# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:51:46 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (3E,6Z,8E)-3,7-dimethyl-8-[(4S)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-3,6-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC\C(=C/C(C)=C\C\C=C(/C)CC(O)=O)c2ccccc12
#
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
 29V  29V  '(3E,6Z,8E)-3,7-dimethyl-8-[(4S)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-3,6-dienoic acid'  ligand  49  23  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_29V
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
 29V  C4'  C  CH3   0  -0.663   4.6046  -0.4981   2.5371
 29V  C1'  C  CH2   0  -0.431   3.0388  -1.7580   1.0492
 29V  C2'  C  CH2   0  -0.517   2.4961  -1.9115  -0.3658
 29V  C8   C  C1    0  -0.386   0.7804  -0.3413  -1.2643
 29V  C5   C  CR6   0   0.090   4.0825   0.3924   0.2170
 29V  C6   C  CR6   0   0.089   3.0249   0.5144  -0.7002
 29V  C4   C  CR16  0  -0.307   5.0196   1.4238   0.2958
 29V  C2   C  CR16  0  -0.258   3.8793   2.6775  -1.3989
 29V  C18  C  CH1   0  -0.298   4.2562  -0.8388   1.0886
 29V  C3   C  CR16  0  -0.255   4.9249   2.5585  -0.4919
 29V  C1   C  CR16  0  -0.316   2.9503   1.6589  -1.5022
 29V  C7   C  C     0   0.106   2.0270  -0.5678  -0.8351
 29V  C9   C  C     0   0.043  -0.2612  -1.3806  -1.4520
 29V  C19  C  CH3   0  -0.711  -0.1719  -2.1711  -2.7261
 29V  C10  C  C1    0  -0.222  -1.2395  -1.5704  -0.5648
 29V  C11  C  CH2   0  -0.571  -1.4114  -0.8177   0.7230
 29V  C12  C  C1    0  -0.240  -2.5163   0.1902   0.6047
 29V  C13  C  C     0   0.121  -3.7005   0.1899   1.2185
 29V  C20  C  CH3   0  -0.726  -4.1598  -0.8362   2.2101
 29V  C14  C  CH2   0  -0.658  -4.6712   1.3085   0.9629
 29V  C15  C  C     0   0.552  -5.8665   0.8884   0.1435
 29V  O1   O  O     0  -0.436  -5.9655  -0.1486  -0.4614
 29V  O2   O  OH1   0  -0.595  -6.8107   1.8250   0.1407
 29V  H1   H  HCH3  0   0.233   4.7026  -1.4146   3.1210
 29V  H2   H  HCH3  0   0.235   5.5443   0.0453   2.6283
 29V  H3   H  HCH3  0   0.223   3.8198   0.1073   2.9945
 29V  H4   H  HCH2  0   0.223   2.2478  -1.3547   1.6910
 29V  H5   H  HCH2  0   0.241   3.3129  -2.7306   1.4639
 29V  H6   H  HCH2  0   0.238   3.2899  -2.2862  -1.0217
 29V  H7   H  HCH2  0   0.248   1.6844  -2.6386  -0.3886
 29V  H8   H  H     0   0.249   0.4809   0.6738  -1.5127
 29V  H9   H  HCR6  0   0.249   5.8475   1.3391   0.9885
 29V  H10  H  HCR6  0   0.252   3.7986   3.5507  -2.0332
 29V  H11  H  HCH1  0   0.245   5.0989  -1.4013   0.6664
 29V  H12  H  HCR6  0   0.252   5.6677   3.3408  -0.4045
 29V  H13  H  HCR6  0   0.247   2.1629   1.7423  -2.2405
 29V  H14  H  HCH3  0   0.237   0.7708  -2.7220  -2.7755
 29V  H15  H  HCH3  0   0.235  -0.9890  -2.8870  -2.8189
 29V  H16  H  HCH3  0   0.238  -0.1927  -1.5141  -3.5989
 29V  H17  H  H     0   0.230  -2.0028  -2.3130  -0.7825
 29V  H18  H  HCH2  0   0.252  -1.6029  -1.5241   1.5327
 29V  H19  H  HCH2  0   0.249  -0.4816  -0.3014   0.9770
 29V  H20  H  H     0   0.233  -2.3068   0.9987  -0.0920
 29V  H21  H  HCH3  0   0.238  -4.3380  -0.3721   3.1835
 29V  H22  H  HCH3  0   0.241  -5.1062  -1.2849   1.9014
 29V  H23  H  HCH3  0   0.243  -3.4460  -1.6446   2.3521
 29V  H24  H  HCH2  0   0.281  -5.0280   1.7368   1.9052
 29V  H25  H  HCH2  0   0.299  -4.1870   2.1307   0.4262
 29V  H26  H  HOH1  0   0.479  -7.5515   1.5469  -0.4186

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
 29V  C19  C9   single    1.502  0.020  1.502
 29V  C10  C9   double    1.334  0.020  1.334
 29V  C10  C11  single    1.502  0.020  1.502
 29V  C9   C8   single    1.483  0.020  1.483
 29V  C12  C11  single    1.500  0.020  1.500
 29V  C12  C13  double    1.334  0.020  1.334
 29V  C14  C13  single    1.503  0.020  1.503
 29V  C14  C15  single    1.509  0.020  1.509
 29V  C13  C20  single    1.499  0.020  1.499
 29V  C8   C7   double    1.338  0.020  1.338
 29V  O1   C15  double    1.205  0.020  1.205
 29V  C15  O2   single    1.330  0.020  1.330
 29V  C7   C2'  single    1.499  0.020  1.499
 29V  C7   C6   single    1.478  0.020  1.478
 29V  C1   C6   aromatic  1.400  0.020  1.400
 29V  C1   C2   aromatic  1.382  0.020  1.382
 29V  C2'  C1'  single    1.523  0.020  1.523
 29V  C6   C5   aromatic  1.405  0.020  1.405
 29V  C2   C3   aromatic  1.389  0.020  1.389
 29V  C1'  C18  single    1.526  0.020  1.526
 29V  C5   C18  single    1.518  0.020  1.518
 29V  C5   C4   aromatic  1.396  0.020  1.396
 29V  C3   C4   aromatic  1.385  0.020  1.385
 29V  C18  C4'  single    1.528  0.020  1.528
 29V  C4'  H1   single    0.970  0.020  1.090
 29V  C4'  H2   single    0.970  0.020  1.090
 29V  C4'  H3   single    0.970  0.020  1.090
 29V  C1'  H4   single    0.970  0.020  1.090
 29V  C1'  H5   single    0.970  0.020  1.090
 29V  C2'  H6   single    0.970  0.020  1.090
 29V  C2'  H7   single    0.970  0.020  1.090
 29V  C8   H8   single    0.930  0.020  1.080
 29V  C4   H9   single    0.930  0.020  1.080
 29V  C2   H10  single    0.930  0.020  1.080
 29V  C18  H11  single    0.970  0.020  1.090
 29V  C3   H12  single    0.930  0.020  1.080
 29V  C1   H13  single    0.930  0.020  1.080
 29V  C19  H14  single    0.970  0.020  1.090
 29V  C19  H15  single    0.970  0.020  1.090
 29V  C19  H16  single    0.970  0.020  1.090
 29V  C10  H17  single    0.930  0.020  1.080
 29V  C11  H18  single    0.970  0.020  1.090
 29V  C11  H19  single    0.970  0.020  1.090
 29V  C12  H20  single    0.930  0.020  1.080
 29V  C20  H21  single    0.970  0.020  1.090
 29V  C20  H22  single    0.970  0.020  1.090
 29V  C20  H23  single    0.970  0.020  1.090
 29V  C14  H24  single    0.970  0.020  1.090
 29V  C14  H25  single    0.970  0.020  1.090
 29V  O2   H26  single    0.850  0.020  0.980

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
 29V  H3   C4'  H2   107.97  3.000
 29V  H3   C4'  H1   107.83  3.000
 29V  H2   C4'  H1   107.26  3.000
 29V  H3   C4'  C18  110.91  3.000
 29V  H2   C4'  C18  112.78  3.000
 29V  H1   C4'  C18  109.90  3.000
 29V  H5   C1'  H4   106.65  3.000
 29V  H5   C1'  C18  109.05  3.000
 29V  H4   C1'  C18  109.83  3.000
 29V  H5   C1'  C2'  110.63  3.000
 29V  H4   C1'  C2'  108.90  3.000
 29V  C18  C1'  C2'  111.65  3.000
 29V  H7   C2'  H6   107.39  3.000
 29V  H7   C2'  C7   111.01  3.000
 29V  H6   C2'  C7   110.23  3.000
 29V  H7   C2'  C1'  110.61  3.000
 29V  H6   C2'  C1'  109.41  3.000
 29V  C7   C2'  C1'  108.18  3.000
 29V  H8   C8   C9   115.59  3.000
 29V  H8   C8   C7   119.22  3.000
 29V  C9   C8   C7   125.19  3.000
 29V  C18  C5   C4   119.34  3.000
 29V  C4   C5   C6   118.55  3.000
 29V  C18  C5   C6   122.08  3.000
 29V  C7   C6   C1   120.69  3.000
 29V  C1   C6   C5   119.02  3.000
 29V  C7   C6   C5   120.27  3.000
 29V  H9   C4   C3   118.71  3.000
 29V  H9   C4   C5   119.45  3.000
 29V  C3   C4   C5   121.84  3.000
 29V  H10  C2   C1   120.05  3.000
 29V  H10  C2   C3   120.51  3.000
 29V  C1   C2   C3   119.43  3.000
 29V  H11  C18  C5   106.41  3.000
 29V  H11  C18  C1'  107.09  3.000
 29V  C5   C18  C1'  112.48  3.000
 29V  H11  C18  C4'  107.69  3.000
 29V  C5   C18  C4'  112.91  3.000
 29V  C1'  C18  C4'  109.92  3.000
 29V  H12  C3   C2   120.49  3.000
 29V  H12  C3   C4   119.97  3.000
 29V  C2   C3   C4   119.54  3.000
 29V  H13  C1   C2   118.88  3.000
 29V  H13  C1   C6   119.51  3.000
 29V  C2   C1   C6   121.60  3.000
 29V  C6   C7   C8   122.30  3.000
 29V  C6   C7   C2'  114.62  3.000
 29V  C8   C7   C2'  122.96  3.000
 29V  C10  C9   C19  122.19  3.000
 29V  C10  C9   C8   122.03  3.000
 29V  C19  C9   C8   115.74  3.000
 29V  H16  C19  H15  108.21  3.000
 29V  H16  C19  H14  106.46  3.000
 29V  H15  C19  H14  108.15  3.000
 29V  H16  C19  C9   111.10  3.000
 29V  H15  C19  C9   111.91  3.000
 29V  H14  C19  C9   110.78  3.000
 29V  H17  C10  C11  115.71  3.000
 29V  H17  C10  C9   118.62  3.000
 29V  C11  C10  C9   125.66  3.000
 29V  H19  C11  H18  106.41  3.000
 29V  H19  C11  C12  109.11  3.000
 29V  H18  C11  C12  111.35  3.000
 29V  H19  C11  C10  109.78  3.000
 29V  H18  C11  C10  109.39  3.000
 29V  C12  C11  C10  110.70  3.000
 29V  H20  C12  C13  117.77  3.000
 29V  H20  C12  C11  114.09  3.000
 29V  C13  C12  C11  128.13  3.000
 29V  C14  C13  C20  115.09  3.000
 29V  C20  C13  C12  125.21  3.000
 29V  C14  C13  C12  119.67  3.000
 29V  H23  C20  H22  107.48  3.000
 29V  H23  C20  H21  107.83  3.000
 29V  H22  C20  H21  106.56  3.000
 29V  H23  C20  C13  113.20  3.000
 29V  H22  C20  C13  111.09  3.000
 29V  H21  C20  C13  110.39  3.000
 29V  H25  C14  H24  105.79  3.000
 29V  H25  C14  C15  107.05  3.000
 29V  H24  C14  C15  108.55  3.000
 29V  H25  C14  C13  110.89  3.000
 29V  H24  C14  C13  110.81  3.000
 29V  C15  C14  C13  113.38  3.000
 29V  O2   C15  O1   123.15  3.000
 29V  O2   C15  C14  111.56  3.000
 29V  O1   C15  C14  125.27  3.000
 29V  H26  O2   C15  110.00  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
 29V  CONST_01  C2   C1   C6   C5     0.00   0.0  0
 29V  CONST_02  C2   C3   C4   C5     0.00   0.0  0
 29V  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 29V  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 29V  CONST_05  C1   C6   C5   C4     0.00   0.0  0
 29V  CONST_06  C1   C2   C3   C4     0.00   0.0  0
 29V  CONST_07  H13  C1   C6   C5   180.00   0.0  0
 29V  CONST_08  H12  C3   C4   C5   180.00   0.0  0
 29V  CONST_09  H10  C2   C1   C6   180.00   0.0  0
 29V  CONST_10  H9   C4   C5   C6   180.00   0.0  0
 29V  CONST_11  H26  O2   C15  C14  180.00   0.0  0
 29V  Var_01    C6   C7   C2'  C1'   52.23  30.0  1
 29V  Var_02    C1   C6   C7   C2'  156.47  30.0  1
 29V  Var_03    C7   C2'  C1'  C18  -63.25  30.0  1
 29V  Var_04    C9   C8   C7   C2'   -5.72  30.0  2
 29V  Var_05    C19  C9   C8   C7   -80.41  30.0  2
 29V  Var_06    C11  C10  C9   C8    -1.58   0.0  2
 29V  Var_07    C14  C13  C12  C11  179.73   0.0  2
 29V  Var_08    C12  C11  C10  C9   104.16  30.0  3
 29V  Var_09    C13  C12  C11  C10  112.20  30.0  2
 29V  Var_10    C15  C14  C13  C12  108.80  30.0  2
 29V  Var_11    O1   C15  C14  C13  -12.59  30.0  3
 29V  Var_12    H14  C19  C9   C8    61.57  30.0  3
 29V  Var_13    H21  C20  C13  C12  117.50  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
 29V  chir_01  C18  C1'  C5  C4'  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
 29V  plan-1  C14  0.020
 29V  plan-1  C15  0.020
 29V  plan-1  O1   0.020
 29V  plan-1  O2   0.020
 29V  plan-1  H26  0.020
 29V  plan-2  C5   0.020
 29V  plan-2  C6   0.020
 29V  plan-2  C4   0.020
 29V  plan-2  C2   0.020
 29V  plan-2  C18  0.020
 29V  plan-2  C3   0.020
 29V  plan-2  C1   0.020
 29V  plan-2  C7   0.020
 29V  plan-2  H9   0.020
 29V  plan-2  H10  0.020
 29V  plan-2  H12  0.020
 29V  plan-2  H13  0.020
 29V  plan-3  C8   0.020
 29V  plan-3  C9   0.020
 29V  plan-3  C19  0.020
 29V  plan-3  C10  0.020
 29V  plan-3  C11  0.020
 29V  plan-3  H17  0.020
 29V  plan-4  C11  0.020
 29V  plan-4  C12  0.020
 29V  plan-4  C13  0.020
 29V  plan-4  C20  0.020
 29V  plan-4  C14  0.020
 29V  plan-4  H20  0.020

