# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:14:16 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: N~2~-acetyl-N~5~-carbamoyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](CCCNC(N)=O)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
 OLN  OLN  N~2~-acetyl-N~5~-carbamoyl-L-ornithine  ligand  29  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OLN
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
 OLN  CA    C  CH1    0  -0.189  -0.3952  -0.3571  -1.5601
 OLN  C     C  C      0   0.411  -1.4684  -0.0966  -2.6528
 OLN  O     O  O      0  -0.617  -2.5120  -0.7689  -2.5287
 OLN  OXT   O  OC    -1  -0.594  -1.2138   0.7481  -3.5263
 OLN  CB    C  CH2    0  -0.461  -0.9045   0.0909  -0.1915
 OLN  CG    C  CH2    0  -0.455   0.0079  -0.2974   0.9650
 OLN  CD    C  CH2    0  -0.230  -0.5353   0.2060   2.2931
 OLN  NE    N  NH1    0  -0.662   0.3321  -0.1845   3.3826
 OLN  CZ    C  C      0   0.658  -0.0612  -0.0944   4.6786
 OLN  O2    O  O      0  -0.545  -1.2105   0.1840   5.0055
 OLN  NH2   N  NH2    0  -0.844   0.9258  -0.3139   5.5971
 OLN  N1    N  NH1    0  -0.612   0.8616   0.2941  -1.8437
 OLN  C1    C  C      0   0.523   1.6807  -0.1076  -2.8258
 OLN  O1    O  O      0  -0.522   1.5322  -1.1649  -3.4289
 OLN  C2    C  CH3    0  -0.782   2.8253   0.8257  -3.1380
 OLN  HA    H  HCH1   0   0.233  -0.2166  -1.4358  -1.5219
 OLN  HB1   H  HCH2   0   0.222  -1.0524   1.1776  -0.1988
 OLN  HB2   H  HCH2   0   0.240  -1.8907  -0.3500  -0.0367
 OLN  HG1   H  HCH2   0   0.228   0.1072  -1.3863   1.0021
 OLN  HG2   H  HCH2   0   0.227   1.0136   0.1038   0.8050
 OLN  HD1   H  HCH2   0   0.217  -0.6542   1.2953   2.2497
 OLN  HD2   H  HCH2   0   0.231  -1.5285  -0.2121   2.4642
 OLN  HNE   H  HNH1   0   0.388   1.3205  -0.2092   3.1864
 OLN  HH21  H  HNH2   0   0.391   0.6213  -0.4892   6.5401
 OLN  HH22  H  HNH2   0   0.390   1.7527  -0.8216   5.3276
 OLN  HN1   H  HNH1   0   0.387   0.9830   1.2307  -1.4917
 OLN  H21   H  HCH3   0   0.258   3.7580   0.2655  -3.1873
 OLN  H22   H  HCH3   0   0.262   2.6630   1.2745  -4.1192
 OLN  H23   H  HCH3   0   0.244   2.9400   1.6302  -2.4139

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
 OLN  CA   C     single  1.554  0.020  1.554
 OLN  CA   CB    single  1.527  0.020  1.527
 OLN  CA   N1    single  1.444  0.020  1.444
 OLN  CA   HA    single  0.970  0.020  1.090
 OLN  C    O     deloc   1.248  0.020  1.248
 OLN  C    OXT   deloc   1.242  0.020  1.242
 OLN  CB   CG    single  1.523  0.020  1.523
 OLN  CB   HB1   single  0.970  0.020  1.090
 OLN  CB   HB2   single  0.970  0.020  1.090
 OLN  CG   CD    single  1.521  0.020  1.521
 OLN  CG   HG1   single  0.970  0.020  1.090
 OLN  CG   HG2   single  0.970  0.020  1.090
 OLN  CD   NE    single  1.446  0.020  1.446
 OLN  CD   HD1   single  0.970  0.020  1.090
 OLN  CD   HD2   single  0.970  0.020  1.090
 OLN  NE   CZ    single  1.357  0.020  1.357
 OLN  NE   HNE   single  0.890  0.020  1.040
 OLN  CZ   O2    double  1.227  0.020  1.227
 OLN  CZ   NH2   single  1.366  0.020  1.366
 OLN  NH2  HH21  single  0.890  0.020  1.040
 OLN  NH2  HH22  single  0.890  0.020  1.040
 OLN  N1   C1    single  1.340  0.020  1.340
 OLN  N1   HN1   single  0.860  0.020  1.020
 OLN  C1   O1    double  1.226  0.020  1.226
 OLN  C1   C2    single  1.510  0.020  1.510
 OLN  C2   H21   single  0.970  0.020  1.090
 OLN  C2   H22   single  0.970  0.020  1.090
 OLN  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
 OLN  HA    CA   N1    108.03  3.000
 OLN  HA    CA   CB    108.20  3.000
 OLN  N1    CA   CB    109.51  3.000
 OLN  HA    CA   C     107.62  3.000
 OLN  N1    CA   C     112.81  3.000
 OLN  CB    CA   C     110.53  3.000
 OLN  OXT   C    O     127.46  3.000
 OLN  OXT   C    CA    117.86  3.000
 OLN  O     C    CA    114.68  3.000
 OLN  HB2   CB   HB1   106.22  3.000
 OLN  HB2   CB   CG    109.31  3.000
 OLN  HB1   CB   CG    109.77  3.000
 OLN  HB2   CB   CA    108.05  3.000
 OLN  HB1   CB   CA    109.24  3.000
 OLN  CG    CB   CA    113.94  3.000
 OLN  HG2   CG   HG1   106.64  3.000
 OLN  HG2   CG   CD    109.55  3.000
 OLN  HG1   CG   CD    109.41  3.000
 OLN  HG2   CG   CB    110.24  3.000
 OLN  HG1   CG   CB    109.50  3.000
 OLN  CD    CG   CB    111.39  3.000
 OLN  HD2   CD   HD1   106.74  3.000
 OLN  HD2   CD   NE    108.92  3.000
 OLN  HD1   CD   NE    111.29  3.000
 OLN  HD2   CD   CG    109.59  3.000
 OLN  HD1   CD   CG    109.45  3.000
 OLN  NE    CD   CG    110.75  3.000
 OLN  HNE   NE   CZ    118.14  3.000
 OLN  HNE   NE   CD    116.62  3.000
 OLN  CZ    NE   CD    121.84  3.000
 OLN  NH2   CZ   O2    122.29  3.000
 OLN  NH2   CZ   NE    114.96  3.000
 OLN  O2    CZ   NE    122.75  3.000
 OLN  HH22  NH2  HH21  114.29  3.000
 OLN  HH22  NH2  CZ    119.63  3.000
 OLN  HH21  NH2  CZ    116.07  3.000
 OLN  HN1   N1   C1    117.44  3.000
 OLN  HN1   N1   CA    117.09  3.000
 OLN  C1    N1   CA    122.73  3.000
 OLN  C2    C1   O1    121.55  3.000
 OLN  C2    C1   N1    115.44  3.000
 OLN  O1    C1   N1    123.01  3.000
 OLN  H23   C2   H22   108.06  3.000
 OLN  H23   C2   H21   108.67  3.000
 OLN  H22   C2   H21   107.36  3.000
 OLN  H23   C2   C1    113.53  3.000
 OLN  H22   C2   C1    109.12  3.000
 OLN  H21   C2   C1    109.91  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
 OLN  CONST_01  O1   C1  N1  CA     0.00   0.0  0
 OLN  CONST_02  C2   C1  N1  CA   180.00   0.0  0
 OLN  CONST_03  O2   CZ  NE  CD     0.00   0.0  0
 OLN  CONST_04  NH2  CZ  NE  CD   180.00   0.0  0
 OLN  CONST_05  HNE  NE  CZ  O2   180.00   0.0  0
 OLN  CONST_08  HN1  N1  C1  O1   180.00   0.0  0
 OLN  Var_01    CD   CG  CB  CA   178.58  30.0  3
 OLN  Var_02    NE   CD  CG  CB   179.28  30.0  3
 OLN  Var_03    CZ   NE  CD  CG  -166.50  30.0  3
 OLN  Var_04    H21  C2  C1  N1   131.65  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
 OLN  chir_01  CA  C  CB  N1  positiv

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
 OLN  plan-1  CD    0.020
 OLN  plan-1  NE    0.020
 OLN  plan-1  CZ    0.020
 OLN  plan-1  O2    0.020
 OLN  plan-1  NH2   0.020
 OLN  plan-1  HNE   0.020
 OLN  plan-1  HH21  0.020
 OLN  plan-1  HH22  0.020
 OLN  plan-2  CA    0.020
 OLN  plan-2  N1    0.020
 OLN  plan-2  C1    0.020
 OLN  plan-2  O1    0.020
 OLN  plan-2  C2    0.020
 OLN  plan-2  HN1   0.020
 OLN  plan-3  CA    0.020
 OLN  plan-3  C     0.020
 OLN  plan-3  O     0.020
 OLN  plan-3  OXT   0.020

