# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 22:08:14 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: methyl hydrogen (R)-hexylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[P@](O)(=O)OC
#
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
 MHH  MHH  'methyl hydrogen (R)-hexylphosphonate'  ligand  28  11  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MHH
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
 MHH  C1   C  CH2   0  -0.747   0.3958  -0.6573   0.1746
 MHH  C2   C  CH2   0  -0.432  -0.8509   0.2010  -0.0366
 MHH  C3   C  CH2   0  -0.406  -2.1312  -0.6010   0.1587
 MHH  C7   C  CH3   0  -0.413   4.4139  -0.5581  -0.0012
 MHH  P    P  P     0   1.388   1.9137   0.2505  -0.1519
 MHH  O1   O  O2    0  -0.591   3.0326  -0.8330   0.2451
 MHH  O2   O  OH1   0  -0.754   2.0202   1.4329   0.9390
 MHH  C4   C  CH2   0  -0.408  -3.3884   0.2336  -0.0466
 MHH  C5   C  CH2   0  -0.419  -4.6741  -0.5654   0.1264
 MHH  C6   C  CH3   0  -0.662  -5.9244   0.2768  -0.0853
 MHH  O3   O  O     0  -0.722   2.0510   0.8390  -1.5070
 MHH  H1   H  HCH2  0   0.282   0.4231  -1.0579   1.1914
 MHH  H1A  H  HCH2  0   0.283   0.3842  -1.5153  -0.5030
 MHH  H2   H  HCH2  0   0.231  -0.8424   1.0462   0.6570
 MHH  H2A  H  HCH2  0   0.233  -0.8386   0.6258  -1.0441
 MHH  H3   H  HCH2  0   0.215  -2.1367  -1.4467  -0.5377
 MHH  H3A  H  HCH2  0   0.215  -2.1388  -1.0336   1.1647
 MHH  H7   H  HCH3  0   0.233   4.7354   0.3607   0.4913
 MHH  H7A  H  HCH3  0   0.251   4.9813  -1.3899   0.4082
 MHH  H7B  H  HCH3  0   0.237   4.6163  -0.4809  -1.0693
 MHH  HO2  H  HOH1  0   0.489   1.9405   1.1547   1.8606
 MHH  H4   H  HCH2  0   0.209  -3.3870   1.0738   0.6566
 MHH  H4A  H  HCH2  0   0.209  -3.3706   0.6775  -1.0481
 MHH  H5   H  HCH2  0   0.211  -4.6756  -1.4047  -0.5760
 MHH  H5A  H  HCH2  0   0.211  -4.6933  -1.0088   1.1268
 MHH  H6   H  HCH3  0   0.216  -5.9737   1.0993   0.6310
 MHH  H6A  H  HCH3  0   0.216  -5.9405   0.7123  -1.0862
 MHH  H6B  H  HCH3  0   0.226  -6.8326  -0.3162   0.0295

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
 MHH  C1  C2   single  1.528  0.020  1.528
 MHH  P   C1   single  1.798  0.020  1.798
 MHH  C1  H1   single  0.970  0.020  1.090
 MHH  C1  H1A  single  0.970  0.020  1.090
 MHH  C2  C3   single  1.523  0.020  1.523
 MHH  C2  H2   single  0.970  0.020  1.090
 MHH  C2  H2A  single  0.970  0.020  1.090
 MHH  C3  C4   single  1.523  0.020  1.523
 MHH  C3  H3   single  0.970  0.020  1.090
 MHH  C3  H3A  single  0.970  0.020  1.090
 MHH  C7  O1   single  1.430  0.020  1.430
 MHH  C7  H7   single  0.970  0.020  1.090
 MHH  C7  H7A  single  0.970  0.020  1.090
 MHH  C7  H7B  single  0.970  0.020  1.090
 MHH  O3  P    double  1.484  0.020  1.484
 MHH  P   O2   single  1.612  0.020  1.612
 MHH  P   O1   single  1.607  0.020  1.607
 MHH  O2  HO2  single  0.850  0.020  0.980
 MHH  C4  C5   single  1.524  0.020  1.524
 MHH  C4  H4   single  0.970  0.020  1.090
 MHH  C4  H4A  single  0.970  0.020  1.090
 MHH  C5  C6   single  1.522  0.020  1.522
 MHH  C5  H5   single  0.970  0.020  1.090
 MHH  C5  H5A  single  0.970  0.020  1.090
 MHH  C6  H6   single  0.970  0.020  1.090
 MHH  C6  H6A  single  0.970  0.020  1.090
 MHH  C6  H6B  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
 MHH  H1A  C1  H1   106.81  3.000
 MHH  H1A  C1  P    107.01  3.000
 MHH  H1   C1  P    109.44  3.000
 MHH  H1A  C1  C2   110.27  3.000
 MHH  H1   C1  C2   110.77  3.000
 MHH  P    C1  C2   112.33  3.000
 MHH  H2A  C2  H2   106.51  3.000
 MHH  H2A  C2  C3   109.40  3.000
 MHH  H2   C2  C3   109.40  3.000
 MHH  H2A  C2  C1   109.66  3.000
 MHH  H2   C2  C1   109.89  3.000
 MHH  C3   C2  C1   111.85  3.000
 MHH  H3A  C3  H3   106.20  3.000
 MHH  H3A  C3  C4   109.55  3.000
 MHH  H3   C3  C4   109.46  3.000
 MHH  H3A  C3  C2   109.37  3.000
 MHH  H3   C3  C2   109.22  3.000
 MHH  C4   C3  C2   112.83  3.000
 MHH  H7B  C7  H7A  109.05  3.000
 MHH  H7B  C7  H7   109.15  3.000
 MHH  H7A  C7  H7   108.69  3.000
 MHH  H7B  C7  O1   111.21  3.000
 MHH  H7A  C7  O1   107.00  3.000
 MHH  H7   C7  O1   111.65  3.000
 MHH  O3   P   O2   108.72  3.000
 MHH  O2   P   O1   106.33  3.000
 MHH  O3   P   O1   115.37  3.000
 MHH  O1   P   C1   101.68  3.000
 MHH  O2   P   C1   107.64  3.000
 MHH  O3   P   C1   116.37  3.000
 MHH  P    O1  C7   120.02  3.000
 MHH  HO2  O2  P    115.40  3.000
 MHH  H4A  C4  H4   106.02  3.000
 MHH  H4A  C4  C5   109.27  3.000
 MHH  H4   C4  C5   109.29  3.000
 MHH  H4A  C4  C3   109.38  3.000
 MHH  H4   C4  C3   109.43  3.000
 MHH  C5   C4  C3   113.20  3.000
 MHH  H5A  C5  H5   106.02  3.000
 MHH  H5A  C5  C6   109.68  3.000
 MHH  H5   C5  C6   109.50  3.000
 MHH  H5A  C5  C4   109.34  3.000
 MHH  H5   C5  C4   109.30  3.000
 MHH  C6   C5  C4   112.78  3.000
 MHH  H6B  C6  H6A  107.52  3.000
 MHH  H6B  C6  H6   107.63  3.000
 MHH  H6A  C6  H6   107.47  3.000
 MHH  H6B  C6  C5   111.63  3.000
 MHH  H6A  C6  C5   111.13  3.000
 MHH  H6   C6  C5   111.26  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
 MHH  Var_01  C4  C3  C2  C1   180.00  30.0  3
 MHH  Var_02  O3  P   C1  C2   -57.76  30.0  1
 MHH  Var_03  C5  C4  C3  C2   179.14  30.0  3
 MHH  Var_04  P   C1  C2  C3   176.47  30.0  1
 MHH  Var_05  C6  C5  C4  C3  -179.81  30.0  3
 MHH  Var_06  H7  C7  O1  P     57.23  30.0  3
 MHH  Var_07  H6  C6  C5  C4   -60.52  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
 MHH  chir_01  P  O3  O2  O1  both

