# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 10:30:16 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: {[(R)-hydroxy{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}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)=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
 5A3  5A3  '{[(R)-hydroxy{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}phosphoryl]methyl}phosphonic acid'  ligand  48  40  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5A3
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
 5A3  O31  O  O      0  -0.823  -3.9306  -1.8248   2.4748
 5A3  C2   C  CH1    0  -0.057  -2.2549  -0.0125   0.1137
 5A3  C1   C  CH1    0   0.111  -1.5672  -1.2930   0.5899
 5A3  C4   C  CH1    0   0.093  -0.0313   1.0384  -0.4014
 5A3  C5   C  CH1    0  -0.015   0.6469  -0.2799   0.0172
 5A3  C6   C  CH1    0   0.131  -0.2577  -1.5144  -0.1744
 5A3  C3   C  CH1    0   0.097  -1.3343   1.1764   0.3953
 5A3  O11  O  O2     0  -0.653  -2.4101  -2.3986   0.4821
 5A3  O75  O  OP    -1  -0.957   6.5803  -0.1464   0.6031
 5A3  PB5  P  P      0   1.163   5.7691   1.1583   0.6637
 5A3  O55  O  O      0  -0.927   5.3713   1.5575   2.0932
 5A3  O65  O  OP    -1  -0.918   6.4592   2.3100  -0.0967
 5A3  CB5  C  CH2    0  -0.939   4.1905   0.8649  -0.2721
 5A3  O25  O  O      0  -0.819   3.9943  -1.8026  -0.7133
 5A3  O35  O  OP    -1  -0.830   3.1063  -0.8648   1.5520
 5A3  O15  O  O2     0  -0.660   1.8560  -0.4554  -0.6764
 5A3  O16  O  O2     0  -0.688   0.4214  -2.6458   0.2846
 5A3  PA6  P  P      0   1.246   0.6351  -4.0239  -0.6534
 5A3  O46  O  O      0  -0.893  -0.6341  -4.8690  -0.5393
 5A3  O36  O  OP    -1  -0.983   0.8920  -3.5549  -2.0873
 5A3  O26  O  OP    -1  -0.853   1.8319  -4.6801   0.0392
 5A3  PA1  P  P      0   1.244  -3.1379  -2.9870   1.8647
 5A3  O41  O  OP    -1  -0.962  -2.0255  -3.4687   2.8009
 5A3  O21  O  OP    -1  -0.981  -4.0218  -4.1099   1.3174
 5A3  O12  O  O2     0  -0.676  -2.5306  -0.0765  -1.2655
 5A3  PA2  P  P      0   1.200  -4.0613  -0.1065  -1.9417
 5A3  O42  O  O      0  -0.837  -5.0671   0.2840  -0.8628
 5A3  O22  O  OP    -1  -0.956  -3.9477   0.9157  -3.0806
 5A3  O32  O  OP    -1  -1.031  -4.2465  -1.5305  -2.4736
 5A3  O13  O  O2     0  -0.578  -1.9686   2.3891   0.1311
 5A3  PA3  P  P      0   1.192  -2.5230   3.3144   1.4061
 5A3  O43  O  OP    -1  -0.920  -3.2685   4.4388   0.6813
 5A3  O33  O  O      0  -1.006  -3.4287   2.4161   2.2536
 5A3  O23  O  OP    -1  -0.903  -1.2960   3.7940   2.1870
 5A3  O14  O  O2     0  -0.650   0.8340   2.1051  -0.1414
 5A3  PA4  P  P      0   1.232   1.2776   3.1936  -1.3466
 5A3  O24  O  OP    -1  -0.897   2.3509   4.0034  -0.6120
 5A3  O44  O  OP    -1  -1.002   1.7930   2.3710  -2.5292
 5A3  O34  O  O      0  -0.950   0.0449   4.0172  -1.7159
 5A3  H1   H  HCH1   0   0.258  -3.1720   0.1183   0.6918
 5A3  H2   H  HCH1   0   0.098  -1.2904  -1.1235   1.6447
 5A3  H3   H  HCH1   0   0.186  -0.2795   0.9867  -1.4686
 5A3  H4   H  HCH1   0   0.171   0.8533  -0.2036   1.0956
 5A3  H5   H  HCH1   0   0.167  -0.4903  -1.6144  -1.2409
 5A3  H6   H  HCH1   0   0.154  -1.0542   1.1102   1.4611
 5A3  H9   H  HCH2   0   0.214   3.5217   1.7127  -0.1176
 5A3  H10  H  HCH2   0   0.155   4.4034   0.8817  -1.3465
 5A3  PA5  P  P      0   1.252   3.3204  -0.6973   0.0642

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
 5A3  O42  PA2  deloc   1.526  0.020  1.526
 5A3  O31  PA1  deloc   1.533  0.020  1.533
 5A3  O32  PA2  deloc   1.531  0.020  1.531
 5A3  PA2  O22  deloc   1.535  0.020  1.535
 5A3  PA2  O12  single  1.674  0.020  1.674
 5A3  O21  PA1  deloc   1.530  0.020  1.530
 5A3  PA1  O11  single  1.670  0.020  1.670
 5A3  PA1  O41  deloc   1.532  0.020  1.532
 5A3  O11  C1   single  1.394  0.020  1.394
 5A3  O12  C2   single  1.408  0.020  1.408
 5A3  C2   C1   single  1.529  0.020  1.529
 5A3  C2   C3   single  1.530  0.020  1.530
 5A3  C1   C6   single  1.532  0.020  1.532
 5A3  O46  PA6  deloc   1.529  0.020  1.529
 5A3  O33  PA3  deloc   1.532  0.020  1.532
 5A3  O43  PA3  deloc   1.532  0.020  1.532
 5A3  O13  PA3  single  1.670  0.020  1.670
 5A3  O13  C3   single  1.394  0.020  1.394
 5A3  PA3  O23  deloc   1.531  0.020  1.531
 5A3  C3   C4   single  1.533  0.020  1.533
 5A3  C6   O16  single  1.397  0.020  1.397
 5A3  C6   C5   single  1.542  0.020  1.542
 5A3  PA6  O36  deloc   1.530  0.020  1.530
 5A3  PA6  O16  single  1.681  0.020  1.681
 5A3  PA6  O26  deloc   1.531  0.020  1.531
 5A3  C4   C5   single  1.540  0.020  1.540
 5A3  C4   O14  single  1.398  0.020  1.398
 5A3  C5   O15  single  1.405  0.020  1.405
 5A3  O15  PA5  single  1.659  0.020  1.659
 5A3  O14  PA4  single  1.683  0.020  1.683
 5A3  O34  PA4  deloc   1.528  0.020  1.528
 5A3  O24  PA4  deloc   1.532  0.020  1.532
 5A3  PA4  O44  deloc   1.530  0.020  1.530
 5A3  PA5  CB5  single  1.820  0.020  1.820
 5A3  PA5  O25  deloc   1.510  0.020  1.510
 5A3  PA5  O35  deloc   1.512  0.020  1.512
 5A3  CB5  PB5  single  1.858  0.020  1.858
 5A3  O55  PB5  deloc   1.537  0.020  1.537
 5A3  PB5  O75  deloc   1.538  0.020  1.538
 5A3  PB5  O65  deloc   1.543  0.020  1.543
 5A3  C2   H1   single  0.970  0.020  1.090
 5A3  C1   H2   single  0.970  0.020  1.090
 5A3  C4   H3   single  0.970  0.020  1.090
 5A3  C5   H4   single  0.970  0.020  1.090
 5A3  C6   H5   single  0.970  0.020  1.090
 5A3  C3   H6   single  0.970  0.020  1.090
 5A3  CB5  H9   single  0.970  0.020  1.090
 5A3  CB5  H10  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
 5A3  H1   C2   O12  111.08  3.000
 5A3  H1   C2   C3   108.35  3.000
 5A3  O12  C2   C3   109.48  3.000
 5A3  H1   C2   C1   108.24  3.000
 5A3  C3   C2   C1   108.83  3.000
 5A3  O12  C2   C1   110.79  3.000
 5A3  H2   C1   O11  110.32  3.000
 5A3  H2   C1   C6   106.53  3.000
 5A3  O11  C1   C6   111.31  3.000
 5A3  H2   C1   C2   106.37  3.000
 5A3  C6   C1   C2   110.48  3.000
 5A3  O11  C1   C2   111.59  3.000
 5A3  H3   C4   O14  110.91  3.000
 5A3  H3   C4   C3   108.51  3.000
 5A3  O14  C4   C3   111.14  3.000
 5A3  H3   C4   C5   108.88  3.000
 5A3  O14  C4   C5   109.27  3.000
 5A3  C3   C4   C5   108.06  3.000
 5A3  H4   C5   O15  109.33  3.000
 5A3  H4   C5   C6   106.69  3.000
 5A3  O15  C5   C6   110.08  3.000
 5A3  H4   C5   C4   106.83  3.000
 5A3  O15  C5   C4   110.59  3.000
 5A3  C6   C5   C4   113.14  3.000
 5A3  H5   C6   O16  110.42  3.000
 5A3  H5   C6   C5   108.56  3.000
 5A3  O16  C6   C5   108.80  3.000
 5A3  H5   C6   C1   108.49  3.000
 5A3  C5   C6   C1   108.88  3.000
 5A3  O16  C6   C1   111.63  3.000
 5A3  H6   C3   O13  110.53  3.000
 5A3  H6   C3   C4   106.29  3.000
 5A3  O13  C3   C4   111.50  3.000
 5A3  H6   C3   C2   106.49  3.000
 5A3  C4   C3   C2   110.23  3.000
 5A3  O13  C3   C2   111.56  3.000
 5A3  PA1  O11  C1   118.61  3.000
 5A3  CB5  PB5  O65  104.45  3.000
 5A3  O65  PB5  O55  112.35  3.000
 5A3  CB5  PB5  O55  106.83  3.000
 5A3  O65  PB5  O75  112.21  3.000
 5A3  O55  PB5  O75  113.18  3.000
 5A3  CB5  PB5  O75  107.12  3.000
 5A3  H10  CB5  H9   104.25  3.000
 5A3  H10  CB5  PA5  106.70  3.000
 5A3  H9   CB5  PA5  110.36  3.000
 5A3  H10  CB5  PB5  109.05  3.000
 5A3  H9   CB5  PB5  109.08  3.000
 5A3  PA5  CB5  PB5  116.66  3.000
 5A3  PA5  O15  C5   123.89  3.000
 5A3  PA6  O16  C6   122.86  3.000
 5A3  O26  PA6  O36  115.09  3.000
 5A3  O26  PA6  O46  112.23  3.000
 5A3  O36  PA6  O46  112.25  3.000
 5A3  O26  PA6  O16  101.44  3.000
 5A3  O36  PA6  O16  107.03  3.000
 5A3  O46  PA6  O16  107.82  3.000
 5A3  O21  PA1  O41  114.03  3.000
 5A3  O41  PA1  O11  107.48  3.000
 5A3  O21  PA1  O11  102.37  3.000
 5A3  O41  PA1  O31  111.76  3.000
 5A3  O11  PA1  O31  106.72  3.000
 5A3  O21  PA1  O31  113.57  3.000
 5A3  PA2  O12  C2   125.15  3.000
 5A3  O32  PA2  O22  111.75  3.000
 5A3  O22  PA2  O42  113.77  3.000
 5A3  O32  PA2  O42  113.82  3.000
 5A3  O22  PA2  O12  102.72  3.000
 5A3  O32  PA2  O12  105.53  3.000
 5A3  O42  PA2  O12  108.22  3.000
 5A3  PA3  O13  C3   119.23  3.000
 5A3  O23  PA3  O33  112.05  3.000
 5A3  O23  PA3  O43  113.67  3.000
 5A3  O33  PA3  O43  113.87  3.000
 5A3  O23  PA3  O13  107.26  3.000
 5A3  O43  PA3  O13  101.95  3.000
 5A3  O33  PA3  O13  107.09  3.000
 5A3  PA4  O14  C4   121.56  3.000
 5A3  O34  PA4  O44  112.01  3.000
 5A3  O44  PA4  O24  114.76  3.000
 5A3  O34  PA4  O24  113.34  3.000
 5A3  O44  PA4  O14  107.13  3.000
 5A3  O24  PA4  O14  100.55  3.000
 5A3  O34  PA4  O14  107.99  3.000
 5A3  O15  PA5  O35  109.29  3.000
 5A3  O35  PA5  O25  119.25  3.000
 5A3  O15  PA5  O25  105.71  3.000
 5A3  O35  PA5  CB5  110.16  3.000
 5A3  O25  PA5  CB5  108.66  3.000
 5A3  O15  PA5  CB5  102.38  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
 5A3  Var_01  O42  PA2  O12  C2     13.52  30.0  3
 5A3  Var_02  O21  PA1  O11  C1    176.63  30.0  3
 5A3  Var_03  O34  PA4  O14  C4     68.67  30.0  3
 5A3  Var_04  CB5  PA5  O15  C5   -109.90  30.0  3
 5A3  Var_05  O46  PA6  O16  C6    -83.00  30.0  3
 5A3  Var_06  O33  PA3  O13  C3    -54.06  30.0  3
 5A3  Var_07  PA5  CB5  PB5  O75    45.27  30.0  3
 5A3  Var_08  O15  PA5  CB5  PB5   168.54  30.0  1

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
 5A3  chir_01  C2  O12  C1  C3  negativ
 5A3  chir_02  C1  O11  C6  C2  negativ
 5A3  chir_03  C4  O14  C3  C5  positiv
 5A3  chir_04  C5  O15  C4  C6  negativ
 5A3  chir_05  C6  O16  C1  C5  negativ
 5A3  chir_06  C3  O13  C2  C4  negativ

