# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 14:42:03 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: N~5~-acetyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)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
 ORQ  ORQ  'N~5~-acetyl-L-ornithine  '  L-peptide  25  12  .  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_ORQ
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
 ORQ  N    N  NH2    0  -0.794  22.4599  23.7639  40.7633
 ORQ  CA   C  CH1    0  -0.184  23.6776  23.6937  41.5694
 ORQ  CB   C  CH2    0  -0.422  24.8271  24.2920  40.7562
 ORQ  CG   C  CH2    0  -0.432  26.1841  24.2344  41.4434
 ORQ  CD   C  CH2    0  -0.300  27.3285  24.7418  40.5719
 ORQ  NE   N  NH1    0  -0.596  27.5870  23.9096  39.4161
 ORQ  O1   O  O      0  -0.498  27.5734  23.3389  37.2473
 ORQ  C    C  C      0   0.384  23.5730  24.4072  42.9379
 ORQ  O    O  O      0  -0.613  24.0319  23.8084  43.9321
 ORQ  C1   C  C      0   0.487  27.3185  24.1599  38.1200
 ORQ  C2   C  CH3    0  -0.805  26.7090  25.5013  37.7883
 ORQ  OXT  O  OC    -1  -0.611  23.0565  25.5454  42.9225
 ORQ  H    H  HNH2   0   0.321  22.1623  24.7340  40.7513
 ORQ  H2   H  HNH2   0   0.333  21.7168  23.2742  41.2486
 ORQ  HA   H  HCH1   0   0.194  23.9006  22.6350  41.7393
 ORQ  HB2  H  HCH2   0   0.204  24.5877  25.3357  40.5200
 ORQ  HB3  H  HCH2   0   0.215  24.8735  23.7617  39.8002
 ORQ  HG2  H  HCH2   0   0.216  26.4009  23.2098  41.7623
 ORQ  HG3  H  HCH2   0   0.228  26.1764  24.8408  42.3524
 ORQ  HD2  H  HCH2   0   0.253  28.2430  24.7897  41.1670
 ORQ  HD3  H  HCH2   0   0.248  27.1237  25.7607  40.2448
 ORQ  HE   H  HNH1   0   0.383  27.9836  23.0001  39.6050
 ORQ  H21  H  HCH3   0   0.263  26.5094  25.5504  36.7211
 ORQ  H22  H  HCH3   0   0.263  27.3824  26.3190  38.0500
 ORQ  H23  H  HCH3   0   0.264  25.7748  25.6685  38.3247

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
 ORQ  N   CA   single  1.458  0.019  1.458
 ORQ  N   H    single  0.860  0.020  0.860
 ORQ  N   H2   single  0.890  0.020  1.040
 ORQ  CA  CB   single  1.530  0.020  1.530
 ORQ  CA  C    single  1.525  0.021  1.525
 ORQ  CA  HA   single  0.970  0.020  0.970
 ORQ  CB  CG   single  1.522  0.020  1.522
 ORQ  CB  HB2  single  0.970  0.020  1.090
 ORQ  CB  HB3  single  0.970  0.020  1.090
 ORQ  CG  CD   single  1.525  0.020  1.525
 ORQ  CG  HG2  single  0.970  0.020  1.090
 ORQ  CG  HG3  single  0.970  0.020  1.090
 ORQ  CD  NE   single  1.448  0.020  1.448
 ORQ  CD  HD2  single  0.970  0.020  1.090
 ORQ  CD  HD3  single  0.970  0.020  1.090
 ORQ  NE  C1   single  1.347  0.020  1.347
 ORQ  NE  HE   single  0.860  0.020  1.020
 ORQ  O1  C1   double  1.225  0.020  1.225
 ORQ  C   O    deloc   1.231  0.020  1.231
 ORQ  C   OXT  deloc   1.250  0.020  1.250
 ORQ  C1  C2   single  1.510  0.020  1.510
 ORQ  C2  H21  single  0.970  0.020  1.090
 ORQ  C2  H22  single  0.970  0.020  1.090
 ORQ  C2  H23  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
 ORQ  H2   N   H    104.63  3.000
 ORQ  H2   N   CA   108.86  3.000
 ORQ  H    N   CA   114.00  3.000
 ORQ  HA   CA  C    109.00  3.000
 ORQ  HA   CA  CB   109.00  3.000
 ORQ  C    CA  CB   110.10  1.900
 ORQ  HA   CA  N    110.00  3.000
 ORQ  C    CA  N    111.00  2.800
 ORQ  CB   CA  N    110.50  1.700
 ORQ  HB3  CB  HB2  106.40  3.000
 ORQ  HB3  CB  CG   109.78  3.000
 ORQ  HB2  CB  CG   109.15  3.000
 ORQ  HB3  CB  CA   107.86  3.000
 ORQ  HB2  CB  CA   108.82  3.000
 ORQ  CG   CB  CA   114.52  3.000
 ORQ  HG3  CG  HG2  106.16  3.000
 ORQ  HG3  CG  CD   107.21  3.000
 ORQ  HG2  CG  CD   109.22  3.000
 ORQ  HG3  CG  CB   110.38  3.000
 ORQ  HG2  CG  CB   110.09  3.000
 ORQ  CD   CG  CB   113.47  3.000
 ORQ  HD3  CD  HD2  106.26  3.000
 ORQ  HD3  CD  NE   109.36  3.000
 ORQ  HD2  CD  NE   108.11  3.000
 ORQ  HD3  CD  CG   109.98  3.000
 ORQ  HD2  CD  CG   109.36  3.000
 ORQ  NE   CD  CG   113.51  3.000
 ORQ  HE   NE  C1   115.18  3.000
 ORQ  HE   NE  CD   116.01  3.000
 ORQ  C1   NE  CD   128.74  3.000
 ORQ  OXT  C   O    126.77  3.000
 ORQ  OXT  C   CA   115.92  3.000
 ORQ  O    C   CA   120.80  1.700
 ORQ  C2   C1  O1   121.52  3.000
 ORQ  C2   C1  NE   117.18  3.000
 ORQ  O1   C1  NE   121.29  3.000
 ORQ  H23  C2  H22  107.21  3.000
 ORQ  H23  C2  H21  108.59  3.000
 ORQ  H22  C2  H21  108.36  3.000
 ORQ  H23  C2  C1   111.96  3.000
 ORQ  H22  C2  C1   111.34  3.000
 ORQ  H21  C2  C1   109.27  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
 ORQ  CONST_01  O1   C1  NE  CD   180.00   0.0  0
 ORQ  CONST_02  C2   C1  NE  CD     0.00   0.0  0
 ORQ  CONST_03  HE   NE  C1  O1     0.00   0.0  0
 ORQ  Var_01    CD   CG  CB  CA   175.72  30.0  3
 ORQ  Var_02    NE   CD  CG  CB   -66.28  30.0  3
 ORQ  Var_03    C1   NE  CD  CG   107.27  30.0  3
 ORQ  Var_04    H21  C2  C1  NE  -177.70  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
 ORQ  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
 ORQ  plan-1  CD   0.020
 ORQ  plan-1  NE   0.020
 ORQ  plan-1  O1   0.020
 ORQ  plan-1  C1   0.020
 ORQ  plan-1  C2   0.020
 ORQ  plan-1  HE   0.020
 ORQ  plan-2  CA   0.020
 ORQ  plan-2  C    0.020
 ORQ  plan-2  O    0.020
 ORQ  plan-2  OXT  0.020

