# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:15:00 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[3,3,3-tris(fluoranyl)-2,2-bis(oxidanyl)propyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC(O)(O)C(F)(F)F)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
 K5H  K5H  '(2~{R})-2-azanyl-3-[3,3,3-tris(fluoranyl)-2,2-bis(oxidanyl)propyl]sulfanyl-propanoic acid'  L-peptide  24  15  .  2022-07-25  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_K5H
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
 K5H  N     N  NH2    0  -0.738   3.4428   1.5293  -0.4485
 K5H  CA    C  CH1    0  -0.196   2.9488   0.4496   0.3853
 K5H  C     C  C      0   0.360   3.9722  -0.6576   0.7571
 K5H  O     O  O      0  -0.645   5.0975  -0.5992   0.2293
 K5H  C03   C  CH2    0  -0.524   1.7563  -0.2062  -0.2966
 K5H  C05   C  CH2    0  -0.621  -0.9318   0.0714  -1.0200
 K5H  C06   C  CT     0   0.380  -1.8873   0.1963   0.1794
 K5H  C09   C  CT     0   1.014  -2.9773  -0.8895   0.1200
 K5H  F10   F  F      0  -0.328  -3.8267  -0.7878   1.1429
 K5H  F11   F  F      0  -0.347  -3.6934  -0.7816  -1.0059
 K5H  F12   F  F      0  -0.336  -2.4631  -2.1224   0.1483
 K5H  O07   O  OH1    0  -0.665  -1.2572  -0.0040   1.3868
 K5H  O08   O  OH1    0  -0.639  -2.5115   1.4431   0.2101
 K5H  S04   S  S2     0  -0.006   0.5567   1.0831  -0.7756
 K5H  H1    H  HNH2   0   0.352   4.1372   2.0541   0.0688
 K5H  H011  H  HNH2   0   0.310   3.9547   1.1252  -1.2250
 K5H  H021  H  HCH1   0   0.185   2.5877   0.8950   1.3189
 K5H  H031  H  HCH2   0   0.207   2.0681  -0.7409  -1.1975
 K5H  H032  H  HCH2   0   0.287   1.2794  -0.9181   0.3739
 K5H  H052  H  HCH2   0   0.303  -0.6263  -0.9627  -1.1817
 K5H  H051  H  HCH2   0   0.248  -1.4248   0.4027  -1.9353
 K5H  H071  H  HOH1   0   0.480  -0.4742   0.5695   1.4038
 K5H  H081  H  HOH1   0   0.482  -2.6385   1.7855  -0.6816
 K5H  OXT   O  OC    -1  -0.562   3.5615  -1.5221   1.5579

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
 K5H  F10  C09   single  1.333  0.020  1.333
 K5H  C09  F12   single  1.336  0.020  1.336
 K5H  C09  F11   single  1.339  0.020  1.339
 K5H  C09  C06   single  1.540  0.020  1.540
 K5H  O08  C06   single  1.395  0.020  1.395
 K5H  N    CA    single  1.458  0.019  1.458
 K5H  C06  C05   single  1.539  0.020  1.539
 K5H  C06  O07   single  1.377  0.020  1.377
 K5H  C05  S04   single  1.816  0.020  1.816
 K5H  C    CA    single  1.525  0.021  1.525
 K5H  C    O     deloc   1.231  0.020  1.231
 K5H  S04  C03   single  1.825  0.020  1.825
 K5H  CA   C03   single  1.522  0.020  1.522
 K5H  N    H1    single  0.890  0.020  1.040
 K5H  N    H011  single  0.890  0.020  1.040
 K5H  CA   H021  single  0.970  0.020  1.090
 K5H  C03  H031  single  0.970  0.020  1.090
 K5H  C03  H032  single  0.970  0.020  1.090
 K5H  C05  H052  single  0.970  0.020  1.090
 K5H  C05  H051  single  0.970  0.020  1.090
 K5H  O07  H071  single  0.850  0.020  0.980
 K5H  O08  H081  single  0.850  0.020  0.980
 K5H  C    OXT   deloc   1.248  0.020  1.248

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
 K5H  H011  N    H1    104.57  3.000
 K5H  H011  N    CA    108.38  3.000
 K5H  H1    N    CA    109.00  3.000
 K5H  H021  CA   C03   107.38  3.000
 K5H  H021  CA   C     107.64  3.000
 K5H  C03   CA   C     108.44  3.000
 K5H  H021  CA   N     107.42  3.000
 K5H  C03   CA   N     109.26  3.000
 K5H  C     CA   N     111.00  2.800
 K5H  OXT   C    O     127.04  3.000
 K5H  OXT   C    CA    115.51  3.000
 K5H  O     C    CA    120.80  1.700
 K5H  H032  C03  H031  108.24  3.000
 K5H  H032  C03  S04   109.62  3.000
 K5H  H031  C03  S04   108.47  3.000
 K5H  H032  C03  CA    110.44  3.000
 K5H  H031  C03  CA    110.89  3.000
 K5H  S04   C03  CA    109.16  3.000
 K5H  H051  C05  H052  106.87  3.000
 K5H  H051  C05  S04   108.31  3.000
 K5H  H052  C05  S04   108.58  3.000
 K5H  H051  C05  C06   110.40  3.000
 K5H  H052  C05  C06   111.51  3.000
 K5H  S04   C05  C06   111.03  3.000
 K5H  O08   C06  O07   108.40  3.000
 K5H  O07   C06  C09   104.79  3.000
 K5H  O08   C06  C09   108.33  3.000
 K5H  O07   C06  C05   112.81  3.000
 K5H  O08   C06  C05   111.57  3.000
 K5H  C09   C06  C05   110.63  3.000
 K5H  F12   C09  F11   107.34  3.000
 K5H  F11   C09  F10   107.36  3.000
 K5H  F12   C09  F10   107.41  3.000
 K5H  F11   C09  C06   110.75  3.000
 K5H  F12   C09  C06   112.18  3.000
 K5H  F10   C09  C06   111.56  3.000
 K5H  H071  O07  C06   107.38  3.000
 K5H  H081  O08  C06   110.87  3.000
 K5H  C05   S04  C03   100.40  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
 K5H  Var_01  C06   C05  S04  C03   102.34  30.0  1
 K5H  Var_02  F10   C09  C06  C05  -179.21  30.0  3
 K5H  Var_03  S04   C05  C06  C09  -167.18  30.0  3
 K5H  Var_04  H031  C03  S04  C05    77.20  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
 K5H  chir_01  CA  N  C  C03  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
 K5H  plan-1  CA   0.020
 K5H  plan-1  C    0.020
 K5H  plan-1  O    0.020
 K5H  plan-1  OXT  0.020

