# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:45:19 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (3S)-3-amino-4-(4-hydroxyphenyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC(O)=O)Cc1ccc(O)cc1
#
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
 B3Y  B3Y  '(3S)-3-amino-4-(4-hydroxyphenyl)butanoic acid'  L-peptide  27  14  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3Y
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
 B3Y  O    O  O     0  -0.447  -0.5755  -1.7823  -1.7282
 B3Y  C    C  C     0   0.552  -1.1690  -2.3504  -0.8425
 B3Y  CA   C  CH2   0  -0.594  -0.6336  -2.6408   0.5318
 B3Y  CB   C  CH1   0  -0.085   0.5628  -1.7917   0.9828
 B3Y  N    N  NH2   0  -0.793   1.8035  -2.0223   0.2617
 B3Y  CG   C  CH2   0  -0.514   0.2631  -0.2855   0.9908
 B3Y  CD   C  CR6   0   0.103  -1.0077   0.0636   1.7123
 B3Y  CE2  C  CR16  0  -0.300  -2.1564   0.4333   1.0210
 B3Y  CF2  C  CR16  0  -0.369  -3.3457   0.7152   1.6803
 B3Y  CZ   C  CR6   0   0.337  -3.4074   0.6275   3.0669
 B3Y  OH   O  OH1   0  -0.636  -4.5335   0.8831   3.7666
 B3Y  CF1  C  CR16  0  -0.323  -2.2654   0.2642   3.7786
 B3Y  CE1  C  CR16  0  -0.294  -1.0884  -0.0108   3.1028
 B3Y  OXT  O  OH1   0  -0.594  -2.4010  -2.8257  -1.0000
 B3Y  HXT  H  HOH1  0   0.477  -2.7041  -2.6616  -1.9058
 B3Y  HA1  H  HCH2  0   0.294  -0.3388  -3.6965   0.5430
 B3Y  HA2  H  HCH2  0   0.272  -1.4485  -2.5615   1.2544
 B3Y  HB   H  HCH1  0   0.241   0.7429  -2.0874   2.0216
 B3Y  H    H  HNH2  0   0.341   1.6667  -1.8295  -0.7225
 B3Y  H2   H  HNH2  0   0.345   2.0592  -3.0003   0.3230
 B3Y  HG2  H  HCH2  0   0.248   1.1144   0.2156   1.4580
 B3Y  HG3  H  HCH2  0   0.241   0.2136   0.0824  -0.0362
 B3Y  HE2  H  HCR6  0   0.248  -2.1290   0.5105  -0.0600
 B3Y  HF2  H  HCR6  0   0.267  -4.2216   1.0044   1.1101
 B3Y  HOH  H  HOH1  0   0.472  -5.2553   1.1029   3.1674
 B3Y  HF1  H  HCR6  0   0.260  -2.3044   0.2011   4.8592
 B3Y  HE1  H  HCR6  0   0.248  -0.2112  -0.2907   3.6754

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
 B3Y  O    C    double    1.231  0.020  1.231
 B3Y  C    CA   single    1.525  0.021  1.525
 B3Y  C    OXT  single    1.330  0.020  1.330
 B3Y  CA   CB   single    1.530  0.020  1.530
 B3Y  CA   HA1  single    0.970  0.020  1.090
 B3Y  CA   HA2  single    0.970  0.020  1.090
 B3Y  CB   CG   single    1.536  0.020  1.536
 B3Y  CB   N    single    1.453  0.020  1.453
 B3Y  CB   HB   single    0.970  0.020  1.090
 B3Y  N    H    single    0.860  0.020  0.860
 B3Y  N    H2   single    0.890  0.020  1.040
 B3Y  CG   CD   single    1.502  0.020  1.502
 B3Y  CG   HG2  single    0.970  0.020  1.090
 B3Y  CG   HG3  single    0.970  0.020  1.090
 B3Y  CD   CE2  aromatic  1.391  0.020  1.391
 B3Y  CD   CE1  aromatic  1.395  0.020  1.395
 B3Y  CE2  CF2  aromatic  1.389  0.020  1.389
 B3Y  CE2  HE2  single    0.930  0.020  1.080
 B3Y  CF2  CZ   aromatic  1.391  0.020  1.391
 B3Y  CF2  HF2  single    0.930  0.020  1.080
 B3Y  CZ   CF1  aromatic  1.394  0.020  1.394
 B3Y  CZ   OH   single    1.350  0.020  1.350
 B3Y  OH   HOH  single    0.850  0.020  0.980
 B3Y  CF1  CE1  aromatic  1.385  0.020  1.385
 B3Y  CF1  HF1  single    0.930  0.020  1.080
 B3Y  CE1  HE1  single    0.930  0.020  1.080
 B3Y  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
 B3Y  OXT  C    CA   111.67  3.000
 B3Y  OXT  C    O    122.43  3.000
 B3Y  CA   C    O    120.80  1.700
 B3Y  HA2  CA   HA1  105.30  3.000
 B3Y  HA2  CA   CB   110.31  3.000
 B3Y  HA1  CA   CB   108.68  3.000
 B3Y  HA2  CA   C    108.97  3.000
 B3Y  HA1  CA   C    106.92  3.000
 B3Y  CB   CA   C    110.10  1.900
 B3Y  HB   CB   CG   106.97  3.000
 B3Y  HB   CB   N    106.70  3.000
 B3Y  CG   CB   N    108.95  3.000
 B3Y  HB   CB   CA   104.93  3.000
 B3Y  N    CB   CA   110.50  1.700
 B3Y  CG   CB   CA   113.08  3.000
 B3Y  H2   N    H    106.07  3.000
 B3Y  H2   N    CB   109.80  3.000
 B3Y  H    N    CB   109.68  3.000
 B3Y  HG3  CG   HG2  106.43  3.000
 B3Y  HG3  CG   CD   109.57  3.000
 B3Y  HG2  CG   CD   110.31  3.000
 B3Y  HG3  CG   CB   109.53  3.000
 B3Y  HG2  CG   CB   107.46  3.000
 B3Y  CD   CG   CB   113.29  3.000
 B3Y  CE1  CD   CE2  117.51  3.000
 B3Y  CE1  CD   CG   121.01  3.000
 B3Y  CE2  CD   CG   121.44  3.000
 B3Y  HE2  CE2  CF2  118.72  3.000
 B3Y  HE2  CE2  CD   119.59  3.000
 B3Y  CF2  CE2  CD   121.69  3.000
 B3Y  HF2  CF2  CZ   120.35  3.000
 B3Y  HF2  CF2  CE2  119.75  3.000
 B3Y  CZ   CF2  CE2  119.90  3.000
 B3Y  CF1  CZ   OH   117.91  3.000
 B3Y  OH   CZ   CF2  122.81  3.000
 B3Y  CF1  CZ   CF2  119.29  3.000
 B3Y  HOH  OH   CZ   110.22  3.000
 B3Y  HF1  CF1  CE1  120.39  3.000
 B3Y  HF1  CF1  CZ   119.68  3.000
 B3Y  CE1  CF1  CZ   119.93  3.000
 B3Y  HE1  CE1  CF1  118.76  3.000
 B3Y  HE1  CE1  CD   119.57  3.000
 B3Y  CF1  CE1  CD   121.67  3.000
 B3Y  HXT  OXT  C    109.88  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
 B3Y  CONST_01  CZ   CF2  CE2  CD      0.00   0.0  0
 B3Y  CONST_02  CZ   CF1  CE1  CD      0.00   0.0  0
 B3Y  CONST_03  CF1  CE1  CD   CE2     0.00   0.0  0
 B3Y  CONST_04  CF1  CZ   CF2  CE2     0.00   0.0  0
 B3Y  CONST_05  CE1  CD   CE2  CF2     0.00   0.0  0
 B3Y  CONST_06  CE1  CF1  CZ   CF2     0.00   0.0  0
 B3Y  CONST_07  CF2  CE2  CD   CG    180.00   0.0  0
 B3Y  CONST_08  CF1  CE1  CD   CG    180.00   0.0  0
 B3Y  CONST_09  OH   CZ   CF2  CE2   180.00   0.0  0
 B3Y  CONST_10  CE1  CF1  CZ   OH    180.00   0.0  0
 B3Y  CONST_11  HF2  CF2  CE2  CD    180.00   0.0  0
 B3Y  CONST_12  HF1  CF1  CE1  CD    180.00   0.0  0
 B3Y  CONST_13  HE1  CE1  CD   CE2   180.00   0.0  0
 B3Y  CONST_14  HE2  CE2  CF2  CZ    180.00   0.0  0
 B3Y  CONST_15  HXT  OXT  C    O       0.00   0.0  0
 B3Y  Var_01    CE2  CD   CG   CB   -105.77  30.0  2
 B3Y  Var_02    CB   CA   C    O      19.69  30.0  3

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
 B3Y  chir_01  CB  CA  CG  N  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
 B3Y  plan-1  CG   0.020
 B3Y  plan-1  CD   0.020
 B3Y  plan-1  CE2  0.020
 B3Y  plan-1  CF2  0.020
 B3Y  plan-1  CZ   0.020
 B3Y  plan-1  OH   0.020
 B3Y  plan-1  CF1  0.020
 B3Y  plan-1  CE1  0.020
 B3Y  plan-1  HE2  0.020
 B3Y  plan-1  HF2  0.020
 B3Y  plan-1  HF1  0.020
 B3Y  plan-1  HE1  0.020
 B3Y  plan-2  O    0.020
 B3Y  plan-2  C    0.020
 B3Y  plan-2  CA   0.020
 B3Y  plan-2  OXT  0.020
 B3Y  plan-2  HXT  0.020

