# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:48:44 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: N~5~-(N-methoxycarbamimidoyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CONC(=N)NCCC[C@H](N)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
 1KJ  1KJ  N~5~-(N-methoxycarbamimidoyl)-L-ornithine  ligand  30  14  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1KJ
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
 1KJ  OA2  O  OH1   0  -0.594  -4.4147  -1.1350  -1.3590
 1KJ  C    C  C     0   0.521  -4.4193  -0.3782  -0.2670
 1KJ  OA1  O  O     0  -0.440  -5.2721  -0.4488   0.5824
 1KJ  CA   C  CH1   0  -0.209  -3.2271   0.5703  -0.2198
 1KJ  N    N  NH2   0  -0.776  -3.3529   1.6024   0.7797
 1KJ  CB   C  CH2   0  -0.436  -1.9418  -0.2393  -0.0046
 1KJ  CG   C  CH2   0  -0.446  -0.6834   0.6107  -0.1098
 1KJ  CD   C  CH2   0  -0.272   0.5618  -0.2290   0.1230
 1KJ  NE   N  NH1   0  -0.669   1.7572   0.5768  -0.0037
 1KJ  CZ   C  C     0   0.577   2.9868   0.0542   0.3076
 1KJ  NH2  N  N     0  -0.692   3.2484  -1.0390   0.9071
 1KJ  NH1  N  NH1   0  -0.411   4.0150   0.8810  -0.1522
 1KJ  OH   O  O2    0  -0.391   5.2487   0.6148   0.4045
 1KJ  C1   C  CH3   0  -0.381   6.0572  -0.0938  -0.5131
 1KJ  H1   H  HOH1  0   0.481  -5.1745  -1.7364  -1.3516
 1KJ  H2   H  HCH1  0   0.268  -3.1635   1.0506  -1.2025
 1KJ  H3   H  HNH2  0   0.354  -4.1790   2.1617   0.6109
 1KJ  H4   H  HNH2  0   0.343  -3.4736   1.1882   1.6960
 1KJ  H6   H  HCH2  0   0.234  -1.9842  -0.7180   0.9804
 1KJ  H7   H  HCH2  0   0.246  -1.8924  -1.0469  -0.7384
 1KJ  H8   H  HCH2  0   0.228  -0.6411   1.0695  -1.1035
 1KJ  H9   H  HCH2  0   0.240  -0.7147   1.4255   0.6147
 1KJ  H10  H  HCH2  0   0.234   0.5221  -0.6438   1.1332
 1KJ  H11  H  HCH2  0   0.224   0.5749  -1.0805  -0.5702
 1KJ  H12  H  HNH1  0   0.384   1.7468   1.2199  -0.7822
 1KJ  H13  H  H     0   0.335   2.4060  -1.5705   1.0895
 1KJ  H15  H  HNH1  0   0.388   3.8238   1.8697  -0.0398
 1KJ  H16  H  HCH3  0   0.215   5.6272  -1.0649  -0.7678
 1KJ  H17  H  HCH3  0   0.212   6.2277   0.4738  -1.4317
 1KJ  H18  H  HCH3  0   0.229   7.0130  -0.2528  -0.0148

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
 1KJ  C1   OH   single  1.413  0.020  1.413
 1KJ  OH   NH1  single  1.379  0.020  1.379
 1KJ  NH1  CZ   single  1.397  0.020  1.397
 1KJ  CD   NE   single  1.447  0.020  1.447
 1KJ  CD   CG   single  1.520  0.020  1.520
 1KJ  CZ   NH2  double  1.274  0.020  1.274
 1KJ  CZ   NE   single  1.372  0.020  1.372
 1KJ  OA1  C    double  1.206  0.020  1.206
 1KJ  CB   CG   single  1.522  0.020  1.522
 1KJ  CB   CA   single  1.534  0.020  1.534
 1KJ  C    CA   single  1.524  0.020  1.524
 1KJ  C    OA2  single  1.329  0.020  1.329
 1KJ  CA   N    single  1.442  0.020  1.442
 1KJ  OA2  H1   single  0.850  0.020  0.980
 1KJ  CA   H2   single  0.970  0.020  1.090
 1KJ  N    H3   single  0.890  0.020  1.040
 1KJ  N    H4   single  0.890  0.020  1.040
 1KJ  CB   H6   single  0.970  0.020  1.090
 1KJ  CB   H7   single  0.970  0.020  1.090
 1KJ  CG   H8   single  0.970  0.020  1.090
 1KJ  CG   H9   single  0.970  0.020  1.090
 1KJ  CD   H10  single  0.970  0.020  1.090
 1KJ  CD   H11  single  0.970  0.020  1.090
 1KJ  NE   H12  single  0.890  0.020  1.040
 1KJ  NH2  H13  single  0.890  0.020  1.040
 1KJ  NH1  H15  single  0.890  0.020  1.040
 1KJ  C1   H16  single  0.970  0.020  1.090
 1KJ  C1   H17  single  0.970  0.020  1.090
 1KJ  C1   H18  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
 1KJ  H1   OA2  C    110.15  3.000
 1KJ  CA   C    OA1  124.60  3.000
 1KJ  CA   C    OA2  112.16  3.000
 1KJ  OA1  C    OA2  123.24  3.000
 1KJ  H2   CA   CB   107.97  3.000
 1KJ  H2   CA   N    108.23  3.000
 1KJ  CB   CA   N    110.70  3.000
 1KJ  H2   CA   C    106.89  3.000
 1KJ  N    CA   C    113.49  3.000
 1KJ  CB   CA   C    109.34  3.000
 1KJ  H4   N    H3   106.24  3.000
 1KJ  H4   N    CA   110.16  3.000
 1KJ  H3   N    CA   110.56  3.000
 1KJ  H7   CB   H6   106.42  3.000
 1KJ  H7   CB   CG   109.21  3.000
 1KJ  H6   CB   CG   109.76  3.000
 1KJ  H7   CB   CA   109.50  3.000
 1KJ  H6   CB   CA   108.91  3.000
 1KJ  CG   CB   CA   112.84  3.000
 1KJ  H9   CG   H8   106.91  3.000
 1KJ  H9   CG   CD   109.54  3.000
 1KJ  H8   CG   CD   109.80  3.000
 1KJ  H9   CG   CB   110.34  3.000
 1KJ  H8   CG   CB   109.18  3.000
 1KJ  CD   CG   CB   110.99  3.000
 1KJ  H11  CD   H10  106.84  3.000
 1KJ  H11  CD   NE   111.51  3.000
 1KJ  H10  CD   NE   108.80  3.000
 1KJ  H11  CD   CG   109.97  3.000
 1KJ  H10  CD   CG   108.76  3.000
 1KJ  NE   CD   CG   110.84  3.000
 1KJ  H12  NE   CZ   115.27  3.000
 1KJ  H12  NE   CD   114.43  3.000
 1KJ  CZ   NE   CD   120.55  3.000
 1KJ  NH1  CZ   NH2  120.77  3.000
 1KJ  NH2  CZ   NE   128.15  3.000
 1KJ  NH1  CZ   NE   111.06  3.000
 1KJ  H13  NH2  CZ   111.37  3.000
 1KJ  H15  NH1  OH   108.20  3.000
 1KJ  H15  NH1  CZ   113.71  3.000
 1KJ  OH   NH1  CZ   114.28  3.000
 1KJ  C1   OH   NH1  110.27  3.000
 1KJ  H18  C1   H17  108.86  3.000
 1KJ  H18  C1   H16  108.80  3.000
 1KJ  H17  C1   H16  109.09  3.000
 1KJ  H18  C1   OH   106.15  3.000
 1KJ  H17  C1   OH   111.99  3.000
 1KJ  H16  C1   OH   111.84  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
 1KJ  CONST_01  NH1  CZ   NE  CD   180.00   0.0  0
 1KJ  CONST_02  NH2  CZ   NE  CD     0.00   0.0  0
 1KJ  CONST_05  H1   OA2  C   OA1    0.00   0.0  0
 1KJ  CONST_07  H13  NH2  CZ  NE     0.00   0.0  0
 1KJ  Var_01    CD   CG   CB  CA   179.46  30.0  3
 1KJ  Var_02    NE   CD   CG  CB   178.88  30.0  2
 1KJ  Var_03    CZ   NE   CD  CG   172.97  30.0  3
 1KJ  Var_04    H16  C1   OH  NH1  -62.40  30.0  3

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
 1KJ  chir_01  CA  CB  C  N  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
 1KJ  plan-1  CD   0.020
 1KJ  plan-1  NE   0.020
 1KJ  plan-1  CZ   0.020
 1KJ  plan-1  NH2  0.020
 1KJ  plan-1  NH1  0.020
 1KJ  plan-1  OH   0.020
 1KJ  plan-1  H12  0.020
 1KJ  plan-1  H13  0.020
 1KJ  plan-1  H15  0.020
 1KJ  plan-2  OA2  0.020
 1KJ  plan-2  C    0.020
 1KJ  plan-2  OA1  0.020
 1KJ  plan-2  CA   0.020
 1KJ  plan-2  H1   0.020

