# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 13:56:23 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (E,4S)-4-hydroxy-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)C[C@H](N=Cc1c(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
 PPJ  PPJ  (E,4S)-4-hydroxy-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-norvaline  ligand  43  24  .  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_PPJ
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
 PPJ  N1    N  N     0  -0.397  -0.9905   7.5533   1.1170
 PPJ  C2    C  CR6   0   0.130  -0.3954   6.4255   1.4495
 PPJ  C6    C  CR16  0  -0.131  -1.4564   7.7176  -0.1206
 PPJ  C2A   C  CH3   0  -0.704   0.1185   6.2650   2.8450
 PPJ  C3    C  CR6   0   0.310  -0.2381   5.3769   0.5176
 PPJ  O3    O  OH1   0  -0.603   0.3761   4.2726   0.9217
 PPJ  C4    C  CR6   0  -0.017  -0.7413   5.5384  -0.7798
 PPJ  C4A   C  C1    0   0.089  -0.6193   4.4518  -1.7488
 PPJ  C5    C  CR6   0   0.004  -1.3686   6.7531  -1.1014
 PPJ  N     N  N     0  -0.436   0.0134   3.3937  -1.4475
 PPJ  C5A   C  CH2   0  -0.293  -1.9321   7.0319  -2.4597
 PPJ  OP4   O  O2    0  -0.562  -0.8432   7.1025  -3.3936
 PPJ  P     P  P     0   1.448  -1.0485   7.0040  -4.9711
 PPJ  OP1   O  OH1   0  -0.740  -1.8063   5.6144  -5.2238
 PPJ  OP2   O  O     0  -0.632   0.2230   7.1670  -5.6963
 PPJ  OP3   O  OH1   0  -0.722  -2.1896   8.0929  -5.1972
 PPJ  CA    C  CH1   0  -0.245   0.1659   2.3476  -2.4212
 PPJ  CB    C  CH2   0  -0.433   1.5625   2.4226  -3.0563
 PPJ  C     C  C     0   0.568  -0.1243   1.0191  -1.7461
 PPJ  CG    C  CH1   0   0.046   2.7062   2.3873  -2.0557
 PPJ  CD    C  CH3   0  -0.657   4.0497   2.4923  -2.7611
 PPJ  O     O  O     0  -0.391  -0.5136   0.8982  -0.6146
 PPJ  OXT   O  OH1   0  -0.583   0.0183   0.0088  -2.5920
 PPJ  OGL   O  OH1   0  -0.634   2.5846   1.1793  -1.3293
 PPJ  HC6   H  HCR6  0   0.234  -1.9297   8.6697  -0.3362
 PPJ  H2A1  H  HCH3  0   0.250  -0.3505   5.4167   3.3469
 PPJ  H2A2  H  HCH3  0   0.245   1.1950   6.0858   2.8587
 PPJ  H2A3  H  HCH3  0   0.243  -0.0884   7.1627   3.4232
 PPJ  HO3   H  HOH1  0   0.484   0.4037   3.6443   0.1447
 PPJ  H4A   H  H     0   0.220  -1.0925   4.5655  -2.7259
 PPJ  H5A1  H  HCH2  0   0.233  -2.6461   6.2574  -2.7523
 PPJ  H5A2  H  HCH2  0   0.258  -2.4654   7.9836  -2.4471
 PPJ  HA    H  HCH1  0   0.244  -0.5694   2.4481  -3.2334
 PPJ  HCB   H  HCH2  0   0.237   1.6186   3.3543  -3.6239
 PPJ  HB1   H  HCH2  0   0.252   1.6724   1.6138  -3.7824
 PPJ  HCG   H  HCH1  0   0.200   2.6037   3.2457  -1.3796
 PPJ  HC1   H  HCH3  0   0.218   4.1247   3.4327  -3.3090
 PPJ  HC2   H  HCH3  0   0.225   4.1873   1.6750  -3.4721
 PPJ  HC3   H  HCH3  0   0.221   4.8718   2.4631  -2.0442
 PPJ  HXT   H  HOH1  0   0.455  -0.1971  -0.8257  -2.1499
 PPJ  HGL   H  HOH1  0   0.431   3.1426   1.2327  -0.5473
 PPJ  HO1   H  HOH1  0   0.467  -2.5555   8.1291  -6.0913
 PPJ  HO2   H  HOH1  0   0.469  -1.3028   4.9834  -5.7541

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
 PPJ  N1   C2    aromatic  1.318  0.020  1.318
 PPJ  N1   C6    aromatic  1.333  0.020  1.333
 PPJ  C2   C2A   single    1.496  0.020  1.496
 PPJ  C2   C3    aromatic  1.412  0.020  1.412
 PPJ  C6   C5    aromatic  1.378  0.020  1.378
 PPJ  C6   HC6   single    0.930  0.020  1.080
 PPJ  C2A  H2A1  single    0.970  0.020  1.090
 PPJ  C2A  H2A2  single    0.970  0.020  1.090
 PPJ  C2A  H2A3  single    0.970  0.020  1.090
 PPJ  C3   O3    single    1.327  0.020  1.327
 PPJ  C3   C4    aromatic  1.401  0.020  1.401
 PPJ  O3   HO3   single    0.850  0.020  0.980
 PPJ  C4   C4A   single    1.461  0.020  1.461
 PPJ  C4   C5    aromatic  1.404  0.020  1.404
 PPJ  C4A  N     double    1.269  0.020  1.269
 PPJ  C4A  H4A   single    0.930  0.020  1.080
 PPJ  C5   C5A   single    1.497  0.020  1.497
 PPJ  N    CA    single    1.437  0.020  1.437
 PPJ  C5A  OP4   single    1.436  0.020  1.436
 PPJ  C5A  H5A1  single    0.970  0.020  1.090
 PPJ  C5A  H5A2  single    0.970  0.020  1.090
 PPJ  OP4  P     single    1.594  0.020  1.594
 PPJ  P    OP1   single    1.603  0.020  1.603
 PPJ  P    OP2   double    1.473  0.020  1.473
 PPJ  P    OP3   single    1.593  0.020  1.593
 PPJ  CA   CB    single    1.536  0.020  1.536
 PPJ  CA   C     single    1.518  0.020  1.518
 PPJ  CA   HA    single    0.970  0.020  1.090
 PPJ  CB   CG    single    1.520  0.020  1.520
 PPJ  CB   HCB   single    0.970  0.020  1.090
 PPJ  CB   HB1   single    0.970  0.020  1.090
 PPJ  C    O     double    1.203  0.020  1.203
 PPJ  C    OXT   single    1.325  0.020  1.325
 PPJ  CG   CD    single    1.521  0.020  1.521
 PPJ  CG   OGL   single    1.415  0.020  1.415
 PPJ  CG   HCG   single    0.970  0.020  1.090
 PPJ  CD   HC1   single    0.970  0.020  1.090
 PPJ  CD   HC2   single    0.970  0.020  1.090
 PPJ  CD   HC3   single    0.970  0.020  1.090
 PPJ  OXT  HXT   single    0.850  0.020  0.980
 PPJ  OGL  HGL   single    0.850  0.020  0.980
 PPJ  HO1  OP3   single    0.850  0.020  0.980
 PPJ  HO2  OP1   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
 PPJ  C6    N1   C2    119.85  3.000
 PPJ  C3    C2   C2A   119.86  3.000
 PPJ  C3    C2   N1    121.30  3.000
 PPJ  C2A   C2   N1    118.84  3.000
 PPJ  HC6   C6   C5    120.03  3.000
 PPJ  HC6   C6   N1    116.45  3.000
 PPJ  C5    C6   N1    123.52  3.000
 PPJ  H2A3  C2A  H2A2  108.44  3.000
 PPJ  H2A3  C2A  H2A1  108.38  3.000
 PPJ  H2A2  C2A  H2A1  106.88  3.000
 PPJ  H2A3  C2A  C2    110.00  3.000
 PPJ  H2A2  C2A  C2    111.61  3.000
 PPJ  H2A1  C2A  C2    111.40  3.000
 PPJ  C4    C3   O3    122.98  3.000
 PPJ  C4    C3   C2    119.06  3.000
 PPJ  O3    C3   C2    117.96  3.000
 PPJ  HO3   O3   C3    107.40  3.000
 PPJ  C5    C4   C4A   121.92  3.000
 PPJ  C5    C4   C3    118.18  3.000
 PPJ  C4A   C4   C3    119.90  3.000
 PPJ  H4A   C4A  N     121.03  3.000
 PPJ  H4A   C4A  C4    118.69  3.000
 PPJ  N     C4A  C4    120.28  3.000
 PPJ  C5A   C5   C4    122.49  3.000
 PPJ  C5A   C5   C6    119.43  3.000
 PPJ  C4    C5   C6    118.08  3.000
 PPJ  CA    N    C4A   119.93  3.000
 PPJ  H5A2  C5A  H5A1  107.57  3.000
 PPJ  H5A2  C5A  OP4   109.58  3.000
 PPJ  H5A1  C5A  OP4   110.85  3.000
 PPJ  H5A2  C5A  C5    109.64  3.000
 PPJ  H5A1  C5A  C5    110.90  3.000
 PPJ  OP4   C5A  C5    108.28  3.000
 PPJ  P     OP4  C5A   122.87  3.000
 PPJ  OP3   P    OP2   118.22  3.000
 PPJ  OP3   P    OP1   103.39  3.000
 PPJ  OP2   P    OP1   115.25  3.000
 PPJ  OP3   P    OP4   100.98  3.000
 PPJ  OP2   P    OP4   111.67  3.000
 PPJ  OP1   P    OP4   105.69  3.000
 PPJ  HO2   OP1  P     113.98  3.000
 PPJ  HO1   OP3  P     115.33  3.000
 PPJ  HA    CA   C     106.29  3.000
 PPJ  HA    CA   CB    107.33  3.000
 PPJ  C     CA   CB    113.60  3.000
 PPJ  HA    CA   N     111.27  3.000
 PPJ  C     CA   N     108.39  3.000
 PPJ  CB    CA   N     109.94  3.000
 PPJ  HB1   CB   HCB   106.31  3.000
 PPJ  HB1   CB   CG    110.16  3.000
 PPJ  HCB   CB   CG    108.86  3.000
 PPJ  HB1   CB   CA    109.28  3.000
 PPJ  HCB   CB   CA    107.65  3.000
 PPJ  CG    CB   CA    114.25  3.000
 PPJ  OXT   C    O     123.97  3.000
 PPJ  OXT   C    CA    111.27  3.000
 PPJ  O     C    CA    124.62  3.000
 PPJ  HCG   CG   OGL   110.09  3.000
 PPJ  HCG   CG   CD    108.31  3.000
 PPJ  OGL   CG   CD    111.90  3.000
 PPJ  HCG   CG   CB    108.49  3.000
 PPJ  OGL   CG   CB    107.05  3.000
 PPJ  CD    CG   CB    110.96  3.000
 PPJ  HC3   CD   HC2   108.22  3.000
 PPJ  HC3   CD   HC1   107.53  3.000
 PPJ  HC2   CD   HC1   108.03  3.000
 PPJ  HC3   CD   CG    111.03  3.000
 PPJ  HC2   CD   CG    111.20  3.000
 PPJ  HC1   CD   CG    110.68  3.000
 PPJ  HXT   OXT  C     109.97  3.000
 PPJ  HGL   OGL  CG    108.67  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
 PPJ  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PPJ  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PPJ  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PPJ  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PPJ  CONST_05  C3    C2   N1   C6     0.00   0.0  0
 PPJ  CONST_06  C3    C4   C5   C6     0.00   0.0  0
 PPJ  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 PPJ  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PPJ  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PPJ  CONST_10  C2A   C2   N1   C6   180.00   0.0  0
 PPJ  CONST_11  C4A   C4   C5   C6   180.00   0.0  0
 PPJ  CONST_12  C4    C3   C2   C2A  180.00   0.0  0
 PPJ  CONST_13  C5A   C5   C4   C3   180.00   0.0  0
 PPJ  CONST_14  C5    C4   C3   O3   180.00   0.0  0
 PPJ  CONST_15  HC6   C6   N1   C2   180.00   0.0  0
 PPJ  CONST_16  HXT   OXT  C    CA   180.00   0.0  0
 PPJ  Var_01    OP4   C5A  C5   C6   112.94  30.0  2
 PPJ  Var_02    N     C4A  C4   C3    -4.38  30.0  2
 PPJ  Var_03    H2A1  C2A  C2   N1   120.27  30.0  2
 PPJ  Var_04    OP1   P    OP4  C5A  -56.57  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
 PPJ  chir_01  CA  N    CB  C   negativ
 PPJ  chir_02  CG  OGL  CD  CB  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
 PPJ  plan-1  N1   0.020
 PPJ  plan-1  C2   0.020
 PPJ  plan-1  C6   0.020
 PPJ  plan-1  C2A  0.020
 PPJ  plan-1  C3   0.020
 PPJ  plan-1  O3   0.020
 PPJ  plan-1  C4   0.020
 PPJ  plan-1  C4A  0.020
 PPJ  plan-1  C5   0.020
 PPJ  plan-1  C5A  0.020
 PPJ  plan-1  HC6  0.020
 PPJ  plan-2  CA   0.020
 PPJ  plan-2  C    0.020
 PPJ  plan-2  O    0.020
 PPJ  plan-2  OXT  0.020
 PPJ  plan-2  HXT  0.020
 PPJ  plan-3  C4   0.020
 PPJ  plan-3  C4A  0.020
 PPJ  plan-3  N    0.020
 PPJ  plan-3  CA   0.020
 PPJ  plan-3  H4A  0.020

