# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:47:11 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-carbamimidoyl-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(cc1)C(N)=N)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
 APH  APH  4-carbamimidoyl-D-phenylalanine  D-peptide  27  15  .  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_APH
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
 APH  N     N  NH2    0  -0.784  16.1356  -14.2788  20.7261
 APH  CA    C  CH1    0  -0.206  16.3704  -12.8983  20.3350
 APH  C     C  C      0   0.383  17.4442  -12.6930  19.2321
 APH  O     O  O      0  -0.598  17.7589  -13.6910  18.5546
 APH  CB    C  CH2    0  -0.517  15.0552  -12.2549  19.8595
 APH  CG    C  CR6    0   0.165  14.0027  -12.2095  20.9274
 APH  CD1   C  CR16   0  -0.311  12.9442  -13.1143  20.9558
 APH  CD2   C  CR16   0  -0.293  14.0735  -11.2615  21.9454
 APH  CE1   C  CR16   0  -0.260  11.9919  -13.0746  21.9610
 APH  CE2   C  CR16   0  -0.278  13.1234  -11.2142  22.9538
 APH  CZ    C  CR6    0   0.029  12.0654  -12.1222  22.9753
 APH  CF    C  C      0   0.329  11.0365  -12.1098  24.0509
 APH  NG1   N  N      0  -0.653  10.4040  -13.1898  24.3112
 APH  NG2   N  NH2    0  -0.822  10.8971  -10.9231  24.7158
 APH  OXT   O  OC    -1  -0.614  17.8767  -11.5293  19.1033
 APH  H     H  HNH2   0   0.323  16.1073  -14.8339  19.8774
 APH  H2    H  HNH2   0   0.334  16.9527  -14.6175  21.2199
 APH  HA    H  HCH1   0   0.216  16.6963  -12.3495  21.2252
 APH  HB2   H  HCH2   0   0.242  15.2700  -11.2405  19.5174
 APH  HB3   H  HCH2   0   0.233  14.6829  -12.8110  18.9932
 APH  HD1   H  HCR6   0   0.242  12.8584  -13.8596  20.1740
 APH  HD2   H  HCR6   0   0.244  14.8896  -10.5478  21.9528
 APH  HE1   H  HCR6   0   0.247  11.1764  -13.7855  21.9611
 APH  HE2   H  HCR6   0   0.250  13.2321  -10.4711  23.7338
 APH  HG1   H  H      0   0.321   9.7113  -13.0421  25.0404
 APH  HG21  H  HNH2   0   0.391  11.1024  -10.0705  24.2210
 APH  HG22  H  HNH2   0   0.389  10.1159  -10.8402  25.3473

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
 APH  N    CA    single    1.458  0.019  1.458
 APH  N    H     single    0.860  0.020  0.860
 APH  N    H2    single    0.890  0.020  1.040
 APH  CA   C     single    1.525  0.021  1.525
 APH  CA   CB    single    1.521  0.033  1.521
 APH  CA   HA    single    0.970  0.020  0.970
 APH  C    O     deloc     1.231  0.020  1.231
 APH  C    OXT   deloc     1.248  0.020  1.248
 APH  CB   CG    single    1.500  0.020  1.500
 APH  CB   HB2   single    0.970  0.020  1.090
 APH  CB   HB3   single    0.970  0.020  1.090
 APH  CG   CD1   aromatic  1.393  0.020  1.393
 APH  CG   CD2   aromatic  1.393  0.020  1.393
 APH  CD1  CE1   aromatic  1.385  0.020  1.385
 APH  CD1  HD1   single    0.930  0.020  1.080
 APH  CD2  CE2   aromatic  1.386  0.020  1.386
 APH  CD2  HD2   single    0.930  0.020  1.080
 APH  CE1  CZ    aromatic  1.393  0.020  1.393
 APH  CE1  HE1   single    0.930  0.020  1.080
 APH  CE2  CZ    aromatic  1.394  0.020  1.394
 APH  CE2  HE2   single    0.930  0.020  1.080
 APH  CZ   CF    single    1.488  0.020  1.488
 APH  CF   NG1   double    1.278  0.020  1.278
 APH  CF   NG2   single    1.367  0.020  1.367
 APH  NG1  HG1   single    0.890  0.020  1.040
 APH  NG2  HG21  single    0.890  0.020  1.040
 APH  NG2  HG22  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
 APH  H2    N    H     104.32  3.000
 APH  H2    N    CA    108.57  3.000
 APH  H     N    CA    114.00  3.000
 APH  HA    CA   CB    109.00  3.000
 APH  HA    CA   C     110.00  3.000
 APH  CB    CA   C     110.50  1.500
 APH  HA    CA   N     110.00  3.000
 APH  CB    CA   N     110.40  1.500
 APH  C     CA   N     111.00  2.800
 APH  OXT   C    O     127.07  3.000
 APH  OXT   C    CA    120.80  1.700
 APH  O     C    CA    120.80  1.700
 APH  HB3   CB   HB2   106.91  3.000
 APH  HB3   CB   CG    109.88  3.000
 APH  HB2   CB   CG    109.45  3.000
 APH  HB3   CB   CA    108.82  3.000
 APH  HB2   CB   CA    108.48  3.000
 APH  CG    CB   CA    113.09  3.000
 APH  CD2   CG   CD1   117.77  3.000
 APH  CD2   CG   CB    120.35  3.000
 APH  CD1   CG   CB    121.88  3.000
 APH  HD1   CD1  CE1   119.27  3.000
 APH  HD1   CD1  CG    119.49  3.000
 APH  CE1   CD1  CG    121.24  3.000
 APH  HD2   CD2  CE2   119.24  3.000
 APH  HD2   CD2  CG    119.43  3.000
 APH  CE2   CD2  CG    121.33  3.000
 APH  HE1   CE1  CZ    119.26  3.000
 APH  HE1   CE1  CD1   119.96  3.000
 APH  CZ    CE1  CD1   120.77  3.000
 APH  HE2   CE2  CZ    120.79  3.000
 APH  HE2   CE2  CD2   118.59  3.000
 APH  CZ    CE2  CD2   120.60  3.000
 APH  CF    CZ   CE2   122.02  3.000
 APH  CF    CZ   CE1   119.69  3.000
 APH  CE2   CZ   CE1   118.29  3.000
 APH  NG2   CF   NG1   125.71  3.000
 APH  NG2   CF   CZ    115.41  3.000
 APH  NG1   CF   CZ    118.82  3.000
 APH  HG1   NG1  CF    111.13  3.000
 APH  HG22  NG2  HG21  113.34  3.000
 APH  HG22  NG2  CF    117.07  3.000
 APH  HG21  NG2  CF    118.37  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
 APH  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 APH  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 APH  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 APH  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 APH  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 APH  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 APH  CONST_07  CE1   CD1  CG   CB    180.00   0.0  0
 APH  CONST_08  CE2   CD2  CG   CB    180.00   0.0  0
 APH  CONST_09  CF    CZ   CE1  CD1   180.00   0.0  0
 APH  CONST_10  CF    CZ   CE2  CD2   180.00   0.0  0
 APH  CONST_11  HE1   CE1  CD1  CG    180.00   0.0  0
 APH  CONST_12  HE2   CE2  CD2  CG    180.00   0.0  0
 APH  CONST_13  HD2   CD2  CG   CD1   180.00   0.0  0
 APH  CONST_14  HD1   CD1  CG   CD2   180.00   0.0  0
 APH  CONST_15  HG1   NG1  CF   CZ    180.00   0.0  0
 APH  CONST_17  HG22  NG2  CF   CZ    180.00   0.0  0
 APH  Var_01    CD1   CG   CB   CA   -102.14  30.0  2
 APH  Var_02    NG1   CF   CZ   CE1    24.22  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
 APH  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
 APH  plan-1  CB    0.020
 APH  plan-1  CG    0.020
 APH  plan-1  CD1   0.020
 APH  plan-1  CD2   0.020
 APH  plan-1  CE1   0.020
 APH  plan-1  CE2   0.020
 APH  plan-1  CZ    0.020
 APH  plan-1  CF    0.020
 APH  plan-1  HD1   0.020
 APH  plan-1  HD2   0.020
 APH  plan-1  HE1   0.020
 APH  plan-1  HE2   0.020
 APH  plan-2  CZ    0.020
 APH  plan-2  CF    0.020
 APH  plan-2  NG1   0.020
 APH  plan-2  NG2   0.020
 APH  plan-2  HG1   0.020
 APH  plan-2  HG21  0.020
 APH  plan-2  HG22  0.020
 APH  plan-3  CA    0.020
 APH  plan-3  C     0.020
 APH  plan-3  O     0.020
 APH  plan-3  OXT   0.020

