# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:15:04 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2E,4E,6Z,8E)-3,7-dimethyl-8-(6-methyl-3,4-dihydronaphthalen-1(2H)-ylidene)octa-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/C=C/C=C(C)\C=C1/CCCc2cc(C)ccc12)=C\C(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
 2VZ  2VZ  '(2E,4E,6Z,8E)-3,7-dimethyl-8-(6-methyl-3,4-dihydronaphthalen-1(2H)-ylidene)octa-2,4,6-trienoic acid'  ligand  46  23  .  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_2VZ
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
 2VZ  C2'  C  CH2    0  -0.535  -2.9389  -2.3858  -0.7521
 2VZ  C1'  C  CH2    0  -0.447  -3.5268  -1.8508  -2.0565
 2VZ  C18  C  CH2    0  -0.500  -4.5384  -0.7542  -1.7727
 2VZ  C5   C  CR6    0   0.074  -4.0605   0.2367  -0.7436
 2VZ  C4   C  CR16   0  -0.343  -4.7610   1.4311  -0.5901
 2VZ  C3   C  CR6    0   0.099  -4.4120   2.3857   0.3555
 2VZ  C6'  C  CH3    0  -0.723  -5.2122   3.6435   0.5237
 2VZ  C2   C  CR16   0  -0.302  -3.3132   2.1148   1.1711
 2VZ  C1   C  CR16   0  -0.304  -2.6051   0.9370   1.0329
 2VZ  C6   C  CR6    0   0.083  -2.9460  -0.0213   0.0692
 2VZ  C7   C  C      0   0.097  -2.1822  -1.2801  -0.0739
 2VZ  C8   C  C1     0  -0.396  -0.8894  -1.3339   0.3105
 2VZ  C9   C  C      0   0.109   0.0329  -2.4601   0.3978
 2VZ  C19  C  CH3    0  -0.756  -0.4662  -3.8740   0.5345
 2VZ  C10  C  C1     0  -0.288   1.3724  -2.2505   0.4526
 2VZ  C11  C  C1     0  -0.250   2.0752  -0.9992   0.3092
 2VZ  C12  C  C1     0  -0.286   3.4137  -0.9083   0.4404
 2VZ  C13  C  C      0   0.168   4.2092   0.3057   0.3113
 2VZ  C20  C  CH3    0  -0.771   3.4869   1.5752  -0.0300
 2VZ  C14  C  C1     0  -0.480   5.5422   0.1929   0.4875
 2VZ  C15  C  C      0   0.393   6.6299   1.2358   0.3972
 2VZ  O1   O  OC    -1  -0.617   7.7844   0.7646   0.3066
 2VZ  O2   O  O      0  -0.593   6.3337   2.4483   0.4244
 2VZ  H1   H  HCH2   0   0.240  -3.7550  -2.7388  -0.1110
 2VZ  H2   H  HCH2   0   0.259  -2.3053  -3.2416  -0.9607
 2VZ  H3   H  HCH2   0   0.231  -2.7171  -1.4668  -2.6834
 2VZ  H4   H  HCH2   0   0.243  -4.0010  -2.6607  -2.6133
 2VZ  H5   H  HCH2   0   0.250  -4.8050  -0.2296  -2.6931
 2VZ  H6   H  HCH2   0   0.246  -5.4674  -1.2064  -1.4085
 2VZ  H7   H  HCR6   0   0.237  -5.6112   1.6156  -1.2397
 2VZ  H8   H  HCH3   0   0.248  -6.0103   3.5014   1.2557
 2VZ  H9   H  HCH3   0   0.243  -4.5940   4.4675   0.8794
 2VZ  H10  H  HCH3   0   0.243  -5.6815   3.9500  -0.4108
 2VZ  H11  H  HCR6   0   0.244  -3.0151   2.8294   1.9295
 2VZ  H12  H  HCR6   0   0.244  -1.7797   0.7530   1.7088
 2VZ  H13  H  H      0   0.231  -0.4581  -0.3939   0.6353
 2VZ  H14  H  HCH3   0   0.246  -0.7050  -4.3266  -0.4295
 2VZ  H15  H  HCH3   0   0.253   0.2957  -4.5017   0.9959
 2VZ  H16  H  HCH3   0   0.242  -1.3660  -3.9270   1.1477
 2VZ  H17  H  H      0   0.234   2.0054  -3.1200   0.6105
 2VZ  H18  H  H      0   0.250   1.5048  -0.1077   0.0739
 2VZ  H19  H  H      0   0.234   3.9662  -1.8173   0.6670
 2VZ  H20  H  HCH3   0   0.231   2.7245   1.8029   0.7186
 2VZ  H21  H  HCH3   0   0.271   4.1710   2.4132  -0.0893
 2VZ  H22  H  HCH3   0   0.232   2.9661   1.4751  -0.9852
 2VZ  H23  H  H      0   0.216   5.9132  -0.8069   0.7013

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
 2VZ  C19  C9   single    1.506  0.020  1.506
 2VZ  C10  C9   double    1.357  0.020  1.357
 2VZ  C10  C11  single    1.442  0.020  1.442
 2VZ  C12  C11  double    1.348  0.020  1.348
 2VZ  C12  C13  single    1.457  0.020  1.457
 2VZ  C9   C8   single    1.458  0.020  1.458
 2VZ  C14  C13  double    1.349  0.020  1.349
 2VZ  C14  C15  single    1.510  0.020  1.510
 2VZ  C13  C20  single    1.500  0.020  1.500
 2VZ  O2   C15  deloc     1.249  0.020  1.249
 2VZ  C15  O1   deloc     1.250  0.020  1.250
 2VZ  C2'  C1'  single    1.528  0.020  1.528
 2VZ  C2'  C7   single    1.502  0.020  1.502
 2VZ  C8   C7   double    1.350  0.020  1.350
 2VZ  C1'  C18  single    1.519  0.020  1.519
 2VZ  C7   C6   single    1.479  0.020  1.479
 2VZ  C18  C5   single    1.506  0.020  1.506
 2VZ  C6   C5   aromatic  1.403  0.020  1.403
 2VZ  C6   C1   aromatic  1.401  0.020  1.401
 2VZ  C5   C4   aromatic  1.393  0.020  1.393
 2VZ  C1   C2   aromatic  1.381  0.020  1.381
 2VZ  C4   C3   aromatic  1.388  0.020  1.388
 2VZ  C2   C3   aromatic  1.395  0.020  1.395
 2VZ  C3   C6'  single    1.500  0.020  1.500
 2VZ  C2'  H1   single    0.970  0.020  1.090
 2VZ  C2'  H2   single    0.970  0.020  1.090
 2VZ  C1'  H3   single    0.970  0.020  1.090
 2VZ  C1'  H4   single    0.970  0.020  1.090
 2VZ  C18  H5   single    0.970  0.020  1.090
 2VZ  C18  H6   single    0.970  0.020  1.090
 2VZ  C4   H7   single    0.930  0.020  1.080
 2VZ  C6'  H8   single    0.970  0.020  1.090
 2VZ  C6'  H9   single    0.970  0.020  1.090
 2VZ  C6'  H10  single    0.970  0.020  1.090
 2VZ  C2   H11  single    0.930  0.020  1.080
 2VZ  C1   H12  single    0.930  0.020  1.080
 2VZ  C8   H13  single    0.930  0.020  1.080
 2VZ  C19  H14  single    0.970  0.020  1.090
 2VZ  C19  H15  single    0.970  0.020  1.090
 2VZ  C19  H16  single    0.970  0.020  1.090
 2VZ  C10  H17  single    0.930  0.020  1.080
 2VZ  C11  H18  single    0.930  0.020  1.080
 2VZ  C12  H19  single    0.930  0.020  1.080
 2VZ  C20  H20  single    0.970  0.020  1.090
 2VZ  C20  H21  single    0.970  0.020  1.090
 2VZ  C20  H22  single    0.970  0.020  1.090
 2VZ  C14  H23  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
 2VZ  H2   C2'  H1   107.05  3.000
 2VZ  H2   C2'  C7   111.92  3.000
 2VZ  H1   C2'  C7   110.38  3.000
 2VZ  H2   C2'  C1'  109.68  3.000
 2VZ  H1   C2'  C1'  109.00  3.000
 2VZ  C7   C2'  C1'  108.77  3.000
 2VZ  H4   C1'  H3   106.85  3.000
 2VZ  H4   C1'  C18  109.98  3.000
 2VZ  H3   C1'  C18  110.29  3.000
 2VZ  H4   C1'  C2'  110.06  3.000
 2VZ  H3   C1'  C2'  109.12  3.000
 2VZ  C18  C1'  C2'  110.46  3.000
 2VZ  H6   C18  H5   105.74  3.000
 2VZ  H6   C18  C5   108.27  3.000
 2VZ  H5   C18  C5   109.70  3.000
 2VZ  H6   C18  C1'  109.21  3.000
 2VZ  H5   C18  C1'  110.60  3.000
 2VZ  C5   C18  C1'  113.04  3.000
 2VZ  C6   C5   C4   119.55  3.000
 2VZ  C4   C5   C18  118.67  3.000
 2VZ  C6   C5   C18  121.78  3.000
 2VZ  H7   C4   C3   119.18  3.000
 2VZ  H7   C4   C5   118.27  3.000
 2VZ  C3   C4   C5   122.55  3.000
 2VZ  C2   C3   C6'  121.15  3.000
 2VZ  C6'  C3   C4   121.25  3.000
 2VZ  C2   C3   C4   117.57  3.000
 2VZ  H10  C6'  H9   108.15  3.000
 2VZ  H10  C6'  H8   107.25  3.000
 2VZ  H9   C6'  H8   107.10  3.000
 2VZ  H10  C6'  C3   111.68  3.000
 2VZ  H9   C6'  C3   111.59  3.000
 2VZ  H8   C6'  C3   110.85  3.000
 2VZ  H11  C2   C1   119.42  3.000
 2VZ  H11  C2   C3   119.86  3.000
 2VZ  C1   C2   C3   120.72  3.000
 2VZ  H12  C1   C6   119.91  3.000
 2VZ  H12  C1   C2   118.25  3.000
 2VZ  C6   C1   C2   121.83  3.000
 2VZ  C7   C6   C1   121.53  3.000
 2VZ  C1   C6   C5   117.76  3.000
 2VZ  C7   C6   C5   120.70  3.000
 2VZ  C8   C7   C6   120.06  3.000
 2VZ  C6   C7   C2'  114.21  3.000
 2VZ  C8   C7   C2'  125.58  3.000
 2VZ  H13  C8   C9   113.58  3.000
 2VZ  H13  C8   C7   115.59  3.000
 2VZ  C9   C8   C7   130.81  3.000
 2VZ  C10  C9   C19  117.95  3.000
 2VZ  C10  C9   C8   120.50  3.000
 2VZ  C19  C9   C8   121.40  3.000
 2VZ  H16  C19  H15  108.11  3.000
 2VZ  H16  C19  H14  107.22  3.000
 2VZ  H15  C19  H14  106.75  3.000
 2VZ  H16  C19  C9   111.74  3.000
 2VZ  H15  C19  C9   110.34  3.000
 2VZ  H14  C19  C9   112.44  3.000
 2VZ  H17  C10  C11  115.13  3.000
 2VZ  H17  C10  C9   117.20  3.000
 2VZ  C11  C10  C9   127.66  3.000
 2VZ  H18  C11  C12  119.21  3.000
 2VZ  H18  C11  C10  118.59  3.000
 2VZ  C12  C11  C10  122.19  3.000
 2VZ  H19  C12  C13  115.94  3.000
 2VZ  H19  C12  C11  117.93  3.000
 2VZ  C13  C12  C11  126.13  3.000
 2VZ  C14  C13  C20  125.18  3.000
 2VZ  C20  C13  C12  117.54  3.000
 2VZ  C14  C13  C12  117.27  3.000
 2VZ  H22  C20  H21  108.91  3.000
 2VZ  H22  C20  H20  106.60  3.000
 2VZ  H21  C20  H20  108.48  3.000
 2VZ  H22  C20  C13  110.55  3.000
 2VZ  H21  C20  C13  111.28  3.000
 2VZ  H20  C20  C13  110.88  3.000
 2VZ  H23  C14  C15  113.65  3.000
 2VZ  H23  C14  C13  116.07  3.000
 2VZ  C15  C14  C13  130.26  3.000
 2VZ  O2   C15  O1   125.92  3.000
 2VZ  O1   C15  C14  114.16  3.000
 2VZ  O2   C15  C14  119.91  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
 2VZ  CONST_01  C2   C1   C6   C5     0.00   0.0  0
 2VZ  CONST_02  C2   C3   C4   C5     0.00   0.0  0
 2VZ  CONST_03  C1   C6   C5   C4     0.00   0.0  0
 2VZ  CONST_04  C1   C2   C3   C4     0.00   0.0  0
 2VZ  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 2VZ  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 2VZ  CONST_07  C6'  C3   C4   C5   180.00   0.0  0
 2VZ  CONST_08  C1   C2   C3   C6'  180.00   0.0  0
 2VZ  CONST_09  H7   C4   C5   C18    0.00   0.0  0
 2VZ  CONST_10  H12  C1   C6   C5   180.00   0.0  0
 2VZ  CONST_11  H11  C2   C3   C4   180.00   0.0  0
 2VZ  Var_01    C5   C18  C1'  C2'   44.79  30.0  1
 2VZ  Var_02    C5   C6   C7   C2'  -20.27  30.0  1
 2VZ  Var_03    C6   C7   C2'  C1'   50.78  30.0  1
 2VZ  Var_04    C6   C5   C18  C1'  -13.83  30.0  1
 2VZ  Var_05    C7   C2'  C1'  C18  -63.71  30.0  1
 2VZ  Var_06    C9   C8   C7   C2'  -11.48  30.0  2
 2VZ  Var_07    H8   C6'  C3   C4    89.91  30.0  2
 2VZ  Var_08    C19  C9   C8   C7   -22.99  30.0  2
 2VZ  Var_09    C11  C10  C9   C8    -6.41   0.0  2
 2VZ  Var_10    C13  C12  C11  C10  179.88   0.0  2
 2VZ  Var_11    C15  C14  C13  C12  178.71   0.0  2
 2VZ  Var_12    C12  C11  C10  C9   177.09  30.0  2
 2VZ  Var_13    C14  C13  C12  C11  179.57  30.0  2
 2VZ  Var_14    O2   C15  C14  C13   16.25  30.0  2
 2VZ  Var_15    H14  C19  C9   C8    84.92  30.0  3
 2VZ  Var_16    H20  C20  C13  C12   58.50  30.0  3

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
 2VZ  plan-1  C14  0.020
 2VZ  plan-1  C15  0.020
 2VZ  plan-1  O1   0.020
 2VZ  plan-1  O2   0.020
 2VZ  plan-2  C18  0.020
 2VZ  plan-2  C5   0.020
 2VZ  plan-2  C4   0.020
 2VZ  plan-2  C3   0.020
 2VZ  plan-2  C6'  0.020
 2VZ  plan-2  C2   0.020
 2VZ  plan-2  C1   0.020
 2VZ  plan-2  C6   0.020
 2VZ  plan-2  C7   0.020
 2VZ  plan-2  H7   0.020
 2VZ  plan-2  H11  0.020
 2VZ  plan-2  H12  0.020
 2VZ  plan-3  C8   0.020
 2VZ  plan-3  C9   0.020
 2VZ  plan-3  C19  0.020
 2VZ  plan-3  C10  0.020
 2VZ  plan-3  C11  0.020
 2VZ  plan-3  H17  0.020
 2VZ  plan-4  C10  0.020
 2VZ  plan-4  C11  0.020
 2VZ  plan-4  C12  0.020
 2VZ  plan-4  C13  0.020
 2VZ  plan-4  H18  0.020
 2VZ  plan-4  H19  0.020
 2VZ  plan-5  C12  0.020
 2VZ  plan-5  C13  0.020
 2VZ  plan-5  C20  0.020
 2VZ  plan-5  C14  0.020
 2VZ  plan-5  C15  0.020
 2VZ  plan-5  H23  0.020

