# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:40:39 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: propane-1,3-diylbis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CCC[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
 7PA  7PA  'propane-1,3-diylbis(phosphonic acid)'  ligand  21  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7PA
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
 7PA  O1   O  O     0  -0.722  -0.9679   1.9219   2.0657
 7PA  O2   O  OH1   0  -0.746  -2.8037   0.5154   3.2678
 7PA  C1   C  CH2   0  -0.741  -0.5680  -1.9513  -0.6553
 7PA  C2   C  CH2   0  -0.452  -0.9504  -0.5628  -0.1467
 7PA  P1   P  P     0   1.370   0.2492  -1.9068  -2.2556
 7PA  C3   C  CH2   0  -0.741  -1.6291  -0.6673   1.2173
 7PA  P2   P  P     0   1.369  -2.0682   0.9369   1.8992
 7PA  O3   O  O     0  -0.722  -0.4726  -1.2338  -3.3665
 7PA  O4   O  OH1   0  -0.746   0.5514  -3.4687  -2.5023
 7PA  O5   O  OH1   0  -0.751  -3.2330   1.4202   0.8966
 7PA  O6   O  OH1   0  -0.750   1.6646  -1.2295  -1.8901
 7PA  HO2  H  HOH1  0   0.491  -2.8786   1.2340   3.9101
 7PA  H11  H  HCH2  0   0.289   0.0827  -2.4584   0.0613
 7PA  H12  H  HCH2  0   0.290  -1.4616  -2.5711  -0.7646
 7PA  H21  H  HCH2  0   0.255  -1.6179  -0.0796  -0.8621
 7PA  H22  H  HCH2  0   0.254  -0.0608   0.0646  -0.0673
 7PA  H31  H  HCH2  0   0.290  -0.9576  -1.1472   1.9342
 7PA  H32  H  HCH2  0   0.289  -2.5256  -1.2898   1.1592
 7PA  HO4  H  HOH1  0   0.491   0.7558  -3.6892  -3.4211
 7PA  HO5  H  HOH1  0   0.490  -3.3932   2.3734   0.9150
 7PA  HO6  H  HOH1  0   0.490   2.1200  -0.8443  -2.6509

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
 7PA  O1  P2   double  1.486  0.020  1.486
 7PA  O2  P2   single  1.610  0.020  1.610
 7PA  O2  HO2  single  0.850  0.020  0.980
 7PA  C1  C2   single  1.527  0.020  1.527
 7PA  C1  P1   single  1.797  0.020  1.797
 7PA  C1  H11  single  0.970  0.020  1.090
 7PA  C1  H12  single  0.970  0.020  1.090
 7PA  C2  C3   single  1.527  0.020  1.527
 7PA  C2  H21  single  0.970  0.020  1.090
 7PA  C2  H22  single  0.970  0.020  1.090
 7PA  P1  O3   double  1.486  0.020  1.486
 7PA  P1  O4   single  1.610  0.020  1.610
 7PA  P1  O6   single  1.611  0.020  1.611
 7PA  C3  P2   single  1.798  0.020  1.798
 7PA  C3  H31  single  0.970  0.020  1.090
 7PA  C3  H32  single  0.970  0.020  1.090
 7PA  P2  O5   single  1.611  0.020  1.611
 7PA  O4  HO4  single  0.850  0.020  0.980
 7PA  O5  HO5  single  0.850  0.020  0.980
 7PA  O6  HO6  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
 7PA  HO2  O2  P2   113.93  3.000
 7PA  H12  C1  H11  106.81  3.000
 7PA  H12  C1  P1   107.26  3.000
 7PA  H11  C1  P1   108.94  3.000
 7PA  H12  C1  C2   110.13  3.000
 7PA  H11  C1  C2   110.64  3.000
 7PA  P1   C1  C2   112.82  3.000
 7PA  H22  C2  H21  106.96  3.000
 7PA  H22  C2  C3   109.67  3.000
 7PA  H21  C2  C3   110.12  3.000
 7PA  H22  C2  C1   110.04  3.000
 7PA  H21  C2  C1   109.72  3.000
 7PA  C3   C2  C1   110.27  3.000
 7PA  O6   P1  O4   106.12  3.000
 7PA  O6   P1  O3   113.95  3.000
 7PA  O4   P1  O3   114.59  3.000
 7PA  O6   P1  C1   101.99  3.000
 7PA  O4   P1  C1   101.41  3.000
 7PA  O3   P1  C1   117.13  3.000
 7PA  H32  C3  H31  106.77  3.000
 7PA  H32  C3  P2   109.16  3.000
 7PA  H31  C3  P2   107.04  3.000
 7PA  H32  C3  C2   110.85  3.000
 7PA  H31  C3  C2   110.05  3.000
 7PA  P2   C3  C2   112.73  3.000
 7PA  O5   P2  C3   102.02  3.000
 7PA  O5   P2  O2   106.09  3.000
 7PA  C3   P2  O2   101.56  3.000
 7PA  O5   P2  O1   113.96  3.000
 7PA  C3   P2  O1   116.95  3.000
 7PA  O2   P2  O1   114.61  3.000
 7PA  HO4  O4  P1   113.99  3.000
 7PA  HO5  O5  P2   113.82  3.000
 7PA  HO6  O6  P1   113.75  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
 7PA  Var_01  C2  C3  P2  O1   -56.87  30.0  2
 7PA  Var_02  P2  C3  C2  C1   178.46  30.0  3
 7PA  Var_03  O3  P1  C1  C2   -55.79  30.0  3
 7PA  Var_04  C3  C2  C1  P1  -179.57  30.0  3

