# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 01:01:05 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S,4R)-2-amino-4-carboxypentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C[C@H](N)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
 SYM  SYM  (2S,4R)-2-amino-4-carboxypentanoate  ligand  21  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SYM
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
 SYM  CB    C  CH2    0  -0.409  -0.0330   0.5635   0.6883
 SYM  CG1   C  CH1    0  -0.357   1.4145   0.7470   0.2484
 SYM  CG2   C  CH3    0  -0.659   2.2622   1.3558   1.3735
 SYM  CD    C  C      0   0.550   2.0477  -0.5593  -0.1636
 SYM  OE1   O  OH1    0  -0.596   3.0059  -0.3914  -1.0724
 SYM  OE2   O  O      0  -0.449   1.7728  -1.6411   0.2963
 SYM  C     C  C      0   0.386  -2.3994  -0.0538   0.1991
 SYM  OT1   O  OC    -1  -0.621  -2.5663  -1.0872   0.8790
 SYM  OT2   O  O      0  -0.609  -3.2374   0.8500   0.0051
 SYM  N     N  NH2    0  -0.788  -0.9314   1.0852  -1.5269
 SYM  CA    C  CH1    0  -0.218  -0.9944   0.1358  -0.4251
 SYM  HB1   H  HCH2   0   0.227  -0.0831  -0.1565   1.5076
 SYM  HB2   H  HCH2   0   0.222  -0.3766   1.5208   1.0970
 SYM  HG1   H  HCH1   0   0.259   1.4400   1.4238  -0.6076
 SYM  HG21  H  HCH3   0   0.241   3.2890   1.5406   1.0578
 SYM  HG22  H  HCH3   0   0.243   1.8316   2.3101   1.6769
 SYM  HG23  H  HCH3   0   0.229   2.2862   0.7054   2.2491
 SYM  HE1   H  HOH1   0   0.475   3.4323  -1.2409  -1.2606
 SYM  HN2   H  HNH2   0   0.323  -1.4533   1.9096  -1.2494
 SYM  HA    H  HCH1   0   0.214  -0.6674  -0.8379  -0.8046
 SYM  HN1   H  HNH2   0   0.336  -1.4546   0.7098  -2.3090

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
 SYM  CB   CG1   single  1.524  0.020  1.524
 SYM  CB   CA    single  1.532  0.020  1.532
 SYM  CB   HB1   single  0.970  0.020  1.090
 SYM  CB   HB2   single  0.970  0.020  1.090
 SYM  CG1  CG2   single  1.535  0.020  1.535
 SYM  CG1  CD    single  1.509  0.020  1.509
 SYM  CG1  HG1   single  0.970  0.020  1.090
 SYM  CG2  HG21  single  0.970  0.020  1.090
 SYM  CG2  HG22  single  0.970  0.020  1.090
 SYM  CG2  HG23  single  0.970  0.020  1.090
 SYM  CD   OE1   single  1.331  0.020  1.331
 SYM  CD   OE2   double  1.207  0.020  1.207
 SYM  OE1  HE1   single  0.850  0.020  0.980
 SYM  C    OT1   single  1.248  0.020  1.248
 SYM  C    OT2   double  1.248  0.020  1.248
 SYM  C    CA    single  1.549  0.020  1.549
 SYM  N    CA    single  1.456  0.020  1.456
 SYM  N    HN1   single  0.890  0.020  1.040
 SYM  N    HN2   single  0.890  0.020  1.040
 SYM  CA   HA    single  0.970  0.020  1.090

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
 SYM  HB2   CB   HB1   106.37  3.000
 SYM  HB2   CB   CA    108.55  3.000
 SYM  HB1   CB   CA    109.42  3.000
 SYM  HB2   CB   CG1   107.47  3.000
 SYM  HB1   CB   CG1   109.85  3.000
 SYM  CA    CB   CG1   114.83  3.000
 SYM  HG1   CG1  CD    108.23  3.000
 SYM  HG1   CG1  CG2   108.42  3.000
 SYM  CD    CG1  CG2   108.17  3.000
 SYM  HG1   CG1  CB    108.86  3.000
 SYM  CD    CG1  CB    111.91  3.000
 SYM  CG2   CG1  CB    111.15  3.000
 SYM  HG23  CG2  HG22  107.89  3.000
 SYM  HG23  CG2  HG21  108.22  3.000
 SYM  HG22  CG2  HG21  107.72  3.000
 SYM  HG23  CG2  CG1   111.35  3.000
 SYM  HG22  CG2  CG1   109.46  3.000
 SYM  HG21  CG2  CG1   112.04  3.000
 SYM  OE2   CD   OE1   122.48  3.000
 SYM  OE2   CD   CG1   125.18  3.000
 SYM  OE1   CD   CG1   112.28  3.000
 SYM  HE1   OE1  CD    109.80  3.000
 SYM  CA    C    OT2   117.24  3.000
 SYM  CA    C    OT1   116.24  3.000
 SYM  OT2   C    OT1   126.49  3.000
 SYM  HN2   N    HN1   104.28  3.000
 SYM  HN2   N    CA    107.50  3.000
 SYM  HN1   N    CA    108.68  3.000
 SYM  HA    CA   N     107.74  3.000
 SYM  HA    CA   C     107.55  3.000
 SYM  N     CA   C     115.09  3.000
 SYM  HA    CA   CB    108.23  3.000
 SYM  N     CA   CB    109.93  3.000
 SYM  C     CA   CB    108.09  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
 SYM  CONST_01  HE1  OE1  CD  CG1  180.00  0.0  0

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
 SYM  chir_01  CG1  CB  CG2  CD  negativ
 SYM  chir_02  CA   N   C    CB  positiv

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
 SYM  plan-1  CG1  0.020
 SYM  plan-1  CD   0.020
 SYM  plan-1  OE1  0.020
 SYM  plan-1  OE2  0.020
 SYM  plan-1  HE1  0.020
 SYM  plan-2  C    0.020
 SYM  plan-2  OT1  0.020
 SYM  plan-2  OT2  0.020
 SYM  plan-2  CA   0.020

