# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:57:56 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2E,4E,6Z,8E)-3,7-dimethyl-8-(7-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/CCCc2ccc(C)cc12)=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
 2VP  2VP  '(2E,4E,6Z,8E)-3,7-dimethyl-8-(7-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_2VP
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
 2VP  C2'  C  CH2    0  -0.526  -2.4808  -2.1263  -0.8622
 2VP  C1'  C  CH2    0  -0.446  -2.6249  -1.5280  -2.2583
 2VP  C18  C  CH2    0  -0.500  -3.7702  -0.5310  -2.2883
 2VP  C5   C  CR6    0   0.032  -3.7408   0.4295  -1.1280
 2VP  C4   C  CR16   0  -0.283  -4.5040   1.5946  -1.1898
 2VP  C3   C  CR16   0  -0.301  -4.5392   2.4958  -0.1422
 2VP  C2   C  CR6    0   0.106  -3.8096   2.2525   1.0228
 2VP  C7'  C  CH3    0  -0.723  -3.8702   3.2064   2.1808
 2VP  C1   C  CR16   0  -0.377  -3.0506   1.0952   1.0838
 2VP  C6   C  CR6    0   0.133  -2.9845   0.1795   0.0247
 2VP  C7   C  C      0   0.101  -2.1474  -1.0378   0.1186
 2VP  C8   C  C1     0  -0.396  -1.1098  -1.1200   0.9643
 2VP  C9   C  C      0   0.061  -0.2596  -2.3073   1.1838
 2VP  C19  C  CH3    0  -0.719  -0.9177  -3.5363   1.7411
 2VP  C10  C  C1     0  -0.275   1.0745  -2.2579   1.0089
 2VP  C11  C  C1     0  -0.247   1.8065  -1.1155   0.5125
 2VP  C12  C  C1     0  -0.289   3.1469  -1.0992   0.3906
 2VP  C13  C  C      0   0.172   3.9472   0.0217  -0.0895
 2VP  C20  C  CH3    0  -0.773   3.2143   1.2677  -0.4888
 2VP  C14  C  C1     0  -0.487   5.2850  -0.1459  -0.1371
 2VP  C15  C  C      0   0.393   6.3776   0.8073  -0.5566
 2VP  O2   O  O      0  -0.593   6.0940   1.9800  -0.8802
 2VP  O1   O  OC    -1  -0.618   7.5261   0.3131  -0.5369
 2VP  H1   H  HCH2   0   0.241  -3.4221  -2.6134  -0.5828
 2VP  H2   H  HCH2   0   0.249  -1.7087  -2.8952  -0.8681
 2VP  H3   H  HCH2   0   0.229  -1.6892  -1.0358  -2.5383
 2VP  H4   H  HCH2   0   0.242  -2.7978  -2.3180  -2.9910
 2VP  H5   H  HCH2   0   0.249  -3.7691   0.0276  -3.2272
 2VP  H6   H  HCH2   0   0.244  -4.7206  -1.0760  -2.2655
 2VP  H7   H  HCR6   0   0.244  -5.0802   1.7987  -2.0857
 2VP  H8   H  HCR6   0   0.244  -5.1399   3.3943  -0.2255
 2VP  H9   H  HCH3   0   0.246  -4.8037   3.0964   2.7364
 2VP  H10  H  HCH3   0   0.242  -3.0517   3.0412   2.8803
 2VP  H11  H  HCH3   0   0.242  -3.8198   4.2423   1.8439
 2VP  H12  H  HCR6   0   0.238  -2.5043   0.8858   1.9958
 2VP  H13  H  H      0   0.251  -0.8494  -0.2473   1.5571
 2VP  H14  H  HCH3   0   0.244  -1.7787  -3.8494   1.1486
 2VP  H15  H  HCH3   0   0.239  -0.2222  -4.3735   1.7985
 2VP  H16  H  HCH3   0   0.244  -1.2946  -3.3420   2.7487
 2VP  H17  H  H      0   0.232   1.6600  -3.1401   1.2546
 2VP  H18  H  H      0   0.252   1.2303  -0.2405   0.2298
 2VP  H19  H  H      0   0.233   3.6990  -1.9898   0.6822
 2VP  H20  H  HCH3   0   0.232   2.6846   1.6931   0.3669
 2VP  H21  H  HCH3   0   0.272   3.8947   2.0132  -0.8815
 2VP  H22  H  HCH3   0   0.230   2.4564   1.0462  -1.2434
 2VP  H23  H  H      0   0.212   5.6568  -1.1163   0.1833

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
 2VP  C19  C9   single    1.501  0.020  1.501
 2VP  C10  C9   double    1.346  0.020  1.346
 2VP  C10  C11  single    1.445  0.020  1.445
 2VP  C12  C11  double    1.346  0.020  1.346
 2VP  C12  C13  single    1.459  0.020  1.459
 2VP  C9   C8   single    1.477  0.020  1.477
 2VP  C14  C13  double    1.349  0.020  1.349
 2VP  C14  C15  single    1.509  0.020  1.509
 2VP  C13  C20  single    1.500  0.020  1.500
 2VP  O2   C15  deloc     1.249  0.020  1.249
 2VP  C2'  C1'  single    1.526  0.020  1.526
 2VP  C2'  C7   single    1.503  0.020  1.503
 2VP  C15  O1   deloc     1.250  0.020  1.250
 2VP  C8   C7   double    1.341  0.020  1.341
 2VP  C1'  C18  single    1.519  0.020  1.519
 2VP  C7   C6   single    1.480  0.020  1.480
 2VP  C18  C5   single    1.507  0.020  1.507
 2VP  C6   C5   aromatic  1.401  0.020  1.401
 2VP  C6   C1   aromatic  1.402  0.020  1.402
 2VP  C5   C4   aromatic  1.394  0.020  1.394
 2VP  C1   C2   aromatic  1.385  0.020  1.385
 2VP  C4   C3   aromatic  1.382  0.020  1.382
 2VP  C2   C3   aromatic  1.396  0.020  1.396
 2VP  C2   C7'  single    1.502  0.020  1.502
 2VP  C2'  H1   single    0.970  0.020  1.090
 2VP  C2'  H2   single    0.970  0.020  1.090
 2VP  C1'  H3   single    0.970  0.020  1.090
 2VP  C1'  H4   single    0.970  0.020  1.090
 2VP  C18  H5   single    0.970  0.020  1.090
 2VP  C18  H6   single    0.970  0.020  1.090
 2VP  C4   H7   single    0.930  0.020  1.080
 2VP  C3   H8   single    0.930  0.020  1.080
 2VP  C7'  H9   single    0.970  0.020  1.090
 2VP  C7'  H10  single    0.970  0.020  1.090
 2VP  C7'  H11  single    0.970  0.020  1.090
 2VP  C1   H12  single    0.930  0.020  1.080
 2VP  C8   H13  single    0.930  0.020  1.080
 2VP  C19  H14  single    0.970  0.020  1.090
 2VP  C19  H15  single    0.970  0.020  1.090
 2VP  C19  H16  single    0.970  0.020  1.090
 2VP  C10  H17  single    0.930  0.020  1.080
 2VP  C11  H18  single    0.930  0.020  1.080
 2VP  C12  H19  single    0.930  0.020  1.080
 2VP  C20  H20  single    0.970  0.020  1.090
 2VP  C20  H21  single    0.970  0.020  1.090
 2VP  C20  H22  single    0.970  0.020  1.090
 2VP  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
 2VP  H2   C2'  H1   107.24  3.000
 2VP  H2   C2'  C7   110.95  3.000
 2VP  H1   C2'  C7   110.25  3.000
 2VP  H2   C2'  C1'  109.80  3.000
 2VP  H1   C2'  C1'  109.05  3.000
 2VP  C7   C2'  C1'  109.52  3.000
 2VP  H4   C1'  H3   106.82  3.000
 2VP  H4   C1'  C18  110.03  3.000
 2VP  H3   C1'  C18  110.16  3.000
 2VP  H4   C1'  C2'  110.21  3.000
 2VP  H3   C1'  C2'  109.26  3.000
 2VP  C18  C1'  C2'  110.29  3.000
 2VP  H6   C18  H5   105.85  3.000
 2VP  H6   C18  C5   108.54  3.000
 2VP  H5   C18  C5   109.62  3.000
 2VP  H6   C18  C1'  109.10  3.000
 2VP  H5   C18  C1'  110.60  3.000
 2VP  C5   C18  C1'  112.87  3.000
 2VP  C6   C5   C4   118.76  3.000
 2VP  C4   C5   C18  119.21  3.000
 2VP  C6   C5   C18  122.03  3.000
 2VP  H7   C4   C3   119.33  3.000
 2VP  H7   C4   C5   118.99  3.000
 2VP  C3   C4   C5   121.68  3.000
 2VP  H8   C3   C2   119.88  3.000
 2VP  H8   C3   C4   119.75  3.000
 2VP  C2   C3   C4   120.37  3.000
 2VP  C1   C2   C7'  121.26  3.000
 2VP  C7'  C2   C3   120.78  3.000
 2VP  C1   C2   C3   117.95  3.000
 2VP  H11  C7'  H10  107.92  3.000
 2VP  H11  C7'  H9   107.01  3.000
 2VP  H10  C7'  H9   107.48  3.000
 2VP  H11  C7'  C2   111.31  3.000
 2VP  H10  C7'  C2   111.63  3.000
 2VP  H9   C7'  C2   111.28  3.000
 2VP  H12  C1   C6   119.07  3.000
 2VP  H12  C1   C2   118.34  3.000
 2VP  C6   C1   C2   122.57  3.000
 2VP  C7   C6   C1   121.06  3.000
 2VP  C1   C6   C5   118.66  3.000
 2VP  C7   C6   C5   120.27  3.000
 2VP  C8   C7   C6   121.86  3.000
 2VP  C6   C7   C2'  115.40  3.000
 2VP  C8   C7   C2'  122.60  3.000
 2VP  H13  C8   C9   115.26  3.000
 2VP  H13  C8   C7   118.70  3.000
 2VP  C9   C8   C7   126.04  3.000
 2VP  C10  C9   C19  120.84  3.000
 2VP  C10  C9   C8   121.44  3.000
 2VP  C19  C9   C8   117.45  3.000
 2VP  H16  C19  H15  107.93  3.000
 2VP  H16  C19  H14  106.23  3.000
 2VP  H15  C19  H14  108.16  3.000
 2VP  H16  C19  C9   110.35  3.000
 2VP  H15  C19  C9   111.63  3.000
 2VP  H14  C19  C9   112.29  3.000
 2VP  H17  C10  C11  116.52  3.000
 2VP  H17  C10  C9   118.33  3.000
 2VP  C11  C10  C9   125.15  3.000
 2VP  H18  C11  C12  119.70  3.000
 2VP  H18  C11  C10  117.27  3.000
 2VP  C12  C11  C10  123.04  3.000
 2VP  H19  C12  C13  116.04  3.000
 2VP  H19  C12  C11  118.12  3.000
 2VP  C13  C12  C11  125.84  3.000
 2VP  C14  C13  C20  125.34  3.000
 2VP  C20  C13  C12  117.26  3.000
 2VP  C14  C13  C12  117.40  3.000
 2VP  H22  C20  H21  108.97  3.000
 2VP  H22  C20  H20  106.48  3.000
 2VP  H21  C20  H20  108.69  3.000
 2VP  H22  C20  C13  110.77  3.000
 2VP  H21  C20  C13  111.19  3.000
 2VP  H20  C20  C13  110.60  3.000
 2VP  H23  C14  C15  113.45  3.000
 2VP  H23  C14  C13  116.07  3.000
 2VP  C15  C14  C13  130.48  3.000
 2VP  O1   C15  O2   125.70  3.000
 2VP  O1   C15  C14  114.26  3.000
 2VP  O2   C15  C14  120.04  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
 2VP  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 2VP  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 2VP  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 2VP  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 2VP  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 2VP  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 2VP  CONST_07  C7'  C2   C3   C4    180.00   0.0  0
 2VP  CONST_08  C6   C1   C2   C7'   180.00   0.0  0
 2VP  CONST_09  H7   C4   C5   C18     0.00   0.0  0
 2VP  CONST_10  H12  C1   C6   C5    180.00   0.0  0
 2VP  CONST_11  H8   C3   C4   C5    180.00   0.0  0
 2VP  Var_01    C5   C18  C1'  C2'    46.83  30.0  1
 2VP  Var_02    C5   C6   C7   C2'   -17.60  30.0  1
 2VP  Var_03    C6   C7   C2'  C1'    47.32  30.0  1
 2VP  Var_04    C6   C5   C18  C1'   -17.12  30.0  1
 2VP  Var_05    C7   C2'  C1'  C18   -62.28  30.0  1
 2VP  Var_06    C9   C8   C7   C2'    -7.83  30.0  2
 2VP  Var_07    H9   C7'  C2   C3     76.25  30.0  2
 2VP  Var_08    C19  C9   C8   C7    -62.96  30.0  2
 2VP  Var_09    C11  C10  C9   C8     -4.54   0.0  2
 2VP  Var_10    C13  C12  C11  C10  -179.37   0.0  2
 2VP  Var_11    C15  C14  C13  C12  -178.95   0.0  2
 2VP  Var_12    C12  C11  C10  C9    178.01  30.0  2
 2VP  Var_13    C14  C13  C12  C11   179.70  30.0  2
 2VP  Var_14    O2   C15  C14  C13     3.17  30.0  2
 2VP  Var_15    H14  C19  C9   C8     54.30  30.0  3
 2VP  Var_16    H20  C20  C13  C12    62.38  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
 2VP  plan-1  C14  0.020
 2VP  plan-1  C15  0.020
 2VP  plan-1  O2   0.020
 2VP  plan-1  O1   0.020
 2VP  plan-2  C18  0.020
 2VP  plan-2  C5   0.020
 2VP  plan-2  C4   0.020
 2VP  plan-2  C3   0.020
 2VP  plan-2  C2   0.020
 2VP  plan-2  C7'  0.020
 2VP  plan-2  C1   0.020
 2VP  plan-2  C6   0.020
 2VP  plan-2  C7   0.020
 2VP  plan-2  H7   0.020
 2VP  plan-2  H8   0.020
 2VP  plan-2  H12  0.020
 2VP  plan-3  C8   0.020
 2VP  plan-3  C9   0.020
 2VP  plan-3  C19  0.020
 2VP  plan-3  C10  0.020
 2VP  plan-3  C11  0.020
 2VP  plan-3  H17  0.020
 2VP  plan-4  C10  0.020
 2VP  plan-4  C11  0.020
 2VP  plan-4  C12  0.020
 2VP  plan-4  C13  0.020
 2VP  plan-4  H18  0.020
 2VP  plan-4  H19  0.020
 2VP  plan-5  C12  0.020
 2VP  plan-5  C13  0.020
 2VP  plan-5  C20  0.020
 2VP  plan-5  C14  0.020
 2VP  plan-5  C15  0.020
 2VP  plan-5  H23  0.020

