# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:03:53 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2R)-2-amino-4-phenylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCc1ccccc1)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
 HMF  HMF  '(2R)-2-amino-4-phenylbutanoic acid'  D-peptide  25  13  .  2016-04-22  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_HMF
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
 HMF  N    N  NH2    0  -0.799  17.3783  -16.2817  22.3794
 HMF  CA   C  CH1    0  -0.175  17.9184  -15.5781  23.5391
 HMF  C    C  C      0   0.407  17.0399  -14.3414  23.8396
 HMF  O    O  O      0  -0.605  15.8055  -14.5244  23.7962
 HMF  OXT  O  OC    -1  -0.600  17.6220  -13.2759  24.1290
 HMF  CB   C  CH2    0  -0.446  18.0036  -16.4746  24.7835
 HMF  CG   C  CH2    0  -0.515  18.7034  -15.8608  26.0020
 HMF  C1   C  CR6    0   0.123  20.1825  -15.6644  25.8053
 HMF  C2   C  CR16   0  -0.309  21.0718  -16.7043  26.0737
 HMF  C6   C  CR16   0  -0.307  20.7012  -14.4582  25.3365
 HMF  C3   C  CR16   0  -0.241  22.4383  -16.5468  25.8833
 HMF  C5   C  CR16   0  -0.243  22.0674  -14.2947  25.1464
 HMF  C4   C  CR16   0  -0.273  22.9423  -15.3380  25.4204
 HMF  H    H  HNH2   0   0.327  17.8152  -17.1931  22.3009
 HMF  H2   H  HNH2   0   0.323  16.3950  -16.4544  22.5522
 HMF  HA   H  HCH1   0   0.200  18.9276  -15.2381  23.2869
 HMF  HB2  H  HCH2   0   0.214  16.9875  -16.7661  25.0680
 HMF  HB3  H  HCH2   0   0.215  18.5247  -17.4001  24.5135
 HMF  HG2  H  HCH2   0   0.239  18.2342  -14.9100  26.2603
 HMF  HG3  H  HCH2   0   0.236  18.5468  -16.5248  26.8556
 HMF  HC2  H  HCR6   0   0.241  20.6893  -17.6494  26.4433
 HMF  H6   H  HCR6   0   0.247  20.0190  -13.6497  25.1038
 HMF  H3   H  HCR6   0   0.247  23.1106  -17.3670  26.1017
 HMF  H5   H  HCR6   0   0.246  22.4492  -13.3486  24.7831
 HMF  H4   H  HCR6   0   0.247  24.0074  -15.2105  25.2750

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
 HMF  N   CA   single    1.458  0.019  1.458
 HMF  N   H    single    0.860  0.020  0.860
 HMF  N   H2   single    0.890  0.020  1.040
 HMF  CA  C    single    1.525  0.021  1.525
 HMF  CA  CB   single    1.521  0.033  1.521
 HMF  CA  HA   single    0.970  0.020  0.970
 HMF  C   O    deloc     1.231  0.020  1.231
 HMF  C   OXT  deloc     1.248  0.020  1.248
 HMF  CB  CG   single    1.533  0.020  1.533
 HMF  CB  HB2  single    0.970  0.020  1.090
 HMF  CB  HB3  single    0.970  0.020  1.090
 HMF  CG  C1   single    1.505  0.020  1.505
 HMF  CG  HG2  single    0.970  0.020  1.090
 HMF  CG  HG3  single    0.970  0.020  1.090
 HMF  C1  C2   aromatic  1.394  0.020  1.394
 HMF  C1  C6   aromatic  1.394  0.020  1.394
 HMF  C2  C3   aromatic  1.389  0.020  1.389
 HMF  C2  HC2  single    0.930  0.020  1.080
 HMF  C6  C5   aromatic  1.389  0.020  1.389
 HMF  C6  H6   single    0.930  0.020  1.080
 HMF  C3  C4   aromatic  1.389  0.020  1.389
 HMF  C3  H3   single    0.930  0.020  1.080
 HMF  C5  C4   aromatic  1.389  0.020  1.389
 HMF  C5  H5   single    0.930  0.020  1.080
 HMF  C4  H4   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
 HMF  H2   N   H    106.16  3.000
 HMF  H2   N   CA   107.80  3.000
 HMF  H    N   CA   114.00  3.000
 HMF  HA   CA  CB   109.00  3.000
 HMF  HA   CA  C    110.00  3.000
 HMF  CB   CA  C    110.50  1.500
 HMF  HA   CA  N    110.00  3.000
 HMF  CB   CA  N    110.40  1.500
 HMF  C    CA  N    111.00  2.800
 HMF  OXT  C   O    126.45  3.000
 HMF  OXT  C   CA   120.80  1.700
 HMF  O    C   CA   120.80  1.700
 HMF  HB3  CB  HB2  106.29  3.000
 HMF  HB3  CB  CG   108.47  3.000
 HMF  HB2  CB  CG   108.88  3.000
 HMF  HB3  CB  CA   108.64  3.000
 HMF  HB2  CB  CA   108.33  3.000
 HMF  CG   CB  CA   115.81  3.000
 HMF  HG3  CG  HG2  106.44  3.000
 HMF  HG3  CG  C1   108.80  3.000
 HMF  HG2  CG  C1   109.86  3.000
 HMF  HG3  CG  CB   108.19  3.000
 HMF  HG2  CG  CB   109.92  3.000
 HMF  C1   CG  CB   113.38  3.000
 HMF  C6   C1  C2   118.20  3.000
 HMF  C6   C1  CG   121.50  3.000
 HMF  C2   C1  CG   120.29  3.000
 HMF  HC2  C2  C3   119.52  3.000
 HMF  HC2  C2  C1   119.37  3.000
 HMF  C3   C2  C1   121.11  3.000
 HMF  H6   C6  C5   120.15  3.000
 HMF  H6   C6  C1   118.92  3.000
 HMF  C5   C6  C1   120.92  3.000
 HMF  H3   C3  C4   120.07  3.000
 HMF  H3   C3  C2   119.83  3.000
 HMF  C4   C3  C2   120.10  3.000
 HMF  H5   C5  C4   120.02  3.000
 HMF  H5   C5  C6   119.71  3.000
 HMF  C4   C5  C6   120.27  3.000
 HMF  H4   C4  C5   120.32  3.000
 HMF  H4   C4  C3   120.28  3.000
 HMF  C5   C4  C3   119.40  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
 HMF  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 HMF  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 HMF  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 HMF  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 HMF  CONST_05  C3   C2  C1  C6    0.00   0.0  0
 HMF  CONST_06  C3   C4  C5  C6    0.00   0.0  0
 HMF  CONST_07  C3   C2  C1  CG  180.00   0.0  0
 HMF  CONST_08  C5   C6  C1  CG  180.00   0.0  0
 HMF  CONST_09  H3   C3  C2  C1  180.00   0.0  0
 HMF  CONST_10  H5   C5  C6  C1  180.00   0.0  0
 HMF  CONST_11  H6   C6  C1  C2  180.00   0.0  0
 HMF  CONST_12  H4   C4  C3  C2  180.00   0.0  0
 HMF  CONST_13  HC2  C2  C1  C6  180.00   0.0  0
 HMF  Var_01    C2   C1  CG  CB  -86.05  30.0  2
 HMF  Var_02    C1   CG  CB  CA  -68.68  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
 HMF  chir_01  CA  N  C  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
 HMF  plan-1  CG   0.020
 HMF  plan-1  C1   0.020
 HMF  plan-1  C2   0.020
 HMF  plan-1  C6   0.020
 HMF  plan-1  C3   0.020
 HMF  plan-1  C5   0.020
 HMF  plan-1  C4   0.020
 HMF  plan-1  HC2  0.020
 HMF  plan-1  H6   0.020
 HMF  plan-1  H3   0.020
 HMF  plan-1  H5   0.020
 HMF  plan-1  H4   0.020
 HMF  plan-2  CA   0.020
 HMF  plan-2  C    0.020
 HMF  plan-2  O    0.020
 HMF  plan-2  OXT  0.020

