# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:29:27 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  57  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  -0.594    5.2878   2.0218   1.6949
 6AS  C1   C  C      0   0.394    6.1517   2.0825   0.7946
 6AS  O12  O  OC    -1  -0.615    7.2874   2.5925   0.9049
 6AS  C2   C  C1     0  -0.458    5.8590   1.5113  -0.5740
 6AS  C3   C  C      0   0.139    4.7944   0.8201  -1.0247
 6AS  C6   C  CH3    0  -0.747    4.7732   0.3563  -2.4551
 6AS  C4   C  C1     0  -0.321    3.6447   0.4745  -0.1893
 6AS  C5   C  C1     0  -0.233    2.5858  -0.2099  -0.6290
 6AS  C1'  C  CT     0   0.157    1.4012  -0.5959   0.2198
 6AS  C2'  C  C      0   0.202    0.1086  -0.2207  -0.5265
 6AS  C7'  C  CH3    0  -0.720    0.1542   1.0835  -1.2560
 6AS  O1'  O  OH1    0  -0.655    1.3708   0.0992   1.4467
 6AS  C6'  C  CT     0  -0.125    1.4648  -2.1098   0.5607
 6AS  C8'  C  CH3    0  -0.637    2.5917  -2.4049   1.5502
 6AS  C9'  C  CH3    0  -0.660    1.7021  -2.9510  -0.6994
 6AS  C5'  C  CH2    0  -0.548    0.1343  -2.5190   1.1921
 6AS  C4'  C  C      0   0.435   -1.0458  -2.2406   0.3093
 6AS  O4'  O  O      0  -0.402   -2.0126  -2.9746   0.2792
 6AS  C3'  C  C      0  -0.320   -0.9978  -0.9894  -0.4776
 6AS  S    S  S2     0  -0.003   -2.4574  -0.5891  -1.3954
 6AS  CA1  C  CH2    0  -0.539   -3.5800  -0.0644  -0.0578
 6AS  CA2  C  CH2    0  -0.424   -4.9296   0.3231  -0.6419
 6AS  CA3  C  CH2    0  -0.410   -5.8794   0.8341   0.4361
 6AS  CA4  C  CH2    0  -0.408   -7.2468   1.2264  -0.1087
 6AS  CA5  C  CH2    0  -0.420   -8.1824   1.7680   0.9655
 6AS  CA6  C  CH3    0  -0.662   -9.5492   2.1595   0.4217
 6AS  H2   H  H      0   0.209    6.6524   1.6883  -1.2950
 6AS  H3   H  HCH3   0   0.237    4.7155  -0.7328  -2.5201
 6AS  H4   H  HCH3   0   0.236    3.9064   0.7499  -2.9911
 6AS  H5   H  HCH3   0   0.249    5.6671   0.6755  -2.9886
 6AS  H6   H  H      0   0.258    3.6978   0.8024   0.8396
 6AS  H7   H  H      0   0.274    2.5326  -0.5422  -1.6599
 6AS  H8   H  HCH3   0   0.268    0.5689   0.9464  -2.2578
 6AS  H9   H  HCH3   0   0.267   -0.8341   1.5212  -1.3705
 6AS  H10  H  HCH3   0   0.248    0.8032   1.8016  -0.7528
 6AS  H11  H  HOH1   0   0.453    1.4602   1.0441   1.2786
 6AS  H12  H  HCH3   0   0.233    2.4176  -1.9517   2.5253
 6AS  H13  H  HCH3   0   0.229    2.6689  -3.4836   1.6986
 6AS  H14  H  HCH3   0   0.239    3.5553  -2.0558   1.1785
 6AS  H15  H  HCH3   0   0.241    2.7034  -2.7942  -1.1013
 6AS  H16  H  HCH3   0   0.241    1.6137  -4.0099  -0.4502
 6AS  H17  H  HCH3   0   0.236    0.9885  -2.7436  -1.4983
 6AS  H18  H  HCH2   0   0.264    0.1444  -3.5805   1.4490
 6AS  H19  H  HCH2   0   0.282   -0.0288  -1.9709   2.1269
 6AS  H20  H  HCH2   0   0.264   -3.6933  -0.8779   0.6590
 6AS  H21  H  HCH2   0   0.261   -3.1270   0.7843   0.4568
 6AS  H22  H  HCH2   0   0.228   -4.7943   1.0956  -1.4051
 6AS  H23  H  HCH2   0   0.229   -5.3726  -0.5410  -1.1459
 6AS  H24  H  HCH2   0   0.215   -6.0015   0.0673   1.2083
 6AS  H25  H  HCH2   0   0.214   -5.4271   1.6982   0.9341
 6AS  H26  H  HCH2   0   0.209   -7.1230   1.9796  -0.8946
 6AS  H27  H  HCH2   0   0.209   -7.7099   0.3584  -0.5907
 6AS  H28  H  HCH2   0   0.212   -8.3011   1.0182   1.7538
 6AS  H29  H  HCH2   0   0.211   -7.7175   2.6365   1.4426
 6AS  H30  H  HCH3   0   0.216   -9.4599   2.9248  -0.3513
 6AS  H31  H  HCH3   0   0.216  -10.0598   1.3028  -0.0219
 6AS  H32  H  HCH3   0   0.226  -10.1933   2.5569   1.2070

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  1.504  0.020  1.504
 6AS  CA1  S    single  1.823  0.020  1.823
 6AS  O4'  C4'  double  1.214  0.020  1.214
 6AS  C3   C2   double  1.347  0.020  1.347
 6AS  C3   C4   single  1.463  0.020  1.463
 6AS  C4'  C5'  single  1.500  0.020  1.500
 6AS  C4'  C3'  single  1.479  0.020  1.479
 6AS  C2   C1   single  1.512  0.020  1.512
 6AS  S    C3'  single  1.770  0.020  1.770
 6AS  C5'  C6'  single  1.529  0.020  1.529
 6AS  C3'  C2'  double  1.348  0.020  1.348
 6AS  C5   C4   double  1.335  0.020  1.335
 6AS  C5   C1'  single  1.508  0.020  1.508
 6AS  C2'  C1'  single  1.539  0.020  1.539
 6AS  C2'  C7'  single  1.495  0.020  1.495
 6AS  C1   O11  deloc   1.249  0.020  1.249
 6AS  C1   O12  deloc   1.250  0.020  1.250
 6AS  C1'  C6'  single  1.553  0.020  1.553
 6AS  C1'  O1'  single  1.410  0.020  1.410
 6AS  C6'  C9'  single  1.534  0.020  1.534
 6AS  C6'  C8'  single  1.528  0.020  1.528
 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  114.21  3.000
 6AS  O12  C1   O11  125.78  3.000
 6AS  C2   C1   O11  120.02  3.000
 6AS  H2   C2   C3   116.02  3.000
 6AS  H2   C2   C1   113.44  3.000
 6AS  C3   C2   C1   130.54  3.000
 6AS  C4   C3   C6   117.34  3.000
 6AS  C4   C3   C2   123.47  3.000
 6AS  C6   C3   C2   119.19  3.000
 6AS  H5   C6   H4   107.79  3.000
 6AS  H5   C6   H3   107.85  3.000
 6AS  H4   C6   H3   106.74  3.000
 6AS  H5   C6   C3   111.35  3.000
 6AS  H4   C6   C3   111.51  3.000
 6AS  H3   C6   C3   111.39  3.000
 6AS  H6   C4   C5   120.51  3.000
 6AS  H6   C4   C3   115.67  3.000
 6AS  C5   C4   C3   123.81  3.000
 6AS  H7   C5   C1'  114.72  3.000
 6AS  H7   C5   C4   120.59  3.000
 6AS  C1'  C5   C4   124.68  3.000
 6AS  C6'  C1'  O1'  106.88  3.000
 6AS  O1'  C1'  C2'  106.48  3.000
 6AS  C6'  C1'  C2'  112.24  3.000
 6AS  O1'  C1'  C5   112.36  3.000
 6AS  C6'  C1'  C5   109.94  3.000
 6AS  C2'  C1'  C5   108.94  3.000
 6AS  C3'  C2'  C7'  122.69  3.000
 6AS  C7'  C2'  C1'  115.06  3.000
 6AS  C3'  C2'  C1'  122.19  3.000
 6AS  H10  C7'  H9   108.93  3.000
 6AS  H10  C7'  H8   106.24  3.000
 6AS  H9   C7'  H8   107.40  3.000
 6AS  H10  C7'  C2'  111.55  3.000
 6AS  H9   C7'  C2'  112.01  3.000
 6AS  H8   C7'  C2'  110.45  3.000
 6AS  H11  O1'  C1'  109.23  3.000
 6AS  C5'  C6'  C9'  109.10  3.000
 6AS  C9'  C6'  C8'  108.18  3.000
 6AS  C5'  C6'  C8'  108.82  3.000
 6AS  C8'  C6'  C1'  111.13  3.000
 6AS  C9'  C6'  C1'  111.14  3.000
 6AS  C5'  C6'  C1'  108.42  3.000
 6AS  H14  C8'  H13  107.47  3.000
 6AS  H14  C8'  H12  108.25  3.000
 6AS  H13  C8'  H12  107.51  3.000
 6AS  H14  C8'  C6'  111.66  3.000
 6AS  H13  C8'  C6'  109.33  3.000
 6AS  H12  C8'  C6'  112.42  3.000
 6AS  H17  C9'  H16  107.38  3.000
 6AS  H17  C9'  H15  107.67  3.000
 6AS  H16  C9'  H15  107.35  3.000
 6AS  H17  C9'  C6'  113.33  3.000
 6AS  H16  C9'  C6'  109.39  3.000
 6AS  H15  C9'  C6'  111.47  3.000
 6AS  H19  C5'  H18  106.67  3.000
 6AS  H19  C5'  C4'  106.99  3.000
 6AS  H18  C5'  C4'  109.03  3.000
 6AS  H19  C5'  C6'  110.37  3.000
 6AS  H18  C5'  C6'  110.44  3.000
 6AS  C4'  C5'  C6'  113.08  3.000
 6AS  C3'  C4'  O4'  121.61  3.000
 6AS  C3'  C4'  C5'  116.41  3.000
 6AS  O4'  C4'  C5'  121.93  3.000
 6AS  S    C3'  C4'  116.14  3.000
 6AS  S    C3'  C2'  121.94  3.000
 6AS  C4'  C3'  C2'  121.89  3.000
 6AS  CA1  S    C3'  101.09  3.000
 6AS  H21  CA1  H20  108.27  3.000
 6AS  H21  CA1  CA2  110.57  3.000
 6AS  H20  CA1  CA2  110.52  3.000
 6AS  H21  CA1  S    108.31  3.000
 6AS  H20  CA1  S    109.37  3.000
 6AS  CA2  CA1  S    109.75  3.000
 6AS  H23  CA2  H22  106.64  3.000
 6AS  H23  CA2  CA3  109.76  3.000
 6AS  H22  CA2  CA3  109.48  3.000
 6AS  H23  CA2  CA1  109.57  3.000
 6AS  H22  CA2  CA1  109.76  3.000
 6AS  CA3  CA2  CA1  111.51  3.000
 6AS  H25  CA3  H24  106.13  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  109.47  3.000
 6AS  CA4  CA3  CA2  113.11  3.000
 6AS  H27  CA4  H26  106.08  3.000
 6AS  H27  CA4  CA5  109.40  3.000
 6AS  H26  CA4  CA5  109.31  3.000
 6AS  H27  CA4  CA3  109.44  3.000
 6AS  H26  CA4  CA3  109.40  3.000
 6AS  CA5  CA4  CA3  112.98  3.000
 6AS  H29  CA5  H28  106.01  3.000
 6AS  H29  CA5  CA6  109.45  3.000
 6AS  H28  CA5  CA6  109.64  3.000
 6AS  H29  CA5  CA4  109.18  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  107.51  3.000
 6AS  H32  CA6  CA5  111.51  3.000
 6AS  H31  CA6  CA5  111.30  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  Var_01  C4'  C3'  C2'  C1'     0.59  30.0  1
 6AS  Var_02  C4'  C5'  C6'  C1'    57.72  30.0  1
 6AS  Var_03  C5'  C4'  C3'  C2'     7.75  30.0  1
 6AS  Var_04  C3'  C4'  C5'  C6'   -38.05  30.0  1
 6AS  Var_05  H8   C7'  C2'  C1'    86.44  30.0  3
 6AS  Var_06  H15  C9'  C6'  C1'    68.68  30.0  3
 6AS  Var_07  H12  C8'  C6'  C1'    65.82  30.0  3
 6AS  Var_08  C1'  C5   C4   C3    178.96   0.0  2
 6AS  Var_09  CA2  CA1  S    C3'  -179.60  30.0  1
 6AS  Var_10  C6   C3   C2   C1   -179.45   0.0  2
 6AS  Var_11  C3   C2   C1   O11    -5.11  30.0  2
 6AS  Var_12  C5   C4   C3   C2    179.98  30.0  2
 6AS  Var_13  CA3  CA2  CA1  S    -177.22  30.0  1
 6AS  Var_14  CA4  CA3  CA2  CA1  -179.70  30.0  3
 6AS  Var_15  CA5  CA4  CA3  CA2  -178.62  30.0  1
 6AS  Var_16  CA6  CA5  CA4  CA3  -179.97  30.0  1
 6AS  Var_17  H3   C6   C3   C2    119.10  30.0  3
 6AS  Var_18  H30  CA6  CA5  CA4   -59.11  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-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

