# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 22:28:29 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (3S)-3-amino-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)c1ccccc1
#
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
 SFE  SFE  '(3S)-3-amino-3-phenylpropanoic acid'  peptide  23  12  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SFE
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
 SFE  N     N  NH2   0  -0.786   0.9747   1.6466  -0.5046
 SFE  O     O  O     0  -0.454   3.1942  -0.7998  -1.0125
 SFE  OXT   O  OH1   0  -0.587   3.5264  -0.0505   1.0592
 SFE  CZ    C  CR16  0  -0.272  -3.7141  -0.3138   0.3741
 SFE  CE2   C  CR16  0  -0.240  -3.0391  -1.1864  -0.4706
 SFE  CE1   C  CR16  0  -0.236  -3.0382   0.7694   0.9185
 SFE  CD2   C  CR16  0  -0.308  -1.6993  -0.9734  -0.7623
 SFE  CD1   C  CR16  0  -0.327  -1.6969   0.9786   0.6223
 SFE  CA    C  CH2   0  -0.550   1.3002  -0.5533   0.4374
 SFE  C     C  C     0   0.543   2.7580  -0.4834   0.0673
 SFE  CG    C  CR6   0   0.147  -1.0104   0.1094  -0.2195
 SFE  CB    C  CH1   0  -0.175   0.4647   0.2900  -0.5319
 SFE  HN1   H  HNH2  0   0.357   0.4553   2.2353  -1.1437
 SFE  HN2   H  HNH2  0   0.350   0.8693   2.0539   0.4163
 SFE  HB    H  HCH1  0   0.257   0.6349  -0.0993  -1.5399
 SFE  HA1C  H  HCH2  0   0.290   0.9860  -1.5984   0.3882
 SFE  HA2C  H  HCH2  0   0.266   1.1373  -0.2152   1.4626
 SFE  HD2   H  HCR6  0   0.248  -1.1813  -1.6578  -1.4258
 SFE  HE2   H  HCR6  0   0.254  -3.5579  -2.0305  -0.9065
 SFE  HXT   H  HOH1  0   0.478   4.4523  -0.0319   0.7729
 SFE  HD1   H  HCR6  0   0.236  -1.1922   1.8352   1.0516
 SFE  HE1   H  HCR6  0   0.255  -3.5565   1.4576   1.5740
 SFE  HZ    H  HCR6  0   0.255  -4.7596  -0.4746   0.6026

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
 SFE  N    CB    single    1.450  0.020  1.450
 SFE  CA   CB    single    1.521  0.033  1.521
 SFE  CA   C     single    1.525  0.021  1.525
 SFE  CD2  CG    aromatic  1.393  0.020  1.393
 SFE  CD2  CE2   aromatic  1.388  0.020  1.388
 SFE  O    C     double    1.231  0.020  1.231
 SFE  OXT  C     single    1.327  0.020  1.327
 SFE  CG   CD1   aromatic  1.391  0.020  1.391
 SFE  CG   CB    single    1.519  0.020  1.519
 SFE  CD1  CE1   aromatic  1.389  0.020  1.389
 SFE  CE1  CZ    aromatic  1.388  0.020  1.388
 SFE  CZ   CE2   aromatic  1.389  0.020  1.389
 SFE  N    HN1   single    0.890  0.020  1.040
 SFE  N    HN2   single    0.890  0.020  1.040
 SFE  CB   HB    single    0.970  0.020  1.090
 SFE  CA   HA1C  single    0.970  0.020  1.090
 SFE  CA   HA2C  single    0.970  0.020  1.090
 SFE  CD2  HD2   single    0.930  0.020  1.080
 SFE  CE2  HE2   single    0.930  0.020  1.080
 SFE  CD1  HD1   single    0.930  0.020  1.080
 SFE  CE1  HE1   single    0.930  0.020  1.080
 SFE  CZ   HZ    single    0.930  0.020  1.080
 SFE  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
 SFE  HN2   N    HN1   106.67  3.000
 SFE  HN2   N    CB    110.91  3.000
 SFE  HN1   N    CB    110.60  3.000
 SFE  HXT   OXT  C     109.79  3.000
 SFE  HZ    CZ   CE1   120.24  3.000
 SFE  HZ    CZ   CE2   120.29  3.000
 SFE  CE1   CZ   CE2   119.47  3.000
 SFE  HE2   CE2  CD2   119.85  3.000
 SFE  HE2   CE2  CZ    120.12  3.000
 SFE  CD2   CE2  CZ    120.03  3.000
 SFE  HE1   CE1  CD1   119.70  3.000
 SFE  HE1   CE1  CZ    120.04  3.000
 SFE  CD1   CE1  CZ    120.26  3.000
 SFE  HD2   CD2  CG    119.50  3.000
 SFE  HD2   CD2  CE2   119.53  3.000
 SFE  CG    CD2  CE2   120.98  3.000
 SFE  HD1   CD1  CG    120.27  3.000
 SFE  HD1   CD1  CE1   118.98  3.000
 SFE  CG    CD1  CE1   120.75  3.000
 SFE  HA2C  CA   HA1C  107.20  3.000
 SFE  HA2C  CA   CB    110.01  3.000
 SFE  HA1C  CA   CB    109.95  3.000
 SFE  HA2C  CA   C     111.15  3.000
 SFE  HA1C  CA   C     108.17  3.000
 SFE  CB    CA   C     110.50  1.500
 SFE  CA    C    OXT   120.80  1.700
 SFE  OXT   C    O     123.02  3.000
 SFE  CA    C    O     120.80  1.700
 SFE  CB    CG   CD1   121.97  3.000
 SFE  CB    CG   CD2   119.51  3.000
 SFE  CD1   CG   CD2   118.51  3.000
 SFE  HB    CB   CG    107.36  3.000
 SFE  HB    CB   CA    107.59  3.000
 SFE  CG    CB   CA    109.51  3.000
 SFE  HB    CB   N     107.19  3.000
 SFE  CG    CB   N     116.69  3.000
 SFE  CA    CB   N     110.40  1.500

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
 SFE  CONST_01  CG   CD1  CE1  CZ     0.00   0.0  0
 SFE  CONST_02  CG   CD2  CE2  CZ     0.00   0.0  0
 SFE  CONST_03  CD1  CG   CD2  CE2    0.00   0.0  0
 SFE  CONST_04  CD1  CE1  CZ   CE2    0.00   0.0  0
 SFE  CONST_05  CD2  CG   CD1  CE1    0.00   0.0  0
 SFE  CONST_06  CD2  CE2  CZ   CE1    0.00   0.0  0
 SFE  CONST_07  CB   CG   CD2  CE2  180.00   0.0  0
 SFE  CONST_08  CB   CG   CD1  CE1  180.00   0.0  0
 SFE  CONST_09  HD1  CD1  CE1  CZ   180.00   0.0  0
 SFE  CONST_10  HD2  CD2  CE2  CZ   180.00   0.0  0
 SFE  CONST_11  HE1  CE1  CZ   CE2  180.00   0.0  0
 SFE  CONST_12  HE2  CE2  CZ   CE1  180.00   0.0  0
 SFE  CONST_13  HZ   CZ   CE2  CD2  180.00   0.0  0
 SFE  CONST_14  HXT  OXT  C    O      0.00   0.0  0
 SFE  Var_01    CB   CA   C    O    -57.52  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
 SFE  chir_01  CB  N  CA  CG  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
 SFE  plan-1  CZ   0.020
 SFE  plan-1  CE2  0.020
 SFE  plan-1  CE1  0.020
 SFE  plan-1  CD2  0.020
 SFE  plan-1  CD1  0.020
 SFE  plan-1  CG   0.020
 SFE  plan-1  CB   0.020
 SFE  plan-1  HD2  0.020
 SFE  plan-1  HE2  0.020
 SFE  plan-1  HD1  0.020
 SFE  plan-1  HE1  0.020
 SFE  plan-1  HZ   0.020
 SFE  plan-2  O    0.020
 SFE  plan-2  OXT  0.020
 SFE  plan-2  CA   0.020
 SFE  plan-2  C    0.020
 SFE  plan-2  HXT  0.020

