# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 16:42:14 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 8-chloranyl-9-oxidanylidene-xanthene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2C(=O)c3c(Cl)cccc3Oc2c1
#
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
 J5R  J5R  "8-chloranyl-9-oxidanylidene-xanthene-3-carboxylic acid"  ligand  25  19  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J5R
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
 J5R  CAD  C   C      0   0.412  -21.9444   0.7751   -2.4343
 J5R  CAE  C   CR66   0  -0.032  -21.1040  -0.3078   -8.8442
 J5R  CAF  C   CR66   0   0.342  -21.5564   0.9797   -8.5187
 J5R  CAG  C   CR6    0  -0.109  -20.9177  -0.5802  -10.2140
 J5R  CAH  C   CR16   0  -0.327  -21.8049   1.9496   -9.4858
 J5R  CAI  C   CR16   0  -0.208  -21.1596   0.3713  -11.1821
 J5R  CAJ  C   CR16   0  -0.261  -21.6028   1.6374  -10.8099
 J5R  CAK  C   CR66   0  -0.122  -21.1284  -0.7650   -6.4080
 J5R  CAL  C   CR66   0   0.389  -21.5827   0.5335   -6.2144
 J5R  CAM  C   CR6    0   0.445  -20.8543  -1.2733   -7.7557
 J5R  CAO  C   CR16   0  -0.283  -21.1958  -1.0820   -4.0174
 J5R  CAP  C   CR6    0  -0.099  -21.6574   0.2295   -3.8370
 J5R  CAQ  C   CR16   0  -0.285  -20.9397  -1.5701   -5.2778
 J5R  CAR  C   CR16   0  -0.386  -21.8517   1.0331   -4.9457
 J5R  OAC  O   O      0  -0.575  -22.4128   1.9258   -2.3800
 J5R  OAN  O   O      0  -0.474  -21.7807   1.3716   -7.2533
 J5R  OAS  O   OC    -1  -0.576  -21.6794   0.0140   -1.4874
 J5R  H1   H   HCR6   0   0.286  -22.1503   2.9295   -9.1843
 J5R  H2   H   HCR6   0   0.288  -21.0062   0.1335  -12.2252
 J5R  H3   H   HCR6   0   0.283  -21.7910   2.3804  -11.5731
 J5R  H4   H   HCR6   0   0.251  -21.0435  -1.7129   -3.1530
 J5R  H5   H   HCR6   0   0.262  -20.5881  -2.5849   -5.4087
 J5R  H6   H   HCR6   0   0.266  -22.2059   2.0492   -4.8310
 J5R  OAA  O   O      0  -0.392  -20.4503  -2.4065   -7.9359
 J5R  CLA  CL  CL     0  -0.095  -20.3795  -2.1210  -10.7749

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
 J5R  CAI  CAJ  aromatic  1.392  0.020  1.392
 J5R  CAI  CAG  aromatic  1.379  0.020  1.379
 J5R  CAJ  CAH  aromatic  1.375  0.020  1.375
 J5R  CLA  CAG  single    1.726  0.020  1.726
 J5R  CAG  CAE  aromatic  1.409  0.020  1.409
 J5R  CAH  CAF  aromatic  1.392  0.020  1.392
 J5R  CAE  CAF  aromatic  1.403  0.020  1.403
 J5R  CAE  CAM  single    1.476  0.020  1.476
 J5R  CAF  OAN  single    1.344  0.020  1.344
 J5R  OAA  CAM  double    1.216  0.020  1.216
 J5R  CAM  CAK  single    1.466  0.020  1.466
 J5R  OAN  CAL  single    1.349  0.020  1.349
 J5R  CAK  CAL  aromatic  1.389  0.020  1.389
 J5R  CAK  CAQ  aromatic  1.400  0.020  1.400
 J5R  CAL  CAR  aromatic  1.390  0.020  1.390
 J5R  CAQ  CAO  aromatic  1.376  0.020  1.376
 J5R  CAR  CAP  aromatic  1.383  0.020  1.383
 J5R  CAO  CAP  aromatic  1.402  0.020  1.402
 J5R  CAP  CAD  single    1.532  0.020  1.532
 J5R  CAD  OAC  deloc     1.244  0.020  1.244
 J5R  CAD  OAS  deloc     1.243  0.020  1.243
 J5R  CAH  H1   single    0.930  0.020  1.080
 J5R  CAI  H2   single    0.930  0.020  1.080
 J5R  CAJ  H3   single    0.930  0.020  1.080
 J5R  CAO  H4   single    0.930  0.020  1.080
 J5R  CAQ  H5   single    0.930  0.020  1.080
 J5R  CAR  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
 J5R  OAS  CAD  OAC  127.84  3.000
 J5R  OAS  CAD  CAP  116.05  3.000
 J5R  OAC  CAD  CAP  116.11  3.000
 J5R  CAM  CAE  CAG  124.61  3.000
 J5R  CAM  CAE  CAF  118.92  3.000
 J5R  CAG  CAE  CAF  116.46  3.000
 J5R  OAN  CAF  CAH  114.92  3.000
 J5R  OAN  CAF  CAE  122.69  3.000
 J5R  CAH  CAF  CAE  122.40  3.000
 J5R  CLA  CAG  CAI  116.27  3.000
 J5R  CLA  CAG  CAE  121.99  3.000
 J5R  CAI  CAG  CAE  121.74  3.000
 J5R  H1   CAH  CAJ  121.39  3.000
 J5R  H1   CAH  CAF  119.63  3.000
 J5R  CAJ  CAH  CAF  118.98  3.000
 J5R  H2   CAI  CAJ  120.22  3.000
 J5R  H2   CAI  CAG  120.06  3.000
 J5R  CAJ  CAI  CAG  119.72  3.000
 J5R  H3   CAJ  CAI  119.44  3.000
 J5R  H3   CAJ  CAH  119.86  3.000
 J5R  CAI  CAJ  CAH  120.70  3.000
 J5R  CAQ  CAK  CAM  121.15  3.000
 J5R  CAQ  CAK  CAL  117.96  3.000
 J5R  CAM  CAK  CAL  120.89  3.000
 J5R  OAN  CAL  CAR  116.82  3.000
 J5R  CAR  CAL  CAK  121.77  3.000
 J5R  OAN  CAL  CAK  121.41  3.000
 J5R  OAA  CAM  CAK  121.42  3.000
 J5R  CAK  CAM  CAE  114.79  3.000
 J5R  OAA  CAM  CAE  123.79  3.000
 J5R  H4   CAO  CAQ  119.96  3.000
 J5R  H4   CAO  CAP  119.31  3.000
 J5R  CAQ  CAO  CAP  120.73  3.000
 J5R  CAR  CAP  CAO  119.12  3.000
 J5R  CAO  CAP  CAD  120.84  3.000
 J5R  CAR  CAP  CAD  120.04  3.000
 J5R  H5   CAQ  CAO  120.27  3.000
 J5R  H5   CAQ  CAK  119.04  3.000
 J5R  CAO  CAQ  CAK  120.69  3.000
 J5R  H6   CAR  CAP  120.44  3.000
 J5R  H6   CAR  CAL  119.84  3.000
 J5R  CAP  CAR  CAL  119.72  3.000
 J5R  CAL  OAN  CAF  121.29  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
 J5R  CONST_01  CAJ  CAI  CAG  CAE     0.00   0.0  0
 J5R  CONST_02  CAJ  CAH  CAF  CAE     0.00   0.0  0
 J5R  CONST_03  CAL  OAN  CAF  CAE     0.00   0.0  0
 J5R  CONST_04  CAL  CAK  CAM  CAE     0.00   0.0  0
 J5R  CONST_05  CAQ  CAK  CAM  CAE   180.00   0.0  0
 J5R  CONST_06  CAI  CAJ  CAH  CAF     0.00   0.0  0
 J5R  CONST_07  CAI  CAG  CAE  CAF     0.00   0.0  0
 J5R  CONST_08  CAK  CAM  CAE  CAF     0.00   0.0  0
 J5R  CONST_09  CAK  CAL  OAN  CAF     0.00   0.0  0
 J5R  CONST_10  CAR  CAL  OAN  CAF   180.00   0.0  0
 J5R  CONST_11  CAH  CAJ  CAI  CAG     0.00   0.0  0
 J5R  CONST_12  CAH  CAF  CAE  CAG     0.00   0.0  0
 J5R  CONST_13  CAK  CAM  CAE  CAG   180.00   0.0  0
 J5R  CONST_14  CAL  OAN  CAF  CAH   180.00   0.0  0
 J5R  CONST_15  CAP  CAR  CAL  CAK     0.00   0.0  0
 J5R  CONST_16  CAP  CAO  CAQ  CAK     0.00   0.0  0
 J5R  CONST_17  CAO  CAQ  CAK  CAL     0.00   0.0  0
 J5R  CONST_18  CAO  CAP  CAR  CAL     0.00   0.0  0
 J5R  CONST_19  CAR  CAL  CAK  CAQ     0.00   0.0  0
 J5R  CONST_20  CAR  CAP  CAO  CAQ     0.00   0.0  0
 J5R  CONST_21  CAL  CAR  CAP  CAD   180.00   0.0  0
 J5R  CONST_22  CAQ  CAO  CAP  CAD   180.00   0.0  0
 J5R  CONST_23  CLA  CAG  CAE  CAF   180.00   0.0  0
 J5R  CONST_24  OAA  CAM  CAE  CAF   180.00   0.0  0
 J5R  CONST_25  OAA  CAM  CAE  CAG     0.00   0.0  0
 J5R  CONST_26  CLA  CAG  CAI  CAJ   180.00   0.0  0
 J5R  CONST_27  OAA  CAM  CAK  CAL   180.00   0.0  0
 J5R  CONST_28  CLA  CAG  CAE  CAM     0.00   0.0  0
 J5R  CONST_29  OAA  CAM  CAK  CAQ     0.00   0.0  0
 J5R  CONST_30  H2   CAI  CAG  CAE   180.00   0.0  0
 J5R  CONST_31  H1   CAH  CAF  CAE   180.00   0.0  0
 J5R  CONST_32  H3   CAJ  CAH  CAF   180.00   0.0  0
 J5R  CONST_33  H3   CAJ  CAI  CAG   180.00   0.0  0
 J5R  CONST_34  H2   CAI  CAJ  CAH   180.00   0.0  0
 J5R  CONST_35  H1   CAH  CAJ  CAI   180.00   0.0  0
 J5R  CONST_36  H6   CAR  CAL  CAK   180.00   0.0  0
 J5R  CONST_37  H4   CAO  CAQ  CAK   180.00   0.0  0
 J5R  CONST_38  H5   CAQ  CAK  CAL   180.00   0.0  0
 J5R  CONST_39  H5   CAQ  CAK  CAM     0.00   0.0  0
 J5R  CONST_40  H6   CAR  CAP  CAO   180.00   0.0  0
 J5R  CONST_41  H5   CAQ  CAO  CAP   180.00   0.0  0
 J5R  CONST_42  H4   CAO  CAP  CAR   180.00   0.0  0
 J5R  CONST_43  H1   CAH  CAF  OAN     0.00   0.0  0
 J5R  CONST_44  H6   CAR  CAL  OAN     0.00   0.0  0
 J5R  Var_01    OAC  CAD  CAP  CAO  -176.57  30.0  2
 J5R  Var_02    OAS  CAD  CAP  CAO     3.50  30.0  2
 J5R  Var_03    OAC  CAD  CAP  CAR     3.50  30.0  2
 J5R  Var_04    OAS  CAD  CAP  CAR  -176.43  30.0  2

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
 J5R  plan-1  CAE  0.020
 J5R  plan-1  CAK  0.020
 J5R  plan-1  CAM  0.020
 J5R  plan-1  OAA  0.020
 J5R  plan-2  CAE  0.020
 J5R  plan-2  CAF  0.020
 J5R  plan-2  CAG  0.020
 J5R  plan-2  CAH  0.020
 J5R  plan-2  CAI  0.020
 J5R  plan-2  CAJ  0.020
 J5R  plan-2  CAM  0.020
 J5R  plan-2  OAN  0.020
 J5R  plan-2  H1   0.020
 J5R  plan-2  H2   0.020
 J5R  plan-2  H3   0.020
 J5R  plan-2  CLA  0.020
 J5R  plan-3  CAD  0.020
 J5R  plan-3  CAK  0.020
 J5R  plan-3  CAL  0.020
 J5R  plan-3  CAM  0.020
 J5R  plan-3  CAO  0.020
 J5R  plan-3  CAP  0.020
 J5R  plan-3  CAQ  0.020
 J5R  plan-3  CAR  0.020
 J5R  plan-3  OAN  0.020
 J5R  plan-3  H4   0.020
 J5R  plan-3  H5   0.020
 J5R  plan-3  H6   0.020
 J5R  plan-4  CAD  0.020
 J5R  plan-4  CAP  0.020
 J5R  plan-4  OAC  0.020
 J5R  plan-4  OAS  0.020

