# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 03:45:08 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: 4-methylsulfanyl-2-oxidanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@@H](O)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
 H9L  H9L  "4-methylsulfanyl-2-oxidanyl-butanoic acid"  ligand  18  9  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_H9L
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
 H9L  C01  C  CH3    0  -0.761  -33.1423  -12.2226  -48.9316
 H9L  S    S  S2     0  -0.052  -32.6532  -10.5146  -49.2579
 H9L  C02  C  CH2    0  -0.540  -31.2965  -10.3414  -48.0614
 H9L  C03  C  CH2    0  -0.436  -30.7151   -8.9383  -48.1396
 H9L  C04  C  CH1    0  -0.077  -29.5933   -8.7187  -47.1262
 H9L  C    C  C      0   0.395  -29.0608   -7.2655  -47.1963
 H9L  O01  O  OH1    0  -0.696  -28.5262   -9.6103  -47.3310
 H9L  O02  O  OC    -1  -0.604  -27.8332   -7.1787  -47.4339
 H9L  O    O  O      0  -0.586  -29.8675   -6.3416  -47.0182
 H9L  H1   H  HCH3   0   0.269  -33.9729  -12.4647  -49.5923
 H9L  H2   H  HCH3   0   0.258  -32.3248  -12.9134  -49.1342
 H9L  H3   H  HCH3   0   0.258  -33.4709  -12.3476  -47.9005
 H9L  H4   H  HCH2   0   0.250  -31.6840  -10.5368  -47.0580
 H9L  H5   H  HCH2   0   0.257  -30.5359  -11.0925  -48.2800
 H9L  H6   H  HCH2   0   0.223  -30.3386   -8.7483  -49.1500
 H9L  H7   H  HCH2   0   0.228  -31.5025   -8.2070  -47.9476
 H9L  H9   H  HCH1   0   0.192  -30.0168   -8.8702  -46.1205
 H9L  H10  H  HOH1   0   0.423  -27.7871   -8.9916  -47.4950

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
 H9L  C01  S    single  1.806  0.020  1.806
 H9L  O    C    deloc   1.239  0.020  1.239
 H9L  S    C02  single  1.817  0.020  1.817
 H9L  C03  C02  single  1.521  0.020  1.521
 H9L  C03  C04  single  1.528  0.020  1.528
 H9L  C04  C    single  1.549  0.020  1.549
 H9L  C04  O01  single  1.406  0.020  1.406
 H9L  C    O02  deloc   1.253  0.020  1.253
 H9L  C01  H1   single  0.970  0.020  1.090
 H9L  C01  H2   single  0.970  0.020  1.090
 H9L  C01  H3   single  0.970  0.020  1.090
 H9L  C02  H4   single  0.970  0.020  1.090
 H9L  C02  H5   single  0.970  0.020  1.090
 H9L  C03  H6   single  0.970  0.020  1.090
 H9L  C03  H7   single  0.970  0.020  1.090
 H9L  C04  H9   single  0.970  0.020  1.090
 H9L  O01  H10  single  0.850  0.020  0.980

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
 H9L  H3   C01  H2   109.25  3.000
 H9L  H3   C01  H1   108.59  3.000
 H9L  H2   C01  H1   108.58  3.000
 H9L  H3   C01  S    111.17  3.000
 H9L  H2   C01  S    111.28  3.000
 H9L  H1   C01  S    107.89  3.000
 H9L  C02  S    C01   99.98  3.000
 H9L  H5   C02  H4   107.93  3.000
 H9L  H5   C02  C03  111.00  3.000
 H9L  H4   C02  C03  110.34  3.000
 H9L  H5   C02  S    108.83  3.000
 H9L  H4   C02  S    108.82  3.000
 H9L  C03  C02  S    109.85  3.000
 H9L  H7   C03  H6   107.10  3.000
 H9L  H7   C03  C04  108.46  3.000
 H9L  H6   C03  C04  109.55  3.000
 H9L  H7   C03  C02  109.47  3.000
 H9L  H6   C03  C02  109.82  3.000
 H9L  C04  C03  C02  112.29  3.000
 H9L  H9   C04  O01  109.73  3.000
 H9L  H9   C04  C    107.60  3.000
 H9L  O01  C04  C    109.11  3.000
 H9L  H9   C04  C03  107.67  3.000
 H9L  O01  C04  C03  111.70  3.000
 H9L  C    C04  C03  110.93  3.000
 H9L  O    C    O02  127.81  3.000
 H9L  O02  C    C04  114.22  3.000
 H9L  O    C    C04  117.97  3.000
 H9L  H10  O01  C04  101.36  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
 H9L  Var_01  C03  C02  S    C01  -179.42  30.0  3
 H9L  Var_02  C04  C03  C02  S     178.37  30.0  1
 H9L  Var_03  H4   C02  S    C01   -58.52  30.0  3
 H9L  Var_04  H5   C02  S    C01    58.87  30.0  3
 H9L  Var_05  H6   C03  C02  S     -59.47  30.0  1
 H9L  Var_06  H7   C03  C02  S      57.85  30.0  1
 H9L  Var_07  H1   C01  S    C02   179.65  30.0  3
 H9L  Var_08  H2   C01  S    C02   -61.33  30.0  3
 H9L  Var_09  H3   C01  S    C02    60.69  30.0  3
 H9L  Var_10  H4   C02  C03  C04    58.39  30.0  3
 H9L  Var_11  H5   C02  C03  C04   -61.22  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
 H9L  chir_01  C04  C03  C  O01  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
 H9L  plan-1  C04  0.020
 H9L  plan-1  C    0.020
 H9L  plan-1  O02  0.020
 H9L  plan-1  O    0.020

