# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:11:30 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: (1R,2R,3R,4R,5S,6S)-6-hydroxycyclohexane-1,2,3,4,5-pentayl pentakis[dihydrogen (phosphate)]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 5IP  5IP  '(1R,2R,3R,4R,5S,6S)-6-hydroxycyclohexane-1,2,3,4,5-pentayl pentakis[dihydrogen (phosphate)]'  ligand  39  32  .  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_5IP
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
 5IP  O46   O  OP    -1  -0.926  -4.4645  -0.6249  -0.6610
 5IP  P6    P  P      0   1.213  -3.0674  -1.0362  -0.1881
 5IP  O26   O  OP    -1  -0.903  -2.4494  -0.0583   0.8105
 5IP  O36   O  O      0  -0.918  -2.9636  -2.4994   0.2456
 5IP  O16   O  O2     0  -0.666  -2.2078  -0.9110  -1.6281
 5IP  C6    C  CH1    0   0.015  -0.8789  -1.3824  -1.7472
 5IP  C1    C  CH1    0   0.051  -0.7257  -1.8988  -3.1893
 5IP  O11   O  O2     0  -0.644   0.4427  -2.6471  -3.3782
 5IP  P1    P  P      0   1.206   0.4036  -4.3130  -3.1941
 5IP  O41   O  O      0  -0.909   0.0789  -4.6094  -1.7291
 5IP  O31   O  OP    -1  -0.925   1.8298  -4.6878  -3.6036
 5IP  O21   O  OP    -1  -0.923  -0.6704  -4.8286  -4.1557
 5IP  C5    C  CH1    0   0.049   0.1179  -0.2701  -1.3886
 5IP  O15   O  O2     0  -0.647   1.3885  -0.8334  -1.1720
 5IP  P5    P  P      0   1.211   2.2980  -0.2889   0.1261
 5IP  O45   O  O      0  -0.918   2.4122   1.2332  -0.0028
 5IP  O35   O  OP    -1  -0.922   3.6160  -1.0345  -0.0899
 5IP  O25   O  OP    -1  -0.921   1.5447  -0.7192   1.3871
 5IP  C4    C  CH1    0  -0.012   0.2265   0.8403  -2.4425
 5IP  O14   O  OH1    0  -0.695  -0.8706   1.7373  -2.2536
 5IP  C3    C  CH1    0   0.034   0.2636   0.3546  -3.9024
 5IP  O13   O  O2     0  -0.652   1.5524  -0.0690  -4.2480
 5IP  P3    P  P      0   1.208   2.5582   1.0110  -5.0507
 5IP  O43   O  O      0  -0.913   2.0416   1.0906  -6.4878
 5IP  O33   O  OP    -1  -0.921   3.9146   0.3140  -4.9264
 5IP  O23   O  OP    -1  -0.918   2.4650   2.3470  -4.3075
 5IP  C2    C  CH1    0   0.092  -0.7939  -0.7173  -4.1492
 5IP  O12   O  O2     0  -0.668  -0.7794  -1.1431  -5.4853
 5IP  P2    P  P      0   1.216  -2.0363  -0.6464  -6.4777
 5IP  O22   O  OP    -1  -0.923  -1.5897  -1.1986  -7.8332
 5IP  O32   O  O      0  -0.924  -3.2998  -1.3129  -5.9250
 5IP  O42   O  OP    -1  -0.914  -2.0934   0.8804  -6.4025
 5IP  H6    H  HCH1   0   0.193  -0.7099  -2.2251  -1.0701
 5IP  H1    H  HCH1   0   0.145  -1.6085  -2.5195  -3.4055
 5IP  H5    H  HCH1   0   0.185  -0.2704   0.1787  -0.4660
 5IP  H4    H  HCH1   0   0.216   1.1680   1.3638  -2.2540
 5IP  HO14  H  HOH1   0   0.420  -0.7821   2.4090  -2.9363
 5IP  H3    H  HCH1   0   0.156  -0.0378   1.1995  -4.5428
 5IP  H2    H  HCH1   0   0.151  -1.7472  -0.2321  -3.9102

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
 5IP  O46  P6    deloc   1.531  0.020  1.531
 5IP  P6   O36   deloc   1.530  0.020  1.530
 5IP  P6   O16   single  1.682  0.020  1.682
 5IP  P6   O26   deloc   1.528  0.020  1.528
 5IP  O16  C6    single  1.415  0.020  1.415
 5IP  C6   C1    single  1.539  0.020  1.539
 5IP  C6   C5    single  1.536  0.020  1.536
 5IP  C6   H6    single  0.970  0.020  1.090
 5IP  C1   C2    single  1.524  0.020  1.524
 5IP  C1   O11   single  1.400  0.020  1.400
 5IP  C1   H1    single  0.970  0.020  1.090
 5IP  O11  P1    single  1.677  0.020  1.677
 5IP  P1   O41   deloc   1.529  0.020  1.529
 5IP  P1   O31   deloc   1.530  0.020  1.530
 5IP  P1   O21   deloc   1.531  0.020  1.531
 5IP  C5   C4    single  1.535  0.020  1.535
 5IP  C5   O15   single  1.407  0.020  1.407
 5IP  C5   H5    single  0.970  0.020  1.090
 5IP  O15  P5    single  1.676  0.020  1.676
 5IP  P5   O45   deloc   1.532  0.020  1.532
 5IP  P5   O35   deloc   1.530  0.020  1.530
 5IP  P5   O25   deloc   1.531  0.020  1.531
 5IP  C4   C3    single  1.539  0.020  1.539
 5IP  C4   O14   single  1.430  0.020  1.430
 5IP  C4   H4    single  0.970  0.020  1.090
 5IP  O14  HO14  single  0.850  0.020  0.980
 5IP  C3   O13   single  1.400  0.020  1.400
 5IP  C3   C2    single  1.526  0.020  1.526
 5IP  C3   H3    single  0.970  0.020  1.090
 5IP  O13  P3    single  1.680  0.020  1.680
 5IP  P3   O43   deloc   1.529  0.020  1.529
 5IP  P3   O23   deloc   1.532  0.020  1.532
 5IP  P3   O33   deloc   1.530  0.020  1.530
 5IP  C2   O12   single  1.402  0.020  1.402
 5IP  C2   H2    single  0.970  0.020  1.090
 5IP  O12  P2    single  1.677  0.020  1.677
 5IP  P2   O32   deloc   1.532  0.020  1.532
 5IP  P2   O42   deloc   1.530  0.020  1.530
 5IP  P2   O22   deloc   1.530  0.020  1.530

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
 5IP  O16   P6   O36  106.22  3.000
 5IP  O16   P6   O26  107.77  3.000
 5IP  O36   P6   O26  113.54  3.000
 5IP  O26   P6   O46  113.50  3.000
 5IP  O16   P6   O46  100.49  3.000
 5IP  O36   P6   O46  113.98  3.000
 5IP  C6    O16  P6   121.82  3.000
 5IP  H6    C6   C5   108.24  3.000
 5IP  H6    C6   C1   107.82  3.000
 5IP  C5    C6   C1   113.40  3.000
 5IP  H6    C6   O16  110.46  3.000
 5IP  C5    C6   O16  110.39  3.000
 5IP  C1    C6   O16  106.50  3.000
 5IP  H1    C1   C2   106.12  3.000
 5IP  H1    C1   O11  109.97  3.000
 5IP  C2    C1   O11  111.51  3.000
 5IP  H1    C1   C6   107.06  3.000
 5IP  O11   C1   C6   112.87  3.000
 5IP  C2    C1   C6   109.00  3.000
 5IP  P1    O11  C1   119.78  3.000
 5IP  O21   P1   O31  113.78  3.000
 5IP  O21   P1   O41  112.79  3.000
 5IP  O31   P1   O41  114.00  3.000
 5IP  O21   P1   O11  106.38  3.000
 5IP  O31   P1   O11  101.08  3.000
 5IP  O41   P1   O11  107.62  3.000
 5IP  H5    C5   C4   107.85  3.000
 5IP  H5    C5   O15  110.74  3.000
 5IP  C4    C5   O15  109.36  3.000
 5IP  H5    C5   C6   105.25  3.000
 5IP  O15   C5   C6   109.40  3.000
 5IP  C4    C5   C6   114.18  3.000
 5IP  P5    O15  C5   118.65  3.000
 5IP  O25   P5   O35  113.79  3.000
 5IP  O25   P5   O45  112.66  3.000
 5IP  O35   P5   O45  114.09  3.000
 5IP  O25   P5   O15  106.24  3.000
 5IP  O35   P5   O15  101.53  3.000
 5IP  O45   P5   O15  107.34  3.000
 5IP  H4    C4   C3   107.08  3.000
 5IP  H4    C4   O14  109.73  3.000
 5IP  C3    C4   O14  109.99  3.000
 5IP  H4    C4   C5   106.80  3.000
 5IP  O14   C4   C5   107.99  3.000
 5IP  C3    C4   C5   115.13  3.000
 5IP  HO14  O14  C4   105.89  3.000
 5IP  H3    C3   C2   104.78  3.000
 5IP  H3    C3   O13  109.89  3.000
 5IP  C2    C3   O13  112.68  3.000
 5IP  H3    C3   C4   107.62  3.000
 5IP  C2    C3   C4   111.01  3.000
 5IP  O13   C3   C4   110.60  3.000
 5IP  P3    O13  C3   118.33  3.000
 5IP  O23   P3   O33  114.32  3.000
 5IP  O33   P3   O43  113.55  3.000
 5IP  O23   P3   O43  112.96  3.000
 5IP  O33   P3   O13  101.48  3.000
 5IP  O23   P3   O13  107.00  3.000
 5IP  O43   P3   O13  106.28  3.000
 5IP  H2    C2   O12  110.56  3.000
 5IP  H2    C2   C3   104.86  3.000
 5IP  O12   C2   C3   111.11  3.000
 5IP  H2    C2   C1   104.17  3.000
 5IP  O12   C2   C1   111.36  3.000
 5IP  C3    C2   C1   114.32  3.000
 5IP  P2    O12  C2   117.78  3.000
 5IP  O42   P2   O32  112.69  3.000
 5IP  O42   P2   O22  114.50  3.000
 5IP  O32   P2   O22  113.79  3.000
 5IP  O22   P2   O12  101.45  3.000
 5IP  O42   P2   O12  107.13  3.000
 5IP  O32   P2   O12  106.01  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
 5IP  Var_01  O41  P1  O11  C1  -64.73  30.0  3
 5IP  Var_02  O45  P5  O15  C5  -54.50  30.0  3
 5IP  Var_03  O43  P3  O13  C3  -74.36  30.0  3
 5IP  Var_04  O32  P2  O12  C2  -65.78  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
 5IP  chir_01  C6  O16  C1  C5  negativ
 5IP  chir_02  C1  O11  C2  C6  positiv
 5IP  chir_03  C5  O15  C4  C6  negativ
 5IP  chir_04  C4  O14  C5  C3  negativ
 5IP  chir_05  C3  O13  C2  C4  negativ
 5IP  chir_06  C2  O12  C1  C3  negativ

