# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:07:18 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: N~5~-(N-nitrocarbamimidoyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)N[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
 NRG  NRG  N~5~-(N-nitrocarbamimidoyl)-L-ornithine  L-peptide  27  15  .  2022-09-22  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_NRG
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
 NRG  N     N  NH2    0  -0.818   8.3397  15.6301  35.4668
 NRG  CA    C  CH1    0  -0.222   8.7661  15.9918  34.1220
 NRG  CB    C  CH2    0  -0.385   8.4327  14.8726  33.1388
 NRG  CG    C  CH2    0  -0.476   9.1160  13.5558  33.4860
 NRG  CD    C  CH2    0  -0.279   8.8531  12.4437  32.4805
 NRG  NE    N  NH1    0  -0.649   7.4482  12.0752  32.4838
 NRG  CZ    C  C      0   0.617   6.7331  11.5323  31.4740
 NRG  NH1   N  NC1    0  -0.526   7.5672  11.1020  30.4148
 NRG  NH2   N  N      0  -0.652   5.4811  11.3324  31.4068
 NRG  C     C  C      0   0.415   8.1439  17.3430  33.6899
 NRG  OA1   O  O      0  -0.611   8.2022  17.6204  32.4761
 NRG  OA2   O  OC    -1  -0.608   7.6704  18.0662  34.5901
 NRG  N1    N  N      1   0.614   7.2195  11.1107  29.1180
 NRG  O2    O  O     -1  -0.429   7.9083  10.4310  28.3873
 NRG  O3    O  O      0  -0.401   6.3017  11.8038  28.7621
 NRG  HN1   H  HNH2   0   0.333   9.0559  15.0842  35.9264
 NRG  HN2   H  HNH2   0   0.334   8.2324  16.4831  35.9998
 NRG  HCA   H  HCH1   0   0.196   9.8593  16.1512  34.0729
 NRG  HCB1  H  HCH2   0   0.204   7.3469  14.7346  33.1156
 NRG  HCB2  H  HCH2   0   0.209   8.7347  15.1777  32.1350
 NRG  HCG1  H  HCH2   0   0.235  10.1991  13.7033  33.5305
 NRG  HCG2  H  HCH2   0   0.228   8.8131  13.2151  34.4816
 NRG  HCD1  H  HCH2   0   0.245   9.1351  12.7841  31.4830
 NRG  HCD2  H  HCH2   0   0.243   9.4836  11.5810  32.7216
 NRG  HNE   H  HNH1   0   0.402   6.9550  12.1833  33.3565
 NRG  HNH1  H  HNC1   0   0.444   8.3830  10.5330  30.5986
 NRG  HNH2  H  H      0   0.337   5.0081  11.7389  32.2065

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
 NRG  N    CA    single  1.458  0.019  1.458
 NRG  N    HN1   single  0.890  0.020  1.040
 NRG  N    HN2   single  0.890  0.020  1.040
 NRG  CA   CB    single  1.521  0.033  1.521
 NRG  CA   C     single  1.525  0.021  1.525
 NRG  CA   HCA   single  0.970  0.020  1.090
 NRG  CB   CG    single  1.524  0.020  1.524
 NRG  CB   HCB1  single  0.970  0.020  1.090
 NRG  CB   HCB2  single  0.970  0.020  1.090
 NRG  CG   CD    single  1.522  0.020  1.522
 NRG  CG   HCG1  single  0.970  0.020  1.090
 NRG  CG   HCG2  single  0.970  0.020  1.090
 NRG  CD   NE    single  1.452  0.020  1.452
 NRG  CD   HCD1  single  0.970  0.020  1.090
 NRG  CD   HCD2  single  0.970  0.020  1.090
 NRG  NE   CZ    single  1.351  0.020  1.351
 NRG  NE   HNE   single  0.860  0.020  1.020
 NRG  CZ   NH1   single  1.415  0.020  1.415
 NRG  CZ   NH2   double  1.270  0.020  1.270
 NRG  NH1  N1    single  1.343  0.020  1.343
 NRG  NH1  HNH1  single  0.860  0.020  1.020
 NRG  NH2  HNH2  single  0.890  0.020  1.040
 NRG  C    OA1   deloc   1.246  0.020  1.246
 NRG  C    OA2   deloc   1.248  0.020  1.248
 NRG  N1   O2    single  1.213  0.020  1.213
 NRG  N1   O3    double  1.204  0.020  1.204

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
 NRG  HN2   N    HN1   106.91  3.000
 NRG  HN2   N    CA    107.95  3.000
 NRG  HN1   N    CA    110.27  3.000
 NRG  HCA   CA   C     105.01  3.000
 NRG  HCA   CA   CB    107.03  3.000
 NRG  C     CA   CB    110.50  1.500
 NRG  HCA   CA   N     111.48  3.000
 NRG  C     CA   N     111.00  2.800
 NRG  CB    CA   N     110.40  1.500
 NRG  HCB2  CB   HCB1  106.87  3.000
 NRG  HCB2  CB   CG    109.09  3.000
 NRG  HCB1  CB   CG    109.92  3.000
 NRG  HCB2  CB   CA    109.08  3.000
 NRG  HCB1  CB   CA    108.83  3.000
 NRG  CG    CB   CA    112.89  3.000
 NRG  HCG2  CG   HCG1  106.20  3.000
 NRG  HCG2  CG   CD    109.00  3.000
 NRG  HCG1  CG   CD    107.24  3.000
 NRG  HCG2  CG   CB    110.61  3.000
 NRG  HCG1  CG   CB    109.67  3.000
 NRG  CD    CG   CB    113.79  3.000
 NRG  HCD2  CD   HCD1  107.35  3.000
 NRG  HCD2  CD   NE    110.89  3.000
 NRG  HCD1  CD   NE    109.34  3.000
 NRG  HCD2  CD   CG    109.30  3.000
 NRG  HCD1  CD   CG    109.35  3.000
 NRG  NE    CD   CG    110.55  3.000
 NRG  HNE   NE   CZ    115.54  3.000
 NRG  HNE   NE   CD    116.61  3.000
 NRG  CZ    NE   CD    127.75  3.000
 NRG  NH2   CZ   NH1   119.58  3.000
 NRG  NH2   CZ   NE    128.66  3.000
 NRG  NH1   CZ   NE    111.69  3.000
 NRG  HNH1  NH1  N1    112.83  3.000
 NRG  HNH1  NH1  CZ    120.69  3.000
 NRG  N1    NH1  CZ    124.63  3.000
 NRG  HNH2  NH2  CZ    110.80  3.000
 NRG  OA2   C    OA1   126.24  3.000
 NRG  OA2   C    CA    117.17  3.000
 NRG  OA1   C    CA    116.55  3.000
 NRG  O3    N1   O2    125.28  3.000
 NRG  O3    N1   NH1   119.13  3.000
 NRG  O2    N1   NH1   115.55  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
 NRG  CONST_01  NH1   CZ   NE   CD     0.00   0.0  0
 NRG  CONST_02  NH2   CZ   NE   CD   180.00   0.0  0
 NRG  CONST_06  HNH2  NH2  CZ   NE     0.00   0.0  0
 NRG  Var_01    CD    CG   CB   CA  -177.13  30.0  3
 NRG  Var_02    NE    CD   CG   CB   -65.48  30.0  3
 NRG  Var_03    CZ    NE   CD   CG   153.70  30.0  3
 NRG  Var_04    O2    N1   NH1  CZ  -163.32  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
 NRG  chir_01  CA  N  CB  C  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
 NRG  plan-1  CD    0.020
 NRG  plan-1  NE    0.020
 NRG  plan-1  CZ    0.020
 NRG  plan-1  NH1   0.020
 NRG  plan-1  NH2   0.020
 NRG  plan-1  N1    0.020
 NRG  plan-1  HNE   0.020
 NRG  plan-1  HNH1  0.020
 NRG  plan-1  HNH2  0.020
 NRG  plan-2  CA    0.020
 NRG  plan-2  C     0.020
 NRG  plan-2  OA1   0.020
 NRG  plan-2  OA2   0.020
 NRG  plan-3  NH1   0.020
 NRG  plan-3  N1    0.020
 NRG  plan-3  O2    0.020
 NRG  plan-3  O3    0.020

