# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:34:40 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2E,4E,6Z,8E)-3,7-dimethyl-8-(6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-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=C\1CCCCc2ccccc\12)=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
 3RB  3RB  '(2E,4E,6Z,8E)-3,7-dimethyl-8-(6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-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_3RB
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
 3RB  C4   C  CR16  0  -0.321  -3.7810   2.5744  -0.1679
 3RB  C5   C  CR6   0   0.116  -2.8431   1.5815   0.1014
 3RB  C6   C  CR6   0   0.034  -3.1267   0.2648  -0.2868
 3RB  C7   C  C     0   0.076  -2.1716  -0.8367  -0.0103
 3RB  C8   C  C1    0  -0.342  -1.7158  -1.5762  -1.0275
 3RB  C10  C  C1    0  -0.268   0.4888  -2.6549  -0.6614
 3RB  C13  C  C     0   0.207   3.2954  -0.1461  -0.0164
 3RB  C15  C  C     0   0.523   5.5844   0.7618   0.5571
 3RB  C20  C  CH3   0  -0.777   2.5965   1.1616  -0.2240
 3RB  C21  C  CH2   0  -0.428  -1.3405   1.3099   2.1506
 3RB  C2'  C  CH2   0  -0.497  -1.8575  -1.1164   1.4367
 3RB  C1'  C  CH2   0  -0.435  -0.8898  -0.1437   2.1122
 3RB  C18  C  CH2   0  -0.537  -1.5463   1.9445   0.7734
 3RB  C3   C  CR16  0  -0.252  -4.9814   2.2879  -0.8048
 3RB  C2   C  CR16  0  -0.262  -5.2576   0.9852  -1.1902
 3RB  C1   C  CR16  0  -0.288  -4.3317  -0.0155  -0.9289
 3RB  C9   C  C     0   0.055  -0.8277  -2.7498  -0.9214
 3RB  C19  C  CH3   0  -0.715  -1.4856  -4.0711  -1.1740
 3RB  C11  C  C1    0  -0.222   1.2125  -1.4171  -0.5008
 3RB  C12  C  C1    0  -0.298   2.5194  -1.3646  -0.1811
 3RB  C14  C  C1    0  -0.475   4.5971  -0.2943   0.3222
 3RB  O1   O  OH1   0  -0.608   6.7837   0.2282   0.8061
 3RB  O2   O  O     0  -0.453   5.4086   1.9612   0.5471
 3RB  H1   H  HCR6  0   0.247  -3.5616   3.5958   0.1211
 3RB  H2   H  H     0   0.259  -2.0637  -1.3462  -2.0329
 3RB  H3   H  H     0   0.242   1.0701  -3.5705  -0.5963
 3RB  H4   H  HCH3  0   0.250   1.8395   1.3050   0.5507
 3RB  H5   H  HCH3  0   0.281   3.2697   2.0084  -0.1923
 3RB  H6   H  HCH3  0   0.253   2.0765   1.1679  -1.1824
 3RB  H7   H  HCH2  0   0.223  -2.2597   1.4020   2.7371
 3RB  H8   H  HCH2  0   0.237  -0.5806   1.8867   2.6835
 3RB  H9   H  HCH2  0   0.238  -2.8012  -1.1097   1.9929
 3RB  H10  H  HCH2  0   0.245  -1.4499  -2.1245   1.5309
 3RB  H11  H  HCH2  0   0.221   0.0840  -0.2049   1.6191
 3RB  H12  H  HCH2  0   0.238  -0.7280  -0.4901   3.1362
 3RB  H13  H  HCH2  0   0.234  -0.7063   1.6705   0.1241
 3RB  H14  H  HCH2  0   0.254  -1.5028   3.0305   0.8737
 3RB  H15  H  HCR6  0   0.252  -5.6929   3.0801  -0.9996
 3RB  H16  H  HCR6  0   0.253  -6.1885   0.7437  -1.6868
 3RB  H17  H  HCR6  0   0.248  -4.5515  -1.0369  -1.2146
 3RB  H18  H  HCH3  0   0.247  -2.2652  -4.2626  -0.4330
 3RB  H19  H  HCH3  0   0.248  -1.9790  -4.0742  -2.1492
 3RB  H20  H  HCH3  0   0.245  -0.7728  -4.8945  -1.1474
 3RB  H21  H  H     0   0.263   0.6554  -0.5015  -0.6676
 3RB  H22  H  H     0   0.247   3.0505  -2.2985  -0.0196
 3RB  H23  H  H     0   0.265   4.9733  -1.3042   0.4394
 3RB  H24  H  HOH1  0   0.478   7.4260   0.9353   0.9634

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
 3RB  C19  C9   single    1.497  0.020  1.497
 3RB  C10  C9   double    1.345  0.020  1.345
 3RB  C10  C11  single    1.443  0.020  1.443
 3RB  C9   C8   single    1.476  0.020  1.476
 3RB  C12  C11  double    1.346  0.020  1.346
 3RB  C12  C13  single    1.454  0.020  1.454
 3RB  C14  C13  double    1.353  0.020  1.353
 3RB  C14  C15  single    1.465  0.020  1.465
 3RB  C13  C20  single    1.497  0.020  1.497
 3RB  O2   C15  double    1.212  0.020  1.212
 3RB  C15  O1   single    1.336  0.020  1.336
 3RB  C1'  C2'  single    1.529  0.020  1.529
 3RB  C1'  C21  single    1.522  0.020  1.522
 3RB  C8   C7   double    1.338  0.020  1.338
 3RB  C2'  C7   single    1.507  0.020  1.507
 3RB  C7   C6   single    1.484  0.020  1.484
 3RB  C21  C18  single    1.530  0.020  1.530
 3RB  C6   C5   aromatic  1.402  0.020  1.402
 3RB  C6   C1   aromatic  1.394  0.020  1.394
 3RB  C18  C5   single    1.505  0.020  1.505
 3RB  C5   C4   aromatic  1.392  0.020  1.392
 3RB  C1   C2   aromatic  1.388  0.020  1.388
 3RB  C4   C3   aromatic  1.389  0.020  1.389
 3RB  C2   C3   aromatic  1.386  0.020  1.386
 3RB  C4   H1   single    0.930  0.020  1.080
 3RB  C8   H2   single    0.930  0.020  1.080
 3RB  C10  H3   single    0.930  0.020  1.080
 3RB  C20  H4   single    0.970  0.020  1.090
 3RB  C20  H5   single    0.970  0.020  1.090
 3RB  C20  H6   single    0.970  0.020  1.090
 3RB  C21  H7   single    0.970  0.020  1.090
 3RB  C21  H8   single    0.970  0.020  1.090
 3RB  C2'  H9   single    0.970  0.020  1.090
 3RB  C2'  H10  single    0.970  0.020  1.090
 3RB  C1'  H11  single    0.970  0.020  1.090
 3RB  C1'  H12  single    0.970  0.020  1.090
 3RB  C18  H13  single    0.970  0.020  1.090
 3RB  C18  H14  single    0.970  0.020  1.090
 3RB  C3   H15  single    0.930  0.020  1.080
 3RB  C2   H16  single    0.930  0.020  1.080
 3RB  C1   H17  single    0.930  0.020  1.080
 3RB  C19  H18  single    0.970  0.020  1.090
 3RB  C19  H19  single    0.970  0.020  1.090
 3RB  C19  H20  single    0.970  0.020  1.090
 3RB  C11  H21  single    0.930  0.020  1.080
 3RB  C12  H22  single    0.930  0.020  1.080
 3RB  C14  H23  single    0.930  0.020  1.080
 3RB  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
 3RB  H1   C4   C3   119.45  3.000
 3RB  H1   C4   C5   118.96  3.000
 3RB  C3   C4   C5   121.59  3.000
 3RB  C18  C5   C6   121.63  3.000
 3RB  C18  C5   C4   119.66  3.000
 3RB  C6   C5   C4   118.69  3.000
 3RB  C1   C6   C7   119.54  3.000
 3RB  C1   C6   C5   119.43  3.000
 3RB  C7   C6   C5   121.03  3.000
 3RB  C2'  C7   C8   123.82  3.000
 3RB  C2'  C7   C6   116.80  3.000
 3RB  C8   C7   C6   119.21  3.000
 3RB  H2   C8   C9   115.27  3.000
 3RB  H2   C8   C7   118.47  3.000
 3RB  C9   C8   C7   126.17  3.000
 3RB  H3   C10  C11  116.62  3.000
 3RB  H3   C10  C9   118.40  3.000
 3RB  C11  C10  C9   124.95  3.000
 3RB  C14  C13  C12  116.74  3.000
 3RB  C14  C13  C20  125.41  3.000
 3RB  C12  C13  C20  117.85  3.000
 3RB  O2   C15  O1   121.79  3.000
 3RB  O1   C15  C14  110.30  3.000
 3RB  O2   C15  C14  127.91  3.000
 3RB  H6   C20  H5   108.53  3.000
 3RB  H6   C20  H4   106.98  3.000
 3RB  H5   C20  H4   107.91  3.000
 3RB  H6   C20  C13  110.46  3.000
 3RB  H5   C20  C13  112.89  3.000
 3RB  H4   C20  C13  109.86  3.000
 3RB  H8   C21  H7   106.16  3.000
 3RB  H8   C21  C18  108.27  3.000
 3RB  H7   C21  C18  109.55  3.000
 3RB  H8   C21  C1'  108.08  3.000
 3RB  H7   C21  C1'  110.04  3.000
 3RB  C18  C21  C1'  114.40  3.000
 3RB  H10  C2'  H9   106.47  3.000
 3RB  H10  C2'  C1'  108.24  3.000
 3RB  H9   C2'  C1'  108.48  3.000
 3RB  H10  C2'  C7   109.40  3.000
 3RB  H9   C2'  C7   107.87  3.000
 3RB  C1'  C2'  C7   115.97  3.000
 3RB  H12  C1'  H11  105.84  3.000
 3RB  H12  C1'  C2'  107.81  3.000
 3RB  H11  C1'  C2'  109.19  3.000
 3RB  H12  C1'  C21  108.83  3.000
 3RB  H11  C1'  C21  109.18  3.000
 3RB  C2'  C1'  C21  115.54  3.000
 3RB  H14  C18  H13  105.81  3.000
 3RB  H14  C18  C21  108.94  3.000
 3RB  H13  C18  C21  109.04  3.000
 3RB  H14  C18  C5   108.38  3.000
 3RB  H13  C18  C5   109.60  3.000
 3RB  C21  C18  C5   114.69  3.000
 3RB  H15  C3   C2   120.45  3.000
 3RB  H15  C3   C4   119.98  3.000
 3RB  C2   C3   C4   119.57  3.000
 3RB  H16  C2   C1   119.95  3.000
 3RB  H16  C2   C3   120.57  3.000
 3RB  C1   C2   C3   119.49  3.000
 3RB  H17  C1   C2   119.65  3.000
 3RB  H17  C1   C6   119.11  3.000
 3RB  C2   C1   C6   121.22  3.000
 3RB  C19  C9   C10  121.65  3.000
 3RB  C10  C9   C8   123.14  3.000
 3RB  C19  C9   C8   115.17  3.000
 3RB  H20  C19  H19  108.36  3.000
 3RB  H20  C19  H18  108.53  3.000
 3RB  H19  C19  H18  106.41  3.000
 3RB  H20  C19  C9   112.05  3.000
 3RB  H19  C19  C9   110.57  3.000
 3RB  H18  C19  C9   110.72  3.000
 3RB  H21  C11  C12  120.15  3.000
 3RB  H21  C11  C10  116.71  3.000
 3RB  C12  C11  C10  123.14  3.000
 3RB  H22  C12  C11  118.45  3.000
 3RB  H22  C12  C13  116.27  3.000
 3RB  C11  C12  C13  125.28  3.000
 3RB  H23  C14  C15  114.86  3.000
 3RB  H23  C14  C13  117.57  3.000
 3RB  C15  C14  C13  127.56  3.000
 3RB  H24  O1   C15  109.52  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
 3RB  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 3RB  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 3RB  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 3RB  CONST_04  H16  C2   C3   C4    180.00   0.0  0
 3RB  CONST_05  H15  C3   C4   C5    180.00   0.0  0
 3RB  CONST_06  H17  C1   C2   C3    180.00   0.0  0
 3RB  CONST_07  H1   C4   C3   C2    180.00   0.0  0
 3RB  CONST_08  H24  O1   C15  C14   180.00   0.0  0
 3RB  Var_01    C19  C9   C8   C7    107.14  30.0  2
 3RB  Var_02    C11  C10  C9   C8     -2.31   0.0  2
 3RB  Var_03    C13  C12  C11  C10   179.58   0.0  2
 3RB  Var_04    C12  C13  C14  C15  -179.46   0.0  2
 3RB  Var_05    O2   C15  C14  C13     3.36  30.0  2
 3RB  Var_06    C11  C12  C13  C20    -0.35  30.0  2
 3RB  Var_07    C12  C11  C10  C9    176.89  30.0  2
 3RB  Var_08    H18  C19  C9   C8    -62.43  30.0  3
 3RB  Var_09    H4   C20  C13  C12    66.00  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
 3RB  plan-1  C15  0.020
 3RB  plan-1  C14  0.020
 3RB  plan-1  O1   0.020
 3RB  plan-1  O2   0.020
 3RB  plan-1  H24  0.020
 3RB  plan-2  C4   0.020
 3RB  plan-2  C5   0.020
 3RB  plan-2  C6   0.020
 3RB  plan-2  C7   0.020
 3RB  plan-2  C18  0.020
 3RB  plan-2  C3   0.020
 3RB  plan-2  C2   0.020
 3RB  plan-2  C1   0.020
 3RB  plan-2  H1   0.020
 3RB  plan-2  H15  0.020
 3RB  plan-2  H16  0.020
 3RB  plan-2  H17  0.020
 3RB  plan-3  C8   0.020
 3RB  plan-3  C10  0.020
 3RB  plan-3  C9   0.020
 3RB  plan-3  C19  0.020
 3RB  plan-3  C11  0.020
 3RB  plan-3  H3   0.020
 3RB  plan-4  C10  0.020
 3RB  plan-4  C13  0.020
 3RB  plan-4  C11  0.020
 3RB  plan-4  C12  0.020
 3RB  plan-4  H21  0.020
 3RB  plan-4  H22  0.020
 3RB  plan-5  C13  0.020
 3RB  plan-5  C15  0.020
 3RB  plan-5  C20  0.020
 3RB  plan-5  C12  0.020
 3RB  plan-5  C14  0.020
 3RB  plan-5  H23  0.020

