# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:20:45 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (2S)-2-aminopent-4-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC#C)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
 LPH  LPH  '(2S)-2-aminopent-4-ynoic acid'  L-peptide  14  8  .  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_LPH
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
 LPH  CD   C  CSP1   0  -0.572  -3.9968   0.3885  27.2166
 LPH  CG   C  CSP    0   0.280  -5.1391   0.7207  27.4016
 LPH  CB   C  CH2    0  -0.564  -6.5291   1.1066  27.6099
 LPH  CA   C  CH1    0  -0.226  -7.4378   0.6665  26.4551
 LPH  N    N  NH2    0  -0.806  -6.9742   1.2477  25.2083
 LPH  C    C  C      0   0.422  -8.9185   1.0443  26.7335
 LPH  OXT  O  OC    -1  -0.600  -9.3037   0.9397  27.9135
 LPH  O    O  O      0  -0.595  -9.6030   1.3751  25.7459
 LPH  H1   H  H      0   0.273  -2.9850   0.0949  27.0555
 LPH  H2   H  HCH2   0   0.252  -6.5845   2.1932  27.7221
 LPH  H3   H  HCH2   0   0.258  -6.8859   0.6704  28.5434
 LPH  H4   H  HCH1   0   0.207  -7.4145  -0.4367  26.4342
 LPH  H5   H  HNH2   0   0.334  -6.2153   0.6982  24.8274
 LPH  H6   H  HNH2   0   0.337  -7.7354   1.2059  24.5439

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
 LPH  N   CA   single  1.458  0.019  1.458
 LPH  O   C    deloc   1.231  0.020  1.231
 LPH  CA  C    single  1.525  0.021  1.525
 LPH  CA  CB   single  1.521  0.033  1.521
 LPH  C   OXT  deloc   1.246  0.020  1.246
 LPH  CD  CG   triple  1.204  0.020  1.204
 LPH  CG  CB   single  1.458  0.020  1.458
 LPH  CD  H1   single  0.913  0.020  1.066
 LPH  CB  H2   single  0.939  0.020  1.096
 LPH  CB  H3   single  0.939  0.020  1.096
 LPH  CA  H4   single  0.939  0.020  1.096
 LPH  N   H5   single  0.868  0.020  1.013
 LPH  N   H6   single  0.868  0.020  1.013

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
 LPH  H1   CD  CG   180.00  3.000
 LPH  CB   CG  CD   180.00  3.000
 LPH  H3   CB  H2   107.04  3.000
 LPH  H3   CB  CA   109.62  3.000
 LPH  H2   CB  CA   109.41  3.000
 LPH  H3   CB  CG   109.18  3.000
 LPH  H2   CB  CG   109.03  3.000
 LPH  CA   CB  CG   112.42  3.000
 LPH  H4   CA  C    105.47  3.000
 LPH  H4   CA  N    112.16  3.000
 LPH  C    CA  N    111.00  2.800
 LPH  H4   CA  CB   106.77  3.000
 LPH  C    CA  CB   110.50  1.500
 LPH  N    CA  CB   110.40  1.500
 LPH  H6   N   H5   107.16  3.000
 LPH  H6   N   CA   107.89  3.000
 LPH  H5   N   CA   110.21  3.000
 LPH  O    C   OXT  127.09  3.000
 LPH  OXT  C   CA   120.80  1.700
 LPH  O    C   CA   120.80  1.700

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
 LPH  Var_01  CA  CB  CG  CD  -19.96  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
 LPH  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
 LPH  plan-1  CA   0.020
 LPH  plan-1  C    0.020
 LPH  plan-1  OXT  0.020
 LPH  plan-1  O    0.020

