# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 09:57:32 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (2R)-amino(2-nitrophenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C(O)=O)c1ccccc1[N+]([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
 PRV  PRV  '(2R)-amino(2-nitrophenyl)ethanoic acid'  L-peptide  21  14  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PRV
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
 PRV  C    C  C      0  -0.125  -3.5525  -38.7254  25.1260
 PRV  N    N  NH2    0  -0.819  -2.1296  -37.1111  26.2945
 PRV  O    O  O      0  -0.638  -2.6833  -39.5661  25.0957
 PRV  N1   N  N      1   0.389  -4.4610  -34.5071  25.1291
 PRV  O1   O  O     -1  -0.261  -4.1161  -33.4232  25.5386
 PRV  O2   O  O      0  -0.384  -4.3979  -34.8421  23.9686
 PRV  CA   C  CH1    0  -0.272  -3.3232  -37.2766  25.4839
 PRV  CG   C  CR6    0   0.250  -4.5335  -36.7360  26.1983
 PRV  CZ   C  CR16   0  -0.205  -6.6611  -35.8269  27.7711
 PRV  CD1  C  CR16   0   0.035  -5.1190  -37.6337  27.1544
 PRV  CD2  C  CR6    0   0.044  -5.0280  -35.4452  26.0959
 PRV  CE1  C  CR16   0  -0.202  -6.2115  -37.1226  27.9150
 PRV  CE2  C  CR16   0  -0.255  -6.0709  -34.9485  26.8677
 PRV  OXT  O  OC    -1  -0.459  -4.6799  -38.8130  27.2717
 PRV  HN   H  HNH2   0   0.344  -1.3226  -37.4539  25.7873
 PRV  HNA  H  HNH2   0   0.340  -1.9670  -36.1232  26.4417
 PRV  HA   H  HCH1   0   0.279  -3.2395  -36.8042  24.4923
 PRV  HZ   H  HCR6   0   0.278  -7.4941  -35.4802  28.3711
 PRV  HD1  H  HCR6   0   0.074  -4.5512  -38.9095  24.6814
 PRV  HE1  H  HCR6   0   0.294  -6.6877  -37.7796  28.6338
 PRV  HE2  H  HCR6   0   0.294  -6.4314  -33.9372  26.7471

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
 PRV  C    O    deloc     1.231  0.020  1.231
 PRV  C    CA   single    1.516  0.018  1.516
 PRV  N    CA   single    1.451  0.016  1.451
 PRV  N1   O1   single    1.209  0.020  1.209
 PRV  N1   O2   double    1.210  0.020  1.210
 PRV  N1   CD2  single    1.462  0.020  1.462
 PRV  CA   CG   single    1.506  0.020  1.506
 PRV  CG   CD1  aromatic  1.436  0.020  1.436
 PRV  CG   CD2  aromatic  1.386  0.020  1.386
 PRV  CZ   CE1  aromatic  1.379  0.020  1.379
 PRV  CZ   CE2  aromatic  1.391  0.020  1.391
 PRV  CD1  CE1  aromatic  1.426  0.020  1.426
 PRV  CD2  CE2  aromatic  1.389  0.020  1.389
 PRV  C    OXT  deloc     2.426  0.020  2.426
 PRV  N    HN   single    0.868  0.020  1.013
 PRV  N    HNA  single    0.868  0.020  1.013
 PRV  CA   HA   single    0.939  0.020  1.096
 PRV  CZ   HZ   single    0.929  0.020  1.085
 PRV  CD1  HD1  single    0.929  0.020  1.085
 PRV  CE1  HE1  single    0.929  0.020  1.085
 PRV  CE2  HE2  single    0.929  0.020  1.085

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
 PRV  OXT  C    CA    84.00  3.000
 PRV  OXT  C    O    109.33  3.000
 PRV  CA   C    O    120.80  2.100
 PRV  HNA  N    HN   105.98  3.000
 PRV  HNA  N    CA   108.93  3.000
 PRV  HN   N    CA   109.67  3.000
 PRV  CD2  N1   O2   118.50  3.000
 PRV  CD2  N1   O1   117.52  3.000
 PRV  O2   N1   O1   123.95  3.000
 PRV  HA   CA   CG   109.53  3.000
 PRV  HA   CA   N    113.02  3.000
 PRV  CG   CA   N    110.78  3.000
 PRV  HA   CA   C    102.10  3.000
 PRV  CG   CA   C    109.57  3.000
 PRV  N    CA   C    113.30  2.900
 PRV  CD2  CG   CD1  119.07  3.000
 PRV  CD2  CG   CA   125.87  3.000
 PRV  CD1  CG   CA   114.78  3.000
 PRV  HZ   CZ   CE2  118.93  3.000
 PRV  HZ   CZ   CE1  119.57  3.000
 PRV  CE2  CZ   CE1  121.51  3.000
 PRV  HD1  CD1  CE1  141.14  3.000
 PRV  HD1  CD1  CG    67.64  3.000
 PRV  CE1  CD1  CG   116.32  3.000
 PRV  CE2  CD2  CG   124.04  3.000
 PRV  CE2  CD2  N1   115.42  3.000
 PRV  CG   CD2  N1   120.54  3.000
 PRV  HE1  CE1  CD1  118.23  3.000
 PRV  HE1  CE1  CZ   119.70  3.000
 PRV  CD1  CE1  CZ   122.07  3.000
 PRV  HE2  CE2  CD2  121.54  3.000
 PRV  HE2  CE2  CZ   121.46  3.000
 PRV  CD2  CE2  CZ   116.97  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
 PRV  CONST_01  CZ   CE1  CD1  CG     0.00  0.0  0
 PRV  CONST_02  CZ   CE2  CD2  CG     0.00  0.0  0
 PRV  CONST_03  CE2  CD2  CG   CD1    0.00  0.0  0
 PRV  CONST_04  CE2  CZ   CE1  CD1    0.00  0.0  0
 PRV  CONST_05  CE1  CD1  CG   CD2    0.00  0.0  0
 PRV  CONST_06  CE1  CZ   CE2  CD2    0.00  0.0  0
 PRV  CONST_07  CD1  CG   CD2  N1   180.00  0.0  0
 PRV  CONST_08  CZ   CE2  CD2  N1   180.00  0.0  0
 PRV  CONST_09  CE1  CD1  CG   CA   180.00  0.0  0
 PRV  CONST_10  CE2  CD2  CG   CA   180.00  0.0  0
 PRV  CONST_11  HE1  CE1  CD1  CG   180.00  0.0  0
 PRV  CONST_12  HE2  CE2  CD2  CG   180.00  0.0  0
 PRV  CONST_14  HZ   CZ   CE1  CD1  180.00  0.0  0

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
 PRV  chir_01  CA  C  N  CG  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
 PRV  plan-1  N1   0.020
 PRV  plan-1  CA   0.020
 PRV  plan-1  CG   0.020
 PRV  plan-1  CZ   0.020
 PRV  plan-1  CD1  0.020
 PRV  plan-1  CD2  0.020
 PRV  plan-1  CE1  0.020
 PRV  plan-1  CE2  0.020
 PRV  plan-1  HZ   0.020
 PRV  plan-1  HD1  0.020
 PRV  plan-1  HE1  0.020
 PRV  plan-1  HE2  0.020
 PRV  plan-2  N1   0.020
 PRV  plan-2  O1   0.020
 PRV  plan-2  O2   0.020
 PRV  plan-2  CD2  0.020
 PRV  plan-3  C    0.020
 PRV  plan-3  O    0.020
 PRV  plan-3  CA   0.020
 PRV  plan-3  OXT  0.020

