# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 21:40:34 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (2Z,4E)-5-[(1S)-3-(hexylsulfanyl)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCSC1=C(C)[C@](O)(\C=C\C(C)=C/C(O)=O)C(C)(C)CC1=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
 6AS  6AS  '(2Z,4E)-5-[(1S)-3-(hexylsulfanyl)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid'  ligand  58  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6AS
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
 6AS  O11  O  O     0  -0.454    5.2403   2.0811   1.7450
 6AS  C1   C  C     0   0.528    6.0035   2.1225   0.8049
 6AS  O12  O  OH1   0  -0.592    7.1808   2.7457   0.8776
 6AS  C2   C  C1    0  -0.416    5.8149   1.5415  -0.5303
 6AS  C3   C  C     0   0.193    4.7663   0.8129  -0.9687
 6AS  C6   C  CH3   0  -0.710    4.7880   0.3251  -2.3870
 6AS  C4   C  C1    0  -0.309    3.6151   0.4621  -0.1427
 6AS  C5   C  C1    0  -0.211    2.5731  -0.2366  -0.5999
 6AS  C1'  C  CT    0   0.156    1.3814  -0.6325   0.2339
 6AS  C2'  C  C     0   0.183    0.0973  -0.2574  -0.5250
 6AS  C7'  C  CH3   0  -0.684    0.1514   1.0445  -1.2587
 6AS  O1'  O  OH1   0  -0.642    1.3439   0.0481   1.4667
 6AS  C6'  C  CT    0  -0.133    1.4550  -2.1500   0.5587
 6AS  C8'  C  CH3   0  -0.619    2.5790  -2.4486   1.5509
 6AS  C9'  C  CH3   0  -0.636    1.7024  -2.9768  -0.7091
 6AS  C5'  C  CH2   0  -0.536    0.1239  -2.5704   1.1807
 6AS  C4'  C  C     0   0.425   -1.0583  -2.2804   0.3041
 6AS  O4'  O  O     0  -0.355   -2.0282  -3.0085   0.2744
 6AS  C3'  C  C     0  -0.323   -1.0089  -1.0251  -0.4789
 6AS  S    S  S2    0   0.049   -2.4667  -0.6207  -1.3969
 6AS  CA1  C  CH2   0  -0.531   -3.5878  -0.0998  -0.0562
 6AS  CA2  C  CH2   0  -0.416   -4.9365   0.2936  -0.6385
 6AS  CA3  C  CH2   0  -0.402   -5.8828   0.8056   0.4421
 6AS  CA4  C  CH2   0  -0.399   -7.2503   1.2026  -0.0992
 6AS  CA5  C  CH2   0  -0.412   -8.1806   1.7484   0.9775
 6AS  CA6  C  CH3   0  -0.644   -9.5475   2.1450   0.4375
 6AS  H1   H  HOH1  0   0.452    7.2900   3.1310   1.7592
 6AS  H2   H  H     0   0.244    6.6211   1.7325  -1.2279
 6AS  H3   H  HCH3  0   0.241    4.7448  -0.7649  -2.4271
 6AS  H4   H  HCH3  0   0.245    3.9284   0.7003  -2.9454
 6AS  H5   H  HCH3  0   0.249    5.6891   0.6461  -2.9047
 6AS  H6   H  H     0   0.262    3.6285   0.7846   0.8876
 6AS  H7   H  H     0   0.274    2.5415  -0.5707  -1.6308
 6AS  H8   H  HCH3  0   0.259    0.5768   0.9036  -2.2556
 6AS  H9   H  HCH3  0   0.269   -0.8358   1.4805  -1.3869
 6AS  H10  H  HCH3  0   0.224    0.7925   1.7676  -0.7517
 6AS  H11  H  HOH1  0   0.434    1.3323   0.9994   1.3109
 6AS  H12  H  HCH3  0   0.229    2.4025  -1.9991   2.5272
 6AS  H13  H  HCH3  0   0.219    2.6536  -3.5279   1.6953
 6AS  H14  H  HCH3  0   0.238    3.5455  -2.1016   1.1845
 6AS  H15  H  HCH3  0   0.234    2.7072  -2.8186  -1.1020
 6AS  H16  H  HCH3  0   0.232    1.6123  -4.0381  -0.4719
 6AS  H17  H  HCH3  0   0.239    0.9950  -2.7614  -1.5113
 6AS  H18  H  HCH2  0   0.252    0.1364  -3.6358   1.4200
 6AS  H19  H  HCH2  0   0.269   -0.0411  -2.0391   2.1247
 6AS  H20  H  HCH2  0   0.263   -3.7029  -0.9163   0.6568
 6AS  H21  H  HCH2  0   0.240   -3.1326   0.7457   0.4617
 6AS  H22  H  HCH2  0   0.220   -4.7993   1.0673  -1.4001
 6AS  H23  H  HCH2  0   0.229   -5.3830  -0.5679  -1.1439
 6AS  H24  H  HCH2  0   0.209   -6.0054   0.0382   1.2135
 6AS  H25  H  HCH2  0   0.203   -5.4271   1.6677   0.9404
 6AS  H26  H  HCH2  0   0.203   -7.1260   1.9550  -0.8858
 6AS  H27  H  HCH2  0   0.205   -7.7180   0.3362  -0.5794
 6AS  H28  H  HCH2  0   0.207   -8.2998   0.9996   1.7666
 6AS  H29  H  HCH2  0   0.205   -7.7109   2.6154   1.4527
 6AS  H30  H  HCH3  0   0.210   -9.4575   2.9108  -0.3349
 6AS  H31  H  HCH3  0   0.211  -10.0620   1.2905  -0.0058
 6AS  H32  H  HCH3  0   0.220  -10.1883   2.5437   1.2248

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
 6AS  CA6  CA5  single  1.522  0.020  1.522
 6AS  CA5  CA4  single  1.524  0.020  1.524
 6AS  CA4  CA3  single  1.523  0.020  1.523
 6AS  CA2  CA3  single  1.525  0.020  1.525
 6AS  CA2  CA1  single  1.521  0.020  1.521
 6AS  C6   C3   single  1.500  0.020  1.500
 6AS  CA1  S    single  1.824  0.020  1.824
 6AS  O4'  C4'  double  1.213  0.020  1.213
 6AS  C3   C2   double  1.350  0.020  1.350
 6AS  C3   C4   single  1.460  0.020  1.460
 6AS  C4'  C5'  single  1.500  0.020  1.500
 6AS  C4'  C3'  single  1.480  0.020  1.480
 6AS  C2   C1   single  1.468  0.020  1.468
 6AS  S    C3'  single  1.770  0.020  1.770
 6AS  C5'  C6'  single  1.528  0.020  1.528
 6AS  C3'  C2'  double  1.347  0.020  1.347
 6AS  C5   C4   double  1.335  0.020  1.335
 6AS  C5   C1'  single  1.507  0.020  1.507
 6AS  C2'  C1'  single  1.538  0.020  1.538
 6AS  C2'  C7'  single  1.495  0.020  1.495
 6AS  C1   O11  double  1.212  0.020  1.212
 6AS  C1   O12  single  1.334  0.020  1.334
 6AS  C1'  C6'  single  1.554  0.020  1.554
 6AS  C1'  O1'  single  1.409  0.020  1.409
 6AS  C6'  C9'  single  1.534  0.020  1.534
 6AS  C6'  C8'  single  1.529  0.020  1.529
 6AS  O12  H1   single  0.850  0.020  0.980
 6AS  C2   H2   single  0.930  0.020  1.080
 6AS  C6   H3   single  0.970  0.020  1.090
 6AS  C6   H4   single  0.970  0.020  1.090
 6AS  C6   H5   single  0.970  0.020  1.090
 6AS  C4   H6   single  0.930  0.020  1.080
 6AS  C5   H7   single  0.930  0.020  1.080
 6AS  C7'  H8   single  0.970  0.020  1.090
 6AS  C7'  H9   single  0.970  0.020  1.090
 6AS  C7'  H10  single  0.970  0.020  1.090
 6AS  O1'  H11  single  0.850  0.020  0.980
 6AS  C8'  H12  single  0.970  0.020  1.090
 6AS  C8'  H13  single  0.970  0.020  1.090
 6AS  C8'  H14  single  0.970  0.020  1.090
 6AS  C9'  H15  single  0.970  0.020  1.090
 6AS  C9'  H16  single  0.970  0.020  1.090
 6AS  C9'  H17  single  0.970  0.020  1.090
 6AS  C5'  H18  single  0.970  0.020  1.090
 6AS  C5'  H19  single  0.970  0.020  1.090
 6AS  CA1  H20  single  0.970  0.020  1.090
 6AS  CA1  H21  single  0.970  0.020  1.090
 6AS  CA2  H22  single  0.970  0.020  1.090
 6AS  CA2  H23  single  0.970  0.020  1.090
 6AS  CA3  H24  single  0.970  0.020  1.090
 6AS  CA3  H25  single  0.970  0.020  1.090
 6AS  CA4  H26  single  0.970  0.020  1.090
 6AS  CA4  H27  single  0.970  0.020  1.090
 6AS  CA5  H28  single  0.970  0.020  1.090
 6AS  CA5  H29  single  0.970  0.020  1.090
 6AS  CA6  H30  single  0.970  0.020  1.090
 6AS  CA6  H31  single  0.970  0.020  1.090
 6AS  CA6  H32  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
 6AS  C2   C1   O12  110.35  3.000
 6AS  O12  C1   O11  121.98  3.000
 6AS  C2   C1   O11  127.67  3.000
 6AS  H1   O12  C1   109.57  3.000
 6AS  H2   C2   C3   117.66  3.000
 6AS  H2   C2   C1   114.86  3.000
 6AS  C3   C2   C1   127.49  3.000
 6AS  C4   C3   C6   117.92  3.000
 6AS  C4   C3   C2   123.95  3.000
 6AS  C6   C3   C2   118.12  3.000
 6AS  H5   C6   H4   107.91  3.000
 6AS  H5   C6   H3   108.06  3.000
 6AS  H4   C6   H3   107.06  3.000
 6AS  H5   C6   C3   111.47  3.000
 6AS  H4   C6   C3   111.13  3.000
 6AS  H3   C6   C3   111.03  3.000
 6AS  H6   C4   C5   119.52  3.000
 6AS  H6   C4   C3   117.29  3.000
 6AS  C5   C4   C3   123.19  3.000
 6AS  H7   C5   C1'  114.96  3.000
 6AS  H7   C5   C4   120.63  3.000
 6AS  C1'  C5   C4   124.40  3.000
 6AS  C6'  C1'  O1'  106.87  3.000
 6AS  O1'  C1'  C2'  106.96  3.000
 6AS  C6'  C1'  C2'  112.39  3.000
 6AS  O1'  C1'  C5   112.23  3.000
 6AS  C6'  C1'  C5   109.55  3.000
 6AS  C2'  C1'  C5   108.85  3.000
 6AS  C3'  C2'  C7'  122.86  3.000
 6AS  C7'  C2'  C1'  115.10  3.000
 6AS  C3'  C2'  C1'  121.98  3.000
 6AS  H10  C7'  H9   108.82  3.000
 6AS  H10  C7'  H8   106.29  3.000
 6AS  H9   C7'  H8   107.31  3.000
 6AS  H10  C7'  C2'  111.73  3.000
 6AS  H9   C7'  C2'  111.98  3.000
 6AS  H8   C7'  C2'  110.45  3.000
 6AS  H11  O1'  C1'  109.61  3.000
 6AS  C5'  C6'  C9'  109.19  3.000
 6AS  C9'  C6'  C8'  108.22  3.000
 6AS  C5'  C6'  C8'  108.81  3.000
 6AS  C8'  C6'  C1'  111.18  3.000
 6AS  C9'  C6'  C1'  111.19  3.000
 6AS  C5'  C6'  C1'  108.21  3.000
 6AS  H14  C8'  H13  107.37  3.000
 6AS  H14  C8'  H12  108.27  3.000
 6AS  H13  C8'  H12  107.49  3.000
 6AS  H14  C8'  C6'  111.81  3.000
 6AS  H13  C8'  C6'  109.23  3.000
 6AS  H12  C8'  C6'  112.46  3.000
 6AS  H17  C9'  H16  107.36  3.000
 6AS  H17  C9'  H15  107.69  3.000
 6AS  H16  C9'  H15  107.19  3.000
 6AS  H17  C9'  C6'  113.38  3.000
 6AS  H16  C9'  C6'  109.35  3.000
 6AS  H15  C9'  C6'  111.61  3.000
 6AS  H19  C5'  H18  106.62  3.000
 6AS  H19  C5'  C4'  106.92  3.000
 6AS  H18  C5'  C4'  109.01  3.000
 6AS  H19  C5'  C6'  110.39  3.000
 6AS  H18  C5'  C6'  110.34  3.000
 6AS  C4'  C5'  C6'  113.29  3.000
 6AS  C3'  C4'  O4'  121.51  3.000
 6AS  C3'  C4'  C5'  116.54  3.000
 6AS  O4'  C4'  C5'  121.90  3.000
 6AS  S    C3'  C4'  116.15  3.000
 6AS  S    C3'  C2'  121.90  3.000
 6AS  C4'  C3'  C2'  121.92  3.000
 6AS  CA1  S    C3'  100.97  3.000
 6AS  H21  CA1  H20  108.30  3.000
 6AS  H21  CA1  CA2  110.56  3.000
 6AS  H20  CA1  CA2  110.52  3.000
 6AS  H21  CA1  S    108.29  3.000
 6AS  H20  CA1  S    109.38  3.000
 6AS  CA2  CA1  S    109.73  3.000
 6AS  H23  CA2  H22  106.64  3.000
 6AS  H23  CA2  CA3  109.78  3.000
 6AS  H22  CA2  CA3  109.48  3.000
 6AS  H23  CA2  CA1  109.58  3.000
 6AS  H22  CA2  CA1  109.77  3.000
 6AS  CA3  CA2  CA1  111.47  3.000
 6AS  H25  CA3  H24  106.12  3.000
 6AS  H25  CA3  CA4  109.28  3.000
 6AS  H24  CA3  CA4  109.42  3.000
 6AS  H25  CA3  CA2  109.18  3.000
 6AS  H24  CA3  CA2  109.48  3.000
 6AS  CA4  CA3  CA2  113.13  3.000
 6AS  H27  CA4  H26  106.07  3.000
 6AS  H27  CA4  CA5  109.41  3.000
 6AS  H26  CA4  CA5  109.30  3.000
 6AS  H27  CA4  CA3  109.45  3.000
 6AS  H26  CA4  CA3  109.41  3.000
 6AS  CA5  CA4  CA3  112.97  3.000
 6AS  H29  CA5  H28  106.00  3.000
 6AS  H29  CA5  CA6  109.45  3.000
 6AS  H28  CA5  CA6  109.65  3.000
 6AS  H29  CA5  CA4  109.17  3.000
 6AS  H28  CA5  CA4  109.32  3.000
 6AS  CA6  CA5  CA4  113.00  3.000
 6AS  H32  CA6  H31  107.60  3.000
 6AS  H32  CA6  H30  107.63  3.000
 6AS  H31  CA6  H30  107.50  3.000
 6AS  H32  CA6  CA5  111.51  3.000
 6AS  H31  CA6  CA5  111.31  3.000
 6AS  H30  CA6  CA5  111.09  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
 6AS  CONST_01  H1   O12  C1   O11     0.00   0.0  0
 6AS  Var_01    C4'  C3'  C2'  C1'    -0.09  30.0  1
 6AS  Var_02    C4'  C5'  C6'  C1'    57.26  30.0  1
 6AS  Var_03    C5'  C4'  C3'  C2'     7.37  30.0  1
 6AS  Var_04    C3'  C4'  C5'  C6'   -37.24  30.0  1
 6AS  Var_05    H8   C7'  C2'  C1'    86.32  30.0  3
 6AS  Var_06    H15  C9'  C6'  C1'    69.29  30.0  3
 6AS  Var_07    H12  C8'  C6'  C1'    65.20  30.0  3
 6AS  Var_08    C1'  C5   C4   C3    178.98   0.0  2
 6AS  Var_09    CA2  CA1  S    C3'  -179.69  30.0  2
 6AS  Var_10    C6   C3   C2   C1    179.69   0.0  2
 6AS  Var_11    C3   C2   C1   O11    -1.89  30.0  2
 6AS  Var_12    C5   C4   C3   C2    178.60  30.0  2
 6AS  Var_13    CA3  CA2  CA1  S    -177.04  30.0  1
 6AS  Var_14    CA4  CA3  CA2  CA1  -179.63  30.0  3
 6AS  Var_15    CA5  CA4  CA3  CA2  -178.47  30.0  1
 6AS  Var_16    CA6  CA5  CA4  CA3  -179.98  30.0  2
 6AS  Var_17    H3   C6   C3   C2    120.06  30.0  3
 6AS  Var_18    H30  CA6  CA5  CA4   -59.21  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
 6AS  chir_01  C1'  C2'  C6'  O1'  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
 6AS  plan-1  C5'  0.020
 6AS  plan-1  C4'  0.020
 6AS  plan-1  O4'  0.020
 6AS  plan-1  C3'  0.020
 6AS  plan-2  O11  0.020
 6AS  plan-2  C1   0.020
 6AS  plan-2  O12  0.020
 6AS  plan-2  C2   0.020
 6AS  plan-2  H1   0.020
 6AS  plan-3  C1   0.020
 6AS  plan-3  C2   0.020
 6AS  plan-3  C3   0.020
 6AS  plan-3  C6   0.020
 6AS  plan-3  C4   0.020
 6AS  plan-3  H2   0.020
 6AS  plan-4  C3   0.020
 6AS  plan-4  C4   0.020
 6AS  plan-4  C5   0.020
 6AS  plan-4  C1'  0.020
 6AS  plan-4  H6   0.020
 6AS  plan-4  H7   0.020

