# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:45:28 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: (1R)-4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)[C@@H](CCCc1cccc(Oc2ccccc2)c1)[S](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
 B65  B65  '(1R)-4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid'  ligand  44  25  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B65
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
 B65  CAL   C  CR16  0  -0.324  16.1521  54.5416  39.8779
 B65  CAH   C  CR16  0  -0.246  16.3218  55.7593  40.5235
 B65  CAG   C  CR16  0  -0.270  15.2260  56.5013  40.9425
 B65  CAI   C  CR16  0  -0.247  13.9460  56.0152  40.7082
 B65  CAM   C  CR16  0  -0.332  13.7601  54.7967  40.0719
 B65  CAU   C  CR6   0   0.349  14.8652  54.0634  39.6560
 B65  OAS   O  O2    0  -0.513  14.6139  52.9004  38.9873
 B65  CAV   C  CR6   0   0.343  15.5208  51.8751  39.0482
 B65  CAO   C  CR16  0  -0.377  15.9668  51.3340  37.8547
 B65  CAN   C  CR16  0  -0.323  15.9323  51.3529  40.2694
 B65  CAJ   C  CR16  0  -0.234  16.8034  50.2762  40.2726
 B65  CAK   C  CR16  0  -0.315  17.2554  49.7263  39.0789
 B65  CAT   C  CR6   0   0.117  16.8393  50.2461  37.8577
 B65  CAQ   C  CH2   0  -0.511  17.3423  49.6835  36.5563
 B65  CAP   C  CH2   0  -0.443  18.2786  50.6338  35.8052
 B65  CAR   C  CH2   0  -0.441  19.5257  50.9592  36.6229
 B65  CAW   C  CH1   0  -0.749  20.4006  52.0512  35.9954
 B65  PAX   P  P     0   1.407  20.9939  51.6248  34.3061
 B65  OAB   O  OH1   0  -0.727  22.3948  52.3689  34.0942
 B65  OAC   O  OH1   0  -0.732  21.4634  50.1176  34.5125
 B65  OAA   O  O     0  -0.687  19.9679  51.8936  33.2750
 B65  SAY   S  S     0   1.464  21.7705  52.5067  37.0759
 B65  OAF   O  OS    0  -0.637  22.2914  53.7906  36.6675
 B65  OAE   O  OS    0  -0.637  22.6477  51.3656  37.2344
 B65  OAD   O  OS    0  -0.704  21.0361  52.8079  38.4664
 B65  HAL   H  HCR6  0   0.272  17.0189  53.9819  39.5508
 B65  HAH   H  HCR6  0   0.262  17.3245  56.1292  40.6932
 B65  HAG   H  HCR6  0   0.256  15.3686  57.4485  41.4452
 B65  HAI   H  HCR6  0   0.261  13.0814  56.5826  41.0277
 B65  HAM   H  HCR6  0   0.268  12.7631  54.4146  39.8931
 B65  HAO   H  HCR6  0   0.263  15.6267  51.7607  36.9174
 B65  HAN   H  HCR6  0   0.275  15.5748  51.7738  41.2008
 B65  HAJ   H  HCR6  0   0.262  17.1284  49.8581  41.2164
 B65  HAK   H  HCR6  0   0.252  17.9372  48.8848  39.1006
 B65  HAQ   H  HCH2  0   0.248  17.8598  48.7392  36.7400
 B65  HAQA  H  HCH2  0   0.261  16.4955  49.4538  35.9049
 B65  HAP   H  HCH2  0   0.251  18.5437  50.1647  34.8573
 B65  HAPA  H  HCH2  0   0.239  17.7496  51.5580  35.5576
 B65  HAR   H  HCH2  0   0.261  19.1950  51.3170  37.5994
 B65  HARA  H  HCH2  0   0.269  20.1083  50.0525  36.7932
 B65  HAW   H  HCH1  0   0.362  19.8137  52.9696  35.8844
 B65  HAB   H  HOH1  0   0.500  22.3230  53.2885  33.8039
 B65  HAC   H  HOH1  0   0.504  21.5846  49.6193  33.6917
 B65  HAD   H  H     0   0.505  20.9795  52.0234  39.0359

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
 B65  CAL  CAH   aromatic  1.389  0.020  1.389
 B65  CAL  CAU   aromatic  1.391  0.020  1.391
 B65  CAH  CAG   aromatic  1.388  0.020  1.388
 B65  CAG  CAI   aromatic  1.389  0.020  1.389
 B65  CAI  CAM   aromatic  1.387  0.020  1.387
 B65  CAM  CAU   aromatic  1.390  0.020  1.390
 B65  CAU  OAS   single    1.365  0.020  1.365
 B65  OAS  CAV   single    1.370  0.020  1.370
 B65  CAV  CAO   aromatic  1.384  0.020  1.384
 B65  CAV  CAN   aromatic  1.390  0.020  1.390
 B65  CAO  CAT   aromatic  1.395  0.020  1.395
 B65  CAN  CAJ   aromatic  1.385  0.020  1.385
 B65  CAJ  CAK   aromatic  1.390  0.020  1.390
 B65  CAK  CAT   aromatic  1.391  0.020  1.391
 B65  CAT  CAQ   single    1.504  0.020  1.504
 B65  CAQ  CAP   single    1.531  0.020  1.531
 B65  CAP  CAR   single    1.526  0.020  1.526
 B65  CAR  CAW   single    1.534  0.020  1.534
 B65  CAW  PAX   single    1.841  0.020  1.841
 B65  CAW  SAY   single    1.803  0.020  1.803
 B65  PAX  OAB   single    1.600  0.020  1.600
 B65  PAX  OAC   single    1.592  0.020  1.592
 B65  PAX  OAA   double    1.479  0.020  1.479
 B65  SAY  OAF   double    1.444  0.020  1.444
 B65  SAY  OAE   double    1.448  0.020  1.448
 B65  SAY  OAD   single    1.601  0.020  1.601
 B65  CAL  HAL   single    0.930  0.020  1.080
 B65  CAH  HAH   single    0.930  0.020  1.080
 B65  CAG  HAG   single    0.930  0.020  1.080
 B65  CAI  HAI   single    0.930  0.020  1.080
 B65  CAM  HAM   single    0.930  0.020  1.080
 B65  CAO  HAO   single    0.930  0.020  1.080
 B65  CAN  HAN   single    0.930  0.020  1.080
 B65  CAJ  HAJ   single    0.930  0.020  1.080
 B65  CAK  HAK   single    0.930  0.020  1.080
 B65  CAQ  HAQ   single    0.970  0.020  1.090
 B65  CAQ  HAQA  single    0.970  0.020  1.090
 B65  CAP  HAP   single    0.970  0.020  1.090
 B65  CAP  HAPA  single    0.970  0.020  1.090
 B65  CAR  HAR   single    0.970  0.020  1.090
 B65  CAR  HARA  single    0.970  0.020  1.090
 B65  CAW  HAW   single    0.970  0.020  1.090
 B65  OAB  HAB   single    0.850  0.020  0.980
 B65  OAC  HAC   single    0.850  0.020  0.980
 B65  OAD  HAD   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
 B65  HAL   CAL  CAU  121.00  3.000
 B65  HAL   CAL  CAH  119.74  3.000
 B65  CAU   CAL  CAH  119.26  3.000
 B65  HAH   CAH  CAG  120.09  3.000
 B65  HAH   CAH  CAL  119.07  3.000
 B65  CAG   CAH  CAL  120.84  3.000
 B65  HAG   CAG  CAI  120.41  3.000
 B65  HAG   CAG  CAH  120.28  3.000
 B65  CAI   CAG  CAH  119.30  3.000
 B65  HAI   CAI  CAM  119.27  3.000
 B65  HAI   CAI  CAG  120.18  3.000
 B65  CAM   CAI  CAG  120.55  3.000
 B65  HAM   CAM  CAU  119.77  3.000
 B65  HAM   CAM  CAI  120.61  3.000
 B65  CAU   CAM  CAI  119.62  3.000
 B65  OAS   CAU  CAM  116.73  3.000
 B65  OAS   CAU  CAL  122.79  3.000
 B65  CAM   CAU  CAL  120.43  3.000
 B65  CAV   OAS  CAU  119.60  3.000
 B65  CAN   CAV  CAO  121.00  3.000
 B65  CAN   CAV  OAS  121.06  3.000
 B65  CAO   CAV  OAS  117.87  3.000
 B65  HAO   CAO  CAT  120.33  3.000
 B65  HAO   CAO  CAV  119.36  3.000
 B65  CAT   CAO  CAV  120.31  3.000
 B65  HAN   CAN  CAJ  120.52  3.000
 B65  HAN   CAN  CAV  120.78  3.000
 B65  CAJ   CAN  CAV  118.69  3.000
 B65  HAJ   CAJ  CAK  119.90  3.000
 B65  HAJ   CAJ  CAN  119.42  3.000
 B65  CAK   CAJ  CAN  120.67  3.000
 B65  HAK   CAK  CAT  119.75  3.000
 B65  HAK   CAK  CAJ  119.66  3.000
 B65  CAT   CAK  CAJ  120.59  3.000
 B65  CAQ   CAT  CAK  121.31  3.000
 B65  CAQ   CAT  CAO  119.93  3.000
 B65  CAK   CAT  CAO  118.73  3.000
 B65  HAQA  CAQ  HAQ  106.60  3.000
 B65  HAQA  CAQ  CAP  108.18  3.000
 B65  HAQ   CAQ  CAP  109.23  3.000
 B65  HAQA  CAQ  CAT  109.59  3.000
 B65  HAQ   CAQ  CAT  109.65  3.000
 B65  CAP   CAQ  CAT  113.38  3.000
 B65  HAPA  CAP  HAP  106.52  3.000
 B65  HAPA  CAP  CAR  109.66  3.000
 B65  HAP   CAP  CAR  111.03  3.000
 B65  HAPA  CAP  CAQ  109.87  3.000
 B65  HAP   CAP  CAQ  107.95  3.000
 B65  CAR   CAP  CAQ  111.67  3.000
 B65  HARA  CAR  HAR  107.14  3.000
 B65  HARA  CAR  CAW  110.55  3.000
 B65  HAR   CAR  CAW  107.79  3.000
 B65  HARA  CAR  CAP  110.04  3.000
 B65  HAR   CAR  CAP  107.56  3.000
 B65  CAW   CAR  CAP  113.50  3.000
 B65  HAW   CAW  SAY  104.83  3.000
 B65  HAW   CAW  PAX  105.90  3.000
 B65  SAY   CAW  PAX  111.32  3.000
 B65  HAW   CAW  CAR  109.44  3.000
 B65  SAY   CAW  CAR  111.60  3.000
 B65  PAX   CAW  CAR  113.24  3.000
 B65  OAA   PAX  OAC  117.83  3.000
 B65  OAA   PAX  OAB  115.49  3.000
 B65  OAC   PAX  OAB  101.49  3.000
 B65  OAA   PAX  CAW  111.97  3.000
 B65  OAC   PAX  CAW  101.27  3.000
 B65  OAB   PAX  CAW  107.22  3.000
 B65  HAB   OAB  PAX  114.64  3.000
 B65  HAC   OAC  PAX  114.48  3.000
 B65  OAD   SAY  OAE  109.33  3.000
 B65  OAD   SAY  OAF  104.11  3.000
 B65  OAE   SAY  OAF  120.86  3.000
 B65  OAD   SAY  CAW  102.68  3.000
 B65  OAE   SAY  CAW  109.07  3.000
 B65  OAF   SAY  CAW  109.21  3.000
 B65  HAD   OAD  SAY  112.59  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
 B65  CONST_01  CAI  CAG  CAH  CAL     0.00   0.0  0
 B65  CONST_02  CAI  CAM  CAU  CAL     0.00   0.0  0
 B65  CONST_03  CAM  CAU  CAL  CAH     0.00   0.0  0
 B65  CONST_04  CAM  CAI  CAG  CAH     0.00   0.0  0
 B65  CONST_05  CAU  CAL  CAH  CAG     0.00   0.0  0
 B65  CONST_06  CAU  CAM  CAI  CAG     0.00   0.0  0
 B65  CONST_07  CAK  CAT  CAO  CAV     0.00   0.0  0
 B65  CONST_08  CAK  CAJ  CAN  CAV     0.00   0.0  0
 B65  CONST_09  CAJ  CAN  CAV  CAO     0.00   0.0  0
 B65  CONST_10  CAJ  CAK  CAT  CAO     0.00   0.0  0
 B65  CONST_11  CAT  CAO  CAV  CAN     0.00   0.0  0
 B65  CONST_12  CAT  CAK  CAJ  CAN     0.00   0.0  0
 B65  CONST_13  OAS  CAU  CAL  CAH   180.00   0.0  0
 B65  CONST_14  OAS  CAU  CAM  CAI   180.00   0.0  0
 B65  CONST_15  CAT  CAO  CAV  OAS   180.00   0.0  0
 B65  CONST_16  CAJ  CAN  CAV  OAS   180.00   0.0  0
 B65  CONST_17  CAQ  CAT  CAO  CAV   180.00   0.0  0
 B65  CONST_18  CAQ  CAT  CAK  CAJ   180.00   0.0  0
 B65  CONST_19  HAG  CAG  CAH  CAL   180.00   0.0  0
 B65  CONST_20  HAM  CAM  CAU  CAL   180.00   0.0  0
 B65  CONST_21  HAI  CAI  CAG  CAH   180.00   0.0  0
 B65  CONST_22  HAL  CAL  CAH  CAG   180.00   0.0  0
 B65  CONST_23  HAH  CAH  CAG  CAI   180.00   0.0  0
 B65  CONST_24  HAJ  CAJ  CAN  CAV   180.00   0.0  0
 B65  CONST_25  HAN  CAN  CAV  CAO   180.00   0.0  0
 B65  CONST_26  HAK  CAK  CAT  CAO   180.00   0.0  0
 B65  CONST_27  HAO  CAO  CAV  CAN   180.00   0.0  0
 B65  Var_01    CAO  CAV  OAS  CAU  -127.25  30.0  2
 B65  Var_02    CAP  CAQ  CAT  CAO    67.80  30.0  2
 B65  Var_03    CAR  CAP  CAQ  CAT    60.77  30.0  3
 B65  Var_04    CAW  CAR  CAP  CAQ  -172.23  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 B65  chir_01  CAW  CAR  PAX  SAY  positiv

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
 B65  plan-1  CAL  0.020
 B65  plan-1  CAH  0.020
 B65  plan-1  CAG  0.020
 B65  plan-1  CAI  0.020
 B65  plan-1  CAM  0.020
 B65  plan-1  CAU  0.020
 B65  plan-1  OAS  0.020
 B65  plan-1  HAL  0.020
 B65  plan-1  HAH  0.020
 B65  plan-1  HAG  0.020
 B65  plan-1  HAI  0.020
 B65  plan-1  HAM  0.020
 B65  plan-2  OAS  0.020
 B65  plan-2  CAV  0.020
 B65  plan-2  CAO  0.020
 B65  plan-2  CAN  0.020
 B65  plan-2  CAJ  0.020
 B65  plan-2  CAK  0.020
 B65  plan-2  CAT  0.020
 B65  plan-2  CAQ  0.020
 B65  plan-2  HAO  0.020
 B65  plan-2  HAN  0.020
 B65  plan-2  HAJ  0.020
 B65  plan-2  HAK  0.020

