# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 07:02:28 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: 4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-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@]2(O)C(=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
 VE4  VE4  "4-[(E)-({1-carboxy-2-[(3R)-3-hydroxy-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  52  32  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VE4
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
 VE4  C05   C  CH2    0  -0.291  82.7745  14.2825  14.2290
 VE4  C06   C  CR6    0  -0.047  83.4600  14.1407  12.8997
 VE4  C07   C  CR6    0  -0.044  83.0796  14.8749  11.7542
 VE4  C08   C  C1     0  -0.053  81.9135  15.6895  11.7567
 VE4  C10   C  C      0   0.146  80.4649  17.1169  10.4750
 VE4  C11   C  CH2    0  -0.584  79.3872  17.2083  11.4990
 VE4  C12   C  CR5    0   0.079  78.3193  16.0830  11.4219
 VE4  C14   C  CR56   0   0.025  77.2626  16.3429  12.4615
 VE4  C15   C  CR56   0   0.379  76.0947  16.7484  11.8203
 VE4  C17   C  CR5    0   0.549  77.5107  16.2184  10.1129
 VE4  C19   C  CR16   0  -0.306  74.9644  17.1114  12.5270
 VE4  C20   C  CR16   0  -0.259  75.0300  17.0519  13.9181
 VE4  C21   C  CR16   0  -0.262  76.1874  16.6488  14.5712
 VE4  C22   C  CR16   0  -0.322  77.3209  16.2964  13.8381
 VE4  C23   C  C      0   0.452  80.4422  17.8061   9.2135
 VE4  C26   C  CR6    0   0.297  83.8684  14.7667  10.5508
 VE4  C28   C  CR6    0   0.198  84.9565  13.8657  10.5717
 VE4  C29   C  CH3    0  -0.720  85.8083  13.6564   9.3708
 VE4  C31   C  CR16   0  -0.051  84.5386  13.2978  12.8348
 VE4  N09   N  NC1    1  -0.552  81.5551  16.3714  10.6846
 VE4  N16   N  NR15   0  -0.739  76.2828  16.7059  10.4433
 VE4  N30   N  NR16   0  -0.590  85.2331  13.1873  11.6947
 VE4  O01   O  OH1    0  -0.732  81.4334  11.9002  13.0091
 VE4  O03   O  O      0  -0.695  79.1526  12.9736  13.7784
 VE4  O04   O  O2     0  -0.578  81.3588  14.0941  14.1703
 VE4  O13   O  OH1    0  -0.673  78.8828  14.8037  11.4192
 VE4  O18   O  O      0  -0.432  77.8912  15.9279   9.0035
 VE4  O24   O  O      0  -0.497  81.2946  17.7082   8.3430
 VE4  O25   O  OH1    0  -0.615  79.3815  18.6130   9.0737
 VE4  O27   O  OC    -1  -0.592  83.6039  15.4399   9.5052
 VE4  O32   O  OH1    0  -0.731  80.8717  11.8944  15.4112
 VE4  P02   P  P      0   1.482  80.5793  12.7134  14.0733
 VE4  H051  H  HCH2   0   0.272  83.2218  13.6032  14.9582
 VE4  H052  H  HCH2   0   0.273  82.9030  15.2973  14.6084
 VE4  H081  H  H      0   0.278  81.2672  15.7229  12.6157
 VE4  H111  H  HCH2   0   0.278  79.8109  17.1832  12.5090
 VE4  H112  H  HCH2   0   0.289  78.8792  18.1718  11.4329
 VE4  H191  H  HCR6   0   0.268  74.0601  17.4279  12.0239
 VE4  H201  H  HCR6   0   0.260  74.1581  17.3275  14.4970
 VE4  H211  H  HCR6   0   0.254  76.2107  16.6097  15.6519
 VE4  H221  H  HCR6   0   0.257  78.2280  15.9895  14.3458
 VE4  H292  H  HCH3   0   0.263  86.3198  14.5785   9.0904
 VE4  H293  H  HCH3   0   0.255  86.5630  12.8893   9.5386
 VE4  H291  H  HCH3   0   0.262  85.2031  13.3556   8.5149
 VE4  H311  H  HCR6   0   0.314  84.8751  12.6958  13.6651
 VE4  H161  H  HNR5   0   0.409  75.5502  16.8641   9.7670
 VE4  H2    H  HOH1   0   0.505  81.0723  11.0394  12.7544
 VE4  H131  H  HOH1   0   0.460  78.8963  14.4230  12.3097
 VE4  H3    H  HOH1   0   0.472  79.4233  19.0364   8.2052
 VE4  H5    H  HOH1   0   0.499  80.2993  12.1238  16.1569
 VE4  H091  H  HNC1   0   0.449  82.2643  16.2507   9.9126
 VE4  H301  H  HNR6   0   0.438  86.0176  12.5474  11.6817

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
 VE4  O24  C23   double    1.222  0.020  1.222
 VE4  O18  C17   double    1.208  0.020  1.208
 VE4  C23  O25   single    1.340  0.020  1.340
 VE4  C23  C10   single    1.438  0.020  1.438
 VE4  O27  C26   single    1.271  0.020  1.271
 VE4  C29  C28   single    1.487  0.020  1.487
 VE4  C10  N09   double    1.337  0.020  1.337
 VE4  C10  C11   single    1.489  0.020  1.489
 VE4  C17  N16   single    1.362  0.020  1.362
 VE4  C17  C12   single    1.545  0.020  1.545
 VE4  N09  C08   single    1.320  0.020  1.320
 VE4  C26  C28   aromatic  1.413  0.020  1.413
 VE4  C26  C07   aromatic  1.443  0.020  1.443
 VE4  N16  C15   single    1.390  0.020  1.390
 VE4  C28  N30   aromatic  1.341  0.020  1.341
 VE4  C11  C12   single    1.553  0.020  1.553
 VE4  C12  O13   single    1.398  0.020  1.398
 VE4  C12  C14   single    1.505  0.020  1.505
 VE4  C08  C07   double    1.422  0.020  1.422
 VE4  C07  C06   aromatic  1.413  0.020  1.413
 VE4  N30  C31   aromatic  1.340  0.020  1.340
 VE4  C15  C14   aromatic  1.393  0.020  1.393
 VE4  C15  C19   aromatic  1.382  0.020  1.382
 VE4  C14  C22   aromatic  1.379  0.020  1.379
 VE4  C06  C31   aromatic  1.370  0.020  1.370
 VE4  C06  C05   single    1.502  0.020  1.502
 VE4  C19  C20   aromatic  1.394  0.020  1.394
 VE4  O04  C05   single    1.429  0.020  1.429
 VE4  O04  P02   single    1.589  0.020  1.589
 VE4  O03  P02   double    1.480  0.020  1.480
 VE4  C22  C21   aromatic  1.395  0.020  1.395
 VE4  O01  P02   single    1.588  0.020  1.588
 VE4  P02  O32   single    1.596  0.020  1.596
 VE4  C20  C21   aromatic  1.389  0.020  1.389
 VE4  C05  H051  single    0.970  0.020  1.090
 VE4  C05  H052  single    0.970  0.020  1.090
 VE4  C08  H081  single    0.930  0.020  1.080
 VE4  C11  H111  single    0.970  0.020  1.090
 VE4  C11  H112  single    0.970  0.020  1.090
 VE4  C19  H191  single    0.930  0.020  1.080
 VE4  C20  H201  single    0.930  0.020  1.080
 VE4  C21  H211  single    0.930  0.020  1.080
 VE4  C22  H221  single    0.930  0.020  1.080
 VE4  C29  H292  single    0.970  0.020  1.090
 VE4  C29  H293  single    0.970  0.020  1.090
 VE4  C29  H291  single    0.970  0.020  1.090
 VE4  C31  H311  single    0.930  0.020  1.080
 VE4  N16  H161  single    0.860  0.020  1.020
 VE4  O01  H2    single    0.850  0.020  0.980
 VE4  O13  H131  single    0.850  0.020  0.980
 VE4  O25  H3    single    0.850  0.020  0.980
 VE4  O32  H5    single    0.850  0.020  0.980
 VE4  N09  H091  single    0.860  0.020  1.020
 VE4  N30  H301  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
 VE4  H052  C05  H051  107.34  3.000
 VE4  H052  C05  O04   104.69  3.000
 VE4  H051  C05  O04   110.55  3.000
 VE4  H052  C05  C06   109.98  3.000
 VE4  H051  C05  C06   110.19  3.000
 VE4  O04   C05  C06   113.78  3.000
 VE4  C31   C06  C07   119.55  3.000
 VE4  C31   C06  C05   117.33  3.000
 VE4  C07   C06  C05   123.06  3.000
 VE4  C26   C07  C08   119.51  3.000
 VE4  C08   C07  C06   121.12  3.000
 VE4  C26   C07  C06   119.34  3.000
 VE4  H081  C08  N09   118.00  3.000
 VE4  H081  C08  C07   120.78  3.000
 VE4  N09   C08  C07   121.12  3.000
 VE4  N09   C10  C23   114.68  3.000
 VE4  N09   C10  C11   121.09  3.000
 VE4  C23   C10  C11   124.22  3.000
 VE4  H112  C11  H111  104.84  3.000
 VE4  H112  C11  C12   108.45  3.000
 VE4  H111  C11  C12   107.16  3.000
 VE4  H112  C11  C10   110.45  3.000
 VE4  H111  C11  C10   110.65  3.000
 VE4  C12   C11  C10   114.77  3.000
 VE4  O13   C12  C17   106.83  3.000
 VE4  O13   C12  C14   116.25  3.000
 VE4  C17   C12  C14   101.70  3.000
 VE4  C14   C12  C11   108.87  3.000
 VE4  O13   C12  C11   112.70  3.000
 VE4  C17   C12  C11   109.79  3.000
 VE4  C22   C14  C15   120.34  3.000
 VE4  C22   C14  C12   130.86  3.000
 VE4  C15   C14  C12   108.72  3.000
 VE4  N16   C15  C19   128.70  3.000
 VE4  C19   C15  C14   121.80  3.000
 VE4  N16   C15  C14   109.49  3.000
 VE4  O18   C17  N16   126.36  3.000
 VE4  N16   C17  C12   107.32  3.000
 VE4  O18   C17  C12   126.31  3.000
 VE4  H191  C19  C20   121.05  3.000
 VE4  H191  C19  C15   121.51  3.000
 VE4  C20   C19  C15   117.44  3.000
 VE4  H201  C20  C21   119.59  3.000
 VE4  H201  C20  C19   119.02  3.000
 VE4  C21   C20  C19   121.39  3.000
 VE4  H211  C21  C22   119.90  3.000
 VE4  H211  C21  C20   119.88  3.000
 VE4  C22   C21  C20   120.22  3.000
 VE4  H221  C22  C21   120.35  3.000
 VE4  H221  C22  C14   120.84  3.000
 VE4  C21   C22  C14   118.80  3.000
 VE4  O25   C23  O24   121.73  3.000
 VE4  O25   C23  C10   113.12  3.000
 VE4  O24   C23  C10   125.14  3.000
 VE4  O27   C26  C28   120.67  3.000
 VE4  C28   C26  C07   117.16  3.000
 VE4  O27   C26  C07   122.17  3.000
 VE4  N30   C28  C29   119.14  3.000
 VE4  N30   C28  C26   119.60  3.000
 VE4  C29   C28  C26   121.26  3.000
 VE4  H291  C29  H293  108.14  3.000
 VE4  H291  C29  H292  106.95  3.000
 VE4  H293  C29  H292  108.06  3.000
 VE4  H291  C29  C28   110.77  3.000
 VE4  H293  C29  C28   111.81  3.000
 VE4  H292  C29  C28   110.92  3.000
 VE4  H311  C31  N30   116.55  3.000
 VE4  H311  C31  C06   123.51  3.000
 VE4  N30   C31  C06   119.94  3.000
 VE4  H091  N09  C10   119.80  3.000
 VE4  H091  N09  C08   110.65  3.000
 VE4  C10   N09  C08   129.53  3.000
 VE4  H161  N16  C17   123.22  3.000
 VE4  H161  N16  C15   124.09  3.000
 VE4  C17   N16  C15   111.91  3.000
 VE4  H301  N30  C31   117.69  3.000
 VE4  H301  N30  C28   117.97  3.000
 VE4  C31   N30  C28   124.34  3.000
 VE4  H2    O01  P02   115.54  3.000
 VE4  P02   O04  C05   127.09  3.000
 VE4  H131  O13  C12   111.32  3.000
 VE4  H3    O25  C23   108.85  3.000
 VE4  H5    O32  P02   114.59  3.000
 VE4  O32   P02  O04   107.76  3.000
 VE4  O32   P02  O03   115.72  3.000
 VE4  O04   P02  O03   109.41  3.000
 VE4  O32   P02  O01   101.56  3.000
 VE4  O03   P02  O01   118.35  3.000
 VE4  O04   P02  O01   102.83  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
 VE4  CONST_01  C28   C26  C07  C06     0.00   0.0  0
 VE4  CONST_02  C28   N30  C31  C06     0.00   0.0  0
 VE4  CONST_03  N30   C28  C26  C07     0.00   0.0  0
 VE4  CONST_04  N30   C31  C06  C07     0.00   0.0  0
 VE4  CONST_05  C20   C19  C15  C14     0.00   0.0  0
 VE4  CONST_06  C20   C21  C22  C14     0.00   0.0  0
 VE4  CONST_07  C21   C22  C14  C15     0.00   0.0  0
 VE4  CONST_08  C21   C20  C19  C15     0.00   0.0  0
 VE4  CONST_09  C22   C14  C15  C19     0.00   0.0  0
 VE4  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 VE4  CONST_11  C31   N30  C28  C26     0.00   0.0  0
 VE4  CONST_12  C31   C06  C07  C26     0.00   0.0  0
 VE4  CONST_13  C15   N16  C17  C12     0.00   0.0  0
 VE4  CONST_14  C26   C07  C06  C05   180.00   0.0  0
 VE4  CONST_15  N30   C31  C06  C05   180.00   0.0  0
 VE4  CONST_16  O27   C26  C07  C06   180.00   0.0  0
 VE4  CONST_17  C29   C28  C26  C07   180.00   0.0  0
 VE4  CONST_18  C28   C26  C07  C08   180.00   0.0  0
 VE4  CONST_19  C31   C06  C07  C08   180.00   0.0  0
 VE4  CONST_20  C31   N30  C28  C29   180.00   0.0  0
 VE4  CONST_21  O27   C26  C28  N30   180.00   0.0  0
 VE4  CONST_22  O18   C17  N16  C15   180.00   0.0  0
 VE4  CONST_23  H301  N30  C31  C06   180.00   0.0  0
 VE4  CONST_24  H311  C31  C06  C07   180.00   0.0  0
 VE4  CONST_25  H221  C22  C14  C12     0.00   0.0  0
 VE4  CONST_26  H191  C19  C15  C14   180.00   0.0  0
 VE4  CONST_27  H211  C21  C22  C14   180.00   0.0  0
 VE4  CONST_28  H221  C22  C14  C15   180.00   0.0  0
 VE4  CONST_29  H201  C20  C19  C15   180.00   0.0  0
 VE4  CONST_30  H211  C21  C20  C19   180.00   0.0  0
 VE4  CONST_31  H221  C22  C21  C20   180.00   0.0  0
 VE4  CONST_32  H191  C19  C20  C21   180.00   0.0  0
 VE4  CONST_33  H201  C20  C21  C22   180.00   0.0  0
 VE4  CONST_34  H301  N30  C28  C26   180.00   0.0  0
 VE4  CONST_35  H311  C31  N30  C28   180.00   0.0  0
 VE4  CONST_36  H191  C19  C15  N16     0.00   0.0  0
 VE4  CONST_37  H161  N16  C17  C12   180.00   0.0  0
 VE4  CONST_38  H161  N16  C17  O18     0.00   0.0  0
 VE4  CONST_39  H3    O25  C23  C10   180.00   0.0  0
 VE4  CONST_40  H3    O25  C23  O24     0.00   0.0  0
 VE4  Var_01    N09   C08  C07  C06  -179.73   0.0  2
 VE4  Var_02    N09   C08  C07  C26    -1.44   0.0  2
 VE4  Var_03    C08   C07  C06  C05    -7.29  30.0  1
 VE4  Var_04    O04   C05  C06  C07    53.95  30.0  2
 VE4  Var_05    O27   C26  C07  C08     4.30  30.0  1
 VE4  Var_06    O27   C26  C28  C29    -1.16  30.0  1
 VE4  Var_07    O04   C05  C06  C31  -128.98  30.0  2
 VE4  Var_08    H081  C08  C07  C06    -3.26   0.0  2
 VE4  Var_09    H081  C08  C07  C26   175.03   0.0  2
 VE4  Var_10    H311  C31  C06  C05     3.82  30.0  1
 VE4  Var_11    H051  C05  C06  C07   178.74  30.0  2
 VE4  Var_12    H052  C05  C06  C07   -63.12  30.0  2
 VE4  Var_13    H292  C29  C28  C26    62.63  30.0  2
 VE4  Var_14    H293  C29  C28  C26  -176.67  30.0  2
 VE4  Var_15    H291  C29  C28  C26   -55.98  30.0  2
 VE4  Var_16    H301  N30  C28  C29    -0.29  30.0  1
 VE4  Var_17    H051  C05  C06  C31    -4.18  30.0  2
 VE4  Var_18    H052  C05  C06  C31   113.96  30.0  2
 VE4  Var_19    H292  C29  C28  N30  -117.15  30.0  2
 VE4  Var_20    H293  C29  C28  N30     3.55  30.0  2
 VE4  Var_21    H291  C29  C28  N30   124.24  30.0  2
 VE4  Var_22    P02   O04  C05  C06    77.71  30.0  1
 VE4  Var_23    C10   N09  C08  C07   175.62  30.0  1
 VE4  Var_24    C23   C10  C11  C12    94.37  30.0  2
 VE4  Var_25    N09   C10  C11  C12   -86.17  30.0  2
 VE4  Var_26    H091  N09  C08  C07    -2.93  30.0  1
 VE4  Var_27    C23   C10  N09  C08   175.55   0.0  2
 VE4  Var_28    C11   C10  N09  C08    -3.96   0.0  2
 VE4  Var_29    O03   P02  O04  C05  -169.34  30.0  3
 VE4  Var_30    O01   P02  O04  C05   -42.71  30.0  3
 VE4  Var_31    O32   P02  O04  C05    64.07  30.0  3
 VE4  Var_32    O24   C23  C10  C11  -177.40  30.0  2
 VE4  Var_33    O25   C23  C10  C11     3.71  30.0  2
 VE4  Var_34    O24   C23  C10  N09     3.11  30.0  2
 VE4  Var_35    O25   C23  C10  N09  -175.77  30.0  2
 VE4  Var_36    H091  N09  C10  C11   174.48   0.0  2
 VE4  Var_37    H091  N09  C10  C23    -6.02   0.0  2
 VE4  Var_38    H081  C08  N09  C10    -0.95  30.0  2
 VE4  Var_39    H111  C11  C10  C23  -144.22  30.0  3
 VE4  Var_40    H112  C11  C10  C23   -28.59  30.0  3
 VE4  Var_41    H111  C11  C10  N09    35.23  30.0  3
 VE4  Var_42    H112  C11  C10  N09   150.86  30.0  3
 VE4  Var_43    H051  C05  O04  P02   -46.88  30.0  3
 VE4  Var_44    H052  C05  O04  P02  -162.18  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
 VE4  chir_01  C12  C17  O13  C14  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
 VE4  plan-1  C07   0.020
 VE4  plan-1  C26   0.020
 VE4  plan-1  C28   0.020
 VE4  plan-1  O27   0.020
 VE4  plan-2  C12   0.020
 VE4  plan-2  C14   0.020
 VE4  plan-2  C15   0.020
 VE4  plan-2  C17   0.020
 VE4  plan-2  C19   0.020
 VE4  plan-2  C20   0.020
 VE4  plan-2  C21   0.020
 VE4  plan-2  C22   0.020
 VE4  plan-2  N16   0.020
 VE4  plan-2  O18   0.020
 VE4  plan-2  H191  0.020
 VE4  plan-2  H201  0.020
 VE4  plan-2  H211  0.020
 VE4  plan-2  H221  0.020
 VE4  plan-2  H161  0.020
 VE4  plan-3  C10   0.020
 VE4  plan-3  C23   0.020
 VE4  plan-3  O24   0.020
 VE4  plan-3  O25   0.020
 VE4  plan-3  H3    0.020
 VE4  plan-4  C08   0.020
 VE4  plan-4  C10   0.020
 VE4  plan-4  C11   0.020
 VE4  plan-4  C23   0.020
 VE4  plan-4  N09   0.020
 VE4  plan-4  H091  0.020
 VE4  plan-5  C06   0.020
 VE4  plan-5  C07   0.020
 VE4  plan-5  C08   0.020
 VE4  plan-5  C26   0.020
 VE4  plan-5  N09   0.020
 VE4  plan-5  H081  0.020

