# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:18:37 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 6-nitro-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCC[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
 6HN  6HN  '6-nitro-L-norleucine     '  L-peptide  23  12  .  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_6HN
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
 6HN  N1   N  N      1   0.435  17.0590  -15.9298  41.6814
 6HN  N    N  NH2    0  -0.806  22.4294  -12.2454  40.2368
 6HN  CA   C  CH1    0  -0.217  22.3344  -12.3413  41.6864
 6HN  C    C  C      0   0.403  23.3489  -13.3630  42.2591
 6HN  OXT  O  OC    -1  -0.612  23.2296  -13.6258  43.4730
 6HN  O    O  O      0  -0.601  24.2159  -13.8083  41.4812
 6HN  CB   C  CH2    0  -0.397  20.8958  -12.6687  42.0902
 6HN  CG   C  CH2    0  -0.424  20.4121  -14.0348  41.6239
 6HN  CD   C  CH2    0  -0.455  18.9270  -14.2402  41.9100
 6HN  CE   C  CH2    0  -0.320  18.5058  -15.6218  41.4673
 6HN  O2   O  O      0  -0.390  16.6875  -17.0361  41.3693
 6HN  O1   O  O     -1  -0.382  16.3401  -15.0789  42.1429
 6HN  HA   H  HCH1   0   0.200  22.5836  -11.3828  42.1741
 6HN  HB   H  HCH2   0   0.206  20.8021  -12.5987  43.1758
 6HN  HBA  H  HCH2   0   0.203  20.2349  -11.8968  41.6793
 6HN  HG   H  HCH2   0   0.217  20.6000  -14.1408  40.5528
 6HN  HGA  H  HCH2   0   0.216  20.9894  -14.8185  42.1237
 6HN  HD   H  HCH2   0   0.238  18.7373  -14.1103  42.9778
 6HN  HDA  H  HCH2   0   0.239  18.3471  -13.4799  41.3826
 6HN  HE   H  HCH2   0   0.293  19.0473  -16.4040  42.0012
 6HN  HEA  H  HCH2   0   0.294  18.6758  -15.7763  40.4005
 6HN  H    H  HNH2   0   0.327  22.0923  -11.3419  39.9311
 6HN  HN2  H  HNH2   0   0.331  23.4013  -12.3098  39.9661

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
 6HN  N1  CE   single  1.495  0.020  1.495
 6HN  N1  O2   double  1.208  0.020  1.208
 6HN  N1  O1   single  1.206  0.020  1.206
 6HN  N   CA   single  1.458  0.019  1.458
 6HN  N   H    single  0.860  0.020  0.860
 6HN  N   HN2  single  0.890  0.020  1.040
 6HN  CA  C    single  1.525  0.021  1.525
 6HN  CA  CB   single  1.530  0.020  1.530
 6HN  CA  HA   single  0.970  0.020  0.970
 6HN  C   OXT  deloc   1.248  0.020  1.248
 6HN  C   O    deloc   1.231  0.020  1.231
 6HN  CB  CG   single  1.522  0.020  1.522
 6HN  CB  HB   single  0.970  0.020  1.090
 6HN  CB  HBA  single  0.970  0.020  1.090
 6HN  CG  CD   single  1.526  0.020  1.526
 6HN  CG  HG   single  0.970  0.020  1.090
 6HN  CG  HGA  single  0.970  0.020  1.090
 6HN  CD  CE   single  1.511  0.020  1.511
 6HN  CD  HD   single  0.970  0.020  1.090
 6HN  CD  HDA  single  0.970  0.020  1.090
 6HN  CE  HE   single  0.970  0.020  1.090
 6HN  CE  HEA  single  0.970  0.020  1.090

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
 6HN  O1   N1  O2   124.18  3.000
 6HN  O1   N1  CE   119.11  3.000
 6HN  O2   N1  CE   116.71  3.000
 6HN  HN2  N   H    107.24  3.000
 6HN  HN2  N   CA   108.98  3.000
 6HN  H    N   CA   114.00  3.000
 6HN  HA   CA  CB   109.00  3.000
 6HN  HA   CA  C    109.00  3.000
 6HN  CB   CA  C    110.10  1.900
 6HN  HA   CA  N    110.00  3.000
 6HN  CB   CA  N    110.50  1.700
 6HN  C    CA  N    111.00  2.800
 6HN  O    C   OXT  126.73  3.000
 6HN  O    C   CA   120.80  1.700
 6HN  OXT  C   CA   115.84  3.000
 6HN  HBA  CB  HB   106.00  3.000
 6HN  HBA  CB  CG   109.00  3.000
 6HN  HB   CB  CG   109.56  3.000
 6HN  HBA  CB  CA   108.51  3.000
 6HN  HB   CB  CA   109.24  3.000
 6HN  CG   CB  CA   114.21  3.000
 6HN  HGA  CG  HG   106.71  3.000
 6HN  HGA  CG  CD   109.36  3.000
 6HN  HG   CG  CD   109.76  3.000
 6HN  HGA  CG  CB   109.58  3.000
 6HN  HG   CG  CB   109.43  3.000
 6HN  CD   CG  CB   111.87  3.000
 6HN  HDA  CD  HD   107.29  3.000
 6HN  HDA  CD  CE   110.31  3.000
 6HN  HD   CD  CE   110.29  3.000
 6HN  HDA  CD  CG   109.42  3.000
 6HN  HD   CD  CG   109.65  3.000
 6HN  CE   CD  CG   109.84  3.000
 6HN  HEA  CE  HE   107.43  3.000
 6HN  HEA  CE  CD   111.87  3.000
 6HN  HE   CE  CD   111.96  3.000
 6HN  HEA  CE  N1   105.17  3.000
 6HN  HE   CE  N1   105.22  3.000
 6HN  CD   CE  N1   114.61  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
 6HN  Var_01  CG  CD  CE  N1  -179.16  30.0  1
 6HN  Var_02  CD  CG  CB  CA  -173.30  30.0  3
 6HN  Var_03  CE  CD  CG  CB  -178.34  30.0  3
 6HN  Var_04  O2  N1  CE  CD  -178.33  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
 6HN  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
 6HN  plan-1  CA   0.020
 6HN  plan-1  C    0.020
 6HN  plan-1  OXT  0.020
 6HN  plan-1  O    0.020
 6HN  plan-2  N1   0.020
 6HN  plan-2  CE   0.020
 6HN  plan-2  O2   0.020
 6HN  plan-2  O1   0.020

