# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 13:08:47 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2E,6Z,8E)-3,7-dimethyl-8-[(4R)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-2,6-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC\C(=C/C(C)=C\CC/C(C)=C/C(O)=O)c2ccccc12
#
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
 R4M  R4M  '(2E,6Z,8E)-3,7-dimethyl-8-[(4R)-4-methyl-3,4-dihydronaphthalen-1(2H)-ylidene]octa-2,6-dienoic acid'  ligand  48  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R4M
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
 R4M  C2'  C  CH2    0  -0.520  -1.5344   1.1833  -1.0219
 R4M  C1'  C  CH2    0  -0.446  -1.0162  -0.1696  -1.4856
 R4M  C18  C  CH1    0  -0.290  -2.0301  -1.2874  -1.2583
 R4M  C4'  C  CH3    0  -0.662  -1.3332  -2.6411  -1.3979
 R4M  C5   C  CR6    0   0.090  -2.7790  -1.1450   0.0546
 R4M  C4   C  CR16   0  -0.305  -3.6350  -2.1710   0.4598
 R4M  C3   C  CR16   0  -0.256  -4.3670  -2.0918   1.6319
 R4M  C2   C  CR16   0  -0.259  -4.2627  -0.9575   2.4280
 R4M  C1   C  CR16   0  -0.318  -3.4297   0.0738   2.0367
 R4M  C6   C  CR6    0   0.085  -2.6708  -0.0009   0.8625
 R4M  C7   C  C      0   0.102  -1.7941   1.1173   0.4521
 R4M  C8   C  C1     0  -0.386  -1.2520   1.9598   1.3397
 R4M  C9   C  C      0   0.045  -0.3967   3.1288   1.0434
 R4M  C19  C  CH3    0  -0.712  -1.0679   4.4567   1.2606
 R4M  C10  C  C1     0  -0.226   0.8846   3.0423   0.6765
 R4M  C11  C  CH2    0  -0.487   1.6846   1.7971   0.4647
 R4M  C12  C  CH2    0  -0.505   2.2487   1.7062  -0.9618
 R4M  C13  C  C      0   0.160   3.0937   0.4783  -1.1767
 R4M  C20  C  CH3    0  -0.728   4.3348   0.4169  -0.3320
 R4M  C14  C  C1     0  -0.465   2.7142  -0.4457  -2.0687
 R4M  C15  C  C      0   0.383   3.3941  -1.7387  -2.4402
 R4M  O1   O  O      0  -0.605   4.2559  -2.2167  -1.6717
 R4M  O2   O  OC    -1  -0.625   3.0153  -2.2432  -3.5202
 R4M  H1   H  HCH2   0   0.249  -0.8212   1.9726  -1.2581
 R4M  H2   H  HCH2   0   0.239  -2.4661   1.4203  -1.5485
 R4M  H3   H  HCH2   0   0.239  -0.7541  -0.1373  -2.5457
 R4M  H4   H  HCH2   0   0.232  -0.0895  -0.4002  -0.9496
 R4M  H5   H  HCH1   0   0.245  -2.7836  -1.2158  -2.0530
 R4M  H6   H  HCH3   0   0.223  -0.6128  -2.7900  -0.5914
 R4M  H7   H  HCH3   0   0.234  -2.0279  -3.4800  -1.3894
 R4M  H8   H  HCH3   0   0.232  -0.7852  -2.6813  -2.3409
 R4M  H9   H  HCR6   0   0.249  -3.7336  -3.0531  -0.1610
 R4M  H10  H  HCR6   0   0.252  -5.0228  -2.9043   1.9173
 R4M  H11  H  HCR6   0   0.252  -4.8407  -0.8714   3.3390
 R4M  H12  H  HCR6   0   0.247  -3.3854   0.9687   2.6446
 R4M  H13  H  H      0   0.245  -1.4878   1.8319   2.3943
 R4M  H14  H  HCH3   0   0.235  -1.4933   4.5216   2.2651
 R4M  H15  H  HCH3   0   0.236  -0.3752   5.2885   1.1312
 R4M  H16  H  HCH3   0   0.236  -1.8977   4.5904   0.5627
 R4M  H17  H  H      0   0.224   1.4249   3.9739   0.5187
 R4M  H18  H  HCH2   0   0.242   2.5164   1.7913   1.1772
 R4M  H19  H  HCH2   0   0.237   1.0863   0.9087   0.6758
 R4M  H20  H  HCH2   0   0.240   1.4218   1.7266  -1.6758
 R4M  H21  H  HCH2   0   0.231   2.8550   2.5994  -1.1540
 R4M  H22  H  HCH3   0   0.234   4.1200  -0.0032   0.6540
 R4M  H23  H  HCH3   0   0.251   5.1099  -0.1962  -0.7792
 R4M  H24  H  HCH3   0   0.219   4.7272   1.4220  -0.1628
 R4M  H25  H  H      0   0.208   1.7997  -0.2451  -2.6215

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
 R4M  C19  C9   single    1.504  0.020  1.504
 R4M  C10  C9   double    1.336  0.020  1.336
 R4M  C10  C11  single    1.495  0.020  1.495
 R4M  C9   C8   single    1.478  0.020  1.478
 R4M  C12  C11  single    1.537  0.020  1.537
 R4M  C12  C13  single    1.506  0.020  1.506
 R4M  C14  C13  double    1.339  0.020  1.339
 R4M  C14  C15  single    1.507  0.020  1.507
 R4M  C8   C7   double    1.338  0.020  1.338
 R4M  C13  C20  single    1.502  0.020  1.502
 R4M  C15  O1   deloc     1.250  0.020  1.250
 R4M  C15  O2   deloc     1.251  0.020  1.251
 R4M  C7   C2'  single    1.498  0.020  1.498
 R4M  C7   C6   single    1.479  0.020  1.479
 R4M  C1   C6   aromatic  1.400  0.020  1.400
 R4M  C1   C2   aromatic  1.382  0.020  1.382
 R4M  C2'  C1'  single    1.521  0.020  1.521
 R4M  C6   C5   aromatic  1.405  0.020  1.405
 R4M  C2   C3   aromatic  1.390  0.020  1.390
 R4M  C1'  C18  single    1.526  0.020  1.526
 R4M  C5   C18  single    1.518  0.020  1.518
 R4M  C5   C4   aromatic  1.396  0.020  1.396
 R4M  C3   C4   aromatic  1.384  0.020  1.384
 R4M  C18  C4'  single    1.529  0.020  1.529
 R4M  C2'  H1   single    0.970  0.020  1.090
 R4M  C2'  H2   single    0.970  0.020  1.090
 R4M  C1'  H3   single    0.970  0.020  1.090
 R4M  C1'  H4   single    0.970  0.020  1.090
 R4M  C18  H5   single    0.970  0.020  1.090
 R4M  C4'  H6   single    0.970  0.020  1.090
 R4M  C4'  H7   single    0.970  0.020  1.090
 R4M  C4'  H8   single    0.970  0.020  1.090
 R4M  C4   H9   single    0.930  0.020  1.080
 R4M  C3   H10  single    0.930  0.020  1.080
 R4M  C2   H11  single    0.930  0.020  1.080
 R4M  C1   H12  single    0.930  0.020  1.080
 R4M  C8   H13  single    0.930  0.020  1.080
 R4M  C19  H14  single    0.970  0.020  1.090
 R4M  C19  H15  single    0.970  0.020  1.090
 R4M  C19  H16  single    0.970  0.020  1.090
 R4M  C10  H17  single    0.930  0.020  1.080
 R4M  C11  H18  single    0.970  0.020  1.090
 R4M  C11  H19  single    0.970  0.020  1.090
 R4M  C12  H20  single    0.970  0.020  1.090
 R4M  C12  H21  single    0.970  0.020  1.090
 R4M  C20  H22  single    0.970  0.020  1.090
 R4M  C20  H23  single    0.970  0.020  1.090
 R4M  C20  H24  single    0.970  0.020  1.090
 R4M  C14  H25  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
 R4M  H2   C2'  H1   107.19  3.000
 R4M  H2   C2'  C7   109.57  3.000
 R4M  H1   C2'  C7   111.01  3.000
 R4M  H2   C2'  C1'  109.60  3.000
 R4M  H1   C2'  C1'  110.80  3.000
 R4M  C7   C2'  C1'  108.65  3.000
 R4M  H4   C1'  H3   106.15  3.000
 R4M  H4   C1'  C18  109.58  3.000
 R4M  H3   C1'  C18  109.00  3.000
 R4M  H4   C1'  C2'  109.05  3.000
 R4M  H3   C1'  C2'  110.57  3.000
 R4M  C18  C1'  C2'  112.31  3.000
 R4M  H5   C18  C5   106.34  3.000
 R4M  H5   C18  C4'  107.73  3.000
 R4M  C5   C18  C4'  112.76  3.000
 R4M  H5   C18  C1'  107.49  3.000
 R4M  C4'  C18  C1'  109.40  3.000
 R4M  C5   C18  C1'  112.82  3.000
 R4M  H8   C4'  H7   107.37  3.000
 R4M  H8   C4'  H6   107.58  3.000
 R4M  H7   C4'  H6   108.07  3.000
 R4M  H8   C4'  C18  109.90  3.000
 R4M  H7   C4'  C18  112.98  3.000
 R4M  H6   C4'  C18  110.74  3.000
 R4M  C6   C5   C4   118.61  3.000
 R4M  C4   C5   C18  118.98  3.000
 R4M  C6   C5   C18  122.39  3.000
 R4M  H9   C4   C3   118.94  3.000
 R4M  H9   C4   C5   119.20  3.000
 R4M  C3   C4   C5   121.86  3.000
 R4M  H10  C3   C2   120.47  3.000
 R4M  H10  C3   C4   120.05  3.000
 R4M  C2   C3   C4   119.48  3.000
 R4M  H11  C2   C1   120.05  3.000
 R4M  H11  C2   C3   120.47  3.000
 R4M  C1   C2   C3   119.47  3.000
 R4M  H12  C1   C6   119.52  3.000
 R4M  H12  C1   C2   118.84  3.000
 R4M  C6   C1   C2   121.62  3.000
 R4M  C7   C6   C1   120.91  3.000
 R4M  C1   C6   C5   118.94  3.000
 R4M  C7   C6   C5   120.12  3.000
 R4M  C8   C7   C6   122.14  3.000
 R4M  C6   C7   C2'  114.14  3.000
 R4M  C8   C7   C2'  123.68  3.000
 R4M  H13  C8   C9   114.37  3.000
 R4M  H13  C8   C7   118.75  3.000
 R4M  C9   C8   C7   126.80  3.000
 R4M  C10  C9   C19  121.67  3.000
 R4M  C10  C9   C8   123.98  3.000
 R4M  C19  C9   C8   114.27  3.000
 R4M  H16  C19  H15  108.27  3.000
 R4M  H16  C19  H14  106.51  3.000
 R4M  H15  C19  H14  108.13  3.000
 R4M  H16  C19  C9   110.78  3.000
 R4M  H15  C19  C9   111.90  3.000
 R4M  H14  C19  C9   111.03  3.000
 R4M  H17  C10  C11  115.26  3.000
 R4M  H17  C10  C9   117.43  3.000
 R4M  C11  C10  C9   127.31  3.000
 R4M  H19  C11  H18  106.63  3.000
 R4M  H19  C11  C12  109.43  3.000
 R4M  H18  C11  C12  108.95  3.000
 R4M  H19  C11  C10  110.93  3.000
 R4M  H18  C11  C10  108.58  3.000
 R4M  C12  C11  C10  112.15  3.000
 R4M  H21  C12  H20  106.78  3.000
 R4M  H21  C12  C13  109.20  3.000
 R4M  H20  C12  C13  110.28  3.000
 R4M  H21  C12  C11  108.52  3.000
 R4M  H20  C12  C11  109.13  3.000
 R4M  C13  C12  C11  112.75  3.000
 R4M  C14  C13  C20  125.48  3.000
 R4M  C20  C13  C12  114.62  3.000
 R4M  C14  C13  C12  119.91  3.000
 R4M  H24  C20  H23  109.11  3.000
 R4M  H24  C20  H22  106.53  3.000
 R4M  H23  C20  H22  107.16  3.000
 R4M  H24  C20  C13  110.26  3.000
 R4M  H23  C20  C13  112.43  3.000
 R4M  H22  C20  C13  111.13  3.000
 R4M  H25  C14  C15  114.35  3.000
 R4M  H25  C14  C13  116.73  3.000
 R4M  C15  C14  C13  128.92  3.000
 R4M  O2   C15  O1   125.84  3.000
 R4M  O2   C15  C14  114.97  3.000
 R4M  O1   C15  C14  119.18  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
 R4M  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 R4M  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 R4M  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 R4M  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 R4M  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 R4M  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 R4M  CONST_07  H9   C4   C5   C18     0.00   0.0  0
 R4M  CONST_08  H12  C1   C6   C5    180.00   0.0  0
 R4M  CONST_09  H10  C3   C4   C5    180.00   0.0  0
 R4M  CONST_10  H11  C2   C3   C4    180.00   0.0  0
 R4M  Var_01    C1   C6   C7   C2'  -154.50  30.0  1
 R4M  Var_02    C6   C7   C2'  C1'   -53.30  30.0  1
 R4M  Var_03    C7   C2'  C1'  C18    61.72  30.0  1
 R4M  Var_04    C9   C8   C7   C2'     4.23  30.0  2
 R4M  Var_05    C19  C9   C8   C7    107.92  30.0  2
 R4M  Var_06    C11  C10  C9   C8      1.51   0.0  2
 R4M  Var_07    C15  C14  C13  C12  -179.80   0.0  2
 R4M  Var_08    C12  C11  C10  C9    121.28  30.0  3
 R4M  Var_09    C13  C12  C11  C10   178.16  30.0  1
 R4M  Var_10    C14  C13  C12  C11   116.95  30.0  3
 R4M  Var_11    O1   C15  C14  C13    17.63  30.0  2
 R4M  Var_12    H14  C19  C9   C8     53.16  30.0  3
 R4M  Var_13    H22  C20  C13  C12    84.87  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 R4M  chir_01  C18  C1'  C5  C4'  positiv

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
 R4M  plan-1  C14  0.020
 R4M  plan-1  C15  0.020
 R4M  plan-1  O1   0.020
 R4M  plan-1  O2   0.020
 R4M  plan-2  C18  0.020
 R4M  plan-2  C5   0.020
 R4M  plan-2  C4   0.020
 R4M  plan-2  C3   0.020
 R4M  plan-2  C2   0.020
 R4M  plan-2  C1   0.020
 R4M  plan-2  C6   0.020
 R4M  plan-2  C7   0.020
 R4M  plan-2  H9   0.020
 R4M  plan-2  H10  0.020
 R4M  plan-2  H11  0.020
 R4M  plan-2  H12  0.020
 R4M  plan-3  C8   0.020
 R4M  plan-3  C9   0.020
 R4M  plan-3  C19  0.020
 R4M  plan-3  C10  0.020
 R4M  plan-3  C11  0.020
 R4M  plan-3  H17  0.020
 R4M  plan-4  C12  0.020
 R4M  plan-4  C13  0.020
 R4M  plan-4  C20  0.020
 R4M  plan-4  C14  0.020
 R4M  plan-4  C15  0.020
 R4M  plan-4  H25  0.020

