# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 13:27:06 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  28  15  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.804   8.4198  15.7604  35.4957
 NRG  CA    C  CH1    0  -0.195   8.7443  16.0130  34.1064
 NRG  CB    C  CH2    0  -0.415   8.3224  14.8277  33.2275
 NRG  CG    C  CH2    0  -0.487   9.0544  13.5381  33.5832
 NRG  CD    C  CH2    0  -0.281   8.8269  12.4240  32.5719
 NRG  NE    N  NH1    0  -0.650   7.4264  12.0470  32.5259
 NRG  CZ    C  C      0   0.616   6.7396  11.5526  31.4706
 NRG  NH1   N  NC1    0  -0.526   7.6021  11.1761  30.4130
 NRG  NH2   N  N      0  -0.647   5.4911  11.3549  31.3612
 NRG  C     C  C      0   0.540   8.0595  17.2569  33.5731
 NRG  OA1   O  O      0  -0.455   8.3157  17.7278  32.4911
 NRG  OA2   O  OH1    0  -0.579   7.1554  17.7709  34.3917
 NRG  N1    N  N      1   0.615   7.2824  11.2536  29.1104
 NRG  O2    O  O     -1  -0.427   7.9722  10.5954  28.3618
 NRG  O3    O  O      0  -0.400   6.3880  11.9845  28.7710
 NRG  HN1   H  HNH2   0   0.360   8.9358  14.9488  35.8100
 NRG  HN2   H  HNH2   0   0.353   8.7474  16.5222  36.0764
 NRG  HCA   H  HCH1   0   0.250   9.8182  16.1824  33.9318
 NRG  HCB1  H  HCH2   0   0.238   7.2412  14.6890  33.3125
 NRG  HCB2  H  HCH2   0   0.238   8.5339  15.0763  32.1849
 NRG  HCG1  H  HCH2   0   0.251  10.1313  13.7232  33.6246
 NRG  HCG2  H  HCH2   0   0.240   8.7631  13.1798  34.5752
 NRG  HCD1  H  HCH2   0   0.252   9.1390  12.7665  31.5849
 NRG  HCD2  H  HCH2   0   0.250   9.4568  11.5678  32.8346
 NRG  HNE   H  HNH1   0   0.403   6.9191  12.0782  33.3970
 NRG  HNH1  H  HNC1   0   0.444   8.3914  10.5677  30.5874
 NRG  HNH2  H  H      0   0.338   4.9950  11.7239  32.1650
 NRG  HOA2  H  HOH1   0   0.480   6.7638  18.5603  33.9876

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  1.525  0.020  1.525
 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  1.451  0.020  1.451
 NRG  CD   HCD1  single  0.970  0.020  1.090
 NRG  CD   HCD2  single  0.970  0.020  1.090
 NRG  NE   CZ    single  1.353  0.020  1.353
 NRG  NE   HNE   single  0.860  0.020  1.020
 NRG  CZ   NH1   single  1.416  0.020  1.416
 NRG  CZ   NH2   double  1.269  0.020  1.269
 NRG  NH1  N1    single  1.344  0.020  1.344
 NRG  NH1  HNH1  single  0.860  0.020  1.020
 NRG  NH2  HNH2  single  0.890  0.020  1.040
 NRG  C    OA1   double  1.208  0.020  1.208
 NRG  C    OA2   single  1.323  0.020  1.323
 NRG  OA2  HOA2  single  0.850  0.020  0.980
 NRG  N1   O2    single  1.212  0.020  1.212
 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   105.10  3.000
 NRG  HN2   N    CA    110.27  3.000
 NRG  HN1   N    CA    108.88  3.000
 NRG  HCA   CA   C     104.97  3.000
 NRG  HCA   CA   CB    107.22  3.000
 NRG  C     CA   CB    110.50  1.500
 NRG  HCA   CA   N     113.41  3.000
 NRG  C     CA   N     111.00  2.800
 NRG  CB    CA   N     110.40  1.500
 NRG  HCB2  CB   HCB1  107.13  3.000
 NRG  HCB2  CB   CG    108.79  3.000
 NRG  HCB1  CB   CG    110.44  3.000
 NRG  HCB2  CB   CA    108.51  3.000
 NRG  HCB1  CB   CA    108.98  3.000
 NRG  CG    CB   CA    112.81  3.000
 NRG  HCG2  CG   HCG1  106.46  3.000
 NRG  HCG2  CG   CD    108.84  3.000
 NRG  HCG1  CG   CD    107.24  3.000
 NRG  HCG2  CG   CB    111.13  3.000
 NRG  HCG1  CG   CB    109.78  3.000
 NRG  CD    CG   CB    113.10  3.000
 NRG  HCD2  CD   HCD1  107.35  3.000
 NRG  HCD2  CD   NE    111.08  3.000
 NRG  HCD1  CD   NE    109.22  3.000
 NRG  HCD2  CD   CG    109.09  3.000
 NRG  HCD1  CD   CG    109.20  3.000
 NRG  NE    CD   CG    110.83  3.000
 NRG  HNE   NE   CZ    115.45  3.000
 NRG  HNE   NE   CD    116.75  3.000
 NRG  CZ    NE   CD    127.57  3.000
 NRG  NH2   CZ   NH1   119.59  3.000
 NRG  NH2   CZ   NE    128.59  3.000
 NRG  NH1   CZ   NE    111.76  3.000
 NRG  HNH1  NH1  N1    112.80  3.000
 NRG  HNH1  NH1  CZ    120.43  3.000
 NRG  N1    NH1  CZ    124.33  3.000
 NRG  HNH2  NH2  CZ    110.88  3.000
 NRG  OA2   C    OA1   123.21  3.000
 NRG  OA2   C    CA    114.17  3.000
 NRG  OA1   C    CA    122.62  3.000
 NRG  HOA2  OA2  C     109.54  3.000
 NRG  O3    N1   O2    125.33  3.000
 NRG  O3    N1   NH1   119.02  3.000
 NRG  O2    N1   NH1   115.59  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_05  HOA2  OA2  C    CA   180.00   0.0  0
 NRG  CONST_07  HNH2  NH2  CZ   NE     0.00   0.0  0
 NRG  Var_01    CD    CG   CB   CA  -170.00  30.0  3
 NRG  Var_02    NE    CD   CG   CB   -62.99  30.0  3
 NRG  Var_03    CZ    NE   CD   CG   150.56  30.0  3
 NRG  Var_04    O2    N1   NH1  CZ  -162.12  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-2  HOA2  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

