# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 17:22:46 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  53  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 OK
;

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   1.370  -1.0205  -0.3647  -5.3637
 HFP  O1P   O  O     0  -0.713  -0.8497  -1.8283  -5.5306
 HFP  O2P   O  OH1   0  -0.746  -2.5289   0.1869  -5.3971
 HFP  O3P   O  OH1   0  -0.755  -0.2248   0.4099  -6.5312
 HFP  C1    C  CH1   0  -0.245  -0.4220   0.3266  -3.7782
 HFP  O1    O  OH1   0  -0.658  -0.5663   1.7289  -3.7793
 HFP  C2    C  CH2   0  -0.492   1.0025  -0.1374  -3.4966
 HFP  C3    C  CH1   0  -0.224   1.5763   0.3303  -2.1538
 HFP  C4    C  CH3   0  -0.661   3.0592  -0.0304  -2.1058
 HFP  C5    C  CH2   0  -0.410   0.8059  -0.2689  -0.9760
 HFP  C6    C  CH2   0  -0.427   1.2851   0.1915   0.3959
 HFP  C7    C  CH2   0  -0.399   0.4220  -0.3542   1.5280
 HFP  C8    C  CH1   0  -0.220   0.8625   0.0710   2.9320
 HFP  C9    C  CH3   0  -0.670   2.1968  -0.5633   3.3176
 HFP  C10   C  CH2   0  -0.397  -0.2378  -0.2553   3.9452
 HFP  C11   C  CH2   0  -0.430   0.0584   0.1617   5.3813
 HFP  C12   C  CH2   0  -0.394  -1.1329  -0.0566   6.3073
 HFP  C13   C  CH1   0  -0.229  -0.9199   0.3991   7.7522
 HFP  C14   C  CH3   0  -0.651  -2.2201   0.2835   8.5420
 HFP  C15   C  CH3   0  -0.656   0.1918  -0.3813   8.4475
 HFP  HO2   H  HOH1  0   0.495  -3.0614  -0.1672  -6.1231
 HFP  HO3   H  HOH1  0   0.489  -0.4386   1.3446  -6.6458
 HFP  H1    H  HCH1  0   0.277  -1.0946  -0.0637  -3.0082
 HFP  HO1   H  HOH1  0   0.456   0.2275   2.1233  -4.1569
 HFP  H21   H  HCH2  0   0.242   1.6554   0.2130  -4.3047
 HFP  H22   H  HCH2  0   0.246   1.0318  -1.2304  -3.5358
 HFP  H3    H  HCH1  0   0.217   1.4928   1.4219  -2.0985
 HFP  H41   H  HCH3  0   0.215   3.1956  -1.1147  -2.1142
 HFP  H42   H  HCH3  0   0.229   3.5902   0.3761  -2.9684
 HFP  H43   H  HCH3  0   0.233   3.5469   0.3574  -1.2114
 HFP  H51   H  HCH2  0   0.208   0.8662  -1.3627  -1.0352
 HFP  H52   H  HCH2  0   0.223  -0.2567  -0.0217  -1.0677
 HFP  H61   H  HCH2  0   0.208   1.2779   1.2869   0.4356
 HFP  H62   H  HCH2  0   0.219   2.3246  -0.1109   0.5427
 HFP  H71   H  HCH2  0   0.203   0.4016  -1.4496   1.4758
 HFP  H72   H  HCH2  0   0.212  -0.6112  -0.0267   1.3663
 HFP  H8    H  HCH1  0   0.203   0.9935   1.1613   2.9267
 HFP  H91   H  HCH3  0   0.210   2.0960  -1.6471   3.4202
 HFP  H92   H  HCH3  0   0.229   2.9671  -0.3741   2.5691
 HFP  H93   H  HCH3  0   0.229   2.5741  -0.1763   4.2645
 HFP  H101  H  HCH2  0   0.202  -0.4420  -1.3327   3.9167
 HFP  H102  H  HCH2  0   0.211  -1.1623   0.2345   3.6189
 HFP  H111  H  HCH2  0   0.204   0.3426   1.2203   5.4037
 HFP  H112  H  HCH2  0   0.218   0.9227  -0.3932   5.7547
 HFP  H121  H  HCH2  0   0.201  -1.4053  -1.1193   6.3049
 HFP  H122  H  HCH2  0   0.211  -1.9984   0.4759   5.8966
 HFP  H13   H  HCH1  0   0.207  -0.6312   1.4572   7.7296
 HFP  H141  H  HCH3  0   0.222  -2.1003   0.6497   9.5634
 HFP  H142  H  HCH3  0   0.222  -3.0240   0.8560   8.0754
 HFP  H143  H  HCH3  0   0.211  -2.5481  -0.7575   8.6014
 HFP  H151  H  HCH3  0   0.210  -0.0327  -1.4513   8.4533
 HFP  H152  H  HCH3  0   0.226   1.1587  -0.2490   7.9610
 HFP  H153  H  HCH3  0   0.223   0.3042  -0.0629   9.4856

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   double  1.483  0.020  1.483
 HFP  P    O2P   single  1.606  0.020  1.606
 HFP  P    O3P   single  1.611  0.020  1.611
 HFP  P    C1    single  1.830  0.020  1.830
 HFP  O2P  HO2   single  0.850  0.020  0.980
 HFP  O3P  HO3   single  0.850  0.020  0.980
 HFP  C1   O1    single  1.410  0.020  1.410
 HFP  C1   C2    single  1.524  0.020  1.524
 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  1.524  0.020  1.524
 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  1.527  0.020  1.527
 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  1.530  0.020  1.530
 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   106.54  3.000
 HFP  C1    P    O2P   101.27  3.000
 HFP  O3P   P    O2P   106.48  3.000
 HFP  C1    P    O1P   115.63  3.000
 HFP  O3P   P    O1P   109.63  3.000
 HFP  O2P   P    O1P   116.40  3.000
 HFP  HO2   O2P  P     114.00  3.000
 HFP  HO3   O3P  P     116.23  3.000
 HFP  H1    C1   C2    109.62  3.000
 HFP  H1    C1   O1    107.00  3.000
 HFP  C2    C1   O1    113.49  3.000
 HFP  H1    C1   P     105.89  3.000
 HFP  C2    C1   P     110.53  3.000
 HFP  O1    C1   P     109.97  3.000
 HFP  HO1   O1   C1    108.86  3.000
 HFP  H22   C2   H21   106.08  3.000
 HFP  H22   C2   C3    109.03  3.000
 HFP  H21   C2   C3    108.98  3.000
 HFP  H22   C2   C1    108.81  3.000
 HFP  H21   C2   C1    108.85  3.000
 HFP  C3    C2   C1    114.75  3.000
 HFP  H3    C3   C5    108.23  3.000
 HFP  H3    C3   C4    107.91  3.000
 HFP  C5    C3   C4    111.86  3.000
 HFP  H3    C3   C2    108.62  3.000
 HFP  C5    C3   C2    111.49  3.000
 HFP  C4    C3   C2    108.60  3.000
 HFP  H43   C4   H42   107.36  3.000
 HFP  H43   C4   H41   107.66  3.000
 HFP  H42   C4   H41   107.62  3.000
 HFP  H43   C4   C3    112.11  3.000
 HFP  H42   C4   C3    111.08  3.000
 HFP  H41   C4   C3    110.81  3.000
 HFP  H52   C5   H51   105.90  3.000
 HFP  H52   C5   C6    108.20  3.000
 HFP  H51   C5   C6    109.41  3.000
 HFP  H52   C5   C3    109.63  3.000
 HFP  H51   C5   C3    108.74  3.000
 HFP  C6    C5   C3    114.60  3.000
 HFP  H62   C6   H61   106.14  3.000
 HFP  H62   C6   C7    109.87  3.000
 HFP  H61   C6   C7    109.09  3.000
 HFP  H62   C6   C5    109.66  3.000
 HFP  H61   C6   C5    109.41  3.000
 HFP  C7    C6   C5    112.47  3.000
 HFP  H72   C7   H71   105.89  3.000
 HFP  H72   C7   C8    108.87  3.000
 HFP  H71   C7   C8    109.04  3.000
 HFP  H72   C7   C6    108.50  3.000
 HFP  H71   C7   C6    109.43  3.000
 HFP  C8    C7   C6    114.74  3.000
 HFP  H8    C8   C10   107.49  3.000
 HFP  H8    C8   C9    108.02  3.000
 HFP  C10   C8   C9    111.87  3.000
 HFP  H8    C8   C7    107.79  3.000
 HFP  C10   C8   C7    109.92  3.000
 HFP  C9    C8   C7    111.56  3.000
 HFP  H93   C9   H92   106.86  3.000
 HFP  H93   C9   H91   107.59  3.000
 HFP  H92   C9   H91   107.54  3.000
 HFP  H93   C9   C8    111.98  3.000
 HFP  H92   C9   C8    111.83  3.000
 HFP  H91   C9   C8    110.79  3.000
 HFP  H102  C10  H101  105.92  3.000
 HFP  H102  C10  C11   108.79  3.000
 HFP  H101  C10  C11   109.23  3.000
 HFP  H102  C10  C8    108.30  3.000
 HFP  H101  C10  C8    109.02  3.000
 HFP  C11   C10  C8    115.18  3.000
 HFP  H112  C11  H111  106.16  3.000
 HFP  H112  C11  C12   109.73  3.000
 HFP  H111  C11  C12   109.17  3.000
 HFP  H112  C11  C10   109.67  3.000
 HFP  H111  C11  C10   109.50  3.000
 HFP  C12   C11  C10   112.41  3.000
 HFP  H122  C12  H121  105.89  3.000
 HFP  H122  C12  C13   108.61  3.000
 HFP  H121  C12  C13   108.98  3.000
 HFP  H122  C12  C11   108.65  3.000
 HFP  H121  C12  C11   109.35  3.000
 HFP  C13   C12  C11   114.97  3.000
 HFP  H13   C13  C15   108.12  3.000
 HFP  H13   C13  C14   107.94  3.000
 HFP  C15   C13  C14   110.26  3.000
 HFP  H13   C13  C12   107.73  3.000
 HFP  C15   C13  C12   112.30  3.000
 HFP  C14   C13  C12   110.35  3.000
 HFP  H143  C14  H142  107.57  3.000
 HFP  H143  C14  H141  107.54  3.000
 HFP  H142  C14  H141  107.75  3.000
 HFP  H143  C14  C13   110.85  3.000
 HFP  H142  C14  C13   111.50  3.000
 HFP  H141  C14  C13   111.43  3.000
 HFP  H153  C15  H152  107.31  3.000
 HFP  H153  C15  H151  107.56  3.000
 HFP  H152  C15  H151  107.65  3.000
 HFP  H153  C15  C13   111.05  3.000
 HFP  H152  C15  C13   112.37  3.000
 HFP  H151  C15  C13   110.69  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    175.85  30.0  3
 HFP  Var_02  C8    C7   C6   C5    179.69  30.0  3
 HFP  Var_03  C12   C11  C10  C8    173.92  30.0  3
 HFP  Var_04  C13   C12  C11  C10  -177.48  30.0  3
 HFP  Var_05  C14   C13  C12  C11   173.45  30.0  3
 HFP  Var_06  H141  C14  C13  C12  -177.26  30.0  3
 HFP  Var_07  H151  C15  C13  C12   -58.74  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

