# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:59:34 2021
#   Inital geometry file: a 159 line input string
#   Ligand name: phosphono [(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCO[P](O)(=O)O[P](O)(O)=O)CC\C=C(/C)CC\C=C(/C)CCC=C(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
 ELR  ELR  'phosphono [(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate'  ligand  67  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ELR
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
 ELR  C11  C  CH2   0  -0.510   8.3533  -12.0715  -18.1291
 ELR  C12  C  C1    0  -0.248   8.0780  -11.8692  -16.6728
 ELR  C13  C  C     0   0.110   7.9381  -10.7211  -16.0063
 ELR  C14  C  CH3   0  -0.733   7.9354   -9.3615  -16.6412
 ELR  C15  C  CH2   0  -0.483   7.8311  -10.7424  -14.5042
 ELR  C16  C  CH2   0  -0.482   9.0850  -10.1744  -13.8241
 ELR  C17  C  C1    0  -0.243   9.0264  -10.3052  -12.3332
 ELR  C19  C  CH3   0  -0.710   9.7913  -10.7232  -10.0191
 ELR  C20  C  CH3   0  -0.742  11.4081  -10.9984  -11.9331
 ELR  O2A  O  O     0  -0.666  12.5105  -13.5301   -9.3134
 ELR  PA   P  P     0   1.484  13.5013  -14.6161   -9.3763
 ELR  O1A  O  OH1   0  -0.726  15.0432  -14.2480   -9.4236
 ELR  O3A  O  O2    0  -0.695  13.3059  -15.5780   -8.0809
 ELR  PB   P  P     0   1.468  14.2697  -16.6799   -7.3792
 ELR  O2B  O  O     0  -0.679  13.4556  -17.5505   -6.5183
 ELR  O1B  O  OH1   0  -0.728  15.4426  -15.8448   -6.7155
 ELR  O3B  O  OH1   0  -0.734  15.1056  -17.3364   -8.5565
 ELR  O1   O  O2    0  -0.587  13.4557  -15.5988  -10.6156
 ELR  C2   C  CH2   0  -0.462  11.9051  -14.9942  -12.3856
 ELR  C3   C  CH1   0  -0.239  10.5955  -15.2987  -13.1159
 ELR  C4   C  CH3   0  -0.666   9.3930  -15.2244  -12.1752
 ELR  C5   C  CH2   0  -0.402  10.3836  -14.3232  -14.2757
 ELR  C6   C  CH2   0  -0.504  11.4161  -14.3860  -15.4066
 ELR  C7   C  C1    0  -0.248  11.0633  -13.3841  -16.4635
 ELR  C8   C  C     0   0.097  10.2937  -13.5801  -17.5365
 ELR  C10  C  CH3   0  -0.732   9.7259  -14.9124  -17.9287
 ELR  C9   C  CH2   0  -0.468   9.8398  -12.4122  -18.3695
 ELR  C18  C  C     0   0.080  10.0089  -10.6659  -11.5035
 ELR  H1   H  HCH2  0   0.241   8.0991  -11.1896  -18.7192
 ELR  H2   H  HCH2  0   0.230   7.7287  -12.8846  -18.5107
 ELR  H3   H  H     0   0.223   8.0715  -12.7807  -16.0804
 ELR  H4   H  HCH3  0   0.232   7.0458   -8.8009  -16.3425
 ELR  H5   H  HCH3  0   0.237   8.7949   -8.7702  -16.3164
 ELR  H6   H  HCH3  0   0.240   7.9569   -9.3964  -17.7289
 ELR  H7   H  HCH2  0   0.221   6.9582  -10.1680  -14.1729
 ELR  H8   H  HCH2  0   0.230   7.6793  -11.7700  -14.1640
 ELR  H9   H  HCH2  0   0.232   9.9649  -10.6751  -14.2349
 ELR  H10  H  HCH2  0   0.234   9.1900   -9.1164  -14.0898
 ELR  H11  H  H     0   0.216   8.0641  -10.0532  -11.8903
 ELR  H12  H  HCH3  0   0.232   8.7706  -10.4633   -9.7399
 ELR  H13  H  HCH3  0   0.233  10.0108  -11.7221   -9.6330
 ELR  H14  H  HCH3  0   0.229  10.4672  -10.0388   -9.4991
 ELR  H15  H  HCH3  0   0.247  11.7993  -11.8351  -11.3517
 ELR  H16  H  HCH3  0   0.230  11.4903  -11.2517  -12.9889
 ELR  H17  H  HCH3  0   0.241  12.0775  -10.1539  -11.7458
 ELR  H18  H  HOH1  0   0.509  15.3045  -13.5278   -8.8332
 ELR  H19  H  HOH1  0   0.509  15.2214  -15.4631   -5.8549
 ELR  H20  H  HOH1  0   0.508  14.6699  -18.0755   -9.0017
 ELR  H21  H  HCH2  0   0.238  11.3941  -15.9137  -10.4855
 ELR  H22  H  HCH2  0   0.255  12.2934  -16.9611  -11.5756
 ELR  H23  H  HCH2  0   0.244  12.7444  -15.0459  -13.0833
 ELR  H24  H  HCH2  0   0.238  11.8638  -13.9668  -12.0129
 ELR  H25  H  HCH1  0   0.218  10.6513  -16.3140  -13.5289
 ELR  H26  H  HCH3  0   0.230   9.4096  -15.9946  -11.4040
 ELR  H27  H  HCH3  0   0.216   9.3547  -14.2529  -11.6751
 ELR  H28  H  HCH3  0   0.232   8.4614  -15.3439  -12.7304
 ELR  H29  H  HCH2  0   0.219  10.3461  -13.3035  -13.8730
 ELR  H30  H  HCH2  0   0.229   9.3947  -14.5062  -14.7075
 ELR  H31  H  HCH2  0   0.227  11.4505  -15.4031  -15.8064
 ELR  H32  H  HCH2  0   0.231  12.4155  -14.1692  -15.0208
 ELR  H33  H  H     0   0.215  11.3789  -12.3641  -16.2545
 ELR  H34  H  HCH3  0   0.241  10.2008  -15.7476  -17.4172
 ELR  H35  H  HCH3  0   0.236   8.6557  -14.9653  -17.7083
 ELR  H36  H  HCH3  0   0.233   9.8278  -15.0749  -19.0042
 ELR  H37  H  HCH2  0   0.229  10.4383  -11.5315  -18.1251
 ELR  H38  H  HCH2  0   0.226   9.9860  -12.6196  -19.4351
 ELR  C1   C  CH2   0  -0.182  12.1899  -15.9320  -11.2319

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
 ELR  C10  C8   single  1.500  0.020  1.500
 ELR  C9   C8   single  1.505  0.020  1.505
 ELR  C9   C11  single  1.544  0.020  1.544
 ELR  C14  C13  single  1.501  0.020  1.501
 ELR  C8   C7   double  1.335  0.020  1.335
 ELR  C11  C12  single  1.496  0.020  1.496
 ELR  C20  C18  single  1.501  0.020  1.501
 ELR  C7   C6   single  1.498  0.020  1.498
 ELR  C13  C12  double  1.335  0.020  1.335
 ELR  C13  C15  single  1.506  0.020  1.506
 ELR  C6   C5   single  1.533  0.020  1.533
 ELR  C16  C15  single  1.535  0.020  1.535
 ELR  C16  C17  single  1.498  0.020  1.498
 ELR  C18  C17  double  1.336  0.020  1.336
 ELR  C18  C19  single  1.501  0.020  1.501
 ELR  C5   C3   single  1.530  0.020  1.530
 ELR  C3   C2   single  1.530  0.020  1.530
 ELR  C3   C4   single  1.528  0.020  1.528
 ELR  C2   C1   single  1.514  0.020  1.514
 ELR  C1   O1   single  1.447  0.020  1.447
 ELR  O1   PA   single  1.582  0.020  1.582
 ELR  PA   O3A  single  1.625  0.020  1.625
 ELR  PA   O2A  double  1.471  0.020  1.471
 ELR  PA   O1A  single  1.586  0.020  1.586
 ELR  O3A  PB   single  1.623  0.020  1.623
 ELR  O2B  PB   double  1.470  0.020  1.470
 ELR  O3B  PB   single  1.586  0.020  1.586
 ELR  PB   O1B  single  1.585  0.020  1.585
 ELR  C11  H1   single  0.970  0.020  1.090
 ELR  C11  H2   single  0.970  0.020  1.090
 ELR  C12  H3   single  0.930  0.020  1.080
 ELR  C14  H4   single  0.970  0.020  1.090
 ELR  C14  H5   single  0.970  0.020  1.090
 ELR  C14  H6   single  0.970  0.020  1.090
 ELR  C15  H7   single  0.970  0.020  1.090
 ELR  C15  H8   single  0.970  0.020  1.090
 ELR  C16  H9   single  0.970  0.020  1.090
 ELR  C16  H10  single  0.970  0.020  1.090
 ELR  C17  H11  single  0.930  0.020  1.080
 ELR  C19  H12  single  0.970  0.020  1.090
 ELR  C19  H13  single  0.970  0.020  1.090
 ELR  C19  H14  single  0.970  0.020  1.090
 ELR  C20  H15  single  0.970  0.020  1.090
 ELR  C20  H16  single  0.970  0.020  1.090
 ELR  C20  H17  single  0.970  0.020  1.090
 ELR  O1A  H18  single  0.850  0.020  0.980
 ELR  O1B  H19  single  0.850  0.020  0.980
 ELR  O3B  H20  single  0.850  0.020  0.980
 ELR  C1   H21  single  0.970  0.020  1.090
 ELR  C1   H22  single  0.970  0.020  1.090
 ELR  C2   H23  single  0.970  0.020  1.090
 ELR  C2   H24  single  0.970  0.020  1.090
 ELR  C3   H25  single  0.970  0.020  1.090
 ELR  C4   H26  single  0.970  0.020  1.090
 ELR  C4   H27  single  0.970  0.020  1.090
 ELR  C4   H28  single  0.970  0.020  1.090
 ELR  C5   H29  single  0.970  0.020  1.090
 ELR  C5   H30  single  0.970  0.020  1.090
 ELR  C6   H31  single  0.970  0.020  1.090
 ELR  C6   H32  single  0.970  0.020  1.090
 ELR  C7   H33  single  0.930  0.020  1.080
 ELR  C10  H34  single  0.970  0.020  1.090
 ELR  C10  H35  single  0.970  0.020  1.090
 ELR  C10  H36  single  0.970  0.020  1.090
 ELR  C9   H37  single  0.970  0.020  1.090
 ELR  C9   H38  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
 ELR  H2   C11  H1   106.20  3.000
 ELR  H2   C11  C9   109.35  3.000
 ELR  H1   C11  C9   108.57  3.000
 ELR  H2   C11  C12  109.57  3.000
 ELR  H1   C11  C12  111.98  3.000
 ELR  C9   C11  C12  111.02  3.000
 ELR  H3   C12  C13  116.64  3.000
 ELR  H3   C12  C11  114.72  3.000
 ELR  C13  C12  C11  128.44  3.000
 ELR  C15  C13  C14  115.76  3.000
 ELR  C15  C13  C12  119.56  3.000
 ELR  C14  C13  C12  124.62  3.000
 ELR  H6   C14  H5   107.39  3.000
 ELR  H6   C14  H4   107.79  3.000
 ELR  H5   C14  H4   106.34  3.000
 ELR  H6   C14  C13  113.19  3.000
 ELR  H5   C14  C13  111.30  3.000
 ELR  H4   C14  C13  110.52  3.000
 ELR  H8   C15  H7   106.73  3.000
 ELR  H8   C15  C16  108.86  3.000
 ELR  H7   C15  C16  108.82  3.000
 ELR  H8   C15  C13  109.48  3.000
 ELR  H7   C15  C13  110.53  3.000
 ELR  C16  C15  C13  112.25  3.000
 ELR  H10  C16  H9   105.91  3.000
 ELR  H10  C16  C17  109.23  3.000
 ELR  H9   C16  C17  111.46  3.000
 ELR  H10  C16  C15  109.14  3.000
 ELR  H9   C16  C15  108.76  3.000
 ELR  C17  C16  C15  112.13  3.000
 ELR  H11  C17  C18  117.38  3.000
 ELR  H11  C17  C16  114.79  3.000
 ELR  C18  C17  C16  127.82  3.000
 ELR  H14  C19  H13  106.25  3.000
 ELR  H14  C19  H12  107.93  3.000
 ELR  H13  C19  H12  108.39  3.000
 ELR  H14  C19  C18  110.90  3.000
 ELR  H13  C19  C18  110.79  3.000
 ELR  H12  C19  C18  112.33  3.000
 ELR  H17  C20  H16  107.43  3.000
 ELR  H17  C20  H15  106.34  3.000
 ELR  H16  C20  H15  108.12  3.000
 ELR  H17  C20  C18  110.52  3.000
 ELR  H16  C20  C18  113.54  3.000
 ELR  H15  C20  C18  110.58  3.000
 ELR  O1   PA   O3A  104.67  3.000
 ELR  O3A  PA   O1A  106.14  3.000
 ELR  O1   PA   O1A   98.56  3.000
 ELR  O1A  PA   O2A  118.99  3.000
 ELR  O3A  PA   O2A  108.77  3.000
 ELR  O1   PA   O2A  118.19  3.000
 ELR  H18  O1A  PA   114.66  3.000
 ELR  PB   O3A  PA   132.44  3.000
 ELR  O3B  PB   O1B   97.98  3.000
 ELR  O1B  PB   O2B  118.45  3.000
 ELR  O3B  PB   O2B  118.77  3.000
 ELR  O1B  PB   O3A  105.23  3.000
 ELR  O3B  PB   O3A  105.84  3.000
 ELR  O2B  PB   O3A  109.04  3.000
 ELR  H19  O1B  PB   114.27  3.000
 ELR  H20  O3B  PB   114.88  3.000
 ELR  C1   O1   PA   120.13  3.000
 ELR  H24  C2   H23  106.92  3.000
 ELR  H24  C2   C3   108.50  3.000
 ELR  H23  C2   C3   110.08  3.000
 ELR  H24  C2   C1   109.23  3.000
 ELR  H23  C2   C1   108.23  3.000
 ELR  C3   C2   C1   113.67  3.000
 ELR  H25  C3   C5   108.15  3.000
 ELR  H25  C3   C4   108.45  3.000
 ELR  C5   C3   C4   109.05  3.000
 ELR  H25  C3   C2   108.68  3.000
 ELR  C4   C3   C2   111.71  3.000
 ELR  C5   C3   C2   110.70  3.000
 ELR  H28  C4   H27  107.47  3.000
 ELR  H28  C4   H26  107.19  3.000
 ELR  H27  C4   H26  107.74  3.000
 ELR  H28  C4   C3   110.69  3.000
 ELR  H27  C4   C3   110.63  3.000
 ELR  H26  C4   C3   112.90  3.000
 ELR  H30  C5   H29  105.63  3.000
 ELR  H30  C5   C6   108.10  3.000
 ELR  H29  C5   C6   109.39  3.000
 ELR  H30  C5   C3   108.52  3.000
 ELR  H29  C5   C3   108.60  3.000
 ELR  C6   C5   C3   116.09  3.000
 ELR  H32  C6   H31  106.55  3.000
 ELR  H32  C6   C7   109.37  3.000
 ELR  H31  C6   C7   111.80  3.000
 ELR  H32  C6   C5   110.33  3.000
 ELR  H31  C6   C5   109.22  3.000
 ELR  C7   C6   C5   109.53  3.000
 ELR  H33  C7   C8   117.35  3.000
 ELR  H33  C7   C6   115.02  3.000
 ELR  C8   C7   C6   127.19  3.000
 ELR  C9   C8   C10  115.49  3.000
 ELR  C9   C8   C7   120.33  3.000
 ELR  C10  C8   C7   123.96  3.000
 ELR  H36  C10  H35  106.40  3.000
 ELR  H36  C10  H34  107.93  3.000
 ELR  H35  C10  H34  107.16  3.000
 ELR  H36  C10  C8   110.74  3.000
 ELR  H35  C10  C8   111.13  3.000
 ELR  H34  C10  C8   113.17  3.000
 ELR  H38  C9   H37  107.29  3.000
 ELR  H38  C9   C8   110.57  3.000
 ELR  H37  C9   C8   109.67  3.000
 ELR  H38  C9   C11  108.77  3.000
 ELR  H37  C9   C11  108.34  3.000
 ELR  C8   C9   C11  112.06  3.000
 ELR  C20  C18  C19  114.18  3.000
 ELR  C19  C18  C17  121.20  3.000
 ELR  C20  C18  C17  124.59  3.000
 ELR  H22  C1   H21  107.51  3.000
 ELR  H22  C1   C2   111.25  3.000
 ELR  H21  C1   C2   111.94  3.000
 ELR  H22  C1   O1   105.59  3.000
 ELR  H21  C1   O1   110.05  3.000
 ELR  C2   C1   O1   110.28  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
 ELR  Var_01  C14  C13  C12  C11     4.73   0.0  2
 ELR  Var_02  C20  C18  C17  C16     0.97   0.0  2
 ELR  Var_03  C10  C8   C7   C6     -5.23   0.0  2
 ELR  Var_04  C8   C9   C11  C12    53.61  30.0  1
 ELR  Var_05  C16  C15  C13  C12   109.36  30.0  3
 ELR  Var_06  C9   C11  C12  C13   101.48  30.0  2
 ELR  Var_07  C17  C16  C15  C13  -175.06  30.0  2
 ELR  Var_08  C18  C17  C16  C15   138.15  30.0  3
 ELR  Var_09  C2   C1   O1   PA     93.09  30.0  1
 ELR  Var_10  O2B  PB   O3A  PA   -162.01  30.0  3
 ELR  Var_11  O1   PA   O3A  PB     70.63  30.0  2
 ELR  Var_12  C3   C2   C1   O1    178.67  30.0  2
 ELR  Var_13  C7   C6   C5   C3    179.51  30.0  2
 ELR  Var_14  C8   C7   C6   C5    -90.66  30.0  1
 ELR  Var_15  H4   C14  C13  C12   126.99  30.0  3
 ELR  Var_16  H15  C20  C18  C17  -141.37  30.0  3
 ELR  Var_17  H12  C19  C18  C17     1.14  30.0  3
 ELR  Var_18  H34  C10  C8   C7    -15.05  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
 ELR  chir_02  C3  C5   C2   C4   negativ
 ELR  chir_03  PA  O3A  O2A  O1A  both

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
 ELR  plan-1  C6   0.020
 ELR  plan-1  C7   0.020
 ELR  plan-1  C8   0.020
 ELR  plan-1  C10  0.020
 ELR  plan-1  C9   0.020
 ELR  plan-1  H33  0.020
 ELR  plan-2  C11  0.020
 ELR  plan-2  C12  0.020
 ELR  plan-2  C13  0.020
 ELR  plan-2  C14  0.020
 ELR  plan-2  C15  0.020
 ELR  plan-2  H3   0.020
 ELR  plan-3  C16  0.020
 ELR  plan-3  C17  0.020
 ELR  plan-3  C19  0.020
 ELR  plan-3  C20  0.020
 ELR  plan-3  C18  0.020
 ELR  plan-3  H11  0.020

