# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 03:22:35 2022
#   Inital geometry file: a 32 line input string
#   Ligand name: (2S)-amino(hydroxy)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](O)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
 HGY  HGY  '(2S)-amino(hydroxy)ethanoic acid'  peptide  10  6  .  2016-04-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HGY
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
 HGY  OXT  O  OC    -1  -0.610  7.1289  68.9419  105.0637
 HGY  C    C  C      0   0.365  7.4989  69.0295  103.8689
 HGY  O    O  O      0  -0.590  8.6134  68.7626  103.3950
 HGY  CA   C  CH1    0   0.046  6.4031  69.5194  102.8831
 HGY  OB   O  OH1    0  -0.689  5.2518  69.8293  103.6098
 HGY  N    N  NH2    0  -0.798  6.0911  68.5562  101.8375
 HGY  HA   H  HCH1   0   0.183  6.7821  70.4140  102.3671
 HGY  H3   H  HOH1   0   0.425  5.5114  69.5715  104.5161
 HGY  H    H  HNH2   0   0.336  6.9004  68.4576  101.2368
 HGY  H2   H  HNH2   0   0.331  5.9413  67.6392  102.2461

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
 HGY  N   CA   single  1.451  0.016  1.451
 HGY  CA  OB   single  1.396  0.020  1.396
 HGY  CA  C    single  1.516  0.018  1.516
 HGY  O   C    deloc   1.231  0.020  1.231
 HGY  C   OXT  deloc   1.254  0.020  1.254
 HGY  CA  HA   single  0.970  0.020  1.090
 HGY  OB  H3   single  0.850  0.020  0.980
 HGY  N   H    single  0.860  0.020  0.860
 HGY  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
 HGY  CA  C   O    120.80  2.100
 HGY  O   C   OXT  127.91  3.000
 HGY  CA  C   OXT  114.74  3.000
 HGY  HA  CA  N    105.97  3.000
 HGY  HA  CA  OB   110.35  3.000
 HGY  N   CA  OB   110.12  3.000
 HGY  HA  CA  C    108.12  3.000
 HGY  OB  CA  C    108.75  3.000
 HGY  N   CA  C    113.30  2.900
 HGY  H3  OB  CA   101.84  3.000
 HGY  H2  N   H    105.59  3.000
 HGY  H2  N   CA   109.90  3.000
 HGY  H   N   CA   114.00  3.000

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
 HGY  chir_01  CA  N  OB  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
 HGY  plan-1  OXT  0.020
 HGY  plan-1  C    0.020
 HGY  plan-1  O    0.020
 HGY  plan-1  CA   0.020

