# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 11:05:10 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 5-oxo-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CC[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
 ONL  ONL  '5-oxo-L-norleucine       '  L-peptide  20  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_ONL
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
 ONL  N    N  NH2    0  -0.801  76.9438  15.7954  32.0238
 ONL  CA   C  CH1    0  -0.223  75.5311  15.9876  32.3354
 ONL  C    C  C      0   0.385  74.7068  16.6949  31.2272
 ONL  O    O  O      0  -0.612  73.4660  16.6321  31.3473
 ONL  OXT  O  OC    -1  -0.602  75.3414  17.2874  30.3303
 ONL  CB   C  CH2    0  -0.401  75.3782  16.7434  33.6619
 ONL  CG   C  CH2    0  -0.569  76.0088  18.1262  33.6357
 ONL  CD   C  C      0   0.391  75.9457  18.8817  34.9378
 ONL  OD   O  O      0  -0.404  75.3464  18.4676  35.9053
 ONL  CE   C  CH3    0  -0.765  76.6935  20.1891  34.9640
 ONL  HN1  H  HNH2   0   0.334  77.0363  14.9843  31.4245
 ONL  HN2  H  HNH2   0   0.326  77.2290  16.5714  31.4364
 ONL  HA   H  HCH1   0   0.218  75.0877  14.9988  32.4924
 ONL  HB1  H  HCH2   0   0.215  74.3182  16.8192  33.9100
 ONL  HB2  H  HCH2   0   0.215  75.8439  16.1512  34.4540
 ONL  HG1  H  HCH2   0   0.255  77.0621  18.0661  33.3404
 ONL  HG2  H  HCH2   0   0.264  75.5421  18.7644  32.8760
 ONL  HE1  H  HCH3   0   0.254  76.4502  20.7742  35.8484
 ONL  HE2  H  HCH3   0   0.264  77.7673  19.9866  34.9628
 ONL  HE3  H  HCH3   0   0.255  76.4872  20.7775  34.0691

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
 ONL  N   CA   single  1.458  0.019  1.458
 ONL  N   HN1  single  0.890  0.020  1.040
 ONL  N   HN2  single  0.890  0.020  1.040
 ONL  CA  C    single  1.525  0.021  1.525
 ONL  CA  CB   single  1.521  0.033  1.521
 ONL  CA  HA   single  0.970  0.020  0.970
 ONL  C   O    deloc   1.231  0.020  1.231
 ONL  C   OXT  deloc   1.248  0.020  1.248
 ONL  CB  CG   single  1.520  0.020  1.520
 ONL  CB  HB1  single  0.970  0.020  1.090
 ONL  CB  HB2  single  0.970  0.020  1.090
 ONL  CG  CD   single  1.507  0.020  1.507
 ONL  CG  HG1  single  0.970  0.020  1.090
 ONL  CG  HG2  single  0.970  0.020  1.090
 ONL  CD  OD   double  1.211  0.020  1.211
 ONL  CD  CE   single  1.506  0.020  1.506
 ONL  CE  HE1  single  0.970  0.020  1.090
 ONL  CE  HE2  single  0.970  0.020  1.090
 ONL  CE  HE3  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
 ONL  HN2  N   HN1  104.15  3.000
 ONL  HN2  N   CA   107.16  3.000
 ONL  HN1  N   CA   108.67  3.000
 ONL  HA   CA  CB   109.00  3.000
 ONL  HA   CA  C    110.00  3.000
 ONL  CB   CA  C    110.50  1.500
 ONL  HA   CA  N    110.00  3.000
 ONL  CB   CA  N    110.40  1.500
 ONL  C    CA  N    111.00  2.800
 ONL  OXT  C   O    126.75  3.000
 ONL  OXT  C   CA   120.80  1.700
 ONL  O    C   CA   120.80  1.700
 ONL  HB2  CB  HB1  106.67  3.000
 ONL  HB2  CB  CG   109.18  3.000
 ONL  HB1  CB  CG   110.10  3.000
 ONL  HB2  CB  CA   108.49  3.000
 ONL  HB1  CB  CA   109.12  3.000
 ONL  CG   CB  CA   113.07  3.000
 ONL  HG2  CG  HG1  104.73  3.000
 ONL  HG2  CG  CD   106.80  3.000
 ONL  HG1  CG  CD   107.50  3.000
 ONL  HG2  CG  CB   111.40  3.000
 ONL  HG1  CG  CB   110.71  3.000
 ONL  CD   CG  CB   115.08  3.000
 ONL  CE   CD  OD   121.91  3.000
 ONL  CE   CD  CG   115.43  3.000
 ONL  OD   CD  CG   122.66  3.000
 ONL  HE3  CE  HE2  106.56  3.000
 ONL  HE3  CE  HE1  109.54  3.000
 ONL  HE2  CE  HE1  108.68  3.000
 ONL  HE3  CE  CD   111.11  3.000
 ONL  HE2  CE  CD   109.09  3.000
 ONL  HE1  CE  CD   111.71  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
 ONL  Var_01  CD   CG  CB  CA  -177.06  30.0  3
 ONL  Var_02  OD   CD  CG  CB    -5.60  30.0  3
 ONL  Var_03  HE1  CE  CD  CG   168.66  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
 ONL  chir_01  CA  N  C  CB  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
 ONL  plan-1  CG   0.020
 ONL  plan-1  CD   0.020
 ONL  plan-1  OD   0.020
 ONL  plan-1  CE   0.020
 ONL  plan-2  CA   0.020
 ONL  plan-2  C    0.020
 ONL  plan-2  O    0.020
 ONL  plan-2  OXT  0.020

