# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 12:47:44 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 ORN  ORN  'L-ornithine              '  L-peptide  20  9  .  2016-04-26  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_ORN
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
 ORN  N    N  NH2    0  -0.795  60.2250  198.2688  50.6203
 ORN  CA   C  CH1    0  -0.218  59.0444  198.2639  49.7627
 ORN  CB   C  CH2    0  -0.404  58.2486  196.9695  49.9665
 ORN  CG   C  CH2    0  -0.440  57.6494  196.8070  51.3591
 ORN  CD   C  CH2    0  -0.267  56.8907  195.4979  51.5124
 ORN  NE   N  NH2    0  -0.797  56.3044  195.3819  52.8414
 ORN  C    C  C      0   0.382  58.1012  199.4854  49.9190
 ORN  O    O  O      0  -0.605  58.2546  200.2036  50.9279
 ORN  OXT  O  OC    -1  -0.616  57.2420  199.6250  49.0238
 ORN  H    H  HNH2   0   0.331  60.8489  199.0004  50.3014
 ORN  H2   H  HNH2   0   0.324  59.9362  198.5806  51.5406
 ORN  HA   H  HCH1   0   0.211  59.3998  198.2523  48.7263
 ORN  HB2  H  HCH2   0   0.205  57.4475  196.9279  49.2239
 ORN  HB3  H  HCH2   0   0.203  58.9095  196.1215  49.7598
 ORN  HG2  H  HCH2   0   0.206  58.4436  196.8476  52.1125
 ORN  HG3  H  HCH2   0   0.213  56.9671  197.6324  51.5811
 ORN  HD2  H  HCH2   0   0.207  56.0780  195.4702  50.7804
 ORN  HD3  H  HCH2   0   0.183  57.5614  194.6647  51.2549
 ORN  HE1  H  HNH2   0   0.342  55.7828  194.5167  52.9050
 ORN  HE2  H  HNH2   0   0.334  57.0466  195.2998  53.5258

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
 ORN  N   CA   single  1.458  0.019  1.458
 ORN  N   H    single  0.860  0.020  0.860
 ORN  N   H2   single  0.890  0.020  1.040
 ORN  CA  CB   single  1.521  0.033  1.521
 ORN  CA  C    single  1.525  0.021  1.525
 ORN  CA  HA   single  0.970  0.020  0.970
 ORN  CB  CG   single  1.525  0.020  1.525
 ORN  CB  HB2  single  0.970  0.020  1.090
 ORN  CB  HB3  single  0.970  0.020  1.090
 ORN  CG  CD   single  1.521  0.020  1.521
 ORN  CG  HG2  single  0.970  0.020  1.090
 ORN  CG  HG3  single  0.970  0.020  1.090
 ORN  CD  NE   single  1.457  0.020  1.457
 ORN  CD  HD2  single  0.970  0.020  1.090
 ORN  CD  HD3  single  0.970  0.020  1.090
 ORN  NE  HE1  single  0.890  0.020  1.040
 ORN  NE  HE2  single  0.890  0.020  1.040
 ORN  C   O    deloc   1.231  0.020  1.231
 ORN  C   OXT  deloc   1.249  0.020  1.249

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
 ORN  H2   N   H    103.83  3.000
 ORN  H2   N   CA   107.71  3.000
 ORN  H    N   CA   114.00  3.000
 ORN  HA   CA  C    109.00  3.000
 ORN  HA   CA  CB   109.00  3.000
 ORN  C    CA  CB   110.50  1.500
 ORN  HA   CA  N    110.00  3.000
 ORN  C    CA  N    111.00  2.800
 ORN  CB   CA  N    110.40  1.500
 ORN  HB3  CB  HB2  106.54  3.000
 ORN  HB3  CB  CG   109.09  3.000
 ORN  HB2  CB  CG   109.17  3.000
 ORN  HB3  CB  CA   108.39  3.000
 ORN  HB2  CB  CA   108.80  3.000
 ORN  CG   CB  CA   114.55  3.000
 ORN  HG3  CG  HG2  106.54  3.000
 ORN  HG3  CG  CD   108.54  3.000
 ORN  HG2  CG  CD   108.92  3.000
 ORN  HG3  CG  CB   110.50  3.000
 ORN  HG2  CG  CB   109.84  3.000
 ORN  CD   CG  CB   112.33  3.000
 ORN  HD3  CD  HD2  106.08  3.000
 ORN  HD3  CD  NE   113.48  3.000
 ORN  HD2  CD  NE   108.01  3.000
 ORN  HD3  CD  CG   108.92  3.000
 ORN  HD2  CD  CG   108.96  3.000
 ORN  NE   CD  CG   111.18  3.000
 ORN  HE2  NE  HE1  105.42  3.000
 ORN  HE2  NE  CD   109.14  3.000
 ORN  HE1  NE  CD   109.44  3.000
 ORN  OXT  C   O    126.86  3.000
 ORN  OXT  C   CA   115.74  3.000
 ORN  O    C   CA   120.80  1.700

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
 ORN  Var_01  CD   CG  CB  CA  -179.09  30.0  3
 ORN  Var_02  NE   CD  CG  CB  -178.74  30.0  3
 ORN  Var_03  HE1  NE  CD  CG   178.24  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
 ORN  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
 ORN  plan-1  CA   0.020
 ORN  plan-1  C    0.020
 ORN  plan-1  O    0.020
 ORN  plan-1  OXT  0.020

