# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:51:35 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (2S,3E)-2,6-diaminohex-3-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC/C=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
 LYH  LYH  '(2S,3E)-2,6-diaminohex-3-enoic acid'  L-peptide  21  10  .  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
;

data_comp_LYH
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
 LYH  N    N  NH2    0  -0.807  62.1305  -136.1685  38.0396
 LYH  CA   C  CH1    0  -0.252  61.5111  -135.4938  39.1631
 LYH  C    C  C      0   0.414  62.5744  -135.0239  40.2043
 LYH  O    O  O      0  -0.595  63.7655  -135.0616  39.8452
 LYH  CB   C  C1     0  -0.210  60.4667  -136.3429  39.8278
 LYH  CG   C  C1     0  -0.229  60.2026  -137.6183  39.5562
 LYH  CD   C  CH2    0  -0.478  59.1727  -138.4421  40.2661
 LYH  CE   C  CH2    0  -0.282  59.8036  -139.5313  41.1320
 LYH  NZ   N  NH2    0  -0.796  60.5535  -138.9423  42.2304
 LYH  OXT  O  OC    -1  -0.602  62.1272  -134.6189  41.2933
 LYH  H    H  HNH2   0   0.331  61.5359  -136.1027  37.2241
 LYH  H2   H  HNH2   0   0.336  62.9965  -135.6952  37.8215
 LYH  HA   H  HCH1   0   0.205  61.0001  -134.5619  38.8580
 LYH  HB   H  H      0   0.216  59.8819  -135.8421  40.5937
 LYH  HG   H  H      0   0.219  60.7870  -138.1278  38.7945
 LYH  HD1  H  HCH2   0   0.221  58.5441  -137.8065  40.8958
 LYH  HD2  H  HCH2   0   0.225  58.5131  -138.9235  39.5374
 LYH  HE1  H  HCH2   0   0.217  59.0098  -140.1550  41.5507
 LYH  HE2  H  HCH2   0   0.187  60.4049  -140.1886  40.4869
 LYH  HZ1  H  HNH2   0   0.342  61.0162  -139.6723  42.7567
 LYH  HZ2  H  HNH2   0   0.338  61.2929  -138.3611  41.8535

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
 LYH  N   CA   single  1.458  0.019  1.458
 LYH  CA  C    single  1.525  0.021  1.525
 LYH  CA  CB   single  1.521  0.033  1.521
 LYH  C   O    deloc   1.231  0.020  1.231
 LYH  C   OXT  deloc   1.245  0.020  1.245
 LYH  CB  CG   double  1.330  0.020  1.330
 LYH  CG  CD   single  1.498  0.020  1.498
 LYH  CD  CE   single  1.528  0.020  1.528
 LYH  CE  NZ   single  1.455  0.020  1.455
 LYH  N   H    single  0.860  0.020  0.860
 LYH  N   H2   single  0.890  0.020  1.040
 LYH  CA  HA   single  0.970  0.020  0.970
 LYH  CB  HB   single  0.930  0.020  1.080
 LYH  CG  HG   single  0.930  0.020  1.080
 LYH  CD  HD1  single  0.970  0.020  1.090
 LYH  CD  HD2  single  0.970  0.020  1.090
 LYH  CE  HE1  single  0.970  0.020  1.090
 LYH  CE  HE2  single  0.970  0.020  1.090
 LYH  NZ  HZ1  single  0.890  0.020  1.040
 LYH  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
 LYH  H2   N   H    107.41  3.000
 LYH  H2   N   CA   108.39  3.000
 LYH  H    N   CA   114.00  3.000
 LYH  HA   CA  CB   109.00  3.000
 LYH  HA   CA  C    110.00  3.000
 LYH  CB   CA  C    110.50  1.500
 LYH  HA   CA  N    110.00  3.000
 LYH  CB   CA  N    110.40  1.500
 LYH  C    CA  N    111.00  2.800
 LYH  OXT  C   O    127.30  3.000
 LYH  OXT  C   CA   120.80  1.700
 LYH  O    C   CA   120.80  1.700
 LYH  HB   CB  CG   118.63  3.000
 LYH  HB   CB  CA   115.22  3.000
 LYH  CG   CB  CA   126.15  3.000
 LYH  HG   CG  CD   116.37  3.000
 LYH  HG   CG  CB   119.06  3.000
 LYH  CD   CG  CB   124.54  3.000
 LYH  HD2  CD  HD1  107.02  3.000
 LYH  HD2  CD  CE   108.22  3.000
 LYH  HD1  CD  CE   108.99  3.000
 LYH  HD2  CD  CG   109.92  3.000
 LYH  HD1  CD  CG   110.39  3.000
 LYH  CE   CD  CG   112.13  3.000
 LYH  HE2  CE  HE1  106.31  3.000
 LYH  HE2  CE  NZ   113.77  3.000
 LYH  HE1  CE  NZ   108.43  3.000
 LYH  HE2  CE  CD   108.63  3.000
 LYH  HE1  CE  CD   108.90  3.000
 LYH  NZ   CE  CD   110.62  3.000
 LYH  HZ2  NZ  HZ1  105.88  3.000
 LYH  HZ2  NZ  CE   109.12  3.000
 LYH  HZ1  NZ  CE   109.65  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
 LYH  Var_01  CD   CG  CB  CA   178.45   0.0  2
 LYH  Var_02  CE   CD  CG  CB  -110.90  30.0  3
 LYH  Var_03  NZ   CE  CD  CG    66.05  30.0  3
 LYH  Var_04  HZ1  NZ  CE  CD  -176.18  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
 LYH  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
 LYH  plan-1  CA   0.020
 LYH  plan-1  C    0.020
 LYH  plan-1  O    0.020
 LYH  plan-1  OXT  0.020
 LYH  plan-2  CA   0.020
 LYH  plan-2  CB   0.020
 LYH  plan-2  CG   0.020
 LYH  plan-2  CD   0.020
 LYH  plan-2  HB   0.020
 LYH  plan-2  HG   0.020

