# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 04:27:52 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-nitro-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)[N+]([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
 PPN  PPN  '4-nitro-L-phenylalanine  '  L-peptide  24  15  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_PPN
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
 PPN  N    N  NH2    0  -0.794  -18.0202  -0.8036  -0.4606
 PPN  CA   C  CH1    0  -0.175  -18.7731  -2.0266  -0.6867
 PPN  C    C  C      0   0.411  -20.0648  -1.6945  -1.4693
 PPN  O    O  O      0  -0.608  -20.7605  -0.7764  -0.9860
 PPN  OXT  O  OC    -1  -0.599  -20.3099  -2.3682  -2.4865
 PPN  CB   C  CH2    0  -0.534  -19.1311  -2.7513   0.6328
 PPN  CG   C  CR6    0   0.151  -19.8372  -4.0524   0.4188
 PPN  CD1  C  CR16   0  -0.305  -19.1138  -5.2158   0.1539
 PPN  CD2  C  CR16   0  -0.290  -21.2295  -4.1299   0.4431
 PPN  CE1  C  CR16   0  -0.251  -19.7491  -6.4217  -0.0772
 PPN  CE2  C  CR16   0  -0.253  -21.8868  -5.3251   0.2174
 PPN  CZ   C  CR6    0   0.227  -21.1366  -6.4643  -0.0415
 PPN  N1   N  N      1   0.326  -21.8164  -7.7247  -0.2749
 PPN  O1   O  O      0  -0.381  -23.0254  -7.7372  -0.2344
 PPN  O2   O  O     -1  -0.382  -21.1425  -8.7040  -0.4990
 PPN  H    H  HNH2   0   0.334  -17.2587  -0.9779   0.1846
 PPN  H2   H  HNH2   0   0.329  -18.6321  -0.1343  -0.0085
 PPN  HA   H  HCH1   0   0.205  -18.1563  -2.7050  -1.2840
 PPN  HB2  H  HCH2   0   0.244  -18.2051  -2.9290   1.1868
 PPN  HB3  H  HCH2   0   0.239  -19.7482  -2.0828   1.2377
 PPN  HD1  H  HCR6   0   0.263  -18.0315  -5.1787   0.1354
 PPN  HD2  H  HCR6   0   0.261  -21.8099  -3.2377   0.6403
 PPN  HE1  H  HCR6   0   0.291  -19.1662  -7.3092  -0.2769
 PPN  HE2  H  HCR6   0   0.290  -22.9663  -5.3618   0.2465

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
 PPN  N    CA   single    1.458  0.019  1.458
 PPN  N    H    single    0.860  0.020  0.860
 PPN  N    H2   single    0.890  0.020  1.040
 PPN  CA   C    single    1.525  0.021  1.525
 PPN  CA   CB   single    1.530  0.020  1.530
 PPN  CA   HA   single    0.970  0.020  0.970
 PPN  C    O    deloc     1.231  0.020  1.231
 PPN  C    OXT  deloc     1.244  0.020  1.244
 PPN  CB   CG   single    1.496  0.020  1.496
 PPN  CB   HB2  single    0.970  0.020  1.090
 PPN  CB   HB3  single    0.970  0.020  1.090
 PPN  CG   CD1  aromatic  1.395  0.020  1.395
 PPN  CG   CD2  aromatic  1.395  0.020  1.395
 PPN  CD1  CE1  aromatic  1.383  0.020  1.383
 PPN  CD1  HD1  single    0.930  0.020  1.080
 PPN  CD2  CE2  aromatic  1.383  0.020  1.383
 PPN  CD2  HD2  single    0.930  0.020  1.080
 PPN  CE1  CZ   aromatic  1.389  0.020  1.389
 PPN  CE1  HE1  single    0.930  0.020  1.080
 PPN  CE2  CZ   aromatic  1.388  0.020  1.388
 PPN  CE2  HE2  single    0.930  0.020  1.080
 PPN  CZ   N1   single    1.451  0.020  1.451
 PPN  N1   O1   double    1.210  0.020  1.210
 PPN  N1   O2   single    1.210  0.020  1.210

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
 PPN  H2   N    H    106.47  3.000
 PPN  H2   N    CA   108.20  3.000
 PPN  H    N    CA   114.00  3.000
 PPN  HA   CA   CB   109.00  3.000
 PPN  HA   CA   C    109.00  3.000
 PPN  CB   CA   C    110.10  1.900
 PPN  HA   CA   N    110.00  3.000
 PPN  CB   CA   N    110.50  1.700
 PPN  C    CA   N    111.00  2.800
 PPN  OXT  C    O    127.19  3.000
 PPN  OXT  C    CA   117.51  3.000
 PPN  O    C    CA   120.80  1.700
 PPN  HB3  CB   HB2  107.29  3.000
 PPN  HB3  CB   CG   110.17  3.000
 PPN  HB2  CB   CG   109.32  3.000
 PPN  HB3  CB   CA   108.44  3.000
 PPN  HB2  CB   CA   108.19  3.000
 PPN  CG   CB   CA   113.24  3.000
 PPN  CD2  CG   CD1  118.33  3.000
 PPN  CD2  CG   CB   121.14  3.000
 PPN  CD1  CG   CB   120.51  3.000
 PPN  HD1  CD1  CE1  119.09  3.000
 PPN  HD1  CD1  CG   119.52  3.000
 PPN  CE1  CD1  CG   121.38  3.000
 PPN  HD2  CD2  CE2  119.17  3.000
 PPN  HD2  CD2  CG   119.51  3.000
 PPN  CE2  CD2  CG   121.32  3.000
 PPN  HE1  CE1  CZ   121.24  3.000
 PPN  HE1  CE1  CD1  119.97  3.000
 PPN  CZ   CE1  CD1  118.79  3.000
 PPN  HE2  CE2  CZ   121.14  3.000
 PPN  HE2  CE2  CD2  119.99  3.000
 PPN  CZ   CE2  CD2  118.87  3.000
 PPN  N1   CZ   CE2  119.31  3.000
 PPN  N1   CZ   CE1  119.39  3.000
 PPN  CE2  CZ   CE1  121.30  3.000
 PPN  O2   N1   O1   123.68  3.000
 PPN  O2   N1   CZ   118.16  3.000
 PPN  O1   N1   CZ   118.16  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
 PPN  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PPN  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PPN  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PPN  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PPN  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PPN  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PPN  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PPN  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PPN  CONST_09  N1   CZ   CE1  CD1  180.00   0.0  0
 PPN  CONST_10  N1   CZ   CE2  CD2  180.00   0.0  0
 PPN  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 PPN  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 PPN  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 PPN  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 PPN  CONST_15  O1   N1   CZ   CE1  180.00   0.0  0
 PPN  CONST_16  O2   N1   CZ   CE1    0.00   0.0  0
 PPN  CONST_17  O1   N1   CZ   CE2    0.00   0.0  0
 PPN  CONST_18  O2   N1   CZ   CE2  180.00   0.0  0
 PPN  Var_01    CD1  CG   CB   CA    83.35  30.0  2

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
 PPN  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
 PPN  plan-1  CB   0.020
 PPN  plan-1  CG   0.020
 PPN  plan-1  CD1  0.020
 PPN  plan-1  CD2  0.020
 PPN  plan-1  CE1  0.020
 PPN  plan-1  CE2  0.020
 PPN  plan-1  CZ   0.020
 PPN  plan-1  N1   0.020
 PPN  plan-1  HD1  0.020
 PPN  plan-1  HD2  0.020
 PPN  plan-1  HE1  0.020
 PPN  plan-1  HE2  0.020
 PPN  plan-2  CZ   0.020
 PPN  plan-2  N1   0.020
 PPN  plan-2  O1   0.020
 PPN  plan-2  O2   0.020
 PPN  plan-3  CA   0.020
 PPN  plan-3  C    0.020
 PPN  plan-3  O    0.020
 PPN  plan-3  OXT  0.020

