# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 11:19:04 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridinium-4-yl}methyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH+]cc(CO[P](O)(O)=O)c(CN[C@@H](CCC(O)=O)C(O)=O)c1O
#
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
 PPE  PPE  'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridinium-4-yl}methyl)-L-glutamic acid'  ligand  45  25  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PPE
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
 PPE  N1    N  NR16  1  -0.618  43.7408  15.5621  44.9142
 PPE  C2    C  CR6   0   0.304  44.7133  14.9745  45.6085
 PPE  C2A   C  CH3   0  -0.715  44.8873  15.3004  47.0457
 PPE  C3    C  CR6   0   0.301  45.5366  14.0716  44.9279
 PPE  O3    O  OH1   0  -0.574  46.5051  13.5374  45.6697
 PPE  C4    C  CR6   0   0.069  45.3144  13.7945  43.5776
 PPE  C4A   C  CH2   0  -0.318  46.2122  12.8463  42.8280
 PPE  C5    C  CR6   0  -0.028  44.2805  14.4708  42.9160
 PPE  C6    C  CR16  0  -0.024  43.4987  15.3526  43.6180
 PPE  C5A   C  CH2   0  -0.215  43.9801  14.2527  41.4640
 PPE  OP4   O  O2    0  -0.638  43.2118  13.0501  41.3573
 PPE  P     P  P     0   1.339  42.2975  12.7830  40.0714
 PPE  OP1   O  O     0  -0.696  41.4191  13.8917  39.6600
 PPE  OP2   O  OH1   0  -0.646  41.6200  11.3979  40.4460
 PPE  OP3   O  OH1   0  -0.628  43.4001  12.3289  38.9983
 PPE  NA    N  NH1   0  -0.629  47.2213  13.5882  42.0854
 PPE  CAA   C  CH1   0  -0.195  48.5278  12.9671  42.0684
 PPE  CBA   C  CH2   0  -0.483  48.5937  11.7955  41.0863
 PPE  CGA   C  CH2   0  -0.552  48.3684  12.1895  39.6288
 PPE  CDA   C  C     0   0.561  46.9620  12.5813  39.2694
 PPE  OE1   O  O     0  -0.482  46.6597  13.5666  38.6398
 PPE  OE2   O  OH1   0  -0.521  46.0752  11.6694  39.6526
 PPE  CA    C  C     0   0.612  49.5717  14.0259  41.7591
 PPE  OA    O  O     0  -0.488  49.3390  15.2041  41.6609
 PPE  OXT   O  OH1   0  -0.590  50.7804  13.5027  41.6428
 PPE  HN1   H  HNR6  0   0.464  43.1423  16.2185  45.4039
 PPE  H2A1  H  HCH3  0   0.290  44.7991  14.4003  47.6539
 PPE  H2A2  H  HCH3  0   0.276  45.8771  15.7210  47.2234
 PPE  H2A3  H  HCH3  0   0.299  44.1433  16.0190  47.3821
 PPE  HO3   H  HOH1  0   0.460  47.0372  12.8952  45.1855
 PPE  H4A1  H  HCH2  0   0.277  46.6690  12.1272  43.5226
 PPE  H4A2  H  HCH2  0   0.281  45.6106  12.2265  42.1626
 PPE  H6    H  HCR6  0   0.344  42.6808  15.9090  43.1866
 PPE  H5A1  H  HCH2  0   0.231  43.4236  15.1070  41.0738
 PPE  H5A2  H  HCH2  0   0.231  44.9014  14.1678  40.8858
 PPE  HOP2  H  HOH1  0   0.520  40.7937  11.4740  40.9428
 PPE  HOP3  H  HOH1  0   0.527  43.1427  12.4378  38.0715
 PPE  HNA   H  HNH1  0   0.338  47.2935  14.5404  42.4175
 PPE  HAA   H  HCH1  0   0.310  48.8023  12.5684  43.0617
 PPE  HBA1  H  HCH2  0   0.274  49.5673  11.3139  41.1728
 PPE  HBA2  H  HCH2  0   0.249  47.8686  11.0391  41.3922
 PPE  HGA1  H  HCH2  0   0.260  49.0371  12.9952  39.3239
 PPE  HGA2  H  HCH2  0   0.254  48.6243  11.3293  39.0025
 PPE  HOE2  H  HOH1  0   0.493  45.1781  11.9190  39.3592
 PPE  HXT   H  HOH1  0   0.476  51.4328  14.1974  41.4657

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
 PPE  N1   C2    aromatic  1.331  0.020  1.331
 PPE  N1   C6    aromatic  1.335  0.020  1.335
 PPE  N1   HN1   single    0.860  0.020  1.020
 PPE  C2   C2A   single    1.484  0.020  1.484
 PPE  C2   C3    aromatic  1.399  0.020  1.399
 PPE  C2A  H2A1  single    0.970  0.020  1.090
 PPE  C2A  H2A2  single    0.970  0.020  1.090
 PPE  C2A  H2A3  single    0.970  0.020  1.090
 PPE  C3   O3    single    1.332  0.020  1.332
 PPE  C3   C4    aromatic  1.396  0.020  1.396
 PPE  O3   HO3   single    0.850  0.020  0.980
 PPE  C4   C4A   single    1.506  0.020  1.506
 PPE  C4   C5    aromatic  1.401  0.020  1.401
 PPE  C4A  NA    single    1.456  0.020  1.456
 PPE  C4A  H4A1  single    0.970  0.020  1.090
 PPE  C4A  H4A2  single    0.970  0.020  1.090
 PPE  C5   C6    aromatic  1.372  0.020  1.372
 PPE  C5   C5A   single    1.499  0.020  1.499
 PPE  C6   H6    single    0.930  0.020  1.080
 PPE  C5A  OP4   single    1.431  0.020  1.431
 PPE  C5A  H5A1  single    0.970  0.020  1.090
 PPE  C5A  H5A2  single    0.970  0.020  1.090
 PPE  OP4  P     single    1.600  0.020  1.600
 PPE  P    OP1   double    1.473  0.020  1.473
 PPE  P    OP2   single    1.587  0.020  1.587
 PPE  P    OP3   single    1.604  0.020  1.604
 PPE  OP2  HOP2  single    0.850  0.020  0.980
 PPE  OP3  HOP3  single    0.850  0.020  0.980
 PPE  NA   CAA   single    1.447  0.020  1.447
 PPE  NA   HNA   single    0.890  0.020  1.040
 PPE  CAA  CBA   single    1.530  0.020  1.530
 PPE  CAA  CA    single    1.519  0.020  1.519
 PPE  CAA  HAA   single    0.970  0.020  1.090
 PPE  CBA  CGA   single    1.527  0.020  1.527
 PPE  CBA  HBA1  single    0.970  0.020  1.090
 PPE  CBA  HBA2  single    0.970  0.020  1.090
 PPE  CGA  CDA   single    1.503  0.020  1.503
 PPE  CGA  HGA1  single    0.970  0.020  1.090
 PPE  CGA  HGA2  single    0.970  0.020  1.090
 PPE  CDA  OE1   double    1.208  0.020  1.208
 PPE  CDA  OE2   single    1.329  0.020  1.329
 PPE  OE2  HOE2  single    0.850  0.020  0.980
 PPE  CA   OA    double    1.205  0.020  1.205
 PPE  CA   OXT   single    1.322  0.020  1.322
 PPE  OXT  HXT   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
 PPE  HN1   N1   C6    117.59  3.000
 PPE  HN1   N1   C2    117.70  3.000
 PPE  C6    N1   C2    124.71  3.000
 PPE  C3    C2   C2A   122.95  3.000
 PPE  C3    C2   N1    117.46  3.000
 PPE  C2A   C2   N1    119.59  3.000
 PPE  H2A3  C2A  H2A2  108.40  3.000
 PPE  H2A3  C2A  H2A1  108.52  3.000
 PPE  H2A2  C2A  H2A1  107.53  3.000
 PPE  H2A3  C2A  C2    111.37  3.000
 PPE  H2A2  C2A  C2    110.44  3.000
 PPE  H2A1  C2A  C2    110.47  3.000
 PPE  C4    C3   O3    125.09  3.000
 PPE  C4    C3   C2    120.33  3.000
 PPE  O3    C3   C2    114.58  3.000
 PPE  HO3   O3   C3    112.87  3.000
 PPE  C5    C4   C4A   120.58  3.000
 PPE  C5    C4   C3    118.57  3.000
 PPE  C4A   C4   C3    120.77  3.000
 PPE  H4A2  C4A  H4A1  104.06  3.000
 PPE  H4A2  C4A  NA    111.15  3.000
 PPE  H4A1  C4A  NA    111.56  3.000
 PPE  H4A2  C4A  C4    109.45  3.000
 PPE  H4A1  C4A  C4    110.19  3.000
 PPE  NA    C4A  C4    110.26  3.000
 PPE  C5A   C5   C6    118.36  3.000
 PPE  C5A   C5   C4    122.35  3.000
 PPE  C6    C5   C4    119.28  3.000
 PPE  H6    C6   C5    123.98  3.000
 PPE  H6    C6   N1    116.40  3.000
 PPE  C5    C6   N1    119.62  3.000
 PPE  H5A2  C5A  H5A1  107.57  3.000
 PPE  H5A2  C5A  OP4   110.39  3.000
 PPE  H5A1  C5A  OP4   110.94  3.000
 PPE  H5A2  C5A  C5    110.82  3.000
 PPE  H5A1  C5A  C5    109.54  3.000
 PPE  OP4   C5A  C5    107.59  3.000
 PPE  P     OP4  C5A   120.46  3.000
 PPE  OP3   P    OP2   101.79  3.000
 PPE  OP3   P    OP1   115.86  3.000
 PPE  OP2   P    OP1   117.93  3.000
 PPE  OP3   P    OP4   101.07  3.000
 PPE  OP2   P    OP4   101.53  3.000
 PPE  OP1   P    OP4   116.07  3.000
 PPE  HOP2  OP2  P     114.67  3.000
 PPE  HOP3  OP3  P     115.20  3.000
 PPE  HNA   NA   CAA   110.10  3.000
 PPE  HNA   NA   C4A   111.22  3.000
 PPE  CAA   NA   C4A   114.41  3.000
 PPE  HAA   CAA  CA    105.30  3.000
 PPE  HAA   CAA  CBA   106.86  3.000
 PPE  CA    CAA  CBA   111.93  3.000
 PPE  HAA   CAA  NA    111.63  3.000
 PPE  CA    CAA  NA    108.90  3.000
 PPE  CBA   CAA  NA    112.03  3.000
 PPE  HBA2  CBA  HBA1  105.37  3.000
 PPE  HBA2  CBA  CGA   110.39  3.000
 PPE  HBA1  CBA  CGA   108.77  3.000
 PPE  HBA2  CBA  CAA   108.79  3.000
 PPE  HBA1  CBA  CAA   109.02  3.000
 PPE  CGA   CBA  CAA   114.13  3.000
 PPE  HGA2  CGA  HGA1  106.10  3.000
 PPE  HGA2  CGA  CDA   106.66  3.000
 PPE  HGA1  CGA  CDA   108.32  3.000
 PPE  HGA2  CGA  CBA   108.00  3.000
 PPE  HGA1  CGA  CBA   111.54  3.000
 PPE  CDA   CGA  CBA   115.69  3.000
 PPE  OE2   CDA  OE1   122.90  3.000
 PPE  OE2   CDA  CGA   112.13  3.000
 PPE  OE1   CDA  CGA   124.85  3.000
 PPE  HOE2  OE2  CDA   110.56  3.000
 PPE  OXT   CA   OA    123.80  3.000
 PPE  OXT   CA   CAA   111.74  3.000
 PPE  OA    CA   CAA   124.44  3.000
 PPE  HXT   OXT  CA    110.35  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
 PPE  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PPE  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PPE  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PPE  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PPE  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 PPE  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PPE  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 PPE  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PPE  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PPE  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 PPE  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 PPE  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 PPE  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 PPE  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 PPE  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PPE  CONST_16  HN1   N1   C2   C3   180.00   0.0  0
 PPE  CONST_17  HXT   OXT  CA   CAA  180.00   0.0  0
 PPE  CONST_18  HOE2  OE2  CDA  CGA  180.00   0.0  0
 PPE  Var_01    NA    C4A  C4   C3   -97.46  30.0  2
 PPE  Var_02    OP4   C5A  C5   C4    80.28  30.0  2
 PPE  Var_03    H2A1  C2A  C2   N1   121.33  30.0  2
 PPE  Var_04    CAA   NA   C4A  C4   141.83  30.0  3
 PPE  Var_05    OP1   P    OP4  C5A  -48.38  30.0  3
 PPE  Var_06    CDA   CGA  CBA  CAA  -71.31  30.0  3
 PPE  Var_07    OE1   CDA  CGA  CBA  132.28  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
 PPE  chir_01  CAA  NA  CBA  CA  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
 PPE  plan-1  N1    0.020
 PPE  plan-1  C2    0.020
 PPE  plan-1  C2A   0.020
 PPE  plan-1  C3    0.020
 PPE  plan-1  O3    0.020
 PPE  plan-1  C4    0.020
 PPE  plan-1  C4A   0.020
 PPE  plan-1  C5    0.020
 PPE  plan-1  C6    0.020
 PPE  plan-1  C5A   0.020
 PPE  plan-1  HN1   0.020
 PPE  plan-1  H6    0.020
 PPE  plan-2  CGA   0.020
 PPE  plan-2  CDA   0.020
 PPE  plan-2  OE1   0.020
 PPE  plan-2  OE2   0.020
 PPE  plan-2  HOE2  0.020
 PPE  plan-3  CAA   0.020
 PPE  plan-3  CA    0.020
 PPE  plan-3  OA    0.020
 PPE  plan-3  OXT   0.020
 PPE  plan-3  HXT   0.020

