# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:58:43 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: (2S,4S)-2-amino-4-hydroxypentanedioic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@H](O)C(O)=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
 3GL  3GL  '(2S,4S)-2-amino-4-hydroxypentanedioic acid (non-preferred name)'  L-peptide  18  11  .  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_3GL
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
 3GL  N     N  NH2    0  -0.820  127.6463  83.5747  112.3474
 3GL  CA    C  CH1    0  -0.213  128.4736  84.4243  113.1958
 3GL  C     C  C      0   0.409  128.8381  83.6947  114.5166
 3GL  CB    C  CH2    0  -0.411  127.7740  85.7568  113.4619
 3GL  CG    C  CH1    0  -0.088  127.3562  86.5007  112.1966
 3GL  OH    O  OH1    0  -0.704  128.4555  86.7372  111.3470
 3GL  CD    C  C      0   0.394  126.6855  87.8528  112.5343
 3GL  OE1   O  OC    -1  -0.610  127.2374  88.8498  112.0088
 3GL  OE2   O  O      0  -0.591  125.6896  87.8444  113.2740
 3GL  O     O  O      0  -0.607  129.3010  84.4005  115.4342
 3GL  OXT   O  OC    -1  -0.604  128.6767  82.4564  114.5442
 3GL  HN1   H  HNH2   0   0.328  127.8287  83.7709  111.3725
 3GL  HN2   H  HNH2   0   0.331  127.9210  82.6152  112.5135
 3GL  HA    H  HCH1   0   0.192  129.4417  84.6517  112.7190
 3GL  HB1C  H  HCH2   0   0.195  126.8774  85.5752  114.0605
 3GL  HB2C  H  HCH2   0   0.197  128.4329  86.3948  114.0565
 3GL  HG    H  HCH1   0   0.183  126.6079  85.8869  111.6722
 3GL  HH    H  HOH1   0   0.420  128.4339  87.7115  111.2725

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
 3GL  N   CA    single  1.458  0.019  1.458
 3GL  CA  C     single  1.525  0.021  1.525
 3GL  CA  CB    single  1.530  0.020  1.530
 3GL  C   O     deloc   1.231  0.020  1.231
 3GL  CB  CG    single  1.526  0.020  1.526
 3GL  CG  OH    single  1.409  0.020  1.409
 3GL  CG  CD    single  1.547  0.020  1.547
 3GL  CD  OE1   deloc   1.255  0.020  1.255
 3GL  CD  OE2   deloc   1.241  0.020  1.241
 3GL  C   OXT   deloc   1.249  0.020  1.249
 3GL  N   HN1   single  0.890  0.020  1.040
 3GL  N   HN2   single  0.890  0.020  1.040
 3GL  CA  HA    single  0.970  0.020  0.970
 3GL  CB  HB1C  single  0.970  0.020  1.090
 3GL  CB  HB2C  single  0.970  0.020  1.090
 3GL  CG  HG    single  0.970  0.020  1.090
 3GL  OH  HH    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
 3GL  HN2   N   HN1   107.06  3.000
 3GL  HN2   N   CA    107.64  3.000
 3GL  HN1   N   CA    110.22  3.000
 3GL  HA    CA  CB    109.00  3.000
 3GL  HA    CA  C     109.00  3.000
 3GL  CB    CA  C     110.10  1.900
 3GL  HA    CA  N     110.00  3.000
 3GL  CB    CA  N     110.50  1.700
 3GL  C     CA  N     111.00  2.800
 3GL  OXT   C   O     126.37  3.000
 3GL  OXT   C   CA    117.03  3.000
 3GL  O     C   CA    120.80  1.700
 3GL  HB2C  CB  HB1C  107.07  3.000
 3GL  HB2C  CB  CG    109.36  3.000
 3GL  HB1C  CB  CG    108.08  3.000
 3GL  HB2C  CB  CA    109.13  3.000
 3GL  HB1C  CB  CA    109.02  3.000
 3GL  CG    CB  CA    113.95  3.000
 3GL  HG    CG  CD    107.26  3.000
 3GL  HG    CG  OH    109.66  3.000
 3GL  CD    CG  OH    108.85  3.000
 3GL  HG    CG  CB    108.02  3.000
 3GL  CD    CG  CB    111.34  3.000
 3GL  OH    CG  CB    111.60  3.000
 3GL  HH    OH  CG    101.30  3.000
 3GL  OE2   CD  OE1   127.46  3.000
 3GL  OE2   CD  CG    118.18  3.000
 3GL  OE1   CD  CG    114.36  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
 3GL  chir_01  CA  N   C   CB  positiv
 3GL  chir_02  CG  OH  CB  CD  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
 3GL  plan-1  CA   0.020
 3GL  plan-1  C    0.020
 3GL  plan-1  O    0.020
 3GL  plan-1  OXT  0.020
 3GL  plan-2  CG   0.020
 3GL  plan-2  CD   0.020
 3GL  plan-2  OE1  0.020
 3GL  plan-2  OE2  0.020

