# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 14:17:08 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (3S)-7-methylsulfanyl-3-oxidanyl-hept-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC\C=C/[C@@H](O)CC(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
 1KC  1KC  '(3S)-7-methylsulfanyl-3-oxidanyl-hept-4-enoic acid'  ligand  25  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1KC
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
 1KC  CAS  C  CH2    0  -0.599  -2.4774  -0.6556   0.3573
 1KC  CBA  C  C      0   0.410  -3.9793  -0.6930   0.0207
 1KC  OAH  O  O      0  -0.616  -4.6875   0.1831   0.5569
 1KC  OAX  O  OH1    0  -0.666  -2.0263   1.2420  -1.0876
 1KC  CBI  C  CH1    0   0.002  -1.8712   0.7383   0.2208
 1KC  CAO  C  C1     0  -0.243  -0.4434   0.7413   0.6871
 1KC  CAM  C  C1     0  -0.221   0.6145   1.0839  -0.0401
 1KC  CAP  C  CH2    0  -0.481   2.0296   1.0368   0.4475
 1KC  CAQ  C  CH2    0  -0.538   2.8153  -0.0584  -0.2690
 1KC  SAY  S  S2     0  -0.051   4.5613   0.0057   0.2253
 1KC  CAB  C  CH3    0  -0.763   5.1988  -1.4110  -0.6955
 1KC  H1   H  HCH2   0   0.232  -2.3444  -0.9936   1.3914
 1KC  H2   H  HCH2   0   0.212  -1.9175  -1.3599  -0.2667
 1KC  H35  H  HCH1   0   0.229  -2.4427   1.4139   0.8658
 1KC  H36  H  H      0   0.237  -0.2973   0.4170   1.7156
 1KC  H38  H  H      0   0.233   0.4807   1.4107  -1.0679
 1KC  H40  H  HCH2   0   0.241   2.5114   2.0021   0.2623
 1KC  H41  H  HCH2   0   0.244   2.0587   0.8657   1.5262
 1KC  H42  H  HCH2   0   0.261   2.4061  -1.0387  -0.0168
 1KC  H43  H  HCH2   0   0.260   2.7456   0.0657  -1.3521
 1KC  H44  H  HCH3   0   0.260   4.7286  -2.3373  -0.3685
 1KC  H45  H  HCH3   0   0.260   5.0448  -1.2871  -1.7666
 1KC  H46  H  HCH3   0   0.272   6.2682  -1.4767  -0.5034
 1KC  OXT  O  OC    -1  -0.617  -4.3711  -1.6026  -0.7369
 1KC  H3   H  HOH1   0   0.442  -1.6594   0.5976  -1.7026

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
 1KC  OAX  CBI  single  1.410  0.020  1.410
 1KC  CBI  CAS  single  1.526  0.020  1.526
 1KC  CBI  CAO  single  1.502  0.020  1.502
 1KC  CAM  CAP  single  1.498  0.020  1.498
 1KC  CAM  CAO  double  1.329  0.020  1.329
 1KC  CAP  CAQ  single  1.526  0.020  1.526
 1KC  CAQ  SAY  single  1.816  0.020  1.816
 1KC  CAS  CBA  single  1.540  0.020  1.540
 1KC  CBA  OAH  deloc   1.248  0.020  1.248
 1KC  SAY  CAB  single  1.806  0.020  1.806
 1KC  CAS  H1   single  0.970  0.020  1.090
 1KC  CAS  H2   single  0.970  0.020  1.090
 1KC  CBI  H35  single  0.970  0.020  1.090
 1KC  CAO  H36  single  0.930  0.020  1.080
 1KC  CAM  H38  single  0.930  0.020  1.080
 1KC  CAP  H40  single  0.970  0.020  1.090
 1KC  CAP  H41  single  0.970  0.020  1.090
 1KC  CAQ  H42  single  0.970  0.020  1.090
 1KC  CAQ  H43  single  0.970  0.020  1.090
 1KC  CAB  H44  single  0.970  0.020  1.090
 1KC  CAB  H45  single  0.970  0.020  1.090
 1KC  CAB  H46  single  0.970  0.020  1.090
 1KC  OAX  H3   single  0.850  0.020  0.980
 1KC  CBA  OXT  deloc   1.247  0.020  1.247

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
 1KC  H2   CAS  H1   106.09  3.000
 1KC  H2   CAS  CBI  109.48  3.000
 1KC  H1   CAS  CBI  108.53  3.000
 1KC  H2   CAS  CBA  111.02  3.000
 1KC  H1   CAS  CBA  108.49  3.000
 1KC  CBI  CAS  CBA  112.96  3.000
 1KC  OXT  CBA  OAH  126.51  3.000
 1KC  OXT  CBA  CAS  117.20  3.000
 1KC  OAH  CBA  CAS  116.28  3.000
 1KC  H3   OAX  CBI  108.14  3.000
 1KC  H35  CBI  CAO  108.18  3.000
 1KC  H35  CBI  OAX  105.58  3.000
 1KC  CAO  CBI  OAX  113.06  3.000
 1KC  H35  CBI  CAS  107.67  3.000
 1KC  CAO  CBI  CAS  110.59  3.000
 1KC  OAX  CBI  CAS  111.44  3.000
 1KC  H36  CAO  CAM  119.16  3.000
 1KC  H36  CAO  CBI  114.86  3.000
 1KC  CAM  CAO  CBI  125.98  3.000
 1KC  H38  CAM  CAP  115.70  3.000
 1KC  H38  CAM  CAO  119.81  3.000
 1KC  CAP  CAM  CAO  124.48  3.000
 1KC  H41  CAP  H40  107.06  3.000
 1KC  H41  CAP  CAQ  109.71  3.000
 1KC  H40  CAP  CAQ  109.08  3.000
 1KC  H41  CAP  CAM  110.58  3.000
 1KC  H40  CAP  CAM  109.46  3.000
 1KC  CAQ  CAP  CAM  110.86  3.000
 1KC  H43  CAQ  H42  107.88  3.000
 1KC  H43  CAQ  SAY  109.10  3.000
 1KC  H42  CAQ  SAY  109.22  3.000
 1KC  H43  CAQ  CAP  110.55  3.000
 1KC  H42  CAQ  CAP  110.05  3.000
 1KC  SAY  CAQ  CAP  109.99  3.000
 1KC  CAB  SAY  CAQ   99.96  3.000
 1KC  H46  CAB  H45  108.63  3.000
 1KC  H46  CAB  H44  108.66  3.000
 1KC  H45  CAB  H44  109.33  3.000
 1KC  H46  CAB  SAY  107.71  3.000
 1KC  H45  CAB  SAY  111.23  3.000
 1KC  H44  CAB  SAY  111.21  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
 1KC  Var_01  CAP  CAM  CAO  CBI  -178.15   0.0  2
 1KC  Var_02  CBI  CAS  CBA  OAH   -48.21  30.0  2
 1KC  Var_03  CAQ  CAP  CAM  CAO   111.32  30.0  3
 1KC  Var_04  SAY  CAQ  CAP  CAM   174.76  30.0  3
 1KC  Var_05  H44  CAB  SAY  CAQ   -62.35  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
 1KC  chir_01  CBI  OAX  CAS  CAO  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
 1KC  plan-1  CAS  0.020
 1KC  plan-1  CBA  0.020
 1KC  plan-1  OAH  0.020
 1KC  plan-1  OXT  0.020
 1KC  plan-2  CBI  0.020
 1KC  plan-2  CAO  0.020
 1KC  plan-2  CAM  0.020
 1KC  plan-2  CAP  0.020
 1KC  plan-2  H36  0.020
 1KC  plan-2  H38  0.020

