# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:20:12 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (4S)-4-hydroxy-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@H](O)C[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
 LYO  LYO  '(4S)-4-hydroxy-L-lysine  '  L-peptide  24  11  .  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_LYO
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
 LYO  N    N  NH2    0  -0.814  61.3278  -136.2615  37.6816
 LYO  CA   C  CH1    0  -0.208  60.8345  -136.3943  39.0489
 LYO  C    C  C      0   0.424  61.9253  -135.9179  40.0433
 LYO  O    O  O      0  -0.601  62.7090  -135.0427  39.6270
 LYO  CB   C  CH2    0  -0.432  60.3852  -137.8374  39.2886
 LYO  CG   C  CH1    0   0.040  59.3135  -137.9965  40.3567
 LYO  OG   O  OH1    0  -0.680  58.0839  -137.5740  39.7772
 LYO  CD   C  CH2    0  -0.448  59.1915  -139.4279  40.8802
 LYO  CE   C  CH2    0  -0.304  60.4387  -139.9649  41.5750
 LYO  NZ   N  NH2    0  -0.826  60.8636  -139.0987  42.6665
 LYO  OXT  O  OC    -1  -0.590  61.9205  -136.4067  41.1941
 LYO  H    H  HNH2   0   0.326  60.5437  -136.2550  37.0414
 LYO  H2   H  HNH2   0   0.330  61.7822  -135.3618  37.5966
 LYO  HA   H  HCH1   0   0.200  59.9651  -135.7372  39.2296
 LYO  HB1  H  HCH2   0   0.209  59.9812  -138.2502  38.3571
 LYO  HB2  H  HCH2   0   0.223  61.2559  -138.4494  39.5312
 LYO  HG   H  HCH1   0   0.195  59.5604  -137.3409  41.1982
 LYO  HOG  H  HOH1   0   0.439  57.4352  -137.4979  40.4832
 LYO  HD1  H  HCH2   0   0.212  58.3553  -139.4660  41.5876
 LYO  HD2  H  HCH2   0   0.209  58.9330  -140.0957  40.0515
 LYO  HE1  H  HCH2   0   0.220  60.2014  -140.9486  41.9875
 LYO  HE2  H  HCH2   0   0.188  61.2247  -140.1378  40.8263
 LYO  HZ1  H  HNH2   0   0.337  61.6194  -139.5465  43.1690
 LYO  HZ2  H  HNH2   0   0.352  61.2547  -138.2455  42.2792

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
 LYO  N   CA   single  1.458  0.019  1.458
 LYO  CA  C    single  1.525  0.021  1.525
 LYO  CA  CB   single  1.530  0.020  1.530
 LYO  C   O    deloc   1.231  0.020  1.231
 LYO  CB  CG   single  1.521  0.020  1.521
 LYO  CG  OG   single  1.423  0.020  1.423
 LYO  CG  CD   single  1.529  0.020  1.529
 LYO  CD  CE   single  1.525  0.020  1.525
 LYO  CE  NZ   single  1.457  0.020  1.457
 LYO  C   OXT  deloc   1.250  0.020  1.250
 LYO  N   H    single  0.860  0.020  0.860
 LYO  N   H2   single  0.890  0.020  1.040
 LYO  CA  HA   single  0.970  0.020  0.970
 LYO  CB  HB1  single  0.970  0.020  1.090
 LYO  CB  HB2  single  0.970  0.020  1.090
 LYO  CG  HG   single  0.970  0.020  1.090
 LYO  OG  HOG  single  0.850  0.020  0.980
 LYO  CD  HD1  single  0.970  0.020  1.090
 LYO  CD  HD2  single  0.970  0.020  1.090
 LYO  CE  HE1  single  0.970  0.020  1.090
 LYO  CE  HE2  single  0.970  0.020  1.090
 LYO  NZ  HZ1  single  0.890  0.020  1.040
 LYO  NZ  HZ2  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
 LYO  H2   N   H    106.80  3.000
 LYO  H2   N   CA   108.15  3.000
 LYO  H    N   CA   114.00  3.000
 LYO  HA   CA  CB   109.00  3.000
 LYO  HA   CA  C    109.00  3.000
 LYO  CB   CA  C    110.10  1.900
 LYO  HA   CA  N    110.00  3.000
 LYO  CB   CA  N    110.50  1.700
 LYO  C    CA  N    111.00  2.800
 LYO  OXT  C   O    125.75  3.000
 LYO  OXT  C   CA   117.86  3.000
 LYO  O    C   CA   120.80  1.700
 LYO  HB2  CB  HB1  105.76  3.000
 LYO  HB2  CB  CG   110.32  3.000
 LYO  HB1  CB  CG   107.32  3.000
 LYO  HB2  CB  CA   109.23  3.000
 LYO  HB1  CB  CA   109.28  3.000
 LYO  CG   CB  CA   114.54  3.000
 LYO  HG   CG  CD   108.38  3.000
 LYO  HG   CG  OG   109.26  3.000
 LYO  CD   CG  OG   110.38  3.000
 LYO  HG   CG  CB   108.55  3.000
 LYO  CD   CG  CB   113.23  3.000
 LYO  OG   CG  CB   106.96  3.000
 LYO  HOG  OG  CG   107.89  3.000
 LYO  HD2  CD  HD1  106.68  3.000
 LYO  HD2  CD  CE   108.85  3.000
 LYO  HD1  CD  CE   108.52  3.000
 LYO  HD2  CD  CG   109.30  3.000
 LYO  HD1  CD  CG   108.33  3.000
 LYO  CE   CD  CG   114.85  3.000
 LYO  HE2  CE  HE1  105.71  3.000
 LYO  HE2  CE  NZ   113.29  3.000
 LYO  HE1  CE  NZ   108.41  3.000
 LYO  HE2  CE  CD   109.25  3.000
 LYO  HE1  CE  CD   108.14  3.000
 LYO  NZ   CE  CD   111.74  3.000
 LYO  HZ2  NZ  HZ1  105.87  3.000
 LYO  HZ2  NZ  CE   109.04  3.000
 LYO  HZ1  NZ  CE   109.08  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
 LYO  Var_01  NZ   CE  CD  CG   55.36  30.0  3
 LYO  Var_02  HZ1  NZ  CE  CD  173.10  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
 LYO  chir_01  CA  N   C   CB  positiv
 LYO  chir_02  CG  OG  CD  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
 LYO  plan-1  CA   0.020
 LYO  plan-1  C    0.020
 LYO  plan-1  O    0.020
 LYO  plan-1  OXT  0.020

