# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:51:39 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (2S,3S)-3-amino-2-hydroxy-4-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[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
 005  005  '(2S,3S)-3-amino-2-hydroxy-4-phenylbutanoic acid'  peptide  27  14  .  2022-03-07  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_005
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
 005  C     C  C     0   0.528   3.1176  -0.2913  -0.3679
 005  N     N  NH2   0  -0.791   0.6551  -1.4560  -0.1826
 005  O     O  O     0  -0.451   3.3555   0.1475  -1.4663
 005  CA    C  CH1   0  -0.049   2.0920   0.3418   0.5627
 005  CD    C  CR6   0   0.132  -1.7684   0.2747   0.4852
 005  CG    C  CH2   0  -0.520  -0.3873   0.4950   1.0303
 005  CH    C  CR16  0  -0.273  -4.3009  -0.1657  -0.6314
 005  CB1   C  CH1   0  -0.131   0.6889  -0.0288   0.0651
 005  OB2   O  OH1   0  -0.652   2.2965   1.7262   0.6362
 005  CE1   C  CR16  0  -0.322  -2.4980  -0.8700   0.8001
 005  CE2   C  CR16  0  -0.305  -2.3292   1.1946  -0.4004
 005  CZ1   C  CR16  0  -0.240  -3.7546  -1.0897   0.2487
 005  CZ2   C  CR16  0  -0.240  -3.5833   0.9798  -0.9540
 005  OXT   O  OH1   0  -0.584   3.7319  -1.3360   0.1601
 005  HN    H  HNH2  0   0.345   0.6714  -1.9705   0.6908
 005  HNA   H  HNH2  0   0.362  -0.2087  -1.7111  -0.6447
 005  HA    H  HCH1  0   0.263   2.2306  -0.0454   1.5761
 005  HG    H  HCH2  0   0.251  -0.2266   1.5608   1.2065
 005  HGA   H  HCH2  0   0.246  -0.2730  -0.0096   1.9950
 005  HH    H  HCR6  0   0.254  -5.2802  -0.3344  -1.0601
 005  HB1   H  HCH1  0   0.248   0.5473   0.4635  -0.9051
 005  HOB2  H  HOH1  0   0.449   2.1707   2.1018  -0.2428
 005  HE1   H  HCR6  0   0.248  -2.0827  -1.5948   1.4910
 005  HE2   H  HCR6  0   0.246  -1.7781   2.0927  -0.6573
 005  HZ1   H  HCR6  0   0.254  -4.3068  -1.9838   0.5094
 005  HZ2   H  HCR6  0   0.254  -4.0032   1.7086  -1.6357
 005  HXT   H  HOH1  0   0.481   4.3625  -1.7103  -0.4744

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
 005  C    CA    single    1.525  0.021  1.525
 005  C    O     double    1.231  0.020  1.231
 005  C    OXT   single    1.322  0.020  1.322
 005  N    CB1   single    1.449  0.020  1.449
 005  N    HN    single    0.890  0.020  1.040
 005  N    HNA   single    0.890  0.020  1.040
 005  CA   OB2   single    1.401  0.020  1.401
 005  CA   HA    single    0.970  0.020  0.970
 005  CD   CG    single    1.501  0.020  1.501
 005  CG   HG    single    0.970  0.020  1.090
 005  CG   HGA   single    0.970  0.020  1.090
 005  CH   CZ1   aromatic  1.388  0.020  1.388
 005  CH   CZ2   aromatic  1.390  0.020  1.390
 005  CH   HH    single    0.930  0.020  1.080
 005  CB1  CA    single    1.534  0.020  1.534
 005  CB1  CG    single    1.538  0.020  1.538
 005  CB1  HB1   single    0.970  0.020  1.090
 005  OB2  HOB2  single    0.850  0.020  0.980
 005  CE1  CD    aromatic  1.394  0.020  1.394
 005  CE1  HE1   single    0.930  0.020  1.080
 005  CE2  CD    aromatic  1.395  0.020  1.395
 005  CE2  HE2   single    0.930  0.020  1.080
 005  CZ1  CE1   aromatic  1.390  0.020  1.390
 005  CZ1  HZ1   single    0.930  0.020  1.080
 005  CZ2  CE2   aromatic  1.388  0.020  1.388
 005  CZ2  HZ2   single    0.930  0.020  1.080
 005  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
 005  OXT   C    CA   120.80  1.700
 005  OXT   C    O    124.02  3.000
 005  CA    C    O    120.80  1.700
 005  HNA   N    HN   106.21  3.000
 005  HNA   N    CB1  110.25  3.000
 005  HN    N    CB1  110.63  3.000
 005  HA    CA   OB2  106.42  3.000
 005  HA    CA   CB1  109.32  3.000
 005  OB2   CA   CB1  112.90  3.000
 005  CB1   CA   C    108.51  3.000
 005  HA    CA   C    110.00  3.000
 005  OB2   CA   C    110.15  3.000
 005  CE2   CD   CE1  118.35  3.000
 005  CE2   CD   CG   120.25  3.000
 005  CE1   CD   CG   121.35  3.000
 005  HGA   CG   HG   106.99  3.000
 005  HGA   CG   CB1  108.85  3.000
 005  HG    CG   CB1  109.31  3.000
 005  CB1   CG   CD   111.47  3.000
 005  HGA   CG   CD   110.40  3.000
 005  HG    CG   CD   109.71  3.000
 005  HH    CH   CZ2  120.25  3.000
 005  HH    CH   CZ1  120.23  3.000
 005  CZ2   CH   CZ1  119.52  3.000
 005  HB1   CB1  CG   108.18  3.000
 005  HB1   CB1  CA   107.25  3.000
 005  CG    CB1  CA   110.75  3.000
 005  HB1   CB1  N    106.72  3.000
 005  CG    CB1  N    115.25  3.000
 005  CA    CB1  N    108.34  3.000
 005  HOB2  OB2  CA   108.54  3.000
 005  HE1   CE1  CZ1  119.58  3.000
 005  CZ1   CE1  CD   120.90  3.000
 005  HE1   CE1  CD   119.51  3.000
 005  HE2   CE2  CZ2  119.53  3.000
 005  CZ2   CE2  CD   120.98  3.000
 005  HE2   CE2  CD   119.49  3.000
 005  HZ1   CZ1  CE1  119.74  3.000
 005  HZ1   CZ1  CH   120.11  3.000
 005  CE1   CZ1  CH   120.15  3.000
 005  HZ2   CZ2  CE2  119.84  3.000
 005  HZ2   CZ2  CH   120.05  3.000
 005  CE2   CZ2  CH   120.11  3.000
 005  HXT   OXT  C    110.23  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
 005  CONST_01  CH   CZ1  CE1  CD     0.00   0.0  0
 005  CONST_02  CH   CZ2  CE2  CD     0.00   0.0  0
 005  CONST_03  CZ2  CE2  CD   CE1    0.00   0.0  0
 005  CONST_04  CZ2  CH   CZ1  CE1    0.00   0.0  0
 005  CONST_05  CZ1  CE1  CD   CE2    0.00   0.0  0
 005  CONST_06  CZ1  CH   CZ2  CE2    0.00   0.0  0
 005  CONST_07  CZ1  CE1  CD   CG   180.00   0.0  0
 005  CONST_08  CZ2  CE2  CD   CG   180.00   0.0  0
 005  CONST_09  HZ1  CZ1  CE1  CD   180.00   0.0  0
 005  CONST_10  HZ2  CZ2  CE2  CD   180.00   0.0  0
 005  CONST_11  HE1  CE1  CZ1  CH   180.00   0.0  0
 005  CONST_12  HE2  CE2  CZ2  CH   180.00   0.0  0
 005  CONST_13  HH   CH   CZ1  CE1  180.00   0.0  0
 005  CONST_14  HXT  OXT  C    O      0.00   0.0  0
 005  Var_01    CE1  CD   CG   CB1   92.74  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
 005  chir_01  CA   C  OB2  CB1  negativ
 005  chir_02  CB1  N  CG   CA   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
 005  plan-1  CD   0.020
 005  plan-1  CG   0.020
 005  plan-1  CH   0.020
 005  plan-1  CE1  0.020
 005  plan-1  CE2  0.020
 005  plan-1  CZ1  0.020
 005  plan-1  CZ2  0.020
 005  plan-1  HH   0.020
 005  plan-1  HE1  0.020
 005  plan-1  HE2  0.020
 005  plan-1  HZ1  0.020
 005  plan-1  HZ2  0.020
 005  plan-2  C    0.020
 005  plan-2  O    0.020
 005  plan-2  CA   0.020
 005  plan-2  OXT  0.020
 005  plan-2  HXT  0.020

