# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:33:04 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: (2S)-2-aminopent-4-enoic 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
 2AG  2AG  '(2S)-2-aminopent-4-enoic acid'  L-peptide  16  8  .  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_2AG
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
 2AG  C1A   C  C2     0  -0.542  -11.2453  20.1971  -55.9318
 2AG  C1E   C  C1     0  -0.148  -11.1372  19.3398  -56.9416
 2AG  CB    C  CH2    0  -0.491  -10.0962  18.2706  -57.0375
 2AG  CA    C  CH1    0  -0.185  -10.6516  16.8359  -57.0163
 2AG  C     C  C      0   0.381  -11.6092  16.6252  -58.2148
 2AG  O     O  O      0  -0.606  -11.0741  16.3160  -59.3001
 2AG  OXT   O  OC    -1  -0.610  -12.8249  16.8138  -58.0067
 2AG  N     N  NH2    0  -0.792   -9.5202  15.9153  -56.9774
 2AG  H1A   H  H      0   0.225  -10.5664  20.1735  -55.0866
 2AG  H1AA  H  H      0   0.228  -12.0177  20.9553  -55.9103
 2AG  H1E   H  H      0   0.234  -11.8428  19.4140  -57.7630
 2AG  HB2   H  HCH2   0   0.220   -9.5280  18.3991  -57.9667
 2AG  HB3   H  HCH2   0   0.227   -9.3855  18.3773  -56.2142
 2AG  HA    H  HCH1   0   0.203  -11.2161  16.7121  -56.0871
 2AG  H     H  HNH2   0   0.334   -9.8701  14.9777  -56.8170
 2AG  H2    H  HNH2   0   0.323   -9.1264  15.8832  -57.9122

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
 2AG  C1E  C1A   double  1.329  0.020  1.329
 2AG  C1A  H1A   single  0.930  0.020  1.080
 2AG  C1A  H1AA  single  0.930  0.020  1.080
 2AG  CB   C1E   single  1.495  0.020  1.495
 2AG  C1E  H1E   single  0.930  0.020  1.080
 2AG  CA   CB    single  1.521  0.033  1.521
 2AG  CB   HB2   single  0.970  0.020  1.090
 2AG  CB   HB3   single  0.970  0.020  1.090
 2AG  C    CA    single  1.525  0.021  1.525
 2AG  CA   N     single  1.458  0.019  1.458
 2AG  CA   HA    single  0.970  0.020  0.970
 2AG  O    C     deloc   1.231  0.020  1.231
 2AG  C    OXT   deloc   1.248  0.020  1.248
 2AG  N    H     single  0.860  0.020  0.860
 2AG  N    H2    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
 2AG  H1AA  C1A  H1A  116.52  3.000
 2AG  H1AA  C1A  C1E  121.66  3.000
 2AG  H1A   C1A  C1E  121.82  3.000
 2AG  H1E   C1E  CB   116.93  3.000
 2AG  H1E   C1E  C1A  118.56  3.000
 2AG  CB    C1E  C1A  124.51  3.000
 2AG  HB3   CB   HB2  106.85  3.000
 2AG  HB3   CB   CA   108.39  3.000
 2AG  HB2   CB   CA   107.94  3.000
 2AG  HB3   CB   C1E  109.55  3.000
 2AG  HB2   CB   C1E  109.35  3.000
 2AG  CA    CB   C1E  114.49  3.000
 2AG  HA    CA   N    110.00  3.000
 2AG  HA    CA   C    109.00  3.000
 2AG  N     CA   C    111.00  2.800
 2AG  HA    CA   CB   109.00  3.000
 2AG  N     CA   CB   110.40  1.500
 2AG  C     CA   CB   110.50  1.500
 2AG  OXT   C    O    126.86  3.000
 2AG  OXT   C    CA   116.93  3.000
 2AG  O     C    CA   120.80  1.700
 2AG  H2    N    H    104.50  3.000
 2AG  H2    N    CA   107.23  3.000
 2AG  H     N    CA   114.00  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
 2AG  Var_01  CA   CB   C1E  C1A  115.84  30.0  1
 2AG  Var_02  H1A  C1A  C1E  CB    -0.16   0.0  2

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
 2AG  chir_01  CA  CB  C  N  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
 2AG  plan-1  CA    0.020
 2AG  plan-1  C     0.020
 2AG  plan-1  O     0.020
 2AG  plan-1  OXT   0.020
 2AG  plan-2  C1A   0.020
 2AG  plan-2  C1E   0.020
 2AG  plan-2  CB    0.020
 2AG  plan-2  H1A   0.020
 2AG  plan-2  H1AA  0.020
 2AG  plan-2  H1E   0.020

