# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:19:33 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (5R)-5-hydroxy-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](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
 LYZ  LYZ  '(5R)-5-hydroxy-L-lysine  '  L-peptide  24  11  .  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_LYZ
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
 LYZ  N    N  NH2    0  -0.799  17.7842  47.0967  22.1283
 LYZ  CA   C  CH1    0  -0.204  16.6011  47.8938  22.4146
 LYZ  C    C  C      0   0.401  15.5857  47.8107  21.2487
 LYZ  O    O  O      0  -0.615  14.4029  48.0854  21.5357
 LYZ  CB   C  CH2    0  -0.423  16.8776  49.3768  22.7166
 LYZ  CG   C  CH2    0  -0.446  17.7451  49.6008  23.9495
 LYZ  CD   C  CH1    0   0.060  18.0171  51.0632  24.2589
 LYZ  CE   C  CH2    0  -0.298  19.0265  51.2157  25.3917
 LYZ  NZ   N  NH2    0  -0.814  19.2163  52.6203  25.7339
 LYZ  OH   O  OH1    0  -0.677  16.7885  51.6885  24.5812
 LYZ  OXT  O  OC    -1  -0.603  16.0330  47.5217  20.1206
 LYZ  H    H  HNH2   0   0.332  18.5154  47.2904  22.8010
 LYZ  H2   H  HNH2   0   0.322  18.1431  47.3707  21.2221
 LYZ  HA   H  HCH1   0   0.193  16.1180  47.4693  23.3035
 LYZ  HB2  H  HCH2   0   0.200  17.3604  49.8347  21.8446
 LYZ  HB3  H  HCH2   0   0.214  15.9220  49.8880  22.8500
 LYZ  HG2  H  HCH2   0   0.213  17.2783  49.1279  24.8214
 LYZ  HG3  H  HCH2   0   0.211  18.7161  49.1115  23.8206
 LYZ  HD   H  HCH1   0   0.183  18.4544  51.5333  23.3641
 LYZ  HE2  H  HCH2   0   0.195  18.7115  50.5992  26.2460
 LYZ  HE3  H  HCH2   0   0.220  19.9805  50.8086  25.0494
 LYZ  HZ1  H  HNH2   0   0.351  20.1077  52.7433  26.1944
 LYZ  HZ2  H  HNH2   0   0.342  18.5223  52.9071  26.4114
 LYZ  HH   H  HOH1   0   0.442  16.9475  52.6363  24.6349

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
 LYZ  N   CA   single  1.458  0.019  1.458
 LYZ  N   H    single  0.860  0.020  0.860
 LYZ  N   H2   single  0.890  0.020  1.040
 LYZ  CA  C    single  1.525  0.021  1.525
 LYZ  CA  CB   single  1.530  0.020  1.530
 LYZ  CA  HA   single  0.970  0.020  0.970
 LYZ  C   O    deloc   1.231  0.020  1.231
 LYZ  C   OXT  deloc   1.248  0.020  1.248
 LYZ  CB  CG   single  1.524  0.020  1.524
 LYZ  CB  HB2  single  0.970  0.020  1.090
 LYZ  CB  HB3  single  0.970  0.020  1.090
 LYZ  CG  CD   single  1.519  0.020  1.519
 LYZ  CG  HG2  single  0.970  0.020  1.090
 LYZ  CG  HG3  single  0.970  0.020  1.090
 LYZ  CD  CE   single  1.525  0.020  1.525
 LYZ  CD  OH   single  1.416  0.020  1.416
 LYZ  CD  HD   single  0.970  0.020  1.090
 LYZ  CE  NZ   single  1.458  0.020  1.458
 LYZ  CE  HE2  single  0.970  0.020  1.090
 LYZ  CE  HE3  single  0.970  0.020  1.090
 LYZ  NZ  HZ1  single  0.890  0.020  1.040
 LYZ  NZ  HZ2  single  0.890  0.020  1.040
 LYZ  OH  HH   single  0.850  0.020  0.980

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
 LYZ  H2   N   H    106.67  3.000
 LYZ  H2   N   CA   108.43  3.000
 LYZ  H    N   CA   114.00  3.000
 LYZ  HA   CA  CB   109.00  3.000
 LYZ  HA   CA  C    109.00  3.000
 LYZ  CB   CA  C    110.10  1.900
 LYZ  HA   CA  N    110.00  3.000
 LYZ  CB   CA  N    110.50  1.700
 LYZ  C    CA  N    111.00  2.800
 LYZ  OXT  C   O    126.79  3.000
 LYZ  OXT  C   CA   117.27  3.000
 LYZ  O    C   CA   120.80  1.700
 LYZ  HB3  CB  HB2  106.67  3.000
 LYZ  HB3  CB  CG   109.30  3.000
 LYZ  HB2  CB  CG   109.34  3.000
 LYZ  HB3  CB  CA   108.54  3.000
 LYZ  HB2  CB  CA   108.99  3.000
 LYZ  CG   CB  CA   113.75  3.000
 LYZ  HG3  CG  HG2  106.16  3.000
 LYZ  HG3  CG  CD   107.18  3.000
 LYZ  HG2  CG  CD   109.23  3.000
 LYZ  HG3  CG  CB   110.12  3.000
 LYZ  HG2  CG  CB   109.74  3.000
 LYZ  CD   CG  CB   114.09  3.000
 LYZ  HD   CD  OH   109.94  3.000
 LYZ  HD   CD  CE   107.34  3.000
 LYZ  OH   CD  CE   111.17  3.000
 LYZ  HD   CD  CG   108.45  3.000
 LYZ  OH   CD  CG   108.43  3.000
 LYZ  CE   CD  CG   111.47  3.000
 LYZ  HE3  CE  HE2  106.54  3.000
 LYZ  HE3  CE  NZ   108.59  3.000
 LYZ  HE2  CE  NZ   113.27  3.000
 LYZ  HE3  CE  CD   107.95  3.000
 LYZ  HE2  CE  CD   109.36  3.000
 LYZ  NZ   CE  CD   110.91  3.000
 LYZ  HZ2  NZ  HZ1  105.39  3.000
 LYZ  HZ2  NZ  CE   109.94  3.000
 LYZ  HZ1  NZ  CE   109.81  3.000
 LYZ  HH   OH  CD   107.71  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
 LYZ  Var_01  CD   CG  CB  CA  -179.70  30.0  3
 LYZ  Var_02  HZ1  NZ  CE  CD  -157.74  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
 LYZ  chir_01  CA  N   C   CB  positiv
 LYZ  chir_02  CD  OH  CG  CE  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
 LYZ  plan-1  CA   0.020
 LYZ  plan-1  C    0.020
 LYZ  plan-1  O    0.020
 LYZ  plan-1  OXT  0.020

