# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:18:04 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  59  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   0.525  -6.7414   2.3015  -0.0017
 8V6  C2   C  C1    0  -0.444  -5.3934   2.8802   0.0342
 8V6  C3   C  C     0   0.183  -4.2146   2.2206   0.0354
 8V6  C4   C  C1    0  -0.322  -4.0916   0.7673   0.0028
 8V6  C5   C  C1    0  -0.200  -2.9147   0.1328  -0.0037
 8V6  C6   C  CH3   0  -0.755  -2.9536   3.0321   0.0771
 8V6  O11  O  O     0  -0.455  -7.0445   1.1285  -0.0276
 8V6  O12  O  OH1   0  -0.607  -7.6616   3.2682  -0.0021
 8V6  C1'  C  CT    0   0.185  -2.7364  -1.3656  -0.0714
 8V6  C6'  C  CT    0  -0.108  -2.0887  -1.9090   1.2368
 8V6  C9'  C  CH3   0  -0.647  -2.8128  -1.3711   2.4717
 8V6  C5'  C  CH2   0  -0.466  -0.6274  -1.4550   1.2898
 8V6  C8'  C  CH3   0  -0.651  -2.1558  -3.4413   1.2690
 8V6  O1   O  OH1   0  -0.669  -3.9687  -2.0304  -0.2098
 8V6  C2'  C  C     0   0.120  -1.8421  -1.6234  -1.2851
 8V6  C7'  C  CH3   0  -0.747  -2.5038  -1.5375  -2.6291
 8V6  C3'  C  C1    0  -0.315  -0.5379  -1.8655  -1.1690
 8V6  C4'  C  CH1   0   0.050   0.1956  -1.9861   0.1317
 8V6  O4'  O  O2    0  -0.497   1.4154  -1.2551   0.1116
 8V6  CA1  C  CH2   0  -0.332   2.4686  -1.9145  -0.5468
 8V6  CA2  C  CSP   0  -0.006   3.6862  -1.1312  -0.3848
 8V6  CA3  C  CSP   0   0.184   4.7016  -0.4960  -0.2565
 8V6  CA4  C  CR6   0  -0.129   5.8988   0.2615  -0.0953
 8V6  CA5  C  CR16  0  -0.277   6.0254   1.1750   0.9557
 8V6  CA6  C  CR16  0  -0.287   7.1883   1.9087   1.1080
 8V6  CA7  C  CR6   0   0.096   8.2609   1.7571   0.2288
 8V6  CA0  C  CH3   0  -0.723   9.5262   2.5386   0.4224
 8V6  CA8  C  CR16  0  -0.296   8.1263   0.8463  -0.8166
 8V6  CA9  C  CR16  0  -0.274   6.9654   0.1079  -0.9827
 8V6  H1   H  H     0   0.265  -5.3659   3.9627   0.0607
 8V6  H2   H  H     0   0.259  -5.0081   0.1966   0.0015
 8V6  H3   H  H     0   0.280  -1.9924   0.7037   0.0032
 8V6  H4   H  HCH3  0   0.254  -2.3618   2.7903   0.9615
 8V6  H5   H  HCH3  0   0.257  -2.3234   2.8283  -0.7899
 8V6  H6   H  HCH3  0   0.262  -3.1650   4.0988   0.0964
 8V6  H7   H  HOH1  0   0.479  -8.5464   2.8752  -0.0222
 8V6  H8   H  HCH3  0   0.234  -3.8817  -1.5820   2.4358
 8V6  H9   H  HCH3  0   0.231  -2.4099  -1.8440   3.3695
 8V6  H10  H  HCH3  0   0.229  -2.6893  -0.2931   2.5840
 8V6  H11  H  HCH2  0   0.240  -0.5704  -0.3623   1.2877
 8V6  H12  H  HCH2  0   0.249  -0.1865  -1.7835   2.2352
 8V6  H13  H  HCH3  0   0.230  -1.7961  -3.9063   0.3505
 8V6  H14  H  HCH3  0   0.227  -1.5422  -3.8139   2.0918
 8V6  H15  H  HCH3  0   0.239  -3.1724  -3.7935   1.4384
 8V6  H16  H  HOH1  0   0.456  -4.4403  -1.6861  -0.9756
 8V6  H17  H  HCH3  0   0.242  -3.0568  -0.6014  -2.7461
 8V6  H18  H  HCH3  0   0.256  -1.7687  -1.5874  -3.4306
 8V6  H19  H  HCH3  0   0.246  -3.2136  -2.3523  -2.7877
 8V6  H20  H  H     0   0.244   0.0398  -2.0249  -2.0760
 8V6  H21  H  HCH1  0   0.225   0.4278  -3.0487   0.3047
 8V6  H22  H  HCH2  0   0.246   2.6248  -2.9211  -0.1337
 8V6  H23  H  HCH2  0   0.245   2.2720  -2.0466  -1.6189
 8V6  H24  H  HCR6  0   0.258   5.2068   1.3104   1.6506
 8V6  H25  H  HCR6  0   0.254   7.2632   2.6146   1.9265
 8V6  H26  H  HCH3  0   0.251  10.1086   2.1358   1.2536
 8V6  H27  H  HCH3  0   0.246  10.1567   2.5074  -0.4649
 8V6  H28  H  HCH3  0   0.247   9.3189   3.5837   0.6540
 8V6  H29  H  HCR6  0   0.255   8.9410   0.7096  -1.5172
 8V6  H30  H  HCR6  0   0.258   6.8845  -0.5915  -1.8043

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  1.383  0.020  1.383
 8V6  CA5  CA4  aromatic  1.398  0.020  1.398
 8V6  CA6  CA7  aromatic  1.395  0.020  1.395
 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  1.396  0.020  1.396
 8V6  CA7  CA0  single    1.500  0.020  1.500
 8V6  CA7  CA8  aromatic  1.393  0.020  1.393
 8V6  CA9  CA8  aromatic  1.386  0.020  1.386
 8V6  C3'  C4'  single    1.498  0.020  1.498
 8V6  C3'  C2'  double    1.331  0.020  1.331
 8V6  O4'  C4'  single    1.422  0.020  1.422
 8V6  C4'  C5'  single    1.517  0.020  1.517
 8V6  C7'  C2'  single    1.501  0.020  1.501
 8V6  C2'  C1'  single    1.530  0.020  1.530
 8V6  C8'  C6'  single    1.534  0.020  1.534
 8V6  C5'  C6'  single    1.531  0.020  1.531
 8V6  C6'  C1'  single    1.558  0.020  1.558
 8V6  C6'  C9'  single    1.529  0.020  1.529
 8V6  C1'  O1   single    1.407  0.020  1.407
 8V6  C1'  C5   single    1.511  0.020  1.511
 8V6  C5   C4   double    1.337  0.020  1.337
 8V6  C4   C3   single    1.459  0.020  1.459
 8V6  C6   C3   single    1.500  0.020  1.500
 8V6  C3   C2   double    1.351  0.020  1.351
 8V6  O11  C1   double    1.212  0.020  1.212
 8V6  C2   C1   single    1.467  0.020  1.467
 8V6  C1   O12  single    1.335  0.020  1.335
 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  O12  H7   single    0.850  0.020  0.980
 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  121.92  3.000
 8V6  O12  C1   C2   110.34  3.000
 8V6  O11  C1   C2   127.74  3.000
 8V6  H1   C2   C3   117.76  3.000
 8V6  H1   C2   C1   114.72  3.000
 8V6  C3   C2   C1   127.52  3.000
 8V6  C6   C3   C4   117.95  3.000
 8V6  C6   C3   C2   118.00  3.000
 8V6  C4   C3   C2   124.06  3.000
 8V6  H2   C4   C5   119.76  3.000
 8V6  H2   C4   C3   117.06  3.000
 8V6  C5   C4   C3   123.16  3.000
 8V6  H3   C5   C1'  114.96  3.000
 8V6  H3   C5   C4   119.91  3.000
 8V6  C1'  C5   C4   125.09  3.000
 8V6  H6   C6   H5   108.03  3.000
 8V6  H6   C6   H4   107.96  3.000
 8V6  H5   C6   H4   106.82  3.000
 8V6  H6   C6   C3   111.57  3.000
 8V6  H5   C6   C3   111.25  3.000
 8V6  H4   C6   C3   111.01  3.000
 8V6  H7   O12  C1   109.63  3.000
 8V6  C2'  C1'  O1   110.76  3.000
 8V6  O1   C1'  C6'  106.38  3.000
 8V6  C2'  C1'  C6'  111.38  3.000
 8V6  O1   C1'  C5   111.70  3.000
 8V6  C6'  C1'  C5   110.95  3.000
 8V6  C2'  C1'  C5   105.77  3.000
 8V6  C8'  C6'  C5'  109.70  3.000
 8V6  C5'  C6'  C9'  108.64  3.000
 8V6  C8'  C6'  C9'  108.28  3.000
 8V6  C9'  C6'  C1'  111.02  3.000
 8V6  C5'  C6'  C1'  108.82  3.000
 8V6  C8'  C6'  C1'  110.36  3.000
 8V6  H10  C9'  H9   107.56  3.000
 8V6  H10  C9'  H8   107.79  3.000
 8V6  H9   C9'  H8   107.77  3.000
 8V6  H10  C9'  C6'  112.16  3.000
 8V6  H9   C9'  C6'  109.69  3.000
 8V6  H8   C9'  C6'  111.69  3.000
 8V6  H12  C5'  H11  106.29  3.000
 8V6  H12  C5'  C4'  109.65  3.000
 8V6  H11  C5'  C4'  108.66  3.000
 8V6  H12  C5'  C6'  109.00  3.000
 8V6  H11  C5'  C6'  110.22  3.000
 8V6  C4'  C5'  C6'  112.81  3.000
 8V6  H15  C8'  H14  107.27  3.000
 8V6  H15  C8'  H13  107.52  3.000
 8V6  H14  C8'  H13  107.68  3.000
 8V6  H15  C8'  C6'  111.54  3.000
 8V6  H14  C8'  C6'  109.40  3.000
 8V6  H13  C8'  C6'  113.19  3.000
 8V6  H16  O1   C1'  109.77  3.000
 8V6  C3'  C2'  C7'  121.36  3.000
 8V6  C7'  C2'  C1'  116.31  3.000
 8V6  C3'  C2'  C1'  122.29  3.000
 8V6  H19  C7'  H18  107.32  3.000
 8V6  H19  C7'  H17  107.13  3.000
 8V6  H18  C7'  H17  107.58  3.000
 8V6  H19  C7'  C2'  111.96  3.000
 8V6  H18  C7'  C2'  111.04  3.000
 8V6  H17  C7'  C2'  111.58  3.000
 8V6  H20  C3'  C4'  116.89  3.000
 8V6  H20  C3'  C2'  118.33  3.000
 8V6  C4'  C3'  C2'  124.75  3.000
 8V6  H21  C4'  O4'  108.50  3.000
 8V6  H21  C4'  C3'  108.50  3.000
 8V6  O4'  C4'  C3'  111.49  3.000
 8V6  H21  C4'  C5'  109.41  3.000
 8V6  O4'  C4'  C5'  107.23  3.000
 8V6  C3'  C4'  C5'  111.66  3.000
 8V6  CA1  O4'  C4'  114.08  3.000
 8V6  H23  CA1  H22  106.39  3.000
 8V6  H23  CA1  CA2  108.84  3.000
 8V6  H22  CA1  CA2  109.38  3.000
 8V6  H23  CA1  O4'  112.30  3.000
 8V6  H22  CA1  O4'  111.09  3.000
 8V6  CA2  CA1  O4'  108.77  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  120.75  3.000
 8V6  CA5  CA4  CA3  120.53  3.000
 8V6  H24  CA5  CA6  119.92  3.000
 8V6  H24  CA5  CA4  119.73  3.000
 8V6  CA6  CA5  CA4  120.35  3.000
 8V6  H25  CA6  CA7  119.59  3.000
 8V6  H25  CA6  CA5  119.13  3.000
 8V6  CA7  CA6  CA5  121.28  3.000
 8V6  CA8  CA7  CA0  121.27  3.000
 8V6  CA8  CA7  CA6  118.01  3.000
 8V6  CA0  CA7  CA6  120.71  3.000
 8V6  H28  CA0  H27  108.10  3.000
 8V6  H28  CA0  H26  107.05  3.000
 8V6  H27  CA0  H26  107.51  3.000
 8V6  H28  CA0  CA7  111.50  3.000
 8V6  H27  CA0  CA7  111.62  3.000
 8V6  H26  CA0  CA7  110.85  3.000
 8V6  H29  CA8  CA9  119.03  3.000
 8V6  H29  CA8  CA7  119.68  3.000
 8V6  CA9  CA8  CA7  121.29  3.000
 8V6  H30  CA9  CA8  119.88  3.000
 8V6  H30  CA9  CA4  119.78  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  CONST_15  H7   O12  C1   C2    180.00   0.0  0
 8V6  Var_01    C4'  C3'  C2'  C1'     3.29  30.0  1
 8V6  Var_02    C4'  C5'  C6'  C1'   -61.34  30.0  1
 8V6  Var_03    H17  C7'  C2'  C1'    51.57  30.0  3
 8V6  Var_04    H13  C8'  C6'  C1'    49.61  30.0  3
 8V6  Var_05    H8   C9'  C6'  C1'    54.76  30.0  3
 8V6  Var_06    H26  CA0  CA7  CA6    74.75  30.0  2
 8V6  Var_07    C1'  C5   C4   C3   -178.41   0.0  2
 8V6  Var_08    CA2  CA1  O4'  C4'  -174.43  30.0  2
 8V6  Var_09    C4   C3   C2   C1     -0.14   0.0  2
 8V6  Var_10    C5   C4   C3   C2    179.58  30.0  3
 8V6  Var_11    O11  C1   C2   C3      0.55  30.0  2
 8V6  Var_12    H4   C6   C3   C2    120.14  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
 8V6  plan-4  H7   0.020

