# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 08:18:14 2021
#   Inital geometry file: a 153 line input string
#   Ligand name: [2,3-diphosphonooxy-5-(3,4,5-triphosphonooxyphenyl)phenyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1cc(cc(O[P](O)(O)=O)c1O[P](O)(O)=O)c2cc(O[P](O)(O)=O)c(O[P](O)(O)=O)c(O[P](O)(O)=O)c2
#
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
 B6K  B6K  '[2,3-diphosphonooxy-5-(3,4,5-triphosphonooxyphenyl)phenyl] dihydrogen phosphate'  ligand  58  42  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B6K
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
 B6K  C1    C  CR6   0   0.105  44.0471  -55.6003  14.6881
 B6K  C2    C  CR16  0  -0.403  44.7032  -55.8114  13.4775
 B6K  C3    C  CR6   0   0.331  45.5760  -54.8592  12.9799
 B6K  O3    O  O2    0  -0.611  46.2211  -55.0152  11.7892
 B6K  P3    P  P     0   1.439  47.4262  -56.0949  11.5505
 B6K  C4    C  CR6   0   0.236  45.7860  -53.6727  13.6745
 B6K  O4    O  O2    0  -0.583  46.5521  -52.6835  13.1278
 B6K  P4    P  P     0   1.492  48.1195  -52.4988  13.4368
 B6K  C5    C  CR6   0   0.356  45.1514  -53.4772  14.8936
 B6K  O5    O  O2    0  -0.612  45.4396  -52.3474  15.6050
 B6K  P5    P  P     0   1.441  44.6076  -50.9744  15.3746
 B6K  C6    C  CR16  0  -0.400  44.2831  -54.4262  15.3988
 B6K  C14   C  CR6   0   0.101  43.1013  -56.6072  15.2066
 B6K  C15   C  CR16  0  -0.405  43.0114  -56.8569  16.5735
 B6K  C16   C  CR6   0   0.372  42.1161  -57.7938  17.0557
 B6K  O16   O  O2    0  -0.611  41.9989  -57.9726  18.4030
 B6K  P16   P  P     0   1.430  42.3973  -59.3690  19.1295
 B6K  C17   C  CR6   0   0.254  41.2931  -58.4968  16.1836
 B6K  O17   O  O2    0  -0.606  40.3828  -59.3662  16.6966
 B6K  P17   P  P     0   1.473  40.2700  -60.9298  16.2676
 B6K  C18   C  CR6   0   0.336  41.3831  -58.2403  14.8219
 B6K  O18   O  O2    0  -0.623  40.5555  -58.9562  13.9992
 B6K  P18   P  P     0   1.458  39.3220  -58.2331  13.2269
 B6K  C19   C  CR16  0  -0.399  42.2793  -57.3107  14.3296
 B6K  O31   O  OH1   0  -0.771  48.2226  -56.1355  12.9050
 B6K  O32   O  O     0  -0.684  48.1091  -55.7309  10.2980
 B6K  O33   O  OH1   0  -0.726  46.7605  -57.5386  11.6109
 B6K  O41   O  O     0  -0.711  48.8197  -53.7768  13.7281
 B6K  O42   O  OH1   0  -0.712  48.2436  -51.4114  14.5820
 B6K  O43   O  OH1   0  -0.703  48.4769  -51.7191  12.1155
 B6K  O51   O  OH1   0  -0.721  43.4393  -51.1675  16.4324
 B6K  O52   O  OH1   0  -0.719  45.5597  -49.9305  16.0971
 B6K  O53   O  O     0  -0.684  44.2231  -50.7115  13.9788
 B6K  O61   O  OH1   0  -0.715  43.2208  -58.7415  20.3309
 B6K  O62   O  O     0  -0.690  43.0569  -60.3246  18.2222
 B6K  O63   O  OH1   0  -0.742  41.0667  -59.8650  19.8388
 B6K  O71   O  OH1   0  -0.719  38.8290  -61.0629  15.6117
 B6K  O72   O  OH1   0  -0.746  39.9904  -61.4748  17.7438
 B6K  O73   O  O     0  -0.675  41.4074  -61.4652  15.5087
 B6K  O81   O  OH1   0  -0.723  38.5044  -59.5188  12.7769
 B6K  O82   O  O     0  -0.674  39.7157  -57.2711  12.1854
 B6K  O83   O  OH1   0  -0.724  38.4871  -57.6856  14.4582
 B6K  H2    H  HCR6  0   0.289  44.5490  -56.7283  12.9249
 B6K  H6    H  HCR6  0   0.289  43.7838  -54.2313  16.3388
 B6K  H15   H  HCR6  0   0.288  43.6505  -56.3399  17.2778
 B6K  H19   H  HCR6  0   0.291  42.3181  -57.1254  13.2643
 B6K  HO31  H  HOH1  0   0.503  48.5346  -55.2454  13.2434
 B6K  HO33  H  HOH1  0   0.505  46.4559  -57.8671  10.7540
 B6K  HO42  H  HOH1  0   0.514  48.5008  -51.7525  15.4505
 B6K  HO43  H  HOH1  0   0.518  49.3727  -51.3529  12.0806
 B6K  HO51  H  HOH1  0   0.508  42.6591  -50.6196  16.2677
 B6K  HO52  H  HOH1  0   0.504  46.2535  -49.5583  15.5350
 B6K  H161  H  HOH1  0   0.509  43.5049  -59.3789  21.0007
 B6K  H163  H  HOH1  0   0.505  40.5566  -60.4965  19.2991
 B6K  H171  H  HOH1  0   0.499  38.8172  -61.1019  14.6449
 B6K  H172  H  HOH1  0   0.519  39.9199  -62.4378  17.8192
 B6K  H181  H  HOH1  0   0.513  38.7007  -59.8348  11.8836
 B6K  H183  H  HOH1  0   0.511  37.9566  -56.8996  14.2668

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
 B6K  C2   C1    aromatic  1.393  0.020  1.393
 B6K  C1   C14   single    1.476  0.020  1.476
 B6K  C1   C6    aromatic  1.393  0.020  1.393
 B6K  C3   C2    aromatic  1.384  0.020  1.384
 B6K  C2   H2    single    0.930  0.020  1.080
 B6K  O3   C3    single    1.363  0.020  1.363
 B6K  C3   C4    aromatic  1.391  0.020  1.391
 B6K  P3   O3    single    1.636  0.020  1.636
 B6K  O32  P3    double    1.472  0.020  1.472
 B6K  P3   O33   single    1.591  0.020  1.591
 B6K  P3   O31   single    1.572  0.020  1.572
 B6K  O4   C4    single    1.365  0.020  1.365
 B6K  C4   C5    aromatic  1.388  0.020  1.388
 B6K  O4   P4    single    1.608  0.020  1.608
 B6K  O41  P4    double    1.486  0.020  1.486
 B6K  P4   O43   single    1.575  0.020  1.575
 B6K  P4   O42   single    1.584  0.020  1.584
 B6K  C5   C6    aromatic  1.382  0.020  1.382
 B6K  C5   O5    single    1.366  0.020  1.366
 B6K  O5   P5    single    1.622  0.020  1.622
 B6K  O53  P5    double    1.471  0.020  1.471
 B6K  P5   O51   single    1.588  0.020  1.588
 B6K  P5   O52   single    1.587  0.020  1.587
 B6K  C6   H6    single    0.930  0.020  1.080
 B6K  C19  C14   aromatic  1.393  0.020  1.393
 B6K  C14  C15   aromatic  1.392  0.020  1.392
 B6K  C15  C16   aromatic  1.383  0.020  1.383
 B6K  C15  H15   single    0.930  0.020  1.080
 B6K  C17  C16   aromatic  1.390  0.020  1.390
 B6K  C16  O16   single    1.364  0.020  1.364
 B6K  O16  P16   single    1.624  0.020  1.624
 B6K  O62  P16   double    1.474  0.020  1.474
 B6K  P16  O63   single    1.587  0.020  1.587
 B6K  P16  O61   single    1.586  0.020  1.586
 B6K  C18  C17   aromatic  1.389  0.020  1.389
 B6K  C17  O17   single    1.359  0.020  1.359
 B6K  O17  P17   single    1.625  0.020  1.625
 B6K  O73  P17   double    1.468  0.020  1.468
 B6K  P17  O71   single    1.589  0.020  1.589
 B6K  P17  O72   single    1.598  0.020  1.598
 B6K  O18  C18   single    1.369  0.020  1.369
 B6K  C19  C18   aromatic  1.382  0.020  1.382
 B6K  P18  O18   single    1.625  0.020  1.625
 B6K  O82  P18   double    1.471  0.020  1.471
 B6K  O81  P18   single    1.589  0.020  1.589
 B6K  P18  O83   single    1.585  0.020  1.585
 B6K  C19  H19   single    0.930  0.020  1.080
 B6K  O31  HO31  single    0.850  0.020  0.980
 B6K  O33  HO33  single    0.850  0.020  0.980
 B6K  O42  HO42  single    0.850  0.020  0.980
 B6K  O43  HO43  single    0.850  0.020  0.980
 B6K  O51  HO51  single    0.850  0.020  0.980
 B6K  O52  HO52  single    0.850  0.020  0.980
 B6K  O61  H161  single    0.850  0.020  0.980
 B6K  O63  H163  single    0.850  0.020  0.980
 B6K  O71  H171  single    0.850  0.020  0.980
 B6K  O72  H172  single    0.850  0.020  0.980
 B6K  O81  H181  single    0.850  0.020  0.980
 B6K  O83  H183  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
 B6K  C14   C1   C6   120.30  3.000
 B6K  C6    C1   C2   119.44  3.000
 B6K  C14   C1   C2   120.26  3.000
 B6K  H2    C2   C3   119.30  3.000
 B6K  H2    C2   C1   120.35  3.000
 B6K  C3    C2   C1   120.34  3.000
 B6K  C4    C3   O3   117.54  3.000
 B6K  C4    C3   C2   120.16  3.000
 B6K  O3    C3   C2   122.26  3.000
 B6K  P3    O3   C3   123.49  3.000
 B6K  O33   P3   O32  116.79  3.000
 B6K  O33   P3   O31   98.97  3.000
 B6K  O32   P3   O31  120.30  3.000
 B6K  O31   P3   O3   105.34  3.000
 B6K  O33   P3   O3   106.57  3.000
 B6K  O32   P3   O3   107.62  3.000
 B6K  C5    C4   O4   120.41  3.000
 B6K  C5    C4   C3   119.32  3.000
 B6K  O4    C4   C3   120.18  3.000
 B6K  P4    O4   C4   123.58  3.000
 B6K  O43   P4   O42  104.41  3.000
 B6K  O42   P4   O41  114.31  3.000
 B6K  O43   P4   O41  118.89  3.000
 B6K  O42   P4   O4   107.11  3.000
 B6K  O43   P4   O4    96.71  3.000
 B6K  O41   P4   O4   113.46  3.000
 B6K  C6    C5   O5   120.68  3.000
 B6K  O5    C5   C4   118.52  3.000
 B6K  C6    C5   C4   120.77  3.000
 B6K  P5    O5   C5   121.20  3.000
 B6K  O53   P5   O52  118.11  3.000
 B6K  O52   P5   O51  102.60  3.000
 B6K  O53   P5   O51  117.48  3.000
 B6K  O52   P5   O5   100.63  3.000
 B6K  O51   P5   O5   100.36  3.000
 B6K  O53   P5   O5   114.84  3.000
 B6K  H6    C6   C5   118.93  3.000
 B6K  H6    C6   C1   121.13  3.000
 B6K  C5    C6   C1   119.93  3.000
 B6K  C19   C14  C15  119.30  3.000
 B6K  C15   C14  C1   120.58  3.000
 B6K  C19   C14  C1   120.11  3.000
 B6K  H15   C15  C16  118.63  3.000
 B6K  H15   C15  C14  120.99  3.000
 B6K  C16   C15  C14  120.38  3.000
 B6K  C17   C16  O16  120.16  3.000
 B6K  O16   C16  C15  119.27  3.000
 B6K  C17   C16  C15  120.49  3.000
 B6K  P16   O16  C16  122.25  3.000
 B6K  O63   P16  O62  116.60  3.000
 B6K  O63   P16  O61  102.73  3.000
 B6K  O62   P16  O61  119.38  3.000
 B6K  O61   P16  O16   97.25  3.000
 B6K  O63   P16  O16  105.25  3.000
 B6K  O62   P16  O16  113.08  3.000
 B6K  C18   C17  O17  122.12  3.000
 B6K  O17   C17  C16  118.90  3.000
 B6K  C18   C17  C16  118.91  3.000
 B6K  P17   O17  C17  124.21  3.000
 B6K  O73   P17  O72  119.24  3.000
 B6K  O72   P17  O71  101.19  3.000
 B6K  O73   P17  O71  117.30  3.000
 B6K  O72   P17  O17   95.53  3.000
 B6K  O71   P17  O17  104.62  3.000
 B6K  O73   P17  O17  115.68  3.000
 B6K  C19   C18  O18  121.98  3.000
 B6K  C19   C18  C17  121.04  3.000
 B6K  O18   C18  C17  116.97  3.000
 B6K  P18   O18  C18  120.78  3.000
 B6K  O83   P18  O82  117.70  3.000
 B6K  O83   P18  O81  103.21  3.000
 B6K  O82   P18  O81  117.79  3.000
 B6K  O83   P18  O18  100.62  3.000
 B6K  O81   P18  O18   99.51  3.000
 B6K  O82   P18  O18  115.10  3.000
 B6K  H19   C19  C18  119.29  3.000
 B6K  H19   C19  C14  120.81  3.000
 B6K  C18   C19  C14  119.88  3.000
 B6K  HO31  O31  P3   115.20  3.000
 B6K  HO33  O33  P3   113.98  3.000
 B6K  HO42  O42  P4   115.32  3.000
 B6K  HO43  O43  P4   115.30  3.000
 B6K  HO51  O51  P5   114.27  3.000
 B6K  HO52  O52  P5   114.76  3.000
 B6K  H161  O61  P16  114.61  3.000
 B6K  H163  O63  P16  113.19  3.000
 B6K  H171  O71  P17  115.27  3.000
 B6K  H172  O72  P17  115.06  3.000
 B6K  H181  O81  P18  114.92  3.000
 B6K  H183  O83  P18  114.57  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
 B6K  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 B6K  CONST_02  C18  C19  C14  C1    180.00   0.0  0
 B6K  CONST_03  C16  C15  C14  C1    180.00   0.0  0
 B6K  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 B6K  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 B6K  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 B6K  CONST_09  C14  C1   C2   C3    180.00   0.0  0
 B6K  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 B6K  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 B6K  CONST_12  C14  C1   C6   C5    180.00   0.0  0
 B6K  CONST_15  C17  C18  C19  C14     0.00   0.0  0
 B6K  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 B6K  CONST_17  C18  C19  C14  C15     0.00   0.0  0
 B6K  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 B6K  CONST_19  C19  C14  C15  C16     0.00   0.0  0
 B6K  CONST_20  C19  C18  C17  C16     0.00   0.0  0
 B6K  CONST_21  O3   C3   C2   C1    180.00   0.0  0
 B6K  CONST_22  O5   C5   C6   C1    180.00   0.0  0
 B6K  CONST_23  O4   C4   C3   C2    180.00   0.0  0
 B6K  CONST_24  O5   C5   C4   C3    180.00   0.0  0
 B6K  CONST_25  C5   C4   C3   O3    180.00   0.0  0
 B6K  CONST_26  C6   C5   C4   O4    180.00   0.0  0
 B6K  CONST_27  O18  C18  C19  C14   180.00   0.0  0
 B6K  CONST_28  O16  C16  C15  C14   180.00   0.0  0
 B6K  CONST_29  O17  C17  C16  C15   180.00   0.0  0
 B6K  CONST_30  O18  C18  C17  C16   180.00   0.0  0
 B6K  CONST_31  C18  C17  C16  O16   180.00   0.0  0
 B6K  CONST_32  C19  C18  C17  O17   180.00   0.0  0
 B6K  CONST_33  H19  C19  C14  C1      0.00   0.0  0
 B6K  CONST_34  H15  C15  C14  C1      0.00   0.0  0
 B6K  CONST_35  H6   C6   C1   C2    180.00   0.0  0
 B6K  CONST_36  H2   C2   C3   C4    180.00   0.0  0
 B6K  Var_01    C4   C3   O3   P3    111.39  30.0  2
 B6K  Var_02    C5   C4   O4   P4     88.46  30.0  2
 B6K  Var_03    C6   C5   O5   P5    -93.64  30.0  1
 B6K  Var_04    C17  C16  O16  P16    67.74  30.0  3
 B6K  Var_05    C18  C17  O17  P17    57.58  30.0  2
 B6K  Var_06    C19  C18  O18  P18   -70.15  30.0  2
 B6K  Var_07    O32  P3   O3   C3   -164.85  30.0  2
 B6K  Var_08    O41  P4   O4   C4     30.67  30.0  3
 B6K  Var_09    O53  P5   O5   C5    -37.12  30.0  3
 B6K  Var_10    O62  P16  O16  C16     7.87  30.0  3
 B6K  Var_11    O73  P17  O17  C17    13.66  30.0  3
 B6K  Var_12    O82  P18  O18  C18    67.70  30.0  2

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
 B6K  plan-1  C1   0.020
 B6K  plan-1  C2   0.020
 B6K  plan-1  C3   0.020
 B6K  plan-1  O3   0.020
 B6K  plan-1  C4   0.020
 B6K  plan-1  O4   0.020
 B6K  plan-1  C5   0.020
 B6K  plan-1  O5   0.020
 B6K  plan-1  C6   0.020
 B6K  plan-1  C14  0.020
 B6K  plan-1  H2   0.020
 B6K  plan-1  H6   0.020
 B6K  plan-2  C1   0.020
 B6K  plan-2  C14  0.020
 B6K  plan-2  C15  0.020
 B6K  plan-2  C16  0.020
 B6K  plan-2  O16  0.020
 B6K  plan-2  C17  0.020
 B6K  plan-2  O17  0.020
 B6K  plan-2  C18  0.020
 B6K  plan-2  O18  0.020
 B6K  plan-2  C19  0.020
 B6K  plan-2  H15  0.020
 B6K  plan-2  H19  0.020

