# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:48:55 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (3S,7S,8E)-8-[3-ethyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-dimethyloctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1=C(CCC(C)C)/C(CCC1)=C/[C@@H](C)CCC[C@H](C)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
 3SV  3SV  '(3S,7S,8E)-8-[3-ethyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-dimethyloctanoic acid'  ligand  64  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3SV
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
 3SV  C5'  C  CH3    0  -0.662   4.3199  -3.7452  -0.7940
 3SV  C3'  C  CH1    0  -0.229   2.9916  -3.2262  -0.2512
 3SV  C4'  C  CH3    0  -0.653   2.4203  -4.1987   0.7761
 3SV  C2'  C  CH2    0  -0.389   3.1209  -1.8298   0.3567
 3SV  C1'  C  CH2    0  -0.572   3.6125  -0.7548  -0.6150
 3SV  C1   C  C      0   0.111   3.5405   0.6346  -0.0269
 3SV  C2   C  C      0   0.026   4.6167   1.1865   0.5694
 3SV  C6'  C  CH2    0  -0.519   5.9374   0.4771   0.7215
 3SV  C7'  C  CH3    0  -0.654   6.9094   0.7868  -0.4173
 3SV  C3   C  CH2    0  -0.488   4.6120   2.5833   1.1245
 3SV  C4   C  CH2    0  -0.442   3.4516   3.4152   0.6156
 3SV  C5   C  CH2    0  -0.515   2.1609   2.6219   0.7388
 3SV  C6   C  C      0   0.078   2.2367   1.3344  -0.0439
 3SV  C7   C  C1     0  -0.269   1.1646   0.8313  -0.6749
 3SV  C8   C  CH1    0  -0.297  -0.2323   1.3821  -0.7119
 3SV  C19  C  CH3    0  -0.652  -0.4919   2.0584  -2.0607
 3SV  C9   C  CH2    0  -0.396  -1.2195   0.2393  -0.4396
 3SV  C10  C  CH2    0  -0.430  -2.6844   0.6529  -0.3605
 3SV  C11  C  CH2    0  -0.393  -3.5846  -0.5152   0.0281
 3SV  C12  C  CH1    0  -0.210  -5.0861  -0.2298  -0.0378
 3SV  C20  C  CH3    0  -0.668  -5.4848   0.9140   0.8902
 3SV  C13  C  CH2    0  -0.556  -5.8753  -1.4951   0.2845
 3SV  C14  C  C      0   0.404  -7.3936  -1.4270   0.0453
 3SV  O1   O  OC    -1  -0.628  -8.1046  -2.1682   0.7570
 3SV  O2   O  O      0  -0.613  -7.7997  -0.6732  -0.8627
 3SV  H1   H  HCH3   0   0.226   4.2187  -4.7663  -1.1667
 3SV  H2   H  HCH3   0   0.228   4.6960  -3.1373  -1.6175
 3SV  H3   H  HCH3   0   0.212   5.0834  -3.7539  -0.0116
 3SV  H4   H  HCH1   0   0.210   2.2840  -3.1639  -1.0873
 3SV  H5   H  HCH3   0   0.212   3.0937  -4.3022   1.6305
 3SV  H6   H  HCH3   0   0.222   1.4547  -3.8581   1.1552
 3SV  H7   H  HCH3   0   0.223   2.2774  -5.1919   0.3464
 3SV  H8   H  HCH2   0   0.224   2.1485  -1.5281   0.7586
 3SV  H9   H  HCH2   0   0.210   3.8054  -1.8717   1.2127
 3SV  H10  H  HCH2   0   0.244   4.6326  -0.9788  -0.9252
 3SV  H11  H  HCH2   0   0.233   3.0239  -0.8047  -1.5347
 3SV  H12  H  HCH2   0   0.238   6.3910   0.7979   1.6644
 3SV  H13  H  HCH2   0   0.236   5.8071  -0.6027   0.8081
 3SV  H14  H  HCH3   0   0.224   7.0700   1.8609  -0.5210
 3SV  H15  H  HCH3   0   0.229   7.8811   0.3248  -0.2374
 3SV  H16  H  HCH3   0   0.223   6.5331   0.4144  -1.3708
 3SV  H17  H  HCH2   0   0.235   4.5847   2.5334   2.2206
 3SV  H18  H  HCH2   0   0.237   5.5649   3.0657   0.8820
 3SV  H19  H  HCH2   0   0.231   3.3779   4.3511   1.1733
 3SV  H20  H  HCH2   0   0.220   3.6191   3.6814  -0.4322
 3SV  H21  H  HCH2   0   0.230   1.9849   2.3949   1.7971
 3SV  H22  H  HCH2   0   0.240   1.3184   3.2287   0.4082
 3SV  H23  H  H      0   0.215   1.2702  -0.0939  -1.2340
 3SV  H24  H  HCH1   0   0.225  -0.3666   2.1290   0.0759
 3SV  H25  H  HCH3   0   0.214  -0.4047   1.3399  -2.8796
 3SV  H26  H  HCH3   0   0.228  -1.4884   2.4996  -2.1091
 3SV  H27  H  HCH3   0   0.228   0.2308   2.8553  -2.2391
 3SV  H28  H  HCH2   0   0.205  -1.0990  -0.5247  -1.2170
 3SV  H29  H  HCH2   0   0.218  -0.9359  -0.2409   0.5033
 3SV  H30  H  HCH2   0   0.211  -2.7883   1.4685   0.3621
 3SV  H31  H  HCH2   0   0.211  -3.0143   1.0528  -1.3248
 3SV  H32  H  HCH2   0   0.207  -3.3611  -1.3604  -0.6332
 3SV  H33  H  HCH2   0   0.199  -3.3264  -0.8496   1.0405
 3SV  H34  H  HCH1   0   0.197  -5.3280   0.0647  -1.0646
 3SV  H35  H  HCH3   0   0.227  -6.5617   1.0823   0.8652
 3SV  H36  H  HCH3   0   0.203  -5.2027   0.6936   1.9237
 3SV  H37  H  HCH3   0   0.222  -5.0044   1.8532   0.6116
 3SV  H38  H  HCH2   0   0.223  -5.4907  -2.3188  -0.3327
 3SV  H39  H  HCH2   0   0.198  -5.6807  -1.7961   1.3198

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
 3SV  C19  C8   single  1.531  0.020  1.531
 3SV  C8   C9   single  1.535  0.020  1.535
 3SV  C8   C7   single  1.502  0.020  1.502
 3SV  C9   C10  single  1.524  0.020  1.524
 3SV  C11  C10  single  1.525  0.020  1.525
 3SV  C11  C12  single  1.530  0.020  1.530
 3SV  C13  C12  single  1.526  0.020  1.526
 3SV  C13  C14  single  1.539  0.020  1.539
 3SV  C5   C4   single  1.520  0.020  1.520
 3SV  C5   C6   single  1.509  0.020  1.509
 3SV  C4   C3   single  1.516  0.020  1.516
 3SV  C12  C20  single  1.526  0.020  1.526
 3SV  C7   C6   double  1.342  0.020  1.342
 3SV  O2   C14  deloc   1.248  0.020  1.248
 3SV  C14  O1   deloc   1.250  0.020  1.250
 3SV  C6   C1   single  1.480  0.020  1.480
 3SV  C3   C2   single  1.503  0.020  1.503
 3SV  C1   C2   double  1.348  0.020  1.348
 3SV  C1   C1'  single  1.510  0.020  1.510
 3SV  C2   C6'  single  1.507  0.020  1.507
 3SV  C1'  C2'  single  1.530  0.020  1.530
 3SV  C6'  C7'  single  1.529  0.020  1.529
 3SV  C2'  C3'  single  1.529  0.020  1.529
 3SV  C3'  C4'  single  1.526  0.020  1.526
 3SV  C3'  C5'  single  1.526  0.020  1.526
 3SV  C5'  H1   single  0.970  0.020  1.090
 3SV  C5'  H2   single  0.970  0.020  1.090
 3SV  C5'  H3   single  0.970  0.020  1.090
 3SV  C3'  H4   single  0.970  0.020  1.090
 3SV  C4'  H5   single  0.970  0.020  1.090
 3SV  C4'  H6   single  0.970  0.020  1.090
 3SV  C4'  H7   single  0.970  0.020  1.090
 3SV  C2'  H8   single  0.970  0.020  1.090
 3SV  C2'  H9   single  0.970  0.020  1.090
 3SV  C1'  H10  single  0.970  0.020  1.090
 3SV  C1'  H11  single  0.970  0.020  1.090
 3SV  C6'  H12  single  0.970  0.020  1.090
 3SV  C6'  H13  single  0.970  0.020  1.090
 3SV  C7'  H14  single  0.970  0.020  1.090
 3SV  C7'  H15  single  0.970  0.020  1.090
 3SV  C7'  H16  single  0.970  0.020  1.090
 3SV  C3   H17  single  0.970  0.020  1.090
 3SV  C3   H18  single  0.970  0.020  1.090
 3SV  C4   H19  single  0.970  0.020  1.090
 3SV  C4   H20  single  0.970  0.020  1.090
 3SV  C5   H21  single  0.970  0.020  1.090
 3SV  C5   H22  single  0.970  0.020  1.090
 3SV  C7   H23  single  0.930  0.020  1.080
 3SV  C8   H24  single  0.970  0.020  1.090
 3SV  C19  H25  single  0.970  0.020  1.090
 3SV  C19  H26  single  0.970  0.020  1.090
 3SV  C19  H27  single  0.970  0.020  1.090
 3SV  C9   H28  single  0.970  0.020  1.090
 3SV  C9   H29  single  0.970  0.020  1.090
 3SV  C10  H30  single  0.970  0.020  1.090
 3SV  C10  H31  single  0.970  0.020  1.090
 3SV  C11  H32  single  0.970  0.020  1.090
 3SV  C11  H33  single  0.970  0.020  1.090
 3SV  C12  H34  single  0.970  0.020  1.090
 3SV  C20  H35  single  0.970  0.020  1.090
 3SV  C20  H36  single  0.970  0.020  1.090
 3SV  C20  H37  single  0.970  0.020  1.090
 3SV  C13  H38  single  0.970  0.020  1.090
 3SV  C13  H39  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
 3SV  H3   C5'  H2   107.69  3.000
 3SV  H3   C5'  H1   107.55  3.000
 3SV  H2   C5'  H1   107.19  3.000
 3SV  H3   C5'  C3'  110.86  3.000
 3SV  H2   C5'  C3'  112.29  3.000
 3SV  H1   C5'  C3'  111.03  3.000
 3SV  H4   C3'  C2'  107.80  3.000
 3SV  H4   C3'  C4'  107.93  3.000
 3SV  C2'  C3'  C4'  110.25  3.000
 3SV  H4   C3'  C5'  108.04  3.000
 3SV  C4'  C3'  C5'  110.41  3.000
 3SV  C2'  C3'  C5'  112.25  3.000
 3SV  H7   C4'  H6   107.74  3.000
 3SV  H7   C4'  H5   107.59  3.000
 3SV  H6   C4'  H5   107.64  3.000
 3SV  H7   C4'  C3'  111.34  3.000
 3SV  H6   C4'  C3'  111.48  3.000
 3SV  H5   C4'  C3'  110.86  3.000
 3SV  H9   C2'  H8   106.17  3.000
 3SV  H9   C2'  C1'  108.78  3.000
 3SV  H8   C2'  C1'  108.96  3.000
 3SV  H9   C2'  C3'  109.16  3.000
 3SV  H8   C2'  C3'  108.83  3.000
 3SV  C1'  C2'  C3'  114.61  3.000
 3SV  H11  C1'  H10  104.79  3.000
 3SV  H11  C1'  C1   110.12  3.000
 3SV  H10  C1'  C1   110.15  3.000
 3SV  H11  C1'  C2'  109.22  3.000
 3SV  H10  C1'  C2'  109.70  3.000
 3SV  C1   C1'  C2'  112.56  3.000
 3SV  C6   C1   C2   120.97  3.000
 3SV  C2   C1   C1'  120.71  3.000
 3SV  C6   C1   C1'  118.19  3.000
 3SV  C3   C2   C6'  113.76  3.000
 3SV  C6'  C2   C1   123.46  3.000
 3SV  C3   C2   C1   122.77  3.000
 3SV  H13  C6'  H12  105.73  3.000
 3SV  H13  C6'  C7'  109.61  3.000
 3SV  H12  C6'  C7'  108.59  3.000
 3SV  H13  C6'  C2   111.67  3.000
 3SV  H12  C6'  C2   108.19  3.000
 3SV  C7'  C6'  C2   112.75  3.000
 3SV  H16  C7'  H15  107.87  3.000
 3SV  H16  C7'  H14  107.68  3.000
 3SV  H15  C7'  H14  107.55  3.000
 3SV  H16  C7'  C6'  111.27  3.000
 3SV  H15  C7'  C6'  110.96  3.000
 3SV  H14  C7'  C6'  111.34  3.000
 3SV  H18  C3   H17  105.24  3.000
 3SV  H18  C3   C4   110.48  3.000
 3SV  H17  C3   C4   109.95  3.000
 3SV  H18  C3   C2   108.96  3.000
 3SV  H17  C3   C2   109.07  3.000
 3SV  C4   C3   C2   112.85  3.000
 3SV  H20  C4   H19  106.92  3.000
 3SV  H20  C4   C5   109.55  3.000
 3SV  H19  C4   C5   110.40  3.000
 3SV  H20  C4   C3   109.75  3.000
 3SV  H19  C4   C3   110.52  3.000
 3SV  C5   C4   C3   109.65  3.000
 3SV  H22  C5   H21  106.49  3.000
 3SV  H22  C5   C6   110.90  3.000
 3SV  H21  C5   C6   109.40  3.000
 3SV  H22  C5   C4   109.96  3.000
 3SV  H21  C5   C4   108.81  3.000
 3SV  C6   C5   C4   111.15  3.000
 3SV  C7   C6   C5   121.58  3.000
 3SV  C7   C6   C1   122.14  3.000
 3SV  C5   C6   C1   116.22  3.000
 3SV  H23  C7   C8   112.96  3.000
 3SV  H23  C7   C6   118.93  3.000
 3SV  C8   C7   C6   128.11  3.000
 3SV  H24  C8   C9   107.56  3.000
 3SV  H24  C8   C19  108.18  3.000
 3SV  C9   C8   C19  112.10  3.000
 3SV  H24  C8   C7   110.30  3.000
 3SV  C9   C8   C7   108.71  3.000
 3SV  C19  C8   C7   109.96  3.000
 3SV  H27  C19  H26  107.61  3.000
 3SV  H27  C19  H25  107.76  3.000
 3SV  H26  C19  H25  107.79  3.000
 3SV  H27  C19  C8   110.76  3.000
 3SV  H26  C19  C8   111.88  3.000
 3SV  H25  C19  C8   110.86  3.000
 3SV  H29  C9   H28  106.04  3.000
 3SV  H29  C9   C10  108.85  3.000
 3SV  H28  C9   C10  109.36  3.000
 3SV  H29  C9   C8   108.22  3.000
 3SV  H28  C9   C8   108.80  3.000
 3SV  C10  C9   C8   115.18  3.000
 3SV  H31  C10  H30  106.29  3.000
 3SV  H31  C10  C11  109.04  3.000
 3SV  H30  C10  C11  110.27  3.000
 3SV  H31  C10  C9   110.06  3.000
 3SV  H30  C10  C9   109.13  3.000
 3SV  C11  C10  C9   111.88  3.000
 3SV  H33  C11  H32  105.89  3.000
 3SV  H33  C11  C12  109.12  3.000
 3SV  H32  C11  C12  108.54  3.000
 3SV  H33  C11  C10  109.25  3.000
 3SV  H32  C11  C10  108.45  3.000
 3SV  C12  C11  C10  115.18  3.000
 3SV  H34  C12  C13  107.87  3.000
 3SV  H34  C12  C20  108.11  3.000
 3SV  C13  C12  C20  110.98  3.000
 3SV  H34  C12  C11  107.90  3.000
 3SV  C20  C12  C11  111.72  3.000
 3SV  C13  C12  C11  110.11  3.000
 3SV  H37  C20  H36  107.53  3.000
 3SV  H37  C20  H35  107.23  3.000
 3SV  H36  C20  H35  107.91  3.000
 3SV  H37  C20  C12  112.02  3.000
 3SV  H36  C20  C12  110.87  3.000
 3SV  H35  C20  C12  111.09  3.000
 3SV  H39  C13  H38  105.24  3.000
 3SV  H39  C13  C14  109.53  3.000
 3SV  H38  C13  C14  106.94  3.000
 3SV  H39  C13  C12  109.61  3.000
 3SV  H38  C13  C12  108.78  3.000
 3SV  C14  C13  C12  116.16  3.000
 3SV  O2   C14  O1   125.98  3.000
 3SV  O1   C14  C13  116.53  3.000
 3SV  O2   C14  C13  117.45  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
 3SV  Var_01  C4   C5   C6   C1     37.95  30.0  1
 3SV  Var_02  C4   C3   C2   C1    -15.96  30.0  1
 3SV  Var_03  C5   C4   C3   C2     47.78  30.0  1
 3SV  Var_04  C5   C6   C1   C2     -5.14  30.0  1
 3SV  Var_05  C6   C5   C4   C3    -58.88  30.0  1
 3SV  Var_06  C6   C1   C2   C3     -6.40  30.0  1
 3SV  Var_07  C8   C7   C6   C1    176.15  30.0  2
 3SV  Var_08  C7'  C6'  C2   C1     93.55  30.0  3
 3SV  Var_09  C1   C1'  C2'  C3'   172.01  30.0  2
 3SV  Var_10  H14  C7'  C6'  C2     55.64  30.0  3
 3SV  Var_11  C1'  C2'  C3'  C5'    59.72  30.0  3
 3SV  Var_12  C11  C10  C9   C8   -175.18  30.0  3
 3SV  Var_13  C12  C11  C10  C9   -172.78  30.0  2
 3SV  Var_14  O2   C14  C13  C12    30.04  30.0  3
 3SV  Var_15  H5   C4'  C3'  C5'    61.73  30.0  3
 3SV  Var_16  H1   C5'  C3'  C4'    53.02  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
 3SV  chir_01  C8   C19  C9   C7   negativ
 3SV  chir_02  C12  C11  C13  C20  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
 3SV  plan-1  C13  0.020
 3SV  plan-1  C14  0.020
 3SV  plan-1  O1   0.020
 3SV  plan-1  O2   0.020

