# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 14:11:17 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)O[C@H]1[C@H](NC(=O)C(F)(F)[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
 KDJ  KDJ  '(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid'  ligand  48  41  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KDJ
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
 KDJ  N15  N  NH1    0  -0.645  -1.7275   0.8196   0.2397
 KDJ  C3   C  CH1    0   0.057   1.9355   0.7766  -0.6103
 KDJ  C4   C  CH1    0   0.026   0.6809   1.2402   0.1306
 KDJ  C5   C  CH1    0  -0.042  -0.4781   0.3057  -0.2710
 KDJ  C6   C  CH1    0   0.089  -0.1863  -1.1468   0.1564
 KDJ  C1   C  CH1    0   0.115   1.1000  -1.5838  -0.5622
 KDJ  C2   C  CH1    0   0.046   2.2683  -0.6616  -0.1909
 KDJ  O75  O  OP    -1  -0.997  -5.6894   1.8165  -1.9999
 KDJ  PB5  P  P      0   1.124  -5.7684   1.3107  -0.5609
 KDJ  O85  O  O      0  -0.835  -6.5930   2.2172   0.3610
 KDJ  O95  O  OP    -1  -0.883  -6.0700  -0.1738  -0.4019
 KDJ  C45  C  CT     0   0.290  -4.0278   1.5564   0.1292
 KDJ  F55  F  F      0  -0.396  -3.6871   2.8923  -0.0673
 KDJ  F65  F  F      0  -0.362  -4.0446   1.4082   1.4942
 KDJ  C25  C  C      0   0.553  -2.8580   0.7575  -0.4533
 KDJ  O35  O  O      0  -0.482  -2.9963   0.2213  -1.5486
 KDJ  O14  O  O2     0  -0.673   0.3595   2.5726  -0.1663
 KDJ  PA4  P  P      0   1.219  -0.0534   3.5888   1.1117
 KDJ  O34  O  OP    -1  -0.845   1.2339   3.9198   1.8587
 KDJ  O44  O  OP    -1  -0.995  -0.6793   4.7725   0.3857
 KDJ  O24  O  O      0  -0.886  -1.0261   2.7695   1.9873
 KDJ  O13  O  O2     0  -0.587   3.0058   1.6402  -0.3820
 KDJ  PA3  P  P      0   1.200   3.8946   2.1728  -1.6992
 KDJ  O33  O  O      0  -0.885   4.3729   0.9286  -2.4502
 KDJ  O43  O  OP    -1  -1.008   2.9549   3.0376  -2.5441
 KDJ  O23  O  OP    -1  -1.003   5.0115   2.9646  -1.0157
 KDJ  O12  O  O2     0  -0.576   2.5007  -0.7033   1.1929
 KDJ  PA2  P  P      0   1.186   3.9116  -1.2311   1.9266
 KDJ  O32  O  O      0  -0.950   4.9404  -1.4968   0.8321
 KDJ  O42  O  OP    -1  -0.898   4.2822  -0.0717   2.8596
 KDJ  O22  O  OP    -1  -0.985   3.5011  -2.4803   2.7123
 KDJ  O11  O  O2     0  -0.609   1.3953  -2.9198  -0.3000
 KDJ  PA1  P  P      0   1.205   1.8327  -3.9147  -1.5719
 KDJ  O31  O  OP    -1  -1.008   2.1083  -5.2342  -0.8462
 KDJ  O41  O  O      0  -0.850   0.6365  -3.9734  -2.5262
 KDJ  O21  O  OP    -1  -0.909   3.0671  -3.2922  -2.2294
 KDJ  O16  O  O2     0  -0.556  -1.2448  -1.9909  -0.1711
 KDJ  PA6  P  P      0   1.181  -2.1924  -2.7094   1.0236
 KDJ  O36  O  OP    -1  -1.053  -2.9210  -3.7867   0.2143
 KDJ  O46  O  O      0  -0.888  -1.2210  -3.2735   2.0657
 KDJ  O26  O  OP    -1  -0.927  -3.1056  -1.6313   1.5953
 KDJ  H1   H  HNH1   0   0.377  -1.6429   1.4976   1.0218
 KDJ  H2   H  HCH1   0   0.239   1.6821   0.7513  -1.6839
 KDJ  H3   H  HCH1   0   0.170   0.8698   1.1222   1.2039
 KDJ  H4   H  HCH1   0   0.246  -0.5455   0.3120  -1.3681
 KDJ  H5   H  HCH1   0   0.138   0.0037  -1.1650   1.2368
 KDJ  H6   H  HCH1   0   0.095   0.9139  -1.4389  -1.6414
 KDJ  H7   H  HCH1   0   0.178   3.1519  -0.9846  -0.7474

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
 KDJ  O32  PA2  deloc   1.526  0.020  1.526
 KDJ  O42  PA2  deloc   1.534  0.020  1.534
 KDJ  O41  PA1  deloc   1.531  0.020  1.531
 KDJ  O31  PA1  deloc   1.531  0.020  1.531
 KDJ  PA2  O22  deloc   1.532  0.020  1.532
 KDJ  PA2  O12  single  1.676  0.020  1.676
 KDJ  PA1  O11  single  1.673  0.020  1.673
 KDJ  PA1  O21  deloc   1.531  0.020  1.531
 KDJ  O11  C1   single  1.393  0.020  1.393
 KDJ  O12  C2   single  1.404  0.020  1.404
 KDJ  O46  PA6  deloc   1.532  0.020  1.532
 KDJ  C2   C1   single  1.534  0.020  1.534
 KDJ  C2   C3   single  1.535  0.020  1.535
 KDJ  C1   C6   single  1.537  0.020  1.537
 KDJ  O33  PA3  deloc   1.530  0.020  1.530
 KDJ  O43  PA3  deloc   1.531  0.020  1.531
 KDJ  O13  PA3  single  1.676  0.020  1.676
 KDJ  O13  C3   single  1.394  0.020  1.394
 KDJ  C6   O16  single  1.393  0.020  1.393
 KDJ  C6   C5   single  1.542  0.020  1.542
 KDJ  PA6  O36  deloc   1.532  0.020  1.532
 KDJ  PA6  O16  single  1.686  0.020  1.686
 KDJ  PA6  O26  deloc   1.524  0.020  1.524
 KDJ  PA3  O23  deloc   1.530  0.020  1.530
 KDJ  C3   C4   single  1.529  0.020  1.529
 KDJ  C4   C5   single  1.542  0.020  1.542
 KDJ  C4   O14  single  1.402  0.020  1.402
 KDJ  O24  PA4  deloc   1.544  0.020  1.544
 KDJ  C5   N15  single  1.444  0.020  1.444
 KDJ  N15  C25  single  1.327  0.020  1.327
 KDJ  O14  PA4  single  1.684  0.020  1.684
 KDJ  PA4  O34  deloc   1.525  0.020  1.525
 KDJ  PA4  O44  deloc   1.523  0.020  1.523
 KDJ  O85  PB5  deloc   1.533  0.020  1.533
 KDJ  C25  O35  double  1.227  0.020  1.227
 KDJ  C25  C45  single  1.532  0.020  1.532
 KDJ  F55  C45  single  1.393  0.020  1.393
 KDJ  C45  PB5  single  1.888  0.020  1.888
 KDJ  C45  F65  single  1.373  0.020  1.373
 KDJ  PB5  O95  deloc   1.523  0.020  1.523
 KDJ  PB5  O75  deloc   1.527  0.020  1.527
 KDJ  N15  H1   single  0.890  0.020  1.040
 KDJ  C3   H2   single  0.970  0.020  1.090
 KDJ  C4   H3   single  0.970  0.020  1.090
 KDJ  C5   H4   single  0.970  0.020  1.090
 KDJ  C6   H5   single  0.970  0.020  1.090
 KDJ  C1   H6   single  0.970  0.020  1.090
 KDJ  C2   H7   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
 KDJ  H1   N15  C25  119.54  3.000
 KDJ  H1   N15  C5   115.34  3.000
 KDJ  C25  N15  C5   122.38  3.000
 KDJ  H2   C3   O13  110.48  3.000
 KDJ  H2   C3   C2   107.11  3.000
 KDJ  O13  C3   C2   111.67  3.000
 KDJ  H2   C3   C4   106.86  3.000
 KDJ  O13  C3   C4   111.27  3.000
 KDJ  C2   C3   C4   109.25  3.000
 KDJ  H3   C4   O14  110.43  3.000
 KDJ  H3   C4   C5   108.62  3.000
 KDJ  O14  C4   C5   110.39  3.000
 KDJ  H3   C4   C3   107.48  3.000
 KDJ  O14  C4   C3   111.93  3.000
 KDJ  C5   C4   C3   107.87  3.000
 KDJ  H4   C5   C6   107.07  3.000
 KDJ  H4   C5   C4   107.61  3.000
 KDJ  C6   C5   C4   110.89  3.000
 KDJ  H4   C5   N15  107.33  3.000
 KDJ  C4   C5   N15  110.03  3.000
 KDJ  C6   C5   N15  113.63  3.000
 KDJ  H5   C6   O16  110.68  3.000
 KDJ  H5   C6   C1   108.10  3.000
 KDJ  O16  C6   C1   110.72  3.000
 KDJ  H5   C6   C5   108.75  3.000
 KDJ  O16  C6   C5   111.22  3.000
 KDJ  C1   C6   C5   107.26  3.000
 KDJ  H6   C1   O11  110.21  3.000
 KDJ  H6   C1   C2   106.61  3.000
 KDJ  O11  C1   C2   111.69  3.000
 KDJ  H6   C1   C6   106.17  3.000
 KDJ  C2   C1   C6   110.69  3.000
 KDJ  O11  C1   C6   111.23  3.000
 KDJ  H7   C2   O12  111.05  3.000
 KDJ  H7   C2   C1   108.35  3.000
 KDJ  O12  C2   C1   110.29  3.000
 KDJ  H7   C2   C3   108.25  3.000
 KDJ  C1   C2   C3   109.40  3.000
 KDJ  O12  C2   C3   109.46  3.000
 KDJ  C45  PB5  O95  105.73  3.000
 KDJ  O95  PB5  O85  114.01  3.000
 KDJ  C45  PB5  O85  101.48  3.000
 KDJ  O95  PB5  O75  115.55  3.000
 KDJ  C45  PB5  O75  104.69  3.000
 KDJ  O85  PB5  O75  113.48  3.000
 KDJ  C25  C45  F65  109.34  3.000
 KDJ  F65  C45  F55  104.28  3.000
 KDJ  C25  C45  F55  105.06  3.000
 KDJ  F65  C45  PB5  109.75  3.000
 KDJ  F55  C45  PB5  107.38  3.000
 KDJ  C25  C45  PB5  119.81  3.000
 KDJ  O35  C25  C45  118.77  3.000
 KDJ  C45  C25  N15  115.31  3.000
 KDJ  O35  C25  N15  125.61  3.000
 KDJ  PA4  O14  C4   117.96  3.000
 KDJ  O24  PA4  O44  115.08  3.000
 KDJ  O44  PA4  O34  114.31  3.000
 KDJ  O24  PA4  O34  111.67  3.000
 KDJ  O44  PA4  O14  102.00  3.000
 KDJ  O34  PA4  O14  107.20  3.000
 KDJ  O24  PA4  O14  105.34  3.000
 KDJ  PA3  O13  C3   118.38  3.000
 KDJ  O23  PA3  O43  113.71  3.000
 KDJ  O23  PA3  O33  114.32  3.000
 KDJ  O43  PA3  O33  112.35  3.000
 KDJ  O23  PA3  O13  101.56  3.000
 KDJ  O43  PA3  O13  106.72  3.000
 KDJ  O33  PA3  O13  107.05  3.000
 KDJ  PA2  O12  C2   125.48  3.000
 KDJ  O22  PA2  O42  111.67  3.000
 KDJ  O22  PA2  O32  114.00  3.000
 KDJ  O42  PA2  O32  113.90  3.000
 KDJ  O22  PA2  O12  104.82  3.000
 KDJ  O42  PA2  O12  103.40  3.000
 KDJ  O32  PA2  O12  107.97  3.000
 KDJ  PA1  O11  C1   118.86  3.000
 KDJ  O21  PA1  O41  112.20  3.000
 KDJ  O21  PA1  O31  114.14  3.000
 KDJ  O41  PA1  O31  113.76  3.000
 KDJ  O21  PA1  O11  107.19  3.000
 KDJ  O31  PA1  O11  101.49  3.000
 KDJ  O41  PA1  O11  107.00  3.000
 KDJ  PA6  O16  C6   121.25  3.000
 KDJ  O26  PA6  O46  112.65  3.000
 KDJ  O26  PA6  O36  114.24  3.000
 KDJ  O46  PA6  O36  113.70  3.000
 KDJ  O26  PA6  O16  107.53  3.000
 KDJ  O36  PA6  O16  101.11  3.000
 KDJ  O46  PA6  O16  106.41  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
 KDJ  CONST_01  O35  C25  N15  C5     0.00   0.0  0
 KDJ  CONST_02  C45  C25  N15  C5   180.00   0.0  0
 KDJ  CONST_03  H1   N15  C25  C45    0.00   0.0  0
 KDJ  Var_01    O33  PA3  O13  C3   -54.92  30.0  3
 KDJ  Var_02    O24  PA4  O14  C4   -44.85  30.0  3
 KDJ  Var_03    O46  PA6  O16  C6   -46.43  30.0  3
 KDJ  Var_04    O41  PA1  O11  C1   -62.47  30.0  2
 KDJ  Var_05    O32  PA2  O12  C2     6.54  30.0  3
 KDJ  Var_06    F55  C45  C25  N15   70.55  30.0  3
 KDJ  Var_07    C25  C45  PB5  O75  -65.27  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
 KDJ  chir_01  C3  C2   O13  C4  positiv
 KDJ  chir_02  C4  O14  C5   C3  negativ
 KDJ  chir_03  C5  N15  C6   C4  positiv
 KDJ  chir_04  C6  O16  C1   C5  negativ
 KDJ  chir_05  C1  O11  C2   C6  positiv
 KDJ  chir_06  C2  O12  C3   C1  positiv

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
 KDJ  plan-1  N15  0.020
 KDJ  plan-1  C5   0.020
 KDJ  plan-1  C45  0.020
 KDJ  plan-1  C25  0.020
 KDJ  plan-1  O35  0.020
 KDJ  plan-1  H1   0.020

