# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:17:38 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCCC(/C)=C/CC[C@@](C)(O)C=C
#
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
 28U  28U  (3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol  ligand  42  16  .  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_28U
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
 28U  C4   C  CH3   0  -0.665   4.3349  -0.2453  -1.6424
 28U  C5   C  CH2   0  -0.445   2.2082  -0.2506  -0.2573
 28U  C6   C  CH2   0  -0.496   1.6038   1.0348  -0.8274
 28U  C7   C  C1    0  -0.265   0.1083   0.9512  -0.8528
 28U  C8   C  C     0   0.110  -0.7641   1.5225  -0.0188
 28U  C10  C  CH3   0  -0.729  -0.3880   2.4227   1.1209
 28U  C13  C  C     0   0.090  -4.8216  -0.9057  -0.0548
 28U  C15  C  CH3   0  -0.721  -4.0551  -1.8985  -0.8775
 28U  O16  O  OH1   0  -0.672   4.2760   0.8038   0.4680
 28U  C3   C  CT    0   0.172   3.7473  -0.3026  -0.2331
 28U  C2   C  C1    0  -0.168   4.1505  -1.6125   0.4001
 28U  C1   C  C2    0  -0.547   4.9399  -1.7568   1.4568
 28U  C9   C  CH2   0  -0.481  -2.2381   1.2540  -0.1713
 28U  C11  C  CH2   0  -0.494  -2.7785   0.2675   0.8780
 28U  C12  C  C1    0  -0.267  -4.2495   0.0255   0.7130
 28U  C14  C  CH3   0  -0.706  -6.3140  -1.0185  -0.1667
 28U  H1   H  HCH3  0   0.238   4.0716   0.6833  -2.1498
 28U  H2   H  HCH3  0   0.239   5.4229  -0.3169  -1.6090
 28U  H3   H  HCH3  0   0.228   3.9629  -1.0736  -2.2455
 28U  H4   H  HCH2  0   0.236   1.8396  -0.3878   0.7659
 28U  H5   H  HCH2  0   0.229   1.8363  -1.1105  -0.8229
 28U  H6   H  HCH2  0   0.231   1.9488   1.8935  -0.2503
 28U  H7   H  HCH2  0   0.236   1.9587   1.1891  -1.8500
 28U  H8   H  H     0   0.219  -0.2989   0.3145  -1.6361
 28U  H11  H  HCH3  0   0.236  -0.7963   3.4253   0.9688
 28U  H12  H  HCH3  0   0.237  -0.8057   2.0600   2.0625
 28U  H13  H  HCH3  0   0.238   0.6870   2.5195   1.2594
 28U  H15  H  HCH3  0   0.237  -2.9769  -1.8251  -0.7489
 28U  H16  H  HCH3  0   0.235  -4.3540  -2.9204  -0.6314
 28U  H17  H  HCH3  0   0.237  -4.2708  -1.7613  -1.9403
 28U  H18  H  HOH1  0   0.444   3.8932   0.8141   1.3524
 28U  H19  H  H     0   0.248   3.7326  -2.4969  -0.0737
 28U  H20  H  H     0   0.233   5.3913  -0.9161   1.9688
 28U  H21  H  H     0   0.238   5.1668  -2.7382   1.8521
 28U  H22  H  HCH2  0   0.226  -2.8013   2.1910  -0.1001
 28U  H23  H  HCH2  0   0.235  -2.4436   0.8444  -1.1638
 28U  H24  H  HCH2  0   0.233  -2.2090  -0.6619   0.8040
 28U  H25  H  HCH2  0   0.235  -2.5917   0.6575   1.8818
 28U  H26  H  H     0   0.221  -4.9020   0.7131   1.2456
 28U  H28  H  HCH3  0   0.230  -6.6563  -2.0109   0.1383
 28U  H29  H  HCH3  0   0.235  -6.8301  -0.2801   0.4463
 28U  H30  H  HCH3  0   0.230  -6.6397  -0.8847  -1.2019

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
 28U  C7   C6   single  1.498  0.020  1.498
 28U  C7   C8   double  1.335  0.020  1.335
 28U  C6   C5   single  1.531  0.020  1.531
 28U  C8   C9   single  1.506  0.020  1.506
 28U  C8   C10  single  1.500  0.020  1.500
 28U  C9   C11  single  1.538  0.020  1.538
 28U  C5   C3   single  1.540  0.020  1.540
 28U  C11  C12  single  1.500  0.020  1.500
 28U  C4   C3   single  1.528  0.020  1.528
 28U  C3   C2   single  1.510  0.020  1.510
 28U  C3   O16  single  1.413  0.020  1.413
 28U  C12  C13  double  1.336  0.020  1.336
 28U  C2   C1   double  1.327  0.020  1.327
 28U  C14  C13  single  1.501  0.020  1.501
 28U  C13  C15  single  1.500  0.020  1.500
 28U  C4   H1   single  0.970  0.020  1.090
 28U  C4   H2   single  0.970  0.020  1.090
 28U  C4   H3   single  0.970  0.020  1.090
 28U  C5   H4   single  0.970  0.020  1.090
 28U  C5   H5   single  0.970  0.020  1.090
 28U  C6   H6   single  0.970  0.020  1.090
 28U  C6   H7   single  0.970  0.020  1.090
 28U  C7   H8   single  0.930  0.020  1.080
 28U  C10  H11  single  0.970  0.020  1.090
 28U  C10  H12  single  0.970  0.020  1.090
 28U  C10  H13  single  0.970  0.020  1.090
 28U  C15  H15  single  0.970  0.020  1.090
 28U  C15  H16  single  0.970  0.020  1.090
 28U  C15  H17  single  0.970  0.020  1.090
 28U  O16  H18  single  0.850  0.020  0.980
 28U  C2   H19  single  0.930  0.020  1.080
 28U  C1   H20  single  0.930  0.020  1.080
 28U  C1   H21  single  0.930  0.020  1.080
 28U  C9   H22  single  0.970  0.020  1.090
 28U  C9   H23  single  0.970  0.020  1.090
 28U  C11  H24  single  0.970  0.020  1.090
 28U  C11  H25  single  0.970  0.020  1.090
 28U  C12  H26  single  0.930  0.020  1.080
 28U  C14  H28  single  0.970  0.020  1.090
 28U  C14  H29  single  0.970  0.020  1.090
 28U  C14  H30  single  0.970  0.020  1.090

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
 28U  H3   C4   H2   107.90  3.000
 28U  H3   C4   H1   107.89  3.000
 28U  H2   C4   H1   108.12  3.000
 28U  H3   C4   C3   110.52  3.000
 28U  H2   C4   C3   110.66  3.000
 28U  H1   C4   C3   111.61  3.000
 28U  H5   C5   H4   105.65  3.000
 28U  H5   C5   C3   108.74  3.000
 28U  H4   C5   C3   108.49  3.000
 28U  H5   C5   C6   109.46  3.000
 28U  H4   C5   C6   108.66  3.000
 28U  C3   C5   C6   115.39  3.000
 28U  H7   C6   H6   106.33  3.000
 28U  H7   C6   C7   108.42  3.000
 28U  H6   C6   C7   111.64  3.000
 28U  H7   C6   C5   109.80  3.000
 28U  H6   C6   C5   109.83  3.000
 28U  C7   C6   C5   110.71  3.000
 28U  H8   C7   C8   117.08  3.000
 28U  H8   C7   C6   114.73  3.000
 28U  C8   C7   C6   128.15  3.000
 28U  C9   C8   C10  115.43  3.000
 28U  C10  C8   C7   124.56  3.000
 28U  C9   C8   C7   120.00  3.000
 28U  H13  C10  H12  107.31  3.000
 28U  H13  C10  H11  107.77  3.000
 28U  H12  C10  H11  106.36  3.000
 28U  H13  C10  C8   113.44  3.000
 28U  H12  C10  C8   111.08  3.000
 28U  H11  C10  C8   110.55  3.000
 28U  C14  C13  C12  121.41  3.000
 28U  C14  C13  C15  114.68  3.000
 28U  C12  C13  C15  123.91  3.000
 28U  H17  C15  H16  106.40  3.000
 28U  H17  C15  H15  107.57  3.000
 28U  H16  C15  H15  107.91  3.000
 28U  H17  C15  C13  110.45  3.000
 28U  H16  C15  C13  110.83  3.000
 28U  H15  C15  C13  113.38  3.000
 28U  H18  O16  C3   108.37  3.000
 28U  C2   C3   O16  111.81  3.000
 28U  O16  C3   C5   110.82  3.000
 28U  C2   C3   C5   107.62  3.000
 28U  O16  C3   C4   106.53  3.000
 28U  C2   C3   C4   108.46  3.000
 28U  C5   C3   C4   111.63  3.000
 28U  H19  C2   C1   119.17  3.000
 28U  H19  C2   C3   114.87  3.000
 28U  C1   C2   C3   125.96  3.000
 28U  H21  C1   H20  116.36  3.000
 28U  H21  C1   C2   120.95  3.000
 28U  H20  C1   C2   122.69  3.000
 28U  H23  C9   H22  106.43  3.000
 28U  H23  C9   C11  108.24  3.000
 28U  H22  C9   C11  108.88  3.000
 28U  H23  C9   C8   110.04  3.000
 28U  H22  C9   C8   110.13  3.000
 28U  C11  C9   C8   112.90  3.000
 28U  H25  C11  H24  106.06  3.000
 28U  H25  C11  C12  109.04  3.000
 28U  H24  C11  C12  111.50  3.000
 28U  H25  C11  C9   109.73  3.000
 28U  H24  C11  C9   108.44  3.000
 28U  C12  C11  C9   111.90  3.000
 28U  H26  C12  C11  115.64  3.000
 28U  H26  C12  C13  117.74  3.000
 28U  C11  C12  C13  126.57  3.000
 28U  H30  C14  H29  107.97  3.000
 28U  H30  C14  H28  106.38  3.000
 28U  H29  C14  H28  108.05  3.000
 28U  H30  C14  C13  110.95  3.000
 28U  H29  C14  C13  112.22  3.000
 28U  H28  C14  C13  111.03  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
 28U  Var_01  C9   C8   C7   C6   -176.71   0.0  2
 28U  Var_02  C11  C12  C13  C15     1.12   0.0  2
 28U  Var_03  C8   C7   C6   C5    103.06  30.0  2
 28U  Var_04  C3   C5   C6   C7    177.71  30.0  3
 28U  Var_05  C11  C9   C8   C7    103.53  30.0  3
 28U  Var_06  C12  C11  C9   C8    179.51  30.0  3
 28U  Var_07  C9   C11  C12  C13    88.72  30.0  1
 28U  Var_08  H20  C1   C2   C3     -0.85   0.0  2
 28U  Var_09  H11  C10  C8   C7    117.03  30.0  3
 28U  Var_10  H28  C14  C13  C15    58.94  30.0  3
 28U  Var_11  H15  C15  C13  C12     3.15  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
 28U  chir_01  C3  C4  C2  O16  negativ

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
 28U  plan-1  C6   0.020
 28U  plan-1  C7   0.020
 28U  plan-1  C8   0.020
 28U  plan-1  C10  0.020
 28U  plan-1  C9   0.020
 28U  plan-1  H8   0.020
 28U  plan-2  C13  0.020
 28U  plan-2  C15  0.020
 28U  plan-2  C11  0.020
 28U  plan-2  C12  0.020
 28U  plan-2  C14  0.020
 28U  plan-2  H26  0.020
 28U  plan-3  C3   0.020
 28U  plan-3  C2   0.020
 28U  plan-3  C1   0.020
 28U  plan-3  H19  0.020
 28U  plan-3  H20  0.020
 28U  plan-3  H21  0.020

