# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:06:57 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: (2~{S})-2-[2-(4-chlorophenyl)sulfanylethanoylamino]-3-methyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)CSc1ccc(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
 JVK  JVK  '(2~{S})-2-[2-(4-chlorophenyl)sulfanylethanoylamino]-3-methyl-butanoic acid'  ligand  34  19  .  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_JVK
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
 JVK  C    C   CR16   0  -0.240   -5.2114  -0.6743  -2.9480
 JVK  N    N   NH1    0  -0.600   -7.7069  -2.6054  -5.2215
 JVK  S    S   S2     0   0.040   -4.7229  -2.0277  -5.3289
 JVK  C1   C   CR6    0  -0.117   -5.1482  -0.6271  -4.3378
 JVK  C2   C   CR16   0  -0.256   -5.3829   0.5798  -4.9904
 JVK  C3   C   CR16   0  -0.202   -5.6752   1.7268  -4.2694
 JVK  C4   C   CR6    0  -0.047   -5.7483   1.6585  -2.8875
 JVK  C5   C   CR16   0  -0.197   -5.5229   0.4644  -2.2212
 JVK  C6   C   CH2    0  -0.700   -5.5418  -3.3797  -4.4503
 JVK  C7   C   C      0   0.541   -7.0474  -3.2385  -4.2510
 JVK  C8   C   CH1    0  -0.209   -9.1455  -2.4984  -5.3179
 JVK  C9   C   C      0   0.420   -9.6100  -2.8339  -6.7590
 JVK  C10  C   CH1    0  -0.217   -9.6547  -1.1050  -4.8998
 JVK  C11  C   CH3    0  -0.655   -9.2830  -0.7702  -3.4600
 JVK  C12  C   CH3    0  -0.672   -9.1755  -0.0015  -5.8389
 JVK  O    O   O      0  -0.496   -7.5625  -3.7367  -3.2588
 JVK  CL   CL  CL     0  -0.126   -6.1257   3.0842  -1.9803
 JVK  O1   O   OC    -1  -0.597  -10.8358  -2.9962  -6.8960
 JVK  O2   O   O      0  -0.594   -8.7332  -2.8827  -7.6427
 JVK  H1   H   HCR6   0   0.279   -5.0182  -1.5932  -2.4109
 JVK  H2   H   HNH1   0   0.384   -7.1991  -2.3500  -6.0566
 JVK  H3   H   HCR6   0   0.280   -5.3500   0.6304  -6.0713
 JVK  H4   H   HCR6   0   0.283   -5.8580   2.6586  -4.7871
 JVK  H5   H   HCR6   0   0.283   -5.5771   0.4168  -1.1418
 JVK  H6   H   HCH2   0   0.326   -5.3479  -4.2642  -5.0638
 JVK  H7   H   HCH2   0   0.302   -5.0730  -3.5611  -3.4845
 JVK  H8   H   HCH1   0   0.238   -9.5830  -3.2323  -4.6367
 JVK  H9   H   HCH1   0   0.217  -10.7456  -1.1562  -4.9624
 JVK  H10  H   HCH3   0   0.220   -9.6105  -1.5455  -2.7658
 JVK  H11  H   HCH3   0   0.217   -8.2037  -0.6507  -3.3439
 JVK  H12  H   HCH3   0   0.223   -9.7485   0.1686  -3.1544
 JVK  H13  H   HCH3   0   0.223   -9.5489   0.9690  -5.5070
 JVK  H14  H   HCH3   0   0.220   -8.0852   0.0621  -5.8532
 JVK  H15  H   HCH3   0   0.228   -9.5185  -0.1467  -6.8638

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
 JVK  O2   C9   deloc     1.246  0.020  1.246
 JVK  C12  C10  single    1.526  0.020  1.526
 JVK  C9   O1   deloc     1.244  0.020  1.244
 JVK  C9   C8   single    1.551  0.020  1.551
 JVK  N    C8   single    1.446  0.020  1.446
 JVK  N    C7   single    1.333  0.020  1.333
 JVK  S    C6   single    1.808  0.020  1.808
 JVK  S    C1   single    1.768  0.020  1.768
 JVK  C8   C10  single    1.541  0.020  1.541
 JVK  C6   C7   single    1.525  0.020  1.525
 JVK  C10  C11  single    1.524  0.020  1.524
 JVK  C7   O    double    1.224  0.020  1.224
 JVK  C2   C1   aromatic  1.392  0.020  1.392
 JVK  C2   C3   aromatic  1.386  0.020  1.386
 JVK  C1   C    aromatic  1.392  0.020  1.392
 JVK  C3   C4   aromatic  1.386  0.020  1.386
 JVK  C    C5   aromatic  1.386  0.020  1.386
 JVK  C4   C5   aromatic  1.386  0.020  1.386
 JVK  C4   CL   single    1.731  0.020  1.731
 JVK  C    H1   single    0.930  0.020  1.080
 JVK  N    H2   single    0.860  0.020  1.020
 JVK  C2   H3   single    0.930  0.020  1.080
 JVK  C3   H4   single    0.930  0.020  1.080
 JVK  C5   H5   single    0.930  0.020  1.080
 JVK  C6   H6   single    0.970  0.020  1.090
 JVK  C6   H7   single    0.970  0.020  1.090
 JVK  C8   H8   single    0.970  0.020  1.090
 JVK  C10  H9   single    0.970  0.020  1.090
 JVK  C11  H10  single    0.970  0.020  1.090
 JVK  C11  H11  single    0.970  0.020  1.090
 JVK  C11  H12  single    0.970  0.020  1.090
 JVK  C12  H13  single    0.970  0.020  1.090
 JVK  C12  H14  single    0.970  0.020  1.090
 JVK  C12  H15  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
 JVK  H1   C    C5   118.53  3.000
 JVK  H1   C    C1   121.09  3.000
 JVK  C5   C    C1   120.38  3.000
 JVK  H2   N    C8   115.23  3.000
 JVK  H2   N    C7   118.24  3.000
 JVK  C8   N    C7   125.16  3.000
 JVK  C6   S    C1   102.18  3.000
 JVK  C2   C1   S    117.69  3.000
 JVK  C2   C1   C    119.33  3.000
 JVK  S    C1   C    122.94  3.000
 JVK  H3   C2   C3   119.15  3.000
 JVK  H3   C2   C1   120.23  3.000
 JVK  C3   C2   C1   120.62  3.000
 JVK  H4   C3   C4   120.73  3.000
 JVK  H4   C3   C2   119.98  3.000
 JVK  C4   C3   C2   119.29  3.000
 JVK  CL   C4   C5   119.54  3.000
 JVK  CL   C4   C3   119.57  3.000
 JVK  C5   C4   C3   120.89  3.000
 JVK  H5   C5   C4   120.63  3.000
 JVK  H5   C5   C    119.88  3.000
 JVK  C4   C5   C    119.49  3.000
 JVK  H7   C6   H6   106.64  3.000
 JVK  H7   C6   C7   108.94  3.000
 JVK  H6   C6   C7   108.85  3.000
 JVK  H7   C6   S    111.13  3.000
 JVK  H6   C6   S    104.59  3.000
 JVK  C7   C6   S    116.19  3.000
 JVK  O    C7   C6   118.93  3.000
 JVK  O    C7   N    125.11  3.000
 JVK  C6   C7   N    115.92  3.000
 JVK  H8   C8   C10  107.80  3.000
 JVK  H8   C8   C9   108.30  3.000
 JVK  C10  C8   C9   110.41  3.000
 JVK  H8   C8   N    107.88  3.000
 JVK  C10  C8   N    112.18  3.000
 JVK  C9   C8   N    110.12  3.000
 JVK  O2   C9   O1   127.60  3.000
 JVK  O1   C9   C8   115.19  3.000
 JVK  O2   C9   C8   117.18  3.000
 JVK  H9   C10  C12  108.16  3.000
 JVK  H9   C10  C11  107.91  3.000
 JVK  C12  C10  C11  110.23  3.000
 JVK  H9   C10  C8   105.77  3.000
 JVK  C11  C10  C8   111.98  3.000
 JVK  C12  C10  C8   112.52  3.000
 JVK  H12  C11  H11  107.31  3.000
 JVK  H12  C11  H10  107.77  3.000
 JVK  H11  C11  H10  107.87  3.000
 JVK  H12  C11  C10  110.45  3.000
 JVK  H11  C11  C10  111.44  3.000
 JVK  H10  C11  C10  111.82  3.000
 JVK  H15  C12  H14  108.03  3.000
 JVK  H15  C12  H13  107.26  3.000
 JVK  H14  C12  H13  107.08  3.000
 JVK  H15  C12  C10  112.53  3.000
 JVK  H14  C12  C10  111.32  3.000
 JVK  H13  C12  C10  110.39  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
 JVK  CONST_01  C3   C2   C1   C      0.00   0.0  0
 JVK  CONST_02  C3   C4   C5   C      0.00   0.0  0
 JVK  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 JVK  CONST_04  C4   C5   C    C1     0.00   0.0  0
 JVK  CONST_05  C5   C    C1   C2     0.00   0.0  0
 JVK  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 JVK  CONST_07  CL   C4   C5   C    180.00   0.0  0
 JVK  CONST_08  C3   C2   C1   S    180.00   0.0  0
 JVK  CONST_09  C5   C    C1   S    180.00   0.0  0
 JVK  CONST_10  CL   C4   C3   C2   180.00   0.0  0
 JVK  CONST_11  H3   C2   C1   C    180.00   0.0  0
 JVK  CONST_12  H4   C3   C2   C1   180.00   0.0  0
 JVK  CONST_13  H5   C5   C    C1   180.00   0.0  0
 JVK  CONST_14  H1   C    C1   C2   180.00   0.0  0
 JVK  CONST_15  C8   N    C7   C6   180.00   0.0  0
 JVK  CONST_16  O    C7   N    C8     0.00   0.0  0
 JVK  CONST_17  H2   N    C7   C6     0.00   0.0  0
 JVK  Var_01    C7   C6   S    C1    57.04  30.0  3
 JVK  Var_02    S    C6   C7   N     32.91  30.0  2
 JVK  Var_03    H13  C12  C10  C8  -179.56  30.0  3
 JVK  Var_04    H10  C11  C10  C8   -53.69  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
 JVK  chir_01  C8  C9  N  C10  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
 JVK  plan-1  C   0.020
 JVK  plan-1  S   0.020
 JVK  plan-1  C1  0.020
 JVK  plan-1  C2  0.020
 JVK  plan-1  C3  0.020
 JVK  plan-1  C4  0.020
 JVK  plan-1  C5  0.020
 JVK  plan-1  CL  0.020
 JVK  plan-1  H1  0.020
 JVK  plan-1  H3  0.020
 JVK  plan-1  H4  0.020
 JVK  plan-1  H5  0.020
 JVK  plan-2  N   0.020
 JVK  plan-2  C6  0.020
 JVK  plan-2  C7  0.020
 JVK  plan-2  C8  0.020
 JVK  plan-2  O   0.020
 JVK  plan-2  H2  0.020
 JVK  plan-3  C8  0.020
 JVK  plan-3  C9  0.020
 JVK  plan-3  O1  0.020
 JVK  plan-3  O2  0.020

