3.000
 PFV  C19  C16  C18  110.48  3.000
 PFV  C17  C16  C18  108.22  3.000
 PFV  C19  C16  O15  111.30  3.000
 PFV  C17  C16  O15  107.99  3.000
 PFV  C18  C16  O15  105.09  3.000
 PFV  H8   C19  H7   107.21  3.000
 PFV  H8   C19  H6   108.54  3.000
 PFV  H7   C19  H6   108.86  3.000
 PFV  H8   C19  C16  110.97  3.000
 PFV  H7   C19  C16  108.57  3.000
 PFV  H6   C19  C16  112.54  3.000
 PFV  H9   C26  C31  119.16  3.000
 PFV  H9   C26  C27  118.28  3.000
 PFV  C31  C26  C27  122.55  3.000
 PFV  H10  N35  C34  117.18  3.000
 PFV  H10  N35  C36  119.30  3.000
 PFV  C34  N35  C36  120.81  3.000
 PFV  N28  C27  C26  118.71  3.000
 PFV  C26  C27  C34  122.74  3.000
 PFV  N28  C27  C34  118.54  3.000
 PFV  C29  N28  O38  117.25  3.000
 PFV  C29  N28  C27  123.15  3.000
 PFV  O38  N28  C27  119.49  3.000
 PFV  H11  O38  N28  106.66  3.000
 PFV  H12  C29  C30  123.65  3.000
 PFV  H12  C29  N28  116.65  3.000
 PFV  C30  C29  N28  119.70  3.000
 PFV  C31  C30  O33  117.45  3.000
 PFV  C31  C30  C29  121.19  3.000
 PFV  O33  C30  C29  121.36  3.000
 PFV  H13  O33  C30  106.26  3.000
 PFV  O32  C31  C30  119.22  3.000
 PFV  O32  C31  C26  126.13  3.000
 PFV  C30  C31  C26  114.64  3.000
 PFV  H14  N4   C3   117.88  3.000
 PFV  H14  N4   C36  120.00  3.000
 PFV  C3   N4   C36  121.80  3.000
 PFV  H16  C3   H15  106.97  3.000
 PFV  H16  C3   C2   108.42  3.000
 PFV  H15  C3   C2   109.86  3.000
 PFV  H16  C3   N4   108.37  3.000
 PFV  H15  C3   N4   109.60  3.000
 PFV  C2   C3   N4   113.41  3.000
 PFV  H17  C2   CA   108.28  3.000
 PFV  H17  C2   N1   110.77  3.000
 PFV  CA   C2   N1   108.57  3.000
 PFV  H17  C2   C3   108.37  3.000
 PFV  N1   C2   C3   110.26  3.000
 PFV  CA   C2   C3   110.58  3.000
 PFV  H18  N1   S22  111.35  3.000
 PFV  H18  N1   C2   112.75  3.000
 PFV  S22  N1   C2   119.06  3.000
 PFV  O23  S22  O24  103.49  3.000
 PFV  O24  S22  O25  111.08  3.000
 PFV  O23  S22  O25  119.14  3.000
 PFV  O24  S22  N1   100.50  3.000
 PFV  O25  S22  N1   107.25  3.000
 PFV  O23  S22  N1   113.77  3.000
 PFV  H26  O24  S22  112.43  3.000
 PFV  H19  CA   N    109.13  3.000
 PFV  H19  CA   C    106.45  3.000
 PFV  N    CA   C    111.83  3.000
 PFV  H19  CA   C2   108.10  3.000
 PFV  N    CA   C2   110.81  3.000
 PFV  C    CA   C2   110.34  3.000
 PFV  H20  C    O    121.93  3.000
 PFV  H20  C    CA   113.99  3.000
 PFV  O    C    CA   124.07  3.000
 PFV  H21  N    C5   118.65  3.000
 PFV  H21  N    CA   117.23  3.000
 PFV  C5   N    CA   124.12  3.000
 PFV  O7   C5   N    125.32  3.000
 PFV  N    C5   C6   113.70  3.000
 PFV  O7   C5   C6   120.98  3.000
 PFV  O15  N8   C6   112.07  3.000
 PFV  O20  C17  O21  123.97  3.000
 PFV  O20  C17  C16  111.70  3.000
 PFV  O21  C17  C16  124.27  3.000
 PFV  H22  O20  C17  110.14  3.000
 PFV  C12  N13  C9   110.81  3.000
 PFV  S11  C12  N14  120.77  3.000
 PFV  N14  C12  N13  124.66  3.000
 PFV  S11  C12  N13  114.51  3.000
 PFV  H24  N14  H23  114.37  3.000
 PFV  H24  N14  C12  115.92  3.000
 PFV  H23  N14  C12  118.91  3.000
 PFV  C10  S11  C12   88.87  3.000
 PFV  H25  C10  S11  121.00  3.000
 PFV  H25  C10  C9   129.40  3.000
 PFV  S11  C10  C9   109.57  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
 PFV  CONST_01  C12  S11  C10  C9     0.00   0.0  0
 PFV  CONST_02  S11  C12  N13  C9     0.00   0.0  0
 PFV  CONST_03  S11  C10  C9   N13    0.00   0.0  0
 PFV  CONST_04  C10  S11  C12  N13    0.00   0.0  0
 PFV  CONST_05  C10  C9   N13  C12    0.00   0.0  0
 PFV  CONST_06  S11  C10  C9   C6   180.00   0.0  0
 PFV  CONST_07  C12  N13  C9   C6   180.00   0.0  0
 PFV  CONST_08  N14  C12  N13  C9   180.00   0.0  0
 PFV  CONST_09  C10  S11  C12  N14  180.00   0.0  0
 PFV  CONST_10  H25  C10  C9   N13  180.00   0.0  0
 PFV  CONST_13  O37  C36  N35  C34    0.00   0.0  0
 PFV  CONST_14  CA   N    C5   C6   180.00   0.0  0
 PFV  CONST_15  C3   N4   C36  O37    0.00   0.0  0
 PFV  CONST_16  O7   C5   N    CA     0.00   0.0  0
 PFV  CONST_17  N4   C36  N35  C34  180.00   0.0  0
 PFV  CONST_18  C3   N4   C36  N35  180.00   0.0  0
 PFV  CONST_19  H21  N    C5   C6     0.00   0.0  0
 PFV  CONST_20  H14  N4   C36  O37  180.00   0.0  0
 PFV  CONST_21  H10  N35  C36  O37  180.00   0.0  0
 PFV  CONST_22  H22  O20  C17  C16  180.00   0.0  0
 PFV  Var_01    N35  C34  C27  C26  112.13  30.0  3
 PFV  Var_02    C10  C9   C6   C5    12.71  30.0  2
 PFV  Var_03    C27  C34  N35  C36  -72.70  30.0  3
 PFV  Var_04    O7   C5   C6   C9    91.97  30.0  2
 PFV  Var_05    C5   C6   N8   O15   -2.80   0.0  2
 PFV  Var_06    C2   C3   N4   C36  -90.19  30.0  3
 PFV  Var_07    O21  C17  C16  O15  -18.39  30.0  3
 PFV  Var_08    O23  S22  N1   C2    88.60  30.0  2
 PFV  Var_09    C17  C16  O15  N8   -64.89  30.0  3
 PFV  Var_10    H3   C18  C16  O15  172.56  30.0  3
 PFV  Var_11    H6   C19  C16  O15  -68.19  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
 PFV  chir_01  C2  C3  CA  N1  positiv
 PFV  chir_02  CA  N   C2  C   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
 PFV  plan-1  C6   0.020
 PFV  plan-1  C9   0.020
 PFV  plan-1  N13  0.020
 PFV  plan-1  C12  0.020
 PFV  plan-1  N14  0.020
 PFV  plan-1  S11  0.020
 PFV  plan-1  C10  0.020
 PFV  plan-1  H25  0.020
 PFV  plan-2  C16  0.020
 PFV  plan-2  C17  0.020
 PFV  plan-2  O21  0.020
 PFV  plan-2  O20  0.020
 PFV  plan-2  H22  0.020
 PFV  plan-3  CA   0.020
 PFV  plan-3  C    0.020
 PFV  plan-3  O    0.020
 PFV  plan-3  H20  0.020
 PFV  plan-4  C6   0.020
 PFV  plan-4  C9   0.020
 PFV  plan-4  O15  0.020
 PFV  plan-4  C5   0.020
 PFV  plan-4  N8   0.020
 PFV  plan-5  C34  0.020
 PFV  plan-5  C26  0.020
 PFV  plan-5  C27  0.020
 PFV  plan-5  N28  0.020
 PFV  plan-5  O38  0.020
 PFV  plan-5  C29  0.020
 PFV  plan-5  C30  0.020
 PFV  plan-5  O33  0.020
 PFV  plan-5  C31  0.020
 PFV  plan-5  O32  0.020
 PFV  plan-5  H9   0.020
 PFV  plan-5  H12  0.020
 PFV  plan-6  C36  0.020
 PFV  plan-6  C34  0.020
 PFV  plan-6  O37  0.020
 PFV  plan-6  N35  0.020
 PFV  plan-6  N4   0.020
 PFV  plan-6  C3   0.020
 PFV  plan-6  H10  0.020
 PFV  plan-6  H14  0.020
 PFV  plan-7  C6   0.020
 PFV  plan-7  CA   0.020
 PFV  plan-7  N    0.020
 PFV  plan-7  C5   0.020
 PFV  plan-7  O7   0.020
 PFV  plan-7  H21  0.020
 PFV  plan-8  C12  0.020
 PFV  plan-8  N14  0.020
 PFV  plan-8  H23  0.020
 PFV  plan-8  H24  0.020

