# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:09:37 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S})-2-[3-(4-chlorophenyl)sulfanylpropanoylamino]-3-methyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)CCSc1ccc(Cl)cc1)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
 K7Z  K7Z  '(2~{S})-2-[3-(4-chlorophenyl)sulfanylpropanoylamino]-3-methyl-butanoic acid'  ligand  37  20  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K7Z
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
 K7Z  C13  C   C      0   0.421  13.3040  -3.2667   2.3266
 K7Z  C10  C   CR6    0  -0.046   7.3125   2.3202  -1.7422
 K7Z  C9   C   CR16   0  -0.201   8.0039   1.1279  -1.8997
 K7Z  C8   C   CR16   0  -0.247   8.2264   0.3204  -0.7963
 K7Z  C7   C   CR6    0  -0.112   7.7340   0.6842   0.4555
 K7Z  C6   C   CH2    0  -0.555   7.5508  -1.9681   1.4265
 K7Z  C11  C   CR16   0  -0.200   6.8304   2.7068  -0.5030
 K7Z  N    N   NH1    0  -0.612  10.9848  -2.5966   1.8804
 K7Z  C    C   CH3    0  -0.655  12.0162  -0.1708   0.3296
 K7Z  O    O   O      0  -0.510   9.9270  -2.7351  -0.1195
 K7Z  C1   C   CH1    0  -0.221  12.7939  -0.9766   1.3635
 K7Z  O1   O   OC    -1  -0.594  12.8388  -3.7032   3.3978
 K7Z  C2   C   CH3    0  -0.663  12.7120  -0.2989   2.7284
 K7Z  O2   O   O      0  -0.596  14.4670  -3.3858   1.9017
 K7Z  C3   C   CH1    0  -0.209  12.3466  -2.4519   1.4170
 K7Z  C5   C   CH2    0  -0.559   8.6043  -2.9774   1.8534
 K7Z  C12  C   CR16   0  -0.265   7.0349   1.8795   0.5921
 K7Z  S    S   S2     0   0.009   8.0492  -0.2743   1.9073
 K7Z  H2   H   HCR6   0   0.283   8.7911  -0.5953  -0.9174
 K7Z  H3   H   HCH2   0   0.292   6.5965  -2.1925   1.9012
 K7Z  H4   H   HCH2   0   0.284   7.4015  -1.9966   0.3488
 K7Z  H5   H   HCR6   0   0.281   6.2871   3.6348  -0.3874
 K7Z  H6   H   HNH1   0   0.383  10.8961  -2.7574   2.8727
 K7Z  H7   H   HCH3   0   0.220  12.4270   0.8372   0.2442
 K7Z  H8   H   HCH3   0   0.217  12.0571  -0.6321  -0.6579
 K7Z  H9   H   HCH3   0   0.217  10.9656  -0.0704   0.6094
 K7Z  H10  H   HCH1   0   0.217  13.8420  -0.9990   1.0520
 K7Z  H12  H   HCH3   0   0.227  13.3027  -0.8147   3.4863
 K7Z  H13  H   HCH3   0   0.224  13.0809   0.7262   2.6687
 K7Z  H14  H   HCH3   0   0.210  11.6794  -0.2528   3.0817
 K7Z  H15  H   HCH1   0   0.237  12.4058  -2.8562   0.4030
 K7Z  H16  H   HCH2   0   0.279   8.2338  -3.9784   1.6142
 K7Z  H17  H   HCH2   0   0.259   8.7435  -2.9452   2.9358
 K7Z  H18  H   HCR6   0   0.275   6.6391   2.1704   1.5564
 K7Z  CL   CL  CL     0  -0.126   7.0503   3.3409  -3.1168
 K7Z  C4   C   C      0   0.555   9.9079  -2.7593   1.1079
 K7Z  H1   H   HCR6   0   0.281   8.3828   0.8346  -2.8695

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
 K7Z  CL   C10  single    1.732  0.020  1.732
 K7Z  C9   C10  aromatic  1.387  0.020  1.387
 K7Z  C9   C8   aromatic  1.385  0.020  1.385
 K7Z  C10  C11  aromatic  1.385  0.020  1.385
 K7Z  C8   C7   aromatic  1.394  0.020  1.394
 K7Z  C11  C12  aromatic  1.388  0.020  1.388
 K7Z  O    C4   double    1.228  0.020  1.228
 K7Z  C    C1   single    1.524  0.020  1.524
 K7Z  C7   C12  aromatic  1.391  0.020  1.391
 K7Z  C7   S    single    1.768  0.020  1.768
 K7Z  C4   C5   single    1.518  0.020  1.518
 K7Z  C4   N    single    1.335  0.020  1.335
 K7Z  C6   S    single    1.830  0.020  1.830
 K7Z  C6   C5   single    1.520  0.020  1.520
 K7Z  C1   C3   single    1.543  0.020  1.543
 K7Z  C1   C2   single    1.526  0.020  1.526
 K7Z  C3   N    single    1.446  0.020  1.446
 K7Z  C3   C13  single    1.552  0.020  1.552
 K7Z  O2   C13  deloc     1.244  0.020  1.244
 K7Z  C13  O1   deloc     1.247  0.020  1.247
 K7Z  C9   H1   single    0.930  0.020  1.080
 K7Z  C8   H2   single    0.930  0.020  1.080
 K7Z  C6   H3   single    0.970  0.020  1.090
 K7Z  C6   H4   single    0.970  0.020  1.090
 K7Z  C11  H5   single    0.930  0.020  1.080
 K7Z  N    H6   single    0.860  0.020  1.020
 K7Z  C    H7   single    0.970  0.020  1.090
 K7Z  C    H8   single    0.970  0.020  1.090
 K7Z  C    H9   single    0.970  0.020  1.090
 K7Z  C1   H10  single    0.970  0.020  1.090
 K7Z  C2   H12  single    0.970  0.020  1.090
 K7Z  C2   H13  single    0.970  0.020  1.090
 K7Z  C2   H14  single    0.970  0.020  1.090
 K7Z  C3   H15  single    0.970  0.020  1.090
 K7Z  C5   H16  single    0.970  0.020  1.090
 K7Z  C5   H17  single    0.970  0.020  1.090
 K7Z  C12  H18  single    0.930  0.020  1.080

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
 K7Z  C3   C13  O2   115.27  3.000
 K7Z  O2   C13  O1   127.51  3.000
 K7Z  C3   C13  O1   117.21  3.000
 K7Z  CL   C10  C11  119.54  3.000
 K7Z  C11  C10  C9   121.00  3.000
 K7Z  CL   C10  C9   119.46  3.000
 K7Z  H1   C9   C8   119.98  3.000
 K7Z  H1   C9   C10  120.63  3.000
 K7Z  C8   C9   C10  119.38  3.000
 K7Z  H2   C8   C7   120.37  3.000
 K7Z  H2   C8   C9   119.19  3.000
 K7Z  C7   C8   C9   120.44  3.000
 K7Z  S    C7   C12  118.34  3.000
 K7Z  S    C7   C8   122.22  3.000
 K7Z  C12  C7   C8   119.34  3.000
 K7Z  H4   C6   H3   107.82  3.000
 K7Z  H4   C6   S    108.77  3.000
 K7Z  H3   C6   S    108.35  3.000
 K7Z  H4   C6   C5   110.84  3.000
 K7Z  H3   C6   C5   110.37  3.000
 K7Z  S    C6   C5   110.61  3.000
 K7Z  H5   C11  C12  120.08  3.000
 K7Z  H5   C11  C10  120.67  3.000
 K7Z  C12  C11  C10  119.24  3.000
 K7Z  H6   N    C3   114.45  3.000
 K7Z  H6   N    C4   118.59  3.000
 K7Z  C3   N    C4   125.90  3.000
 K7Z  H9   C    H8   107.88  3.000
 K7Z  H9   C    H7   107.30  3.000
 K7Z  H8   C    H7   107.80  3.000
 K7Z  H9   C    C1   111.45  3.000
 K7Z  H8   C    C1   111.80  3.000
 K7Z  H7   C    C1   110.43  3.000
 K7Z  H10  C1   C3   105.55  3.000
 K7Z  H10  C1   C2   108.38  3.000
 K7Z  C3   C1   C2   112.22  3.000
 K7Z  H10  C1   C    107.86  3.000
 K7Z  C2   C1   C    110.15  3.000
 K7Z  C3   C1   C    112.41  3.000
 K7Z  H14  C2   H13  107.32  3.000
 K7Z  H14  C2   H12  107.89  3.000
 K7Z  H13  C2   H12  107.42  3.000
 K7Z  H14  C2   C1   111.02  3.000
 K7Z  H13  C2   C1   110.49  3.000
 K7Z  H12  C2   C1   112.49  3.000
 K7Z  H15  C3   C1   107.81  3.000
 K7Z  H15  C3   N    108.14  3.000
 K7Z  C1   C3   N    112.33  3.000
 K7Z  H15  C3   C13  108.43  3.000
 K7Z  N    C3   C13  109.92  3.000
 K7Z  C1   C3   C13  110.10  3.000
 K7Z  H17  C5   H16  106.68  3.000
 K7Z  H17  C5   C4   111.91  3.000
 K7Z  H16  C5   C4   108.36  3.000
 K7Z  H17  C5   C6   110.32  3.000
 K7Z  H16  C5   C6   108.15  3.000
 K7Z  C4   C5   C6   111.22  3.000
 K7Z  H18  C12  C11  119.28  3.000
 K7Z  H18  C12  C7   120.14  3.000
 K7Z  C11  C12  C7   120.58  3.000
 K7Z  C6   S    C7   103.74  3.000
 K7Z  C5   C4   O    120.48  3.000
 K7Z  C5   C4   N    115.22  3.000
 K7Z  O    C4   N    124.29  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
 K7Z  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 K7Z  CONST_02  C7   C12  C11  C10     0.00   0.0  0
 K7Z  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 K7Z  CONST_04  C12  C7   C8   C9      0.00   0.0  0
 K7Z  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 K7Z  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 K7Z  CONST_07  S    C7   C8   C9    180.00   0.0  0
 K7Z  CONST_08  CL   C10  C9   C8    180.00   0.0  0
 K7Z  CONST_09  S    C7   C12  C11   180.00   0.0  0
 K7Z  CONST_10  C12  C11  C10  CL    180.00   0.0  0
 K7Z  CONST_11  H2   C8   C9   C10   180.00   0.0  0
 K7Z  CONST_12  H18  C12  C11  C10   180.00   0.0  0
 K7Z  CONST_13  H5   C11  C10  C9    180.00   0.0  0
 K7Z  CONST_14  H1   C9   C8   C7    180.00   0.0  0
 K7Z  CONST_15  C3   N    C4   O       0.00   0.0  0
 K7Z  CONST_16  C5   C4   N    C3    180.00   0.0  0
 K7Z  CONST_17  H6   N    C4   O     180.00   0.0  0
 K7Z  Var_01    C12  C7   S    C6    131.94  30.0  1
 K7Z  Var_02    C5   C6   S    C7    133.91  30.0  1
 K7Z  Var_03    O    C4   C5   C6    -54.48  30.0  2
 K7Z  Var_04    S    C6   C5   C4    -65.25  30.0  2
 K7Z  Var_05    H12  C2   C1   C    -176.80  30.0  3
 K7Z  Var_06    H7   C    C1   C2     59.98  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
 K7Z  chir_01  C3  C1  N  C13  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
 K7Z  plan-1  C10  0.020
 K7Z  plan-1  C9   0.020
 K7Z  plan-1  C8   0.020
 K7Z  plan-1  C7   0.020
 K7Z  plan-1  C11  0.020
 K7Z  plan-1  C12  0.020
 K7Z  plan-1  S    0.020
 K7Z  plan-1  H2   0.020
 K7Z  plan-1  H5   0.020
 K7Z  plan-1  H18  0.020
 K7Z  plan-1  CL   0.020
 K7Z  plan-1  H1   0.020
 K7Z  plan-2  N    0.020
 K7Z  plan-2  O    0.020
 K7Z  plan-2  C3   0.020
 K7Z  plan-2  C5   0.020
 K7Z  plan-2  H6   0.020
 K7Z  plan-2  C4   0.020
 K7Z  plan-3  C13  0.020
 K7Z  plan-3  O1   0.020
 K7Z  plan-3  O2   0.020
 K7Z  plan-3  C3   0.020

