# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 05:13:58 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 4-chloranyl-9-oxidanylidene-xanthene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(Cl)c2Oc3ccccc3C(=O)c2c1
#
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
 HH9  HH9  "4-chloranyl-9-oxidanylidene-xanthene-2-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_HH9
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
 HH9  CAA  C   CR6    0  -0.107  -20.9905  -0.0166   -6.5185
 HH9  CAB  C   CR6    0   0.370  -21.9315   0.7856   -7.1610
 HH9  CAC  C   C1     0  -0.292  -20.0919  -0.7513   -7.3011
 HH9  CAD  C   C1     0  -0.334  -21.9849   0.8684   -8.5493
 HH9  CAE  C   C1     0  -0.244  -20.1363  -0.6807   -8.6755
 HH9  CAF  C   C1     0  -0.247  -21.0874   0.1337   -9.2963
 HH9  CAG  C   CR6    0   0.435  -20.9568  -0.0837   -5.0538
 HH9  CAH  C   CR66   0  -0.094  -21.9783   0.7266   -4.3784
 HH9  CAJ  C   CR66   0   0.453  -22.8692   1.4821   -5.1383
 HH9  CAK  C   CR16   0  -0.350  -22.0783   0.7489   -2.9853
 HH9  CAL  C   CR6    0  -0.097  -23.0488   1.4939   -2.3461
 HH9  CAM  C   CR6    0  -0.154  -23.8515   2.2396   -4.4983
 HH9  CAN  C   CR16   0  -0.265  -23.9388   2.2413   -3.1242
 HH9  CAO  C   C      0   0.414  -23.1603   1.5061   -0.8214
 HH9  OAI  O   O      0  -0.465  -22.8366   1.5197   -6.4784
 HH9  OAP  O   O      0  -0.578  -24.1073   2.1585   -0.3471
 HH9  OAQ  O   OC    -1  -0.577  -22.2933   0.8608   -0.2066
 HH9  OAS  O   O      0  -0.400  -20.1499  -0.7622   -4.4439
 HH9  CL1  CL  CL     0  -0.101  -24.9526   3.1646   -5.4527
 HH9  H1   H   H      0   0.270  -19.3605  -1.3782   -6.8085
 HH9  H2   H   H      0   0.283  -22.7243   1.4995   -9.0250
 HH9  H3   H   H      0   0.268  -19.4398  -1.2524   -9.2732
 HH9  H4   H   H      0   0.275  -21.1252   0.1919  -10.3760
 HH9  H5   H   HCR6   0   0.260  -21.3811   0.1645   -2.4005
 HH9  H6   H   HCR6   0   0.278  -24.7070   2.8282   -2.6389

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
 HH9  CAF  CAE  aromatic  1.398  0.020  1.398
 HH9  CAF  CAD  aromatic  1.380  0.020  1.380
 HH9  CAE  CAC  aromatic  1.377  0.020  1.377
 HH9  CAD  CAB  aromatic  1.392  0.020  1.392
 HH9  CAC  CAA  aromatic  1.400  0.020  1.400
 HH9  CAB  CAA  aromatic  1.393  0.020  1.393
 HH9  CAB  OAI  single    1.351  0.020  1.351
 HH9  CAA  CAG  single    1.467  0.020  1.467
 HH9  OAI  CAJ  single    1.341  0.020  1.341
 HH9  CL1  CAM  single    1.726  0.020  1.726
 HH9  CAJ  CAM  aromatic  1.396  0.020  1.396
 HH9  CAJ  CAH  aromatic  1.394  0.020  1.394
 HH9  CAG  OAS  double    1.218  0.020  1.218
 HH9  CAG  CAH  single    1.468  0.020  1.468
 HH9  CAM  CAN  aromatic  1.377  0.020  1.377
 HH9  CAH  CAK  aromatic  1.397  0.020  1.397
 HH9  CAN  CAL  aromatic  1.399  0.020  1.399
 HH9  CAK  CAL  aromatic  1.380  0.020  1.380
 HH9  CAL  CAO  single    1.529  0.020  1.529
 HH9  CAO  OAP  deloc     1.244  0.020  1.244
 HH9  CAO  OAQ  deloc     1.243  0.020  1.243
 HH9  CAC  H1   single    0.930  0.020  1.080
 HH9  CAD  H2   single    0.930  0.020  1.080
 HH9  CAE  H3   single    0.930  0.020  1.080
 HH9  CAF  H4   single    0.930  0.020  1.080
 HH9  CAK  H5   single    0.930  0.020  1.080
 HH9  CAN  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
 HH9  CAG  CAA  CAC  121.30  3.000
 HH9  CAG  CAA  CAB  120.15  3.000
 HH9  CAC  CAA  CAB  118.54  3.000
 HH9  OAI  CAB  CAD  116.49  3.000
 HH9  OAI  CAB  CAA  122.17  3.000
 HH9  CAD  CAB  CAA  121.34  3.000
 HH9  H1   CAC  CAE  120.39  3.000
 HH9  H1   CAC  CAA  118.91  3.000
 HH9  CAE  CAC  CAA  120.69  3.000
 HH9  H2   CAD  CAF  121.14  3.000
 HH9  H2   CAD  CAB  119.96  3.000
 HH9  CAF  CAD  CAB  118.91  3.000
 HH9  H3   CAE  CAF  120.06  3.000
 HH9  H3   CAE  CAC  120.26  3.000
 HH9  CAF  CAE  CAC  119.68  3.000
 HH9  H4   CAF  CAE  119.90  3.000
 HH9  H4   CAF  CAD  119.27  3.000
 HH9  CAE  CAF  CAD  120.84  3.000
 HH9  OAS  CAG  CAH  122.54  3.000
 HH9  CAH  CAG  CAA  114.72  3.000
 HH9  OAS  CAG  CAA  122.74  3.000
 HH9  CAK  CAH  CAJ  119.30  3.000
 HH9  CAK  CAH  CAG  121.15  3.000
 HH9  CAJ  CAH  CAG  119.55  3.000
 HH9  OAI  CAJ  CAM  117.39  3.000
 HH9  CAM  CAJ  CAH  119.61  3.000
 HH9  OAI  CAJ  CAH  123.00  3.000
 HH9  H5   CAK  CAL  119.64  3.000
 HH9  H5   CAK  CAH  118.98  3.000
 HH9  CAL  CAK  CAH  121.38  3.000
 HH9  CAO  CAL  CAN  120.28  3.000
 HH9  CAO  CAL  CAK  121.15  3.000
 HH9  CAN  CAL  CAK  118.57  3.000
 HH9  CL1  CAM  CAN  120.71  3.000
 HH9  CAN  CAM  CAJ  120.19  3.000
 HH9  CL1  CAM  CAJ  119.10  3.000
 HH9  H6   CAN  CAM  119.57  3.000
 HH9  H6   CAN  CAL  119.49  3.000
 HH9  CAM  CAN  CAL  120.94  3.000
 HH9  OAQ  CAO  OAP  127.92  3.000
 HH9  OAQ  CAO  CAL  115.98  3.000
 HH9  OAP  CAO  CAL  116.10  3.000
 HH9  CAJ  OAI  CAB  120.40  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
 HH9  CONST_01  CAF  CAE  CAC  CAA     0.00   0.0  0
 HH9  CONST_02  CAF  CAD  CAB  CAA     0.00   0.0  0
 HH9  CONST_03  CAJ  OAI  CAB  CAA     0.00   0.0  0
 HH9  CONST_04  CAJ  CAH  CAG  CAA     0.00   0.0  0
 HH9  CONST_05  CAK  CAH  CAG  CAA   180.00   0.0  0
 HH9  CONST_06  CAE  CAF  CAD  CAB     0.00   0.0  0
 HH9  CONST_07  CAE  CAC  CAA  CAB     0.00   0.0  0
 HH9  CONST_08  CAH  CAG  CAA  CAB     0.00   0.0  0
 HH9  CONST_09  CAM  CAJ  OAI  CAB   180.00   0.0  0
 HH9  CONST_10  CAH  CAJ  OAI  CAB     0.00   0.0  0
 HH9  CONST_11  CAD  CAF  CAE  CAC     0.00   0.0  0
 HH9  CONST_12  CAD  CAB  CAA  CAC     0.00   0.0  0
 HH9  CONST_13  CAH  CAG  CAA  CAC   180.00   0.0  0
 HH9  CONST_14  CAJ  OAI  CAB  CAD   180.00   0.0  0
 HH9  CONST_15  CAN  CAM  CAJ  CAH     0.00   0.0  0
 HH9  CONST_16  CAN  CAL  CAK  CAH     0.00   0.0  0
 HH9  CONST_17  CAL  CAN  CAM  CAJ     0.00   0.0  0
 HH9  CONST_18  CAL  CAK  CAH  CAJ     0.00   0.0  0
 HH9  CONST_19  CAM  CAJ  CAH  CAK     0.00   0.0  0
 HH9  CONST_20  CAM  CAN  CAL  CAK     0.00   0.0  0
 HH9  CONST_21  OAS  CAG  CAA  CAB   180.00   0.0  0
 HH9  CONST_22  OAS  CAG  CAA  CAC     0.00   0.0  0
 HH9  CONST_23  CL1  CAM  CAJ  CAH   180.00   0.0  0
 HH9  CONST_24  CAO  CAL  CAK  CAH   180.00   0.0  0
 HH9  CONST_25  OAS  CAG  CAH  CAJ   180.00   0.0  0
 HH9  CONST_26  OAS  CAG  CAH  CAK     0.00   0.0  0
 HH9  CONST_27  CL1  CAM  CAN  CAL   180.00   0.0  0
 HH9  CONST_28  CAO  CAL  CAN  CAM   180.00   0.0  0
 HH9  CONST_29  CL1  CAM  CAJ  OAI     0.00   0.0  0
 HH9  CONST_30  H3   CAE  CAC  CAA   180.00   0.0  0
 HH9  CONST_31  H2   CAD  CAB  CAA   180.00   0.0  0
 HH9  CONST_32  H4   CAF  CAD  CAB   180.00   0.0  0
 HH9  CONST_33  H1   CAC  CAA  CAB   180.00   0.0  0
 HH9  CONST_34  H4   CAF  CAE  CAC   180.00   0.0  0
 HH9  CONST_35  H3   CAE  CAF  CAD   180.00   0.0  0
 HH9  CONST_36  H2   CAD  CAF  CAE   180.00   0.0  0
 HH9  CONST_37  H1   CAC  CAE  CAF   180.00   0.0  0
 HH9  CONST_38  H1   CAC  CAA  CAG     0.00   0.0  0
 HH9  CONST_39  H5   CAK  CAH  CAG     0.00   0.0  0
 HH9  CONST_40  H6   CAN  CAM  CAJ   180.00   0.0  0
 HH9  CONST_41  H5   CAK  CAH  CAJ   180.00   0.0  0
 HH9  CONST_42  H6   CAN  CAL  CAK   180.00   0.0  0
 HH9  CONST_43  H5   CAK  CAL  CAN   180.00   0.0  0
 HH9  CONST_44  H2   CAD  CAB  OAI     0.00   0.0  0
 HH9  Var_01    OAP  CAO  CAL  CAK  -176.71  30.0  2
 HH9  Var_02    OAQ  CAO  CAL  CAK     3.21  30.0  2
 HH9  Var_03    OAP  CAO  CAL  CAN     3.11  30.0  2
 HH9  Var_04    OAQ  CAO  CAL  CAN  -176.97  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
 HH9  plan-1  CAA  0.020
 HH9  plan-1  CAG  0.020
 HH9  plan-1  CAH  0.020
 HH9  plan-1  OAS  0.020
 HH9  plan-2  CAA  0.020
 HH9  plan-2  CAB  0.020
 HH9  plan-2  CAC  0.020
 HH9  plan-2  CAD  0.020
 HH9  plan-2  CAE  0.020
 HH9  plan-2  CAF  0.020
 HH9  plan-2  CAG  0.020
 HH9  plan-2  OAI  0.020
 HH9  plan-2  H1   0.020
 HH9  plan-2  H2   0.020
 HH9  plan-2  H3   0.020
 HH9  plan-2  H4   0.020
 HH9  plan-3  CAG  0.020
 HH9  plan-3  CAH  0.020
 HH9  plan-3  CAJ  0.020
 HH9  plan-3  CAK  0.020
 HH9  plan-3  CAL  0.020
 HH9  plan-3  CAM  0.020
 HH9  plan-3  CAN  0.020
 HH9  plan-3  CAO  0.020
 HH9  plan-3  OAI  0.020
 HH9  plan-3  CL1  0.020
 HH9  plan-3  H5   0.020
 HH9  plan-3  H6   0.020
 HH9  plan-4  CAL  0.020
 HH9  plan-4  CAO  0.020
 HH9  plan-4  OAP  0.020
 HH9  plan-4  OAQ  0.020

