# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 00:55:00 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R)-2-methyl-3-phenylpropyl hydrogen (S)-hexylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[P@@](O)(=O)OC[C@H](C)Cc1ccccc1
#
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
 2HR  2HR  '(2R)-2-methyl-3-phenylpropyl hydrogen (S)-hexylphosphonate'  ligand  47  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2HR
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
 2HR  C6    C  CH3   0  -0.662   8.6224   1.9923   6.0739
 2HR  C5    C  CH2   0  -0.419   7.3466   1.3238   5.5807
 2HR  C4    C  CH2   0  -0.412   6.1013   1.8288   6.2981
 2HR  C3    C  CH2   0  -0.405   4.8210   1.1442   5.8380
 2HR  C2    C  CH2   0  -0.443   3.5880   1.6517   6.5753
 2HR  C1    C  CH2   0  -0.771   2.3272   0.8920   6.1650
 2HR  P     P  P     0   1.391   0.8415   1.5242   6.9617
 2HR  O     O  OH1   0  -0.752  -0.2518   0.4351   6.4999
 2HR  O1    O  O2    0  -0.590   1.0210   1.3339   8.5473
 2HR  C7    C  CH2   0  -0.175   1.4733   0.1080   9.1303
 2HR  C8    C  CH1   0  -0.271   1.1784   0.1189  10.6189
 2HR  C9    C  CH3   0  -0.661  -0.3181   0.0703  10.9062
 2HR  C10   C  CH2   0  -0.484   1.8285   1.3094  11.3396
 2HR  C11   C  CR6   0   0.116   3.3011   1.4516  11.0727
 2HR  C16   C  CR16  0  -0.308   4.2127   0.5320  11.5916
 2HR  C15   C  CR16  0  -0.242   5.5695   0.6421  11.3217
 2HR  C14   C  CR16  0  -0.273   6.0416   1.6810  10.5281
 2HR  C13   C  CR16  0  -0.233   5.1456   2.6058  10.0110
 2HR  C12   C  CR16  0  -0.308   3.7876   2.4878  10.2798
 2HR  O2    O  O     0  -0.713   0.4936   2.9382   6.6784
 2HR  H61   H  HCH3  0   0.226   9.5029   1.6070   5.5585
 2HR  H62   H  HCH3  0   0.216   8.5906   3.0714   5.9126
 2HR  H63   H  HCH3  0   0.215   8.7647   1.8255   7.1435
 2HR  H51   H  HCH2  0   0.211   7.4253   0.2405   5.7155
 2HR  H52   H  HCH2  0   0.211   7.2383   1.4876   4.5041
 2HR  H41   H  HCH2  0   0.214   6.2178   1.6785   7.3768
 2HR  H42   H  HCH2  0   0.208   6.0101   2.9110   6.1535
 2HR  H31   H  HCH2  0   0.213   4.9135   0.0636   5.9920
 2HR  H32   H  HCH2  0   0.215   4.6905   1.2891   4.7604
 2HR  H21   H  HCH2  0   0.247   3.7521   1.5546   7.6520
 2HR  H22   H  HCH2  0   0.232   3.4580   2.7199   6.3819
 2HR  H11   H  HCH2  0   0.291   2.1707   0.9702   5.0853
 2HR  H12A  H  HCH2  0   0.279   2.4359  -0.1734   6.3864
 2HR  HO    H  HOH1  0   0.490  -1.1653   0.6877   6.6913
 2HR  H71   H  HCH2  0   0.242   0.9762  -0.7488   8.6655
 2HR  H72   H  HCH2  0   0.238   2.5484   0.0012   8.9600
 2HR  H8    H  HCH1  0   0.243   1.6330  -0.8016  11.0027
 2HR  H91   H  HCH3  0   0.231  -0.7839  -0.7955  10.4328
 2HR  H92   H  HCH3  0   0.232  -0.5034  -0.0004  11.9787
 2HR  H93   H  HCH3  0   0.225  -0.8237   0.9660  10.5422
 2HR  H101  H  HCH2  0   0.248   1.6582   1.1864  12.4128
 2HR  H102  H  HCH2  0   0.241   1.3154   2.2298  11.0515
 2HR  H16   H  HCR6  0   0.245   3.8570  -0.2819  12.2140
 2HR  H15   H  HCR6  0   0.252   6.2603  -0.0828  11.7336
 2HR  H14   H  HCR6  0   0.251   7.0994   1.7682  10.3145
 2HR  H13   H  HCR6  0   0.250   5.5027   3.4190   9.3919
 2HR  H12   H  HCR6  0   0.246   3.0945   3.2087   9.8617

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
 2HR  C6   C5    single    1.522  0.020  1.522
 2HR  C6   H61   single    0.970  0.020  1.090
 2HR  C6   H62   single    0.970  0.020  1.090
 2HR  C6   H63   single    0.970  0.020  1.090
 2HR  C5   C4    single    1.523  0.020  1.523
 2HR  C5   H51   single    0.970  0.020  1.090
 2HR  C5   H52   single    0.970  0.020  1.090
 2HR  C4   C3    single    1.523  0.020  1.523
 2HR  C4   H41   single    0.970  0.020  1.090
 2HR  C4   H42   single    0.970  0.020  1.090
 2HR  C3   C2    single    1.524  0.020  1.524
 2HR  C3   H31   single    0.970  0.020  1.090
 2HR  C3   H32   single    0.970  0.020  1.090
 2HR  C2   C1    single    1.528  0.020  1.528
 2HR  C2   H21   single    0.970  0.020  1.090
 2HR  C2   H22   single    0.970  0.020  1.090
 2HR  C1   P     single    1.801  0.020  1.801
 2HR  C1   H11   single    0.970  0.020  1.090
 2HR  C1   H12A  single    0.970  0.020  1.090
 2HR  P    O     single    1.611  0.020  1.611
 2HR  P    O1    single    1.607  0.020  1.607
 2HR  P    O2    double    1.484  0.020  1.484
 2HR  O    HO    single    0.850  0.020  0.980
 2HR  O1   C7    single    1.431  0.020  1.431
 2HR  C7   C8    single    1.518  0.020  1.518
 2HR  C7   H71   single    0.970  0.020  1.090
 2HR  C7   H72   single    0.970  0.020  1.090
 2HR  C8   C9    single    1.525  0.020  1.525
 2HR  C8   C10   single    1.536  0.020  1.536
 2HR  C8   H8    single    0.970  0.020  1.090
 2HR  C9   H91   single    0.970  0.020  1.090
 2HR  C9   H92   single    0.970  0.020  1.090
 2HR  C9   H93   single    0.970  0.020  1.090
 2HR  C10  C11   single    1.503  0.020  1.503
 2HR  C10  H101  single    0.970  0.020  1.090
 2HR  C10  H102  single    0.970  0.020  1.090
 2HR  C11  C16   aromatic  1.395  0.020  1.395
 2HR  C11  C12   aromatic  1.393  0.020  1.393
 2HR  C16  C15   aromatic  1.388  0.020  1.388
 2HR  C16  H16   single    0.930  0.020  1.080
 2HR  C15  C14   aromatic  1.390  0.020  1.390
 2HR  C15  H15   single    0.930  0.020  1.080
 2HR  C14  C13   aromatic  1.388  0.020  1.388
 2HR  C14  H14   single    0.930  0.020  1.080
 2HR  C13  C12   aromatic  1.389  0.020  1.389
 2HR  C13  H13   single    0.930  0.020  1.080
 2HR  C12  H12   single    0.930  0.020  1.080

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
 2HR  H63   C6   H62   107.43  3.000
 2HR  H63   C6   H61   107.68  3.000
 2HR  H62   C6   H61   107.64  3.000
 2HR  H63   C6   C5    111.07  3.000
 2HR  H62   C6   C5    111.21  3.000
 2HR  H61   C6   C5    111.62  3.000
 2HR  H52   C5   H51   106.05  3.000
 2HR  H52   C5   C4    109.43  3.000
 2HR  H51   C5   C4    109.20  3.000
 2HR  H52   C5   C6    109.63  3.000
 2HR  H51   C5   C6    109.54  3.000
 2HR  C4    C5   C6    112.77  3.000
 2HR  H42   C4   H41   105.92  3.000
 2HR  H42   C4   C3    109.52  3.000
 2HR  H41   C4   C3    108.98  3.000
 2HR  H42   C4   C5    109.47  3.000
 2HR  H41   C4   C5    109.35  3.000
 2HR  C3    C4   C5    113.33  3.000
 2HR  H32   C3   H31   106.20  3.000
 2HR  H32   C3   C2    109.61  3.000
 2HR  H31   C3   C2    109.20  3.000
 2HR  H32   C3   C4    109.75  3.000
 2HR  H31   C3   C4    109.27  3.000
 2HR  C2    C3   C4    112.61  3.000
 2HR  H22   C2   H21   106.18  3.000
 2HR  H22   C2   C1    109.89  3.000
 2HR  H21   C2   C1    110.12  3.000
 2HR  H22   C2   C3    109.64  3.000
 2HR  H21   C2   C3    108.99  3.000
 2HR  C1    C2   C3    111.85  3.000
 2HR  H12A  C1   H11   106.49  3.000
 2HR  H12A  C1   P     109.54  3.000
 2HR  H11   C1   P     107.07  3.000
 2HR  H12A  C1   C2    110.36  3.000
 2HR  H11   C1   C2    110.34  3.000
 2HR  P     C1   C2    112.79  3.000
 2HR  O2    P    O1    109.11  3.000
 2HR  O2    P    O     115.50  3.000
 2HR  O1    P    O     106.18  3.000
 2HR  O2    P    C1    116.34  3.000
 2HR  O1    P    C1    107.63  3.000
 2HR  O     P    C1    101.29  3.000
 2HR  HO    O    P     114.07  3.000
 2HR  C7    O1   P     122.60  3.000
 2HR  H72   C7   H71   107.70  3.000
 2HR  H72   C7   C8    110.15  3.000
 2HR  H71   C7   C8    109.51  3.000
 2HR  H72   C7   O1    109.33  3.000
 2HR  H71   C7   O1    110.75  3.000
 2HR  C8    C7   O1    109.39  3.000
 2HR  H8    C8   C10   108.12  3.000
 2HR  H8    C8   C9    108.32  3.000
 2HR  C10   C8   C9    110.59  3.000
 2HR  H8    C8   C7    104.88  3.000
 2HR  C10   C8   C7    112.55  3.000
 2HR  C9    C8   C7    112.05  3.000
 2HR  H93   C9   H92   107.61  3.000
 2HR  H93   C9   H91   107.99  3.000
 2HR  H92   C9   H91   107.62  3.000
 2HR  H93   C9   C8    111.46  3.000
 2HR  H92   C9   C8    110.74  3.000
 2HR  H91   C9   C8    111.26  3.000
 2HR  H102  C10  H101  106.29  3.000
 2HR  H102  C10  C11   109.49  3.000
 2HR  H101  C10  C11   109.72  3.000
 2HR  H102  C10  C8    109.30  3.000
 2HR  H101  C10  C8    107.90  3.000
 2HR  C11   C10  C8    113.87  3.000
 2HR  C12   C11  C16   118.30  3.000
 2HR  C12   C11  C10   120.91  3.000
 2HR  C16   C11  C10   120.78  3.000
 2HR  H16   C16  C15   119.46  3.000
 2HR  H16   C16  C11   119.60  3.000
 2HR  C15   C16  C11   120.95  3.000
 2HR  H15   C15  C14   120.06  3.000
 2HR  H15   C15  C16   119.78  3.000
 2HR  C14   C15  C16   120.16  3.000
 2HR  H14   C14  C13   120.24  3.000
 2HR  H14   C14  C15   120.31  3.000
 2HR  C13   C14  C15   119.45  3.000
 2HR  H13   C13  C12   119.79  3.000
 2HR  H13   C13  C14   120.04  3.000
 2HR  C12   C13  C14   120.16  3.000
 2HR  H12   C12  C13   119.60  3.000
 2HR  H12   C12  C11   119.42  3.000
 2HR  C13   C12  C11   120.98  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
 2HR  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 2HR  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 2HR  CONST_03  C13  C12  C11  C16     0.00   0.0  0
 2HR  CONST_04  C13  C14  C15  C16     0.00   0.0  0
 2HR  CONST_05  C12  C11  C16  C15     0.00   0.0  0
 2HR  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 2HR  CONST_07  C15  C16  C11  C10   180.00   0.0  0
 2HR  CONST_08  C13  C12  C11  C10   180.00   0.0  0
 2HR  CONST_09  H15  C15  C16  C11   180.00   0.0  0
 2HR  CONST_10  H13  C13  C12  C11   180.00   0.0  0
 2HR  CONST_11  H12  C12  C11  C16   180.00   0.0  0
 2HR  CONST_12  H14  C14  C15  C16   180.00   0.0  0
 2HR  CONST_13  H16  C16  C15  C14   180.00   0.0  0
 2HR  Var_01    C16  C11  C10  C8    -70.14  30.0  2
 2HR  Var_02    C3   C4   C5   C6   -178.61  30.0  3
 2HR  Var_03    C2   C3   C4   C5    179.44  30.0  3
 2HR  Var_04    C1   C2   C3   C4   -176.36  30.0  3
 2HR  Var_05    P    C1   C2   C3   -177.22  30.0  3
 2HR  Var_06    O    P    C1   C2   -172.97  30.0  3
 2HR  Var_07    C8   C7   O1   P    -164.67  30.0  3
 2HR  Var_08    H61  C6   C5   C4    179.18  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
 2HR  chir_02  C8  C7  C9  C10  positiv
 2HR  chir_03  P   O   O1  O2   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
 2HR  plan-1  C10  0.020
 2HR  plan-1  C11  0.020
 2HR  plan-1  C16  0.020
 2HR  plan-1  C15  0.020
 2HR  plan-1  C14  0.020
 2HR  plan-1  C13  0.020
 2HR  plan-1  C12  0.020
 2HR  plan-1  H16  0.020
 2HR  plan-1  H15  0.020
 2HR  plan-1  H14  0.020
 2HR  plan-1  H13  0.020
 2HR  plan-1  H12  0.020

