# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:02:29 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-methyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C[C@H](N)C(O)=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
 4PH  4PH  '4-methyl-L-phenylalanine '  L-peptide  25  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_4PH
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
 4PH  CA    C  CH1    0  -0.190  13.4460  15.2848  19.3562
 4PH  CB    C  CH2    0  -0.495  12.9630  16.4396  18.4676
 4PH  CG    C  CR6    0   0.116  12.0118  17.3778  19.1534
 4PH  CD2   C  CR16   0  -0.296  10.6494  17.3659  18.8695
 4PH  CD1   C  CR16   0  -0.300  12.4648  18.2884  20.1063
 4PH  CE2   C  CR16   0  -0.283   9.7717  18.2272  19.5148
 4PH  CE1   C  CR16   0  -0.284  11.5892  19.1477  20.7532
 4PH  CZ    C  CR6    0   0.079  10.2240  19.1318  20.4714
 4PH  C     C  C      0   0.394  12.2322  14.5282  19.9456
 4PH  C33   C  CH3    0  -0.720   9.2718  20.0417  21.1923
 4PH  O     O  O      0  -0.614  11.5823  13.8320  19.1350
 4PH  N     N  NH2    0  -0.793  14.3368  14.4474  18.5559
 4PH  OXT   O  OC    -1  -0.607  11.9954  14.6781  21.1601
 4PH  HA    H  HCH1   0   0.201  14.0345  15.7071  20.1768
 4PH  HB2   H  HCH2   0   0.232  13.8402  16.9897  18.1165
 4PH  HB3   H  HCH2   0   0.224  12.4815  16.0177  17.5805
 4PH  HD2   H  HCR6   0   0.237  10.2656  16.6744  18.1283
 4PH  HD1   H  HCR6   0   0.238  13.5222  18.3296  20.3441
 4PH  HE2   H  HCR6   0   0.238   8.7170  18.1964  19.2651
 4PH  HE1   H  HCR6   0   0.238  11.9742  19.8471  21.4869
 4PH  H33   H  HCH3   0   0.243   8.8676  19.5590  22.0848
 4PH  H33A  H  HCH3   0   0.239   9.7625  20.9591  21.5168
 4PH  H33B  H  HCH3   0   0.240   8.4245  20.3166  20.5640
 4PH  H     H  HNH2   0   0.336  14.7682  13.7561  19.1583
 4PH  H2    H  HNH2   0   0.325  13.7557  13.9115  17.9194

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
 4PH  CB   CA    single    1.530  0.020  1.530
 4PH  N    CA    single    1.458  0.019  1.458
 4PH  CA   C     single    1.525  0.021  1.525
 4PH  CA   HA    single    0.970  0.020  0.970
 4PH  CB   CG    single    1.502  0.020  1.502
 4PH  CB   HB2   single    0.970  0.020  1.090
 4PH  CB   HB3   single    0.970  0.020  1.090
 4PH  CD2  CG    aromatic  1.392  0.020  1.392
 4PH  CG   CD1   aromatic  1.394  0.020  1.394
 4PH  CD2  CE2   aromatic  1.389  0.020  1.389
 4PH  CD2  HD2   single    0.930  0.020  1.080
 4PH  CD1  CE1   aromatic  1.387  0.020  1.387
 4PH  CD1  HD1   single    0.930  0.020  1.080
 4PH  CE2  CZ    aromatic  1.392  0.020  1.392
 4PH  CE2  HE2   single    0.930  0.020  1.080
 4PH  CZ   CE1   aromatic  1.394  0.020  1.394
 4PH  CE1  HE1   single    0.930  0.020  1.080
 4PH  CZ   C33   single    1.501  0.020  1.501
 4PH  O    C     deloc     1.231  0.020  1.231
 4PH  C    OXT   deloc     1.246  0.020  1.246
 4PH  C33  H33   single    0.970  0.020  1.090
 4PH  C33  H33A  single    0.970  0.020  1.090
 4PH  C33  H33B  single    0.970  0.020  1.090
 4PH  N    H     single    0.860  0.020  0.860
 4PH  N    H2    single    0.890  0.020  1.040

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
 4PH  HA    CA   N     110.00  3.000
 4PH  HA    CA   C     109.00  3.000
 4PH  N     CA   C     111.00  2.800
 4PH  HA    CA   CB    109.00  3.000
 4PH  C     CA   CB    110.10  1.900
 4PH  N     CA   CB    110.50  1.700
 4PH  HB3   CB   HB2   106.67  3.000
 4PH  HB3   CB   CG    109.42  3.000
 4PH  HB2   CB   CG    109.90  3.000
 4PH  HB3   CB   CA    108.53  3.000
 4PH  HB2   CB   CA    108.18  3.000
 4PH  CG    CB   CA    113.89  3.000
 4PH  CD1   CG   CD2   117.59  3.000
 4PH  CD1   CG   CB    120.97  3.000
 4PH  CD2   CG   CB    121.44  3.000
 4PH  HD2   CD2  CE2   119.32  3.000
 4PH  HD2   CD2  CG    119.44  3.000
 4PH  CE2   CD2  CG    121.24  3.000
 4PH  HD1   CD1  CE1   119.32  3.000
 4PH  HD1   CD1  CG    119.45  3.000
 4PH  CE1   CD1  CG    121.24  3.000
 4PH  HE2   CE2  CZ    119.52  3.000
 4PH  HE2   CE2  CD2   119.35  3.000
 4PH  CZ    CE2  CD2   121.13  3.000
 4PH  HE1   CE1  CZ    119.47  3.000
 4PH  HE1   CE1  CD1   119.41  3.000
 4PH  CZ    CE1  CD1   121.12  3.000
 4PH  C33   CZ   CE1   121.13  3.000
 4PH  C33   CZ   CE2   121.17  3.000
 4PH  CE1   CZ   CE2   117.68  3.000
 4PH  OXT   C    O     126.85  3.000
 4PH  OXT   C    CA    117.49  3.000
 4PH  O     C    CA    120.80  1.700
 4PH  H33B  C33  H33A  108.02  3.000
 4PH  H33B  C33  H33   107.15  3.000
 4PH  H33A  C33  H33   107.18  3.000
 4PH  H33B  C33  CZ    111.66  3.000
 4PH  H33A  C33  CZ    111.56  3.000
 4PH  H33   C33  CZ    111.05  3.000
 4PH  H2    N    H     104.86  3.000
 4PH  H2    N    CA    107.28  3.000
 4PH  H     N    CA    114.00  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
 4PH  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 4PH  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 4PH  CONST_03  CE1  CD1  CG   CD2     0.00   0.0  0
 4PH  CONST_04  CE1  CZ   CE2  CD2     0.00   0.0  0
 4PH  CONST_05  CE2  CD2  CG   CD1     0.00   0.0  0
 4PH  CONST_06  CE2  CZ   CE1  CD1     0.00   0.0  0
 4PH  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 4PH  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 4PH  CONST_09  C33  CZ   CE2  CD2   180.00   0.0  0
 4PH  CONST_10  C33  CZ   CE1  CD1   180.00   0.0  0
 4PH  CONST_11  HE2  CE2  CD2  CG    180.00   0.0  0
 4PH  CONST_12  HE1  CE1  CD1  CG    180.00   0.0  0
 4PH  CONST_13  HD1  CD1  CG   CD2   180.00   0.0  0
 4PH  CONST_14  HD2  CD2  CG   CD1   180.00   0.0  0
 4PH  Var_01    CD2  CG   CB   CA   -105.50  30.0  2
 4PH  Var_02    H33  C33  CZ   CE2    87.71  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
 4PH  chir_01  CA  CB  N  C  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
 4PH  plan-1  CB   0.020
 4PH  plan-1  CG   0.020
 4PH  plan-1  CD2  0.020
 4PH  plan-1  CD1  0.020
 4PH  plan-1  CE2  0.020
 4PH  plan-1  CE1  0.020
 4PH  plan-1  CZ   0.020
 4PH  plan-1  C33  0.020
 4PH  plan-1  HD2  0.020
 4PH  plan-1  HD1  0.020
 4PH  plan-1  HE2  0.020
 4PH  plan-1  HE1  0.020
 4PH  plan-2  CA   0.020
 4PH  plan-2  C    0.020
 4PH  plan-2  O    0.020
 4PH  plan-2  OXT  0.020

