# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:02:27 2022
#   Inital geometry file: a 167 line input string
#   Ligand name: {[(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C[P](O)(=O)O[C@@H]1[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H](O[P](O)(=O)C[P](O)(O)=O)[C@H]1O[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
 5A2  5A2  '{[(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)'  ligand  54  44  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5A2
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
 5A2  C1   C  CH1    0   0.088  -0.1263   2.2053   0.6787
 5A2  C2   C  CH1    0  -0.010   1.1450   1.5786   0.0980
 5A2  C3   C  CH1    0   0.059   1.1377   0.0895   0.4387
 5A2  C4   C  CH1    0   0.096  -0.0837  -0.6168  -0.1575
 5A2  C5   C  CH1    0   0.026  -1.3759   0.0895   0.2895
 5A2  C6   C  CH1    0   0.094  -1.3689   1.6039   0.0139
 5A2  O55  O  OP    -1  -1.007  -4.8469  -5.2093  -1.1148
 5A2  PB5  P  P      0   1.132  -5.2516  -3.8881  -0.4292
 5A2  O65  O  O      0  -0.840  -6.3726  -3.1643  -1.1914
 5A2  O75  O  OP    -1  -0.890  -5.5501  -4.0671   1.0684
 5A2  C5B  C  CH2    0  -1.008  -3.7330  -2.8247  -0.5404
 5A2  O35  O  OP    -1  -0.954  -3.2858  -1.5559   1.8793
 5A2  O25  O  O      0  -0.711  -4.9791  -0.5258   0.2278
 5A2  O15  O  O2     0  -0.621  -2.4772  -0.5080  -0.3441
 5A2  O14  O  O2     0  -0.652  -0.1285  -1.9568   0.2423
 5A2  PA4  P  P      0   1.262   0.1681  -3.2604  -0.7884
 5A2  O34  O  O      0  -0.851  -0.3294  -2.8462  -2.1730
 5A2  O44  O  OP    -1  -1.003   1.6697  -3.5498  -0.7576
 5A2  O24  O  OP    -1  -0.960  -0.6377  -4.3745  -0.1104
 5A2  O16  O  O2     0  -0.633  -2.5425   2.1587   0.5300
 5A2  PA6  P  P      0   1.268  -3.5565   3.1283  -0.4010
 5A2  O36  O  O      0  -0.881  -3.7474   2.4241  -1.7447
 5A2  O46  O  OP    -1  -0.937  -4.8028   3.1853   0.4864
 5A2  O26  O  OP    -1  -1.016  -2.8823   4.4917  -0.5592
 5A2  O11  O  O2     0  -0.573  -0.1126   3.5931   0.5720
 5A2  PA1  P  P      0   1.226   0.1803   4.4948   1.9497
 5A2  O41  O  OP    -1  -0.920  -0.9816   4.2298   2.9098
 5A2  O21  O  O      0  -1.020   1.5195   4.0170   2.5202
 5A2  O31  O  OP    -1  -0.985   0.2152   5.9212   1.3971
 5A2  O12  O  O2     0  -0.660   1.1835   1.7614  -1.2946
 5A2  PA2  P  P      0   1.203   2.4962   2.3877  -2.1407
 5A2  O42  O  OP    -1  -0.940   3.4088   1.2180  -2.5113
 5A2  O22  O  OP    -1  -0.875   1.7845   2.9748  -3.3681
 5A2  O32  O  O      0  -0.983   3.1573   3.4368  -1.2526
 5A2  O13  O  O2     0  -0.601   2.2935  -0.5402  -0.0318
 5A2  PA3  P  P      0   1.238   3.6141  -0.7837   0.9210
 5A2  O23  O  OP    -1  -0.851   3.2867  -1.7913   2.0034
 5A2  O33  O  O      0  -0.872   4.1387   0.5465   1.4191
 5A2  C3B  C  CH2    0  -0.991   4.6599  -1.4764  -0.3904
 5A2  PB3  P  P      0   1.147   6.4499  -1.8291  -0.0335
 5A2  O53  O  O      0  -0.852   6.4838  -2.6862   1.2404
 5A2  O63  O  OP    -1  -1.009   6.9352  -2.5947  -1.2809
 5A2  O73  O  OP    -1  -0.948   7.1440  -0.4691   0.1275
 5A2  H1   H  HCH1   0   0.212  -0.1704   1.9053   1.7406
 5A2  H2   H  HCH1   0   0.228   2.0076   2.0508   0.5797
 5A2  H3   H  HCH1   0   0.226   1.0658   0.0086   1.5371
 5A2  H4   H  HCH1   0   0.163  -0.0160  -0.5428  -1.2505
 5A2  H5   H  HCH1   0   0.150  -1.4615  -0.0399   1.3785
 5A2  H6   H  HCH1   0   0.159  -1.2975   1.7647  -1.0698
 5A2  H9   H  HCH2   0   0.169  -2.8411  -3.4029  -0.2852
 5A2  H10  H  HCH2   0   0.201  -3.5854  -2.5425  -1.5889
 5A2  H21  H  HCH2   0   0.215   4.1529  -2.3927  -0.7135
 5A2  H22  H  HCH2   0   0.244   4.5839  -0.7799  -1.2332
 5A2  PA5  P  P      0   1.250  -3.7023  -1.3012   0.4444

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
 5A2  O32  PA2  deloc   1.525  0.020  1.525
 5A2  O22  PA2  deloc   1.536  0.020  1.536
 5A2  O21  PA1  deloc   1.532  0.020  1.532
 5A2  PA2  O42  deloc   1.529  0.020  1.529
 5A2  PA2  O12  single  1.683  0.020  1.683
 5A2  O41  PA1  deloc   1.530  0.020  1.530
 5A2  PA1  O11  single  1.672  0.020  1.672
 5A2  PA1  O31  deloc   1.530  0.020  1.530
 5A2  O33  PA3  deloc   1.514  0.020  1.514
 5A2  O53  PB3  deloc   1.536  0.020  1.536
 5A2  O11  C1   single  1.392  0.020  1.392
 5A2  O12  C2   single  1.405  0.020  1.405
 5A2  C2   C1   single  1.532  0.020  1.532
 5A2  C2   C3   single  1.528  0.020  1.528
 5A2  PA3  O23  deloc   1.515  0.020  1.515
 5A2  PA3  O13  single  1.647  0.020  1.647
 5A2  PA3  C3B  single  1.815  0.020  1.815
 5A2  C1   C6   single  1.532  0.020  1.532
 5A2  O36  PA6  deloc   1.529  0.020  1.529
 5A2  PB3  O63  deloc   1.542  0.020  1.542
 5A2  PB3  C3B  single  1.859  0.020  1.859
 5A2  PB3  O73  deloc   1.535  0.020  1.535
 5A2  O13  C3   single  1.398  0.020  1.398
 5A2  C3   C4   single  1.532  0.020  1.532
 5A2  C6   O16  single  1.397  0.020  1.397
 5A2  C6   C5   single  1.539  0.020  1.539
 5A2  O46  PA6  deloc   1.531  0.020  1.531
 5A2  PA6  O16  single  1.684  0.020  1.684
 5A2  PA6  O26  deloc   1.529  0.020  1.529
 5A2  C4   C5   single  1.539  0.020  1.539
 5A2  C4   O14  single  1.399  0.020  1.399
 5A2  O34  PA4  deloc   1.528  0.020  1.528
 5A2  C5   O15  single  1.404  0.020  1.404
 5A2  O14  PA4  single  1.688  0.020  1.688
 5A2  O24  PA4  deloc   1.533  0.020  1.533
 5A2  O15  PA5  single  1.659  0.020  1.659
 5A2  PA4  O44  deloc   1.530  0.020  1.530
 5A2  O65  PB5  deloc   1.537  0.020  1.537
 5A2  PA5  O25  deloc   1.509  0.020  1.509
 5A2  PA5  O35  deloc   1.516  0.020  1.516
 5A2  PA5  C5B  single  1.814  0.020  1.814
 5A2  PB5  C5B  single  1.857  0.020  1.857
 5A2  PB5  O55  deloc   1.543  0.020  1.543
 5A2  PB5  O75  deloc   1.538  0.020  1.538
 5A2  C1   H1   single  0.970  0.020  1.090
 5A2  C2   H2   single  0.970  0.020  1.090
 5A2  C3   H3   single  0.970  0.020  1.090
 5A2  C4   H4   single  0.970  0.020  1.090
 5A2  C5   H5   single  0.970  0.020  1.090
 5A2  C6   H6   single  0.970  0.020  1.090
 5A2  C5B  H9   single  0.970  0.020  1.090
 5A2  C5B  H10  single  0.970  0.020  1.090
 5A2  C3B  H21  single  0.970  0.020  1.090
 5A2  C3B  H22  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
 5A2  H1   C1   O11  110.18  3.000
 5A2  H1   C1   C6   106.16  3.000
 5A2  O11  C1   C6   111.47  3.000
 5A2  H1   C1   C2   106.65  3.000
 5A2  C6   C1   C2   110.36  3.000
 5A2  O11  C1   C2   111.75  3.000
 5A2  H2   C2   O12  111.00  3.000
 5A2  H2   C2   C3   109.02  3.000
 5A2  O12  C2   C3   110.37  3.000
 5A2  H2   C2   C1   108.10  3.000
 5A2  C3   C2   C1   108.08  3.000
 5A2  O12  C2   C1   110.20  3.000
 5A2  H3   C3   O13  110.85  3.000
 5A2  H3   C3   C4   107.56  3.000
 5A2  O13  C3   C4   108.70  3.000
 5A2  H3   C3   C2   107.08  3.000
 5A2  C4   C3   C2   111.50  3.000
 5A2  O13  C3   C2   111.11  3.000
 5A2  H4   C4   O14  110.56  3.000
 5A2  H4   C4   C5   108.07  3.000
 5A2  O14  C4   C5   109.25  3.000
 5A2  H4   C4   C3   107.90  3.000
 5A2  O14  C4   C3   110.85  3.000
 5A2  C5   C4   C3   110.17  3.000
 5A2  H5   C5   O15  109.62  3.000
 5A2  H5   C5   C6   107.06  3.000
 5A2  O15  C5   C6   109.96  3.000
 5A2  H5   C5   C4   107.39  3.000
 5A2  O15  C5   C4   109.40  3.000
 5A2  C6   C5   C4   113.31  3.000
 5A2  H6   C6   O16  111.17  3.000
 5A2  H6   C6   C5   108.73  3.000
 5A2  O16  C6   C5   108.71  3.000
 5A2  H6   C6   C1   108.55  3.000
 5A2  C5   C6   C1   108.19  3.000
 5A2  O16  C6   C1   111.42  3.000
 5A2  C5B  PB5  O75  106.48  3.000
 5A2  O75  PB5  O65  113.35  3.000
 5A2  C5B  PB5  O65  107.28  3.000
 5A2  O75  PB5  O55  112.59  3.000
 5A2  C5B  PB5  O55  104.44  3.000
 5A2  O65  PB5  O55  111.98  3.000
 5A2  H10  C5B  H9   104.46  3.000
 5A2  H10  C5B  PA5  107.51  3.000
 5A2  H9   C5B  PA5  107.67  3.000
 5A2  H10  C5B  PB5  108.36  3.000
 5A2  H9   C5B  PB5  110.51  3.000
 5A2  PA5  C5B  PB5  117.52  3.000
 5A2  PA5  O15  C5   124.63  3.000
 5A2  PA4  O14  C4   124.02  3.000
 5A2  O24  PA4  O44  111.69  3.000
 5A2  O44  PA4  O34  112.90  3.000
 5A2  O24  PA4  O34  115.25  3.000
 5A2  O44  PA4  O14  107.84  3.000
 5A2  O24  PA4  O14  101.47  3.000
 5A2  O34  PA4  O14  106.66  3.000
 5A2  PA6  O16  C6   122.03  3.000
 5A2  O26  PA6  O46  112.68  3.000
 5A2  O26  PA6  O36  112.01  3.000
 5A2  O46  PA6  O36  115.14  3.000
 5A2  O26  PA6  O16  107.77  3.000
 5A2  O46  PA6  O16  101.02  3.000
 5A2  O36  PA6  O16  107.21  3.000
 5A2  PA1  O11  C1   118.43  3.000
 5A2  O31  PA1  O21  113.91  3.000
 5A2  O31  PA1  O41  113.91  3.000
 5A2  O21  PA1  O41  112.09  3.000
 5A2  O31  PA1  O11  102.07  3.000
 5A2  O41  PA1  O11  106.89  3.000
 5A2  O21  PA1  O11  106.96  3.000
 5A2  PA2  O12  C2   124.62  3.000
 5A2  O32  PA2  O22  113.79  3.000
 5A2  O22  PA2  O42  112.05  3.000
 5A2  O32  PA2  O42  114.11  3.000
 5A2  O42  PA2  O12  107.62  3.000
 5A2  O22  PA2  O12  100.52  3.000
 5A2  O32  PA2  O12  107.54  3.000
 5A2  PA3  O13  C3   122.34  3.000
 5A2  C3B  PA3  O33  111.93  3.000
 5A2  C3B  PA3  O23  112.77  3.000
 5A2  O33  PA3  O23  115.10  3.000
 5A2  C3B  PA3  O13   95.77  3.000
 5A2  O23  PA3  O13  109.79  3.000
 5A2  O33  PA3  O13  109.78  3.000
 5A2  H22  C3B  H21  105.82  3.000
 5A2  H22  C3B  PB3  109.57  3.000
 5A2  H21  C3B  PB3  110.08  3.000
 5A2  H22  C3B  PA3  105.85  3.000
 5A2  H21  C3B  PA3  105.41  3.000
 5A2  PB3  C3B  PA3  119.25  3.000
 5A2  O73  PB3  O63  112.48  3.000
 5A2  O73  PB3  O53  113.42  3.000
 5A2  O63  PB3  O53  112.76  3.000
 5A2  O73  PB3  C3B  106.70  3.000
 5A2  O63  PB3  C3B  104.00  3.000
 5A2  O53  PB3  C3B  106.64  3.000
 5A2  O15  PA5  O25  108.11  3.000
 5A2  O25  PA5  O35  117.04  3.000
 5A2  O15  PA5  O35  109.11  3.000
 5A2  O35  PA5  C5B  112.17  3.000
 5A2  O25  PA5  C5B  109.82  3.000
 5A2  O15  PA5  C5B   98.98  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
 5A2  Var_01  O21  PA1  O11  C1     56.05  30.0  2
 5A2  Var_02  O32  PA2  O12  C2    -34.46  30.0  3
 5A2  Var_03  O33  PA3  O13  C3    -59.70  30.0  1
 5A2  Var_04  O34  PA4  O14  C4    -32.68  30.0  3
 5A2  Var_05  O25  PA5  O15  C5    115.20  30.0  3
 5A2  Var_06  O36  PA6  O16  C6     46.29  30.0  3
 5A2  Var_07  PA5  C5B  PB5  O55  -168.25  30.0  3
 5A2  Var_08  O15  PA5  C5B  PB5  -162.20  30.0  1
 5A2  Var_09  PB3  C3B  PA3  O13   173.39  30.0  3
 5A2  Var_10  O53  PB3  C3B  PA3    52.10  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
 5A2  chir_01  C1  O11  C2  C6  positiv
 5A2  chir_02  C2  O12  C3  C1  positiv
 5A2  chir_03  C3  O13  C2  C4  negativ
 5A2  chir_04  C4  O14  C5  C3  negativ
 5A2  chir_05  C5  O15  C4  C6  negativ
 5A2  chir_06  C6  O16  C1  C5  negativ

