# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 18:13:16 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: methyl L-phenylalaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)Cc1ccccc1
#
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
 0A9  0A9  'methyl L-phenylalaninate '  L-peptide  26  13  .  2012-08-28  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0A9
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
 0A9  N     N  NH2   0  -0.795   9.6023  34.3400   1.7096
 0A9  CA    C  CH1   0  -0.189   8.8767  33.5359   0.7511
 0A9  C     C  C     0   0.584   7.3813  33.7985   0.7763
 0A9  CB    C  CH2   0  -0.508   9.0932  32.0385   1.0493
 0A9  CG    C  CR6   0   0.101  10.5455  31.6585   0.9712
 0A9  CD1   C  CR16  0  -0.294  11.1782  31.5419  -0.2660
 0A9  CD2   C  CR16  0  -0.305  11.2961  31.4467   2.1247
 0A9  CE1   C  CR16  0  -0.238  12.5255  31.2216  -0.3475
 0A9  CE2   C  CR16  0  -0.239  12.6455  31.1234   2.0475
 0A9  CZ    C  CR16  0  -0.268  13.2646  31.0117   0.8107
 0A9  O     O  O     0  -0.454   6.6347  33.3771  -0.0729
 0A9  CM    C  CH3   0  -0.423   5.5835  34.7755   1.9265
 0A9  OXT   O  O2    0  -0.436   6.9814  34.5061   1.8175
 0A9  HN1   H  HNH2  0   0.358  10.5890  34.1251   1.6339
 0A9  HN2   H  HNH2  0   0.352   9.5183  35.3222   1.4793
 0A9  HA    H  HCH1  0   0.253   9.1830  33.7066  -0.2917
 0A9  HBC1  H  HCH2  0   0.258   8.7018  31.8163   2.0448
 0A9  HBC2  H  HCH2  0   0.262   8.5173  31.4525   0.3311
 0A9  HD1   H  HCR6  0   0.248  10.6092  31.7011  -1.1752
 0A9  HD2   H  HCR6  0   0.249  10.8194  31.5330   3.0941
 0A9  HE1   H  HCR6  0   0.253  13.0000  31.1327  -1.3165
 0A9  HE2   H  HCR6  0   0.253  13.2119  30.9601   2.9555
 0A9  HZ    H  HCR6  0   0.253  14.3157  30.7610   0.7481
 0A9  HMC1  H  HCH3  0   0.250   5.4623  35.3624   2.8322
 0A9  HMC2  H  HCH3  0   0.238   5.2198  35.3474   1.0731
 0A9  HMC3  H  HCH3  0   0.239   5.0069  33.8546   2.0116

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
 0A9  N    CA    single    1.458  0.019  1.458
 0A9  N    HN1   single    0.890  0.020  1.040
 0A9  N    HN2   single    0.890  0.020  1.040
 0A9  CA   C     single    1.525  0.021  1.525
 0A9  CA   CB    single    1.530  0.020  1.530
 0A9  CA   HA    single    0.970  0.020  0.970
 0A9  C    O     double    1.231  0.020  1.231
 0A9  C    OXT   single    1.321  0.020  1.321
 0A9  CB   CG    single    1.503  0.020  1.503
 0A9  CB   HBC1  single    0.970  0.020  1.090
 0A9  CB   HBC2  single    0.970  0.020  1.090
 0A9  CG   CD1   aromatic  1.394  0.020  1.394
 0A9  CG   CD2   aromatic  1.392  0.020  1.392
 0A9  CD1  CE1   aromatic  1.387  0.020  1.387
 0A9  CD1  HD1   single    0.930  0.020  1.080
 0A9  CD2  CE2   aromatic  1.390  0.020  1.390
 0A9  CD2  HD2   single    0.930  0.020  1.080
 0A9  CE1  CZ    aromatic  1.390  0.020  1.390
 0A9  CE1  HE1   single    0.930  0.020  1.080
 0A9  CE2  CZ    aromatic  1.388  0.020  1.388
 0A9  CE2  HE2   single    0.930  0.020  1.080
 0A9  CZ   HZ    single    0.930  0.020  1.080
 0A9  CM   HMC1  single    0.970  0.020  1.090
 0A9  OXT  CM    single    1.428  0.020  1.428
 0A9  CM   HMC2  single    0.970  0.020  1.090
 0A9  CM   HMC3  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
 0A9  HN2   N    HN1   105.65  3.000
 0A9  HN2   N    CA    110.31  3.000
 0A9  HN1   N    CA    108.74  3.000
 0A9  HA    CA   CB    109.00  3.000
 0A9  HA    CA   C     109.00  3.000
 0A9  CB    CA   C     110.10  1.900
 0A9  HA    CA   N     110.00  3.000
 0A9  CB    CA   N     110.50  1.700
 0A9  C     CA   N     111.00  2.800
 0A9  OXT   C    O     123.67  3.000
 0A9  OXT   C    CA    113.82  3.000
 0A9  O     C    CA    120.80  1.700
 0A9  HBC2  CB   HBC1  107.54  3.000
 0A9  HBC2  CB   CG    109.87  3.000
 0A9  HBC1  CB   CG    110.00  3.000
 0A9  HBC2  CB   CA    108.67  3.000
 0A9  HBC1  CB   CA    108.87  3.000
 0A9  CG    CB   CA    111.78  3.000
 0A9  CD2   CG   CD1   118.53  3.000
 0A9  CD2   CG   CB    121.08  3.000
 0A9  CD1   CG   CB    120.37  3.000
 0A9  HD1   CD1  CE1   119.63  3.000
 0A9  HD1   CD1  CG    119.57  3.000
 0A9  CE1   CD1  CG    120.80  3.000
 0A9  HD2   CD2  CE2   119.69  3.000
 0A9  HD2   CD2  CG    119.46  3.000
 0A9  CE2   CD2  CG    120.85  3.000
 0A9  HE1   CE1  CZ    120.03  3.000
 0A9  HE1   CE1  CD1   119.82  3.000
 0A9  CZ    CE1  CD1   120.16  3.000
 0A9  HE2   CE2  CZ    120.13  3.000
 0A9  HE2   CE2  CD2   119.77  3.000
 0A9  CZ    CE2  CD2   120.10  3.000
 0A9  HZ    CZ   CE2   120.23  3.000
 0A9  HZ    CZ   CE1   120.21  3.000
 0A9  CE2   CZ   CE1   119.56  3.000
 0A9  HMC3  CM   HMC2  109.15  3.000
 0A9  HMC3  CM   HMC1  109.42  3.000
 0A9  HMC2  CM   HMC1  109.41  3.000
 0A9  HMC3  CM   OXT   111.38  3.000
 0A9  HMC2  CM   OXT   111.47  3.000
 0A9  HMC1  CM   OXT   105.95  3.000
 0A9  CM    OXT  C     117.24  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
 0A9  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 0A9  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 0A9  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 0A9  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 0A9  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 0A9  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 0A9  CONST_07  CE1   CD1  CG   CB    180.00   0.0  0
 0A9  CONST_08  CE2   CD2  CG   CB    180.00   0.0  0
 0A9  CONST_09  HE1   CE1  CD1  CG    180.00   0.0  0
 0A9  CONST_10  HE2   CE2  CD2  CG    180.00   0.0  0
 0A9  CONST_11  HD2   CD2  CG   CD1   180.00   0.0  0
 0A9  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 0A9  CONST_13  HD1   CD1  CG   CD2   180.00   0.0  0
 0A9  Var_01    CD1   CG   CB   CA    -74.49  30.0  2
 0A9  Var_02    HMC1  CM   OXT  C    -179.82  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
 0A9  chir_01  CA  N  C  CB  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
 0A9  plan-1  CB   0.020
 0A9  plan-1  CG   0.020
 0A9  plan-1  CD1  0.020
 0A9  plan-1  CD2  0.020
 0A9  plan-1  CE1  0.020
 0A9  plan-1  CE2  0.020
 0A9  plan-1  CZ   0.020
 0A9  plan-1  HD1  0.020
 0A9  plan-1  HD2  0.020
 0A9  plan-1  HE1  0.020
 0A9  plan-1  HE2  0.020
 0A9  plan-1  HZ   0.020
 0A9  plan-2  CA   0.020
 0A9  plan-2  C    0.020
 0A9  plan-2  O    0.020
 0A9  plan-2  OXT  0.020

