# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 10:47:30 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: N-formyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC=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
 QPH  QPH  'N-formyl-L-phenylalanine '  L-peptide  24  14  .  2012-08-28  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QPH
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
 QPH  C    C  C      0   0.077  2.0106  -1.2004   1.6928
 QPH  N    N  NH1    0  -0.641  3.4706  -1.3470  -0.1521
 QPH  O    O  O      0  -0.307  1.0628  -1.8644   2.0159
 QPH  CA   C  CH1    0  -0.136  3.3438  -1.7511   1.2341
 QPH  CB   C  CH2    0  -0.470  4.5023  -1.1991   2.0800
 QPH  CG   C  CR6    0   0.074  4.3238  -1.4324   3.5544
 QPH  CZ   C  CR16   0  -0.242  3.9586  -1.8796   6.2968
 QPH  CD1  C  CR16   0  -0.309  4.3851  -2.7236   4.0824
 QPH  CD2  C  CR16   0  -0.274  4.0708  -0.3738   4.4223
 QPH  CE1  C  CR16   0  -0.226  4.2066  -2.9469   5.4402
 QPH  CE2  C  CR16   0  -0.277  3.8921  -0.5924   5.7835
 QPH  H    H  HNH1   0   0.353  2.6278   0.5419   1.2215
 QPH  HA   H  HCH1   0   0.199  3.3078  -2.8370   1.3750
 QPH  HZ   H  HCR6   0   0.239  3.8218  -2.0524   7.3566
 QPH  HB2  H  HCH2   0   0.267  5.4209  -1.6739   1.7280
 QPH  HB3  H  HCH2   0   0.231  4.6208  -0.1298   1.8860
 QPH  HD1  H  HCR6   0   0.242  4.5821  -3.5623   3.4241
 QPH  HD2  H  HCR6   0   0.246  4.0191   0.6363   4.0284
 QPH  HE1  H  HCR6   0   0.254  4.2644  -3.9547   5.8313
 QPH  HE2  H  HCR6   0   0.259  3.6995   0.2467   6.4400
 QPH  O1   O  O      0  -0.264  4.2963  -3.4359  -0.7576
 QPH  CN   C  C1     0   0.207  3.9392  -2.2571  -0.9699
 QPH  HNA  H  H      0   0.137  4.0065  -1.8662  -2.0082
 QPH  OXT  O  OC    -1  -0.640  1.8954   0.1291   1.7284

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
 QPH  CA   C    single    1.525  0.021  1.525
 QPH  O    C    deloc     1.231  0.020  1.231
 QPH  CN   N    single    1.310  0.020  1.310
 QPH  H    N    single    0.860  0.020  0.860
 QPH  N    CA   single    1.458  0.019  1.458
 QPH  HA   CA   single    0.970  0.020  0.970
 QPH  CA   CB   single    1.530  0.020  1.530
 QPH  HB2  CB   single    0.970  0.020  1.090
 QPH  HB3  CB   single    0.970  0.020  1.090
 QPH  CB   CG   single    1.503  0.020  1.503
 QPH  CG   CD1  aromatic  1.396  0.020  1.396
 QPH  CG   CD2  aromatic  1.392  0.020  1.392
 QPH  CE1  CZ   aromatic  1.391  0.020  1.391
 QPH  CE2  CZ   aromatic  1.387  0.020  1.387
 QPH  CZ   HZ   single    0.930  0.020  1.080
 QPH  HD1  CD1  single    0.930  0.020  1.080
 QPH  CD1  CE1  aromatic  1.387  0.020  1.387
 QPH  HD2  CD2  single    0.930  0.020  1.080
 QPH  CD2  CE2  aromatic  1.390  0.020  1.390
 QPH  CE1  HE1  single    0.930  0.020  1.080
 QPH  CE2  HE2  single    0.930  0.020  1.080
 QPH  CN   O1   double    1.250  0.020  1.250
 QPH  HNA  CN   single    0.930  0.020  1.080
 QPH  C    OXT  deloc     1.335  0.020  1.335

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
 QPH  OXT  C    CA   116.51  3.000
 QPH  OXT  C    O    118.37  3.000
 QPH  CA   C    O    120.80  1.700
 QPH  CN   N    H    174.34  3.000
 QPH  H    N    CA   114.00  3.000
 QPH  CN   N    CA   115.76  3.000
 QPH  HA   CA   CB   109.00  3.000
 QPH  CB   CA   N    110.50  1.700
 QPH  HA   CA   N    110.00  3.000
 QPH  CB   CA   C    110.10  1.900
 QPH  HA   CA   C    109.00  3.000
 QPH  N    CA   C    111.00  2.800
 QPH  HB3  CB   HB2  106.07  3.000
 QPH  HB3  CB   CG   109.79  3.000
 QPH  HB2  CB   CG   110.39  3.000
 QPH  CG   CB   CA   113.24  3.000
 QPH  HB3  CB   CA   109.59  3.000
 QPH  HB2  CB   CA   107.49  3.000
 QPH  CD2  CG   CD1  118.39  3.000
 QPH  CD2  CG   CB   121.00  3.000
 QPH  CD1  CG   CB   120.61  3.000
 QPH  HZ   CZ   CE2  120.28  3.000
 QPH  HZ   CZ   CE1  120.20  3.000
 QPH  CE2  CZ   CE1  119.51  3.000
 QPH  HD1  CD1  CE1  119.54  3.000
 QPH  CE1  CD1  CG   120.88  3.000
 QPH  HD1  CD1  CG   119.58  3.000
 QPH  HD2  CD2  CE2  119.71  3.000
 QPH  CE2  CD2  CG   120.95  3.000
 QPH  HD2  CD2  CG   119.35  3.000
 QPH  HE1  CE1  CD1  119.77  3.000
 QPH  HE1  CE1  CZ   120.09  3.000
 QPH  CD1  CE1  CZ   120.14  3.000
 QPH  HE2  CE2  CD2  119.65  3.000
 QPH  HE2  CE2  CZ   120.22  3.000
 QPH  CD2  CE2  CZ   120.13  3.000
 QPH  HNA  CN   O1   118.23  3.000
 QPH  HNA  CN   N    111.13  3.000
 QPH  O1   CN   N    130.64  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
 QPH  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 QPH  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 QPH  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 QPH  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 QPH  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 QPH  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 QPH  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 QPH  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 QPH  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 QPH  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 QPH  CONST_11  HD1  CD1  CE1  CZ   180.00   0.0  0
 QPH  CONST_12  HD2  CD2  CE2  CZ   180.00   0.0  0
 QPH  CONST_13  HZ   CZ   CE1  CD1  180.00   0.0  0
 QPH  CONST_14  O1   CN   N    CA     0.00   0.0  0
 QPH  CONST_15  O1   CN   N    H    180.00   0.0  0
 QPH  Var_01    CD1  CG   CB   CA    68.36  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
 QPH  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
 QPH  plan-1  CB   0.020
 QPH  plan-1  CG   0.020
 QPH  plan-1  CZ   0.020
 QPH  plan-1  CD1  0.020
 QPH  plan-1  CD2  0.020
 QPH  plan-1  CE1  0.020
 QPH  plan-1  CE2  0.020
 QPH  plan-1  HZ   0.020
 QPH  plan-1  HD1  0.020
 QPH  plan-1  HD2  0.020
 QPH  plan-1  HE1  0.020
 QPH  plan-1  HE2  0.020
 QPH  plan-2  N    0.020
 QPH  plan-2  CA   0.020
 QPH  plan-2  H    0.020
 QPH  plan-2  O1   0.020
 QPH  plan-2  CN   0.020
 QPH  plan-2  HNA  0.020
 QPH  plan-3  C    0.020
 QPH  plan-3  O    0.020
 QPH  plan-3  CA   0.020
 QPH  plan-3  OXT  0.020

