# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 04:29:01 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-[(E)-({1-carboxy-2-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH+]cc(CO[P](O)(O)=O)c(C=[NH+][C-](C[C@@H]2C(=O)Nc3ccccc23)C(O)=O)c1[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
 VCS  VCS  "4-[(E)-({1-carboxy-2-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-id-1-yl}iminio)methyl]-2-methyl-5-[(phosphonooxy)methyl]pyridin-1-ium-3-olate"  ligand  51  31  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VCS
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
 VCS  C05   C  CH2    0  -0.324  81.9705  14.5543  13.9784
 VCS  C06   C  CR6    0  -0.048  82.7851  14.3879  12.7299
 VCS  C07   C  CR6    0  -0.037  82.4977  15.1025  11.5472
 VCS  C08   C  C1     0  -0.069  81.3790  15.9779  11.4737
 VCS  C10   C  C     -1   0.153  80.0361  17.3823  10.0720
 VCS  C11   C  CH2    0  -0.542  78.9540  17.5326  11.0808
 VCS  C12   C  CR15   0  -0.470  78.0927  16.2556  11.2563
 VCS  C13   C  CR56   0   0.076  77.0617  16.4012  12.3313
 VCS  C14   C  CR56   0   0.377  75.7987  16.2977  11.7502
 VCS  C16   C  CR5    0   0.555  77.2515  15.9822  10.0134
 VCS  C18   C  CR16   0  -0.306  74.6393  16.4179  12.4928
 VCS  C19   C  CR16   0  -0.265  74.7737  16.6480  13.8609
 VCS  C20   C  CR16   0  -0.262  76.0248  16.7503  14.4556
 VCS  C21   C  CR16   0  -0.329  77.1824  16.6276  13.6861
 VCS  C22   C  C      0   0.449  80.0186  17.9381   8.7449
 VCS  C25   C  CR6    0   0.298  83.3359  14.9241  10.3886
 VCS  C27   C  CR6    0   0.200  84.3937  13.9943  10.4973
 VCS  C28   C  CH3    0  -0.721  85.2958  13.7219   9.3474
 VCS  C30   C  CR16   0  -0.043  83.8381  13.5111  12.7510
 VCS  N09   N  NC1    1  -0.552  81.0886  16.6106  10.3478
 VCS  N15   N  NR15   0  -0.739  75.9426  16.0606  10.3892
 VCS  N29   N  NR16   1  -0.591  84.5902  13.3464  11.6549
 VCS  O01   O  O      0  -0.689  78.6744  12.6288  13.4048
 VCS  O03   O  OH1    0  -0.736  81.1391  11.7127  13.2997
 VCS  O04   O  O2     0  -0.578  80.6013  14.1887  13.7704
 VCS  O17   O  O      0  -0.442  77.6540  15.7490   8.8940
 VCS  O23   O  O      0  -0.493  80.8882  17.7648   7.9052
 VCS  O24   O  OH1    0  -0.612  78.9421  18.6967   8.5050
 VCS  O26   O  OC    -1  -0.593  83.1426  15.5636   9.3064
 VCS  P02   P  P      0   1.458  80.0499  12.6939  13.9277
 VCS  O31   O  OH1    0  -0.738  80.2862  12.2758  15.4490
 VCS  H052  H  HCH2   0   0.275  82.4118  13.9839  14.7990
 VCS  H051  H  HCH2   0   0.272  81.9489  15.5996  14.2906
 VCS  H081  H  H      0   0.288  80.7285  16.1255  12.3207
 VCS  H111  H  HCH2   0   0.277  79.3778  17.7784  12.0611
 VCS  H112  H  HCH2   0   0.288  78.3009  18.3671  10.8305
 VCS  H121  H  HCR5   0   0.310  78.7398  15.3896  11.4359
 VCS  H181  H  HCR6   0   0.265  73.6622  16.3369  12.0347
 VCS  H191  H  HCR6   0   0.256  73.8831  16.7472  14.4679
 VCS  H201  H  HCR6   0   0.252  76.1023  16.9255  15.5203
 VCS  H211  H  HCR6   0   0.253  78.1591  16.7082  14.1480
 VCS  H281  H  HCH3   0   0.263  85.8141  14.6303   9.0372
 VCS  H282  H  HCH3   0   0.256  86.0466  12.9698   9.5857
 VCS  H283  H  HCH3   0   0.263  84.7261  13.3716   8.4856
 VCS  H301  H  HCR6   0   0.315  84.1083  12.9231  13.6145
 VCS  H151  H  HNR5   0   0.408  75.1733  15.9282   9.7496
 VCS  H2    H  HOH1   0   0.502  81.1652  11.7126  12.3328
 VCS  H3    H  HOH1   0   0.474  78.9941  19.0370   7.6013
 VCS  H5    H  HOH1   0   0.500  79.6555  12.6668  16.0690
 VCS  H091  H  HNC1   0   0.452  81.8145  16.4047   9.6059
 VCS  H291  H  HNR6   0   0.439  85.3541  12.6839  11.7071

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
 VCS  O23  C22   double    1.221  0.020  1.221
 VCS  O24  C22   single    1.339  0.020  1.339
 VCS  C22  C10   single    1.439  0.020  1.439
 VCS  O17  C16   double    1.212  0.020  1.212
 VCS  O26  C25   single    1.272  0.020  1.272
 VCS  C28  C27   single    1.487  0.020  1.487
 VCS  C16  N15   single    1.364  0.020  1.364
 VCS  C16  C12   single    1.526  0.020  1.526
 VCS  C10  N09   single    1.334  0.020  1.334
 VCS  C10  C11   single    1.487  0.020  1.487
 VCS  N09  C08   double    1.324  0.020  1.324
 VCS  C25  C27   aromatic  1.413  0.020  1.413
 VCS  C25  C07   aromatic  1.441  0.020  1.441
 VCS  N15  C14   single    1.389  0.020  1.389
 VCS  C27  N29   aromatic  1.341  0.020  1.341
 VCS  C11  C12   single    1.550  0.020  1.550
 VCS  C12  C13   single    1.497  0.020  1.497
 VCS  C08  C07   single    1.422  0.020  1.422
 VCS  C07  C06   aromatic  1.411  0.020  1.411
 VCS  C14  C13   aromatic  1.394  0.020  1.394
 VCS  C14  C18   aromatic  1.382  0.020  1.382
 VCS  N29  C30   aromatic  1.339  0.020  1.339
 VCS  C13  C21   aromatic  1.379  0.020  1.379
 VCS  C06  C30   aromatic  1.370  0.020  1.370
 VCS  C06  C05   single    1.500  0.020  1.500
 VCS  C18  C19   aromatic  1.394  0.020  1.394
 VCS  O04  C05   single    1.432  0.020  1.432
 VCS  O04  P02   single    1.601  0.020  1.601
 VCS  O01  P02   double    1.473  0.020  1.473
 VCS  C21  C20   aromatic  1.395  0.020  1.395
 VCS  O03  P02   single    1.595  0.020  1.595
 VCS  P02  O31   single    1.595  0.020  1.595
 VCS  C19  C20   aromatic  1.389  0.020  1.389
 VCS  C05  H052  single    0.970  0.020  1.090
 VCS  C05  H051  single    0.970  0.020  1.090
 VCS  C08  H081  single    0.930  0.020  1.080
 VCS  C11  H111  single    0.970  0.020  1.090
 VCS  C11  H112  single    0.970  0.020  1.090
 VCS  C12  H121  single    0.970  0.020  1.090
 VCS  C18  H181  single    0.930  0.020  1.080
 VCS  C19  H191  single    0.930  0.020  1.080
 VCS  C20  H201  single    0.930  0.020  1.080
 VCS  C21  H211  single    0.930  0.020  1.080
 VCS  C28  H281  single    0.970  0.020  1.090
 VCS  C28  H282  single    0.970  0.020  1.090
 VCS  C28  H283  single    0.970  0.020  1.090
 VCS  C30  H301  single    0.930  0.020  1.080
 VCS  N15  H151  single    0.860  0.020  1.020
 VCS  O03  H2    single    0.850  0.020  0.980
 VCS  O24  H3    single    0.850  0.020  0.980
 VCS  O31  H5    single    0.850  0.020  0.980
 VCS  N09  H091  single    0.860  0.020  1.020
 VCS  N29  H291  single    0.860  0.020  1.020

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
 VCS  H051  C05  H052  107.05  3.000
 VCS  H051  C05  O04   105.50  3.000
 VCS  H052  C05  O04   111.22  3.000
 VCS  H051  C05  C06   110.81  3.000
 VCS  H052  C05  C06   110.36  3.000
 VCS  O04   C05  C06   111.71  3.000
 VCS  C30   C06  C07   119.56  3.000
 VCS  C30   C06  C05   118.39  3.000
 VCS  C07   C06  C05   122.05  3.000
 VCS  C25   C07  C08   119.48  3.000
 VCS  C08   C07  C06   121.00  3.000
 VCS  C25   C07  C06   119.51  3.000
 VCS  H081  C08  N09   118.07  3.000
 VCS  H081  C08  C07   121.21  3.000
 VCS  N09   C08  C07   120.70  3.000
 VCS  N09   C10  C22   115.07  3.000
 VCS  N09   C10  C11   119.50  3.000
 VCS  C22   C10  C11   125.30  3.000
 VCS  H112  C11  H111  105.41  3.000
 VCS  H112  C11  C12   108.91  3.000
 VCS  H111  C11  C12   107.36  3.000
 VCS  H112  C11  C10   110.97  3.000
 VCS  H111  C11  C10   110.37  3.000
 VCS  C12   C11  C10   113.44  3.000
 VCS  H121  C12  C16   108.51  3.000
 VCS  H121  C12  C13   111.47  3.000
 VCS  C16   C12  C13   102.88  3.000
 VCS  H121  C12  C11   109.96  3.000
 VCS  C13   C12  C11   112.57  3.000
 VCS  C16   C12  C11   111.21  3.000
 VCS  C21   C13  C14   120.07  3.000
 VCS  C21   C13  C12   131.41  3.000
 VCS  C14   C13  C12   108.51  3.000
 VCS  N15   C14  C18   128.92  3.000
 VCS  C18   C14  C13   121.98  3.000
 VCS  N15   C14  C13   109.10  3.000
 VCS  O17   C16  N15   125.74  3.000
 VCS  N15   C16  C12   107.12  3.000
 VCS  O17   C16  C12   127.14  3.000
 VCS  H181  C18  C19   120.99  3.000
 VCS  H181  C18  C14   121.56  3.000
 VCS  C19   C18  C14   117.44  3.000
 VCS  H191  C19  C20   119.62  3.000
 VCS  H191  C19  C18   119.10  3.000
 VCS  C20   C19  C18   121.28  3.000
 VCS  H201  C20  C21   119.84  3.000
 VCS  H201  C20  C19   119.85  3.000
 VCS  C21   C20  C19   120.31  3.000
 VCS  H211  C21  C20   120.42  3.000
 VCS  H211  C21  C13   120.66  3.000
 VCS  C20   C21  C13   118.92  3.000
 VCS  O24   C22  O23   121.99  3.000
 VCS  O24   C22  C10   113.20  3.000
 VCS  O23   C22  C10   124.80  3.000
 VCS  O26   C25  C27   120.69  3.000
 VCS  C27   C25  C07   117.08  3.000
 VCS  O26   C25  C07   122.24  3.000
 VCS  N29   C27  C28   119.35  3.000
 VCS  N29   C27  C25   119.62  3.000
 VCS  C28   C27  C25   121.03  3.000
 VCS  H283  C28  H282  108.12  3.000
 VCS  H283  C28  H281  106.91  3.000
 VCS  H282  C28  H281  108.04  3.000
 VCS  H283  C28  C27   110.67  3.000
 VCS  H282  C28  C27   112.07  3.000
 VCS  H281  C28  C27   110.83  3.000
 VCS  H301  C30  N29   116.57  3.000
 VCS  H301  C30  C06   123.60  3.000
 VCS  N29   C30  C06   119.84  3.000
 VCS  H091  N09  C10   120.59  3.000
 VCS  H091  N09  C08   110.67  3.000
 VCS  C10   N09  C08   128.71  3.000
 VCS  H151  N15  C16   123.32  3.000
 VCS  H151  N15  C14   124.36  3.000
 VCS  C16   N15  C14   112.28  3.000
 VCS  H291  N29  C30   117.51  3.000
 VCS  H291  N29  C27   118.11  3.000
 VCS  C30   N29  C27   124.38  3.000
 VCS  H2    O03  P02   114.34  3.000
 VCS  P02   O04  C05   123.59  3.000
 VCS  H3    O24  C22   108.88  3.000
 VCS  O31   P02  O04   106.70  3.000
 VCS  O31   P02  O03    96.50  3.000
 VCS  O04   P02  O03   107.49  3.000
 VCS  O31   P02  O01   117.73  3.000
 VCS  O03   P02  O01   118.08  3.000
 VCS  O04   P02  O01   109.15  3.000
 VCS  H5    O31  P02   114.13  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
 VCS  CONST_01  C27   C25  C07  C06      0.00   0.0  0
 VCS  CONST_02  C27   N29  C30  C06      0.00   0.0  0
 VCS  CONST_03  N29   C27  C25  C07      0.00   0.0  0
 VCS  CONST_04  N29   C30  C06  C07      0.00   0.0  0
 VCS  CONST_05  C19   C18  C14  C13      0.00   0.0  0
 VCS  CONST_06  C19   C20  C21  C13      0.00   0.0  0
 VCS  CONST_07  C20   C21  C13  C14      0.00   0.0  0
 VCS  CONST_08  C20   C19  C18  C14      0.00   0.0  0
 VCS  CONST_09  C21   C13  C14  C18      0.00   0.0  0
 VCS  CONST_10  C21   C20  C19  C18      0.00   0.0  0
 VCS  CONST_11  C30   N29  C27  C25      0.00   0.0  0
 VCS  CONST_12  C30   C06  C07  C25      0.00   0.0  0
 VCS  CONST_13  C14   N15  C16  C12      0.00   0.0  0
 VCS  CONST_14  C25   C07  C06  C05    180.00   0.0  0
 VCS  CONST_15  N29   C30  C06  C05    180.00   0.0  0
 VCS  CONST_16  O26   C25  C07  C06    180.00   0.0  0
 VCS  CONST_17  C28   C27  C25  C07    180.00   0.0  0
 VCS  CONST_18  C27   C25  C07  C08    180.00   0.0  0
 VCS  CONST_19  C30   C06  C07  C08    180.00   0.0  0
 VCS  CONST_20  C30   N29  C27  C28    180.00   0.0  0
 VCS  CONST_21  O26   C25  C27  N29    180.00   0.0  0
 VCS  CONST_22  O17   C16  N15  C14    180.00   0.0  0
 VCS  CONST_23  H291  N29  C30  C06    180.00   0.0  0
 VCS  CONST_24  H301  C30  C06  C07    180.00   0.0  0
 VCS  CONST_25  H211  C21  C13  C12      0.00   0.0  0
 VCS  CONST_26  H181  C18  C14  C13    180.00   0.0  0
 VCS  CONST_27  H201  C20  C21  C13    180.00   0.0  0
 VCS  CONST_28  H211  C21  C13  C14    180.00   0.0  0
 VCS  CONST_29  H191  C19  C18  C14    180.00   0.0  0
 VCS  CONST_30  H201  C20  C19  C18    180.00   0.0  0
 VCS  CONST_31  H211  C21  C20  C19    180.00   0.0  0
 VCS  CONST_32  H181  C18  C19  C20    180.00   0.0  0
 VCS  CONST_33  H191  C19  C20  C21    180.00   0.0  0
 VCS  CONST_34  H291  N29  C27  C25    180.00   0.0  0
 VCS  CONST_35  H301  C30  N29  C27    180.00   0.0  0
 VCS  CONST_36  H181  C18  C14  N15      0.00   0.0  0
 VCS  CONST_37  H151  N15  C16  C12    180.00   0.0  0
 VCS  CONST_38  H151  N15  C16  O17      0.00   0.0  0
 VCS  CONST_39  H3    O24  C22  C10    180.00   0.0  0
 VCS  CONST_40  H3    O24  C22  O23      0.00   0.0  0
 VCS  Var_01    N09   C08  C07  C06   -177.71  30.0  1
 VCS  Var_02    O04   C05  C06  C07     60.87  30.0  2
 VCS  Var_03    N09   C08  C07  C25      1.14  30.0  1
 VCS  Var_04    O04   C05  C06  C30   -119.10  30.0  2
 VCS  Var_05    H081  C08  C07  C06      0.61  30.0  1
 VCS  Var_06    H052  C05  C06  C07   -174.86  30.0  2
 VCS  Var_07    H051  C05  C06  C07    -56.45  30.0  2
 VCS  Var_08    H281  C28  C27  C25     60.24  30.0  2
 VCS  Var_09    H282  C28  C27  C25   -178.98  30.0  2
 VCS  Var_10    H283  C28  C27  C25    -58.20  30.0  2
 VCS  Var_11    H081  C08  C07  C25    179.46  30.0  1
 VCS  Var_12    H052  C05  C06  C30      5.18  30.0  2
 VCS  Var_13    H051  C05  C06  C30    123.58  30.0  2
 VCS  Var_14    H281  C28  C27  N29   -119.72  30.0  2
 VCS  Var_15    H282  C28  C27  N29      1.07  30.0  2
 VCS  Var_16    H283  C28  C27  N29    121.85  30.0  2
 VCS  Var_17    C10   N09  C08  C07    174.62   0.0  2
 VCS  Var_18    P02   O04  C05  C06     87.08  30.0  1
 VCS  Var_19    C22   C10  C11  C12    104.38  30.0  3
 VCS  Var_20    N09   C10  C11  C12    -71.19  30.0  3
 VCS  Var_21    H091  N09  C08  C07     -3.22   0.0  2
 VCS  Var_22    O01   P02  O04  C05   -169.61  30.0  3
 VCS  Var_23    O03   P02  O04  C05    -40.42  30.0  3
 VCS  Var_24    O31   P02  O04  C05     62.19  30.0  3
 VCS  Var_25    C22   C10  N09  C08    179.50  30.0  2
 VCS  Var_26    C11   C10  N09  C08     -4.49  30.0  2
 VCS  Var_27    O23   C22  C10  C11   -176.93  30.0  3
 VCS  Var_28    O24   C22  C10  C11      3.76  30.0  3
 VCS  Var_29    O23   C22  C10  N09     -1.19  30.0  3
 VCS  Var_30    O24   C22  C10  N09    179.50  30.0  3
 VCS  Var_31    H081  C08  N09  C10     -3.75   0.0  2
 VCS  Var_32    H091  N09  C10  C11    173.17  30.0  2
 VCS  Var_33    H091  N09  C10  C22     -2.84  30.0  2
 VCS  Var_34    H111  C11  C10  C22   -135.10  30.0  3
 VCS  Var_35    H112  C11  C10  C22    -18.62  30.0  3
 VCS  Var_36    H111  C11  C10  N09     49.34  30.0  3
 VCS  Var_37    H112  C11  C10  N09    165.82  30.0  3
 VCS  Var_38    H052  C05  O04  P02    -36.72  30.0  3
 VCS  Var_39    H051  C05  O04  P02   -152.44  30.0  3
 VCS  Var_40    H091  N09  C08  H081   178.41   0.0  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
 VCS  chir_01  C12  C16  C11  C13  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
 VCS  plan-1  C05   0.020
 VCS  plan-1  C06   0.020
 VCS  plan-1  C07   0.020
 VCS  plan-1  C08   0.020
 VCS  plan-1  C25   0.020
 VCS  plan-1  C27   0.020
 VCS  plan-1  C28   0.020
 VCS  plan-1  C30   0.020
 VCS  plan-1  N29   0.020
 VCS  plan-1  O26   0.020
 VCS  plan-1  H301  0.020
 VCS  plan-1  H291  0.020
 VCS  plan-2  C12   0.020
 VCS  plan-2  C13   0.020
 VCS  plan-2  C14   0.020
 VCS  plan-2  C16   0.020
 VCS  plan-2  C18   0.020
 VCS  plan-2  C19   0.020
 VCS  plan-2  C20   0.020
 VCS  plan-2  C21   0.020
 VCS  plan-2  N15   0.020
 VCS  plan-2  O17   0.020
 VCS  plan-2  H181  0.020
 VCS  plan-2  H191  0.020
 VCS  plan-2  H201  0.020
 VCS  plan-2  H211  0.020
 VCS  plan-2  H151  0.020
 VCS  plan-3  C10   0.020
 VCS  plan-3  C22   0.020
 VCS  plan-3  O23   0.020
 VCS  plan-3  O24   0.020
 VCS  plan-3  H3    0.020
 VCS  plan-4  C07   0.020
 VCS  plan-4  C08   0.020
 VCS  plan-4  C10   0.020
 VCS  plan-4  N09   0.020
 VCS  plan-4  H081  0.020
 VCS  plan-4  H091  0.020

