# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 17:53:34 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: [2-oxo-2-({[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy}amino)ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(C)=C\CC\C(C)=C\CONC(=O)C[P](O)(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
 FII  FII  '[2-oxo-2-({[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy}amino)ethyl]phosphonic acid'  ligand  52  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FII
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
 FII  C1    C  CH3    0  -0.705  -0.5323   0.8665  10.3159
 FII  C2    C  C      0   0.077  -0.4955   0.9925   8.8197
 FII  C6    C  CH3    0  -0.721   0.3545   2.1220   8.3174
 FII  C10   C  C1     0  -0.251  -1.1752   0.1434   8.0444
 FII  C11   C  CH2    0  -0.491  -1.2326   0.0981   6.5500
 FII  C12   C  CH2    0  -0.481  -0.5711  -1.1748   5.9987
 FII  C15   C  C      0   0.109  -0.5981  -1.2560   4.4948
 FII  C18   C  CH3    0  -0.733  -1.9544  -1.4397   3.8802
 FII  C22   C  C1     0  -0.264   0.5395  -1.1516   3.8025
 FII  C23   C  CH2    0  -0.493   0.7305  -1.1562   2.3186
 FII  C24   C  CH2    0  -0.484   1.2331   0.2091   1.8242
 FII  C27   C  C      0   0.158   1.5063   0.2638   0.3457
 FII  C30   C  CH3    0  -0.747   2.6335  -0.5947  -0.1455
 FII  C34   C  C1     0  -0.363   0.7788   1.0573  -0.4459
 FII  C35   C  CH2    0  -0.183   0.9865   1.2282  -1.9170
 FII  O36   O  O2     0  -0.400   0.3498   0.1442  -2.5959
 FII  N42   N  NH1    0  -0.402   0.5627   0.2414  -3.9492
 FII  C43   C  C      0   0.475   1.4748  -0.5876  -4.5085
 FII  O44   O  O      0  -0.504   2.2540  -1.2776  -3.8624
 FII  C45   C  CH2    0  -0.858   1.4365  -0.5235  -6.0099
 FII  P46   P  P      0   1.183  -0.2905  -0.7785  -6.7202
 FII  O49   O  O      0  -0.876  -1.1110   0.3352  -6.0185
 FII  O50   O  OP    -1  -0.879  -0.1377  -0.5647  -8.2225
 FII  O51   O  OP    -1  -0.880  -0.6953  -2.1875  -6.2980
 FII  H11   H  HCH3   0   0.230   0.4696   0.6951  10.7189
 FII  H12   H  HCH3   0   0.229  -0.8974   1.7867  10.7794
 FII  H13   H  HCH3   0   0.235  -1.1712   0.0463  10.6431
 FII  H61   H  HCH3   0   0.239   0.3566   2.2211   7.2339
 FII  H62   H  HCH3   0   0.234   0.0167   3.0724   8.7382
 FII  H63   H  HCH3   0   0.234   1.3907   1.9935   8.6410
 FII  H101  H  H      0   0.220  -1.7443  -0.6396   8.5423
 FII  H111  H  HCH2   0   0.233  -2.2809   0.1260   6.2366
 FII  H112  H  HCH2   0   0.236  -0.7548   0.9691   6.0990
 FII  H121  H  HCH2   0   0.233   0.4631  -1.2114   6.3499
 FII  H122  H  HCH2   0   0.224  -1.0779  -2.0477   6.4263
 FII  H181  H  HCH3   0   0.243  -1.9193  -1.6026   2.8050
 FII  H182  H  HCH3   0   0.234  -2.4668  -2.2944   4.3293
 FII  H183  H  HCH3   0   0.239  -2.5923  -0.5702   4.0566
 FII  H221  H  H      0   0.221   1.4568  -1.0178   4.3737
 FII  H231  H  HCH2   0   0.235   1.4627  -1.9278   2.0623
 FII  H232  H  HCH2   0   0.240  -0.1896  -1.4122   1.7905
 FII  H241  H  HCH2   0   0.239   0.4985   0.9721   2.0926
 FII  H242  H  HCH2   0   0.232   2.1549   0.4580   2.3623
 FII  H301  H  HCH3   0   0.244   2.4747  -1.6374   0.1365
 FII  H302  H  HCH3   0   0.261   2.7566  -0.5744  -1.2260
 FII  H303  H  HCH3   0   0.236   3.5742  -0.2894   0.3198
 FII  H341  H  H      0   0.234  -0.0277   1.6308   0.0012
 FII  H351  H  HCH2   0   0.222   0.5563   2.1793  -2.2486
 FII  H352  H  HCH2   0   0.214   2.0513   1.2482  -2.1679
 FII  HN1   H  HNH1   0   0.405  -0.2675   0.4667  -4.5447
 FII  H451  H  HCH2   0   0.239   1.7919   0.4617  -6.3282
 FII  H452  H  HCH2   0   0.229   2.1351  -1.2609  -6.4089

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
 FII  C1   C2    single  1.502  0.020  1.502
 FII  C1   H11   single  0.970  0.020  1.090
 FII  C1   H12   single  0.970  0.020  1.090
 FII  C1   H13   single  0.970  0.020  1.090
 FII  C2   C6    single  1.500  0.020  1.500
 FII  C2   C10   double  1.336  0.020  1.336
 FII  C6   H61   single  0.970  0.020  1.090
 FII  C6   H62   single  0.970  0.020  1.090
 FII  C6   H63   single  0.970  0.020  1.090
 FII  C10  C11   single  1.496  0.020  1.496
 FII  C10  H101  single  0.930  0.020  1.080
 FII  C11  C12   single  1.537  0.020  1.537
 FII  C11  H111  single  0.970  0.020  1.090
 FII  C11  H112  single  0.970  0.020  1.090
 FII  C12  C15   single  1.506  0.020  1.506
 FII  C12  H121  single  0.970  0.020  1.090
 FII  C12  H122  single  0.970  0.020  1.090
 FII  C15  C18   single  1.500  0.020  1.500
 FII  C15  C22   double  1.336  0.020  1.336
 FII  C18  H181  single  0.970  0.020  1.090
 FII  C18  H182  single  0.970  0.020  1.090
 FII  C18  H183  single  0.970  0.020  1.090
 FII  C22  C23   single  1.496  0.020  1.496
 FII  C22  H221  single  0.930  0.020  1.080
 FII  C23  C24   single  1.537  0.020  1.537
 FII  C23  H231  single  0.970  0.020  1.090
 FII  C23  H232  single  0.970  0.020  1.090
 FII  C24  C27   single  1.505  0.020  1.505
 FII  C24  H241  single  0.970  0.020  1.090
 FII  C24  H242  single  0.970  0.020  1.090
 FII  C27  C30   single  1.500  0.020  1.500
 FII  C27  C34   double  1.336  0.020  1.336
 FII  C30  H301  single  0.970  0.020  1.090
 FII  C30  H302  single  0.970  0.020  1.090
 FII  C30  H303  single  0.970  0.020  1.090
 FII  C34  C35   single  1.496  0.020  1.496
 FII  C34  H341  single  0.930  0.020  1.080
 FII  C35  O36   single  1.429  0.020  1.429
 FII  C35  H351  single  0.970  0.020  1.090
 FII  C35  H352  single  0.970  0.020  1.090
 FII  O36  N42   single  1.373  0.020  1.373
 FII  N42  C43   single  1.354  0.020  1.354
 FII  N42  HN1   single  0.890  0.020  1.040
 FII  C43  O44   double  1.225  0.020  1.225
 FII  C43  C45   single  1.503  0.020  1.503
 FII  C45  P46   single  1.885  0.020  1.885
 FII  C45  H451  single  0.970  0.020  1.090
 FII  C45  H452  single  0.970  0.020  1.090
 FII  P46  O49   deloc   1.551  0.020  1.551
 FII  P46  O50   deloc   1.525  0.020  1.525
 FII  P46  O51   deloc   1.526  0.020  1.526

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
 FII  H13   C1   H12   108.09  3.000
 FII  H13   C1   H11   107.96  3.000
 FII  H12   C1   H11   106.36  3.000
 FII  H13   C1   C2    112.13  3.000
 FII  H12   C1   C2    111.10  3.000
 FII  H11   C1   C2    110.97  3.000
 FII  C10   C2   C6    124.93  3.000
 FII  C10   C2   C1    120.82  3.000
 FII  C6    C2   C1    114.25  3.000
 FII  H63   C6   H62   106.33  3.000
 FII  H63   C6   H61   107.68  3.000
 FII  H62   C6   H61   107.74  3.000
 FII  H63   C6   C2    110.46  3.000
 FII  H62   C6   C2    110.52  3.000
 FII  H61   C6   C2    113.77  3.000
 FII  H101  C10  C11   114.52  3.000
 FII  H101  C10  C2    117.25  3.000
 FII  C11   C10  C2    128.21  3.000
 FII  H112  C11  H111  106.31  3.000
 FII  H112  C11  C12   108.93  3.000
 FII  H111  C11  C12   109.31  3.000
 FII  H112  C11  C10   111.84  3.000
 FII  H111  C11  C10   108.78  3.000
 FII  C12   C11  C10   111.52  3.000
 FII  H122  C12  H121  106.59  3.000
 FII  H122  C12  C15   109.77  3.000
 FII  H121  C12  C15   109.64  3.000
 FII  H122  C12  C11   108.70  3.000
 FII  H121  C12  C11   108.65  3.000
 FII  C15   C12  C11   113.27  3.000
 FII  C22   C15  C18   124.55  3.000
 FII  C22   C15  C12   119.87  3.000
 FII  C18   C15  C12   115.58  3.000
 FII  H183  C18  H182  106.40  3.000
 FII  H183  C18  H181  107.30  3.000
 FII  H182  C18  H181  107.70  3.000
 FII  H183  C18  C15   111.35  3.000
 FII  H182  C18  C15   110.56  3.000
 FII  H181  C18  C15   113.20  3.000
 FII  H221  C22  C23   114.40  3.000
 FII  H221  C22  C15   117.07  3.000
 FII  C23   C22  C15   128.50  3.000
 FII  H232  C23  H231  106.59  3.000
 FII  H232  C23  C24   109.18  3.000
 FII  H231  C23  C24   109.41  3.000
 FII  H232  C23  C22   111.90  3.000
 FII  H231  C23  C22   108.66  3.000
 FII  C24   C23  C22   110.99  3.000
 FII  H242  C24  H241  106.63  3.000
 FII  H242  C24  C27   108.75  3.000
 FII  H241  C24  C27   109.76  3.000
 FII  H242  C24  C23   108.60  3.000
 FII  H241  C24  C23   108.75  3.000
 FII  C27   C24  C23   114.08  3.000
 FII  C34   C27  C30   123.72  3.000
 FII  C34   C27  C24   120.32  3.000
 FII  C30   C27  C24   115.95  3.000
 FII  H303  C30  H302  108.68  3.000
 FII  H303  C30  H301  106.38  3.000
 FII  H302  C30  H301  106.91  3.000
 FII  H303  C30  C27   110.34  3.000
 FII  H302  C30  C27   113.56  3.000
 FII  H301  C30  C27   110.66  3.000
 FII  H341  C34  C35   116.60  3.000
 FII  H341  C34  C27   118.30  3.000
 FII  C35   C34  C27   125.10  3.000
 FII  H352  C35  H351  107.28  3.000
 FII  H352  C35  O36   109.79  3.000
 FII  H351  C35  O36   109.87  3.000
 FII  H352  C35  C34   111.27  3.000
 FII  H351  C35  C34   110.03  3.000
 FII  O36   C35  C34   108.59  3.000
 FII  N42   O36  C35   110.21  3.000
 FII  HN1   N42  C43   115.56  3.000
 FII  HN1   N42  O36   116.94  3.000
 FII  C43   N42  O36   117.92  3.000
 FII  C45   C43  O44   124.54  3.000
 FII  C45   C43  N42   111.67  3.000
 FII  O44   C43  N42   123.76  3.000
 FII  H452  C45  H451  107.09  3.000
 FII  H452  C45  P46   110.94  3.000
 FII  H451  C45  P46   108.04  3.000
 FII  H452  C45  C43   108.66  3.000
 FII  H451  C45  C43   108.69  3.000
 FII  P46   C45  C43   113.21  3.000
 FII  O51   P46  O50   115.38  3.000
 FII  O51   P46  O49   113.43  3.000
 FII  O50   P46  O49   113.45  3.000
 FII  O51   P46  C45   105.30  3.000
 FII  O50   P46  C45   105.10  3.000
 FII  O49   P46  C45   102.54  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
 FII  CONST_01  O44   C43  N42  O36     0.00   0.0  0
 FII  CONST_02  C45   C43  N42  O36   180.00   0.0  0
 FII  Var_01    C11   C10  C2   C1   -178.58   0.0  2
 FII  Var_02    C23   C22  C15  C12  -177.64   0.0  2
 FII  Var_03    C35   C34  C27  C24   177.89   0.0  2
 FII  Var_04    C12   C11  C10  C2    113.27  30.0  3
 FII  Var_05    C15   C12  C11  C10  -179.59  30.0  3
 FII  Var_06    C18   C15  C12  C11   -67.93  30.0  3
 FII  Var_07    C24   C23  C22  C15   113.54  30.0  3
 FII  Var_08    C27   C24  C23  C22   177.48  30.0  3
 FII  Var_09    C30   C27  C24  C23   -65.85  30.0  3
 FII  Var_10    O36   C35  C34  C27    81.87  30.0  3
 FII  Var_11    C43   N42  O36  C35   103.88  30.0  3
 FII  Var_12    P46   C45  C43  N42   -52.12  30.0  3
 FII  Var_13    O49   P46  C45  C43    56.65  30.0  3
 FII  Var_14    H61   C6   C2   C1   -178.60  30.0  3
 FII  Var_15    H11   C1   C2   C6    -60.08  30.0  3
 FII  Var_16    H181  C18  C15  C12  -173.68  30.0  3
 FII  Var_17    H301  C30  C27  C24    56.09  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
 FII  plan-1  O36   0.020
 FII  plan-1  N42   0.020
 FII  plan-1  C43   0.020
 FII  plan-1  O44   0.020
 FII  plan-1  C45   0.020
 FII  plan-1  HN1   0.020
 FII  plan-2  C1    0.020
 FII  plan-2  C2    0.020
 FII  plan-2  C6    0.020
 FII  plan-2  C10   0.020
 FII  plan-2  C11   0.020
 FII  plan-2  H101  0.020
 FII  plan-3  C12   0.020
 FII  plan-3  C15   0.020
 FII  plan-3  C18   0.020
 FII  plan-3  C22   0.020
 FII  plan-3  C23   0.020
 FII  plan-3  H221  0.020
 FII  plan-4  C24   0.020
 FII  plan-4  C27   0.020
 FII  plan-4  C30   0.020
 FII  plan-4  C34   0.020
 FII  plan-4  C35   0.020
 FII  plan-4  H341  0.020

