# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:57:25 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2-oxoheptyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)C[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
 HPO  HPO  '(2-oxoheptyl)phosphonic acid'  ligand  27  12  .  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_HPO
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
 HPO  C1   C  CH3   0  -0.662  -0.2877   0.0507   6.3318
 HPO  C2   C  CH2   0  -0.420   0.4837  -0.0305   5.0219
 HPO  C3   C  CH2   0  -0.410  -0.4272   0.0217   3.8014
 HPO  C4   C  CH2   0  -0.418   0.3358  -0.0329   2.4831
 HPO  C5   C  CH2   0  -0.550  -0.6040   0.0069   1.2891
 HPO  C6   C  C     0   0.418   0.0688  -0.0109  -0.0553
 HPO  C7   C  CH2   0  -0.878  -0.8625   0.1088  -1.2408
 HPO  O1   O  O     0  -0.391   1.2648  -0.1063  -0.1960
 HPO  P1   P  P     0   1.381  -0.0347  -0.0746  -2.8375
 HPO  O2   O  O     0  -0.711   0.6885  -1.3448  -3.0715
 HPO  O3   O  OH1   0  -0.745  -1.2845   0.2114  -3.8085
 HPO  O4   O  OH1   0  -0.747   0.9707   1.1651  -3.0092
 HPO  H11  H  HCH3  0   0.227   0.3776   0.0092   7.1949
 HPO  H12  H  HCH3  0   0.216  -0.8542   0.9819   6.3959
 HPO  H13  H  HCH3  0   0.216  -0.9989  -0.7730   6.4227
 HPO  H21  H  HCH2  0   0.212   1.2058   0.7900   4.9693
 HPO  H22  H  HCH2  0   0.212   1.0707  -0.9538   4.9957
 HPO  H31  H  HCH2  0   0.212  -1.1409  -0.8083   3.8475
 HPO  H32  H  HCH2  0   0.211  -1.0268   0.9383   3.8371
 HPO  H41  H  HCH2  0   0.224   1.0341   0.8072   2.4329
 HPO  H42  H  HCH2  0   0.225   0.9426  -0.9420   2.4497
 HPO  H51  H  HCH2  0   0.274  -1.3008  -0.8391   1.3184
 HPO  H52  H  HCH2  0   0.269  -1.2450   0.8952   1.3294
 HPO  H71  H  HCH2  0   0.324  -1.6506  -0.6458  -1.1646
 HPO  H72  H  HCH2  0   0.327  -1.3774   1.0738  -1.1925
 HPO  HO3  H  HOH1  0   0.494  -1.1083   0.0325  -4.7426
 HPO  HO4  H  HOH1  0   0.490   0.5711   2.0419  -2.9433

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
 HPO  C1  C2   single  1.522  0.020  1.522
 HPO  C1  H11  single  0.970  0.020  1.090
 HPO  C1  H12  single  0.970  0.020  1.090
 HPO  C1  H13  single  0.970  0.020  1.090
 HPO  C2  C3   single  1.524  0.020  1.524
 HPO  C2  H21  single  0.970  0.020  1.090
 HPO  C2  H22  single  0.970  0.020  1.090
 HPO  C3  C4   single  1.524  0.020  1.524
 HPO  C3  H31  single  0.970  0.020  1.090
 HPO  C3  H32  single  0.970  0.020  1.090
 HPO  C4  C5   single  1.520  0.020  1.520
 HPO  C4  H41  single  0.970  0.020  1.090
 HPO  C4  H42  single  0.970  0.020  1.090
 HPO  C5  C6   single  1.503  0.020  1.503
 HPO  C5  H51  single  0.970  0.020  1.090
 HPO  C5  H52  single  0.970  0.020  1.090
 HPO  C6  C7   single  1.512  0.020  1.512
 HPO  C6  O1   double  1.208  0.020  1.208
 HPO  C7  P1   single  1.808  0.020  1.808
 HPO  C7  H71  single  0.970  0.020  1.090
 HPO  C7  H72  single  0.970  0.020  1.090
 HPO  P1  O2   double  1.480  0.020  1.480
 HPO  P1  O3   single  1.608  0.020  1.608
 HPO  P1  O4   single  1.605  0.020  1.605
 HPO  O3  HO3  single  0.850  0.020  0.980
 HPO  O4  HO4  single  0.850  0.020  0.980

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
 HPO  H13  C1  H12  107.49  3.000
 HPO  H13  C1  H11  107.63  3.000
 HPO  H12  C1  H11  107.61  3.000
 HPO  H13  C1  C2   111.18  3.000
 HPO  H12  C1  C2   111.03  3.000
 HPO  H11  C1  C2   111.70  3.000
 HPO  H22  C2  H21  106.11  3.000
 HPO  H22  C2  C3   109.29  3.000
 HPO  H21  C2  C3   109.29  3.000
 HPO  H22  C2  C1   109.72  3.000
 HPO  H21  C2  C1   109.62  3.000
 HPO  C3   C2  C1   112.61  3.000
 HPO  H32  C3  H31  106.01  3.000
 HPO  H32  C3  C4   109.39  3.000
 HPO  H31  C3  C4   109.59  3.000
 HPO  H32  C3  C2   109.25  3.000
 HPO  H31  C3  C2   109.26  3.000
 HPO  C4   C3  C2   113.10  3.000
 HPO  H42  C4  H41  106.43  3.000
 HPO  H42  C4  C5   109.92  3.000
 HPO  H41  C4  C5   109.79  3.000
 HPO  H42  C4  C3   109.51  3.000
 HPO  H41  C4  C3   109.39  3.000
 HPO  C5   C4  C3   111.65  3.000
 HPO  H52  C5  H51  104.63  3.000
 HPO  H52  C5  C6   107.71  3.000
 HPO  H51  C5  C6   107.41  3.000
 HPO  H52  C5  C4   110.72  3.000
 HPO  H51  C5  C4   110.60  3.000
 HPO  C6   C5  C4   115.18  3.000
 HPO  O1   C6  C7   121.64  3.000
 HPO  O1   C6  C5   123.24  3.000
 HPO  C7   C6  C5   115.12  3.000
 HPO  H72  C7  H71  105.43  3.000
 HPO  H72  C7  P1   110.10  3.000
 HPO  H71  C7  P1   108.75  3.000
 HPO  H72  C7  C6   108.95  3.000
 HPO  H71  C7  C6   109.55  3.000
 HPO  P1   C7  C6   113.73  3.000
 HPO  O4   P1  O3   106.54  3.000
 HPO  O4   P1  O2   109.86  3.000
 HPO  O3   P1  O2   115.90  3.000
 HPO  O4   P1  C7   107.64  3.000
 HPO  O3   P1  C7    99.17  3.000
 HPO  O2   P1  C7   116.77  3.000
 HPO  HO3  O3  P1   114.12  3.000
 HPO  HO4  O4  P1   115.76  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
 HPO  Var_01  C4   C3  C2  C1   178.94  30.0  3
 HPO  Var_02  C5   C4  C3  C2   179.42  30.0  3
 HPO  Var_03  C6   C5  C4  C3   178.65  30.0  3
 HPO  Var_04  C7   C6  C5  C4  -176.64  30.0  3
 HPO  Var_05  P1   C7  C6  C5  -174.48  30.0  3
 HPO  Var_06  O2   P1  C7  C6    58.59  30.0  3
 HPO  Var_07  H11  C1  C2  C3   179.84  30.0  3

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
 HPO  plan-1  C5  0.020
 HPO  plan-1  C6  0.020
 HPO  plan-1  C7  0.020
 HPO  plan-1  O1  0.020

