# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:13:04 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-methyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C[C@H](N)C(O)=O)c1
#
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
 APD  APD  '3-methyl-L-phenylalanine '  ligand  25  13  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_APD
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
 APD  C     C  C      0   0.403   0.4087  -0.0095  -3.0626
 APD  O     O  O      0  -0.604  -0.5343   0.0092  -3.8775
 APD  CA    C  CH1    0  -0.196   0.0974   0.4101  -1.6086
 APD  N     N  NH2    0  -0.796  -1.0738   1.2637  -1.5529
 APD  CB    C  CH2    0  -0.525  -0.0050  -0.8738  -0.7498
 APD  CG    C  CR6    0   0.147  -0.2251  -0.5718   0.7034
 APD  CD1   C  CR16   0  -0.343  -1.5045  -0.5562   1.2561
 APD  CD2   C  CR16   0  -0.353   0.8531  -0.2355   1.5205
 APD  CE1   C  CR16   0  -0.229  -1.6907  -0.2144   2.5891
 APD  CE2   C  CR6    0   0.116   0.6867   0.1072   2.8594
 APD  CZ    C  CR16   0  -0.321  -0.6041   0.1171   3.3855
 APD  C5    C  CH3    0  -0.724   1.8734   0.4316   3.7209
 APD  OXT   O  OC    -1  -0.619   1.5799  -0.3748  -3.2872
 APD  HA    H  HCH1   0   0.211   0.9547   0.9783  -1.2313
 APD  HN1   H  HNH2   0   0.327  -1.8230   0.8174  -2.0673
 APD  HN2   H  HNH2   0   0.335  -1.3946   1.3614  -0.5968
 APD  HBC1  H  HCH2   0   0.237   0.9134  -1.4525  -0.8708
 APD  HBC2  H  HCH2   0   0.233  -0.8253  -1.4882  -1.1332
 APD  HD1   H  HCR6   0   0.245  -2.3593  -0.8159   0.6422
 APD  HD2   H  HCR6   0   0.235   1.8543  -0.2436   1.0996
 APD  HE1   H  HCR6   0   0.249  -2.6891  -0.2046   3.0083
 APD  HZ    H  HCR6   0   0.243  -0.7586   0.3836   4.4245
 APD  H5C1  H  HCH3   0   0.247   2.3487  -0.4793   4.0907
 APD  H5C2  H  HCH3   0   0.242   2.6304   0.9879   3.1683
 APD  H5C3  H  HCH3   0   0.242   1.5866   1.0235   4.5898

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
 APD  C    O     deloc     1.246  0.020  1.246
 APD  C    CA    single    1.545  0.020  1.545
 APD  C    OXT   deloc     1.247  0.020  1.247
 APD  CA   N     single    1.450  0.020  1.450
 APD  CA   CB    single    1.548  0.020  1.548
 APD  CA   HA    single    0.970  0.020  1.090
 APD  N    HN1   single    0.890  0.020  1.040
 APD  N    HN2   single    0.890  0.020  1.040
 APD  CB   CG    single    1.501  0.020  1.501
 APD  CB   HBC1  single    0.970  0.020  1.090
 APD  CB   HBC2  single    0.970  0.020  1.090
 APD  CG   CD1   aromatic  1.394  0.020  1.394
 APD  CG   CD2   aromatic  1.394  0.020  1.394
 APD  CD1  CE1   aromatic  1.389  0.020  1.389
 APD  CD1  HD1   single    0.930  0.020  1.080
 APD  CD2  CE2   aromatic  1.392  0.020  1.392
 APD  CD2  HD2   single    0.930  0.020  1.080
 APD  CE1  CZ    aromatic  1.387  0.020  1.387
 APD  CE1  HE1   single    0.930  0.020  1.080
 APD  CE2  CZ    aromatic  1.394  0.020  1.394
 APD  CE2  C5    single    1.502  0.020  1.502
 APD  CZ   HZ    single    0.930  0.020  1.080
 APD  C5   H5C1  single    0.970  0.020  1.090
 APD  C5   H5C2  single    0.970  0.020  1.090
 APD  C5   H5C3  single    0.970  0.020  1.090

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
 APD  OXT   C    CA    115.99  3.000
 APD  OXT   C    O     126.66  3.000
 APD  CA    C    O     117.31  3.000
 APD  HA    CA   CB    106.91  3.000
 APD  HA    CA   N     108.27  3.000
 APD  CB    CA   N     114.42  3.000
 APD  HA    CA   C     107.90  3.000
 APD  CB    CA   C     108.07  3.000
 APD  N     CA   C     111.02  3.000
 APD  HN2   N    HN1   106.72  3.000
 APD  HN2   N    CA    110.41  3.000
 APD  HN1   N    CA    108.58  3.000
 APD  HBC2  CB   HBC1  107.10  3.000
 APD  HBC2  CB   CG    110.02  3.000
 APD  HBC1  CB   CG    109.71  3.000
 APD  HBC2  CB   CA    108.72  3.000
 APD  HBC1  CB   CA    108.80  3.000
 APD  CG    CB   CA    112.34  3.000
 APD  CD2   CG   CD1   118.35  3.000
 APD  CD2   CG   CB    120.18  3.000
 APD  CD1   CG   CB    121.39  3.000
 APD  HD1   CD1  CE1   119.80  3.000
 APD  HD1   CD1  CG    119.78  3.000
 APD  CE1   CD1  CG    120.43  3.000
 APD  HD2   CD2  CE2   119.00  3.000
 APD  HD2   CD2  CG    118.95  3.000
 APD  CE2   CD2  CG    122.05  3.000
 APD  HE1   CE1  CZ    119.85  3.000
 APD  HE1   CE1  CD1   119.83  3.000
 APD  CZ    CE1  CD1   120.32  3.000
 APD  C5    CE2  CZ    120.91  3.000
 APD  C5    CE2  CD2   120.70  3.000
 APD  CZ    CE2  CD2   118.38  3.000
 APD  HZ    CZ   CE2   119.71  3.000
 APD  HZ    CZ   CE1   119.83  3.000
 APD  CE2   CZ   CE1   120.46  3.000
 APD  H5C3  C5   H5C2  108.05  3.000
 APD  H5C3  C5   H5C1  107.32  3.000
 APD  H5C2  C5   H5C1  107.16  3.000
 APD  H5C3  C5   CE2   111.52  3.000
 APD  H5C2  C5   CE2   111.60  3.000
 APD  H5C1  C5   CE2   110.98  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
 APD  CONST_01  CZ    CE1  CD1  CG     0.00   0.0  0
 APD  CONST_02  CZ    CE2  CD2  CG     0.00   0.0  0
 APD  CONST_03  CE2   CD2  CG   CD1    0.00   0.0  0
 APD  CONST_04  CE2   CZ   CE1  CD1    0.00   0.0  0
 APD  CONST_05  CE1   CD1  CG   CD2    0.00   0.0  0
 APD  CONST_06  CE1   CZ   CE2  CD2    0.00   0.0  0
 APD  CONST_07  CE1   CD1  CG   CB   180.00   0.0  0
 APD  CONST_08  CE2   CD2  CG   CB   180.00   0.0  0
 APD  CONST_09  C5    CE2  CD2  CG   180.00   0.0  0
 APD  CONST_10  C5    CE2  CZ   CE1  180.00   0.0  0
 APD  CONST_11  HE1   CE1  CD1  CG   180.00   0.0  0
 APD  CONST_12  HD2   CD2  CG   CD1  180.00   0.0  0
 APD  CONST_13  HZ    CZ   CE1  CD1  180.00   0.0  0
 APD  CONST_14  HD1   CD1  CG   CD2  180.00   0.0  0
 APD  Var_01    CD1   CG   CB   CA    95.34  30.0  2
 APD  Var_02    H5C1  C5   CE2  CD2  -81.80  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
 APD  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
 APD  plan-1  CB   0.020
 APD  plan-1  CG   0.020
 APD  plan-1  CD1  0.020
 APD  plan-1  CD2  0.020
 APD  plan-1  CE1  0.020
 APD  plan-1  CE2  0.020
 APD  plan-1  CZ   0.020
 APD  plan-1  C5   0.020
 APD  plan-1  HD1  0.020
 APD  plan-1  HD2  0.020
 APD  plan-1  HE1  0.020
 APD  plan-1  HZ   0.020
 APD  plan-2  C    0.020
 APD  plan-2  O    0.020
 APD  plan-2  CA   0.020
 APD  plan-2  OXT  0.020

