# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 12:00:37 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1cc(O[P](O)(O)=O)c(c(O[P](O)(O)=O)c1)c2cc(O[P](O)(O)=O)cc(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
 B5F  B5F  'biphenyl-2,3',4,5',6-pentayl pentakis[dihydrogen (phosphate)]'  ligand  52  37  .  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_B5F
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
 B5F  C1    C  CR6   0  -0.059   1.1607  52.4237  -49.0645
 B5F  C2    C  CR6   0   0.439   1.2696  53.7880  -48.8365
 B5F  O2    O  O2    0  -0.589   1.0019  54.6298  -49.8774
 B5F  P2    P  P     0   1.445   2.1583  55.2849  -50.8092
 B5F  C3    C  CR16  0  -0.467   1.5833  54.2987  -47.5865
 B5F  C4    C  CR6   0   0.297   1.7917  53.4068  -46.5420
 B5F  O4    O  O2    0  -0.612   2.1546  53.8753  -45.3066
 B5F  P4    P  P     0   1.470   1.0348  54.3907  -44.2542
 B5F  C5    C  CR16  0  -0.353   1.6698  52.0390  -46.7249
 B5F  C6    C  CR6   0   0.297   1.3578  51.5816  -47.9915
 B5F  O6    O  O2    0  -0.604   1.1386  50.2647  -48.2655
 B5F  P6    P  P     0   1.427   2.2220  49.0850  -48.1549
 B5F  C1'   C  CR6   0   0.026   0.8054  51.8489  -50.3809
 B5F  C2'   C  CR16  0  -0.213  -0.4877  52.0096  -50.8572
 B5F  O21   O  O     0  -0.838   1.5314  55.8987  -51.9879
 B5F  O22   O  OH1   0  -0.734   3.0277  56.2128  -49.8436
 B5F  O23   O  OH1   0  -0.610   3.2278  54.1311  -51.0155
 B5F  C3'   C  CR6   0   0.259  -0.8474  51.4208  -52.0563
 B5F  O3'   O  O2    0  -0.577  -2.1110  51.6353  -52.5494
 B5F  P3'   P  P     0   1.487  -3.2630  50.5126  -52.3716
 B5F  O31   O  OH1   0  -0.692  -4.4774  51.2232  -53.1033
 B5F  O32   O  O     0  -0.783  -2.8855  49.1602  -52.8188
 B5F  O33   O  OH1   0  -0.721  -3.6249  50.6937  -50.8355
 B5F  C4'   C  CR16  0  -0.391   0.0413  50.6458  -52.7738
 B5F  O41   O  OH1   0  -0.762   1.9582  54.8492  -43.0491
 B5F  O42   O  O     0  -0.751   0.0797  55.3689  -44.8015
 B5F  O43   O  OH1   0  -0.659   0.4488  53.0087  -43.7401
 B5F  C5'   C  CR6   0   0.347   1.3319  50.4950  -52.2923
 B5F  O5'   O  O2    0  -0.567   2.1780  49.7418  -53.0719
 B5F  P5'   P  P     0   1.450   2.8774  48.3136  -52.7070
 B5F  O51   O  O     0  -0.754   3.2571  47.6692  -53.9705
 B5F  O52   O  OH1   0  -0.710   4.1011  48.6447  -51.7133
 B5F  O53   O  OH1   0  -0.662   1.8788  47.5091  -51.7926
 B5F  C6'   C  CR16  0  -0.315   1.7336  51.1080  -51.1115
 B5F  O61   O  OH1   0  -0.662   3.6483  49.7452  -48.3132
 B5F  O62   O  OH1   0  -0.705   2.2958  48.6560  -46.6358
 B5F  O63   O  O     0  -0.767   1.8549  48.0441  -49.1539
 B5F  H3    H  HCR6  0   0.310   1.6648  55.3681  -47.4286
 B5F  H5    H  HCR6  0   0.331   1.8017  51.3575  -45.8964
 B5F  H2'   H  HCR6  0   0.270  -1.2097  52.5892  -50.2985
 B5F  HO22  H  HOH1  0   0.514   2.6478  57.0791  -49.6681
 B5F  HO23  H  HOH1  0   0.515   3.1037  53.6012  -51.8196
 B5F  HO31  H  HOH1  0   0.496  -4.5464  51.0339  -54.0557
 B5F  HO33  H  HOH1  0   0.515  -4.0040  49.9031  -50.4148
 B5F  H4'   H  HCR6  0   0.326  -0.2554  50.1806  -53.7038
 B5F  HO41  H  HOH1  0   0.501   2.2633  55.7717  -43.0987
 B5F  HO43  H  HOH1  0   0.484  -0.4607  53.0571  -43.3868
 B5F  HO52  H  HOH1  0   0.505   4.9293  48.9062  -52.1720
 B5F  HO53  H  HOH1  0   0.523   1.9815  47.4717  -50.7944
 B5F  H6'   H  HCR6  0   0.257   2.7569  51.0380  -50.7727
 B5F  HO61  H  HOH1  0   0.547   4.0917  49.5246  -49.1726
 B5F  HO62  H  HOH1  0   0.518   1.4723  48.2625  -46.2714

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
 B5F  C1'  C1    single    1.480  0.020  1.480
 B5F  C1   C2    aromatic  1.388  0.020  1.388
 B5F  C1   C6    aromatic  1.378  0.020  1.378
 B5F  O2   C2    single    1.365  0.020  1.365
 B5F  C2   C3    aromatic  1.386  0.020  1.386
 B5F  P2   O2    single    1.623  0.020  1.623
 B5F  O21  P2    double    1.469  0.020  1.469
 B5F  P2   O23   single    1.587  0.020  1.587
 B5F  P2   O22   single    1.597  0.020  1.597
 B5F  C3   C4    aromatic  1.389  0.020  1.389
 B5F  C3   H3    single    0.930  0.020  1.080
 B5F  C5   C4    aromatic  1.385  0.020  1.385
 B5F  C4   O4    single    1.370  0.020  1.370
 B5F  O4   P4    single    1.621  0.020  1.621
 B5F  O42  P4    double    1.473  0.020  1.473
 B5F  P4   O43   single    1.587  0.020  1.587
 B5F  P4   O41   single    1.586  0.020  1.586
 B5F  C6   C5    aromatic  1.382  0.020  1.382
 B5F  C5   H5    single    0.930  0.020  1.080
 B5F  C6   O6    single    1.363  0.020  1.363
 B5F  O6   P6    single    1.606  0.020  1.606
 B5F  O63  P6    double    1.489  0.020  1.489
 B5F  O61  P6    single    1.580  0.020  1.580
 B5F  P6   O62   single    1.580  0.020  1.580
 B5F  C6'  C1'   aromatic  1.394  0.020  1.394
 B5F  C2'  C1'   aromatic  1.387  0.020  1.387
 B5F  C3'  C2'   aromatic  1.383  0.020  1.383
 B5F  C2'  H2'   single    0.930  0.020  1.080
 B5F  O22  HO22  single    0.850  0.020  0.980
 B5F  O23  HO23  single    0.850  0.020  0.980
 B5F  C4'  C3'   aromatic  1.380  0.020  1.380
 B5F  O3'  C3'   single    1.373  0.020  1.373
 B5F  P3'  O3'   single    1.618  0.020  1.618
 B5F  O32  P3'   double    1.474  0.020  1.474
 B5F  O31  P3'   single    1.586  0.020  1.586
 B5F  P3'  O33   single    1.589  0.020  1.589
 B5F  O31  HO31  single    0.850  0.020  0.980
 B5F  O33  HO33  single    0.850  0.020  0.980
 B5F  C4'  C5'   aromatic  1.386  0.020  1.386
 B5F  C4'  H4'   single    0.930  0.020  1.080
 B5F  O41  HO41  single    0.850  0.020  0.980
 B5F  O43  HO43  single    0.850  0.020  0.980
 B5F  O5'  C5'   single    1.375  0.020  1.375
 B5F  C5'  C6'   aromatic  1.390  0.020  1.390
 B5F  O5'  P5'   single    1.632  0.020  1.632
 B5F  O51  P5'   double    1.468  0.020  1.468
 B5F  P5'  O53   single    1.575  0.020  1.575
 B5F  P5'  O52   single    1.611  0.020  1.611
 B5F  O52  HO52  single    0.850  0.020  0.980
 B5F  O53  HO53  single    0.850  0.020  0.980
 B5F  C6'  H6'   single    0.930  0.020  1.080
 B5F  O61  HO61  single    0.850  0.020  0.980
 B5F  O62  HO62  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
 B5F  C1'   C1   C6   119.32  3.000
 B5F  C6    C1   C2   117.49  3.000
 B5F  C1'   C1   C2   123.16  3.000
 B5F  C3    C2   O2   120.32  3.000
 B5F  C3    C2   C1   121.88  3.000
 B5F  O2    C2   C1   117.75  3.000
 B5F  P2    O2   C2   123.15  3.000
 B5F  O23   P2   O22   97.71  3.000
 B5F  O22   P2   O21  118.34  3.000
 B5F  O23   P2   O21  119.15  3.000
 B5F  O22   P2   O2   105.98  3.000
 B5F  O23   P2   O2   105.15  3.000
 B5F  O21   P2   O2   108.97  3.000
 B5F  H3    C3   C4   120.84  3.000
 B5F  H3    C3   C2   120.78  3.000
 B5F  C4    C3   C2   118.38  3.000
 B5F  C5    C4   O4   118.68  3.000
 B5F  O4    C4   C3   119.87  3.000
 B5F  C5    C4   C3   121.43  3.000
 B5F  P4    O4   C4   120.74  3.000
 B5F  O43   P4   O42  117.35  3.000
 B5F  O43   P4   O41  102.75  3.000
 B5F  O42   P4   O41  117.90  3.000
 B5F  O41   P4   O4   100.55  3.000
 B5F  O43   P4   O4   100.87  3.000
 B5F  O42   P4   O4   114.71  3.000
 B5F  H5    C5   C6   121.42  3.000
 B5F  H5    C5   C4   120.70  3.000
 B5F  C6    C5   C4   117.88  3.000
 B5F  O6    C6   C5   122.71  3.000
 B5F  O6    C6   C1   114.26  3.000
 B5F  C5    C6   C1   122.92  3.000
 B5F  P6    O6   C6   125.99  3.000
 B5F  O63   P6   O62  117.83  3.000
 B5F  O62   P6   O61   99.65  3.000
 B5F  O63   P6   O61  116.59  3.000
 B5F  O62   P6   O6   107.29  3.000
 B5F  O61   P6   O6   107.18  3.000
 B5F  O63   P6   O6   107.52  3.000
 B5F  C6'   C1'  C2'  120.14  3.000
 B5F  C2'   C1'  C1   118.96  3.000
 B5F  C6'   C1'  C1   120.85  3.000
 B5F  H2'   C2'  C3'  120.15  3.000
 B5F  H2'   C2'  C1'  120.46  3.000
 B5F  C3'   C2'  C1'  119.38  3.000
 B5F  HO22  O22  P2   114.75  3.000
 B5F  HO23  O23  P2   114.73  3.000
 B5F  C4'   C3'  O3'  119.57  3.000
 B5F  O3'   C3'  C2'  118.95  3.000
 B5F  C4'   C3'  C2'  121.47  3.000
 B5F  P3'   O3'  C3'  120.47  3.000
 B5F  O33   P3'  O32  117.16  3.000
 B5F  O33   P3'  O31  102.74  3.000
 B5F  O32   P3'  O31  117.86  3.000
 B5F  O33   P3'  O3'  100.92  3.000
 B5F  O31   P3'  O3'  100.58  3.000
 B5F  O32   P3'  O3'  114.90  3.000
 B5F  HO31  O31  P3'  114.73  3.000
 B5F  HO33  O33  P3'  114.49  3.000
 B5F  H4'   C4'  C5'  120.50  3.000
 B5F  H4'   C4'  C3'  120.79  3.000
 B5F  C5'   C4'  C3'  118.69  3.000
 B5F  HO41  O41  P4   114.71  3.000
 B5F  HO43  O43  P4   114.70  3.000
 B5F  C6'   C5'  O5'  123.05  3.000
 B5F  C6'   C5'  C4'  121.09  3.000
 B5F  O5'   C5'  C4'  115.83  3.000
 B5F  P5'   O5'  C5'  128.06  3.000
 B5F  O53   P5'  O52  103.21  3.000
 B5F  O52   P5'  O51  115.13  3.000
 B5F  O53   P5'  O51  116.07  3.000
 B5F  O52   P5'  O5'  106.48  3.000
 B5F  O53   P5'  O5'  107.77  3.000
 B5F  O51   P5'  O5'  107.61  3.000
 B5F  HO52  O52  P5'  114.03  3.000
 B5F  HO53  O53  P5'  122.10  3.000
 B5F  H6'   C6'  C5'  120.78  3.000
 B5F  H6'   C6'  C1'  120.05  3.000
 B5F  C5'   C6'  C1'  119.15  3.000
 B5F  HO61  O61  P6   113.42  3.000
 B5F  HO62  O62  P6   115.22  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
 B5F  CONST_01  C5'  C6'  C1'  C1    180.00   0.0  0
 B5F  CONST_02  C3'  C2'  C1'  C1    180.00   0.0  0
 B5F  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 B5F  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 B5F  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 B5F  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 B5F  CONST_09  C1'  C1   C2   C3    180.00   0.0  0
 B5F  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 B5F  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 B5F  CONST_12  C1'  C1   C6   C5    180.00   0.0  0
 B5F  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 B5F  CONST_16  C4'  C3'  C2'  C1'     0.00   0.0  0
 B5F  CONST_17  C5'  C6'  C1'  C2'     0.00   0.0  0
 B5F  CONST_18  C5'  C4'  C3'  C2'     0.00   0.0  0
 B5F  CONST_19  C6'  C1'  C2'  C3'     0.00   0.0  0
 B5F  CONST_20  C6'  C5'  C4'  C3'     0.00   0.0  0
 B5F  CONST_21  O6   C6   C1   C2    180.00   0.0  0
 B5F  CONST_22  O4   C4   C3   C2    180.00   0.0  0
 B5F  CONST_23  C1'  C1   C2   O2      0.00   0.0  0
 B5F  CONST_24  C6   C1   C2   O2    180.00   0.0  0
 B5F  CONST_25  C4   C3   C2   O2    180.00   0.0  0
 B5F  CONST_26  O6   C6   C5   C4    180.00   0.0  0
 B5F  CONST_27  C6   C5   C4   O4    180.00   0.0  0
 B5F  CONST_28  C1'  C1   C6   O6      0.00   0.0  0
 B5F  CONST_29  O5'  C5'  C6'  C1'   180.00   0.0  0
 B5F  CONST_30  O3'  C3'  C2'  C1'   180.00   0.0  0
 B5F  CONST_31  O5'  C5'  C4'  C3'   180.00   0.0  0
 B5F  CONST_32  C5'  C4'  C3'  O3'   180.00   0.0  0
 B5F  CONST_33  H6'  C6'  C1'  C1      0.00   0.0  0
 B5F  CONST_34  H2'  C2'  C1'  C1      0.00   0.0  0
 B5F  CONST_35  H3   C3   C2   C1    180.00   0.0  0
 B5F  CONST_36  H5   C5   C6   C1    180.00   0.0  0
 B5F  CONST_37  H4'  C4'  C3'  C2'   180.00   0.0  0
 B5F  Var_01    C3   C2   O2   P2     84.58  30.0  2
 B5F  Var_02    C5   C4   O4   P4    -97.13  30.0  3
 B5F  Var_03    C4'  C3'  O3'  P3'    80.45  30.0  2
 B5F  Var_04    C6'  C5'  O5'  P5'    66.42  30.0  2
 B5F  Var_05    O21  P2   O2   C2    168.22  30.0  1
 B5F  Var_06    O42  P4   O4   C4    -50.81  30.0  3
 B5F  Var_07    O63  P6   O6   C6   -150.76  30.0  3
 B5F  Var_08    O32  P3'  O3'  C3'   -51.79  30.0  1
 B5F  Var_09    O51  P5'  O5'  C5'   159.04  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
 B5F  plan-1  C1   0.020
 B5F  plan-1  C2   0.020
 B5F  plan-1  O2   0.020
 B5F  plan-1  C3   0.020
 B5F  plan-1  C4   0.020
 B5F  plan-1  O4   0.020
 B5F  plan-1  C5   0.020
 B5F  plan-1  C6   0.020
 B5F  plan-1  O6   0.020
 B5F  plan-1  C1'  0.020
 B5F  plan-1  H3   0.020
 B5F  plan-1  H5   0.020
 B5F  plan-2  C1   0.020
 B5F  plan-2  C1'  0.020
 B5F  plan-2  C2'  0.020
 B5F  plan-2  C3'  0.020
 B5F  plan-2  O3'  0.020
 B5F  plan-2  C4'  0.020
 B5F  plan-2  C5'  0.020
 B5F  plan-2  O5'  0.020
 B5F  plan-2  C6'  0.020
 B5F  plan-2  H2'  0.020
 B5F  plan-2  H4'  0.020
 B5F  plan-2  H6'  0.020

