# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:23:37 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S)-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
 2HS  2HS  '(2S)-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_2HS
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
 2HS  C6    C  CH3   0  -0.662   3.6697   6.5886  6.6301
 2HS  C5    C  CH2   0  -0.421   4.1019   5.2105  7.1113
 2HS  C4    C  CH2   0  -0.408   3.3495   4.0801  6.4203
 2HS  C3    C  CH2   0  -0.408   3.7650   2.6988  6.9090
 2HS  C2    C  CH2   0  -0.434   3.0165   1.5727  6.2074
 2HS  C1    C  CH2   0  -0.762   3.4091   0.2023  6.7593
 2HS  P     P  P     0   1.385   2.6674  -1.1491  5.8307
 2HS  O     O  OH1   0  -0.757   3.0144  -2.4079  6.7725
 2HS  O1    O  O2    0  -0.593   1.0730  -0.9605  5.8902
 2HS  C7    C  CH2   0  -0.179   0.3277  -0.9473  7.1117
 2HS  C8    C  CH1   0  -0.272  -1.1249  -1.2695  6.8107
 2HS  C9    C  CH3   0  -0.662  -1.8229  -0.1362  6.0668
 2HS  C10   C  CH2   0  -0.483  -1.2872  -2.5917  6.0440
 2HS  C11   C  CR6   0   0.130  -0.5075  -3.7409  6.6193
 2HS  C16   C  CR16  0  -0.368   0.5068  -4.3535  5.8846
 2HS  C15   C  CR16  0  -0.257   1.2482  -5.4028  6.4183
 2HS  C14   C  CR16  0  -0.268   0.9907  -5.8504  7.7076
 2HS  C13   C  CR16  0  -0.234  -0.0213  -5.2520  8.4474
 2HS  C12   C  CR16  0  -0.303  -0.7637  -4.2114  7.9061
 2HS  O2    O  O     0  -0.709   3.0823  -1.2637  4.4112
 2HS  H61   H  HCH3  0   0.226   4.2186   7.3821  7.1383
 2HS  H62   H  HCH3  0   0.216   3.8404   6.7032  5.5580
 2HS  H63   H  HCH3  0   0.216   2.6061   6.7525  6.8120
 2HS  H51   H  HCH2  0   0.212   3.9519   5.1355  8.1928
 2HS  H52   H  HCH2  0   0.212   5.1765   5.0843  6.9456
 2HS  H41   H  HCH2  0   0.209   2.2731   4.2098  6.5775
 2HS  H42   H  HCH2  0   0.210   3.5079   4.1474  5.3383
 2HS  H31   H  HCH2  0   0.215   3.5962   2.6282  7.9888
 2HS  H32   H  HCH2  0   0.216   4.8418   2.5665  6.7594
 2HS  H21   H  HCH2  0   0.230   1.9399   1.7244  6.3272
 2HS  H22   H  HCH2  0   0.235   3.2180   1.6165  5.1337
 2HS  H11   H  HCH2  0   0.288   4.4939   0.0714  6.7141
 2HS  H12A  H  HCH2  0   0.280   3.1278   0.1223  7.8129
 2HS  HO    H  HOH1  0   0.490   2.6400  -3.2525  6.4790
 2HS  H71   H  HCH2  0   0.241   0.7388  -1.6734  7.8171
 2HS  H72   H  HCH2  0   0.241   0.4022   0.0414  7.5752
 2HS  H8    H  HCH1  0   0.244  -1.6031  -1.3779  7.7903
 2HS  H91   H  HCH3  0   0.233  -2.8625  -0.3926  5.8575
 2HS  H92   H  HCH3  0   0.233  -1.8221   0.7822  6.6556
 2HS  H93   H  HCH3  0   0.226  -1.3375   0.0762  5.1131
 2HS  H101  H  HCH2  0   0.244  -0.9969  -2.4446  5.0014
 2HS  H102  H  HCH2  0   0.253  -2.3525  -2.8394  6.0307
 2HS  H16   H  HCR6  0   0.263   0.7118  -4.0130  4.8753
 2HS  H15   H  HCR6  0   0.266   2.0233  -5.8704  5.8239
 2HS  H14   H  HCR6  0   0.257   1.5681  -6.6627  8.1294
 2HS  H13   H  HCR6  0   0.257  -0.2354  -5.5980  9.4505
 2HS  H12   H  HCR6  0   0.251  -1.5537  -3.7611  8.4966

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
 2HS  C6   C5    single    1.522  0.020  1.522
 2HS  C6   H61   single    0.970  0.020  1.090
 2HS  C6   H62   single    0.970  0.020  1.090
 2HS  C6   H63   single    0.970  0.020  1.090
 2HS  C5   C4    single    1.524  0.020  1.524
 2HS  C5   H51   single    0.970  0.020  1.090
 2HS  C5   H52   single    0.970  0.020  1.090
 2HS  C4   C3    single    1.523  0.020  1.523
 2HS  C4   H41   single    0.970  0.020  1.090
 2HS  C4   H42   single    0.970  0.020  1.090
 2HS  C3   C2    single    1.523  0.020  1.523
 2HS  C3   H31   single    0.970  0.020  1.090
 2HS  C3   H32   single    0.970  0.020  1.090
 2HS  C2   C1    single    1.529  0.020  1.529
 2HS  C2   H21   single    0.970  0.020  1.090
 2HS  C2   H22   single    0.970  0.020  1.090
 2HS  C1   P     single    1.800  0.020  1.800
 2HS  C1   H11   single    0.970  0.020  1.090
 2HS  C1   H12A  single    0.970  0.020  1.090
 2HS  P    O     single    1.610  0.020  1.610
 2HS  P    O1    single    1.607  0.020  1.607
 2HS  P    O2    double    1.483  0.020  1.483
 2HS  O    HO    single    0.850  0.020  0.980
 2HS  O1   C7    single    1.431  0.020  1.431
 2HS  C7   C8    single    1.518  0.020  1.518
 2HS  C7   H71   single    0.970  0.020  1.090
 2HS  C7   H72   single    0.970  0.020  1.090
 2HS  C8   C9    single    1.525  0.020  1.525
 2HS  C8   C10   single    1.537  0.020  1.537
 2HS  C8   H8    single    0.970  0.020  1.090
 2HS  C9   H91   single    0.970  0.020  1.090
 2HS  C9   H92   single    0.970  0.020  1.090
 2HS  C9   H93   single    0.970  0.020  1.090
 2HS  C10  C11   single    1.503  0.020  1.503
 2HS  C10  H101  single    0.970  0.020  1.090
 2HS  C10  H102  single    0.970  0.020  1.090
 2HS  C11  C16   aromatic  1.394  0.020  1.394
 2HS  C11  C12   aromatic  1.394  0.020  1.394
 2HS  C16  C15   aromatic  1.391  0.020  1.391
 2HS  C16  H16   single    0.930  0.020  1.080
 2HS  C15  C14   aromatic  1.389  0.020  1.389
 2HS  C15  H15   single    0.930  0.020  1.080
 2HS  C14  C13   aromatic  1.389  0.020  1.389
 2HS  C14  H14   single    0.930  0.020  1.080
 2HS  C13  C12   aromatic  1.388  0.020  1.388
 2HS  C13  H13   single    0.930  0.020  1.080
 2HS  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
 2HS  H63   C6   H62   107.47  3.000
 2HS  H63   C6   H61   107.67  3.000
 2HS  H62   C6   H61   107.61  3.000
 2HS  H63   C6   C5    111.09  3.000
 2HS  H62   C6   C5    111.17  3.000
 2HS  H61   C6   C5    111.63  3.000
 2HS  H52   C5   H51   106.03  3.000
 2HS  H52   C5   C4    109.30  3.000
 2HS  H51   C5   C4    109.25  3.000
 2HS  H52   C5   C6    109.59  3.000
 2HS  H51   C5   C6    109.60  3.000
 2HS  C4    C5   C6    112.84  3.000
 2HS  H42   C4   H41   106.05  3.000
 2HS  H42   C4   C3    109.46  3.000
 2HS  H41   C4   C3    109.23  3.000
 2HS  H42   C4   C5    109.32  3.000
 2HS  H41   C4   C5    109.41  3.000
 2HS  C3    C4   C5    113.13  3.000
 2HS  H32   C3   H31   106.17  3.000
 2HS  H32   C3   C2    109.32  3.000
 2HS  H31   C3   C2    109.31  3.000
 2HS  H32   C3   C4    109.51  3.000
 2HS  H31   C3   C4    109.44  3.000
 2HS  C2    C3   C4    112.87  3.000
 2HS  H22   C2   H21   106.46  3.000
 2HS  H22   C2   C1    110.07  3.000
 2HS  H21   C2   C1    109.73  3.000
 2HS  H22   C2   C3    109.40  3.000
 2HS  H21   C2   C3    109.31  3.000
 2HS  C1    C2   C3    111.73  3.000
 2HS  H12A  C1   H11   106.64  3.000
 2HS  H12A  C1   P     109.65  3.000
 2HS  H11   C1   P     107.31  3.000
 2HS  H12A  C1   C2    110.33  3.000
 2HS  H11   C1   C2    110.31  3.000
 2HS  P     C1   C2    112.40  3.000
 2HS  O2    P    O1    108.79  3.000
 2HS  O2    P    O     116.05  3.000
 2HS  O1    P    O     106.51  3.000
 2HS  O2    P    C1    115.88  3.000
 2HS  O1    P    C1    107.56  3.000
 2HS  O     P    C1    101.33  3.000
 2HS  HO    O    P     114.89  3.000
 2HS  C7    O1   P     123.33  3.000
 2HS  H72   C7   H71   107.54  3.000
 2HS  H72   C7   C8    109.92  3.000
 2HS  H71   C7   C8    110.31  3.000
 2HS  H72   C7   O1    109.53  3.000
 2HS  H71   C7   O1    110.43  3.000
 2HS  C8    C7   O1    109.10  3.000
 2HS  H8    C8   C10   108.35  3.000
 2HS  H8    C8   C9    108.06  3.000
 2HS  C10   C8   C9    110.34  3.000
 2HS  H8    C8   C7    105.15  3.000
 2HS  C10   C8   C7    112.49  3.000
 2HS  C9    C8   C7    112.15  3.000
 2HS  H93   C9   H92   107.91  3.000
 2HS  H93   C9   H91   107.58  3.000
 2HS  H92   C9   H91   107.59  3.000
 2HS  H93   C9   C8    111.56  3.000
 2HS  H92   C9   C8    111.23  3.000
 2HS  H91   C9   C8    110.80  3.000
 2HS  H102  C10  H101  106.13  3.000
 2HS  H102  C10  C11   109.68  3.000
 2HS  H101  C10  C11   109.29  3.000
 2HS  H102  C10  C8    107.68  3.000
 2HS  H101  C10  C8    109.41  3.000
 2HS  C11   C10  C8    114.33  3.000
 2HS  C12   C11  C16   118.16  3.000
 2HS  C12   C11  C10   121.07  3.000
 2HS  C16   C11  C10   120.77  3.000
 2HS  H16   C16  C15   119.54  3.000
 2HS  H16   C16  C11   119.33  3.000
 2HS  C15   C16  C11   121.13  3.000
 2HS  H15   C15  C14   120.20  3.000
 2HS  H15   C15  C16   119.77  3.000
 2HS  C14   C15  C16   120.03  3.000
 2HS  H14   C14  C13   120.29  3.000
 2HS  H14   C14  C15   120.32  3.000
 2HS  C13   C14  C15   119.38  3.000
 2HS  H13   C13  C12   119.68  3.000
 2HS  H13   C13  C14   119.99  3.000
 2HS  C12   C13  C14   120.32  3.000
 2HS  H12   C12  C13   119.25  3.000
 2HS  H12   C12  C11   119.77  3.000
 2HS  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
 2HS  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 2HS  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 2HS  CONST_03  C13  C12  C11  C16     0.00   0.0  0
 2HS  CONST_04  C13  C14  C15  C16     0.00   0.0  0
 2HS  CONST_05  C12  C11  C16  C15     0.00   0.0  0
 2HS  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 2HS  CONST_07  C15  C16  C11  C10   180.00   0.0  0
 2HS  CONST_08  C13  C12  C11  C10   180.00   0.0  0
 2HS  CONST_09  H15  C15  C16  C11   180.00   0.0  0
 2HS  CONST_10  H13  C13  C12  C11   180.00   0.0  0
 2HS  CONST_11  H12  C12  C11  C16   180.00   0.0  0
 2HS  CONST_12  H14  C14  C15  C16   180.00   0.0  0
 2HS  CONST_13  H16  C16  C15  C14   180.00   0.0  0
 2HS  Var_01    C16  C11  C10  C8   -116.82  30.0  2
 2HS  Var_02    C3   C4   C5   C6   -179.31  30.0  3
 2HS  Var_03    C2   C3   C4   C5   -179.59  30.0  3
 2HS  Var_04    C1   C2   C3   C4   -177.53  30.0  3
 2HS  Var_05    P    C1   C2   C3   -174.02  30.0  3
 2HS  Var_06    O    P    C1   C2   -169.96  30.0  3
 2HS  Var_07    C8   C7   O1   P    -159.10  30.0  3
 2HS  Var_08    H61  C6   C5   C4    179.89  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
 2HS  chir_02  C8  C7  C9  C10  negativ
 2HS  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
 2HS  plan-1  C10  0.020
 2HS  plan-1  C11  0.020
 2HS  plan-1  C16  0.020
 2HS  plan-1  C15  0.020
 2HS  plan-1  C14  0.020
 2HS  plan-1  C13  0.020
 2HS  plan-1  C12  0.020
 2HS  plan-1  H16  0.020
 2HS  plan-1  H15  0.020
 2HS  plan-1  H14  0.020
 2HS  plan-1  H13  0.020
 2HS  plan-1  H12  0.020

