# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:33:03 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2R,3S)-3-amino-1-chloro-4-phenylbutan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)[C@@H](O)CCl
#
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
 PHK  PHK  (2R,3S)-3-amino-1-chloro-4-phenylbutan-2-ol  ligand  27  13  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PHK
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
 PHK  CB   C   CH2   0  -0.523  -0.5953   0.0636  -0.9512
 PHK  CG   C   CR6   0   0.165  -2.0149  -0.0516  -0.4754
 PHK  CD1  C   CR16  0  -0.310  -2.7867   1.0778  -0.2138
 PHK  CD2  C   CR16  0  -0.313  -2.5872  -1.3051  -0.2686
 PHK  CE1  C   CR16  0  -0.244  -4.0936   0.9605   0.2405
 PHK  CE2  C   CR16  0  -0.241  -3.8926  -1.4295   0.1885
 PHK  CZ   C   CR16  0  -0.275  -4.6513  -0.2951   0.4459
 PHK  O    O   OH1   0  -0.653   2.2324   1.0079  -1.1320
 PHK  C1   C   CH2   0  -0.487   2.8368  -0.4255   0.7319
 PHK  CL   CL  CL    0  -0.168   4.4967  -0.6541   0.0825
 PHK  C    C   CH1   0   0.032   1.8511  -0.1162  -0.3816
 PHK  N    N   NH2   0  -0.788   0.2101   1.1388   1.0798
 PHK  CA   C   CH1   0  -0.104   0.4229   0.0118   0.1933
 PHK  H6   H   HCH2  0   0.245  -0.4612   0.9941  -1.5101
 PHK  H7   H   HCH2  0   0.249  -0.3798  -0.7498  -1.6485
 PHK  H1   H   HCR6  0   0.240  -2.3637   2.0618  -0.3761
 PHK  H5   H   HCR6  0   0.242  -2.0065  -2.1976  -0.4738
 PHK  H2   H   HCR6  0   0.250  -4.6775   1.8516   0.4338
 PHK  H4   H   HCR6  0   0.251  -4.3183  -2.4134   0.3399
 PHK  H3   H   HCR6  0   0.251  -5.6708  -0.3890   0.7976
 PHK  H9   H   HOH1  0   0.439   2.2932   1.7682  -0.5433
 PHK  H11  H   HCH2  0   0.273   2.8996   0.3778   1.4660
 PHK  H12  H   HCH2  0   0.290   2.5632  -1.3461   1.2437
 PHK  H    H   HCH1  0   0.244   1.8576  -0.9609  -1.0770
 PHK  H13  H   HNH2  0   0.354   0.8419   1.1372   1.8696
 PHK  H14  H   HNH2  0   0.340   0.3210   2.0216   0.5975
 PHK  H8   H   HCH1  0   0.240   0.2333  -0.9016   0.7694

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
 PHK  CB   CG   single    1.502  0.020  1.502
 PHK  CB   CA   single    1.533  0.020  1.533
 PHK  CB   H6   single    0.970  0.020  1.090
 PHK  CB   H7   single    0.970  0.020  1.090
 PHK  CG   CD1  aromatic  1.393  0.020  1.393
 PHK  CG   CD2  aromatic  1.393  0.020  1.393
 PHK  CD1  CE1  aromatic  1.389  0.020  1.389
 PHK  CD1  H1   single    0.930  0.020  1.080
 PHK  CD2  CE2  aromatic  1.389  0.020  1.389
 PHK  CD2  H5   single    0.930  0.020  1.080
 PHK  CE1  CZ   aromatic  1.389  0.020  1.389
 PHK  CE1  H2   single    0.930  0.020  1.080
 PHK  CE2  CZ   aromatic  1.389  0.020  1.389
 PHK  CE2  H4   single    0.930  0.020  1.080
 PHK  CZ   H3   single    0.930  0.020  1.080
 PHK  O    C    single    1.404  0.020  1.404
 PHK  O    H9   single    0.850  0.020  0.980
 PHK  C1   CL   single    1.797  0.020  1.797
 PHK  C1   C    single    1.519  0.020  1.519
 PHK  C1   H11  single    0.970  0.020  1.090
 PHK  C1   H12  single    0.970  0.020  1.090
 PHK  C    CA   single    1.545  0.020  1.545
 PHK  C    H    single    0.970  0.020  1.090
 PHK  N    CA   single    1.450  0.020  1.450
 PHK  N    H13  single    0.890  0.020  1.040
 PHK  N    H14  single    0.890  0.020  1.040
 PHK  CA   H8   single    0.970  0.020  1.090

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
 PHK  H7   CB   H6   106.44  3.000
 PHK  H7   CB   CA   108.68  3.000
 PHK  H6   CB   CA   109.20  3.000
 PHK  H7   CB   CG   109.36  3.000
 PHK  H6   CB   CG   110.07  3.000
 PHK  CA   CB   CG   112.88  3.000
 PHK  CD2  CG   CD1  118.29  3.000
 PHK  CD2  CG   CB   120.29  3.000
 PHK  CD1  CG   CB   121.41  3.000
 PHK  H1   CD1  CE1  119.56  3.000
 PHK  H1   CD1  CG   119.47  3.000
 PHK  CE1  CD1  CG   120.97  3.000
 PHK  H5   CD2  CE2  119.47  3.000
 PHK  H5   CD2  CG   119.49  3.000
 PHK  CE2  CD2  CG   121.03  3.000
 PHK  H2   CE1  CZ   120.07  3.000
 PHK  H2   CE1  CD1  119.76  3.000
 PHK  CZ   CE1  CD1  120.17  3.000
 PHK  H4   CE2  CZ   120.10  3.000
 PHK  H4   CE2  CD2  119.81  3.000
 PHK  CZ   CE2  CD2  120.09  3.000
 PHK  H3   CZ   CE2  120.26  3.000
 PHK  H3   CZ   CE1  120.30  3.000
 PHK  CE2  CZ   CE1  119.44  3.000
 PHK  H9   O    C    108.80  3.000
 PHK  H12  C1   H11  108.74  3.000
 PHK  H12  C1   C    110.72  3.000
 PHK  H11  C1   C    112.39  3.000
 PHK  H12  C1   CL   107.14  3.000
 PHK  H11  C1   CL   106.49  3.000
 PHK  C    C1   CL   111.13  3.000
 PHK  H    C    CA   107.82  3.000
 PHK  H    C    C1   107.75  3.000
 PHK  CA   C    C1   110.12  3.000
 PHK  H    C    O    106.07  3.000
 PHK  CA   C    O    112.56  3.000
 PHK  C1   C    O    112.24  3.000
 PHK  H14  N    H13  107.76  3.000
 PHK  H14  N    CA   111.76  3.000
 PHK  H13  N    CA   112.63  3.000
 PHK  H8   CA   N    107.52  3.000
 PHK  H8   CA   C    106.64  3.000
 PHK  N    CA   C    115.32  3.000
 PHK  H8   CA   CB   107.80  3.000
 PHK  N    CA   CB   109.44  3.000
 PHK  C    CA   CB   109.82  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
 PHK  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 PHK  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 PHK  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PHK  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PHK  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PHK  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PHK  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 PHK  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 PHK  CONST_09  H2   CE1  CD1  CG   180.00   0.0  0
 PHK  CONST_10  H4   CE2  CD2  CG   180.00   0.0  0
 PHK  CONST_11  H5   CD2  CG   CD1  180.00   0.0  0
 PHK  CONST_12  H3   CZ   CE1  CD1  180.00   0.0  0
 PHK  CONST_13  H1   CD1  CG   CD2  180.00   0.0  0
 PHK  Var_01    CA   CB   CG   CD1   93.84  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
 PHK  chir_01  C   O  C1  CA  negativ
 PHK  chir_02  CA  N  CB  C   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
 PHK  plan-1  CB   0.020
 PHK  plan-1  CG   0.020
 PHK  plan-1  CD1  0.020
 PHK  plan-1  CD2  0.020
 PHK  plan-1  CE1  0.020
 PHK  plan-1  CE2  0.020
 PHK  plan-1  CZ   0.020
 PHK  plan-1  H1   0.020
 PHK  plan-1  H5   0.020
 PHK  plan-1  H2   0.020
 PHK  plan-1  H4   0.020
 PHK  plan-1  H3   0.020

