# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:21:57 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (4S)-4-amino-5-hydroxypentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)CCC(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
 GAU  GAU  '(4S)-4-amino-5-hydroxypentanoic acid'  L-peptide  20  9  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_GAU
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
 GAU  N    N  NH2   0  -0.787   1.5650   1.4040  -0.6100
 GAU  CA   C  CH1   0  -0.133   1.4171   0.2109   0.2104
 GAU  CB   C  CH2   0  -0.424   0.0642  -0.4427  -0.0561
 GAU  CG   C  CH2   0  -0.572  -1.0954   0.4702   0.3023
 GAU  CD   C  C     0   0.548  -2.4433  -0.1176  -0.0025
 GAU  OE2  O  OH1   0  -0.599  -3.4310   0.6703   0.4160
 GAU  OE1  O  O     0  -0.448  -2.6389  -1.1685  -0.5621
 GAU  C    C  CH2   0  -0.133   2.5277  -0.8166   0.0194
 GAU  OXT  O  OH1   0  -0.674   3.7668  -0.2117   0.3179
 GAU  H    H  HNH2  0   0.346   2.4645   1.8311  -0.4287
 GAU  H2   H  HNH2  0   0.334   1.5808   1.1364  -1.5888
 GAU  HA   H  HCH1  0   0.222   1.4415   0.5334   1.2588
 GAU  HB2  H  HCH2  0   0.227   0.0064  -0.7298  -1.1105
 GAU  HB3  H  HCH2  0   0.234  -0.0046  -1.3668   0.5228
 GAU  HG2  H  HCH2  0   0.271  -1.0652   0.7241   1.3663
 GAU  HG3  H  HCH2  0   0.282  -1.0086   1.4232  -0.2269
 GAU  HE2  H  HOH1  0   0.477  -4.2862   0.2698   0.2006
 GAU  HO1  H  HCH2  0   0.188   2.3381  -1.6813   0.6698
 GAU  HO2  H  HCH2  0   0.185   2.4977  -1.1816  -1.0175
 GAU  HXT  H  HOH1  0   0.455   4.4676  -0.8288   0.0894

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
 GAU  N    CA   single  1.458  0.019  1.458
 GAU  N    H    single  0.860  0.020  0.860
 GAU  N    H2   single  0.890  0.020  1.040
 GAU  CA   CB   single  1.530  0.020  1.530
 GAU  CA   C    single  1.525  0.021  1.525
 GAU  CA   HA   single  0.970  0.020  0.970
 GAU  CB   CG   single  1.519  0.020  1.519
 GAU  CB   HB2  single  0.970  0.020  1.090
 GAU  CB   HB3  single  0.970  0.020  1.090
 GAU  CG   CD   single  1.502  0.020  1.502
 GAU  CG   HG2  single  0.970  0.020  1.090
 GAU  CG   HG3  single  0.970  0.020  1.090
 GAU  CD   OE2  single  1.331  0.020  1.331
 GAU  CD   OE1  double  1.207  0.020  1.207
 GAU  OE2  HE2  single  0.850  0.020  0.980
 GAU  C    OXT  single  1.411  0.020  1.411
 GAU  C    HO1  single  0.970  0.020  1.090
 GAU  C    HO2  single  0.970  0.020  1.090
 GAU  OXT  HXT  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
 GAU  H2   N    H    105.68  3.000
 GAU  H2   N    CA   109.21  3.000
 GAU  H    N    CA   114.00  3.000
 GAU  HA   CA   C    109.00  3.000
 GAU  HA   CA   CB   109.00  3.000
 GAU  C    CA   CB   110.10  1.900
 GAU  HA   CA   N    110.00  3.000
 GAU  C    CA   N    111.00  2.800
 GAU  CB   CA   N    110.50  1.700
 GAU  HB3  CB   HB2  106.58  3.000
 GAU  HB3  CB   CG   109.59  3.000
 GAU  HB2  CB   CG   110.17  3.000
 GAU  HB3  CB   CA   109.00  3.000
 GAU  HB2  CB   CA   109.11  3.000
 GAU  CG   CB   CA   112.22  3.000
 GAU  HG3  CG   HG2  105.43  3.000
 GAU  HG3  CG   CD   108.31  3.000
 GAU  HG2  CG   CD   108.24  3.000
 GAU  HG3  CG   CB   110.43  3.000
 GAU  HG2  CG   CB   110.35  3.000
 GAU  CD   CG   CB   113.71  3.000
 GAU  OE1  CD   OE2  122.76  3.000
 GAU  OE1  CD   CG   125.49  3.000
 GAU  OE2  CD   CG   111.75  3.000
 GAU  HE2  OE2  CD   109.91  3.000
 GAU  HO2  C    HO1  107.00  3.000
 GAU  HO2  C    OXT  111.45  3.000
 GAU  HO1  C    OXT  111.34  3.000
 GAU  HO2  C    CA   108.78  3.000
 GAU  HO1  C    CA   109.30  3.000
 GAU  OXT  C    CA   108.92  3.000
 GAU  HXT  OXT  C    108.35  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
 GAU  CONST_01  HE2  OE2  CD  CG  180.00   0.0  0
 GAU  Var_01    CD   CG   CB  CA  177.50  30.0  3
 GAU  Var_02    OE2  CD   CG  CB  175.38  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
 GAU  chir_01  CA  N  CB  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
 GAU  plan-1  CG   0.020
 GAU  plan-1  CD   0.020
 GAU  plan-1  OE2  0.020
 GAU  plan-1  OE1  0.020
 GAU  plan-1  HE2  0.020

