# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 11:19:01 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: biphenyl-2,3',4,5',6-pentayl pentakis[dihydrogen (phosphate)]
#   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  42  37  .  2021-08-06  2021-08-06  
;
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  -0.105   0.9867  -0.2472   0.1158
 B5F  C2   C  CR6    0   0.254   1.7497  -1.4160  -0.0171
 B5F  O2   O  O2     0  -0.660   1.0954  -2.5359  -0.3451
 B5F  P2   P  P      0   1.229   1.6028  -4.1478   0.0443
 B5F  C3   C  CR16   0  -0.368   3.1340  -1.3644   0.1620
 B5F  C4   C  CR6    0   0.312   3.7573  -0.1565   0.4765
 B5F  O4   O  O2     0  -0.545   5.0845  -0.2057   0.6945
 B5F  P4   P  P      0   1.184   6.2206   0.9879   0.1476
 B5F  C5   C  CR16   0  -0.436   3.0140   1.0186   0.5924
 B5F  C6   C  CR6    0   0.243   1.6248   0.9697   0.4160
 B5F  O6   O  O2     0  -0.565   0.8265   2.0336   0.5292
 B5F  P6   P  P      0   1.170   1.3032   3.6760   0.8354
 B5F  C1'  C  CR6    0   0.151  -0.4897  -0.3011  -0.0333
 B5F  C2'  C  CR16   0  -0.317  -1.2996  -0.3929   1.0898
 B5F  O21  O  O      0  -0.897   2.8759  -4.3820  -0.7609
 B5F  O22  O  OP    -1  -0.907   1.7920  -4.1334   1.5513
 B5F  O23  O  OP    -1  -0.924   0.3920  -4.9165  -0.4595
 B5F  C3'  C  CR6    0   0.275  -2.6941  -0.4587   0.9726
 B5F  O3'  O  O2     0  -0.638  -3.3759  -0.5769   2.1180
 B5F  P3'  P  P      0   1.141  -5.1044  -0.5805   2.3212
 B5F  O31  O  OP    -1  -0.965  -5.1582  -0.7616   3.8310
 B5F  O32  O  O      0  -0.853  -5.5487   0.7809   1.8185
 B5F  O33  O  OP    -1  -0.858  -5.5889  -1.7739   1.5152
 B5F  C4'  C  CR16   0  -0.316  -3.2837  -0.4154  -0.2955
 B5F  O41  O  OP    -1  -0.968   7.5109   0.2258   0.4117
 B5F  O42  O  O      0  -0.838   5.8755   1.1890  -1.3178
 B5F  O43  O  OP    -1  -0.899   6.0047   2.1961   1.0465
 B5F  C5'  C  CR6    0   0.277  -2.4713  -0.3277  -1.4310
 B5F  O5'  O  O2     0  -0.662  -2.9481  -0.3363  -2.6844
 B5F  P5'  P  P      0   1.127  -4.5002   0.2687  -3.1870
 B5F  O51  O  O      0  -0.781  -4.5436   1.6824  -2.6360
 B5F  O52  O  OP    -1  -0.996  -4.3163   0.1610  -4.6934
 B5F  O53  O  OP    -1  -0.875  -5.5158  -0.7002  -2.6018
 B5F  C6'  C  CR16   0  -0.245  -1.0806  -0.2640  -1.2903
 B5F  O61  O  OP    -1  -0.896   2.1452   4.0598  -0.3689
 B5F  O62  O  OP    -1  -0.998  -0.0743   4.3186   0.8873
 B5F  O63  O  O      0  -0.854   2.0359   3.6331   2.1667
 B5F  H3   H  HCR6   0   0.215   3.7285  -2.2585   0.0359
 B5F  H5   H  HCR6   0   0.212   3.5104   1.9464   0.8335
 B5F  H2'  H  HCR6   0   0.189  -0.8523  -0.4277   2.0770
 B5F  H4'  H  HCR6   0   0.207  -4.3553  -0.4913  -0.4072
 B5F  H6'  H  HCR6   0   0.179  -0.4607  -0.1936  -2.1773

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    1.485  0.020  1.485
 B5F  C1   C2   aromatic  1.402  0.020  1.402
 B5F  C1   C6   aromatic  1.406  0.020  1.406
 B5F  O2   C2   single    1.338  0.020  1.338
 B5F  C2   C3   aromatic  1.397  0.020  1.397
 B5F  P2   O2   single    1.734  0.020  1.734
 B5F  O21  P2   deloc     1.524  0.020  1.524
 B5F  P2   O23  deloc     1.520  0.020  1.520
 B5F  P2   O22  deloc     1.519  0.020  1.519
 B5F  C3   C4   aromatic  1.395  0.020  1.395
 B5F  C3   H3   single    0.930  0.020  1.080
 B5F  C5   C4   aromatic  1.395  0.020  1.395
 B5F  C4   O4   single    1.346  0.020  1.346
 B5F  O4   P4   single    1.736  0.020  1.736
 B5F  O42  P4   deloc     1.519  0.020  1.519
 B5F  P4   O43  deloc     1.521  0.020  1.521
 B5F  P4   O41  deloc     1.522  0.020  1.522
 B5F  C6   C5   aromatic  1.401  0.020  1.401
 B5F  C5   H5   single    0.930  0.020  1.080
 B5F  C6   O6   single    1.335  0.020  1.335
 B5F  O6   P6   single    1.737  0.020  1.737
 B5F  O63  P6   deloc     1.520  0.020  1.520
 B5F  O61  P6   deloc     1.519  0.020  1.519
 B5F  P6   O62  deloc     1.521  0.020  1.521
 B5F  C6'  C1'  aromatic  1.389  0.020  1.389
 B5F  C2'  C1'  aromatic  1.388  0.020  1.388
 B5F  C3'  C2'  aromatic  1.401  0.020  1.401
 B5F  C2'  H2'  single    0.930  0.020  1.080
 B5F  C4'  C3'  aromatic  1.399  0.020  1.399
 B5F  O3'  C3'  single    1.338  0.020  1.338
 B5F  P3'  O3'  single    1.740  0.020  1.740
 B5F  O32  P3'  deloc     1.518  0.020  1.518
 B5F  O31  P3'  deloc     1.522  0.020  1.522
 B5F  P3'  O33  deloc     1.519  0.020  1.519
 B5F  C4'  C5'  aromatic  1.399  0.020  1.399
 B5F  C4'  H4'  single    0.930  0.020  1.080
 B5F  O5'  C5'  single    1.341  0.020  1.341
 B5F  C5'  C6'  aromatic  1.399  0.020  1.399
 B5F  O5'  P5'  single    1.740  0.020  1.740
 B5F  O51  P5'  deloc     1.518  0.020  1.518
 B5F  P5'  O53  deloc     1.521  0.020  1.521
 B5F  P5'  O52  deloc     1.521  0.020  1.521
 B5F  C6'  H6'  single    0.930  0.020  1.080

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   120.26  3.000
 B5F  C6   C1   C2   119.64  3.000
 B5F  C1'  C1   C2   120.08  3.000
 B5F  C3   C2   O2   123.17  3.000
 B5F  C3   C2   C1   119.76  3.000
 B5F  O2   C2   C1   117.06  3.000
 B5F  P2   O2   C2   125.45  3.000
 B5F  O23  P2   O22  115.65  3.000
 B5F  O22  P2   O21  114.93  3.000
 B5F  O23  P2   O21  114.36  3.000
 B5F  O22  P2   O2   104.50  3.000
 B5F  O23  P2   O2    99.36  3.000
 B5F  O21  P2   O2   105.57  3.000
 B5F  H3   C3   C4   119.78  3.000
 B5F  H3   C3   C2   119.97  3.000
 B5F  C4   C3   C2   120.24  3.000
 B5F  C5   C4   O4   122.87  3.000
 B5F  O4   C4   C3   116.45  3.000
 B5F  C5   C4   C3   120.66  3.000
 B5F  P4   O4   C4   124.69  3.000
 B5F  O43  P4   O42  115.64  3.000
 B5F  O43  P4   O41  114.56  3.000
 B5F  O42  P4   O41  115.24  3.000
 B5F  O41  P4   O4    98.97  3.000
 B5F  O43  P4   O4   105.49  3.000
 B5F  O42  P4   O4   104.26  3.000
 B5F  H5   C5   C6   120.93  3.000
 B5F  H5   C5   C4   119.83  3.000
 B5F  C6   C5   C4   119.23  3.000
 B5F  O6   C6   C5   123.67  3.000
 B5F  O6   C6   C1   115.87  3.000
 B5F  C5   C6   C1   120.46  3.000
 B5F  P6   O6   C6   127.18  3.000
 B5F  O63  P6   O62  114.74  3.000
 B5F  O62  P6   O61  114.99  3.000
 B5F  O63  P6   O61  115.74  3.000
 B5F  O62  P6   O6    99.03  3.000
 B5F  O61  P6   O6   104.55  3.000
 B5F  O63  P6   O6   105.06  3.000
 B5F  C6'  C1'  C2'  119.07  3.000
 B5F  C2'  C1'  C1   120.09  3.000
 B5F  C6'  C1'  C1   120.85  3.000
 B5F  H2'  C2'  C3'  119.03  3.000
 B5F  H2'  C2'  C1'  119.88  3.000
 B5F  C3'  C2'  C1'  121.08  3.000
 B5F  C4'  C3'  O3'  124.32  3.000
 B5F  O3'  C3'  C2'  116.08  3.000
 B5F  C4'  C3'  C2'  119.60  3.000
 B5F  P3'  O3'  C3'  127.31  3.000
 B5F  O33  P3'  O32  115.81  3.000
 B5F  O33  P3'  O31  114.94  3.000
 B5F  O32  P3'  O31  115.16  3.000
 B5F  O33  P3'  O3'  104.86  3.000
 B5F  O31  P3'  O3'   98.70  3.000
 B5F  O32  P3'  O3'  104.49  3.000
 B5F  H4'  C4'  C5'  119.78  3.000
 B5F  H4'  C4'  C3'  120.64  3.000
 B5F  C5'  C4'  C3'  119.53  3.000
 B5F  C6'  C5'  O5'  116.59  3.000
 B5F  C6'  C5'  C4'  119.90  3.000
 B5F  O5'  C5'  C4'  123.48  3.000
 B5F  P5'  O5'  C5'  125.79  3.000
 B5F  O53  P5'  O52  114.62  3.000
 B5F  O52  P5'  O51  115.39  3.000
 B5F  O53  P5'  O51  115.76  3.000
 B5F  O52  P5'  O5'   98.83  3.000
 B5F  O53  P5'  O5'  105.25  3.000
 B5F  O51  P5'  O5'  104.15  3.000
 B5F  H6'  C6'  C5'  119.26  3.000
 B5F  H6'  C6'  C1'  119.91  3.000
 B5F  C5'  C6'  C1'  120.82  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     28.08  30.0  2
 B5F  Var_02    C5   C4   O4   P4    -42.03  30.0  2
 B5F  Var_03    C4'  C3'  O3'  P3'    -5.05  30.0  2
 B5F  Var_04    C6'  C5'  O5'  P5'  -151.59  30.0  2
 B5F  Var_05    O21  P2   O2   C2    -67.04  30.0  3
 B5F  Var_06    O42  P4   O4   C4    -48.76  30.0  3
 B5F  Var_07    O63  P6   O6   C6    -59.25  30.0  3
 B5F  Var_08    O32  P3'  O3'  C3'   -61.68  30.0  3
 B5F  Var_09    O51  P5'  O5'  C5'    52.56  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

