# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 09:43:04 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2E,4E,6E)-3-methyl-7-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/C=C/C=C(C)/c1ccc2c(c1)C(C)(C)CCC2(C)C)=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
 R13  R13  '(2E,4E,6E)-3-methyl-7-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid'  ligand  55  25  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R13
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
 R13  C1    C  CT    0  -0.173   1.5687  -0.3338  -4.3071
 R13  C2    C  CH2   0  -0.425   0.8899  -0.8669  -5.5727
 R13  C3    C  CH2   0  -0.423  -0.3650  -0.0961  -5.9244
 R13  C4    C  CT    0  -0.169  -1.4495  -0.2250  -4.8514
 R13  C5    C  CR6   0   0.111  -0.8444  -0.0261  -3.4685
 R13  C6    C  CR16  0  -0.287  -1.7000   0.1905  -2.3825
 R13  C7    C  CR16  0  -0.331  -1.2347   0.3952  -1.1011
 R13  C8    C  CR6   0   0.117   0.1396   0.4009  -0.8424
 R13  C9    C  CR16  0  -0.381   0.9886   0.1838  -1.9235
 R13  C10   C  CR6   0   0.172   0.5332  -0.0623  -3.2207
 R13  C11   C  C     0   0.064   0.6832   0.6286   0.5099
 R13  C12   C  C1    0  -0.294  -0.0378   0.2750   1.5970
 R13  C13   C  C1    0  -0.220   0.3571   0.4333   2.9724
 R13  C14   C  C1    0  -0.301  -0.4002  -0.0049   3.9984
 R13  C15   C  C     0   0.206  -0.0592   0.1252   5.4050
 R13  C16   C  C1    0  -0.475  -0.9512  -0.3660   6.2966
 R13  C17   C  C     0   0.524  -0.8505  -0.3540   7.7579
 R13  C18   C  CH3   0  -0.636  -2.1014  -1.6141  -4.9174
 R13  C19   C  CH3   0  -0.646  -2.5172   0.8358  -5.1448
 R13  C20   C  CH3   0  -0.636   2.3219   0.9662  -4.6224
 R13  C21   C  CH3   0  -0.643   2.5806  -1.3911  -3.8479
 R13  C22   C  CH3   0  -0.761   2.0622   1.2152   0.5959
 R13  C23   C  CH3   0  -0.775   1.2369   0.7913   5.7500
 R13  O1    O  O     0  -0.453   0.0289   0.1269   8.4395
 R13  O2    O  OH1   0  -0.608  -1.9057  -0.9672   8.3019
 R13  H21   H  HCH2  0   0.233   1.6055  -0.8307  -6.3990
 R13  H22   H  HCH2  0   0.227   0.6459  -1.9249  -5.4341
 R13  H31   H  HCH2  0   0.227  -0.1209   0.9622  -6.0625
 R13  H32   H  HCH2  0   0.232  -0.7694  -0.4398  -6.8806
 R13  H6    H  HCR6  0   0.243  -2.7704   0.2111  -2.5429
 R13  H7    H  HCR6  0   0.246  -1.9466   0.5840  -0.3079
 R13  H9    H  HCR6  0   0.240   2.0571   0.1894  -1.7509
 R13  H12   H  H     0   0.246  -1.0022  -0.1994   1.4448
 R13  H13   H  H     0   0.261   1.3015   0.9202   3.1838
 R13  H14   H  H     0   0.248  -1.3429  -0.4951   3.7728
 R13  H16   H  H     0   0.266  -1.8521  -0.8256   5.9065
 R13  H181  H  HCH3  0   0.231  -2.8830  -1.7203  -4.1629
 R13  H182  H  HCH3  0   0.226  -2.5594  -1.7734  -5.8966
 R13  H183  H  HCH3  0   0.230  -1.3784  -2.4145  -4.7525
 R13  H191  H  HCH3  0   0.229  -3.3854   0.7617  -4.4893
 R13  H192  H  HCH3  0   0.228  -2.1074   1.8431  -5.0496
 R13  H193  H  HCH3  0   0.230  -2.8782   0.7199  -6.1691
 R13  H201  H  HCH3  0   0.229   2.8084   1.3710  -3.7336
 R13  H202  H  HCH3  0   0.226   3.0965   0.7821  -5.3700
 R13  H203  H  HCH3  0   0.230   1.6598   1.7399  -5.0146
 R13  H211  H  HCH3  0   0.228   3.1791  -1.0662  -2.9967
 R13  H212  H  HCH3  0   0.228   2.0793  -2.3210  -3.5733
 R13  H213  H  HCH3  0   0.229   3.2732  -1.6131  -4.6630
 R13  H221  H  HCH3  0   0.260   2.2893   1.6126   1.5816
 R13  H222  H  HCH3  0   0.254   2.8220   0.4616   0.3742
 R13  H223  H  HCH3  0   0.252   2.1917   2.0211  -0.1265
 R13  H231  H  HCH3  0   0.280   1.4555   0.7644   6.8096
 R13  H232  H  HCH3  0   0.252   2.0609   0.3184   5.2144
 R13  H233  H  HCH3  0   0.256   1.2149   1.8360   5.4334
 R13  HO2   H  HOH1  0   0.478  -1.8287  -0.9468   9.2667

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
 R13  C1   C2    single    1.532  0.020  1.532
 R13  C1   C10   single    1.525  0.020  1.525
 R13  C1   C20   single    1.535  0.020  1.535
 R13  C1   C21   single    1.534  0.020  1.534
 R13  C2   C3    single    1.514  0.020  1.514
 R13  C2   H21   single    0.970  0.020  1.090
 R13  C2   H22   single    0.970  0.020  1.090
 R13  C3   C4    single    1.531  0.020  1.531
 R13  C3   H31   single    0.970  0.020  1.090
 R13  C3   H32   single    0.970  0.020  1.090
 R13  C4   C5    single    1.523  0.020  1.523
 R13  C4   C18   single    1.536  0.020  1.536
 R13  C4   C19   single    1.533  0.020  1.533
 R13  C5   C6    aromatic  1.399  0.020  1.399
 R13  C5   C10   aromatic  1.400  0.020  1.400
 R13  C6   C7    aromatic  1.379  0.020  1.379
 R13  C6   H6    single    0.930  0.020  1.080
 R13  C7   C8    aromatic  1.398  0.020  1.398
 R13  C7   H7    single    0.930  0.020  1.080
 R13  C8   C9    aromatic  1.392  0.020  1.392
 R13  C8   C11   single    1.475  0.020  1.475
 R13  C9   C10   aromatic  1.397  0.020  1.397
 R13  C9   H9    single    0.930  0.020  1.080
 R13  C11  C12   double    1.352  0.020  1.352
 R13  C11  C22   single    1.501  0.020  1.501
 R13  C12  C13   single    1.440  0.020  1.440
 R13  C12  H12   single    0.930  0.020  1.080
 R13  C13  C14   double    1.348  0.020  1.348
 R13  C13  H13   single    0.930  0.020  1.080
 R13  C14  C15   single    1.453  0.020  1.453
 R13  C14  H14   single    0.930  0.020  1.080
 R13  C15  C16   double    1.353  0.020  1.353
 R13  C15  C23   single    1.498  0.020  1.498
 R13  C16  C17   single    1.465  0.020  1.465
 R13  C16  H16   single    0.930  0.020  1.080
 R13  C17  O1    double    1.212  0.020  1.212
 R13  C17  O2    single    1.336  0.020  1.336
 R13  C18  H181  single    0.970  0.020  1.090
 R13  C18  H182  single    0.970  0.020  1.090
 R13  C18  H183  single    0.970  0.020  1.090
 R13  C19  H191  single    0.970  0.020  1.090
 R13  C19  H192  single    0.970  0.020  1.090
 R13  C19  H193  single    0.970  0.020  1.090
 R13  C20  H201  single    0.970  0.020  1.090
 R13  C20  H202  single    0.970  0.020  1.090
 R13  C20  H203  single    0.970  0.020  1.090
 R13  C21  H211  single    0.970  0.020  1.090
 R13  C21  H212  single    0.970  0.020  1.090
 R13  C21  H213  single    0.970  0.020  1.090
 R13  C22  H221  single    0.970  0.020  1.090
 R13  C22  H222  single    0.970  0.020  1.090
 R13  C22  H223  single    0.970  0.020  1.090
 R13  C23  H231  single    0.970  0.020  1.090
 R13  C23  H232  single    0.970  0.020  1.090
 R13  C23  H233  single    0.970  0.020  1.090
 R13  O2   HO2   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
 R13  C21   C1   C20   108.75  3.000
 R13  C21   C1   C10   110.94  3.000
 R13  C20   C1   C10   109.19  3.000
 R13  C21   C1   C2    107.44  3.000
 R13  C20   C1   C2    110.03  3.000
 R13  C10   C1   C2    110.46  3.000
 R13  H22   C2   H21   105.87  3.000
 R13  H22   C2   C3    109.67  3.000
 R13  H21   C2   C3    110.48  3.000
 R13  H22   C2   C1    109.31  3.000
 R13  H21   C2   C1    108.83  3.000
 R13  C3    C2   C1    112.45  3.000
 R13  H32   C3   H31   106.02  3.000
 R13  H32   C3   C4    108.93  3.000
 R13  H31   C3   C4    109.14  3.000
 R13  H32   C3   C2    110.46  3.000
 R13  H31   C3   C2    109.67  3.000
 R13  C4    C3   C2    112.42  3.000
 R13  C19   C4   C18   108.78  3.000
 R13  C19   C4   C5    111.11  3.000
 R13  C18   C4   C5    109.02  3.000
 R13  C19   C4   C3    107.51  3.000
 R13  C18   C4   C3    110.29  3.000
 R13  C5    C4   C3    110.12  3.000
 R13  C10   C5   C6    117.92  3.000
 R13  C10   C5   C4    123.26  3.000
 R13  C6    C5   C4    118.82  3.000
 R13  H6    C6   C7    117.95  3.000
 R13  H6    C6   C5    119.51  3.000
 R13  C7    C6   C5    122.54  3.000
 R13  H7    C7   C8    120.67  3.000
 R13  H7    C7   C6    119.02  3.000
 R13  C8    C7   C6    120.28  3.000
 R13  C11   C8   C9    120.76  3.000
 R13  C11   C8   C7    122.16  3.000
 R13  C9    C8   C7    117.08  3.000
 R13  H9    C9   C10   118.09  3.000
 R13  H9    C9   C8    118.53  3.000
 R13  C10   C9   C8    123.37  3.000
 R13  C9    C10  C5    118.73  3.000
 R13  C9    C10  C1    118.14  3.000
 R13  C5    C10  C1    123.13  3.000
 R13  C22   C11  C12   123.11  3.000
 R13  C22   C11  C8    116.83  3.000
 R13  C12   C11  C8    120.03  3.000
 R13  H12   C12  C13   115.20  3.000
 R13  H12   C12  C11   118.39  3.000
 R13  C13   C12  C11   126.39  3.000
 R13  H13   C13  C14   119.15  3.000
 R13  H13   C13  C12   118.36  3.000
 R13  C14   C13  C12   122.49  3.000
 R13  H14   C14  C15   116.43  3.000
 R13  H14   C14  C13   118.43  3.000
 R13  C15   C14  C13   125.14  3.000
 R13  C23   C15  C16   125.46  3.000
 R13  C23   C15  C14   117.77  3.000
 R13  C16   C15  C14   116.78  3.000
 R13  H16   C16  C17   114.81  3.000
 R13  H16   C16  C15   117.67  3.000
 R13  C17   C16  C15   127.51  3.000
 R13  O2    C17  O1    121.74  3.000
 R13  O2    C17  C16   110.37  3.000
 R13  O1    C17  C16   127.88  3.000
 R13  H183  C18  H182  107.83  3.000
 R13  H183  C18  H181  107.38  3.000
 R13  H182  C18  H181  107.77  3.000
 R13  H183  C18  C4    112.07  3.000
 R13  H182  C18  C4    110.38  3.000
 R13  H181  C18  C4    111.24  3.000
 R13  H193  C19  H192  107.69  3.000
 R13  H193  C19  H191  107.06  3.000
 R13  H192  C19  H191  108.01  3.000
 R13  H193  C19  C4    109.64  3.000
 R13  H192  C19  C4    111.12  3.000
 R13  H191  C19  C4    113.10  3.000
 R13  H203  C20  H202  107.68  3.000
 R13  H203  C20  H201  107.47  3.000
 R13  H202  C20  H201  107.69  3.000
 R13  H203  C20  C1    112.12  3.000
 R13  H202  C20  C1    110.23  3.000
 R13  H201  C20  C1    111.45  3.000
 R13  H213  C21  H212  107.80  3.000
 R13  H213  C21  H211  107.17  3.000
 R13  H212  C21  H211  108.04  3.000
 R13  H213  C21  C1    109.57  3.000
 R13  H212  C21  C1    111.07  3.000
 R13  H211  C21  C1    112.99  3.000
 R13  H223  C22  H222  107.03  3.000
 R13  H223  C22  H221  107.81  3.000
 R13  H222  C22  H221  106.91  3.000
 R13  H223  C22  C11   111.11  3.000
 R13  H222  C22  C11   110.96  3.000
 R13  H221  C22  C11   112.75  3.000
 R13  H233  C23  H232  106.72  3.000
 R13  H233  C23  H231  108.16  3.000
 R13  H232  C23  H231  108.51  3.000
 R13  H233  C23  C15   109.96  3.000
 R13  H232  C23  C15   110.36  3.000
 R13  H231  C23  C15   112.91  3.000
 R13  HO2   O2   C17   109.46  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
 R13  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 R13  CONST_02  C8    C9   C10  C5      0.00   0.0  0
 R13  CONST_03  C9    C10  C5   C6      0.00   0.0  0
 R13  CONST_04  C9    C8   C7   C6      0.00   0.0  0
 R13  CONST_05  C10   C5   C6   C7      0.00   0.0  0
 R13  CONST_06  C10   C9   C8   C7      0.00   0.0  0
 R13  CONST_07  C11   C8   C7   C6    180.00   0.0  0
 R13  CONST_08  C11   C8   C9   C10   180.00   0.0  0
 R13  CONST_09  H9    C9   C10  C1      0.00   0.0  0
 R13  CONST_10  H6    C6   C5   C4      0.00   0.0  0
 R13  CONST_11  H7    C7   C6   C5    180.00   0.0  0
 R13  CONST_12  HO2   O2   C17  C16   180.00   0.0  0
 R13  Var_01    C4    C3   C2   C1    -63.48  30.0  1
 R13  Var_02    C5    C10  C1   C2    -13.08  30.0  1
 R13  Var_03    C5    C4   C3   C2     45.81  30.0  1
 R13  Var_04    C10   C1   C2   C3     44.14  30.0  1
 R13  Var_05    C6    C5   C4   C3    165.96  30.0  1
 R13  Var_06    C12   C11  C8   C7     28.70  30.0  2
 R13  Var_07    H201  C20  C1   C2    179.55  30.0  3
 R13  Var_08    H211  C21  C1   C2    175.10  30.0  3
 R13  Var_09    H181  C18  C4   C3   -179.58  30.0  3
 R13  Var_10    H191  C19  C4   C3    174.39  30.0  3
 R13  Var_11    C13   C12  C11  C8    179.99   0.0  2
 R13  Var_12    H221  C22  C11  C8    163.83  30.0  3
 R13  Var_13    C15   C14  C13  C12  -179.94   0.0  2
 R13  Var_14    C17   C16  C15  C14  -179.65   0.0  2
 R13  Var_15    C14   C13  C12  C11  -176.86  30.0  2
 R13  Var_16    C16   C15  C14  C13   179.43  30.0  2
 R13  Var_17    O1    C17  C16  C15     2.13  30.0  2
 R13  Var_18    H231  C23  C15  C14  -174.65  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
 R13  plan-1  C16  0.020
 R13  plan-1  C17  0.020
 R13  plan-1  O1   0.020
 R13  plan-1  O2   0.020
 R13  plan-1  HO2  0.020
 R13  plan-2  C1   0.020
 R13  plan-2  C4   0.020
 R13  plan-2  C5   0.020
 R13  plan-2  C6   0.020
 R13  plan-2  C7   0.020
 R13  plan-2  C8   0.020
 R13  plan-2  C9   0.020
 R13  plan-2  C10  0.020
 R13  plan-2  C11  0.020
 R13  plan-2  H6   0.020
 R13  plan-2  H7   0.020
 R13  plan-2  H9   0.020
 R13  plan-3  C8   0.020
 R13  plan-3  C11  0.020
 R13  plan-3  C12  0.020
 R13  plan-3  C13  0.020
 R13  plan-3  C22  0.020
 R13  plan-3  H12  0.020
 R13  plan-4  C12  0.020
 R13  plan-4  C13  0.020
 R13  plan-4  C14  0.020
 R13  plan-4  C15  0.020
 R13  plan-4  H13  0.020
 R13  plan-4  H14  0.020
 R13  plan-5  C14  0.020
 R13  plan-5  C15  0.020
 R13  plan-5  C16  0.020
 R13  plan-5  C17  0.020
 R13  plan-5  C23  0.020
 R13  plan-5  H16  0.020

