# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:02:50 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-bromophenyl hydrogen (S)-phenylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](=O)(Oc1cccc(Br)c1)c2ccccc2
#
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
 62Y  62Y  '3-bromophenyl hydrogen (S)-phenylphosphonate'  ligand  27  17  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_62Y
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
 62Y  CAB  C   CR16  0  -0.233   5.4654   1.2884  -0.2765
 62Y  CAC  C   CR16  0  -0.272   4.2156   1.0171  -0.8136
 62Y  CAD  C   CR6   0  -0.253   3.3510   0.1415  -0.1578
 62Y  CAE  C   CR16  0  -0.263   3.7506  -0.4665   1.0327
 62Y  CAF  C   CR16  0  -0.235   5.0003  -0.1896   1.5644
 62Y  CAG  C   CR16  0  -0.248   5.8578   0.6867   0.9111
 62Y  OAH  O   O     0  -0.673   1.7293  -1.4982  -1.7405
 62Y  OAI  O   OH1   0  -0.730   1.2976   0.9852  -1.7631
 62Y  OAK  O   O2    0  -0.624   0.8260  -0.3269   0.4050
 62Y  CAL  C   CR6   0   0.375  -0.4734  -0.7666   0.2961
 62Y  CAM  C   CR16  0  -0.306  -0.7540  -2.1227   0.3501
 62Y  CAN  C   CR16  0  -0.247  -2.0754  -2.5365   0.2812
 62Y  CAO  C   CR16  0  -0.235  -3.1080  -1.6177   0.1518
 62Y  CAP  C   CR6   0  -0.103  -2.7939  -0.2679   0.0985
 62Y  CAQ  C   CR16  0  -0.293  -1.4820   0.1768   0.1660
 62Y  P    P   P     0   1.375   1.7844  -0.2771  -0.9094
 62Y  BR   BR  BR    0  -0.034  -4.1804   1.0006  -0.0726
 62Y  HAB  H   HCR6  0   0.270   6.1305   1.9720  -0.7866
 62Y  HAC  H   HCR6  0   0.275   3.9250   1.4929  -1.7414
 62Y  HAG  H   HCR6  0   0.271   6.8329   0.9006   1.3286
 62Y  HAE  H   HCR6  0   0.274   3.0943  -1.1514   1.5533
 62Y  HAF  H   HCR6  0   0.270   5.3042  -0.6576   2.4910
 62Y  HAI  H   HOH1  0   0.499   1.2837   1.8360  -1.3035
 62Y  HAM  H   HCR6  0   0.283   0.0449  -2.8434   0.4571
 62Y  HAQ  H   HCR6  0   0.294  -1.2396   1.2309   0.1344
 62Y  HAN  H   HCR6  0   0.279  -2.3071  -3.5921   0.3257
 62Y  HAO  H   HCR6  0   0.284  -4.1335  -1.9564   0.0985

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
 62Y  CAB  CAC  aromatic  1.387  0.020  1.387
 62Y  CAB  CAG  aromatic  1.388  0.020  1.388
 62Y  CAC  CAD  aromatic  1.394  0.020  1.394
 62Y  CAD  CAE  aromatic  1.395  0.020  1.395
 62Y  CAD  P    single    1.787  0.020  1.787
 62Y  CAE  CAF  aromatic  1.386  0.020  1.386
 62Y  CAF  CAG  aromatic  1.389  0.020  1.389
 62Y  OAH  P    double    1.478  0.020  1.478
 62Y  OAI  P    single    1.600  0.020  1.600
 62Y  OAK  CAL  single    1.376  0.020  1.376
 62Y  OAK  P    single    1.627  0.020  1.627
 62Y  CAL  CAM  aromatic  1.386  0.020  1.386
 62Y  CAL  CAQ  aromatic  1.387  0.020  1.387
 62Y  CAM  CAN  aromatic  1.386  0.020  1.386
 62Y  CAN  CAO  aromatic  1.388  0.020  1.388
 62Y  CAO  CAP  aromatic  1.387  0.020  1.387
 62Y  CAP  CAQ  aromatic  1.387  0.020  1.387
 62Y  CAP  BR   single    1.887  0.020  1.887
 62Y  CAB  HAB  single    0.930  0.020  1.080
 62Y  CAC  HAC  single    0.930  0.020  1.080
 62Y  CAG  HAG  single    0.930  0.020  1.080
 62Y  CAE  HAE  single    0.930  0.020  1.080
 62Y  CAF  HAF  single    0.930  0.020  1.080
 62Y  OAI  HAI  single    0.850  0.020  0.980
 62Y  CAM  HAM  single    0.930  0.020  1.080
 62Y  CAQ  HAQ  single    0.930  0.020  1.080
 62Y  CAN  HAN  single    0.930  0.020  1.080
 62Y  CAO  HAO  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
 62Y  HAB  CAB  CAG  120.24  3.000
 62Y  HAB  CAB  CAC  119.67  3.000
 62Y  CAG  CAB  CAC  120.09  3.000
 62Y  HAC  CAC  CAD  120.84  3.000
 62Y  HAC  CAC  CAB  119.20  3.000
 62Y  CAD  CAC  CAB  119.96  3.000
 62Y  P    CAD  CAE  120.52  3.000
 62Y  P    CAD  CAC  119.52  3.000
 62Y  CAE  CAD  CAC  119.83  3.000
 62Y  HAE  CAE  CAF  119.26  3.000
 62Y  HAE  CAE  CAD  120.84  3.000
 62Y  CAF  CAE  CAD  119.90  3.000
 62Y  HAF  CAF  CAG  120.16  3.000
 62Y  HAF  CAF  CAE  119.70  3.000
 62Y  CAG  CAF  CAE  120.14  3.000
 62Y  HAG  CAG  CAF  119.96  3.000
 62Y  HAG  CAG  CAB  119.95  3.000
 62Y  CAF  CAG  CAB  120.09  3.000
 62Y  HAI  OAI  P    116.42  3.000
 62Y  P    OAK  CAL  120.13  3.000
 62Y  CAQ  CAL  CAM  121.46  3.000
 62Y  CAQ  CAL  OAK  118.47  3.000
 62Y  CAM  CAL  OAK  120.06  3.000
 62Y  HAM  CAM  CAN  120.67  3.000
 62Y  HAM  CAM  CAL  120.43  3.000
 62Y  CAN  CAM  CAL  118.89  3.000
 62Y  HAN  CAN  CAO  119.37  3.000
 62Y  HAN  CAN  CAM  119.57  3.000
 62Y  CAO  CAN  CAM  121.06  3.000
 62Y  HAO  CAO  CAP  121.18  3.000
 62Y  HAO  CAO  CAN  120.18  3.000
 62Y  CAP  CAO  CAN  118.64  3.000
 62Y  BR   CAP  CAQ  118.94  3.000
 62Y  BR   CAP  CAO  119.43  3.000
 62Y  CAQ  CAP  CAO  121.63  3.000
 62Y  HAQ  CAQ  CAP  121.52  3.000
 62Y  HAQ  CAQ  CAL  120.16  3.000
 62Y  CAP  CAQ  CAL  118.32  3.000
 62Y  OAK  P    OAI  106.02  3.000
 62Y  OAK  P    OAH  114.01  3.000
 62Y  OAI  P    OAH  109.91  3.000
 62Y  OAK  P    CAD  100.59  3.000
 62Y  OAI  P    CAD  107.84  3.000
 62Y  OAH  P    CAD  117.56  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
 62Y  CONST_01  CAE  CAD  CAC  CAB    0.00   0.0  0
 62Y  CONST_02  CAE  CAF  CAG  CAB    0.00   0.0  0
 62Y  CONST_03  CAF  CAG  CAB  CAC    0.00   0.0  0
 62Y  CONST_04  CAF  CAE  CAD  CAC    0.00   0.0  0
 62Y  CONST_05  CAG  CAB  CAC  CAD    0.00   0.0  0
 62Y  CONST_06  CAG  CAF  CAE  CAD    0.00   0.0  0
 62Y  CONST_07  CAO  CAN  CAM  CAL    0.00   0.0  0
 62Y  CONST_08  CAO  CAP  CAQ  CAL    0.00   0.0  0
 62Y  CONST_09  CAP  CAQ  CAL  CAM    0.00   0.0  0
 62Y  CONST_10  CAP  CAO  CAN  CAM    0.00   0.0  0
 62Y  CONST_11  CAQ  CAL  CAM  CAN    0.00   0.0  0
 62Y  CONST_12  CAQ  CAP  CAO  CAN    0.00   0.0  0
 62Y  CONST_13  P    CAD  CAC  CAB  180.00   0.0  0
 62Y  CONST_14  P    CAD  CAE  CAF  180.00   0.0  0
 62Y  CONST_15  CAN  CAM  CAL  OAK  180.00   0.0  0
 62Y  CONST_16  CAP  CAQ  CAL  OAK  180.00   0.0  0
 62Y  CONST_17  BR   CAP  CAQ  CAL  180.00   0.0  0
 62Y  CONST_18  BR   CAP  CAO  CAN  180.00   0.0  0
 62Y  CONST_19  HAF  CAF  CAG  CAB  180.00   0.0  0
 62Y  CONST_20  HAG  CAG  CAB  CAC  180.00   0.0  0
 62Y  CONST_21  HAE  CAE  CAD  CAC  180.00   0.0  0
 62Y  CONST_22  HAB  CAB  CAC  CAD  180.00   0.0  0
 62Y  CONST_23  HAC  CAC  CAD  CAE  180.00   0.0  0
 62Y  CONST_24  HAN  CAN  CAM  CAL  180.00   0.0  0
 62Y  CONST_25  HAQ  CAQ  CAL  CAM  180.00   0.0  0
 62Y  CONST_26  HAO  CAO  CAN  CAM  180.00   0.0  0
 62Y  CONST_27  HAM  CAM  CAN  CAO  180.00   0.0  0
 62Y  Var_01    OAH  P    CAD  CAC   93.68  30.0  2

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
 62Y  chir_01  P  OAH  OAI  OAK  both

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
 62Y  plan-1  CAB  0.020
 62Y  plan-1  CAC  0.020
 62Y  plan-1  CAD  0.020
 62Y  plan-1  CAE  0.020
 62Y  plan-1  CAF  0.020
 62Y  plan-1  CAG  0.020
 62Y  plan-1  P    0.020
 62Y  plan-1  HAB  0.020
 62Y  plan-1  HAC  0.020
 62Y  plan-1  HAG  0.020
 62Y  plan-1  HAE  0.020
 62Y  plan-1  HAF  0.020
 62Y  plan-2  OAK  0.020
 62Y  plan-2  CAL  0.020
 62Y  plan-2  CAM  0.020
 62Y  plan-2  CAN  0.020
 62Y  plan-2  CAO  0.020
 62Y  plan-2  CAP  0.020
 62Y  plan-2  CAQ  0.020
 62Y  plan-2  BR   0.020
 62Y  plan-2  HAM  0.020
 62Y  plan-2  HAQ  0.020
 62Y  plan-2  HAN  0.020
 62Y  plan-2  HAO  0.020

