# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 21:34:29 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (2~{Z},4~{E})-3-methyl-5-[(1~{S},4~{S})-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C#CCO[C@H]2CC(C)(C)[C@@](O)(\C=C\C(C)=C/C(O)=O)C(=C2)C
#
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
 8V6  8V6  '(2~{Z},4~{E})-3-methyl-5-[(1~{S},4~{S})-2,6,6-trimethyl-4-[3-(4-methylphenyl)prop-2-ynoxy]-1-oxidanyl-cyclohex-2-en-1-yl]penta-2,4-dienoic acid'  ligand  58  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8V6
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
 8V6  C1   C  C      0   0.394  -6.7335   2.4327  -0.0361
 8V6  C2   C  C1     0  -0.464  -5.3186   2.9423   0.1115
 8V6  C3   C  C      0   0.142  -4.1479   2.2764   0.1514
 8V6  C4   C  C1     0  -0.321  -4.0419   0.8205   0.0593
 8V6  C5   C  C1     0  -0.217  -2.8810   0.1582   0.0632
 8V6  C6   C  CH3    0  -0.751  -2.8693   3.0522   0.3117
 8V6  O11  O  O      0  -0.596  -6.9475   1.2090  -0.1697
 8V6  O12  O  OC    -1  -0.617  -7.6065   3.3273  -0.0115
 8V6  C1'  C  CR6    0   0.188  -2.7255  -1.3408  -0.0552
 8V6  C6'  C  CR6    0  -0.105  -2.0800  -1.9437   1.2269
 8V6  C9'  C  CH3    0  -0.645  -2.7887  -1.4399   2.4847
 8V6  C5'  C  C      0  -0.465  -0.6118  -1.5135   1.2890
 8V6  C8'  C  CH3    0  -0.652  -2.1678  -3.4756   1.2061
 8V6  O1   O  OH1    0  -0.673  -3.9679  -1.9850  -0.2123
 8V6  C2'  C  CR6    0   0.124  -1.8421  -1.5757  -1.2816
 8V6  C7'  C  CH3    0  -0.744  -2.5105  -1.4420  -2.6182
 8V6  C3'  C  CR16   0  -0.320  -0.5401  -1.8387  -1.1832
 8V6  C4'  C  CR16   0   0.050   0.1994  -2.0111   0.1082
 8V6  O4'  O  O2     0  -0.498   1.4264  -1.2901   0.1068
 8V6  CA1  C  CH2    0  -0.331   2.4715  -1.9384  -0.5748
 8V6  CA2  C  CSP    0  -0.007   3.6915  -1.1596  -0.4083
 8V6  CA3  C  CSP    0   0.183   4.7066  -0.5255  -0.2720
 8V6  CA4  C  CR6    0  -0.129   5.8998   0.2366  -0.1027
 8V6  CA5  C  CR16   0  -0.277   6.0304   1.1202   0.9715
 8V6  CA6  C  CR16   0  -0.292   7.1880   1.8635   1.1296
 8V6  CA7  C  CR6    0   0.096   8.2494   1.7497   0.2330
 8V6  CA0  C  CH3    0  -0.722   9.5132   2.5333   0.4277
 8V6  CA8  C  CR16   0  -0.291   8.1109   0.8662  -0.8368
 8V6  CA9  C  CR16   0  -0.275   6.9573   0.1199  -1.0084
 8V6  H1   H  H      0   0.207  -5.2566   4.0237   0.1977
 8V6  H2   H  H      0   0.247  -4.9830   0.2914   0.0009
 8V6  H3   H  H      0   0.262  -1.9478   0.7089   0.1170
 8V6  H4   H  HCH3   0   0.237  -2.3381   2.7556   1.2190
 8V6  H5   H  HCH3   0   0.238  -2.1856   2.8776  -0.5219
 8V6  H6   H  HCH3   0   0.248  -3.0575   4.1229   0.3686
 8V6  H8   H  HCH3   0   0.232  -3.8599  -1.6392   2.4487
 8V6  H9   H  HCH3   0   0.227  -2.3838  -1.9444   3.3644
 8V6  H10  H  HCH3   0   0.229  -2.6543  -0.3671   2.6278
 8V6  H11  H  H      0   0.239  -0.5420  -0.4223   1.3271
 8V6  H12  H  H      0   0.246  -0.1702  -1.8817   2.2197
 8V6  H13  H  HCH3   0   0.229  -1.8207  -3.9122   0.2686
 8V6  H14  H  HCH3   0   0.224  -1.5528  -3.8859   2.0100
 8V6  H15  H  HCH3   0   0.237  -3.1879  -3.8206   1.3702
 8V6  H16  H  HOH1   0   0.454  -4.4571  -1.5699  -0.9304
 8V6  H17  H  HCH3   0   0.241  -3.0500  -0.4950  -2.7029
 8V6  H18  H  HCH3   0   0.251  -1.7819  -1.4810  -3.4263
 8V6  H19  H  HCH3   0   0.243  -3.2345  -2.2408  -2.7925
 8V6  H20  H  HCR6   0   0.240   0.0308  -1.9783  -2.0979
 8V6  H21  H  HCR6   0   0.222   0.4236  -3.0811   0.2423
 8V6  H22  H  HCH2   0   0.245   2.6293  -2.9533  -0.1835
 8V6  H23  H  HCH2   0   0.244   2.2645  -2.0484  -1.6477
 8V6  H24  H  HCR6   0   0.258   5.2196   1.2274   1.6802
 8V6  H25  H  HCR6   0   0.254   7.2646   2.5468   1.9667
 8V6  H26  H  HCH3   0   0.252  10.2415   1.9580   1.0033
 8V6  H27  H  HCH3   0   0.246   9.9798   2.7841  -0.5244
 8V6  H28  H  HCH3   0   0.246   9.3306   3.4597   0.9712
 8V6  H29  H  HCR6   0   0.254   8.9176   0.7599  -1.5523
 8V6  H30  H  HCR6   0   0.258   6.8725  -0.5563  -1.8490

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
 8V6  CA5  CA6  aromatic  1.385  0.020  1.385
 8V6  CA5  CA4  aromatic  1.397  0.020  1.397
 8V6  CA6  CA7  aromatic  1.394  0.020  1.394
 8V6  CA1  CA2  single    1.457  0.020  1.457
 8V6  CA1  O4'  single    1.406  0.020  1.406
 8V6  CA2  CA3  triple    1.205  0.020  1.205
 8V6  CA3  CA4  single    1.426  0.020  1.426
 8V6  CA4  CA9  aromatic  1.397  0.020  1.397
 8V6  CA7  CA0  single    1.500  0.020  1.500
 8V6  CA7  CA8  aromatic  1.394  0.020  1.394
 8V6  CA9  CA8  aromatic  1.385  0.020  1.385
 8V6  C3'  C4'  single    1.498  0.020  1.498
 8V6  C3'  C2'  double    1.332  0.020  1.332
 8V6  O4'  C4'  single    1.423  0.020  1.423
 8V6  C4'  C5'  single    1.517  0.020  1.517
 8V6  C7'  C2'  single    1.500  0.020  1.500
 8V6  C2'  C1'  single    1.530  0.020  1.530
 8V6  C8'  C6'  single    1.535  0.020  1.535
 8V6  C5'  C6'  single    1.531  0.020  1.531
 8V6  C6'  C1'  single    1.557  0.020  1.557
 8V6  C6'  C9'  single    1.529  0.020  1.529
 8V6  C1'  O1   single    1.408  0.020  1.408
 8V6  C1'  C5   single    1.512  0.020  1.512
 8V6  C5   C4   double    1.337  0.020  1.337
 8V6  C4   C3   single    1.463  0.020  1.463
 8V6  C6   C3   single    1.504  0.020  1.504
 8V6  C3   C2   double    1.347  0.020  1.347
 8V6  O11  C1   deloc     1.250  0.020  1.250
 8V6  C2   C1   single    1.511  0.020  1.511
 8V6  C1   O12  deloc     1.250  0.020  1.250
 8V6  C2   H1   single    0.930  0.020  1.080
 8V6  C4   H2   single    0.930  0.020  1.080
 8V6  C5   H3   single    0.930  0.020  1.080
 8V6  C6   H4   single    0.970  0.020  1.090
 8V6  C6   H5   single    0.970  0.020  1.090
 8V6  C6   H6   single    0.970  0.020  1.090
 8V6  C9'  H8   single    0.970  0.020  1.090
 8V6  C9'  H9   single    0.970  0.020  1.090
 8V6  C9'  H10  single    0.970  0.020  1.090
 8V6  C5'  H11  single    0.970  0.020  1.090
 8V6  C5'  H12  single    0.970  0.020  1.090
 8V6  C8'  H13  single    0.970  0.020  1.090
 8V6  C8'  H14  single    0.970  0.020  1.090
 8V6  C8'  H15  single    0.970  0.020  1.090
 8V6  O1   H16  single    0.850  0.020  0.980
 8V6  C7'  H17  single    0.970  0.020  1.090
 8V6  C7'  H18  single    0.970  0.020  1.090
 8V6  C7'  H19  single    0.970  0.020  1.090
 8V6  C3'  H20  single    0.930  0.020  1.080
 8V6  C4'  H21  single    0.970  0.020  1.090
 8V6  CA1  H22  single    0.970  0.020  1.090
 8V6  CA1  H23  single    0.970  0.020  1.090
 8V6  CA5  H24  single    0.930  0.020  1.080
 8V6  CA6  H25  single    0.930  0.020  1.080
 8V6  CA0  H26  single    0.970  0.020  1.090
 8V6  CA0  H27  single    0.970  0.020  1.090
 8V6  CA0  H28  single    0.970  0.020  1.090
 8V6  CA8  H29  single    0.930  0.020  1.080
 8V6  CA9  H30  single    0.930  0.020  1.080

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
 8V6  O12  C1   O11  125.68  3.000
 8V6  O12  C1   C2   114.25  3.000
 8V6  O11  C1   C2   120.07  3.000
 8V6  H1   C2   C3   116.09  3.000
 8V6  H1   C2   C1   113.38  3.000
 8V6  C3   C2   C1   130.53  3.000
 8V6  C6   C3   C4   117.29  3.000
 8V6  C6   C3   C2   119.14  3.000
 8V6  C4   C3   C2   123.57  3.000
 8V6  H2   C4   C5   120.91  3.000
 8V6  H2   C4   C3   115.31  3.000
 8V6  C5   C4   C3   123.78  3.000
 8V6  H3   C5   C1'  114.75  3.000
 8V6  H3   C5   C4   119.72  3.000
 8V6  C1'  C5   C4   125.49  3.000
 8V6  H6   C6   H5   107.78  3.000
 8V6  H6   C6   H4   107.92  3.000
 8V6  H5   C6   H4   106.63  3.000
 8V6  H6   C6   C3   111.46  3.000
 8V6  H5   C6   C3   111.61  3.000
 8V6  H4   C6   C3   111.21  3.000
 8V6  C2'  C1'  O1   110.48  3.000
 8V6  O1   C1'  C6'  106.29  3.000
 8V6  C2'  C1'  C6'  111.18  3.000
 8V6  O1   C1'  C5   111.81  3.000
 8V6  C6'  C1'  C5   111.24  3.000
 8V6  C2'  C1'  C5   105.93  3.000
 8V6  C8'  C6'  C5'  109.63  3.000
 8V6  C5'  C6'  C9'  108.57  3.000
 8V6  C8'  C6'  C9'  108.27  3.000
 8V6  C9'  C6'  C1'  110.96  3.000
 8V6  C5'  C6'  C1'  108.79  3.000
 8V6  C8'  C6'  C1'  110.59  3.000
 8V6  H10  C9'  H9   107.64  3.000
 8V6  H10  C9'  H8   107.77  3.000
 8V6  H9   C9'  H8   107.84  3.000
 8V6  H10  C9'  C6'  112.02  3.000
 8V6  H9   C9'  C6'  109.80  3.000
 8V6  H8   C9'  C6'  111.60  3.000
 8V6  H12  C5'  H11  106.28  3.000
 8V6  H12  C5'  C4'  109.64  3.000
 8V6  H11  C5'  C4'  108.68  3.000
 8V6  H12  C5'  C6'  109.09  3.000
 8V6  H11  C5'  C6'  110.05  3.000
 8V6  C4'  C5'  C6'  112.90  3.000
 8V6  H15  C8'  H14  107.30  3.000
 8V6  H15  C8'  H13  107.50  3.000
 8V6  H14  C8'  H13  107.64  3.000
 8V6  H15  C8'  C6'  111.57  3.000
 8V6  H14  C8'  C6'  109.44  3.000
 8V6  H13  C8'  C6'  113.14  3.000
 8V6  H16  O1   C1'  109.52  3.000
 8V6  C3'  C2'  C7'  121.26  3.000
 8V6  C7'  C2'  C1'  116.31  3.000
 8V6  C3'  C2'  C1'  122.39  3.000
 8V6  H19  C7'  H18  107.40  3.000
 8V6  H19  C7'  H17  107.11  3.000
 8V6  H18  C7'  H17  107.68  3.000
 8V6  H19  C7'  C2'  111.86  3.000
 8V6  H18  C7'  C2'  111.09  3.000
 8V6  H17  C7'  C2'  111.47  3.000
 8V6  H20  C3'  C4'  116.82  3.000
 8V6  H20  C3'  C2'  118.46  3.000
 8V6  C4'  C3'  C2'  124.68  3.000
 8V6  H21  C4'  O4'  108.46  3.000
 8V6  H21  C4'  C3'  108.50  3.000
 8V6  O4'  C4'  C3'  111.50  3.000
 8V6  H21  C4'  C5'  109.44  3.000
 8V6  O4'  C4'  C5'  107.20  3.000
 8V6  C3'  C4'  C5'  111.68  3.000
 8V6  CA1  O4'  C4'  114.06  3.000
 8V6  H23  CA1  H22  106.41  3.000
 8V6  H23  CA1  CA2  108.84  3.000
 8V6  H22  CA1  CA2  109.43  3.000
 8V6  H23  CA1  O4'  112.31  3.000
 8V6  H22  CA1  O4'  111.10  3.000
 8V6  CA2  CA1  O4'  108.70  3.000
 8V6  CA3  CA2  CA1  180.00  3.000
 8V6  CA4  CA3  CA2  180.00  3.000
 8V6  CA9  CA4  CA5  118.72  3.000
 8V6  CA9  CA4  CA3  120.78  3.000
 8V6  CA5  CA4  CA3  120.50  3.000
 8V6  H24  CA5  CA6  119.90  3.000
 8V6  H24  CA5  CA4  119.74  3.000
 8V6  CA6  CA5  CA4  120.36  3.000
 8V6  H25  CA6  CA7  119.65  3.000
 8V6  H25  CA6  CA5  119.07  3.000
 8V6  CA7  CA6  CA5  121.28  3.000
 8V6  CA8  CA7  CA0  120.96  3.000
 8V6  CA8  CA7  CA6  118.00  3.000
 8V6  CA0  CA7  CA6  121.03  3.000
 8V6  H28  CA0  H27  108.18  3.000
 8V6  H28  CA0  H26  107.26  3.000
 8V6  H27  CA0  H26  107.23  3.000
 8V6  H28  CA0  CA7  111.58  3.000
 8V6  H27  CA0  CA7  111.57  3.000
 8V6  H26  CA0  CA7  110.80  3.000
 8V6  H29  CA8  CA9  119.05  3.000
 8V6  H29  CA8  CA7  119.66  3.000
 8V6  CA9  CA8  CA7  121.29  3.000
 8V6  H30  CA9  CA8  119.89  3.000
 8V6  H30  CA9  CA4  119.76  3.000
 8V6  CA8  CA9  CA4  120.35  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
 8V6  CONST_01  CA7  CA6  CA5  CA4     0.00   0.0  0
 8V6  CONST_02  CA7  CA8  CA9  CA4     0.00   0.0  0
 8V6  CONST_03  CA8  CA7  CA6  CA5     0.00   0.0  0
 8V6  CONST_04  CA8  CA9  CA4  CA5     0.00   0.0  0
 8V6  CONST_05  CA9  CA4  CA5  CA6     0.00   0.0  0
 8V6  CONST_06  CA9  CA8  CA7  CA6     0.00   0.0  0
 8V6  CONST_07  CA6  CA5  CA4  CA3   180.00   0.0  0
 8V6  CONST_08  CA8  CA9  CA4  CA3   180.00   0.0  0
 8V6  CONST_09  CA0  CA7  CA6  CA5   180.00   0.0  0
 8V6  CONST_10  CA9  CA8  CA7  CA0   180.00   0.0  0
 8V6  CONST_11  H25  CA6  CA5  CA4   180.00   0.0  0
 8V6  CONST_12  H29  CA8  CA9  CA4   180.00   0.0  0
 8V6  CONST_13  H30  CA9  CA4  CA5   180.00   0.0  0
 8V6  CONST_14  H24  CA5  CA6  CA7   180.00   0.0  0
 8V6  Var_01    C4'  C3'  C2'  C1'     3.51  30.0  1
 8V6  Var_02    C4'  C5'  C6'  C1'   -61.38  30.0  1
 8V6  Var_03    H17  C7'  C2'  C1'    51.59  30.0  3
 8V6  Var_04    H13  C8'  C6'  C1'    49.50  30.0  3
 8V6  Var_05    H8   C9'  C6'  C1'    55.22  30.0  3
 8V6  Var_06    H26  CA0  CA7  CA6    92.05  30.0  2
 8V6  Var_07    C1'  C5   C4   C3   -178.82   0.0  2
 8V6  Var_08    CA2  CA1  O4'  C4'  -175.26  30.0  1
 8V6  Var_09    C4   C3   C2   C1     -0.46   0.0  2
 8V6  Var_10    C5   C4   C3   C2    178.18  30.0  2
 8V6  Var_11    O11  C1   C2   C3     -1.29  30.0  2
 8V6  Var_12    H4   C6   C3   C2    119.83  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
 8V6  chir_01  C1'  C6'  C2'  C5   positiv
 8V6  chir_02  C4'  O4'  C5'  C3'  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
 8V6  plan-1  CA2  0.020
 8V6  plan-1  CA3  0.020
 8V6  plan-1  CA4  0.020
 8V6  plan-1  CA5  0.020
 8V6  plan-1  CA6  0.020
 8V6  plan-1  CA7  0.020
 8V6  plan-1  CA0  0.020
 8V6  plan-1  CA8  0.020
 8V6  plan-1  CA9  0.020
 8V6  plan-1  H24  0.020
 8V6  plan-1  H25  0.020
 8V6  plan-1  H29  0.020
 8V6  plan-1  H30  0.020
 8V6  plan-2  C3   0.020
 8V6  plan-2  C4   0.020
 8V6  plan-2  C5   0.020
 8V6  plan-2  C1'  0.020
 8V6  plan-2  H2   0.020
 8V6  plan-2  H3   0.020
 8V6  plan-3  C1   0.020
 8V6  plan-3  C2   0.020
 8V6  plan-3  C3   0.020
 8V6  plan-3  C4   0.020
 8V6  plan-3  C6   0.020
 8V6  plan-3  H1   0.020
 8V6  plan-4  C1   0.020
 8V6  plan-4  C2   0.020
 8V6  plan-4  O11  0.020
 8V6  plan-4  O12  0.020

