# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 01:01:00 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-[difluoro(phosphono)methyl]-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)C(F)(F)[P](O)(O)=O)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
 FTY  FTY  4-[difluoro(phosphono)methyl]-L-phenylalanine  L-peptide  28  19  .  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_FTY
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
 FTY  N    N  NH2    0  -0.796  41.5240   7.0902  23.6026
 FTY  CA   C  CH1    0  -0.193  41.4863   7.8156  22.3468
 FTY  C    C  C      0   0.400  40.2462   7.4090  21.5131
 FTY  O    O  O      0  -0.600  39.7812   6.2694  21.7140
 FTY  OXT  O  OC    -1  -0.611  39.8482   8.2452  20.6782
 FTY  CB   C  CH2    0  -0.520  42.7423   7.6255  21.4625
 FTY  CG   C  CR6    0   0.117  44.0052   8.0644  22.1451
 FTY  CD1  C  CR16   0  -0.310  44.8415   7.1558  22.7885
 FTY  CD2  C  CR16   0  -0.292  44.3576   9.4127  22.1995
 FTY  CE1  C  CR16   0  -0.298  45.9863   7.5730  23.4557
 FTY  CE2  C  CR16   0  -0.284  45.4983   9.8352  22.8635
 FTY  CZ   C  CR6    0  -0.050  46.3364   8.9190  23.4976
 FTY  C1   C  CT     0   0.444  47.5506   9.3852  24.2399
 FTY  F1   F  F      0  -0.380  48.4951   8.3737  24.2063
 FTY  F2   F  F      0  -0.383  48.1366  10.4153  23.5199
 FTY  P    P  P      0   1.101  47.2543   9.9540  26.0300
 FTY  O1P  O  O      0  -0.880  48.6642  10.2340  26.5450
 FTY  O2P  O  OP    -1  -0.874  46.5631   8.7528  26.6700
 FTY  O3P  O  OP    -1  -0.874  46.3765  11.1889  25.8385
 FTY  H    H  HNH2   0   0.334  42.4383   7.1709  24.0312
 FTY  H2   H  HNH2   0   0.324  41.3737   6.1082  23.4063
 FTY  HA   H  HCH1   0   0.204  41.4094   8.8860  22.5688
 FTY  HB2  H  HCH2   0   0.230  42.8187   6.5698  21.1839
 FTY  HB3  H  HCH2   0   0.232  42.6084   8.1923  20.5379
 FTY  HD1  H  HCR6   0   0.241  44.6011   6.0989  22.7593
 FTY  HD2  H  HCR6   0   0.237  43.7290  10.1472  21.7080
 FTY  HE1  H  HCR6   0   0.241  46.6072   6.8293  23.9368
 FTY  HE2  H  HCR6   0   0.240  45.7363  10.8900  22.8798

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
 FTY  N    CA   single    1.458  0.019  1.458
 FTY  N    H    single    0.860  0.020  0.860
 FTY  N    H2   single    0.890  0.020  1.040
 FTY  CA   C    single    1.525  0.021  1.525
 FTY  CA   CB   single    1.530  0.020  1.530
 FTY  CA   HA   single    0.970  0.020  0.970
 FTY  C    O    deloc     1.231  0.020  1.231
 FTY  C    OXT  deloc     1.247  0.020  1.247
 FTY  CB   CG   single    1.501  0.020  1.501
 FTY  CB   HB2  single    0.970  0.020  1.090
 FTY  CB   HB3  single    0.970  0.020  1.090
 FTY  CG   CD1  aromatic  1.392  0.020  1.392
 FTY  CG   CD2  aromatic  1.395  0.020  1.395
 FTY  CD1  CE1  aromatic  1.389  0.020  1.389
 FTY  CD1  HD1  single    0.930  0.020  1.080
 FTY  CD2  CE2  aromatic  1.386  0.020  1.386
 FTY  CD2  HD2  single    0.930  0.020  1.080
 FTY  CE1  CZ   aromatic  1.391  0.020  1.391
 FTY  CE1  HE1  single    0.930  0.020  1.080
 FTY  CE2  CZ   aromatic  1.394  0.020  1.394
 FTY  CE2  HE2  single    0.930  0.020  1.080
 FTY  CZ   C1   single    1.498  0.020  1.498
 FTY  C1   F1   single    1.384  0.020  1.384
 FTY  C1   F2   single    1.387  0.020  1.387
 FTY  C1   P    single    1.902  0.020  1.902
 FTY  P    O1P  deloc     1.527  0.020  1.527
 FTY  P    O2P  deloc     1.526  0.020  1.526
 FTY  P    O3P  deloc     1.527  0.020  1.527

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
 FTY  H2   N    H    107.05  3.000
 FTY  H2   N    CA   108.26  3.000
 FTY  H    N    CA   114.00  3.000
 FTY  HA   CA   CB   109.00  3.000
 FTY  HA   CA   C    109.00  3.000
 FTY  CB   CA   C    110.10  1.900
 FTY  HA   CA   N    110.00  3.000
 FTY  CB   CA   N    110.50  1.700
 FTY  C    CA   N    111.00  2.800
 FTY  OXT  C    O    126.99  3.000
 FTY  OXT  C    CA   116.11  3.000
 FTY  O    C    CA   120.80  1.700
 FTY  HB3  CB   HB2  107.06  3.000
 FTY  HB3  CB   CG   109.65  3.000
 FTY  HB2  CB   CG   109.82  3.000
 FTY  HB3  CB   CA   108.68  3.000
 FTY  HB2  CB   CA   108.69  3.000
 FTY  CG   CB   CA   112.77  3.000
 FTY  CD2  CG   CD1  117.46  3.000
 FTY  CD2  CG   CB   120.86  3.000
 FTY  CD1  CG   CB   121.64  3.000
 FTY  HD1  CD1  CE1  119.24  3.000
 FTY  HD1  CD1  CG   119.37  3.000
 FTY  CE1  CD1  CG   121.39  3.000
 FTY  HD2  CD2  CE2  119.20  3.000
 FTY  HD2  CD2  CG   119.38  3.000
 FTY  CE2  CD2  CG   121.42  3.000
 FTY  HE1  CE1  CZ   120.48  3.000
 FTY  HE1  CE1  CD1  118.69  3.000
 FTY  CZ   CE1  CD1  120.82  3.000
 FTY  HE2  CE2  CZ   120.12  3.000
 FTY  HE2  CE2  CD2  119.06  3.000
 FTY  CZ   CE2  CD2  120.82  3.000
 FTY  C1   CZ   CE2  120.54  3.000
 FTY  C1   CZ   CE1  121.34  3.000
 FTY  CE2  CZ   CE1  118.08  3.000
 FTY  P    C1   F2   109.42  3.000
 FTY  P    C1   F1   110.35  3.000
 FTY  F2   C1   F1   103.99  3.000
 FTY  P    C1   CZ   115.68  3.000
 FTY  F2   C1   CZ   108.46  3.000
 FTY  F1   C1   CZ   108.28  3.000
 FTY  O3P  P    O2P  115.38  3.000
 FTY  O3P  P    O1P  115.13  3.000
 FTY  O2P  P    O1P  114.90  3.000
 FTY  O3P  P    C1   102.32  3.000
 FTY  O2P  P    C1   103.29  3.000
 FTY  O1P  P    C1   103.21  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
 FTY  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 FTY  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 FTY  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 FTY  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 FTY  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 FTY  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 FTY  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 FTY  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 FTY  CONST_09  C1   CZ   CE1  CD1  180.00   0.0  0
 FTY  CONST_10  C1   CZ   CE2  CD2  180.00   0.0  0
 FTY  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 FTY  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 FTY  CONST_13  HD2  CD2  CG   CD1  180.00   0.0  0
 FTY  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 FTY  Var_01    CD1  CG   CB   CA    97.35  30.0  2
 FTY  Var_02    F1   C1   CZ   CE1   30.46  30.0  2
 FTY  Var_03    O1P  P    C1   CZ   174.91  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
 FTY  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
 FTY  plan-1  CB   0.020
 FTY  plan-1  CG   0.020
 FTY  plan-1  CD1  0.020
 FTY  plan-1  CD2  0.020
 FTY  plan-1  CE1  0.020
 FTY  plan-1  CE2  0.020
 FTY  plan-1  CZ   0.020
 FTY  plan-1  C1   0.020
 FTY  plan-1  HD1  0.020
 FTY  plan-1  HD2  0.020
 FTY  plan-1  HE1  0.020
 FTY  plan-1  HE2  0.020
 FTY  plan-2  CA   0.020
 FTY  plan-2  C    0.020
 FTY  plan-2  O    0.020
 FTY  plan-2  OXT  0.020

