# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:33:24 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (3S)-3-amino-4-oxo-5-(2,3,5,6-tetrafluorophenoxy)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)C(=O)COc1c(F)c(F)cc(F)c1F
#
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
 4H0  4H0  '(3S)-3-amino-4-oxo-5-(2,3,5,6-tetrafluorophenoxy)pentanoic acid'  peptide  28  20  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4H0
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
 4H0  N    N  NH2    0  -0.809  3.9056  -1.3250  40.5498
 4H0  CA   C  CH1    0  -0.189  3.0786  -1.9831  39.5565
 4H0  CB   C  CH2    0  -0.600  3.1310  -1.2062  38.2369
 4H0  CG   C  C      0   0.426  2.5046   0.2110  38.2804
 4H0  OD1  O  O      0  -0.601  2.6845   0.8951  37.2578
 4H0  OD2  O  OC    -1  -0.594  1.8707   0.5324  39.3052
 4H0  C    C  C      0   0.377  3.5924  -3.3711  39.2533
 4H0  O    O  O      0  -0.382  2.8553  -4.2719  38.9215
 4H0  C5   C  CH2    0  -0.280  5.0933  -3.6204  39.3510
 4H0  H    H  HNH2   0   0.353  3.5698  -0.3743  40.6410
 4H0  HA   H  HCH1   0   0.230  2.0257  -2.0876  39.8500
 4H0  HB2  H  HCH2   0   0.234  4.1696  -1.1218  37.9007
 4H0  HB3  H  HCH2   0   0.246  2.6068  -1.7725  37.4606
 4H0  H2   H  HNH2   0   0.342  3.7734  -1.7541  41.4563
 4H0  O4   O  O2     0  -0.474  5.4249  -3.9748  40.7004
 4H0  H5   H  HCH2   0   0.265  5.3796  -4.4117  38.6537
 4H0  H8   H  HCH2   0   0.265  5.6665  -2.7226  39.1326
 4H0  C6   C  CR6    0   0.061  5.0293  -5.1973  41.1061
 4H0  C7   C  CR6    0   0.357  3.8881  -5.3430  41.8842
 4H0  C8   C  CR6    0   0.422  3.5090  -6.5870  42.3509
 4H0  C9   C  CR16   0  -0.580  4.2479  -7.7136  42.0535
 4H0  C10  C  CR6    0   0.416  5.3818  -7.5710  41.2792
 4H0  C11  C  CR6    0   0.365  5.7750  -6.3324  40.8095
 4H0  F1   F  F      0  -0.294  3.1550  -4.2706  42.1789
 4H0  F2   F  F      0  -0.296  2.4074  -6.6863  43.0928
 4H0  H9   H  HCR6   0   0.329  3.9471  -8.6860  42.4209
 4H0  F3   F  F      0  -0.297  6.1207  -8.6380  40.9783
 4H0  F4   F  F      0  -0.293  6.8795  -6.2163  40.0759

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
 4H0  N    H    single    0.860  0.020  0.860
 4H0  N    H2   single    0.890  0.020  1.040
 4H0  CA   N    single    1.458  0.019  1.458
 4H0  CA   C    single    1.525  0.021  1.525
 4H0  CA   HA   single    0.970  0.020  0.970
 4H0  CB   CA   single    1.521  0.033  1.521
 4H0  CB   CG   single    1.550  0.020  1.550
 4H0  CB   HB2  single    0.970  0.020  1.090
 4H0  CB   HB3  single    0.970  0.020  1.090
 4H0  CG   OD2  deloc     1.247  0.020  1.247
 4H0  OD1  CG   deloc     1.243  0.020  1.243
 4H0  C    C5   single    1.525  0.020  1.525
 4H0  O    C    double    1.231  0.020  1.231
 4H0  C5   O4   single    1.434  0.020  1.434
 4H0  C5   H5   single    0.970  0.020  1.090
 4H0  C5   H8   single    0.970  0.020  1.090
 4H0  O4   C6   single    1.347  0.020  1.347
 4H0  C6   C7   aromatic  1.389  0.020  1.389
 4H0  C7   C8   aromatic  1.382  0.020  1.382
 4H0  C8   C9   aromatic  1.380  0.020  1.380
 4H0  C9   C10  aromatic  1.380  0.020  1.380
 4H0  C10  C11  aromatic  1.382  0.020  1.382
 4H0  C6   C11  aromatic  1.390  0.020  1.390
 4H0  C7   F1   single    1.332  0.020  1.332
 4H0  C8   F2   single    1.332  0.020  1.332
 4H0  C9   H9   single    0.930  0.020  1.080
 4H0  C10  F3   single    1.332  0.020  1.332
 4H0  C11  F4   single    1.331  0.020  1.331

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
 4H0  H2   N    H    105.92  3.000
 4H0  H2   N    CA   110.29  3.000
 4H0  H    N    CA   114.00  3.000
 4H0  HA   CA   C    110.00  3.000
 4H0  HA   CA   CB   109.00  3.000
 4H0  C    CA   CB   110.50  1.500
 4H0  CB   CA   N    110.40  1.500
 4H0  HA   CA   N    110.00  3.000
 4H0  C    CA   N    111.00  2.800
 4H0  HB3  CB   HB2  106.04  3.000
 4H0  HB3  CB   CG   107.42  3.000
 4H0  HB2  CB   CG   108.75  3.000
 4H0  HB3  CB   CA   109.40  3.000
 4H0  HB2  CB   CA   109.63  3.000
 4H0  CG   CB   CA   115.19  3.000
 4H0  OD2  CG   OD1  127.41  3.000
 4H0  OD1  CG   CB   114.92  3.000
 4H0  OD2  CG   CB   117.65  3.000
 4H0  C5   C    O    119.70  3.000
 4H0  O    C    CA   120.80  1.700
 4H0  C5   C    CA   118.17  3.000
 4H0  H8   C5   H5   109.37  3.000
 4H0  H8   C5   O4   105.73  3.000
 4H0  H5   C5   O4   111.16  3.000
 4H0  H8   C5   C    111.78  3.000
 4H0  H5   C5   C    109.59  3.000
 4H0  O4   C5   C    109.17  3.000
 4H0  C6   O4   C5   116.08  3.000
 4H0  C11  C6   C7   118.34  3.000
 4H0  C11  C6   O4   121.27  3.000
 4H0  C7   C6   O4   120.34  3.000
 4H0  F1   C7   C8   119.94  3.000
 4H0  F1   C7   C6   119.45  3.000
 4H0  C8   C7   C6   120.61  3.000
 4H0  F2   C8   C9   120.15  3.000
 4H0  F2   C8   C7   118.83  3.000
 4H0  C9   C8   C7   121.02  3.000
 4H0  H9   C9   C10  120.77  3.000
 4H0  H9   C9   C8   120.77  3.000
 4H0  C10  C9   C8   118.46  3.000
 4H0  F3   C10  C11  118.90  3.000
 4H0  F3   C10  C9   119.97  3.000
 4H0  C11  C10  C9   121.13  3.000
 4H0  F4   C11  C10  120.11  3.000
 4H0  F4   C11  C6   119.44  3.000
 4H0  C10  C11  C6   120.45  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
 4H0  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 4H0  CONST_02  C9   C10  C11  C6      0.00   0.0  0
 4H0  CONST_03  C10  C11  C6   C7      0.00   0.0  0
 4H0  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 4H0  CONST_05  C11  C6   C7   C8      0.00   0.0  0
 4H0  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 4H0  CONST_07  C8   C7   C6   O4    180.00   0.0  0
 4H0  CONST_08  C10  C11  C6   O4    180.00   0.0  0
 4H0  CONST_09  F2   C8   C7   C6    180.00   0.0  0
 4H0  CONST_10  F3   C10  C11  C6    180.00   0.0  0
 4H0  CONST_11  F4   C11  C6   C7    180.00   0.0  0
 4H0  CONST_12  F3   C10  C9   C8    180.00   0.0  0
 4H0  CONST_13  F1   C7   C8   C9    180.00   0.0  0
 4H0  CONST_14  F4   C11  C10  C9    180.00   0.0  0
 4H0  CONST_15  F2   C8   C9   C10   180.00   0.0  0
 4H0  CONST_16  F1   C7   C6   C11   180.00   0.0  0
 4H0  CONST_17  H9   C9   C8   C7    180.00   0.0  0
 4H0  Var_01    C7   C6   O4   C5   -100.48  30.0  2
 4H0  Var_02    O4   C5   C    CA     87.37  30.0  3
 4H0  Var_03    OD2  CG   CB   CA     -8.91  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
 4H0  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
 4H0  plan-1  O4   0.020
 4H0  plan-1  C6   0.020
 4H0  plan-1  C7   0.020
 4H0  plan-1  C8   0.020
 4H0  plan-1  C9   0.020
 4H0  plan-1  C10  0.020
 4H0  plan-1  C11  0.020
 4H0  plan-1  F1   0.020
 4H0  plan-1  F2   0.020
 4H0  plan-1  H9   0.020
 4H0  plan-1  F3   0.020
 4H0  plan-1  F4   0.020
 4H0  plan-2  CA   0.020
 4H0  plan-2  C    0.020
 4H0  plan-2  O    0.020
 4H0  plan-2  C5   0.020
 4H0  plan-3  CB   0.020
 4H0  plan-3  CG   0.020
 4H0  plan-3  OD1  0.020
 4H0  plan-3  OD2  0.020

