# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:07:59 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: N~5~-hydroxy-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNO)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
 ONH  ONH  'N~5~-hydroxy-L-ornithine '  L-peptide  21  10  .  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_ONH
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
 ONH  C    C  C      0   0.411  100.5336  39.9425  132.9744
 ONH  N    N  NH2    0  -0.817  100.8157  37.5036  133.3375
 ONH  O    O  O      0  -0.601   99.4890  39.6157  132.3749
 ONH  CA   C  CH1    0  -0.217  101.2974  38.8213  133.7298
 ONH  CB   C  CH2    0  -0.390  102.8068  38.9223  133.5164
 ONH  CD   C  CH2    0  -0.254  105.0968  38.0429  134.1202
 ONH  NE   N  NH1    0  -0.370  105.8002  37.0101  134.8626
 ONH  CG   C  CH2    0  -0.461  103.5954  37.8835  134.3046
 ONH  OZ   O  OH1    0  -0.590  107.1881  37.2567  134.7931
 ONH  OXT  O  OC    -1  -0.606  101.0122  41.0904  133.0604
 ONH  HN   H  HNH2   0   0.329  100.8796  36.8615  134.1157
 ONH  HNA  H  HNH2   0   0.333   99.8352  37.5905  133.1036
 ONH  HA   H  HCH1   0   0.191  101.1136  39.0155  134.8016
 ONH  HB   H  HCH2   0   0.197  103.0272  38.8092  132.4489
 ONH  HBA  H  HCH2   0   0.205  103.1403  39.9215  133.8028
 ONH  HD   H  HCH2   0   0.214  105.3495  37.9343  133.0616
 ONH  HDA  H  HCH2   0   0.194  105.4003  39.0554  134.4223
 ONH  HG   H  HCH2   0   0.210  103.3463  37.9733  135.3691
 ONH  HGA  H  HCH2   0   0.218  103.3017  36.8764  133.9973
 ONH  HOZ  H  HOH1   0   0.454  107.5421  36.4701  134.3681
 ONH  HNE  H  HNH1   0   0.347  105.5723  37.1188  135.8463

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
 ONH  O   C    deloc   1.231  0.020  1.231
 ONH  C   OXT  deloc   1.247  0.020  1.247
 ONH  C   CA   single  1.525  0.021  1.525
 ONH  N   CA   single  1.458  0.019  1.458
 ONH  N   HN   single  0.890  0.020  1.040
 ONH  N   HNA  single  0.890  0.020  1.040
 ONH  CB  CA   single  1.521  0.033  1.521
 ONH  CA  HA   single  0.970  0.020  0.970
 ONH  CB  CG   single  1.524  0.020  1.524
 ONH  CB  HB   single  0.970  0.020  1.090
 ONH  CB  HBA  single  0.970  0.020  1.090
 ONH  CD  CG   single  1.521  0.020  1.521
 ONH  CD  NE   single  1.453  0.020  1.453
 ONH  CD  HD   single  0.970  0.020  1.090
 ONH  CD  HDA  single  0.970  0.020  1.090
 ONH  OZ  NE   single  1.411  0.020  1.411
 ONH  CG  HG   single  0.970  0.020  1.090
 ONH  CG  HGA  single  0.970  0.020  1.090
 ONH  OZ  HOZ  single  0.850  0.020  0.980
 ONH  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
 ONH  OXT  C   CA  116.26  3.000
 ONH  CA   C   O   120.80  1.700
 ONH  OXT  C   O   126.56  3.000
 ONH  HNA  N   HN  107.08  3.000
 ONH  HNA  N   CA  107.76  3.000
 ONH  HN   N   CA  110.26  3.000
 ONH  HA   CA  CB  109.00  3.000
 ONH  HA   CA  N   110.00  3.000
 ONH  CB   CA  N   110.40  1.500
 ONH  HA   CA  C   109.00  3.000
 ONH  CB   CA  C   110.50  1.500
 ONH  N    CA  C   111.00  2.800
 ONH  HBA  CB  HB  106.78  3.000
 ONH  HBA  CB  CG  109.28  3.000
 ONH  HB   CB  CG  109.23  3.000
 ONH  HBA  CB  CA  109.01  3.000
 ONH  HB   CB  CA  109.14  3.000
 ONH  CG   CB  CA  113.20  3.000
 ONH  HDA  CD  HD  107.08  3.000
 ONH  HDA  CD  CG  109.61  3.000
 ONH  HD   CD  CG  109.58  3.000
 ONH  HDA  CD  NE  112.36  3.000
 ONH  HD   CD  NE  108.18  3.000
 ONH  CG   CD  NE  109.95  3.000
 ONH  HNE  NE  OZ  104.45  3.000
 ONH  HNE  NE  CD  108.07  3.000
 ONH  OZ   NE  CD  109.06  3.000
 ONH  HGA  CG  HG  106.69  3.000
 ONH  HGA  CG  CD  109.13  3.000
 ONH  HG   CG  CD  109.47  3.000
 ONH  HGA  CG  CB  110.09  3.000
 ONH  HG   CG  CB  109.18  3.000
 ONH  CD   CG  CB  112.12  3.000
 ONH  HOZ  OZ  NE  103.94  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
 ONH  Var_01  CD  CG  CB  CA  -177.61  30.0  3
 ONH  Var_02  NE  CD  CG  CB  -178.54  30.0  1
 ONH  Var_03  OZ  NE  CD  CG  -173.96  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
 ONH  chir_01  CA  C  N  CB  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
 ONH  plan-1  C    0.020
 ONH  plan-1  O    0.020
 ONH  plan-1  CA   0.020
 ONH  plan-1  OXT  0.020

