# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:24:06 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (2~{S})-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCCC(/C)=C/CCC(/C)=C/COC[C@@H](O)CO
#
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
 FV3  FV3  (2~{S})-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol  ligand  53  21  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FV3
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
 FV3  O1   O  OH1   0  -0.674   -3.4353  -28.4633  15.3910
 FV3  C1   C  CH2   0  -0.165   -3.6601  -27.3151  14.5988
 FV3  C2   C  CH1   0  -0.011   -4.9236  -27.5565  13.7905
 FV3  O6   O  OH1   0  -0.673   -4.7881  -28.6943  12.9675
 FV3  C3   C  CH2   0  -0.154   -5.2357  -26.3922  12.8647
 FV3  O5   O  O2    0  -0.483   -5.5349  -25.2603  13.6393
 FV3  C6   C  CH2   0  -0.229   -5.6219  -24.0652  12.8844
 FV3  C7   C  C1    0  -0.323   -6.7010  -24.0687  11.8395
 FV3  C8   C  C     0   0.139   -8.0003  -23.8486  12.0584
 FV3  C10  C  CH3   0  -0.728   -8.5926  -23.5885  13.4092
 FV3  C9   C  CH2   0  -0.498   -8.9711  -23.8433  10.9028
 FV3  C11  C  CH2   0  -0.480   -8.9682  -22.5125  10.1307
 FV3  C12  C  C1    0  -0.270   -9.3764  -21.3446  10.9717
 FV3  C13  C  C     0   0.117   -8.6177  -20.3361  11.4096
 FV3  C14  C  CH3   0  -0.733   -7.1564  -20.1789  11.1088
 FV3  C15  C  CH2   0  -0.469   -9.2082  -19.2709  12.2963
 FV3  C16  C  CH2   0  -0.511   -9.0779  -17.8379  11.7534
 FV3  C17  C  C1    0  -0.244   -9.6865  -17.6698  10.3968
 FV3  C18  C  C     0   0.082  -10.8244  -17.0454  10.0808
 FV3  C20  C  CH3   0  -0.718  -11.7322  -16.3689  11.0651
 FV3  C19  C  CH3   0  -0.703  -11.2965  -16.9731   8.6571
 FV3  H1   H  HOH1  0   0.457   -2.5410  -28.4249  15.7407
 FV3  H2   H  HCH2  0   0.197   -2.8254  -27.1330  13.9084
 FV3  H3   H  HCH2  0   0.200   -3.7800  -26.4168  15.2143
 FV3  H4   H  HCH1  0   0.201   -5.7656  -27.6806  14.4900
 FV3  H5   H  HOH1  0   0.446   -4.4528  -29.4112  13.5160
 FV3  H6   H  HCH2  0   0.215   -6.0788  -26.6659  12.2161
 FV3  H7   H  HCH2  0   0.194   -4.3737  -26.2029  12.2058
 FV3  H8   H  HCH2  0   0.213   -4.6580  -23.8617  12.3990
 FV3  H9   H  HCH2  0   0.232   -5.7849  -23.2696  13.6137
 FV3  H10  H  H     0   0.233   -6.3873  -24.2768  10.8196
 FV3  H11  H  HCH3  0   0.238   -7.8529  -23.4816  14.2001
 FV3  H12  H  HCH3  0   0.244   -9.2062  -22.6859  13.3913
 FV3  H13  H  HCH3  0   0.241   -9.2579  -24.4099  13.6875
 FV3  H14  H  HCH2  0   0.233   -9.9825  -24.0492  11.2646
 FV3  H15  H  HCH2  0   0.243   -8.7231  -24.6441  10.2022
 FV3  H16  H  HCH2  0   0.233   -7.9814  -22.3647   9.6904
 FV3  H17  H  HCH2  0   0.235   -9.6664  -22.6090   9.2933
 FV3  H18  H  H     0   0.217  -10.4211  -21.3492  11.2767
 FV3  H19  H  HCH3  0   0.233   -6.5876  -20.0658  12.0354
 FV3  H20  H  HCH3  0   0.241   -6.7356  -21.0230  10.5672
 FV3  H21  H  HCH3  0   0.237   -6.9673  -19.2794  10.5177
 FV3  H22  H  HCH2  0   0.229  -10.2647  -19.4854  12.4747
 FV3  H23  H  HCH2  0   0.229   -8.7096  -19.3076  13.2718
 FV3  H24  H  HCH2  0   0.232   -8.0195  -17.5631  11.7073
 FV3  H25  H  HCH2  0   0.241   -9.5277  -17.1581  12.4784
 FV3  H26  H  H     0   0.219   -9.1313  -18.1296   9.5822
 FV3  H27  H  HCH3  0   0.238  -11.3860  -16.4304  12.0948
 FV3  H28  H  HCH3  0   0.233  -11.8515  -15.3117  10.8144
 FV3  H29  H  HCH3  0   0.233  -12.7320  -16.8085  11.0243
 FV3  H30  H  HCH3  0   0.234  -10.6171  -17.4802   7.9725
 FV3  H31  H  HCH3  0   0.228  -12.2865  -17.4236   8.5483
 FV3  H32  H  HCH3  0   0.229  -11.3932  -15.9345   8.3294

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
 FV3  C19  C18  single  1.502  0.020  1.502
 FV3  C11  C9   single  1.539  0.020  1.539
 FV3  C11  C12  single  1.496  0.020  1.496
 FV3  C18  C20  single  1.500  0.020  1.500
 FV3  C18  C17  double  1.336  0.020  1.336
 FV3  C14  C13  single  1.500  0.020  1.500
 FV3  C9   C8   single  1.509  0.020  1.509
 FV3  C17  C16  single  1.496  0.020  1.496
 FV3  C12  C13  double  1.336  0.020  1.336
 FV3  C13  C15  single  1.506  0.020  1.506
 FV3  C7   C8   double  1.336  0.020  1.336
 FV3  C7   C6   single  1.502  0.020  1.502
 FV3  C16  C15  single  1.538  0.020  1.538
 FV3  C8   C10  single  1.498  0.020  1.498
 FV3  C3   O5   single  1.404  0.020  1.404
 FV3  C3   C2   single  1.520  0.020  1.520
 FV3  C6   O5   single  1.416  0.020  1.416
 FV3  O6   C2   single  1.411  0.020  1.411
 FV3  C2   C1   single  1.519  0.020  1.519
 FV3  C1   O1   single  1.413  0.020  1.413
 FV3  O1   H1   single  0.850  0.020  0.980
 FV3  C1   H2   single  0.970  0.020  1.090
 FV3  C1   H3   single  0.970  0.020  1.090
 FV3  C2   H4   single  0.970  0.020  1.090
 FV3  O6   H5   single  0.850  0.020  0.980
 FV3  C3   H6   single  0.970  0.020  1.090
 FV3  C3   H7   single  0.970  0.020  1.090
 FV3  C6   H8   single  0.970  0.020  1.090
 FV3  C6   H9   single  0.970  0.020  1.090
 FV3  C7   H10  single  0.930  0.020  1.080
 FV3  C10  H11  single  0.970  0.020  1.090
 FV3  C10  H12  single  0.970  0.020  1.090
 FV3  C10  H13  single  0.970  0.020  1.090
 FV3  C9   H14  single  0.970  0.020  1.090
 FV3  C9   H15  single  0.970  0.020  1.090
 FV3  C11  H16  single  0.970  0.020  1.090
 FV3  C11  H17  single  0.970  0.020  1.090
 FV3  C12  H18  single  0.930  0.020  1.080
 FV3  C14  H19  single  0.970  0.020  1.090
 FV3  C14  H20  single  0.970  0.020  1.090
 FV3  C14  H21  single  0.970  0.020  1.090
 FV3  C15  H22  single  0.970  0.020  1.090
 FV3  C15  H23  single  0.970  0.020  1.090
 FV3  C16  H24  single  0.970  0.020  1.090
 FV3  C16  H25  single  0.970  0.020  1.090
 FV3  C17  H26  single  0.930  0.020  1.080
 FV3  C20  H27  single  0.970  0.020  1.090
 FV3  C20  H28  single  0.970  0.020  1.090
 FV3  C20  H29  single  0.970  0.020  1.090
 FV3  C19  H30  single  0.970  0.020  1.090
 FV3  C19  H31  single  0.970  0.020  1.090
 FV3  C19  H32  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
 FV3  H1   O1   C1   108.64  3.000
 FV3  H3   C1   H2   107.48  3.000
 FV3  H3   C1   C2   109.76  3.000
 FV3  H2   C1   C2   108.90  3.000
 FV3  H3   C1   O1   111.64  3.000
 FV3  H2   C1   O1   111.49  3.000
 FV3  C2   C1   O1   107.55  3.000
 FV3  H4   C2   C3   108.43  3.000
 FV3  H4   C2   O6   110.67  3.000
 FV3  C3   C2   O6   106.39  3.000
 FV3  H4   C2   C1   108.40  3.000
 FV3  O6   C2   C1   111.02  3.000
 FV3  C3   C2   C1   111.91  3.000
 FV3  H5   O6   C2   107.56  3.000
 FV3  H7   C3   H6   106.88  3.000
 FV3  H7   C3   O5   111.00  3.000
 FV3  H6   C3   O5   111.29  3.000
 FV3  H7   C3   C2   109.59  3.000
 FV3  H6   C3   C2   109.05  3.000
 FV3  O5   C3   C2   108.99  3.000
 FV3  C6   O5   C3   113.54  3.000
 FV3  H9   C6   H8   106.94  3.000
 FV3  H9   C6   C7   111.05  3.000
 FV3  H8   C6   C7   108.88  3.000
 FV3  H9   C6   O5   105.55  3.000
 FV3  H8   C6   O5   109.75  3.000
 FV3  C7   C6   O5   114.38  3.000
 FV3  H10  C7   C8   117.77  3.000
 FV3  H10  C7   C6   116.47  3.000
 FV3  C8   C7   C6   125.76  3.000
 FV3  C9   C8   C10  115.82  3.000
 FV3  C10  C8   C7   124.13  3.000
 FV3  C9   C8   C7   120.05  3.000
 FV3  H13  C10  H12  106.47  3.000
 FV3  H13  C10  H11  107.60  3.000
 FV3  H12  C10  H11  108.22  3.000
 FV3  H13  C10  C8   109.87  3.000
 FV3  H12  C10  C8   110.56  3.000
 FV3  H11  C10  C8   113.81  3.000
 FV3  H15  C9   H14  106.50  3.000
 FV3  H15  C9   C11  108.17  3.000
 FV3  H14  C9   C11  109.31  3.000
 FV3  H15  C9   C8   110.02  3.000
 FV3  H14  C9   C8   109.93  3.000
 FV3  C11  C9   C8   112.71  3.000
 FV3  H17  C11  H16  106.27  3.000
 FV3  H17  C11  C12  108.96  3.000
 FV3  H16  C11  C12  111.60  3.000
 FV3  H17  C11  C9   107.85  3.000
 FV3  H16  C11  C9   108.75  3.000
 FV3  C12  C11  C9   113.12  3.000
 FV3  H18  C12  C13  117.16  3.000
 FV3  H18  C12  C11  114.60  3.000
 FV3  C13  C12  C11  128.22  3.000
 FV3  C15  C13  C14  115.20  3.000
 FV3  C15  C13  C12  120.27  3.000
 FV3  C14  C13  C12  124.51  3.000
 FV3  H21  C14  H20  107.60  3.000
 FV3  H21  C14  H19  106.46  3.000
 FV3  H20  C14  H19  107.52  3.000
 FV3  H21  C14  C13  111.30  3.000
 FV3  H20  C14  C13  113.29  3.000
 FV3  H19  C14  C13  110.35  3.000
 FV3  H23  C15  H22  106.73  3.000
 FV3  H23  C15  C16  107.86  3.000
 FV3  H22  C15  C16  108.82  3.000
 FV3  H23  C15  C13  108.77  3.000
 FV3  H22  C15  C13  109.65  3.000
 FV3  C16  C15  C13  114.70  3.000
 FV3  H25  C16  H24  105.68  3.000
 FV3  H25  C16  C17  111.39  3.000
 FV3  H24  C16  C17  109.08  3.000
 FV3  H25  C16  C15  108.13  3.000
 FV3  H24  C16  C15  109.32  3.000
 FV3  C17  C16  C15  112.97  3.000
 FV3  H26  C17  C18  117.08  3.000
 FV3  H26  C17  C16  115.08  3.000
 FV3  C18  C17  C16  127.84  3.000
 FV3  C19  C18  C20  114.21  3.000
 FV3  C20  C18  C17  124.82  3.000
 FV3  C19  C18  C17  120.97  3.000
 FV3  H29  C20  H28  106.29  3.000
 FV3  H29  C20  H27  107.68  3.000
 FV3  H28  C20  H27  107.85  3.000
 FV3  H29  C20  C18  110.34  3.000
 FV3  H28  C20  C18  110.59  3.000
 FV3  H27  C20  C18  113.76  3.000
 FV3  H32  C19  H31  106.35  3.000
 FV3  H32  C19  H30  107.99  3.000
 FV3  H31  C19  H30  108.08  3.000
 FV3  H32  C19  C18  110.96  3.000
 FV3  H31  C19  C18  111.05  3.000
 FV3  H30  C19  C18  112.16  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
 FV3  Var_01  C9   C8   C7   C6    178.22   0.0  2
 FV3  Var_02  C14  C13  C12  C11     0.79   0.0  2
 FV3  Var_03  C19  C18  C17  C16  -179.77   0.0  2
 FV3  Var_04  C7   C6   O5   C3     61.57  30.0  1
 FV3  Var_05  C8   C7   C6   O5     79.88  30.0  1
 FV3  Var_06  C11  C9   C8   C7    -80.28  30.0  1
 FV3  Var_07  C12  C11  C9   C8    -61.58  30.0  2
 FV3  Var_08  C13  C12  C11  C9    109.96  30.0  3
 FV3  Var_09  C16  C15  C13  C12  -122.82  30.0  3
 FV3  Var_10  C17  C16  C15  C13    56.82  30.0  1
 FV3  Var_11  C18  C17  C16  C15   106.58  30.0  2
 FV3  Var_12  H6   C3   O5   C6    -69.68  30.0  2
 FV3  Var_13  H11  C10  C8   C7      6.52  30.0  3
 FV3  Var_14  H19  C14  C13  C12  -126.04  30.0  3
 FV3  Var_15  H30  C19  C18  C17     0.40  30.0  3
 FV3  Var_16  H27  C20  C18  C17    -0.31  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
 FV3  chir_01  C2  C3  O6  C1  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
 FV3  plan-1  C16  0.020
 FV3  plan-1  C17  0.020
 FV3  plan-1  C18  0.020
 FV3  plan-1  C20  0.020
 FV3  plan-1  C19  0.020
 FV3  plan-1  H26  0.020
 FV3  plan-2  C11  0.020
 FV3  plan-2  C12  0.020
 FV3  plan-2  C13  0.020
 FV3  plan-2  C14  0.020
 FV3  plan-2  C15  0.020
 FV3  plan-2  H18  0.020
 FV3  plan-3  C6   0.020
 FV3  plan-3  C7   0.020
 FV3  plan-3  C8   0.020
 FV3  plan-3  C10  0.020
 FV3  plan-3  C9   0.020
 FV3  plan-3  H10  0.020

