# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:59:44 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  47  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  -0.523  -2.2052  -2.0299  -1.0438
 2VZ  C1'  C  CH2   0  -0.448  -2.2551  -1.1273  -2.2731
 2VZ  C18  C  CH2   0  -0.500  -3.4507  -0.1923  -2.1938
 2VZ  C5   C  CR6   0   0.073  -3.6047   0.4588  -0.8430
 2VZ  C4   C  CR16  0  -0.350  -4.4499   1.5613  -0.7197
 2VZ  C3   C  CR6   0   0.101  -4.6718   2.1981   0.4925
 2VZ  C6'  C  CH3   0  -0.725  -5.6001   3.3716   0.6029
 2VZ  C2   C  CR16  0  -0.297  -4.0175   1.6954   1.6192
 2VZ  C1   C  CR16  0  -0.304  -3.1748   0.6073   1.5163
 2VZ  C6   C  CR6   0   0.088  -2.9378  -0.0255   0.2894
 2VZ  C7   C  C     0   0.111  -2.0199  -1.1790   0.1791
 2VZ  C8   C  C1    0  -0.405  -1.0345  -1.3857   1.0628
 2VZ  C9   C  C     0   0.068  -0.1004  -2.5322   1.0537
 2VZ  C19  C  CH3   0  -0.717  -0.6697  -3.8696   1.4147
 2VZ  C10  C  C1    0  -0.275   1.2134  -2.3747   0.8060
 2VZ  C11  C  C1    0  -0.234   1.8291  -1.1219   0.4435
 2VZ  C12  C  C1    0  -0.285   3.1548  -0.9948   0.2403
 2VZ  C13  C  C     0   0.180   3.8699   0.2157  -0.1252
 2VZ  C20  C  CH3   0  -0.733   3.1168   1.4926  -0.3514
 2VZ  C14  C  C1    0  -0.456   5.2158   0.1082  -0.2343
 2VZ  C15  C  C     0   0.520   6.1348   1.1911  -0.5718
 2VZ  O1   O  OH1   0  -0.612   7.3946   0.7475  -0.6318
 2VZ  O2   O  O     0  -0.457   5.8510   2.3522  -0.7760
 2VZ  H1   H  HCH2  0   0.243  -3.1394  -2.5987  -0.9730
 2VZ  H2   H  HCH2  0   0.248  -1.3969  -2.7547  -1.1430
 2VZ  H3   H  HCH2  0   0.230  -1.3276  -0.5505  -2.3293
 2VZ  H4   H  HCH2  0   0.244  -2.3103  -1.7279  -3.1825
 2VZ  H5   H  HCH2  0   0.251  -3.3869   0.5766  -2.9671
 2VZ  H6   H  HCH2  0   0.246  -4.3641  -0.7578  -2.4092
 2VZ  H7   H  HCR6  0   0.239  -4.9494   1.9322  -1.6091
 2VZ  H8   H  HCH3  0   0.247  -6.5143   3.0990   1.1340
 2VZ  H9   H  HCH3  0   0.244  -5.1424   4.1912   1.1579
 2VZ  H10  H  HCH3  0   0.243  -5.8874   3.7494  -0.3775
 2VZ  H11  H  HCR6  0   0.245  -4.1779   2.1566   2.5868
 2VZ  H12  H  HCR6  0   0.245  -2.7042   0.2285   2.4150
 2VZ  H13  H  H     0   0.259  -0.8860  -0.6688   1.8654
 2VZ  H14  H  HCH3  0   0.248  -1.4819  -4.1491   0.7402
 2VZ  H15  H  HCH3  0   0.243   0.0848  -4.6549   1.3847
 2VZ  H16  H  HCH3  0   0.249  -1.1007  -3.8430   2.4185
 2VZ  H17  H  H     0   0.242   1.8646  -3.2420   0.8674
 2VZ  H18  H  H     0   0.260   1.1678  -0.2697   0.3320
 2VZ  H19  H  H     0   0.249   3.7722  -1.8801   0.3660
 2VZ  H20  H  HCH3  0   0.258   3.3478   2.2212   0.4258
 2VZ  H21  H  HCH3  0   0.259   3.3867   1.9465  -1.3023
 2VZ  H22  H  HCH3  0   0.245   2.0417   1.3398  -0.3489
 2VZ  H23  H  H     0   0.264   5.6704  -0.8586  -0.0523
 2VZ  H24  H  HOH1  0   0.477   7.9858   1.4813  -0.8533

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    1.498  0.020  1.498
 2VZ  C10  C9   double    1.346  0.020  1.346
 2VZ  C10  C11  single    1.442  0.020  1.442
 2VZ  C12  C11  double    1.347  0.020  1.347
 2VZ  C12  C13  single    1.453  0.020  1.453
 2VZ  C9   C8   single    1.479  0.020  1.479
 2VZ  C14  C13  double    1.355  0.020  1.355
 2VZ  C14  C15  single    1.460  0.020  1.460
 2VZ  C13  C20  single    1.500  0.020  1.500
 2VZ  O2   C15  double    1.213  0.020  1.213
 2VZ  C15  O1   single    1.337  0.020  1.337
 2VZ  C2'  C1'  single    1.526  0.020  1.526
 2VZ  C2'  C7   single    1.501  0.020  1.501
 2VZ  C8   C7   double    1.340  0.020  1.340
 2VZ  C1'  C18  single    1.520  0.020  1.520
 2VZ  C7   C6   single    1.478  0.020  1.478
 2VZ  C18  C5   single    1.507  0.020  1.507
 2VZ  C6   C5   aromatic  1.401  0.020  1.401
 2VZ  C6   C1   aromatic  1.401  0.020  1.401
 2VZ  C5   C4   aromatic  1.395  0.020  1.395
 2VZ  C1   C2   aromatic  1.380  0.020  1.380
 2VZ  C4   C3   aromatic  1.387  0.020  1.387
 2VZ  C2   C3   aromatic  1.397  0.020  1.397
 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
 2VZ  O1   H24  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
 2VZ  H2   C2'  H1   107.03  3.000
 2VZ  H2   C2'  C7   111.06  3.000
 2VZ  H1   C2'  C7   110.29  3.000
 2VZ  H2   C2'  C1'  110.13  3.000
 2VZ  H1   C2'  C1'  109.34  3.000
 2VZ  C7   C2'  C1'  108.96  3.000
 2VZ  H4   C1'  H3   106.88  3.000
 2VZ  H4   C1'  C18  110.01  3.000
 2VZ  H3   C1'  C18  110.21  3.000
 2VZ  H4   C1'  C2'  110.33  3.000
 2VZ  H3   C1'  C2'  109.01  3.000
 2VZ  C18  C1'  C2'  110.34  3.000
 2VZ  H6   C18  H5   105.83  3.000
 2VZ  H6   C18  C5   108.30  3.000
 2VZ  H5   C18  C5   109.65  3.000
 2VZ  H6   C18  C1'  109.15  3.000
 2VZ  H5   C18  C1'  110.49  3.000
 2VZ  C5   C18  C1'  113.13  3.000
 2VZ  C6   C5   C4   119.37  3.000
 2VZ  C4   C5   C18  118.86  3.000
 2VZ  C6   C5   C18  121.77  3.000
 2VZ  H7   C4   C3   119.06  3.000
 2VZ  H7   C4   C5   118.46  3.000
 2VZ  C3   C4   C5   122.49  3.000
 2VZ  C2   C3   C6'  120.80  3.000
 2VZ  C6'  C3   C4   121.49  3.000
 2VZ  C2   C3   C4   117.70  3.000
 2VZ  H10  C6'  H9   107.95  3.000
 2VZ  H10  C6'  H8   107.68  3.000
 2VZ  H9   C6'  H8   106.95  3.000
 2VZ  H10  C6'  C3   111.61  3.000
 2VZ  H9   C6'  C3   111.44  3.000
 2VZ  H8   C6'  C3   111.01  3.000
 2VZ  H11  C2   C1   119.50  3.000
 2VZ  H11  C2   C3   119.86  3.000
 2VZ  C1   C2   C3   120.65  3.000
 2VZ  H12  C1   C6   119.69  3.000
 2VZ  H12  C1   C2   118.64  3.000
 2VZ  C6   C1   C2   121.65  3.000
 2VZ  C7   C6   C1   121.53  3.000
 2VZ  C1   C6   C5   118.13  3.000
 2VZ  C7   C6   C5   120.35  3.000
 2VZ  C8   C7   C6   121.87  3.000
 2VZ  C6   C7   C2'  115.24  3.000
 2VZ  C8   C7   C2'  122.73  3.000
 2VZ  H13  C8   C9   115.46  3.000
 2VZ  H13  C8   C7   119.08  3.000
 2VZ  C9   C8   C7   125.46  3.000
 2VZ  C10  C9   C19  121.32  3.000
 2VZ  C10  C9   C8   121.80  3.000
 2VZ  C19  C9   C8   116.79  3.000
 2VZ  H16  C19  H15  108.43  3.000
 2VZ  H16  C19  H14  106.28  3.000
 2VZ  H15  C19  H14  108.28  3.000
 2VZ  H16  C19  C9   110.46  3.000
 2VZ  H15  C19  C9   111.95  3.000
 2VZ  H14  C19  C9   111.24  3.000
 2VZ  H17  C10  C11  116.86  3.000
 2VZ  H17  C10  C9   118.77  3.000
 2VZ  C11  C10  C9   124.37  3.000
 2VZ  H18  C11  C12  120.69  3.000
 2VZ  H18  C11  C10  116.62  3.000
 2VZ  C12  C11  C10  122.68  3.000
 2VZ  H19  C12  C13  115.36  3.000
 2VZ  H19  C12  C11  117.70  3.000
 2VZ  C13  C12  C11  126.95  3.000
 2VZ  C14  C13  C20  123.67  3.000
 2VZ  C20  C13  C12  120.01  3.000
 2VZ  C14  C13  C12  116.32  3.000
 2VZ  H22  C20  H21  107.84  3.000
 2VZ  H22  C20  H20  107.59  3.000
 2VZ  H21  C20  H20  106.96  3.000
 2VZ  H22  C20  C13  112.15  3.000
 2VZ  H21  C20  C13  111.26  3.000
 2VZ  H20  C20  C13  110.80  3.000
 2VZ  H23  C14  C15  115.89  3.000
 2VZ  H23  C14  C13  118.29  3.000
 2VZ  C15  C14  C13  125.82  3.000
 2VZ  O2   C15  O1   122.05  3.000
 2VZ  O1   C15  C14  110.94  3.000
 2VZ  O2   C15  C14  127.01  3.000
 2VZ  H24  O1   C15  109.53  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  CONST_12  H24  O1   C15  C14   180.00   0.0  0
 2VZ  Var_01    C5   C18  C1'  C2'    45.95  30.0  1
 2VZ  Var_02    C5   C6   C7   C2'   -19.31  30.0  1
 2VZ  Var_03    C6   C7   C2'  C1'    49.08  30.0  1
 2VZ  Var_04    C6   C5   C18  C1'   -15.90  30.0  1
 2VZ  Var_05    C7   C2'  C1'  C18   -62.68  30.0  1
 2VZ  Var_06    C9   C8   C7   C2'    -6.96  30.0  2
 2VZ  Var_07    H8   C6'  C3   C4    108.84  30.0  2
 2VZ  Var_08    C19  C9   C8   C7    -70.38  30.0  2
 2VZ  Var_09    C11  C10  C9   C8     -4.24   0.0  2
 2VZ  Var_10    C13  C12  C11  C10  -179.97   0.0  2
 2VZ  Var_11    C15  C14  C13  C12  -179.18   0.0  2
 2VZ  Var_12    C12  C11  C10  C9    178.04  30.0  2
 2VZ  Var_13    C14  C13  C12  C11   177.98  30.0  2
 2VZ  Var_14    O2   C15  C14  C13     1.82  30.0  2
 2VZ  Var_15    H14  C19  C9   C8     58.82  30.0  3
 2VZ  Var_16    H20  C20  C13  C12   112.08  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-1  H24  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

