# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 19:28:15 2022
#   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  19  9  .  2022-09-22  2022-09-22
;
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  -0.788   1.6093   1.4128  -0.6295
 GAU  CA   C  CH1    0  -0.127   1.4326   0.2243   0.1944
 GAU  CB   C  CH2    0  -0.409   0.0690  -0.4075  -0.0722
 GAU  CG   C  CH2    0  -0.575  -1.1003   0.4975   0.2759
 GAU  CD   C  C      0   0.409  -2.4990  -0.0713  -0.0146
 GAU  OE2  O  OC    -1  -0.636  -3.4622   0.6295   0.3649
 GAU  OE1  O  O      0  -0.611  -2.5768  -1.1664  -0.6067
 GAU  C    C  CH2    0  -0.134   2.5290  -0.8191   0.0078
 GAU  OXT  O  OH1    0  -0.676   3.7796  -0.2372   0.3108
 GAU  H    H  HNH2   0   0.341   2.5358   1.7934  -0.4817
 GAU  H2   H  HNH2   0   0.329   1.5763   1.1453  -1.6078
 GAU  HA   H  HCH1   0   0.209   1.4619   0.5486   1.2428
 GAU  HB2  H  HCH2   0   0.202   0.0154  -0.7017  -1.1257
 GAU  HB3  H  HCH2   0   0.209  -0.0046  -1.3353   0.5020
 GAU  HG2  H  HCH2   0   0.211  -1.0519   0.7632   1.3382
 GAU  HG3  H  HCH2   0   0.225  -1.0001   1.4491  -0.2551
 GAU  HO1  H  HCH2   0   0.184   2.3234  -1.6814   0.6570
 GAU  HO2  H  HCH2   0   0.181   2.4976  -1.1835  -1.0294
 GAU  HXT  H  HOH1   0   0.453   4.4698  -0.8643   0.0793

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  1.538  0.020  1.538
 GAU  CG   HG2  single  0.970  0.020  1.090
 GAU  CG   HG3  single  0.970  0.020  1.090
 GAU  CD   OE2  deloc   1.250  0.020  1.250
 GAU  CD   OE1  deloc   1.247  0.020  1.247
 GAU  C    OXT  single  1.412  0.020  1.412
 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    105.63  3.000
 GAU  H2   N    CA   109.04  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  105.89  3.000
 GAU  HB3  CB   CG   109.47  3.000
 GAU  HB2  CB   CG   110.05  3.000
 GAU  HB3  CB   CA   108.64  3.000
 GAU  HB2  CB   CA   108.84  3.000
 GAU  CG   CB   CA   113.65  3.000
 GAU  HG3  CG   HG2  104.80  3.000
 GAU  HG3  CG   CD   108.26  3.000
 GAU  HG2  CG   CD   108.24  3.000
 GAU  HG3  CG   CB   109.66  3.000
 GAU  HG2  CG   CB   109.42  3.000
 GAU  CD   CG   CB   115.88  3.000
 GAU  OE1  CD   OE2  126.03  3.000
 GAU  OE1  CD   CG   118.11  3.000
 GAU  OE2  CD   CG   115.86  3.000
 GAU  HO2  C    HO1  106.97  3.000
 GAU  HO2  C    OXT  111.35  3.000
 GAU  HO1  C    OXT  111.24  3.000
 GAU  HO2  C    CA   108.76  3.000
 GAU  HO1  C    CA   109.28  3.000
 GAU  OXT  C    CA   109.18  3.000
 GAU  HXT  OXT  C    108.39  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  Var_01  CD   CG  CB  CA    178.13  30.0  3
 GAU  Var_02  OE2  CD  CG  CB    174.76  30.0  3
 GAU  Var_03  OE1  CD  CG  CB     -5.79  30.0  3
 GAU  Var_04  HG2  CG  CB  CA    -59.19  30.0  3
 GAU  Var_05  HG3  CG  CB  CA     55.23  30.0  3
 GAU  Var_06  HB2  CB  CG  CD     55.78  30.0  1
 GAU  Var_07  HB3  CB  CG  CD    -60.21  30.0  1
 GAU  Var_08  HG2  CG  CD  OE2    51.46  30.0  2
 GAU  Var_09  HG3  CG  CD  OE2   -61.61  30.0  2
 GAU  Var_10  HG2  CG  CD  OE1  -129.09  30.0  2
 GAU  Var_11  HG3  CG  CD  OE1   117.84  30.0  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
 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

