# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 15:14:22 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-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
 PGU  PGU  'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid'  ligand  44  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PGU
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
 PGU  N1    N  N     0  -0.409   6.0926   2.7000   2.7486
 PGU  C2    C  CR6   0   0.133   6.2794   3.6815   1.8806
 PGU  C2A   C  CH3   0  -0.789   7.5555   4.4631   1.9671
 PGU  C3    C  CR6   0   0.255   5.3125   3.9955   0.9107
 PGU  O3    O  OH1   0  -0.619   5.4879   5.0039   0.0347
 PGU  C4    C  CR6   0   0.092   4.1346   3.2578   0.8402
 PGU  C4A   C  CH2   0  -0.371   3.0611   3.5891  -0.1650
 PGU  C5    C  CR6   0  -0.010   3.9638   2.2314   1.7731
 PGU  C6    C  CR16  0  -0.132   4.9686   1.9983   2.6962
 PGU  C5A   C  CH2   0  -0.297   2.7409   1.3701   1.7896
 PGU  O4P   O  O2    0  -0.584   2.8945   0.3531   0.7796
 PGU  P     P  P     0   1.474   1.6881  -0.4812   0.1753
 PGU  O1P   O  O     0  -0.698   2.1343  -1.5332  -0.7562
 PGU  O2P   O  OH1   0  -0.743   0.7888   0.6791  -0.4593
 PGU  O3P   O  OH1   0  -0.749   0.9108  -0.9894   1.4787
 PGU  N     N  NH1   0  -0.576   1.9536   4.2600   0.5004
 PGU  CA    C  CH1   0  -0.210   0.7599   4.3858  -0.2961
 PGU  CB    C  CH2   0  -0.452  -0.4182   4.8761   0.5620
 PGU  CG    C  CH2   0  -0.570  -0.6673   4.0102   1.7873
 PGU  CD    C  C     0   0.547  -1.1405   2.6210   1.4557
 PGU  OE1   O  OH1   0  -0.593  -0.8060   1.7408   2.3935
 PGU  OE2   O  O     0  -0.446  -1.7822   2.3283   0.4769
 PGU  C     C  C     0   0.536   0.9171   5.3389  -1.4745
 PGU  OXT   O  OH1   0  -0.590   0.0423   5.0929  -2.4409
 PGU  O     O  O     0  -0.438   1.7237   6.2340  -1.5163
 PGU  H2A1  H  HCH3  0   0.260   7.3757   5.5194   2.1840
 PGU  H2A2  H  HCH3  0   0.274   8.1783   4.0652   2.7645
 PGU  H2A3  H  HCH3  0   0.259   8.1340   4.4128   1.0410
 PGU  HO3   H  HOH1  0   0.486   6.3336   5.4443   0.1708
 PGU  H4A1  H  HCH2  0   0.247   3.4818   4.1621  -0.9961
 PGU  H4A2  H  HCH2  0   0.256   2.6792   2.6637  -0.6003
 PGU  H6    H  HCR6  0   0.258   4.8579   1.2046   3.4281
 PGU  H5A1  H  HCH2  0   0.264   2.6371   0.8867   2.7623
 PGU  H5A2  H  HCH2  0   0.267   1.8516   1.9719   1.6062
 PGU  HO2P  H  HOH1  0   0.498  -0.0413   0.3945  -0.8638
 PGU  HO3P  H  HOH1  0   0.502   0.3308  -1.7486   1.3317
 PGU  HN    H  HNH1  0   0.352   2.2511   5.1684   0.8377
 PGU  HA    H  HCH1  0   0.278   0.5144   3.3968  -0.6936
 PGU  HB1   H  HCH2  0   0.258  -1.3198   4.9251  -0.0495
 PGU  HB2   H  HCH2  0   0.256  -0.2157   5.8952   0.9011
 PGU  HG1   H  HCH2  0   0.273   0.2175   3.9696   2.4209
 PGU  HG2   H  HCH2  0   0.297  -1.4561   4.4728   2.3904
 PGU  HOE1  H  HOH1  0   0.471  -1.1357   0.8609   2.1584
 PGU  HO    H  HOH1  0   0.481   0.1399   5.7421  -3.1544

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
 PGU  O1P  P     double    1.474  0.020  1.474
 PGU  CA   CB    single    1.538  0.020  1.538
 PGU  CA   C     single    1.524  0.020  1.524
 PGU  CA   N     single    1.440  0.020  1.440
 PGU  O    C     double    1.206  0.020  1.206
 PGU  CB   CG    single    1.521  0.020  1.521
 PGU  O2P  P     single    1.599  0.020  1.599
 PGU  C    OXT   single    1.327  0.020  1.327
 PGU  C4A  N     single    1.456  0.020  1.456
 PGU  C4A  C4    single    1.508  0.020  1.508
 PGU  O3   C3    single    1.347  0.020  1.347
 PGU  P    O4P   single    1.586  0.020  1.586
 PGU  P    O3P   single    1.600  0.020  1.600
 PGU  O4P  C5A   single    1.442  0.020  1.442
 PGU  C3   C4    aromatic  1.392  0.020  1.392
 PGU  C3   C2    aromatic  1.405  0.020  1.405
 PGU  C4   C5    aromatic  1.397  0.020  1.397
 PGU  CG   CD    single    1.505  0.020  1.505
 PGU  C2   C2A   single    1.499  0.020  1.499
 PGU  C2   N1    aromatic  1.323  0.020  1.323
 PGU  C5   C5A   single    1.496  0.020  1.496
 PGU  C5   C6    aromatic  1.384  0.020  1.384
 PGU  N1   C6    aromatic  1.326  0.020  1.326
 PGU  CD   OE2   double    1.206  0.020  1.206
 PGU  CD   OE1   single    1.329  0.020  1.329
 PGU  C2A  H2A1  single    0.970  0.020  1.090
 PGU  C2A  H2A2  single    0.970  0.020  1.090
 PGU  C2A  H2A3  single    0.970  0.020  1.090
 PGU  O3   HO3   single    0.850  0.020  0.980
 PGU  C4A  H4A1  single    0.970  0.020  1.090
 PGU  C4A  H4A2  single    0.970  0.020  1.090
 PGU  C6   H6    single    0.930  0.020  1.080
 PGU  C5A  H5A1  single    0.970  0.020  1.090
 PGU  C5A  H5A2  single    0.970  0.020  1.090
 PGU  O2P  HO2P  single    0.850  0.020  0.980
 PGU  O3P  HO3P  single    0.850  0.020  0.980
 PGU  N    HN    single    0.890  0.020  1.040
 PGU  CA   HA    single    0.970  0.020  1.090
 PGU  CB   HB1   single    0.970  0.020  1.090
 PGU  CB   HB2   single    0.970  0.020  1.090
 PGU  CG   HG1   single    0.970  0.020  1.090
 PGU  CG   HG2   single    0.970  0.020  1.090
 PGU  OE1  HOE1  single    0.850  0.020  0.980
 PGU  OXT  HO    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
 PGU  C6    N1   C2    119.09  3.000
 PGU  C3    C2   C2A   120.61  3.000
 PGU  C2A   C2   N1    117.97  3.000
 PGU  C3    C2   N1    121.42  3.000
 PGU  H2A3  C2A  H2A2  107.54  3.000
 PGU  H2A3  C2A  H2A1  107.43  3.000
 PGU  H2A2  C2A  H2A1  107.60  3.000
 PGU  H2A3  C2A  C2    112.19  3.000
 PGU  H2A2  C2A  C2    109.83  3.000
 PGU  H2A1  C2A  C2    112.04  3.000
 PGU  C4    C3   O3    118.30  3.000
 PGU  C4    C3   C2    119.93  3.000
 PGU  O3    C3   C2    121.77  3.000
 PGU  HO3   O3   C3    111.39  3.000
 PGU  C5    C4   C4A   121.30  3.000
 PGU  C5    C4   C3    117.32  3.000
 PGU  C4A   C4   C3    121.33  3.000
 PGU  H4A2  C4A  H4A1  106.01  3.000
 PGU  H4A2  C4A  N     107.86  3.000
 PGU  H4A1  C4A  N     113.48  3.000
 PGU  H4A2  C4A  C4    109.19  3.000
 PGU  H4A1  C4A  C4    110.37  3.000
 PGU  N     C4A  C4    109.77  3.000
 PGU  C5A   C5   C6    119.28  3.000
 PGU  C6    C5   C4    118.70  3.000
 PGU  C5A   C5   C4    122.02  3.000
 PGU  H6    C6   C5    119.93  3.000
 PGU  H6    C6   N1    116.53  3.000
 PGU  C5    C6   N1    123.54  3.000
 PGU  H5A2  C5A  H5A1  108.49  3.000
 PGU  H5A2  C5A  O4P   111.03  3.000
 PGU  H5A1  C5A  O4P   108.80  3.000
 PGU  H5A2  C5A  C5    110.33  3.000
 PGU  H5A1  C5A  C5    110.04  3.000
 PGU  O4P   C5A  C5    108.14  3.000
 PGU  P     O4P  C5A   123.84  3.000
 PGU  O3P   P    O2P   106.29  3.000
 PGU  O3P   P    O1P   115.78  3.000
 PGU  O2P   P    O1P   115.93  3.000
 PGU  O3P   P    O4P   103.07  3.000
 PGU  O2P   P    O4P   101.38  3.000
 PGU  O1P   P    O4P   112.69  3.000
 PGU  HO2P  O2P  P     115.81  3.000
 PGU  HO3P  O3P  P     114.64  3.000
 PGU  HN    N    CA    110.43  3.000
 PGU  HN    N    C4A   109.98  3.000
 PGU  CA    N    C4A   114.70  3.000
 PGU  HA    CA   C     107.92  3.000
 PGU  HA    CA   CB    108.61  3.000
 PGU  C     CA   CB    108.13  3.000
 PGU  HA    CA   N     107.94  3.000
 PGU  C     CA   N     113.37  3.000
 PGU  CB    CA   N     110.74  3.000
 PGU  HB2   CB   HB1   106.57  3.000
 PGU  HB2   CB   CG    108.13  3.000
 PGU  HB1   CB   CG    110.00  3.000
 PGU  HB2   CB   CA    109.18  3.000
 PGU  HB1   CB   CA    109.56  3.000
 PGU  CG    CB   CA    113.17  3.000
 PGU  HG2   CG   HG1   106.29  3.000
 PGU  HG2   CG   CD    106.54  3.000
 PGU  HG1   CG   CD    110.45  3.000
 PGU  HG2   CG   CB    108.73  3.000
 PGU  HG1   CG   CB    110.91  3.000
 PGU  CD    CG   CB    113.55  3.000
 PGU  OE2   CD   OE1   123.08  3.000
 PGU  OE1   CD   CG    112.13  3.000
 PGU  OE2   CD   CG    124.76  3.000
 PGU  HOE1  OE1  CD    110.16  3.000
 PGU  O     C    OXT   123.61  3.000
 PGU  OXT   C    CA    112.30  3.000
 PGU  O     C    CA    124.08  3.000
 PGU  HO    OXT  C     110.22  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
 PGU  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PGU  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PGU  CONST_03  C5    C4   C3   C2      0.00   0.0  0
 PGU  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 PGU  CONST_05  C6    C5   C4   C3      0.00   0.0  0
 PGU  CONST_06  C6    N1   C2   C3      0.00   0.0  0
 PGU  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PGU  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PGU  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PGU  CONST_10  C4    C3   C2   C2A   180.00   0.0  0
 PGU  CONST_11  C6    N1   C2   C2A   180.00   0.0  0
 PGU  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PGU  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PGU  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PGU  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PGU  CONST_16  HO    OXT  C    CA    180.00   0.0  0
 PGU  CONST_17  HOE1  OE1  CD   CG    180.00   0.0  0
 PGU  Var_01    N     C4A  C4   C3   -104.45  30.0  2
 PGU  Var_02    O4P   C5A  C5   C4     80.88  30.0  2
 PGU  Var_03    H2A1  C2A  C2   N1   -118.23  30.0  2
 PGU  Var_04    CA    N    C4A  C4   -168.11  30.0  3
 PGU  Var_05    O1P   P    O4P  C5A  -175.14  30.0  1
 PGU  Var_06    CD    CG   CB   CA    -66.67  30.0  3
 PGU  Var_07    OE2   CD   CG   CB    -29.39  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
 PGU  chir_01  CA  CB  C  N  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
 PGU  plan-1  N1    0.020
 PGU  plan-1  C2    0.020
 PGU  plan-1  C2A   0.020
 PGU  plan-1  C3    0.020
 PGU  plan-1  O3    0.020
 PGU  plan-1  C4    0.020
 PGU  plan-1  C4A   0.020
 PGU  plan-1  C5    0.020
 PGU  plan-1  C6    0.020
 PGU  plan-1  C5A   0.020
 PGU  plan-1  H6    0.020
 PGU  plan-2  CG    0.020
 PGU  plan-2  CD    0.020
 PGU  plan-2  OE1   0.020
 PGU  plan-2  OE2   0.020
 PGU  plan-2  HOE1  0.020
 PGU  plan-3  CA    0.020
 PGU  plan-3  C     0.020
 PGU  plan-3  OXT   0.020
 PGU  plan-3  O     0.020
 PGU  plan-3  HO    0.020

