# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 10:14:54 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-2-methyl-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@](C)(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
 PMG  PMG  'N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-2-methyl-L-glutamic acid'  ligand  47  26  .  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_PMG
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
 PMG  N1    N  N     0  -0.410  32.7354  77.2920   0.9289
 PMG  C2    C  CR6   0   0.154  32.5496  75.9810   0.9114
 PMG  C2A   C  CH3   0  -0.723  32.1601  75.3021   2.1875
 PMG  C3    C  CR6   0   0.253  32.7078  75.2450  -0.2704
 PMG  O3    O  OH1   0  -0.630  32.4963  73.9098  -0.1885
 PMG  C4    C  CR6   0   0.138  33.0970  75.8756  -1.4474
 PMG  C4A   C  CH2   0  -0.431  33.3680  75.0527  -2.6818
 PMG  C5    C  CR6   0  -0.043  33.2426  77.2665  -1.4099
 PMG  C6    C  CR16  0  -0.130  33.0504  77.9131  -0.2001
 PMG  C5A   C  CH2   0  -0.307  33.5689  78.0789  -2.6240
 PMG  OP4   O  O2    0  -0.584  32.4206  78.0604  -3.4901
 PMG  P     P  P     0   1.481  32.4919  78.4955  -5.0221
 PMG  OP1   O  O     0  -0.697  31.1454  78.5483  -5.6188
 PMG  OP2   O  OH1   0  -0.744  33.5222  77.4270  -5.6045
 PMG  OP3   O  OH1   0  -0.746  33.3505  79.8425  -5.0940
 PMG  N     N  NH1   0  -0.600  34.5584  74.2403  -2.4961
 PMG  CA    C  CT    0  -0.041  35.1820  73.7180  -3.7058
 PMG  CB2   C  CH3   0  -0.673  34.1834  73.3112  -4.8087
 PMG  CB1   C  CH2   0  -0.397  36.1353  74.7884  -4.2549
 PMG  CG    C  CH2   0  -0.574  37.3336  75.1048  -3.3589
 PMG  CD    C  C     0   0.557  36.9971  75.4771  -1.9397
 PMG  OE1   O  OH1   0  -0.594  36.4246  76.6769  -1.8543
 PMG  OE2   O  O     0  -0.455  37.2840  74.8197  -0.9697
 PMG  C     C  C     0   0.570  35.9759  72.4495  -3.3988
 PMG  O     O  O     0  -0.437  36.8578  72.0392  -4.1104
 PMG  OXT   O  OH1   0  -0.588  35.5588  71.8071  -2.3191
 PMG  H2A1  H  HCH3  0   0.250  32.8756  74.5288   2.4717
 PMG  H2A2  H  HCH3  0   0.249  32.1078  76.0316   2.9925
 PMG  H2A3  H  HCH3  0   0.251  31.1861  74.8170   2.1003
 PMG  HO3   H  HOH1  0   0.479  32.1760  73.5531  -1.0252
 PMG  H4A1  H  HCH2  0   0.240  32.4716  74.4672  -2.9398
 PMG  H4A2  H  HCH2  0   0.272  33.5197  75.7090  -3.5342
 PMG  H6    H  HCR6  0   0.259  33.1623  78.9912  -0.1410
 PMG  H5A1  H  HCH2  0   0.272  33.7869  79.1085  -2.3346
 PMG  H5A2  H  HCH2  0   0.258  34.4470  77.6880  -3.1404
 PMG  HP2   H  HOH1  0   0.504  33.7212  77.5085  -6.5470
 PMG  HP3   H  HOH1  0   0.500  32.8293  80.6506  -4.9949
 PMG  HN    H  HNH1  0   0.359  34.3937  73.5144  -1.8158
 PMG  HB21  H  HCH3  0   0.257  34.6976  72.8369  -5.6437
 PMG  HB22  H  HCH3  0   0.251  33.4298  72.6201  -4.4294
 PMG  HB23  H  HCH3  0   0.245  33.6717  74.1907  -5.2007
 PMG  HB11  H  HCH2  0   0.256  36.5177  74.4834  -5.2302
 PMG  HB12  H  HCH2  0   0.246  35.5525  75.6949  -4.4347
 PMG  HG1   H  HCH2  0   0.263  38.0199  74.2602  -3.3287
 PMG  HG2   H  HCH2  0   0.282  37.8797  75.9373  -3.8101
 PMG  HE1   H  HOH1  0   0.470  36.2071  76.8704  -0.9311
 PMG  HXT   H  HOH1  0   0.490  36.0683  70.9911  -2.1972

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
 PMG  N1   C2    aromatic  1.324  0.020  1.324
 PMG  N1   C6    aromatic  1.327  0.020  1.327
 PMG  C2   C2A   single    1.497  0.020  1.497
 PMG  C2   C3    aromatic  1.401  0.020  1.401
 PMG  C2A  H2A1  single    0.970  0.020  1.090
 PMG  C2A  H2A2  single    0.970  0.020  1.090
 PMG  C2A  H2A3  single    0.970  0.020  1.090
 PMG  C3   O3    single    1.354  0.020  1.354
 PMG  C3   C4    aromatic  1.391  0.020  1.391
 PMG  O3   HO3   single    0.850  0.020  0.980
 PMG  C4   C4A   single    1.508  0.020  1.508
 PMG  C4   C5    aromatic  1.399  0.020  1.399
 PMG  C4A  N     single    1.453  0.020  1.453
 PMG  C4A  H4A1  single    0.970  0.020  1.090
 PMG  C4A  H4A2  single    0.970  0.020  1.090
 PMG  C5   C6    aromatic  1.385  0.020  1.385
 PMG  C5   C5A   single    1.497  0.020  1.497
 PMG  C6   H6    single    0.930  0.020  1.080
 PMG  C5A  OP4   single    1.438  0.020  1.438
 PMG  C5A  H5A1  single    0.970  0.020  1.090
 PMG  C5A  H5A2  single    0.970  0.020  1.090
 PMG  OP4  P     single    1.594  0.020  1.594
 PMG  P    OP1   double    1.474  0.020  1.474
 PMG  P    OP2   single    1.595  0.020  1.595
 PMG  P    OP3   single    1.599  0.020  1.599
 PMG  OP2  HP2   single    0.850  0.020  0.980
 PMG  OP3  HP3   single    0.850  0.020  0.980
 PMG  N    CA    single    1.458  0.020  1.458
 PMG  N    HN    single    0.890  0.020  1.040
 PMG  CA   CB2   single    1.542  0.020  1.542
 PMG  CA   CB1   single    1.535  0.020  1.535
 PMG  CA   C     single    1.528  0.020  1.528
 PMG  CB2  HB21  single    0.970  0.020  1.090
 PMG  CB2  HB22  single    0.970  0.020  1.090
 PMG  CB2  HB23  single    0.970  0.020  1.090
 PMG  CB1  CG    single    1.529  0.020  1.529
 PMG  CB1  HB11  single    0.970  0.020  1.090
 PMG  CB1  HB12  single    0.970  0.020  1.090
 PMG  CG   CD    single    1.505  0.020  1.505
 PMG  CG   HG1   single    0.970  0.020  1.090
 PMG  CG   HG2   single    0.970  0.020  1.090
 PMG  CD   OE1   single    1.332  0.020  1.332
 PMG  CD   OE2   double    1.206  0.020  1.206
 PMG  OE1  HE1   single    0.850  0.020  0.980
 PMG  C    O     double    1.205  0.020  1.205
 PMG  C    OXT   single    1.324  0.020  1.324
 PMG  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
 PMG  C6    N1   C2    119.05  3.000
 PMG  C3    C2   C2A   120.67  3.000
 PMG  C3    C2   N1    121.02  3.000
 PMG  C2A   C2   N1    118.30  3.000
 PMG  H2A3  C2A  H2A2  108.32  3.000
 PMG  H2A3  C2A  H2A1  106.91  3.000
 PMG  H2A2  C2A  H2A1  108.30  3.000
 PMG  H2A3  C2A  C2    111.45  3.000
 PMG  H2A2  C2A  C2    109.84  3.000
 PMG  H2A1  C2A  C2    111.89  3.000
 PMG  C4    C3   O3    122.81  3.000
 PMG  C4    C3   C2    120.48  3.000
 PMG  O3    C3   C2    116.69  3.000
 PMG  HO3   O3   C3    111.35  3.000
 PMG  C5    C4   C4A   123.07  3.000
 PMG  C5    C4   C3    117.21  3.000
 PMG  C4A   C4   C3    119.71  3.000
 PMG  H4A2  C4A  H4A1  104.54  3.000
 PMG  H4A2  C4A  N     108.88  3.000
 PMG  H4A1  C4A  N     113.54  3.000
 PMG  H4A2  C4A  C4    109.74  3.000
 PMG  H4A1  C4A  C4    109.61  3.000
 PMG  N     C4A  C4    110.34  3.000
 PMG  C5A   C5   C6    119.03  3.000
 PMG  C5A   C5   C4    122.72  3.000
 PMG  C6    C5   C4    118.23  3.000
 PMG  H6    C6   C5    119.79  3.000
 PMG  H6    C6   N1    116.30  3.000
 PMG  C5    C6   N1    123.90  3.000
 PMG  H5A2  C5A  H5A1  107.62  3.000
 PMG  H5A2  C5A  OP4   110.66  3.000
 PMG  H5A1  C5A  OP4   109.34  3.000
 PMG  H5A2  C5A  C5    111.40  3.000
 PMG  H5A1  C5A  C5    109.90  3.000
 PMG  OP4   C5A  C5    107.90  3.000
 PMG  P     OP4  C5A   122.64  3.000
 PMG  OP3   P    OP2   101.60  3.000
 PMG  OP3   P    OP1   116.25  3.000
 PMG  OP2   P    OP1   117.80  3.000
 PMG  OP3   P    OP4   107.29  3.000
 PMG  OP2   P    OP4   101.36  3.000
 PMG  OP1   P    OP4   110.98  3.000
 PMG  HP2   OP2  P     115.64  3.000
 PMG  HP3   OP3  P     114.21  3.000
 PMG  HN    N    CA    111.83  3.000
 PMG  HN    N    C4A   110.79  3.000
 PMG  CA    N    C4A   116.40  3.000
 PMG  C     CA   CB1   109.16  3.000
 PMG  C     CA   CB2   105.14  3.000
 PMG  CB1   CA   CB2   109.29  3.000
 PMG  C     CA   N     110.68  3.000
 PMG  CB1   CA   N     108.22  3.000
 PMG  CB2   CA   N     114.26  3.000
 PMG  HB23  CB2  HB22  108.17  3.000
 PMG  HB23  CB2  HB21  107.29  3.000
 PMG  HB22  CB2  HB21  108.48  3.000
 PMG  HB23  CB2  CA    110.37  3.000
 PMG  HB22  CB2  CA    111.46  3.000
 PMG  HB21  CB2  CA    110.94  3.000
 PMG  HB12  CB1  HB11  105.77  3.000
 PMG  HB12  CB1  CG    110.04  3.000
 PMG  HB11  CB1  CG    107.88  3.000
 PMG  HB12  CB1  CA    107.83  3.000
 PMG  HB11  CB1  CA    110.03  3.000
 PMG  CG    CB1  CA    114.92  3.000
 PMG  HG2   CG   HG1   106.70  3.000
 PMG  HG2   CG   CD    108.21  3.000
 PMG  HG1   CG   CD    107.86  3.000
 PMG  HG2   CG   CB1   107.89  3.000
 PMG  HG1   CG   CB1   110.47  3.000
 PMG  CD    CG   CB1   115.36  3.000
 PMG  OE2   CD   OE1   122.78  3.000
 PMG  OE2   CD   CG    124.76  3.000
 PMG  OE1   CD   CG    112.29  3.000
 PMG  HE1   OE1  CD    109.74  3.000
 PMG  OXT   C    O     123.15  3.000
 PMG  OXT   C    CA    113.77  3.000
 PMG  O     C    CA    122.98  3.000
 PMG  HXT   OXT  C     110.20  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
 PMG  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PMG  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PMG  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PMG  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PMG  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PMG  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PMG  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PMG  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PMG  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PMG  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PMG  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PMG  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PMG  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PMG  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PMG  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PMG  CONST_16  HXT   OXT  C    CA    180.00   0.0  0
 PMG  CONST_17  HE1   OE1  CD   CG    180.00   0.0  0
 PMG  Var_01    N     C4A  C4   C3    -68.03  30.0  2
 PMG  Var_02    OP4   C5A  C5   C4     69.67  30.0  2
 PMG  Var_03    H2A1  C2A  C2   N1   -121.71  30.0  2
 PMG  Var_04    CA    N    C4A  C4   -161.63  30.0  3
 PMG  Var_05    OP1   P    OP4  C5A  -172.55  30.0  3
 PMG  Var_06    CD    CG   CB1  CA    -53.79  30.0  3
 PMG  Var_07    OE1   CD   CG   CB1   -70.78  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
 PMG  chir_01  CA  CB2  CB1  C  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
 PMG  plan-1  N1   0.020
 PMG  plan-1  C2   0.020
 PMG  plan-1  C2A  0.020
 PMG  plan-1  C3   0.020
 PMG  plan-1  O3   0.020
 PMG  plan-1  C4   0.020
 PMG  plan-1  C4A  0.020
 PMG  plan-1  C5   0.020
 PMG  plan-1  C6   0.020
 PMG  plan-1  C5A  0.020
 PMG  plan-1  H6   0.020
 PMG  plan-2  CG   0.020
 PMG  plan-2  CD   0.020
 PMG  plan-2  OE1  0.020
 PMG  plan-2  OE2  0.020
 PMG  plan-2  HE1  0.020
 PMG  plan-3  CA   0.020
 PMG  plan-3  C    0.020
 PMG  plan-3  O    0.020
 PMG  plan-3  OXT  0.020
 PMG  plan-3  HXT  0.020

