# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:22:16 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [(1S,3R,7R)-1-hydroxy-3,7,11-trimethyldodecyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC[C@@H](C)CCC[C@@H](C)C[C@@H](O)[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
 HFP  HFP  '[(1S,3R,7R)-1-hydroxy-3,7,11-trimethyldodecyl]phosphonic acid'  ligand  51  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HFP
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
 HFP  P     P  P      0   1.157  -1.2742  -0.1722  -5.3531
 HFP  O1P   O  O      0  -0.891  -0.8576  -1.6249  -5.5915
 HFP  O2P   O  OP    -1  -0.901  -2.7851   0.0253  -5.1918
 HFP  O3P   O  OP    -1  -0.906  -0.6289   0.8429  -6.3320
 HFP  C1    C  CH1    0  -0.255  -0.4857   0.4085  -3.7490
 HFP  O1    O  OH1    0  -0.722  -0.3280   1.8218  -3.8795
 HFP  C2    C  CH2    0  -0.406   0.8531  -0.2558  -3.4577
 HFP  C3    C  CH1    0  -0.217   1.5474   0.1934  -2.1665
 HFP  C4    C  CH3    0  -0.660   3.0132  -0.2328  -2.1828
 HFP  C5    C  CH2    0  -0.405   0.8188  -0.3492  -0.9351
 HFP  C6    C  CH2    0  -0.425   1.3110   0.1845   0.4060
 HFP  C7    C  CH2    0  -0.396   0.4732  -0.3342   1.5695
 HFP  C8    C  CH1    0  -0.221   0.8892   0.1660   2.9561
 HFP  C9    C  CH3    0  -0.670   2.2611  -0.3665   3.3604
 HFP  C10   C  CH2    0  -0.395  -0.1921  -0.2037   3.9749
 HFP  C11   C  CH2    0  -0.430   0.0687   0.2411   5.4096
 HFP  C12   C  CH2    0  -0.393  -1.1173  -0.0546   6.3214
 HFP  C13   C  CH1    0  -0.229  -0.9497   0.3819   7.7774
 HFP  C14   C  CH3    0  -0.651  -2.2483   0.1601   8.5475
 HFP  C15   C  CH3    0  -0.657   0.2056  -0.3370   8.4680
 HFP  H1    H  HCH1   0   0.170  -1.1709   0.2257  -2.9104
 HFP  HO1   H  HOH1   0   0.413  -0.2620   1.9163  -4.8518
 HFP  H21   H  HCH2   0   0.190   1.5187  -0.0677  -4.3094
 HFP  H22   H  HCH2   0   0.189   0.7132  -1.3409  -3.4281
 HFP  H3    H  HCH1   0   0.197   1.5150   1.2889  -2.1267
 HFP  H41   H  HCH3   0   0.206   3.1026  -1.3221  -2.2170
 HFP  H42   H  HCH3   0   0.219   3.5252   0.1646  -3.0617
 HFP  H43   H  HCH3   0   0.221   3.5594   0.1148  -1.3044
 HFP  H51   H  HCH2   0   0.196   0.8932  -1.4442  -0.9367
 HFP  H52   H  HCH2   0   0.214  -0.2494  -0.1250  -1.0206
 HFP  H61   H  HCH2   0   0.203   1.2768   1.2801   0.3964
 HFP  H62   H  HCH2   0   0.213   2.3603  -0.0849   0.5518
 HFP  H71   H  HCH2   0   0.200   0.4920  -1.4312   1.5681
 HFP  H72   H  HCH2   0   0.210  -0.5720  -0.0539   1.3954
 HFP  H8    H  HCH1   0   0.202   0.9483   1.2617   2.9143
 HFP  H91   H  HCH3   0   0.209   2.2349  -1.4520   3.4894
 HFP  H92   H  HCH3   0   0.229   3.0188  -0.1426   2.6084
 HFP  H93   H  HCH3   0   0.229   2.6051   0.0694   4.2986
 HFP  H101  H  HCH2   0   0.201  -0.3366  -1.2912   3.9590
 HFP  H102  H  HCH2   0   0.211  -1.1414   0.2288   3.6394
 HFP  H111  H  HCH2   0   0.204   0.2847   1.3156   5.4305
 HFP  H112  H  HCH2   0   0.218   0.9630  -0.2571   5.7921
 HFP  H121  H  HCH2   0   0.201  -1.3312  -1.1306   6.2969
 HFP  H122  H  HCH2   0   0.211  -2.0063   0.4360   5.9089
 HFP  H13   H  HCH1   0   0.207  -0.7332   1.4574   7.7842
 HFP  H141  H  HCH3   0   0.222  -2.1655   0.5103   9.5780
 HFP  H142  H  HCH3   0   0.222  -3.0836   0.6870   8.0824
 HFP  H143  H  HCH3   0   0.211  -2.5053  -0.9017   8.5800
 HFP  H151  H  HCH3   0   0.210   0.0701  -1.4210   8.4246
 HFP  H152  H  HCH3   0   0.226   1.1689  -0.1056   8.0127
 HFP  H153  H  HCH3   0   0.223   0.2691  -0.0556   9.5208

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
 HFP  P    O1P   deloc   1.530  0.020  1.530
 HFP  P    O2P   deloc   1.532  0.020  1.532
 HFP  P    O3P   deloc   1.551  0.020  1.551
 HFP  P    C1    single  1.879  0.020  1.879
 HFP  C1   O1    single  1.428  0.020  1.428
 HFP  C1   C2    single  1.523  0.020  1.523
 HFP  C1   H1    single  0.970  0.020  1.090
 HFP  O1   HO1   single  0.850  0.020  0.980
 HFP  C2   C3    single  1.533  0.020  1.533
 HFP  C2   H21   single  0.970  0.020  1.090
 HFP  C2   H22   single  0.970  0.020  1.090
 HFP  C3   C4    single  1.527  0.020  1.527
 HFP  C3   C5    single  1.530  0.020  1.530
 HFP  C3   H3    single  0.970  0.020  1.090
 HFP  C4   H41   single  0.970  0.020  1.090
 HFP  C4   H42   single  0.970  0.020  1.090
 HFP  C4   H43   single  0.970  0.020  1.090
 HFP  C5   C6    single  1.525  0.020  1.525
 HFP  C5   H51   single  0.970  0.020  1.090
 HFP  C5   H52   single  0.970  0.020  1.090
 HFP  C6   C7    single  1.525  0.020  1.525
 HFP  C6   H61   single  0.970  0.020  1.090
 HFP  C6   H62   single  0.970  0.020  1.090
 HFP  C7   C8    single  1.532  0.020  1.532
 HFP  C7   H71   single  0.970  0.020  1.090
 HFP  C7   H72   single  0.970  0.020  1.090
 HFP  C8   C9    single  1.526  0.020  1.526
 HFP  C8   C10   single  1.531  0.020  1.531
 HFP  C8   H8    single  0.970  0.020  1.090
 HFP  C9   H91   single  0.970  0.020  1.090
 HFP  C9   H92   single  0.970  0.020  1.090
 HFP  C9   H93   single  0.970  0.020  1.090
 HFP  C10  C11   single  1.524  0.020  1.524
 HFP  C10  H101  single  0.970  0.020  1.090
 HFP  C10  H102  single  0.970  0.020  1.090
 HFP  C11  C12   single  1.525  0.020  1.525
 HFP  C11  H111  single  0.970  0.020  1.090
 HFP  C11  H112  single  0.970  0.020  1.090
 HFP  C12  C13   single  1.529  0.020  1.529
 HFP  C12  H121  single  0.970  0.020  1.090
 HFP  C12  H122  single  0.970  0.020  1.090
 HFP  C13  C14   single  1.526  0.020  1.526
 HFP  C13  C15   single  1.526  0.020  1.526
 HFP  C13  H13   single  0.970  0.020  1.090
 HFP  C14  H141  single  0.970  0.020  1.090
 HFP  C14  H142  single  0.970  0.020  1.090
 HFP  C14  H143  single  0.970  0.020  1.090
 HFP  C15  H151  single  0.970  0.020  1.090
 HFP  C15  H152  single  0.970  0.020  1.090
 HFP  C15  H153  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
 HFP  C1    P    O3P    99.32  3.000
 HFP  C1    P    O2P   106.50  3.000
 HFP  O3P   P    O2P   113.10  3.000
 HFP  C1    P    O1P   108.19  3.000
 HFP  O3P   P    O1P   114.20  3.000
 HFP  O2P   P    O1P   114.03  3.000
 HFP  H1    C1   C2    109.26  3.000
 HFP  H1    C1   O1    107.66  3.000
 HFP  C2    C1   O1    110.62  3.000
 HFP  H1    C1   P     109.79  3.000
 HFP  C2    C1   P     113.41  3.000
 HFP  O1    C1   P     105.91  3.000
 HFP  HO1   O1   C1    101.17  3.000
 HFP  H22   C2   H21   105.58  3.000
 HFP  H22   C2   C3    109.00  3.000
 HFP  H21   C2   C3    109.20  3.000
 HFP  H22   C2   C1    108.98  3.000
 HFP  H21   C2   C1    108.06  3.000
 HFP  C3    C2   C1    115.56  3.000
 HFP  H3    C3   C5    108.12  3.000
 HFP  H3    C3   C4    107.91  3.000
 HFP  C5    C3   C4    111.52  3.000
 HFP  H3    C3   C2    108.05  3.000
 HFP  C5    C3   C2    110.99  3.000
 HFP  C4    C3   C2    110.12  3.000
 HFP  H43   C4   H42   107.29  3.000
 HFP  H43   C4   H41   107.55  3.000
 HFP  H42   C4   H41   107.39  3.000
 HFP  H43   C4   C3    112.53  3.000
 HFP  H42   C4   C3    110.93  3.000
 HFP  H41   C4   C3    110.91  3.000
 HFP  H52   C5   H51   105.69  3.000
 HFP  H52   C5   C6    108.17  3.000
 HFP  H51   C5   C6    109.18  3.000
 HFP  H52   C5   C3    109.21  3.000
 HFP  H51   C5   C3    108.68  3.000
 HFP  C6    C5   C3    115.46  3.000
 HFP  H62   C6   H61   106.10  3.000
 HFP  H62   C6   C7    109.99  3.000
 HFP  H61   C6   C7    109.24  3.000
 HFP  H62   C6   C5    109.93  3.000
 HFP  H61   C6   C5    109.39  3.000
 HFP  C7    C6   C5    112.01  3.000
 HFP  H72   C7   H71   105.78  3.000
 HFP  H72   C7   C8    108.62  3.000
 HFP  H71   C7   C8    108.85  3.000
 HFP  H72   C7   C6    108.41  3.000
 HFP  H71   C7   C6    109.25  3.000
 HFP  C8    C7   C6    115.50  3.000
 HFP  H8    C8   C10   107.72  3.000
 HFP  H8    C8   C9    108.05  3.000
 HFP  C10   C8   C9    111.98  3.000
 HFP  H8    C8   C7    107.82  3.000
 HFP  C10   C8   C7    109.38  3.000
 HFP  C9    C8   C7    111.72  3.000
 HFP  H93   C9   H92   106.98  3.000
 HFP  H93   C9   H91   107.63  3.000
 HFP  H92   C9   H91   107.56  3.000
 HFP  H93   C9   C8    111.85  3.000
 HFP  H92   C9   C8    111.73  3.000
 HFP  H91   C9   C8    110.86  3.000
 HFP  H102  C10  H101  105.82  3.000
 HFP  H102  C10  C11   108.74  3.000
 HFP  H101  C10  C11   108.99  3.000
 HFP  H102  C10  C8    108.22  3.000
 HFP  H101  C10  C8    108.83  3.000
 HFP  C11   C10  C8    115.79  3.000
 HFP  H112  C11  H111  106.19  3.000
 HFP  H112  C11  C12   109.80  3.000
 HFP  H111  C11  C12   109.38  3.000
 HFP  H112  C11  C10   109.66  3.000
 HFP  H111  C11  C10   109.73  3.000
 HFP  C12   C11  C10   111.91  3.000
 HFP  H122  C12  H121  105.81  3.000
 HFP  H122  C12  C13   108.63  3.000
 HFP  H121  C12  C13   108.81  3.000
 HFP  H122  C12  C11   108.60  3.000
 HFP  H121  C12  C11   109.17  3.000
 HFP  C13   C12  C11   115.38  3.000
 HFP  H13   C13  C15   108.04  3.000
 HFP  H13   C13  C14   107.90  3.000
 HFP  C15   C13  C14   110.33  3.000
 HFP  H13   C13  C12   107.90  3.000
 HFP  C15   C13  C12   112.30  3.000
 HFP  C14   C13  C12   110.22  3.000
 HFP  H143  C14  H142  107.55  3.000
 HFP  H143  C14  H141  107.54  3.000
 HFP  H142  C14  H141  107.78  3.000
 HFP  H143  C14  C13   110.88  3.000
 HFP  H142  C14  C13   111.48  3.000
 HFP  H141  C14  C13   111.42  3.000
 HFP  H153  C15  H152  107.26  3.000
 HFP  H153  C15  H151  107.53  3.000
 HFP  H152  C15  H151  107.66  3.000
 HFP  H153  C15  C13   111.04  3.000
 HFP  H152  C15  C13   112.32  3.000
 HFP  H151  C15  C13   110.81  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
 HFP  Var_01  C7    C6   C5   C3    176.20  30.0  3
 HFP  Var_02  C8    C7   C6   C5   -179.33  30.0  3
 HFP  Var_03  C12   C11  C10  C8    174.62  30.0  3
 HFP  Var_04  C13   C12  C11  C10  -179.01  30.0  3
 HFP  Var_05  C14   C13  C12  C11   174.32  30.0  3
 HFP  Var_06  H141  C14  C13  C12  -177.25  30.0  3
 HFP  Var_07  H151  C15  C13  C12   -57.14  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
 HFP  chir_01  C1  P    O1  C2  positiv
 HFP  chir_02  C3  C5   C4  C2  negativ
 HFP  chir_03  C8  C10  C9  C7  negativ

