# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 18:02:34 2022
#   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  54  46  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.239   -8.8245  28.2983  -20.2481
 D7I  C1'   C  CR6    0   0.221   -8.3768  24.8672  -17.8047
 D7I  C2    C  CR6    0   0.342   -8.9692  28.5042  -21.6241
 D7I  C2'   C  CR6    0   0.323   -8.0650  23.5224  -17.5959
 D7I  C3    C  CR16   0  -0.527  -10.1651  29.0716  -22.0716
 D7I  C3'   C  CR16   0  -0.489   -7.4139  23.1935  -16.4034
 D7I  C4    C  CR6    0   0.292  -11.1837  29.4674  -21.2061
 D7I  C4'   C  CR6    0   0.293   -7.0524  24.1423  -15.4484
 D7I  C5    C  CR6    0   0.271  -11.0127  29.2854  -19.8200
 D7I  C5'   C  CR6    0   0.270   -7.3647  25.4991  -15.6783
 D7I  C6    C  CR16   0  -0.481   -9.8304  28.7012  -19.3757
 D7I  C6'   C  CR16   0  -0.506   -8.0270  25.8242  -16.8592
 D7I  C7    C  CH2    0  -0.194   -7.2370  26.4960  -20.0482
 D7I  C7'   C  CH2    0  -0.239   -8.3039  25.4218  -20.1029
 D7I  O1    O  O2     0  -0.512   -7.6760  27.7947  -19.6909
 D7I  O1'   O  O2     0  -0.498   -9.0678  25.2696  -18.9215
 D7I  O2    O  O2     0  -0.668   -7.9530  28.1917  -22.4449
 D7I  O2'   O  O2     0  -0.673   -8.3497  22.5978  -18.5339
 D7I  O21   O  OP    -1  -0.877   -6.7347  26.7738  -24.1078
 D7I  O22   O  OP    -1  -0.878   -9.1997  26.2283  -23.5844
 D7I  O23   O  O      0  -0.879   -8.6046  28.3188  -24.9535
 D7I  O4    O  O2     0  -0.666  -12.3056  30.0607  -21.6507
 D7I  O4'   O  O2     0  -0.671   -6.4580  23.7927  -14.2918
 D7I  O41   O  OP    -1  -0.881  -14.6042  30.1587  -22.6410
 D7I  O42   O  OP    -1  -0.889  -13.5082  27.8591  -22.2507
 D7I  O43   O  O      0  -0.882  -12.6628  29.3901  -24.1325
 D7I  O5    O  O2     0  -0.669  -11.9930  29.6562  -18.9728
 D7I  O5'   O  O2     0  -0.660   -7.0348  26.4053  -14.7434
 D7I  O51   O  O      0  -0.883  -13.1555  31.2646  -17.4363
 D7I  O52   O  OP    -1  -0.882  -10.9610  30.1954  -16.6569
 D7I  O53   O  OP    -1  -0.889  -10.9292  31.9690  -18.5198
 D7I  P2    P  P      0   1.232   -8.1573  27.2833  -23.9292
 D7I  P2'   P  P      0   1.201   -9.6252  21.4253  -18.2753
 D7I  P4    P  P      0   1.208  -13.3730  29.2765  -22.7876
 D7I  P4'   P  P      0   1.203   -4.8439  23.1245  -14.2475
 D7I  P5    P  P      0   1.205  -11.7187  30.9000  -17.7773
 D7I  P5'   P  P      0   1.223   -6.5474  28.0383  -15.1216
 D7I  O21'  O  OP    -1  -0.880   -9.0699  20.4660  -17.2293
 D7I  O22'  O  O      0  -0.882   -9.7323  20.8497  -19.6789
 D7I  O23'  O  OP    -1  -0.886  -10.8067  22.2641  -17.8124
 D7I  O41'  O  OP    -1  -0.883   -4.5731  23.2204  -12.7536
 D7I  O42'  O  OP    -1  -0.887   -4.0249  24.0526  -15.1332
 D7I  O43'  O  O      0  -0.882   -4.9897  21.7014  -14.7779
 D7I  O51'  O  OP    -1  -0.876   -6.0425  28.4784  -13.7567
 D7I  O52'  O  O      0  -0.888   -5.4852  27.8667  -16.1968
 D7I  O53'  O  OP    -1  -0.881   -7.8286  28.7277  -15.5807
 D7I  H3    H  HCR6   0   0.231  -10.2952  29.2416  -23.1315
 D7I  H3'   H  HCR6   0   0.224   -7.1733  22.1568  -16.2146
 D7I  H6    H  HCR6   0   0.232   -9.6836  28.5626  -18.3113
 D7I  H6'   H  HCR6   0   0.260   -8.2902  26.8576  -17.0379
 D7I  H71   H  HCH2   0   0.210   -6.7349  26.4934  -21.0207
 D7I  H72   H  HCH2   0   0.220   -6.4866  26.2403  -19.2960
 D7I  H7'2  H  HCH2   0   0.228   -9.0150  25.6352  -20.9039
 D7I  H7'1  H  HCH2   0   0.212   -7.7969  24.4861  -20.3700

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    deloc     1.524  0.020  1.524
 D7I  O43   P4    deloc     1.525  0.020  1.525
 D7I  O41   P4    deloc     1.522  0.020  1.522
 D7I  P4    O4    single    1.746  0.020  1.746
 D7I  P4    O42   deloc     1.522  0.020  1.522
 D7I  P2    O21   deloc     1.522  0.020  1.522
 D7I  P2    O22   deloc     1.523  0.020  1.523
 D7I  P2    O2    single    1.752  0.020  1.752
 D7I  O4    C4    single    1.345  0.020  1.345
 D7I  C3    C4    aromatic  1.394  0.020  1.394
 D7I  C3    C2    aromatic  1.397  0.020  1.397
 D7I  O2    C2    single    1.343  0.020  1.343
 D7I  C4    C5    aromatic  1.408  0.020  1.408
 D7I  C2    C1    aromatic  1.399  0.020  1.399
 D7I  C5    O5    single    1.348  0.020  1.348
 D7I  C5    C6    aromatic  1.392  0.020  1.392
 D7I  C1    C6    aromatic  1.391  0.020  1.391
 D7I  C1    O1    single    1.372  0.020  1.372
 D7I  O5    P5    single    1.747  0.020  1.747
 D7I  O22'  P2'   deloc     1.521  0.020  1.521
 D7I  O51   P5    deloc     1.521  0.020  1.521
 D7I  C7    O1    single    1.417  0.020  1.417
 D7I  C7    C7'   single    1.515  0.020  1.515
 D7I  O53   P5    deloc     1.522  0.020  1.522
 D7I  P5    O52   deloc     1.525  0.020  1.525
 D7I  C7'   O1'   single    1.415  0.020  1.415
 D7I  O21'  P2'   deloc     1.524  0.020  1.524
 D7I  P2'   O2'   single    1.752  0.020  1.752
 D7I  P2'   O23'  deloc     1.521  0.020  1.521
 D7I  O2'   C2'   single    1.347  0.020  1.347
 D7I  O1'   C1'   single    1.374  0.020  1.374
 D7I  C2'   C1'   aromatic  1.396  0.020  1.396
 D7I  C2'   C3'   aromatic  1.398  0.020  1.398
 D7I  C1'   C6'   aromatic  1.390  0.020  1.390
 D7I  C3'   C4'   aromatic  1.394  0.020  1.394
 D7I  O43'  P4'   deloc     1.526  0.020  1.526
 D7I  O42'  P4'   deloc     1.522  0.020  1.522
 D7I  C6'   C5'   aromatic  1.392  0.020  1.392
 D7I  C4'   C5'   aromatic  1.411  0.020  1.411
 D7I  C4'   O4'   single    1.347  0.020  1.347
 D7I  P4'   O4'   single    1.748  0.020  1.748
 D7I  P4'   O41'  deloc     1.521  0.020  1.521
 D7I  O52'  P5'   deloc     1.521  0.020  1.521
 D7I  C5'   O5'   single    1.343  0.020  1.343
 D7I  O5'   P5'   single    1.746  0.020  1.746
 D7I  P5'   O53'  deloc     1.526  0.020  1.526
 D7I  P5'   O51'  deloc     1.520  0.020  1.520
 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

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    117.19  3.000
 D7I  O1    C1   C2    122.68  3.000
 D7I  C6    C1   C2    119.97  3.000
 D7I  O1'   C1'  C6'   118.55  3.000
 D7I  C6'   C1'  C2'   120.35  3.000
 D7I  O1'   C1'  C2'   121.07  3.000
 D7I  O2    C2   C3    123.11  3.000
 D7I  O2    C2   C1    119.25  3.000
 D7I  C3    C2   C1    117.60  3.000
 D7I  O2'   C2'  C3'   122.06  3.000
 D7I  C3'   C2'  C1'   117.26  3.000
 D7I  O2'   C2'  C1'   120.64  3.000
 D7I  H3    C3   C4    118.42  3.000
 D7I  H3    C3   C2    118.73  3.000
 D7I  C4    C3   C2    122.81  3.000
 D7I  H3'   C3'  C4'   118.38  3.000
 D7I  H3'   C3'  C2'   118.58  3.000
 D7I  C4'   C3'  C2'   123.04  3.000
 D7I  O4    C4   C5    118.92  3.000
 D7I  C5    C4   C3    119.05  3.000
 D7I  O4    C4   C3    121.98  3.000
 D7I  O4'   C4'  C5'   119.16  3.000
 D7I  O4'   C4'  C3'   121.75  3.000
 D7I  C5'   C4'  C3'   119.04  3.000
 D7I  O5    C5   C6    122.19  3.000
 D7I  C6    C5   C4    118.14  3.000
 D7I  O5    C5   C4    119.66  3.000
 D7I  O5'   C5'  C6'   123.34  3.000
 D7I  O5'   C5'  C4'   118.75  3.000
 D7I  C6'   C5'  C4'   117.90  3.000
 D7I  H6    C6   C5    118.85  3.000
 D7I  H6    C6   C1    118.76  3.000
 D7I  C5    C6   C1    122.39  3.000
 D7I  H6'   C6'  C5'   118.62  3.000
 D7I  H6'   C6'  C1'   118.97  3.000
 D7I  C5'   C6'  C1'   122.40  3.000
 D7I  H72   C7   H71   107.22  3.000
 D7I  H72   C7   O1    104.70  3.000
 D7I  H71   C7   O1    111.62  3.000
 D7I  H72   C7   C7'   110.03  3.000
 D7I  H71   C7   C7'   106.81  3.000
 D7I  O1    C7   C7'   116.16  3.000
 D7I  H7'1  C7'  H7'2  106.79  3.000
 D7I  H7'1  C7'  O1'   111.16  3.000
 D7I  H7'2  C7'  O1'   106.37  3.000
 D7I  H7'1  C7'  C7    106.74  3.000
 D7I  H7'2  C7'  C7    110.28  3.000
 D7I  O1'   C7'  C7    115.23  3.000
 D7I  C7    O1   C1    119.56  3.000
 D7I  C7'   O1'  C1'   116.03  3.000
 D7I  P2    O2   C2    123.37  3.000
 D7I  P2'   O2'  C2'   120.69  3.000
 D7I  P4    O4   C4    121.82  3.000
 D7I  P4'   O4'  C4'   121.92  3.000
 D7I  P5    O5   C5    120.79  3.000
 D7I  P5'   O5'  C5'   123.30  3.000
 D7I  O23   P2   O22   114.97  3.000
 D7I  O22   P2   O21   115.76  3.000
 D7I  O23   P2   O21   115.03  3.000
 D7I  O22   P2   O2    104.31  3.000
 D7I  O21   P2   O2     99.44  3.000
 D7I  O23   P2   O2    104.56  3.000
 D7I  O23'  P2'  O22'  115.77  3.000
 D7I  O23'  P2'  O21'  114.91  3.000
 D7I  O22'  P2'  O21'  114.89  3.000
 D7I  O23'  P2'  O2'   103.97  3.000
 D7I  O21'  P2'  O2'   104.92  3.000
 D7I  O22'  P2'  O2'    99.70  3.000
 D7I  O43   P4   O42   114.96  3.000
 D7I  O42   P4   O41   115.73  3.000
 D7I  O43   P4   O41   114.74  3.000
 D7I  O42   P4   O4    104.07  3.000
 D7I  O41   P4   O4     99.88  3.000
 D7I  O43   P4   O4    104.84  3.000
 D7I  O43'  P4'  O42'  114.70  3.000
 D7I  O42'  P4'  O41'  115.93  3.000
 D7I  O43'  P4'  O41'  114.66  3.000
 D7I  O41'  P4'  O4'    99.51  3.000
 D7I  O42'  P4'  O4'   104.43  3.000
 D7I  O43'  P4'  O4'   105.04  3.000
 D7I  O53   P5   O52   115.16  3.000
 D7I  O52   P5   O51   114.54  3.000
 D7I  O53   P5   O51   115.53  3.000
 D7I  O52   P5   O5    104.58  3.000
 D7I  O53   P5   O5    104.33  3.000
 D7I  O51   P5   O5    100.12  3.000
 D7I  O53'  P5'  O52'  115.13  3.000
 D7I  O53'  P5'  O51'  114.73  3.000
 D7I  O52'  P5'  O51'  115.80  3.000
 D7I  O51'  P5'  O5'    99.74  3.000
 D7I  O53'  P5'  O5'   104.68  3.000
 D7I  O52'  P5'  O5'   104.04  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   -44.02  30.0  1
 D7I  Var_02    C7    C7'  O1'  C1'  -63.48  30.0  1
 D7I  Var_03    O23   P2   O2   C2    82.35  30.0  2
 D7I  Var_04    O22'  P2'  O2'  C2'  168.64  30.0  3
 D7I  Var_05    O43   P4   O4   C4   -75.97  30.0  3
 D7I  Var_06    O43'  P4'  O4'  C4'  -73.28  30.0  3
 D7I  Var_07    O51   P5   O5   C5   161.94  30.0  3
 D7I  Var_08    O52'  P5'  O5'  C5'  -49.21  30.0  3
 D7I  Var_09    O1'   C7'  C7   O1   -54.88  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

