# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:17:57 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{S},4~{R})-9-fluoranyl-5,5-bis(oxidanyl)-6-oxa-5-boranuidatricyclo[5.4.0.0^{2,4}]undeca-1(11),7,9-triene-8-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(F)ccc2[C@H]3C[C@H]3[B-](O)(O)Oc12
#
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
 QNA  QNA  '(2~{S},4~{R})-9-fluoranyl-5,5-bis(oxidanyl)-6-oxa-5-boranuidatricyclo[5.4.0.0^{2,4}]undeca-1(11),7,9-triene-8-carboxylic acid'  ligand  25  17  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QNA
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
 QNA  C02  C  C      0   0.366  -1.9610  -1.4249   0.2634
 QNA  C09  C  CR6    0   0.067   0.5339   1.4687  -0.0206
 QNA  C10  C  CR6    0   0.353   0.0040   0.1727   0.1272
 QNA  C16  C  CH2    0  -0.503   2.7769   1.1635   1.2354
 QNA  C17  C  CH1    0  -0.349   1.9973   1.6797   0.0511
 QNA  O01  O  OC    -1  -0.601  -2.1258  -2.0791  -0.7804
 QNA  B12  B  B     -1   0.474   2.1560  -0.9197  -0.3545
 QNA  C04  C  CR6    0  -0.350  -1.3811  -0.0283   0.0998
 QNA  C05  C  CR6    0   0.483  -2.1953   1.0700  -0.0821
 QNA  C07  C  CR16   0  -0.444  -1.7179   2.3536  -0.2535
 QNA  C08  C  CR16   0  -0.342  -0.3394   2.5321  -0.2161
 QNA  C15  C  CH1    0  -0.440   2.9032   0.4824  -0.0918
 QNA  F06  F  F      0  -0.332  -3.5356   0.8673  -0.1090
 QNA  O03  O  O      0  -0.607  -2.2183  -1.7765   1.4287
 QNA  O11  O  OC2    0  -0.559   0.7885  -0.8810   0.3136
 QNA  H1   H  HCH2   0   0.227   3.5897   1.7866   1.5925
 QNA  H2   H  HCH2   0   0.222   2.2294   0.6689   2.0305
 QNA  H3   H  HCH1   0   0.229   2.3323   2.6331  -0.3474
 QNA  H5   H  H      0   0.426   1.3230  -1.7679  -1.9839
 QNA  H6   H  HCR6   0   0.251  -2.3930   3.1856  -0.4061
 QNA  H7   H  HCR6   0   0.239   0.0652   3.5303  -0.3415
 QNA  H8   H  HCH1   0   0.203   3.8363   0.6853  -0.6157
 QNA  H9   H  H      0   0.434   2.4845  -2.8616   0.0743
 QNA  O14  O  OB     0  -0.730   1.9636  -1.0751  -1.7992
 QNA  O13  O  OB     0  -0.717   2.8882  -2.0122   0.2742

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
 QNA  C16  C17  single    1.509  0.020  1.509
 QNA  C16  C15  single    1.497  0.020  1.497
 QNA  C08  C09  aromatic  1.390  0.020  1.390
 QNA  C08  C07  aromatic  1.391  0.020  1.391
 QNA  C17  C09  single    1.480  0.020  1.480
 QNA  C17  C15  single    1.508  0.020  1.508
 QNA  C09  C10  aromatic  1.408  0.020  1.408
 QNA  C07  C05  aromatic  1.380  0.020  1.380
 QNA  C10  O11  single    1.327  0.020  1.327
 QNA  C10  C04  aromatic  1.400  0.020  1.400
 QNA  C05  C04  aromatic  1.379  0.020  1.379
 QNA  C05  F06  single    1.356  0.020  1.356
 QNA  C15  B12  single    1.610  0.020  1.610
 QNA  O11  B12  single    1.522  0.020  1.522
 QNA  C04  C02  single    1.521  0.020  1.521
 QNA  O03  C02  deloc     1.244  0.020  1.244
 QNA  O13  B12  single    1.458  0.020  1.458
 QNA  C02  O01  deloc     1.243  0.020  1.243
 QNA  B12  O14  single    1.466  0.020  1.466
 QNA  C16  H1   single    0.970  0.020  1.090
 QNA  C16  H2   single    0.970  0.020  1.090
 QNA  C17  H3   single    0.970  0.020  1.090
 QNA  O14  H5   single    0.850  0.020  0.980
 QNA  C07  H6   single    0.930  0.020  1.080
 QNA  C08  H7   single    0.930  0.020  1.080
 QNA  C15  H8   single    0.970  0.020  1.090
 QNA  O13  H9   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
 QNA  O03  C02  C04  116.04  3.000
 QNA  O03  C02  O01  127.62  3.000
 QNA  C04  C02  O01  116.34  3.000
 QNA  C08  C09  C17  121.26  3.000
 QNA  C17  C09  C10  119.88  3.000
 QNA  C08  C09  C10  118.85  3.000
 QNA  O11  C10  C04  118.28  3.000
 QNA  C04  C10  C09  120.16  3.000
 QNA  O11  C10  C09  121.55  3.000
 QNA  H2   C16  H1   113.51  3.000
 QNA  H2   C16  C15  119.01  3.000
 QNA  H1   C16  C15  119.35  3.000
 QNA  H2   C16  C17  118.07  3.000
 QNA  H1   C16  C17  116.68  3.000
 QNA  C15  C16  C17   60.23  3.000
 QNA  H3   C17  C15  118.48  3.000
 QNA  H3   C17  C16  115.40  3.000
 QNA  C15  C17  C16   59.50  3.000
 QNA  H3   C17  C09  114.34  3.000
 QNA  C15  C17  C09  118.43  3.000
 QNA  C16  C17  C09  120.00  3.000
 QNA  O13  B12  O11  106.31  3.000
 QNA  O13  B12  C15  110.43  3.000
 QNA  O11  B12  C15  108.85  3.000
 QNA  O13  B12  O14  114.31  3.000
 QNA  O11  B12  O14  108.51  3.000
 QNA  C15  B12  O14  108.30  3.000
 QNA  C05  C04  C10  118.19  3.000
 QNA  C05  C04  C02  121.35  3.000
 QNA  C10  C04  C02  120.46  3.000
 QNA  F06  C05  C07  118.59  3.000
 QNA  F06  C05  C04  117.85  3.000
 QNA  C07  C05  C04  123.56  3.000
 QNA  H6   C07  C08  121.57  3.000
 QNA  H6   C07  C05  121.12  3.000
 QNA  C08  C07  C05  117.32  3.000
 QNA  H7   C08  C07  119.01  3.000
 QNA  H7   C08  C09  119.09  3.000
 QNA  C07  C08  C09  121.90  3.000
 QNA  H8   C15  B12  118.77  3.000
 QNA  H8   C15  C17  114.35  3.000
 QNA  B12  C15  C17  115.34  3.000
 QNA  H8   C15  C16  114.45  3.000
 QNA  B12  C15  C16  120.11  3.000
 QNA  C17  C15  C16   60.28  3.000
 QNA  B12  O11  C10  119.31  3.000
 QNA  H5   O14  B12  110.68  3.000
 QNA  H9   O13  B12  111.19  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
 QNA  CONST_01  C05  C07  C08  C09    0.00   0.0  0
 QNA  CONST_02  C05  C04  C10  C09    0.00   0.0  0
 QNA  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 QNA  CONST_04  C07  C05  C04  C10    0.00   0.0  0
 QNA  CONST_05  C08  C09  C10  C04    0.00   0.0  0
 QNA  CONST_06  C08  C07  C05  C04    0.00   0.0  0
 QNA  CONST_07  C09  C10  C04  C02  180.00   0.0  0
 QNA  CONST_08  O11  C10  C04  C02    0.00   0.0  0
 QNA  CONST_09  C07  C05  C04  C02  180.00   0.0  0
 QNA  CONST_10  F06  C05  C04  C10  180.00   0.0  0
 QNA  CONST_11  F06  C05  C07  C08  180.00   0.0  0
 QNA  CONST_12  H6   C07  C08  C09  180.00   0.0  0
 QNA  CONST_13  H7   C08  C09  C10  180.00   0.0  0
 QNA  Var_01    C15  C16  C17  C09  107.33  30.0  1
 QNA  Var_02    C16  C17  C09  C10  -53.00  30.0  1
 QNA  Var_03    C15  B12  O11  C10   47.98  30.0  1
 QNA  Var_04    O11  B12  C15  C16   38.76  30.0  1
 QNA  Var_05    C04  C10  O11  B12  147.07  30.0  1
 QNA  Var_06    O03  C02  C04  C10   90.32  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
 QNA  chir_01  C17  C16  C09  C15  both
 QNA  chir_02  C15  C16  C17  B12  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
 QNA  plan-1  C02  0.020
 QNA  plan-1  O01  0.020
 QNA  plan-1  C04  0.020
 QNA  plan-1  O03  0.020
 QNA  plan-2  C02  0.020
 QNA  plan-2  C09  0.020
 QNA  plan-2  C10  0.020
 QNA  plan-2  C17  0.020
 QNA  plan-2  C04  0.020
 QNA  plan-2  C05  0.020
 QNA  plan-2  C07  0.020
 QNA  plan-2  C08  0.020
 QNA  plan-2  F06  0.020
 QNA  plan-2  O11  0.020
 QNA  plan-2  H6   0.020
 QNA  plan-2  H7   0.020

