# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:25:05 2021
#   Inital geometry file: a 169 line input string
#   Ligand name: [2,4-diphosphonooxy-5-[2-(2,4,5-triphosphonooxyphenoxy)ethoxy]phenyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1cc(O[P](O)(O)=O)c(O[P](O)(O)=O)cc1OCCOc2cc(O[P](O)(O)=O)c(O[P](O)(O)=O)cc2O[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
 D7I  D7I  '[2,4-diphosphonooxy-5-[2-(2,4,5-triphosphonooxyphenoxy)ethoxy]phenyl] dihydrogen phosphate'  ligand  66  46  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D7I
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
 D7I  C1    C  CR6   0   0.298   -9.1809  28.0476  -20.0957
 D7I  C1'   C  CR6   0   0.272   -8.4530  24.7181  -17.3130
 D7I  C2    C  CR6   0   0.319   -8.9298  28.7057  -21.3013
 D7I  C2'   C  CR6   0   0.356   -8.2451  23.3738  -17.0140
 D7I  C3    C  CR16  0  -0.409   -9.9481  29.3699  -21.9657
 D7I  C3'   C  CR16  0  -0.411   -7.3550  23.0044  -16.0211
 D7I  C4    C  CR6   0   0.318  -11.2247  29.3760  -21.4289
 D7I  C4'   C  CR6   0   0.308   -6.6557  23.9813  -15.3332
 D7I  C5    C  CR6   0   0.314  -11.4842  28.7258  -20.2302
 D7I  C5'   C  CR6   0   0.343   -6.8649  25.3252  -15.6185
 D7I  C6    C  CR16  0  -0.409  -10.4626  28.0695  -19.5663
 D7I  C6'   C  CR16  0  -0.407   -7.7699  25.6899  -16.5997
 D7I  C7    C  CH2   0  -0.241   -7.7965  26.1447  -19.8321
 D7I  C7'   C  CH2   0  -0.232   -8.8672  25.0997  -19.6078
 D7I  O1    O  O2    0  -0.487   -8.1751  27.4515  -19.4111
 D7I  O1'   O  O2    0  -0.501   -9.3575  25.0642  -18.2647
 D7I  O2    O  O2    0  -0.605   -7.6351  28.7159  -21.7456
 D7I  O2'   O  O2    0  -0.612   -8.8766  22.3900  -17.7180
 D7I  O21   O  OH1   0  -0.716   -5.6407  28.2430  -23.0931
 D7I  O22   O  OH1   0  -0.733   -7.7572  26.9527  -23.4483
 D7I  O23   O  O     0  -0.683   -7.6416  29.4341  -24.2668
 D7I  O4    O  O2    0  -0.615  -12.2371  30.0700  -22.0375
 D7I  O4'   O  O2    0  -0.607   -5.7911  23.6425  -14.3245
 D7I  O41   O  OH1   0  -0.718  -14.0355  30.6171  -23.6292
 D7I  O42   O  OH1   0  -0.721  -13.8251  28.3057  -22.7462
 D7I  O43   O  O     0  -0.683  -12.0418  29.1369  -24.4649
 D7I  O5    O  O2    0  -0.599  -12.7597  28.7100  -19.7359
 D7I  O5'   O  O2    0  -0.612   -6.1797  26.2556  -14.8912
 D7I  O51   O  O     0  -0.680  -14.7369  29.6212  -18.4824
 D7I  O52   O  OH1   0  -0.729  -12.3244  29.7819  -17.4456
 D7I  O53   O  OH1   0  -0.730  -12.8024  31.2321  -19.2696
 D7I  P2    P  P     0   1.456   -7.2048  28.4327  -23.2782
 D7I  P2'   P  P     0   1.448  -10.4745  22.2549  -17.9452
 D7I  P4    P  P     0   1.442  -12.9584  29.4827  -23.3651
 D7I  P4'   P  P     0   1.458   -4.3021  23.1127  -14.6673
 D7I  P5    P  P     0   1.454  -13.2982  29.8346  -18.6994
 D7I  P5'   P  P     0   1.446   -5.1339  27.2763  -15.5943
 D7I  O21'  O  OH1   0  -0.717  -10.6452  20.7854  -17.3642
 D7I  O22'  O  O     0  -0.682  -10.9109  22.4748  -19.3345
 D7I  O23'  O  OH1   0  -0.734  -11.1398  23.1619  -16.8188
 D7I  O41'  O  OH1   0  -0.716   -3.7434  22.8551  -13.2070
 D7I  O42'  O  OH1   0  -0.742   -3.5712  24.4696  -15.0793
 D7I  O43'  O  O     0  -0.681   -4.2386  22.0121  -15.6426
 D7I  O51'  O  OH1   0  -0.725   -4.0231  27.4323  -14.4694
 D7I  O52'  O  O     0  -0.688   -4.7085  26.8806  -16.9464
 D7I  O53'  O  OH1   0  -0.725   -5.9393  28.6386  -15.4507
 D7I  H3    H  HCR6  0   0.310   -9.7519  29.9101  -22.8817
 D7I  H3'   H  HCR6  0   0.305   -7.2075  21.9587  -15.7859
 D7I  H6    H  HCR6  0   0.293  -10.6634  27.5626  -18.6315
 D7I  H6'   H  HCR6  0   0.300   -7.9508  26.7345  -16.8196
 D7I  H71   H  HCH2  0   0.257   -7.5313  26.1192  -20.8932
 D7I  H72   H  HCH2  0   0.257   -6.8913  25.9127  -19.2697
 D7I  H7'2  H  HCH2  0   0.257   -9.7439  25.2865  -20.2270
 D7I  H7'1  H  HCH2  0   0.258   -8.4566  24.1299  -19.9061
 D7I  H1    H  HOH1  0   0.508   -5.1113  29.0002  -23.3782
 D7I  H2    H  HOH1  0   0.508   -7.8701  26.6637  -24.3644
 D7I  H4    H  HOH1  0   0.508  -13.7230  31.3480  -24.1805
 D7I  H5    H  HOH1  0   0.507  -14.0531  27.6097  -23.3777
 D7I  H7    H  HOH1  0   0.508  -12.5487  29.1068  -16.7909
 D7I  H8    H  HOH1  0   0.505  -13.3051  31.5678  -20.0240
 D7I  H9    H  HOH1  0   0.505  -11.4050  20.3095  -17.7264
 D7I  H10   H  HOH1  0   0.504  -11.4142  24.0387  -17.1209
 D7I  H11   H  HOH1  0   0.510   -3.8707  21.9538  -12.8800
 D7I  H12   H  HOH1  0   0.512   -2.8612  24.3545  -15.7269
 D7I  H13   H  HOH1  0   0.499   -3.4475  26.6582  -14.3785
 D7I  H14   H  HOH1  0   0.507   -5.6269  29.3515  -16.0245

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
 D7I  O23   P2    double    1.473  0.020  1.473
 D7I  O43   P4    double    1.473  0.020  1.473
 D7I  O41   P4    single    1.586  0.020  1.586
 D7I  P4    O4    single    1.621  0.020  1.621
 D7I  P4    O42   single    1.587  0.020  1.587
 D7I  P2    O21   single    1.586  0.020  1.586
 D7I  P2    O22   single    1.589  0.020  1.589
 D7I  P2    O2    single    1.617  0.020  1.617
 D7I  O4    C4    single    1.370  0.020  1.370
 D7I  C3    C4    aromatic  1.385  0.020  1.385
 D7I  C3    C2    aromatic  1.386  0.020  1.386
 D7I  O2    C2    single    1.369  0.020  1.369
 D7I  C4    C5    aromatic  1.388  0.020  1.388
 D7I  C2    C1    aromatic  1.396  0.020  1.396
 D7I  C5    O5    single    1.368  0.020  1.368
 D7I  C5    C6    aromatic  1.384  0.020  1.384
 D7I  C1    C6    aromatic  1.387  0.020  1.387
 D7I  C1    O1    single    1.355  0.020  1.355
 D7I  O5    P5    single    1.621  0.020  1.621
 D7I  O22'  P2'   double    1.473  0.020  1.473
 D7I  O51   P5    double    1.471  0.020  1.471
 D7I  C7    O1    single    1.424  0.020  1.424
 D7I  C7    C7'   single    1.513  0.020  1.513
 D7I  O53   P5    single    1.589  0.020  1.589
 D7I  P5    O52   single    1.588  0.020  1.588
 D7I  C7'   O1'   single    1.430  0.020  1.430
 D7I  O21'  P2'   single    1.589  0.020  1.589
 D7I  P2'   O2'   single    1.620  0.020  1.620
 D7I  P2'   O23'  single    1.592  0.020  1.592
 D7I  O2'   C2'   single    1.365  0.020  1.365
 D7I  O1'   C1'   single    1.358  0.020  1.358
 D7I  C2'   C1'   aromatic  1.393  0.020  1.393
 D7I  C2'   C3'   aromatic  1.384  0.020  1.384
 D7I  C1'   C6'   aromatic  1.386  0.020  1.386
 D7I  C3'   C4'   aromatic  1.384  0.020  1.384
 D7I  O43'  P4'   double    1.472  0.020  1.472
 D7I  O42'  P4'   single    1.595  0.020  1.595
 D7I  C6'   C5'   aromatic  1.384  0.020  1.384
 D7I  C4'   C5'   aromatic  1.390  0.020  1.390
 D7I  C4'   O4'   single    1.371  0.020  1.371
 D7I  P4'   O4'   single    1.617  0.020  1.617
 D7I  P4'   O41'  single    1.585  0.020  1.585
 D7I  O52'  P5'   double    1.472  0.020  1.472
 D7I  C5'   O5'   single    1.365  0.020  1.365
 D7I  O5'   P5'   single    1.622  0.020  1.622
 D7I  P5'   O53'  single    1.589  0.020  1.589
 D7I  P5'   O51'  single    1.589  0.020  1.589
 D7I  C3    H3    single    0.930  0.020  1.080
 D7I  C3'   H3'   single    0.930  0.020  1.080
 D7I  C6    H6    single    0.930  0.020  1.080
 D7I  C6'   H6'   single    0.930  0.020  1.080
 D7I  C7    H71   single    0.970  0.020  1.090
 D7I  C7    H72   single    0.970  0.020  1.090
 D7I  C7'   H7'2  single    0.970  0.020  1.090
 D7I  C7'   H7'1  single    0.970  0.020  1.090
 D7I  O21   H1    single    0.850  0.020  0.980
 D7I  O22   H2    single    0.850  0.020  0.980
 D7I  O41   H4    single    0.850  0.020  0.980
 D7I  O42   H5    single    0.850  0.020  0.980
 D7I  O52   H7    single    0.850  0.020  0.980
 D7I  O53   H8    single    0.850  0.020  0.980
 D7I  O21'  H9    single    0.850  0.020  0.980
 D7I  O23'  H10   single    0.850  0.020  0.980
 D7I  O41'  H11   single    0.850  0.020  0.980
 D7I  O42'  H12   single    0.850  0.020  0.980
 D7I  O51'  H13   single    0.850  0.020  0.980
 D7I  O53'  H14   single    0.850  0.020  0.980

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
 D7I  O1    C1    C6    120.01  3.000
 D7I  O1    C1    C2    120.68  3.000
 D7I  C6    C1    C2    119.23  3.000
 D7I  O1'   C1'   C6'   120.70  3.000
 D7I  C6'   C1'   C2'   119.53  3.000
 D7I  O1'   C1'   C2'   119.73  3.000
 D7I  O2    C2    C3    122.40  3.000
 D7I  O2    C2    C1    116.99  3.000
 D7I  C3    C2    C1    120.52  3.000
 D7I  O2'   C2'   C3'   118.39  3.000
 D7I  C3'   C2'   C1'   120.51  3.000
 D7I  O2'   C2'   C1'   121.06  3.000
 D7I  H3    C3    C4    119.57  3.000
 D7I  H3    C3    C2    120.82  3.000
 D7I  C4    C3    C2    119.58  3.000
 D7I  H3'   C3'   C4'   120.34  3.000
 D7I  H3'   C3'   C2'   120.11  3.000
 D7I  C4'   C3'   C2'   119.55  3.000
 D7I  O4    C4    C5    118.86  3.000
 D7I  C5    C4    C3    120.33  3.000
 D7I  O4    C4    C3    120.74  3.000
 D7I  O4'   C4'   C5'   119.01  3.000
 D7I  O4'   C4'   C3'   120.65  3.000
 D7I  C5'   C4'   C3'   120.29  3.000
 D7I  O5    C5    C6    120.63  3.000
 D7I  C6    C5    C4    119.89  3.000
 D7I  O5    C5    C4    119.45  3.000
 D7I  O5'   C5'   C6'   121.75  3.000
 D7I  O5'   C5'   C4'   118.30  3.000
 D7I  C6'   C5'   C4'   119.93  3.000
 D7I  H6    C6    C5    119.97  3.000
 D7I  H6    C6    C1    119.59  3.000
 D7I  C5    C6    C1    120.44  3.000
 D7I  H6'   C6'   C5'   120.51  3.000
 D7I  H6'   C6'   C1'   119.32  3.000
 D7I  C5'   C6'   C1'   120.17  3.000
 D7I  H72   C7    H71   107.10  3.000
 D7I  H72   C7    O1    105.27  3.000
 D7I  H71   C7    O1    111.87  3.000
 D7I  H72   C7    C7'   111.34  3.000
 D7I  H71   C7    C7'   107.42  3.000
 D7I  O1    C7    C7'   113.69  3.000
 D7I  H7'1  C7'   H7'2  107.39  3.000
 D7I  H7'1  C7'   O1'   111.26  3.000
 D7I  H7'2  C7'   O1'   105.20  3.000
 D7I  H7'1  C7'   C7    107.82  3.000
 D7I  H7'2  C7'   C7    111.52  3.000
 D7I  O1'   C7'   C7    113.52  3.000
 D7I  C7    O1    C1    116.85  3.000
 D7I  C7'   O1'   C1'   115.86  3.000
 D7I  P2    O2    C2    123.92  3.000
 D7I  P2'   O2'   C2'   126.09  3.000
 D7I  H1    O21   P2    114.31  3.000
 D7I  H2    O22   P2    114.85  3.000
 D7I  P4    O4    C4    120.61  3.000
 D7I  P4'   O4'   C4'   120.37  3.000
 D7I  H4    O41   P4    114.57  3.000
 D7I  H5    O42   P4    114.07  3.000
 D7I  P5    O5    C5    122.18  3.000
 D7I  P5'   O5'   C5'   121.44  3.000
 D7I  H7    O52   P5    114.55  3.000
 D7I  H8    O53   P5    115.05  3.000
 D7I  O23   P2    O22   117.27  3.000
 D7I  O22   P2    O21   104.12  3.000
 D7I  O23   P2    O21   116.86  3.000
 D7I  O22   P2    O2     99.91  3.000
 D7I  O21   P2    O2     99.95  3.000
 D7I  O23   P2    O2    115.98  3.000
 D7I  O23'  P2'   O22'  117.30  3.000
 D7I  O23'  P2'   O21'  102.90  3.000
 D7I  O22'  P2'   O21'  116.81  3.000
 D7I  O23'  P2'   O2'   105.40  3.000
 D7I  O21'  P2'   O2'    97.58  3.000
 D7I  O22'  P2'   O2'   114.34  3.000
 D7I  O43   P4    O42   117.19  3.000
 D7I  O42   P4    O41   102.97  3.000
 D7I  O43   P4    O41   117.78  3.000
 D7I  O42   P4    O4    101.09  3.000
 D7I  O41   P4    O4    100.33  3.000
 D7I  O43   P4    O4    114.81  3.000
 D7I  O43'  P4'   O42'  116.43  3.000
 D7I  O42'  P4'   O41'  102.40  3.000
 D7I  O43'  P4'   O41'  118.28  3.000
 D7I  O41'  P4'   O4'   100.52  3.000
 D7I  O42'  P4'   O4'   101.42  3.000
 D7I  O43'  P4'   O4'   115.16  3.000
 D7I  O53   P5    O52    96.96  3.000
 D7I  O52   P5    O51   118.59  3.000
 D7I  O53   P5    O51   119.07  3.000
 D7I  O52   P5    O5    106.14  3.000
 D7I  O53   P5    O5    106.08  3.000
 D7I  O51   P5    O5    108.58  3.000
 D7I  O53'  P5'   O52'  117.39  3.000
 D7I  O53'  P5'   O51'  101.90  3.000
 D7I  O52'  P5'   O51'  118.35  3.000
 D7I  O51'  P5'   O5'   101.87  3.000
 D7I  O53'  P5'   O5'    99.99  3.000
 D7I  O52'  P5'   O5'   114.55  3.000
 D7I  H9    O21'  P2'   113.74  3.000
 D7I  H10   O23'  P2'   114.46  3.000
 D7I  H11   O41'  P4'   114.62  3.000
 D7I  H12   O42'  P4'   114.06  3.000
 D7I  H13   O51'  P5'   113.79  3.000
 D7I  H14   O53'  P5'   114.50  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
 D7I  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 D7I  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 D7I  CONST_03  C4'   C3'  C2'  C1'    0.00   0.0  0
 D7I  CONST_04  C4'   C5'  C6'  C1'    0.00   0.0  0
 D7I  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 D7I  CONST_06  C5    C6   C1   C2     0.00   0.0  0
 D7I  CONST_07  C5'   C6'  C1'  C2'    0.00   0.0  0
 D7I  CONST_08  C5'   C4'  C3'  C2'    0.00   0.0  0
 D7I  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 D7I  CONST_10  C6    C1   C2   C3     0.00   0.0  0
 D7I  CONST_11  C6'   C1'  C2'  C3'    0.00   0.0  0
 D7I  CONST_12  C6'   C5'  C4'  C3'    0.00   0.0  0
 D7I  CONST_13  O5    C5   C6   C1   180.00   0.0  0
 D7I  CONST_14  O5'   C5'  C6'  C1'  180.00   0.0  0
 D7I  CONST_15  O4    C4   C3   C2   180.00   0.0  0
 D7I  CONST_16  O4'   C4'  C3'  C2'  180.00   0.0  0
 D7I  CONST_17  O5    C5   C4   C3   180.00   0.0  0
 D7I  CONST_18  O1    C1   C2   C3   180.00   0.0  0
 D7I  CONST_19  O1'   C1'  C2'  C3'  180.00   0.0  0
 D7I  CONST_20  O5'   C5'  C4'  C3'  180.00   0.0  0
 D7I  CONST_21  O2    C2   C3   C4   180.00   0.0  0
 D7I  CONST_22  O2'   C2'  C3'  C4'  180.00   0.0  0
 D7I  CONST_23  O1    C1   C6   C5   180.00   0.0  0
 D7I  CONST_24  O1'   C1'  C6'  C5'  180.00   0.0  0
 D7I  CONST_25  O4    C4   C5   C6   180.00   0.0  0
 D7I  CONST_26  O2    C2   C1   C6   180.00   0.0  0
 D7I  CONST_27  O2'   C2'  C1'  C6'  180.00   0.0  0
 D7I  CONST_28  O4'   C4'  C5'  C6'  180.00   0.0  0
 D7I  CONST_29  H3    C3   C2   C1   180.00   0.0  0
 D7I  CONST_30  H3'   C3'  C2'  C1'  180.00   0.0  0
 D7I  CONST_31  H6    C6   C1   C2   180.00   0.0  0
 D7I  CONST_32  H6'   C6'  C1'  C2'  180.00   0.0  0
 D7I  Var_01    C7'   C7   O1   C1   -66.33  30.0  2
 D7I  Var_02    C7    C7'  O1'  C1'  -63.70  30.0  2
 D7I  Var_03    O23   P2   O2   C2    66.12  30.0  2
 D7I  Var_04    O22'  P2'  O2'  C2'  111.79  30.0  1
 D7I  Var_05    O43   P4   O4   C4   -53.86  30.0  3
 D7I  Var_06    O43'  P4'  O4'  C4'  -51.10  30.0  2
 D7I  Var_07    O51   P5   O5   C5   173.75  30.0  3
 D7I  Var_08    O52'  P5'  O5'  C5'  -16.43  30.0  3
 D7I  Var_09    O1'   C7'  C7   O1   -52.91  30.0  3

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
 D7I  plan-1  C1'  0.020
 D7I  plan-1  C2'  0.020
 D7I  plan-1  C3'  0.020
 D7I  plan-1  C4'  0.020
 D7I  plan-1  C5'  0.020
 D7I  plan-1  C6'  0.020
 D7I  plan-1  O1'  0.020
 D7I  plan-1  O2'  0.020
 D7I  plan-1  O4'  0.020
 D7I  plan-1  O5'  0.020
 D7I  plan-1  H3'  0.020
 D7I  plan-1  H6'  0.020
 D7I  plan-2  C1   0.020
 D7I  plan-2  C2   0.020
 D7I  plan-2  C3   0.020
 D7I  plan-2  C4   0.020
 D7I  plan-2  C5   0.020
 D7I  plan-2  C6   0.020
 D7I  plan-2  O1   0.020
 D7I  plan-2  O2   0.020
 D7I  plan-2  O4   0.020
 D7I  plan-2  O5   0.020
 D7I  plan-2  H3   0.020
 D7I  plan-2  H6   0.020

