# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 11:19:45 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(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
 PDG  PDG  'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-glutamic acid'  ligand  44  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_PDG
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
 PDG  N1    N  N     0  -0.409   1.6177   3.4850   0.5333
 PDG  C2    C  CR6   0   0.131   0.3112   3.4783   0.3276
 PDG  C2A   C  CH3   0  -0.721  -0.4558   4.7471   0.5374
 PDG  C3    C  CR6   0   0.256  -0.3495   2.3119  -0.0832
 PDG  O3    O  OH1   0  -0.651  -1.6741   2.3656  -0.2874
 PDG  C4    C  CR6   0   0.040   0.3786   1.1396  -0.2838
 PDG  C4A   C  CH2   0  -0.344  -0.3291  -0.0924  -0.7897
 PDG  C5    C  CR6   0  -0.074   1.7559   1.1717  -0.0494
 PDG  C6    C  CR16  0  -0.143   2.3210   2.3708   0.3558
 PDG  C5A   C  CH2   0  -0.212   2.5780  -0.0688  -0.2626
 PDG  OP4   O  O2    0  -0.592   3.9281   0.1851   0.1072
 PDG  P     P  P     0   1.465   5.0123  -0.9839  -0.0133
 PDG  OP1   O  O     0  -0.708   5.0976  -1.6685  -1.3159
 PDG  OP2   O  OH1   0  -0.729   6.2627  -0.1222   0.4647
 PDG  OP3   O  OH1   0  -0.742   4.6754  -2.0463   1.1307
 PDG  NA    N  NH1   0  -0.653  -1.6109  -0.2703  -0.1119
 PDG  CAA   C  CH1   0  -0.192  -2.4672  -1.2867  -0.6856
 PDG  CBA   C  CH2   0  -0.442  -3.8493  -1.2832  -0.0190
 PDG  CGA   C  CH2   0  -0.592  -4.5589   0.0495  -0.1888
 PDG  CDA   C  C     0   0.561  -5.9910   0.0130   0.2703
 PDG  OE1   O  OH1   0  -0.595  -6.6007   1.1748   0.0620
 PDG  OE2   O  O     0  -0.442  -6.5366  -0.9379   0.7719
 PDG  CA    C  C     0   0.538  -1.8799  -2.6868  -0.5572
 PDG  OA    O  O     0  -0.433  -1.0712  -3.0052   0.2775
 PDG  OXT   O  OH1   0  -0.585  -2.3949  -3.5217  -1.4460
 PDG  H2A1  H  HCH3  0   0.246  -0.9270   5.0911  -0.3853
 PDG  H2A2  H  HCH3  0   0.245  -1.2532   4.6157   1.2708
 PDG  H2A3  H  HCH3  0   0.245   0.2108   5.5309   0.8912
 PDG  HO3   H  HOH1  0   0.492  -1.9945   1.4255  -0.2785
 PDG  H4A1  H  HCH2  0   0.281  -0.5340   0.0369  -1.8578
 PDG  H4A2  H  HCH2  0   0.255   0.3097  -0.9747  -0.7061
 PDG  H6    H  HCR6  0   0.255   3.3831   2.4481   0.5487
 PDG  H5A1  H  HCH2  0   0.255   2.1746  -0.8911   0.3378
 PDG  H5A2  H  HCH2  0   0.263   2.5319  -0.3756  -1.3117
 PDG  HP2   H  HOH1  0   0.506   7.1106  -0.5792   0.3807
 PDG  HP3   H  HOH1  0   0.497   4.6561  -1.7021   2.0340
 PDG  HNA   H  HNH1  0   0.379  -1.4569  -0.4581   0.8741
 PDG  HAA   H  HCH1  0   0.289  -2.5961  -1.0594  -1.7486
 PDG  HBA1  H  HCH2  0   0.267  -4.4491  -2.0776  -0.4647
 PDG  HBA2  H  HCH2  0   0.257  -3.7419  -1.5252   1.0414
 PDG  HGA1  H  HCH2  0   0.283  -4.0572   0.8412   0.3724
 PDG  HGA2  H  HCH2  0   0.286  -4.5404   0.3641  -1.2369
 PDG  HE1   H  HOH1  0   0.481  -7.5180   1.1269   0.3694
 PDG  HXT   H  HOH1  0   0.486  -2.0513  -4.4177  -1.3078

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
 PDG  N1   C2    aromatic  1.323  0.020  1.323
 PDG  N1   C6    aromatic  1.330  0.020  1.330
 PDG  C2   C2A   single    1.497  0.020  1.497
 PDG  C2   C3    aromatic  1.402  0.020  1.402
 PDG  C2A  H2A1  single    0.970  0.020  1.090
 PDG  C2A  H2A2  single    0.970  0.020  1.090
 PDG  C2A  H2A3  single    0.970  0.020  1.090
 PDG  C3   O3    single    1.341  0.020  1.341
 PDG  C3   C4    aromatic  1.395  0.020  1.395
 PDG  O3   HO3   single    0.850  0.020  0.980
 PDG  C4   C4A   single    1.508  0.020  1.508
 PDG  C4   C5    aromatic  1.397  0.020  1.397
 PDG  C4A  NA    single    1.461  0.020  1.461
 PDG  C4A  H4A1  single    0.970  0.020  1.090
 PDG  C4A  H4A2  single    0.970  0.020  1.090
 PDG  C5   C6    aromatic  1.386  0.020  1.386
 PDG  C5   C5A   single    1.503  0.020  1.503
 PDG  C6   H6    single    0.930  0.020  1.080
 PDG  C5A  OP4   single    1.423  0.020  1.423
 PDG  C5A  H5A1  single    0.970  0.020  1.090
 PDG  C5A  H5A2  single    0.970  0.020  1.090
 PDG  OP4  P     single    1.599  0.020  1.599
 PDG  P    OP1   double    1.474  0.020  1.474
 PDG  P    OP2   single    1.592  0.020  1.592
 PDG  P    OP3   single    1.597  0.020  1.597
 PDG  OP2  HP2   single    0.850  0.020  0.980
 PDG  OP3  HP3   single    0.850  0.020  0.980
 PDG  NA   CAA   single    1.448  0.020  1.448
 PDG  NA   HNA   single    0.890  0.020  1.040
 PDG  CAA  CBA   single    1.534  0.020  1.534
 PDG  CAA  CA    single    1.524  0.020  1.524
 PDG  CAA  HAA   single    0.970  0.020  1.090
 PDG  CBA  CGA   single    1.519  0.020  1.519
 PDG  CBA  HBA1  single    0.970  0.020  1.090
 PDG  CBA  HBA2  single    0.970  0.020  1.090
 PDG  CGA  CDA   single    1.504  0.020  1.504
 PDG  CGA  HGA1  single    0.970  0.020  1.090
 PDG  CGA  HGA2  single    0.970  0.020  1.090
 PDG  CDA  OE1   single    1.328  0.020  1.328
 PDG  CDA  OE2   double    1.206  0.020  1.206
 PDG  OE1  HE1   single    0.850  0.020  0.980
 PDG  CA   OA    double    1.205  0.020  1.205
 PDG  CA   OXT   single    1.324  0.020  1.324
 PDG  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
 PDG  C6    N1   C2    119.84  3.000
 PDG  C3    C2   C2A   120.30  3.000
 PDG  C3    C2   N1    121.02  3.000
 PDG  C2A   C2   N1    118.68  3.000
 PDG  H2A3  C2A  H2A2  108.42  3.000
 PDG  H2A3  C2A  H2A1  108.20  3.000
 PDG  H2A2  C2A  H2A1  106.89  3.000
 PDG  H2A3  C2A  C2    110.00  3.000
 PDG  H2A2  C2A  C2    111.49  3.000
 PDG  H2A1  C2A  C2    111.70  3.000
 PDG  C4    C3   O3    121.83  3.000
 PDG  C4    C3   C2    119.70  3.000
 PDG  O3    C3   C2    118.47  3.000
 PDG  HO3   O3   C3    106.22  3.000
 PDG  C5    C4   C4A   122.51  3.000
 PDG  C5    C4   C3    118.11  3.000
 PDG  C4A   C4   C3    119.34  3.000
 PDG  H4A2  C4A  H4A1  106.22  3.000
 PDG  H4A2  C4A  NA    112.28  3.000
 PDG  H4A1  C4A  NA    107.63  3.000
 PDG  H4A2  C4A  C4    111.08  3.000
 PDG  H4A1  C4A  C4    108.57  3.000
 PDG  NA    C4A  C4    110.83  3.000
 PDG  C5A   C5   C6    122.16  3.000
 PDG  C5A   C5   C4    119.75  3.000
 PDG  C6    C5   C4    118.08  3.000
 PDG  H6    C6   C5    120.93  3.000
 PDG  H6    C6   N1    115.82  3.000
 PDG  C5    C6   N1    123.25  3.000
 PDG  H5A2  C5A  H5A1  107.44  3.000
 PDG  H5A2  C5A  OP4   109.83  3.000
 PDG  H5A1  C5A  OP4   109.94  3.000
 PDG  H5A2  C5A  C5    110.14  3.000
 PDG  H5A1  C5A  C5    109.90  3.000
 PDG  OP4   C5A  C5    109.56  3.000
 PDG  P     OP4  C5A   119.57  3.000
 PDG  OP3   P    OP2   108.10  3.000
 PDG  OP3   P    OP1   109.65  3.000
 PDG  OP2   P    OP1   118.12  3.000
 PDG  OP3   P    OP4   106.81  3.000
 PDG  OP2   P    OP4    96.56  3.000
 PDG  OP1   P    OP4   116.45  3.000
 PDG  HP2   OP2  P     114.01  3.000
 PDG  HP3   OP3  P     115.89  3.000
 PDG  HNA   NA   CAA   110.16  3.000
 PDG  HNA   NA   C4A   109.87  3.000
 PDG  CAA   NA   C4A   114.88  3.000
 PDG  HAA   CAA  CA    108.54  3.000
 PDG  HAA   CAA  CBA   108.38  3.000
 PDG  CA    CAA  CBA   108.22  3.000
 PDG  HAA   CAA  NA    107.98  3.000
 PDG  CA    CAA  NA    112.57  3.000
 PDG  CBA   CAA  NA    111.04  3.000
 PDG  HBA2  CBA  HBA1  106.82  3.000
 PDG  HBA2  CBA  CGA   110.40  3.000
 PDG  HBA1  CBA  CGA   109.66  3.000
 PDG  HBA2  CBA  CAA   109.42  3.000
 PDG  HBA1  CBA  CAA   108.43  3.000
 PDG  CGA   CBA  CAA   111.97  3.000
 PDG  HGA2  CGA  HGA1  106.01  3.000
 PDG  HGA2  CGA  CDA   108.38  3.000
 PDG  HGA1  CGA  CDA   107.34  3.000
 PDG  HGA2  CGA  CBA   110.57  3.000
 PDG  HGA1  CGA  CBA   111.33  3.000
 PDG  CDA   CGA  CBA   112.91  3.000
 PDG  OE2   CDA  OE1   123.18  3.000
 PDG  OE2   CDA  CGA   125.23  3.000
 PDG  OE1   CDA  CGA   111.58  3.000
 PDG  HE1   OE1  CDA   109.98  3.000
 PDG  OXT   CA   OA    124.02  3.000
 PDG  OXT   CA   CAA   111.90  3.000
 PDG  OA    CA   CAA   124.05  3.000
 PDG  HXT   OXT  CA    110.45  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
 PDG  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PDG  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PDG  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PDG  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PDG  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PDG  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PDG  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PDG  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PDG  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PDG  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PDG  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PDG  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PDG  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PDG  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PDG  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PDG  CONST_16  HXT   OXT  CA   CAA   180.00   0.0  0
 PDG  CONST_17  HE1   OE1  CDA  CGA   180.00   0.0  0
 PDG  Var_01    NA    C4A  C4   C3    -42.92  30.0  2
 PDG  Var_02    OP4   C5A  C5   C4   -176.84  30.0  2
 PDG  Var_03    H2A1  C2A  C2   N1    117.69  30.0  2
 PDG  Var_04    CAA   NA   C4A  C4    169.79  30.0  3
 PDG  Var_05    OP1   P    OP4  C5A    52.18  30.0  3
 PDG  Var_06    CDA   CGA  CBA  CAA   171.28  30.0  3
 PDG  Var_07    OE1   CDA  CGA  CBA  -177.55  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
 PDG  chir_01  CAA  NA  CBA  CA  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
 PDG  plan-1  N1   0.020
 PDG  plan-1  C2   0.020
 PDG  plan-1  C2A  0.020
 PDG  plan-1  C3   0.020
 PDG  plan-1  O3   0.020
 PDG  plan-1  C4   0.020
 PDG  plan-1  C4A  0.020
 PDG  plan-1  C5   0.020
 PDG  plan-1  C6   0.020
 PDG  plan-1  C5A  0.020
 PDG  plan-1  H6   0.020
 PDG  plan-2  CGA  0.020
 PDG  plan-2  CDA  0.020
 PDG  plan-2  OE1  0.020
 PDG  plan-2  OE2  0.020
 PDG  plan-2  HE1  0.020
 PDG  plan-3  CAA  0.020
 PDG  plan-3  CA   0.020
 PDG  plan-3  OA   0.020
 PDG  plan-3  OXT  0.020
 PDG  plan-3  HXT  0.020

