# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 15:09:09 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (2R)-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
 F9D  F9D  '(2R)-2-aminopent-4-ynoic acid'  D-peptide  14  8  .  2019-03-22  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_F9D
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
 F9D  C    C  C      0   0.413  18.9115  2.0189  79.8153
 F9D  O    O  O      0  -0.602  18.8653  0.8414  80.2184
 F9D  CA   C  CH1    0  -0.226  20.0705  2.3586  78.8414
 F9D  N    N  NH2    0  -0.805  19.8327  3.6060  78.1401
 F9D  CB   C  CH2    0  -0.557  20.3141  1.2264  77.8359
 F9D  CG   C  CSP    0   0.274  19.1632  0.9598  76.9835
 F9D  CD   C  CSP1   0  -0.565  18.2103  0.7376  76.2825
 F9D  HA   H  HCH1   0   0.217  20.9792  2.3978  79.4655
 F9D  H    H  HNH2   0   0.335  19.3867  4.2475  78.7815
 F9D  H2   H  HNH2   0   0.332  20.7115  4.0234  77.8642
 F9D  HB2  H  HCH2   0   0.256  20.5835  0.3156  78.3723
 F9D  HB3  H  HCH2   0   0.254  21.1712  1.4768  77.2036
 F9D  HG   H  H      0   0.272  17.3686  0.5400  75.6596
 F9D  OXT  O  OC    -1  -0.598  18.1590  2.9560  80.1446

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
 F9D  CD  CG   triple  1.204  0.020  1.204
 F9D  CG  CB   single  1.457  0.020  1.457
 F9D  CB  CA   single  1.521  0.033  1.521
 F9D  N   CA   single  1.458  0.019  1.458
 F9D  CA  C    single  1.525  0.021  1.525
 F9D  C   O    deloc   1.231  0.020  1.231
 F9D  CA  HA   single  0.970  0.020  0.970
 F9D  N   H    single  0.860  0.020  0.860
 F9D  N   H2   single  0.868  0.020  1.013
 F9D  CB  HB2  single  0.939  0.020  1.096
 F9D  CB  HB3  single  0.939  0.020  1.096
 F9D  CD  HG   single  0.913  0.020  1.066
 F9D  C   OXT  deloc   1.246  0.020  1.246

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
 F9D  OXT  C   CA   120.80  1.700
 F9D  OXT  C   O    127.09  3.000
 F9D  CA   C   O    120.80  1.700
 F9D  HA   CA  CB   109.00  3.000
 F9D  HA   CA  N    110.00  3.000
 F9D  CB   CA  N    110.40  1.500
 F9D  HA   CA  C    110.00  3.000
 F9D  N    CA  C    111.00  2.800
 F9D  CB   CA  C    110.50  1.500
 F9D  H2   N   H    107.13  3.000
 F9D  H2   N   CA   110.14  3.000
 F9D  H    N   CA   114.00  3.000
 F9D  HB3  CB  HB2  106.37  3.000
 F9D  HB3  CB  CG   108.82  3.000
 F9D  HB2  CB  CG   109.28  3.000
 F9D  HB3  CB  CA   109.53  3.000
 F9D  HB2  CB  CA   109.46  3.000
 F9D  CG   CB  CA   113.15  3.000
 F9D  CD   CG  CB   180.00  3.000
 F9D  HG   CD  CG   180.00  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
 F9D  Var_01  HB2  CB  CG  CD  46.59  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
 F9D  chir_01  CA  CB  N  C  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
 F9D  plan-1  C    0.020
 F9D  plan-1  O    0.020
 F9D  plan-1  CA   0.020
 F9D  plan-1  OXT  0.020

