# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:50:50 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-amino-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(N)cc1)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
 HOX  HOX  '4-amino-L-phenylalanine  '  L-peptide  24  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HOX
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
 HOX  O     O  O      0  -0.608   3.0180  55.4997  83.6469
 HOX  C     C  C      0   0.396   1.9175  56.0421  83.4208
 HOX  N     N  NH2    0  -0.809   1.7145  55.1691  81.1159
 HOX  OXT   O  OC    -1  -0.608   1.4715  57.0780  83.9537
 HOX  CA    C  CH1    0  -0.152   1.0042  55.3458  82.3802
 HOX  CB    C  CH2    0  -0.509   0.5785  53.9624  82.8875
 HOX  CG    C  CR6    0   0.101  -0.2713  54.0130  84.1251
 HOX  CZ    C  CR6    0   0.278  -1.8837  54.1564  86.4551
 HOX  NZ    N  NH2    0  -0.859  -2.6762  54.1617  87.5897
 HOX  CD1   C  CR16   0  -0.307  -1.6546  54.1583  84.0456
 HOX  CD2   C  CR16   0  -0.294   0.2854  53.9464  85.4003
 HOX  CE1   C  CR16   0  -0.309  -2.4506  54.2290  85.1782
 HOX  CE2   C  CR16   0  -0.310  -0.4949  54.0156  86.5440
 HOX  HN    H  HNH2   0   0.332   1.0643  54.8144  80.4239
 HOX  HNA   H  HNH2   0   0.335   2.0130  56.0706  80.7632
 HOX  HA    H  HCH1   0   0.173   0.0941  55.9533  82.2656
 HOX  HB    H  HCH2   0   0.224   0.0237  53.4551  82.0909
 HOX  HBA   H  HCH2   0   0.224   1.4799  53.3721  83.0678
 HOX  HNZ   H  HNH2   0   0.373  -2.2135  54.4648  88.4322
 HOX  HNZA  H  HNH2   0   0.372  -3.5711  54.6132  87.4847
 HOX  HD1   H  HCR6   0   0.235  -2.1274  54.2148  83.0709
 HOX  HD2   H  HCR6   0   0.232   1.3592  53.8434  85.5059
 HOX  HE1   H  HCR6   0   0.245  -3.5246  54.3362  85.0745
 HOX  HE2   H  HCR6   0   0.245  -0.0242  53.9576  87.5190

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
 HOX  O    C     deloc     1.231  0.020  1.231
 HOX  CA   C     single    1.525  0.021  1.525
 HOX  C    OXT   deloc     1.247  0.020  1.247
 HOX  N    CA    single    1.458  0.019  1.458
 HOX  N    HN    single    0.890  0.020  1.040
 HOX  N    HNA   single    0.890  0.020  1.040
 HOX  CA   CB    single    1.530  0.020  1.530
 HOX  CA   HA    single    0.970  0.020  0.970
 HOX  CB   CG    single    1.502  0.020  1.502
 HOX  CB   HB    single    0.970  0.020  1.090
 HOX  CB   HBA   single    0.970  0.020  1.090
 HOX  CD1  CG    aromatic  1.393  0.020  1.393
 HOX  CG   CD2   aromatic  1.393  0.020  1.393
 HOX  CE1  CZ    aromatic  1.399  0.020  1.399
 HOX  CZ   CE2   aromatic  1.399  0.020  1.399
 HOX  CZ   NZ    single    1.384  0.020  1.384
 HOX  NZ   HNZ   single    0.890  0.020  1.040
 HOX  NZ   HNZA  single    0.890  0.020  1.040
 HOX  CD1  CE1   aromatic  1.386  0.020  1.386
 HOX  CD1  HD1   single    0.930  0.020  1.080
 HOX  CD2  CE2   aromatic  1.386  0.020  1.386
 HOX  CD2  HD2   single    0.930  0.020  1.080
 HOX  CE1  HE1   single    0.930  0.020  1.080
 HOX  CE2  HE2   single    0.930  0.020  1.080

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
 HOX  CA    C    OXT  116.69  3.000
 HOX  OXT   C    O    126.80  3.000
 HOX  CA    C    O    120.80  1.700
 HOX  HNA   N    HN   105.23  3.000
 HOX  HNA   N    CA   109.70  3.000
 HOX  HN    N    CA   108.75  3.000
 HOX  HA    CA   CB   109.00  3.000
 HOX  HA    CA   N    110.00  3.000
 HOX  CB    CA   N    110.50  1.700
 HOX  HA    CA   C    109.00  3.000
 HOX  CB    CA   C    110.10  1.900
 HOX  N     CA   C    111.00  2.800
 HOX  HBA   CB   HB   106.72  3.000
 HOX  HBA   CB   CG   110.43  3.000
 HOX  HB    CB   CG   109.16  3.000
 HOX  HBA   CB   CA   108.23  3.000
 HOX  HB    CB   CA   108.53  3.000
 HOX  CG    CB   CA   113.52  3.000
 HOX  CD2   CG   CD1  117.01  3.000
 HOX  CD2   CG   CB   121.77  3.000
 HOX  CD1   CG   CB   121.21  3.000
 HOX  CE2   CZ   CE1  117.75  3.000
 HOX  CE2   CZ   NZ   121.12  3.000
 HOX  CE1   CZ   NZ   121.07  3.000
 HOX  HNZA  NZ   HNZ  111.10  3.000
 HOX  HNZA  NZ   CZ   115.13  3.000
 HOX  HNZ   NZ   CZ   115.07  3.000
 HOX  HD1   CD1  CE1  118.77  3.000
 HOX  HD1   CD1  CG   119.31  3.000
 HOX  CE1   CD1  CG   121.92  3.000
 HOX  HD2   CD2  CE2  118.82  3.000
 HOX  HD2   CD2  CG   119.32  3.000
 HOX  CE2   CD2  CG   121.86  3.000
 HOX  HE1   CE1  CD1  119.71  3.000
 HOX  HE1   CE1  CZ   119.59  3.000
 HOX  CD1   CE1  CZ   120.69  3.000
 HOX  HE2   CE2  CD2  119.66  3.000
 HOX  HE2   CE2  CZ   119.58  3.000
 HOX  CD2   CE2  CZ   120.76  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
 HOX  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 HOX  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 HOX  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 HOX  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 HOX  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 HOX  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 HOX  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 HOX  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 HOX  CONST_09  CD1  CE1  CZ   NZ   180.00   0.0  0
 HOX  CONST_10  CD2  CE2  CZ   NZ   180.00   0.0  0
 HOX  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 HOX  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 HOX  CONST_13  HD1  CD1  CE1  CZ   180.00   0.0  0
 HOX  CONST_14  HD2  CD2  CE2  CZ   180.00   0.0  0
 HOX  Var_01    CD1  CG   CB   CA    86.77  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
 HOX  chir_01  CA  C  N  CB  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
 HOX  plan-1  CB    0.020
 HOX  plan-1  CG    0.020
 HOX  plan-1  CZ    0.020
 HOX  plan-1  NZ    0.020
 HOX  plan-1  CD1   0.020
 HOX  plan-1  CD2   0.020
 HOX  plan-1  CE1   0.020
 HOX  plan-1  CE2   0.020
 HOX  plan-1  HD1   0.020
 HOX  plan-1  HD2   0.020
 HOX  plan-1  HE1   0.020
 HOX  plan-1  HE2   0.020
 HOX  plan-2  CZ    0.020
 HOX  plan-2  NZ    0.020
 HOX  plan-2  HNZ   0.020
 HOX  plan-2  HNZA  0.020
 HOX  plan-3  O     0.020
 HOX  plan-3  C     0.020
 HOX  plan-3  OXT   0.020
 HOX  plan-3  CA    0.020

