# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:37:31 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 2,3,5,6-tetrafluoro-4-iodo-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c(F)c(F)c(I)c(F)c1F)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
 V61  V61  2,3,5,6-tetrafluoro-4-iodo-L-phenylalanine  L-peptide  22  17  .  2022-09-22  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_V61
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
 V61  C11  C  CR6    0   0.502  16.0856  6.9774  21.1921
 V61  C13  C  CR6    0   0.400  17.4176  7.0210  20.8177
 V61  N    N  NH2    0  -0.814  19.1147  6.1207  18.0753
 V61  C    C  C      0   0.418  21.1001  7.5971  17.7818
 V61  O    O  O      0  -0.599  21.6584  8.6702  18.0787
 V61  CA   C  CH1    0  -0.215  19.5941  7.4894  18.1505
 V61  C03  C  CH2    0  -0.473  19.3507  8.0657  19.5537
 V61  C04  C  CR6    0  -0.273  17.9080  7.9913  19.9572
 V61  C05  C  CR6    0   0.415  16.9817  8.8998  19.4653
 V61  C07  C  CR6    0   0.505  15.6467  8.8640  19.8177
 V61  C09  C  CR6    0  -0.672  15.1824  7.8976  20.6926
 V61  F06  F  F      0  -0.294  17.3851  9.8505  18.6194
 V61  F08  F  F      0  -0.287  14.8150  9.7716  19.3148
 V61  F12  F  F      0  -0.288  15.6807  6.0430  22.0473
 V61  F14  F  F      0  -0.292  18.2389  6.1071  21.3365
 V61  I10  I  I      0   0.165  13.1815  7.8342  21.2478
 V61  H1   H  HNH2   0   0.335  18.1651  6.0979  17.7294
 V61  H2   H  HNH2   0   0.338  19.6881  5.6352  17.3968
 V61  H5   H  HCH1   0   0.217  19.0745  8.1422  17.4320
 V61  H6   H  HCH2   0   0.248  19.9590  7.5198  20.2751
 V61  H7   H  HCH2   0   0.254  19.6807  9.1032  19.5854
 V61  O1   O  OC    -1  -0.591  21.6071  6.6244  17.1908

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
 V61  O    C    deloc     1.231  0.020  1.231
 V61  C    CA   single    1.525  0.021  1.525
 V61  CA   N    single    1.458  0.019  1.458
 V61  CA   C03  single    1.536  0.020  1.536
 V61  C03  C04  single    1.500  0.020  1.500
 V61  F06  C05  single    1.335  0.020  1.335
 V61  C04  C05  aromatic  1.388  0.020  1.388
 V61  C04  C13  aromatic  1.386  0.020  1.386
 V61  C05  C07  aromatic  1.381  0.020  1.381
 V61  F14  C13  single    1.334  0.020  1.334
 V61  C13  C11  aromatic  1.384  0.020  1.384
 V61  C07  F08  single    1.330  0.020  1.330
 V61  C07  C09  aromatic  1.384  0.020  1.384
 V61  C11  C09  aromatic  1.383  0.020  1.383
 V61  C11  F12  single    1.330  0.020  1.330
 V61  C09  I10  single    2.077  0.020  2.077
 V61  N    H1   single    0.890  0.020  1.040
 V61  N    H2   single    0.890  0.020  1.040
 V61  CA   H5   single    0.970  0.020  1.090
 V61  C03  H6   single    0.970  0.020  1.090
 V61  C03  H7   single    0.970  0.020  1.090
 V61  C    O1   deloc     1.246  0.020  1.246

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
 V61  F12  C11  C09  120.07  3.000
 V61  F12  C11  C13  119.28  3.000
 V61  C09  C11  C13  120.66  3.000
 V61  F14  C13  C04  120.20  3.000
 V61  F14  C13  C11  117.76  3.000
 V61  C04  C13  C11  122.02  3.000
 V61  H2   N    H1   106.98  3.000
 V61  H2   N    CA   107.44  3.000
 V61  H1   N    CA   110.43  3.000
 V61  O1   C    CA   116.92  3.000
 V61  O1   C    O    127.11  3.000
 V61  CA   C    O    120.80  1.700
 V61  H5   CA   C03  107.39  3.000
 V61  H5   CA   C    105.15  3.000
 V61  C03  CA   C    110.13  3.000
 V61  H5   CA   N    111.66  3.000
 V61  C03  CA   N    110.40  3.000
 V61  C    CA   N    111.00  2.800
 V61  H7   C03  H6   106.78  3.000
 V61  H7   C03  C04  109.32  3.000
 V61  H6   C03  C04  109.50  3.000
 V61  H7   C03  CA   109.63  3.000
 V61  H6   C03  CA   109.15  3.000
 V61  C04  C03  CA   112.30  3.000
 V61  C05  C04  C03  120.94  3.000
 V61  C05  C04  C13  116.24  3.000
 V61  C03  C04  C13  122.81  3.000
 V61  F06  C05  C07  118.18  3.000
 V61  C07  C05  C04  122.53  3.000
 V61  F06  C05  C04  119.29  3.000
 V61  F08  C07  C09  120.39  3.000
 V61  C09  C07  C05  120.24  3.000
 V61  F08  C07  C05  119.37  3.000
 V61  I10  C09  C07  120.89  3.000
 V61  I10  C09  C11  120.82  3.000
 V61  C07  C09  C11  118.29  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
 V61  CONST_01  C05  C04  C13  C11    0.00   0.0  0
 V61  CONST_02  C05  C07  C09  C11    0.00   0.0  0
 V61  CONST_03  C07  C05  C04  C13    0.00   0.0  0
 V61  CONST_04  C07  C09  C11  C13    0.00   0.0  0
 V61  CONST_05  C09  C07  C05  C04    0.00   0.0  0
 V61  CONST_06  C09  C11  C13  C04    0.00   0.0  0
 V61  CONST_07  C03  C04  C13  C11  180.00   0.0  0
 V61  CONST_08  F08  C07  C09  C11  180.00   0.0  0
 V61  CONST_09  F06  C05  C04  C13  180.00   0.0  0
 V61  CONST_10  I10  C09  C11  C13  180.00   0.0  0
 V61  CONST_11  C07  C05  C04  C03  180.00   0.0  0
 V61  CONST_12  F08  C07  C05  C04  180.00   0.0  0
 V61  CONST_13  F12  C11  C13  C04  180.00   0.0  0
 V61  CONST_14  F14  C13  C04  C05  180.00   0.0  0
 V61  CONST_15  I10  C09  C07  C05  180.00   0.0  0
 V61  CONST_16  F12  C11  C09  C07  180.00   0.0  0
 V61  CONST_17  F06  C05  C07  C09  180.00   0.0  0
 V61  CONST_18  F14  C13  C11  C09  180.00   0.0  0
 V61  Var_01    CA   C03  C04  C13  101.48  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
 V61  chir_01  CA  C  N  C03  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
 V61  plan-1  C11  0.020
 V61  plan-1  C13  0.020
 V61  plan-1  C03  0.020
 V61  plan-1  C04  0.020
 V61  plan-1  C05  0.020
 V61  plan-1  C07  0.020
 V61  plan-1  C09  0.020
 V61  plan-1  F06  0.020
 V61  plan-1  F08  0.020
 V61  plan-1  F12  0.020
 V61  plan-1  F14  0.020
 V61  plan-1  I10  0.020
 V61  plan-2  C    0.020
 V61  plan-2  O    0.020
 V61  plan-2  CA   0.020
 V61  plan-2  O1   0.020

