# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 02:03:13 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2,3,4,5,6-pentaphosphonooxycyclohexyl) dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[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
 KGN  KGN  '(2,3,4,5,6-pentaphosphonooxycyclohexyl) dihydrogen phosphate'  ligand  42  36  .  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_KGN
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
 KGN  P1   P  P      0   1.172  -1.3395  -2.9185  -2.2933
 KGN  P2   P  P      0   1.195  -3.7488  -0.6439   1.5021
 KGN  P3   P  P      0   1.225  -2.1330   3.2962  -0.6878
 KGN  P4   P  P      0   1.252   2.0978   3.3807   0.6854
 KGN  P5   P  P      0   1.227   3.8255  -0.5809  -1.4965
 KGN  P6   P  P      0   1.230   1.4634  -2.8658   2.3496
 KGN  C1   C  CH1    0  -0.012  -0.6900  -1.4459  -0.1238
 KGN  C2   C  CH1    0   0.089  -1.3553  -0.1919   0.4470
 KGN  C3   C  CH1    0   0.051  -0.7334   1.0796  -0.1553
 KGN  C4   C  CH1    0   0.107   0.7742   1.1043   0.1773
 KGN  C5   C  CH1    0   0.087   1.4355  -0.1476  -0.4248
 KGN  C6   C  CH1    0   0.003   0.8175  -1.4214   0.1553
 KGN  O11  O  O2     0  -0.583  -0.9155  -1.4952  -1.5182
 KGN  O12  O  O2     0  -0.501  -2.7378  -0.2170   0.2462
 KGN  O13  O  O2     0  -0.678  -1.3705   2.2183   0.3396
 KGN  O14  O  O2     0  -0.629   1.3796   2.2573  -0.3242
 KGN  O15  O  O2     0  -0.597   2.8218  -0.1124  -0.2462
 KGN  O16  O  O2     0  -0.654   1.0463  -1.4539   1.5494
 KGN  O21  O  O      0  -0.865  -2.7348  -3.2969  -1.7968
 KGN  O22  O  OP    -1  -0.990  -5.1225  -0.5993   0.8241
 KGN  O23  O  O      0  -0.786  -1.1025   3.8020  -1.6981
 KGN  O24  O  OP    -1  -0.908   0.9997   4.0657   1.4986
 KGN  O25  O  OP    -1  -0.952   5.2082  -0.3220  -0.8886
 KGN  O26  O  OP    -1  -0.962   1.4517  -2.3713   3.8021
 KGN  O31  O  OP    -1  -1.029  -1.3196  -2.4547  -3.7556
 KGN  O32  O  O      0  -0.905  -3.3392  -2.0393   1.9771
 KGN  O33  O  OP    -1  -0.980  -3.2750   2.5423  -1.3759
 KGN  O34  O  O      0  -0.855   3.0801   2.6206   1.5822
 KGN  O35  O  O      0  -1.030   3.5515  -2.0556  -1.7927
 KGN  O36  O  OP    -1  -0.945   0.3929  -3.9106   2.0414
 KGN  O41  O  OP    -1  -1.003  -0.2755  -3.9615  -1.9567
 KGN  O42  O  OP    -1  -0.961  -3.5725   0.4169   2.5949
 KGN  O43  O  OP    -1  -1.000  -2.6221   4.3626   0.2986
 KGN  O44  O  OP    -1  -1.014   2.7795   4.3062  -0.3294
 KGN  O45  O  OP    -1  -0.971   3.4987   0.3250  -2.6903
 KGN  O46  O  O      0  -0.862   2.8542  -3.2620   1.8540
 KGN  H1   H  HCH1   0   0.235  -1.1223  -2.3099   0.3878
 KGN  H2   H  HCH1   0   0.168  -1.1269  -0.1771   1.5214
 KGN  H3   H  HCH1   0   0.150  -0.8320   1.0250  -1.2495
 KGN  H4   H  HCH1   0   0.133   0.8829   1.0547   1.2711
 KGN  H5   H  HCH1   0   0.135   1.1962  -0.1455  -1.4967
 KGN  H6   H  HCH1   0   0.215   1.2788  -2.2748  -0.3492

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
 KGN  O34  P4   deloc   1.532  0.020  1.532
 KGN  O23  P3   deloc   1.529  0.020  1.529
 KGN  O44  P4   deloc   1.533  0.020  1.533
 KGN  P4   O24  deloc   1.528  0.020  1.528
 KGN  P4   O14  single  1.673  0.020  1.673
 KGN  P3   O43  deloc   1.533  0.020  1.533
 KGN  P3   O33  deloc   1.532  0.020  1.532
 KGN  P3   O13  single  1.673  0.020  1.673
 KGN  O14  C4   single  1.396  0.020  1.396
 KGN  O13  C3   single  1.396  0.020  1.396
 KGN  C4   C3   single  1.544  0.020  1.544
 KGN  C4   C5   single  1.539  0.020  1.539
 KGN  O35  P5   deloc   1.529  0.020  1.529
 KGN  O15  C5   single  1.398  0.020  1.398
 KGN  O15  P5   single  1.670  0.020  1.670
 KGN  C3   C2   single  1.538  0.020  1.538
 KGN  O46  P6   deloc   1.529  0.020  1.529
 KGN  C5   C6   single  1.530  0.020  1.530
 KGN  P5   O25  deloc   1.533  0.020  1.533
 KGN  P5   O45  deloc   1.534  0.020  1.534
 KGN  O16  C6   single  1.413  0.020  1.413
 KGN  O16  P6   single  1.676  0.020  1.676
 KGN  C6   C1   single  1.533  0.020  1.533
 KGN  P6   O26  deloc   1.534  0.020  1.534
 KGN  P6   O36  deloc   1.527  0.020  1.527
 KGN  C2   C1   single  1.530  0.020  1.530
 KGN  C2   O12  single  1.397  0.020  1.397
 KGN  O32  P2   deloc   1.530  0.020  1.530
 KGN  O22  P2   deloc   1.533  0.020  1.533
 KGN  C1   O11  single  1.413  0.020  1.413
 KGN  O12  P2   single  1.668  0.020  1.668
 KGN  P2   O42  deloc   1.533  0.020  1.533
 KGN  O11  P1   single  1.675  0.020  1.675
 KGN  O21  P1   deloc   1.529  0.020  1.529
 KGN  O41  P1   deloc   1.527  0.020  1.527
 KGN  P1   O31  deloc   1.534  0.020  1.534
 KGN  C1   H1   single  0.970  0.020  1.090
 KGN  C2   H2   single  0.970  0.020  1.090
 KGN  C3   H3   single  0.970  0.020  1.090
 KGN  C4   H4   single  0.970  0.020  1.090
 KGN  C5   H5   single  0.970  0.020  1.090
 KGN  C6   H6   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
 KGN  O41  P1   O31  114.05  3.000
 KGN  O31  P1   O21  113.34  3.000
 KGN  O41  P1   O21  113.28  3.000
 KGN  O31  P1   O11  100.42  3.000
 KGN  O41  P1   O11  107.57  3.000
 KGN  O21  P1   O11  106.92  3.000
 KGN  O42  P2   O32  112.27  3.000
 KGN  O42  P2   O22  113.47  3.000
 KGN  O32  P2   O22  113.82  3.000
 KGN  O42  P2   O12  106.86  3.000
 KGN  O22  P2   O12  101.70  3.000
 KGN  O32  P2   O12  107.75  3.000
 KGN  O43  P3   O33  113.18  3.000
 KGN  O33  P3   O23  111.62  3.000
 KGN  O43  P3   O23  114.21  3.000
 KGN  O33  P3   O13  107.37  3.000
 KGN  O43  P3   O13  101.45  3.000
 KGN  O23  P3   O13  108.16  3.000
 KGN  O44  P4   O34  113.69  3.000
 KGN  O44  P4   O24  113.64  3.000
 KGN  O34  P4   O24  111.82  3.000
 KGN  O24  P4   O14  108.28  3.000
 KGN  O44  P4   O14  101.35  3.000
 KGN  O34  P4   O14  107.18  3.000
 KGN  O45  P5   O35  112.38  3.000
 KGN  O45  P5   O25  113.65  3.000
 KGN  O35  P5   O25  113.67  3.000
 KGN  O45  P5   O15  106.79  3.000
 KGN  O25  P5   O15  101.41  3.000
 KGN  O35  P5   O15  107.94  3.000
 KGN  O46  P6   O36  113.27  3.000
 KGN  O36  P6   O26  113.97  3.000
 KGN  O46  P6   O26  113.41  3.000
 KGN  O36  P6   O16  107.79  3.000
 KGN  O26  P6   O16  100.29  3.000
 KGN  O46  P6   O16  106.86  3.000
 KGN  H1   C1   O11  111.78  3.000
 KGN  H1   C1   C6   108.43  3.000
 KGN  O11  C1   C6   109.69  3.000
 KGN  H1   C1   C2   107.53  3.000
 KGN  O11  C1   C2   109.10  3.000
 KGN  C6   C1   C2   110.28  3.000
 KGN  H2   C2   O12  110.28  3.000
 KGN  H2   C2   C3   106.72  3.000
 KGN  O12  C2   C3   111.02  3.000
 KGN  H2   C2   C1   106.59  3.000
 KGN  O12  C2   C1   111.22  3.000
 KGN  C3   C2   C1   110.83  3.000
 KGN  H3   C3   O13  110.63  3.000
 KGN  H3   C3   C4   107.61  3.000
 KGN  O13  C3   C4   110.87  3.000
 KGN  H3   C3   C2   108.19  3.000
 KGN  C4   C3   C2   108.88  3.000
 KGN  O13  C3   C2   110.55  3.000
 KGN  H4   C4   O14  110.59  3.000
 KGN  H4   C4   C5   108.06  3.000
 KGN  O14  C4   C5   110.19  3.000
 KGN  H4   C4   C3   108.06  3.000
 KGN  C5   C4   C3   108.80  3.000
 KGN  O14  C4   C3   111.06  3.000
 KGN  H5   C5   O15  109.92  3.000
 KGN  H5   C5   C6   106.48  3.000
 KGN  O15  C5   C6   111.90  3.000
 KGN  H5   C5   C4   106.66  3.000
 KGN  C6   C5   C4   110.82  3.000
 KGN  O15  C5   C4   110.83  3.000
 KGN  H6   C6   O16  111.65  3.000
 KGN  H6   C6   C5   107.73  3.000
 KGN  O16  C6   C5   109.14  3.000
 KGN  H6   C6   C1   108.56  3.000
 KGN  O16  C6   C1   109.77  3.000
 KGN  C5   C6   C1   109.96  3.000
 KGN  C1   O11  P1   121.77  3.000
 KGN  C2   O12  P2   119.75  3.000
 KGN  C3   O13  P3   121.07  3.000
 KGN  C4   O14  P4   121.62  3.000
 KGN  C5   O15  P5   119.54  3.000
 KGN  C6   O16  P6   122.06  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
 KGN  Var_01  O21  P1  O11  C1   66.87  30.0  3
 KGN  Var_02  O32  P2  O12  C2  -57.49  30.0  3
 KGN  Var_03  O23  P3  O13  C3  -57.87  30.0  2
 KGN  Var_04  O34  P4  O14  C4   52.34  30.0  3
 KGN  Var_05  O35  P5  O15  C5  -62.79  30.0  3
 KGN  Var_06  O46  P6  O16  C6   66.72  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
 KGN  chir_01  C1  C6   C2  O11  negativ
 KGN  chir_02  C2  O12  C3  C1   positiv
 KGN  chir_03  C3  O13  C4  C2   negativ
 KGN  chir_04  C4  O14  C5  C3   positiv
 KGN  chir_05  C5  O15  C6  C4   negativ
 KGN  chir_06  C6  O16  C1  C5   negativ

