# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:10:39 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: N~5~-[(1E)-2-hydroxyethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)CO)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
 4JK  4JK  N~5~-[(1E)-2-hydroxyethanimidoyl]-L-ornithine  ligand  28  13  .  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_4JK
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
 4JK  CH    C  CH2   0  -0.225  11.3680  -0.0742  60.5122
 4JK  CZ    C  C     0   0.383  11.4301  -0.5111  59.0674
 4JK  NH    N  N     0  -0.671  10.5111  -1.2640  58.6009
 4JK  NE    N  NH1   0  -0.636  12.5266  -0.0775  58.3813
 4JK  CD    C  CH2   0  -0.286  13.4008   1.0065  58.7866
 4JK  CG    C  CH2   0  -0.454  14.7101   0.9636  58.0140
 4JK  CB    C  CH2   0  -0.424  15.5158  -0.3018  58.2738
 4JK  CA    C  CH1   0  -0.207  16.8808  -0.2778  57.5712
 4JK  C     C  C     0   0.521  17.6846  -1.5010  57.9928
 4JK  OA2   O  O     0  -0.441  17.9238  -2.4435  57.2797
 4JK  OA1   O  OH1   0  -0.594  18.0900  -1.4231  59.2558
 4JK  N     N  NH2   0  -0.776  16.7139  -0.1635  56.1428
 4JK  OH    O  OH1   0  -0.657  10.2457  -0.6298  61.1319
 4JK  HH1C  H  HCH2  0   0.225  12.3021  -0.3804  61.0040
 4JK  HH2C  H  HCH2  0   0.227  11.3523   1.0246  60.5449
 4JK  HH    H  HOH1  0   0.457  10.2499  -0.3339  62.0466
 4JK  HA    H  H     0   0.310  10.6829  -1.4768  57.6209
 4JK  HD1   H  HCH2  0   0.239  12.9263   1.9833  58.6358
 4JK  HD2   H  HCH2  0   0.237  13.6200   0.9213  59.8526
 4JK  HNE   H  HNH1  0   0.379  12.5040  -0.2500  57.3865
 4JK  HG1C  H  HCH2  0   0.237  14.5151   1.0748  56.9450
 4JK  HG2C  H  HCH2  0   0.237  15.2971   1.8369  58.3108
 4JK  HB1C  H  HCH2  0   0.240  15.6608  -0.4188  59.3504
 4JK  HB2C  H  HCH2  0   0.234  14.9592  -1.1818  57.9373
 4JK  HB    H  HCH1  0   0.266  17.4255   0.6043  57.9248
 4JK  HN1   H  HNH2  0   0.354  17.6129  -0.0975  55.6830
 4JK  HN2   H  HNH2  0   0.343  16.2659  -0.9949  55.7769
 4JK  HA1   H  HOH1  0   0.480  18.5745  -2.2258  59.5005

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
 4JK  CH   CZ    single  1.511  0.020  1.511
 4JK  CH   OH    single  1.397  0.020  1.397
 4JK  CZ   NH    double  1.276  0.020  1.276
 4JK  CZ   NE    single  1.364  0.020  1.364
 4JK  NE   CD    single  1.450  0.020  1.450
 4JK  CD   CG    single  1.521  0.020  1.521
 4JK  CG   CB    single  1.522  0.020  1.522
 4JK  CB   CA    single  1.535  0.020  1.535
 4JK  CA   C     single  1.523  0.020  1.523
 4JK  CA   N     single  1.443  0.020  1.443
 4JK  C    OA2   double  1.206  0.020  1.206
 4JK  C    OA1   single  1.329  0.020  1.329
 4JK  CH   HH1C  single  0.970  0.020  1.090
 4JK  CH   HH2C  single  0.970  0.020  1.090
 4JK  OH   HH    single  0.850  0.020  0.980
 4JK  NH   HA    single  0.890  0.020  1.040
 4JK  CD   HD1   single  0.970  0.020  1.090
 4JK  CD   HD2   single  0.970  0.020  1.090
 4JK  CG   HG1C  single  0.970  0.020  1.090
 4JK  CG   HG2C  single  0.970  0.020  1.090
 4JK  CB   HB1C  single  0.970  0.020  1.090
 4JK  CB   HB2C  single  0.970  0.020  1.090
 4JK  CA   HB    single  0.970  0.020  1.090
 4JK  N    HN1   single  0.890  0.020  1.040
 4JK  N    HN2   single  0.890  0.020  1.040
 4JK  OA1  HA1   single  0.850  0.020  0.980
 4JK  NE   HNE   single  0.890  0.020  1.040

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
 4JK  HH2C  CH   HH1C  106.09  3.000
 4JK  HH2C  CH   OH    111.88  3.000
 4JK  HH1C  CH   OH    111.92  3.000
 4JK  HH2C  CH   CZ    108.55  3.000
 4JK  HH1C  CH   CZ    108.21  3.000
 4JK  OH    CH   CZ    110.01  3.000
 4JK  NE    CZ   NH    125.62  3.000
 4JK  NE    CZ   CH    114.97  3.000
 4JK  NH    CZ   CH    119.38  3.000
 4JK  HA    NH   CZ    110.72  3.000
 4JK  HNE   NE   CD    114.61  3.000
 4JK  HNE   NE   CZ    115.04  3.000
 4JK  CD    NE   CZ    125.55  3.000
 4JK  HD2   CD   HD1   106.91  3.000
 4JK  HD2   CD   CG    108.73  3.000
 4JK  HD1   CD   CG    109.14  3.000
 4JK  HD2   CD   NE    109.60  3.000
 4JK  HD1   CD   NE    111.50  3.000
 4JK  CG    CD   NE    110.84  3.000
 4JK  HG2C  CG   HG1C  106.27  3.000
 4JK  HG2C  CG   CB    109.48  3.000
 4JK  HG1C  CG   CB    110.25  3.000
 4JK  HG2C  CG   CD    107.56  3.000
 4JK  HG1C  CG   CD    109.92  3.000
 4JK  CB    CG   CD    113.10  3.000
 4JK  HB2C  CB   HB1C  106.52  3.000
 4JK  HB2C  CB   CA    108.91  3.000
 4JK  HB1C  CB   CA    109.55  3.000
 4JK  HB2C  CB   CG    110.29  3.000
 4JK  HB1C  CB   CG    109.11  3.000
 4JK  CA    CB   CG    112.29  3.000
 4JK  HB    CA   N     108.26  3.000
 4JK  HB    CA   C     107.15  3.000
 4JK  N     CA   C     113.50  3.000
 4JK  HB    CA   CB    107.88  3.000
 4JK  N     CA   CB    110.58  3.000
 4JK  C     CA   CB    109.26  3.000
 4JK  OA1   C    OA2   123.19  3.000
 4JK  OA1   C    CA    112.15  3.000
 4JK  OA2   C    CA    124.66  3.000
 4JK  HA1   OA1  C     110.13  3.000
 4JK  HN2   N    HN1   106.40  3.000
 4JK  HN2   N    CA    110.11  3.000
 4JK  HN1   N    CA    110.63  3.000
 4JK  HH    OH   CH    107.23  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
 4JK  CONST_03  HA   NH   CZ  CH   180.00   0.0  0
 4JK  CONST_04  HNE  NE   CZ  CH   180.00   0.0  0
 4JK  CONST_05  HA1  OA1  C   CA   180.00   0.0  0
 4JK  Var_01    CG   CD   NE  CZ   164.20  30.0  3
 4JK  Var_02    OH   CH   CZ  NH     1.03  30.0  1
 4JK  Var_03    CB   CG   CD  NE   -62.71  30.0  3
 4JK  Var_04    CA   CB   CG  CD  -175.58  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
 4JK  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
 4JK  plan-1  CH   0.020
 4JK  plan-1  CZ   0.020
 4JK  plan-1  NH   0.020
 4JK  plan-1  NE   0.020
 4JK  plan-1  CD   0.020
 4JK  plan-1  HA   0.020
 4JK  plan-1  HNE  0.020
 4JK  plan-2  CA   0.020
 4JK  plan-2  C    0.020
 4JK  plan-2  OA2  0.020
 4JK  plan-2  OA1  0.020
 4JK  plan-2  HA1  0.020

