# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 15:27:42 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (4S,5S)-5-amino-4-hydroxy-6-phenylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)CCC(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
 FOG  FOG  '(4S,5S)-5-amino-4-hydroxy-6-phenylhexanoic acid'  peptide  33  16  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_FOG
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
 FOG  C    C  C     0   0.550  -4.6909  -0.6360   0.1373
 FOG  O1   O  O     0  -0.447  -4.5931  -1.7192  -0.3842
 FOG  CA1  C  CH2   0  -0.579  -3.5492   0.2963   0.4302
 FOG  CM   C  CH2   0  -0.452  -2.1976  -0.2391  -0.0104
 FOG  CH   C  CH1   0   0.052  -1.0598   0.7177   0.3280
 FOG  OH   O  OH1   0  -0.675  -1.2520   1.9924  -0.2552
 FOG  CA   C  CH1   0  -0.096   0.3065   0.1328  -0.0553
 FOG  N    N  NH2   0  -0.804   0.4265   0.0721  -1.5046
 FOG  CB   C  CH2   0  -0.534   1.4444   0.9024   0.6373
 FOG  CG   C  CR6   0   0.149   2.7909   0.2977   0.3648
 FOG  CD1  C  CR16  0  -0.328   3.6176   0.7894  -0.6430
 FOG  CD2  C  CR16  0  -0.307   3.2260  -0.8080   1.0949
 FOG  CE1  C  CR16  0  -0.240   4.8449   0.1969  -0.9138
 FOG  CE2  C  CR16  0  -0.240   4.4508  -1.4040   0.8293
 FOG  CZ   C  CR16  0  -0.274   5.2656  -0.9030  -0.1788
 FOG  OXT  O  OH1   0  -0.599  -5.8573  -0.1257   0.5262
 FOG  HA1  H  HCH2  0   0.278  -3.7681   1.2555  -0.0466
 FOG  HM   H  HCH2  0   0.233  -2.0002  -1.1939   0.4835
 FOG  HA   H  HCH1  0   0.235   0.3277  -0.8974   0.3143
 FOG  H    H  HNH2  0   0.340   0.7641   0.9554  -1.8686
 FOG  H2   H  HNH2  0   0.357   1.1216  -0.6130  -1.7686
 FOG  HB2  H  HCH2  0   0.243   1.4244   1.9443   0.3046
 FOG  HB3  H  HCH2  0   0.242   1.2590   0.9125   1.7152
 FOG  HD1  H  HCR6  0   0.244   3.3056   1.6561  -1.2145
 FOG  HD2  H  HCR6  0   0.244   2.5985  -1.2049   1.8851
 FOG  HE1  H  HCR6  0   0.252   5.4744   0.5991  -1.6976
 FOG  HE2  H  HCR6  0   0.252   4.7720  -2.2586   1.4115
 FOG  HZ   H  HCR6  0   0.253   6.2232  -1.3632  -0.3860
 FOG  HCH  H  HCH1  0   0.223  -1.0631   0.8866   1.4109
 FOG  HO1  H  HOH1  0   0.441  -1.3392   1.8665  -1.2073
 FOG  HM1  H  HCH2  0   0.235  -2.1919  -0.4390  -1.0851
 FOG  HA2  H  HCH2  0   0.275  -3.5509   0.5004   1.5062
 FOG  HXT  H  HOH1  0   0.478  -6.5719  -0.7491   0.3295

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
 FOG  C    O1   double    1.206  0.020  1.206
 FOG  C    CA1  single    1.503  0.020  1.503
 FOG  C    OXT  single    1.331  0.020  1.331
 FOG  CA1  CM   single    1.519  0.020  1.519
 FOG  CA1  HA1  single    0.970  0.020  1.090
 FOG  CA1  HA2  single    0.970  0.020  1.090
 FOG  CM   CH   single    1.525  0.020  1.525
 FOG  CM   HM   single    0.970  0.020  1.090
 FOG  CM   HM1  single    0.970  0.020  1.090
 FOG  CH   OH   single    1.415  0.020  1.415
 FOG  CH   CA   single    1.535  0.020  1.535
 FOG  CH   HCH  single    0.970  0.020  1.090
 FOG  OH   HO1  single    0.850  0.020  0.980
 FOG  CA   N    single    1.458  0.019  1.458
 FOG  CA   CB   single    1.521  0.033  1.521
 FOG  CA   HA   single    0.970  0.020  0.970
 FOG  N    H    single    0.860  0.020  0.860
 FOG  N    H2   single    0.890  0.020  1.040
 FOG  CB   CG   single    1.501  0.020  1.501
 FOG  CB   HB2  single    0.970  0.020  1.090
 FOG  CB   HB3  single    0.970  0.020  1.090
 FOG  CG   CD1  aromatic  1.393  0.020  1.393
 FOG  CG   CD2  aromatic  1.395  0.020  1.395
 FOG  CD1  CE1  aromatic  1.390  0.020  1.390
 FOG  CD1  HD1  single    0.930  0.020  1.080
 FOG  CD2  CE2  aromatic  1.388  0.020  1.388
 FOG  CD2  HD2  single    0.930  0.020  1.080
 FOG  CE1  CZ   aromatic  1.388  0.020  1.388
 FOG  CE1  HE1  single    0.930  0.020  1.080
 FOG  CE2  CZ   aromatic  1.390  0.020  1.390
 FOG  CE2  HE2  single    0.930  0.020  1.080
 FOG  CZ   HZ   single    0.930  0.020  1.080
 FOG  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
 FOG  OXT  C    CA1  111.77  3.000
 FOG  OXT  C    O1   122.79  3.000
 FOG  CA1  C    O1   125.44  3.000
 FOG  HA2  CA1  HA1  105.34  3.000
 FOG  HA2  CA1  CM   110.61  3.000
 FOG  HA1  CA1  CM   111.15  3.000
 FOG  HA2  CA1  C    107.82  3.000
 FOG  HA1  CA1  C    107.89  3.000
 FOG  CM   CA1  C    113.63  3.000
 FOG  HM1  CM   HM   106.48  3.000
 FOG  HM1  CM   CH   109.22  3.000
 FOG  HM   CM   CH   108.25  3.000
 FOG  HM1  CM   CA1  110.74  3.000
 FOG  HM   CM   CA1  109.72  3.000
 FOG  CH   CM   CA1  112.24  3.000
 FOG  HCH  CH   CA   107.95  3.000
 FOG  HCH  CH   OH   105.54  3.000
 FOG  CA   CH   OH   111.18  3.000
 FOG  HCH  CH   CM   108.29  3.000
 FOG  CA   CH   CM   111.70  3.000
 FOG  OH   CH   CM   111.87  3.000
 FOG  HO1  OH   CH   107.55  3.000
 FOG  HA   CA   CB   109.00  3.000
 FOG  HA   CA   N    110.00  3.000
 FOG  CB   CA   N    110.40  1.500
 FOG  HA   CA   CH   106.94  3.000
 FOG  CB   CA   CH   110.82  3.000
 FOG  N    CA   CH   109.75  3.000
 FOG  H2   N    H    105.53  3.000
 FOG  H2   N    CA   110.17  3.000
 FOG  H    N    CA   114.00  3.000
 FOG  HB3  CB   HB2  106.73  3.000
 FOG  HB3  CB   CG   109.55  3.000
 FOG  HB2  CB   CG   110.18  3.000
 FOG  HB3  CB   CA   108.84  3.000
 FOG  HB2  CB   CA   109.03  3.000
 FOG  CG   CB   CA   112.35  3.000
 FOG  CD2  CG   CD1  118.26  3.000
 FOG  CD2  CG   CB   120.28  3.000
 FOG  CD1  CG   CB   121.43  3.000
 FOG  HD1  CD1  CE1  119.49  3.000
 FOG  HD1  CD1  CG   119.53  3.000
 FOG  CE1  CD1  CG   120.97  3.000
 FOG  HD2  CD2  CE2  119.54  3.000
 FOG  HD2  CD2  CG   119.42  3.000
 FOG  CE2  CD2  CG   121.04  3.000
 FOG  HE1  CE1  CZ   120.09  3.000
 FOG  HE1  CE1  CD1  119.75  3.000
 FOG  CZ   CE1  CD1  120.15  3.000
 FOG  HE2  CE2  CZ   120.04  3.000
 FOG  HE2  CE2  CD2  119.86  3.000
 FOG  CZ   CE2  CD2  120.10  3.000
 FOG  HZ   CZ   CE2  120.28  3.000
 FOG  HZ   CZ   CE1  120.24  3.000
 FOG  CE2  CZ   CE1  119.48  3.000
 FOG  HXT  OXT  C    109.90  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
 FOG  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 FOG  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 FOG  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 FOG  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 FOG  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 FOG  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 FOG  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 FOG  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 FOG  CONST_09  HE1  CE1  CD1  CG    180.00   0.0  0
 FOG  CONST_10  HE2  CE2  CD2  CG    180.00   0.0  0
 FOG  CONST_11  HD2  CD2  CG   CD1   180.00   0.0  0
 FOG  CONST_12  HZ   CZ   CE1  CD1   180.00   0.0  0
 FOG  CONST_13  HD1  CD1  CG   CD2   180.00   0.0  0
 FOG  CONST_14  HXT  OXT  C    O1      0.00   0.0  0
 FOG  Var_01    CD1  CG   CB   CA     96.66  30.0  2
 FOG  Var_02    CH   CM   CA1  C    -178.80  30.0  3
 FOG  Var_03    CM   CA1  C    O1      0.64  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
 FOG  chir_01  CH  CM  OH  CA  positiv
 FOG  chir_02  CA  N   CB  CH  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
 FOG  plan-1  CB   0.020
 FOG  plan-1  CG   0.020
 FOG  plan-1  CD1  0.020
 FOG  plan-1  CD2  0.020
 FOG  plan-1  CE1  0.020
 FOG  plan-1  CE2  0.020
 FOG  plan-1  CZ   0.020
 FOG  plan-1  HD1  0.020
 FOG  plan-1  HD2  0.020
 FOG  plan-1  HE1  0.020
 FOG  plan-1  HE2  0.020
 FOG  plan-1  HZ   0.020
 FOG  plan-2  C    0.020
 FOG  plan-2  O1   0.020
 FOG  plan-2  CA1  0.020
 FOG  plan-2  OXT  0.020
 FOG  plan-2  HXT  0.020

