# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 06:59:48 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=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
 PY5  PY5  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-norvaline  ligand  44  23  .  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_PY5
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
 PY5  N1    N  N     0  -0.407   3.6648   0.2884  -0.6188
 PY5  C2    C  CR6   0   0.122   3.6860  -0.1577   0.6267
 PY5  C2A   C  CH3   0  -0.783   4.9856  -0.1139   1.3742
 PY5  C3    C  CR6   0   0.266   2.5263  -0.6573   1.2358
 PY5  O3    O  OH1   0  -0.614   2.5229  -1.1103   2.5019
 PY5  C4    C  CR6   0   0.064   1.3331  -0.7015   0.5210
 PY5  C4A   C  CH2   0  -0.347   0.0777  -1.2174   1.1709
 PY5  C5    C  CR6   0  -0.067   1.3383  -0.2144  -0.7880
 PY5  C6    C  CR16  0  -0.133   2.5310   0.2657  -1.3083
 PY5  C5A   C  CH2   0  -0.212   0.0718  -0.2400  -1.5993
 PY5  O4P   O  O2    0  -0.592   0.2706   0.4868  -2.8064
 PY5  P     P  P     0   1.464  -0.8754   0.4967  -3.9212
 PY5  O1P   O  O     0  -0.706  -2.2300   0.8612  -3.4697
 PY5  O2P   O  OH1   0  -0.729  -0.1343   1.4755  -4.9349
 PY5  O3P   O  OH1   0  -0.741  -0.8973  -0.9632  -4.5682
 PY5  N     N  NH1   0  -0.572  -0.5267  -0.1723   1.9758
 PY5  CA    C  CH1   0  -0.192  -1.7320  -0.5615   2.6616
 PY5  C     C  C     0   0.525  -2.9105  -0.9402   1.7706
 PY5  O     O  O     0  -0.443  -3.7325  -1.7744   2.0602
 PY5  CB    C  CH2   0  -0.434  -2.1865   0.5497   3.6172
 PY5  CG    C  CH2   0  -0.416  -1.2025   0.7804   4.7576
 PY5  CD    C  CH3   0  -0.666  -1.6335   1.9232   5.6655
 PY5  OXT   O  OH1   0  -0.590  -2.9677  -0.2174   0.6583
 PY5  H2A1  H  HCH3  0   0.254   5.3048  -1.1055   1.7066
 PY5  H2A2  H  HCH3  0   0.271   5.7677   0.2832   0.7317
 PY5  H2A3  H  HCH3  0   0.259   4.9267   0.5247   2.2594
 PY5  HO3   H  HOH1  0   0.485   3.4144  -1.1316   2.8663
 PY5  H4A1  H  HCH2  0   0.259   0.3193  -2.0563   1.8270
 PY5  H4A2  H  HCH2  0   0.225  -0.5917  -1.6310   0.4039
 PY5  H6    H  HCR6  0   0.257   2.5841   0.6512  -2.3182
 PY5  H5A1  H  HCH2  0   0.261  -0.2048  -1.2763  -1.8198
 PY5  H5A2  H  HCH2  0   0.254  -0.7536   0.2035  -1.0369
 PY5  HOP2  H  HOH1  0   0.505  -0.7001   1.8098  -5.6437
 PY5  HOP3  H  HOH1  0   0.497  -0.0617  -1.2727  -4.9429
 PY5  HN2   H  HNH1  0   0.352  -0.6782   0.6658   1.4278
 PY5  HA    H  HCH1  0   0.265  -1.5123  -1.4535   3.2577
 PY5  HB1   H  HCH2  0   0.240  -3.1652   0.2914   4.0310
 PY5  HB2   H  HCH2  0   0.230  -2.3252   1.4767   3.0504
 PY5  HG1   H  HCH2  0   0.228  -0.2118   0.9808   4.3458
 PY5  HG2   H  HCH2  0   0.215  -1.1135  -0.1408   5.3411
 PY5  HD1   H  HCH3  0   0.229  -0.9223   2.0737   6.4782
 PY5  HD2   H  HCH3  0   0.218  -1.7061   2.8612   5.1120
 PY5  HD3   H  HCH3  0   0.218  -2.6102   1.7295   6.1128
 PY5  HXT   H  HOH1  0   0.482  -3.7401  -0.4732   0.1322

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
 PY5  N1   C2    aromatic  1.323  0.020  1.323
 PY5  N1   C6    aromatic  1.327  0.020  1.327
 PY5  C2   C2A   single    1.500  0.020  1.500
 PY5  C2   C3    aromatic  1.402  0.020  1.402
 PY5  C2A  H2A1  single    0.970  0.020  1.090
 PY5  C2A  H2A2  single    0.970  0.020  1.090
 PY5  C2A  H2A3  single    0.970  0.020  1.090
 PY5  C3   O3    single    1.345  0.020  1.345
 PY5  C3   C4    aromatic  1.392  0.020  1.392
 PY5  O3   HO3   single    0.850  0.020  0.980
 PY5  C4   C4A   single    1.505  0.020  1.505
 PY5  C4   C5    aromatic  1.397  0.020  1.397
 PY5  C4A  N     single    1.451  0.020  1.451
 PY5  C4A  H4A1  single    0.970  0.020  1.090
 PY5  C4A  H4A2  single    0.970  0.020  1.090
 PY5  C5   C6    aromatic  1.387  0.020  1.387
 PY5  C5   C5A   single    1.504  0.020  1.504
 PY5  C6   H6    single    0.930  0.020  1.080
 PY5  C5A  O4P   single    1.423  0.020  1.423
 PY5  C5A  H5A1  single    0.970  0.020  1.090
 PY5  C5A  H5A2  single    0.970  0.020  1.090
 PY5  O4P  P     single    1.599  0.020  1.599
 PY5  P    O1P   double    1.474  0.020  1.474
 PY5  P    O2P   single    1.592  0.020  1.592
 PY5  P    O3P   single    1.597  0.020  1.597
 PY5  O2P  HOP2  single    0.850  0.020  0.980
 PY5  O3P  HOP3  single    0.850  0.020  0.980
 PY5  N    CA    single    1.440  0.020  1.440
 PY5  N    HN2   single    0.890  0.020  1.040
 PY5  CA   C     single    1.525  0.020  1.525
 PY5  CA   CB    single    1.534  0.020  1.534
 PY5  CA   HA    single    0.970  0.020  1.090
 PY5  C    O     double    1.206  0.020  1.206
 PY5  C    OXT   single    1.328  0.020  1.328
 PY5  CB   CG    single    1.524  0.020  1.524
 PY5  CB   HB1   single    0.970  0.020  1.090
 PY5  CB   HB2   single    0.970  0.020  1.090
 PY5  CG   CD    single    1.522  0.020  1.522
 PY5  CG   HG1   single    0.970  0.020  1.090
 PY5  CG   HG2   single    0.970  0.020  1.090
 PY5  CD   HD1   single    0.970  0.020  1.090
 PY5  CD   HD2   single    0.970  0.020  1.090
 PY5  CD   HD3   single    0.970  0.020  1.090
 PY5  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
 PY5  C6    N1   C2    119.80  3.000
 PY5  C3    C2   C2A   120.70  3.000
 PY5  C3    C2   N1    121.06  3.000
 PY5  C2A   C2   N1    118.24  3.000
 PY5  H2A3  C2A  H2A2  107.69  3.000
 PY5  H2A3  C2A  H2A1  107.42  3.000
 PY5  H2A2  C2A  H2A1  107.51  3.000
 PY5  H2A3  C2A  C2    111.96  3.000
 PY5  H2A2  C2A  C2    109.84  3.000
 PY5  H2A1  C2A  C2    112.21  3.000
 PY5  C4    C3   O3    118.08  3.000
 PY5  C4    C3   C2    119.83  3.000
 PY5  O3    C3   C2    122.09  3.000
 PY5  HO3   O3   C3    111.18  3.000
 PY5  C5    C4   C4A   121.83  3.000
 PY5  C5    C4   C3    117.85  3.000
 PY5  C4A   C4   C3    120.29  3.000
 PY5  H4A2  C4A  H4A1  105.36  3.000
 PY5  H4A2  C4A  N     113.87  3.000
 PY5  H4A1  C4A  N     108.19  3.000
 PY5  H4A2  C4A  C4    109.62  3.000
 PY5  H4A1  C4A  C4    109.77  3.000
 PY5  N     C4A  C4    109.89  3.000
 PY5  C5A   C5   C6    121.84  3.000
 PY5  C5A   C5   C4    119.76  3.000
 PY5  C6    C5   C4    118.39  3.000
 PY5  H6    C6   C5    121.04  3.000
 PY5  H6    C6   N1    115.90  3.000
 PY5  C5    C6   N1    123.07  3.000
 PY5  H5A2  C5A  H5A1  107.27  3.000
 PY5  H5A2  C5A  O4P   109.57  3.000
 PY5  H5A1  C5A  O4P   110.35  3.000
 PY5  H5A2  C5A  C5    110.57  3.000
 PY5  H5A1  C5A  C5    109.71  3.000
 PY5  O4P   C5A  C5    109.34  3.000
 PY5  P     O4P  C5A   119.63  3.000
 PY5  O3P   P    O2P   108.09  3.000
 PY5  O3P   P    O1P   109.73  3.000
 PY5  O2P   P    O1P   118.09  3.000
 PY5  O3P   P    O4P   106.66  3.000
 PY5  O2P   P    O4P    96.55  3.000
 PY5  O1P   P    O4P   116.54  3.000
 PY5  HOP2  O2P  P     114.02  3.000
 PY5  HOP3  O3P  P     115.97  3.000
 PY5  HN2   N    CA    110.86  3.000
 PY5  HN2   N    C4A   110.99  3.000
 PY5  CA    N    C4A   114.71  3.000
 PY5  HA    CA   CB    108.08  3.000
 PY5  HA    CA   C     105.71  3.000
 PY5  CB    CA   C     108.35  3.000
 PY5  HA    CA   N     108.14  3.000
 PY5  CB    CA   N     110.41  3.000
 PY5  C     CA   N     115.82  3.000
 PY5  OXT   C    O     123.24  3.000
 PY5  OXT   C    CA    112.80  3.000
 PY5  O     C    CA    123.91  3.000
 PY5  HB2   CB   HB1   106.40  3.000
 PY5  HB2   CB   CG    109.93  3.000
 PY5  HB1   CB   CG    109.30  3.000
 PY5  HB2   CB   CA    109.15  3.000
 PY5  HB1   CB   CA    109.25  3.000
 PY5  CG    CB   CA    112.61  3.000
 PY5  HG2   CG   HG1   106.38  3.000
 PY5  HG2   CG   CD    109.70  3.000
 PY5  HG1   CG   CD    110.14  3.000
 PY5  HG2   CG   CB    108.92  3.000
 PY5  HG1   CG   CB    109.37  3.000
 PY5  CD    CG   CB    112.16  3.000
 PY5  HD3   CD   HD2   107.50  3.000
 PY5  HD3   CD   HD1   107.61  3.000
 PY5  HD2   CD   HD1   107.62  3.000
 PY5  HD3   CD   CG    111.38  3.000
 PY5  HD2   CD   CG    111.20  3.000
 PY5  HD1   CD   CG    111.32  3.000
 PY5  HXT   OXT  C     110.21  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
 PY5  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PY5  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PY5  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PY5  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PY5  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PY5  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PY5  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PY5  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PY5  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PY5  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PY5  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PY5  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PY5  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PY5  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PY5  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PY5  CONST_16  HXT   OXT  C    CA    180.00   0.0  0
 PY5  Var_01    N     C4A  C4   C3     81.35  30.0  2
 PY5  Var_02    O4P   C5A  C5   C4    171.12  30.0  2
 PY5  Var_03    H2A1  C2A  C2   N1   -120.81  30.0  2
 PY5  Var_04    CA    N    C4A  C4   -179.26  30.0  3
 PY5  Var_05    O1P   P    O4P  C5A    51.61  30.0  3
 PY5  Var_06    CD    CG   CB   CA    177.59  30.0  3
 PY5  Var_07    HD1   CD   CG   CB    179.77  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
 PY5  chir_01  CA  N  C  CB  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
 PY5  plan-1  N1   0.020
 PY5  plan-1  C2   0.020
 PY5  plan-1  C2A  0.020
 PY5  plan-1  C3   0.020
 PY5  plan-1  O3   0.020
 PY5  plan-1  C4   0.020
 PY5  plan-1  C4A  0.020
 PY5  plan-1  C5   0.020
 PY5  plan-1  C6   0.020
 PY5  plan-1  C5A  0.020
 PY5  plan-1  H6   0.020
 PY5  plan-2  CA   0.020
 PY5  plan-2  C    0.020
 PY5  plan-2  O    0.020
 PY5  plan-2  OXT  0.020
 PY5  plan-2  HXT  0.020

