# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:02:48 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: [1-hydroxy-2-(1,1':4',1''-terphenyl-3-yl)ethane-1,1-diyl]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(Cc1cccc(c1)c2ccc(cc2)c3ccccc3)([P](O)(O)=O)[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
 B28  B28  '[1-hydroxy-2-(1,1':4',1''-terphenyl-3-yl)ethane-1,1-diyl]bis(phosphonic acid)'  ligand  45  29  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B28
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
 B28  CAM   C  CR16   0  -0.315   8.6332  -3.6354   3.1019
 B28  CAI   C  CR16   0  -0.240   9.7074  -4.1804   3.7899
 B28  CAH   C  CR16   0  -0.268  10.9810  -3.6486   3.6349
 B28  CAJ   C  CR16   0  -0.240  11.1701  -2.5676   2.7837
 B28  CAN   C  CR16   0  -0.315  10.0951  -2.0221   2.0975
 B28  CAW   C  CR6    0   0.094   8.8085  -2.5460   2.2453
 B28  CAX   C  CR6    0   0.077   7.6645  -1.9579   1.5211
 B28  CAQ   C  CR16   0  -0.301   7.8129  -1.4414   0.2328
 B28  CAS   C  CR16   0  -0.300   6.7405  -0.8793  -0.4408
 B28  CAP   C  CR16   0  -0.304   6.3985  -1.8907   2.1071
 B28  CAR   C  CR16   0  -0.323   5.3246  -1.3299   1.4367
 B28  CAY   C  CR6    0   0.052   5.4769  -0.8128   0.1466
 B28  CAZ   C  CR6    0   0.103   4.3208  -0.1993  -0.5343
 B28  CAT   C  CR16   0  -0.369   3.0492  -0.7307  -0.3307
 B28  CAO   C  CR16   0  -0.345   4.4619   0.9463  -1.3210
 B28  CAK   C  CR16   0  -0.237   3.3368   1.5479  -1.8638
 B28  CAL   C  CR16   0  -0.353   2.0730   1.0245  -1.6145
 B28  CAV   C  CR6    0   0.172   1.9065  -0.1279  -0.8487
 B28  CAU   C  CH2    0  -0.534   0.5341  -0.6679  -0.5649
 B28  CBA   C  CT     0  -0.278   0.0273  -0.4174   0.8774
 B28  PBB   P  P      0   1.194   0.8761  -1.5687   2.1168
 B28  OAD   O  OP    -1  -0.891   1.3942  -2.8073   1.3663
 B28  OAE   O  O      0  -0.891   2.0184  -0.6183   2.6051
 B28  OAA   O  OP    -1  -0.883  -0.0725  -1.9265   3.2611
 B28  PBC   P  P      0   1.171  -1.8393  -0.5358   0.8504
 B28  OAF   O  O      0  -0.935  -2.2906   0.4109  -0.2861
 B28  OAG   O  OP    -1  -0.933  -2.1379  -2.0091   0.5246
 B28  OAB   O  OP    -1  -0.919  -2.3681  -0.0620   2.2103
 B28  OAC   O  OH1    0  -0.755   0.3973   0.9041   1.2847
 B28  HAM   H  HCR6   0   0.253   7.6509  -4.0760   3.2207
 B28  HAI   H  HCR6   0   0.257   9.5502  -5.0283   4.4440
 B28  HAH   H  HCR6   0   0.256  11.8181  -4.0716   4.1747
 B28  HAJ   H  HCR6   0   0.256  12.1566  -2.1398   2.6599
 B28  HAN   H  HCR6   0   0.253  10.2557  -1.1646   1.4559
 B28  HAQ   H  HCR6   0   0.249   8.7729  -1.4979  -0.2655
 B28  HAS   H  HCR6   0   0.246   6.8901  -0.5078  -1.4473
 B28  HAP   H  HCR6   0   0.248   6.2517  -2.2533   3.1172
 B28  HAR   H  HCR6   0   0.288   4.3584  -1.2518   1.9274
 B28  HAT   H  HCR6   0   0.261   2.9259  -1.6359   0.2501
 B28  HAO   H  HCR6   0   0.236   5.4399   1.3842  -1.4825
 B28  HAK   H  HCR6   0   0.238   3.4427   2.4422  -2.4658
 B28  HAL   H  HCR6   0   0.226   1.1999   1.5167  -2.0280
 B28  HAU1  H  HCH2   0   0.201   0.4992  -1.7404  -0.7568
 B28  HAU2  H  HCH2   0   0.196  -0.1624  -0.1898  -1.2588
 B28  HOAC  H  HOH1   0   0.406   1.2042   0.7094   1.8143

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
 B28  CAM  CAI   aromatic  1.387  0.020  1.387
 B28  CAM  CAW   aromatic  1.397  0.020  1.397
 B28  CAM  HAM   single    0.930  0.020  1.080
 B28  CAI  CAH   aromatic  1.389  0.020  1.389
 B28  CAI  HAI   single    0.930  0.020  1.080
 B28  CAH  CAJ   aromatic  1.389  0.020  1.389
 B28  CAH  HAH   single    0.930  0.020  1.080
 B28  CAJ  CAN   aromatic  1.387  0.020  1.387
 B28  CAJ  HAJ   single    0.930  0.020  1.080
 B28  CAN  CAW   aromatic  1.397  0.020  1.397
 B28  CAN  HAN   single    0.930  0.020  1.080
 B28  CAW  CAX   single    1.476  0.020  1.476
 B28  CAX  CAP   aromatic  1.397  0.020  1.397
 B28  CAX  CAQ   aromatic  1.396  0.020  1.396
 B28  CAQ  CAS   aromatic  1.386  0.020  1.386
 B28  CAQ  HAQ   single    0.930  0.020  1.080
 B28  CAS  CAY   aromatic  1.395  0.020  1.395
 B28  CAS  HAS   single    0.930  0.020  1.080
 B28  CAP  CAR   aromatic  1.385  0.020  1.385
 B28  CAP  HAP   single    0.930  0.020  1.080
 B28  CAR  CAY   aromatic  1.398  0.020  1.398
 B28  CAR  HAR   single    0.930  0.020  1.080
 B28  CAY  CAZ   single    1.475  0.020  1.475
 B28  CAZ  CAT   aromatic  1.393  0.020  1.393
 B28  CAZ  CAO   aromatic  1.397  0.020  1.397
 B28  CAT  CAV   aromatic  1.392  0.020  1.392
 B28  CAT  HAT   single    0.930  0.020  1.080
 B28  CAO  CAK   aromatic  1.387  0.020  1.387
 B28  CAO  HAO   single    0.930  0.020  1.080
 B28  CAK  CAL   aromatic  1.390  0.020  1.390
 B28  CAK  HAK   single    0.930  0.020  1.080
 B28  CAL  CAV   aromatic  1.394  0.020  1.394
 B28  CAL  HAL   single    0.930  0.020  1.080
 B28  CAV  CAU   single    1.502  0.020  1.502
 B28  CAU  CBA   single    1.549  0.020  1.549
 B28  CAU  HAU1  single    0.970  0.020  1.090
 B28  CAU  HAU2  single    0.970  0.020  1.090
 B28  CBA  OAC   single    1.432  0.020  1.432
 B28  CBA  PBC   single    1.871  0.020  1.871
 B28  CBA  PBB   single    1.893  0.020  1.893
 B28  PBB  OAE   deloc     1.564  0.020  1.564
 B28  PBB  OAD   deloc     1.538  0.020  1.538
 B28  PBB  OAA   deloc     1.529  0.020  1.529
 B28  PBC  OAF   deloc     1.546  0.020  1.546
 B28  PBC  OAB   deloc     1.534  0.020  1.534
 B28  PBC  OAG   deloc     1.538  0.020  1.538
 B28  OAC  HOAC  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
 B28  HAM   CAM  CAW   119.89  3.000
 B28  HAM   CAM  CAI   119.22  3.000
 B28  CAW   CAM  CAI   120.88  3.000
 B28  HAI   CAI  CAH   120.04  3.000
 B28  HAI   CAI  CAM   119.67  3.000
 B28  CAH   CAI  CAM   120.29  3.000
 B28  HAH   CAH  CAJ   120.31  3.000
 B28  HAH   CAH  CAI   120.26  3.000
 B28  CAJ   CAH  CAI   119.43  3.000
 B28  HAJ   CAJ  CAN   119.63  3.000
 B28  HAJ   CAJ  CAH   120.12  3.000
 B28  CAN   CAJ  CAH   120.25  3.000
 B28  HAN   CAN  CAW   119.75  3.000
 B28  HAN   CAN  CAJ   119.31  3.000
 B28  CAW   CAN  CAJ   120.93  3.000
 B28  CAX   CAW  CAN   120.83  3.000
 B28  CAX   CAW  CAM   120.95  3.000
 B28  CAN   CAW  CAM   118.23  3.000
 B28  CAP   CAX  CAQ   117.77  3.000
 B28  CAQ   CAX  CAW   121.19  3.000
 B28  CAP   CAX  CAW   121.05  3.000
 B28  HAQ   CAQ  CAS   118.92  3.000
 B28  HAQ   CAQ  CAX   119.97  3.000
 B28  CAS   CAQ  CAX   121.10  3.000
 B28  HAS   CAS  CAY   120.01  3.000
 B28  HAS   CAS  CAQ   118.94  3.000
 B28  CAY   CAS  CAQ   121.04  3.000
 B28  HAP   CAP  CAR   118.81  3.000
 B28  HAP   CAP  CAX   119.88  3.000
 B28  CAR   CAP  CAX   121.29  3.000
 B28  HAR   CAR  CAY   119.14  3.000
 B28  HAR   CAR  CAP   120.01  3.000
 B28  CAY   CAR  CAP   120.80  3.000
 B28  CAZ   CAY  CAR   119.63  3.000
 B28  CAZ   CAY  CAS   122.36  3.000
 B28  CAR   CAY  CAS   118.01  3.000
 B28  CAO   CAZ  CAT   119.17  3.000
 B28  CAO   CAZ  CAY   121.45  3.000
 B28  CAT   CAZ  CAY   119.29  3.000
 B28  HAT   CAT  CAV   117.92  3.000
 B28  HAT   CAT  CAZ   120.09  3.000
 B28  CAV   CAT  CAZ   121.99  3.000
 B28  HAO   CAO  CAK   119.92  3.000
 B28  HAO   CAO  CAZ   120.43  3.000
 B28  CAK   CAO  CAZ   119.62  3.000
 B28  HAK   CAK  CAL   119.95  3.000
 B28  HAK   CAK  CAO   119.76  3.000
 B28  CAL   CAK  CAO   120.27  3.000
 B28  HAL   CAL  CAV   119.26  3.000
 B28  HAL   CAL  CAK   119.52  3.000
 B28  CAV   CAL  CAK   121.22  3.000
 B28  CAU   CAV  CAL   120.68  3.000
 B28  CAU   CAV  CAT   121.61  3.000
 B28  CAL   CAV  CAT   117.68  3.000
 B28  HAU2  CAU  HAU1  107.35  3.000
 B28  HAU2  CAU  CBA   108.17  3.000
 B28  HAU1  CAU  CBA   108.21  3.000
 B28  HAU2  CAU  CAV   107.76  3.000
 B28  HAU1  CAU  CAV   110.47  3.000
 B28  CBA   CAU  CAV   114.63  3.000
 B28  OAC   CBA  PBC   108.69  3.000
 B28  PBC   CBA  PBB   114.74  3.000
 B28  OAC   CBA  PBB   105.03  3.000
 B28  PBB   CBA  CAU   111.39  3.000
 B28  PBC   CBA  CAU   107.62  3.000
 B28  OAC   CBA  CAU   109.24  3.000
 B28  OAA   PBB  OAE   111.20  3.000
 B28  OAA   PBB  OAD   112.69  3.000
 B28  OAE   PBB  OAD   113.30  3.000
 B28  OAA   PBB  CBA   110.75  3.000
 B28  OAD   PBB  CBA   108.75  3.000
 B28  OAE   PBB  CBA    99.34  3.000
 B28  OAB   PBC  OAG   114.62  3.000
 B28  OAG   PBC  OAF   111.97  3.000
 B28  OAB   PBC  OAF   111.21  3.000
 B28  OAG   PBC  CBA   104.91  3.000
 B28  OAB   PBC  CBA   108.16  3.000
 B28  OAF   PBC  CBA   105.25  3.000
 B28  HOAC  OAC  CBA   100.50  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
 B28  CONST_01  CAJ  CAH  CAI  CAM    0.00   0.0  0
 B28  CONST_02  CAJ  CAN  CAW  CAM    0.00   0.0  0
 B28  CONST_05  CAN  CAW  CAM  CAI    0.00   0.0  0
 B28  CONST_06  CAX  CAW  CAM  CAI  180.00   0.0  0
 B28  CONST_07  CAN  CAJ  CAH  CAI    0.00   0.0  0
 B28  CONST_08  CAW  CAM  CAI  CAH    0.00   0.0  0
 B28  CONST_09  CAW  CAN  CAJ  CAH    0.00   0.0  0
 B28  CONST_10  CAX  CAW  CAN  CAJ  180.00   0.0  0
 B28  CONST_13  CAR  CAP  CAX  CAW  180.00   0.0  0
 B28  CONST_14  CAS  CAQ  CAX  CAW  180.00   0.0  0
 B28  CONST_15  CAY  CAR  CAP  CAX    0.00   0.0  0
 B28  CONST_16  CAY  CAS  CAQ  CAX    0.00   0.0  0
 B28  CONST_17  CAR  CAP  CAX  CAQ    0.00   0.0  0
 B28  CONST_18  CAR  CAY  CAS  CAQ    0.00   0.0  0
 B28  CONST_19  CAZ  CAY  CAS  CAQ  180.00   0.0  0
 B28  CONST_20  CAP  CAX  CAQ  CAS    0.00   0.0  0
 B28  CONST_21  CAP  CAR  CAY  CAS    0.00   0.0  0
 B28  CONST_24  CAZ  CAY  CAR  CAP  180.00   0.0  0
 B28  CONST_27  CAV  CAT  CAZ  CAY  180.00   0.0  0
 B28  CONST_28  CAK  CAO  CAZ  CAY  180.00   0.0  0
 B28  CONST_29  CAL  CAV  CAT  CAZ    0.00   0.0  0
 B28  CONST_30  CAL  CAK  CAO  CAZ    0.00   0.0  0
 B28  CONST_31  CAK  CAO  CAZ  CAT    0.00   0.0  0
 B28  CONST_32  CAK  CAL  CAV  CAT    0.00   0.0  0
 B28  CONST_33  CAV  CAT  CAZ  CAO    0.00   0.0  0
 B28  CONST_34  CAV  CAL  CAK  CAO    0.00   0.0  0
 B28  CONST_35  CAU  CAV  CAT  CAZ  180.00   0.0  0
 B28  CONST_36  CAU  CAV  CAL  CAK  180.00   0.0  0
 B28  CONST_37  HAH  CAH  CAI  CAM  180.00   0.0  0
 B28  CONST_38  HAN  CAN  CAW  CAM  180.00   0.0  0
 B28  CONST_39  HAJ  CAJ  CAH  CAI  180.00   0.0  0
 B28  CONST_40  HAM  CAM  CAI  CAH  180.00   0.0  0
 B28  CONST_41  HAI  CAI  CAH  CAJ  180.00   0.0  0
 B28  CONST_42  HAP  CAP  CAX  CAW    0.00   0.0  0
 B28  CONST_43  HAQ  CAQ  CAX  CAW    0.00   0.0  0
 B28  CONST_44  HAR  CAR  CAP  CAX  180.00   0.0  0
 B28  CONST_45  HAS  CAS  CAQ  CAX  180.00   0.0  0
 B28  CONST_46  HAT  CAT  CAZ  CAY    0.00   0.0  0
 B28  CONST_47  HAO  CAO  CAZ  CAY    0.00   0.0  0
 B28  CONST_48  HAK  CAK  CAO  CAZ  180.00   0.0  0
 B28  CONST_49  HAL  CAL  CAV  CAT  180.00   0.0  0
 B28  Var_01    CBA  CAU  CAV  CAT   73.00  30.0  2
 B28  Var_02    OAC  CBA  CAU  CAV   40.60  30.0  3
 B28  Var_03    OAF  PBC  CBA  CAU  -51.74  30.0  3
 B28  Var_04    OAE  PBB  CBA  CAU   95.67  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
 B28  plan-1  CAM  0.020
 B28  plan-1  CAI  0.020
 B28  plan-1  CAH  0.020
 B28  plan-1  CAJ  0.020
 B28  plan-1  CAN  0.020
 B28  plan-1  CAW  0.020
 B28  plan-1  CAX  0.020
 B28  plan-1  HAM  0.020
 B28  plan-1  HAI  0.020
 B28  plan-1  HAH  0.020
 B28  plan-1  HAJ  0.020
 B28  plan-1  HAN  0.020
 B28  plan-2  CAW  0.020
 B28  plan-2  CAX  0.020
 B28  plan-2  CAQ  0.020
 B28  plan-2  CAS  0.020
 B28  plan-2  CAP  0.020
 B28  plan-2  CAR  0.020
 B28  plan-2  CAY  0.020
 B28  plan-2  CAZ  0.020
 B28  plan-2  HAQ  0.020
 B28  plan-2  HAS  0.020
 B28  plan-2  HAP  0.020
 B28  plan-2  HAR  0.020
 B28  plan-3  CAY  0.020
 B28  plan-3  CAZ  0.020
 B28  plan-3  CAT  0.020
 B28  plan-3  CAO  0.020
 B28  plan-3  CAK  0.020
 B28  plan-3  CAL  0.020
 B28  plan-3  CAV  0.020
 B28  plan-3  CAU  0.020
 B28  plan-3  HAT  0.020
 B28  plan-3  HAO  0.020
 B28  plan-3  HAK  0.020
 B28  plan-3  HAL  0.020

