# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 18:31:50 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: 2-[3,4-bis(oxidanyl)phenyl]-6-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2c(O)cc3OC(=CC(=O)c3c2O)c4ccc(O)c(O)c4
#
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
 H9R  H9R  "2-[3,4-bis(oxidanyl)phenyl]-6-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5,7-bis(oxidanyl)chromen-4-one"
  ligand  52  32  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H9R
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
 H9R  C4   C  CH1   0   0.016  83.3092  14.7859  49.5515
 H9R  C5   C  CH1   0  -0.013  83.1287  14.2378  50.9763
 H9R  C6   C  CH2   0  -0.162  81.9918  13.2411  51.0566
 H9R  C3   C  CH1   0   0.024  84.5346  15.6872  49.4990
 H9R  C1   C  CH1   0   0.004  85.4169  14.4367  51.4673
 H9R  C2   C  CH1   0  -0.003  85.7482  14.9603  50.0637
 H9R  CAA  C  CR16  0  -0.403  92.1549  11.0733  55.0461
 H9R  CAB  C  CR6   0   0.287  93.2502  10.6470  55.7705
 H9R  CAD  C  CR6   0   0.303  93.5544   9.2779  55.8465
 H9R  CAF  C  CR16  0  -0.326  92.7389   8.3668  55.1912
 H9R  CAG  C  CR16  0  -0.311  91.6446   8.7960  54.4600
 H9R  CAH  C  CR6   0   0.012  91.3439  10.1528  54.3718
 H9R  CAI  C  CR6   0   0.409  90.2051  10.6122  53.5800
 H9R  CAK  C  CR16  0  -0.516  89.6449   9.9462  52.5433
 H9R  CAL  C  CR6   0   0.531  88.5271  10.4956  51.8273
 H9R  CAN  C  CR66  0  -0.348  88.0775  11.7933  52.2811
 H9R  CAO  C  CR6   0   0.406  86.9962  12.4647  51.6593
 H9R  CAQ  C  CR66  0   0.413  88.7201  12.4152  53.3480
 H9R  CAR  C  CR16  0  -0.526  88.3373  13.6554  53.8130
 H9R  CAS  C  CR6   0   0.368  87.2666  14.2914  53.1881
 H9R  CAU  C  CR6   0  -0.175  86.5729  13.7147  52.1089
 H9R  O2   O  OH1   0  -0.668  86.8098  15.8849  50.1040
 H9R  O3   O  OH1   0  -0.665  84.7398  16.0848  48.1671
 H9R  O4   O  OH1   0  -0.666  82.1904  15.5485  49.1611
 H9R  O5   O  O2    0  -0.488  84.2985  13.5824  51.4131
 H9R  O6   O  OH1   0  -0.665  81.8004  12.8720  52.4014
 H9R  OAE  O  OH1   0  -0.616  94.6112   8.8286  56.5391
 H9R  OAJ  O  O     0  -0.468  89.7527  11.8121  53.9731
 H9R  OAP  O  OH1   0  -0.620  86.3903  11.8892  50.6306
 H9R  OAT  O  OH1   0  -0.610  86.8570  15.4935  53.6048
 H9R  H1   H  HCH1  0   0.222  83.4725  13.9398  48.8677
 H9R  H2   H  HCH1  0   0.210  82.9010  15.0891  51.6409
 H9R  H3   H  HCH2  0   0.201  81.0916  13.7051  50.6382
 H9R  H4   H  HCH2  0   0.196  82.2339  12.3755  50.4238
 H9R  H5   H  HCH1  0   0.202  84.3358  16.5610  50.1443
 H9R  H6   H  HCH1  0   0.238  85.1666  15.3146  52.0791
 H9R  H7   H  HCH1  0   0.227  85.9838  14.1161  49.4033
 H9R  H8   H  HCR6  0   0.282  91.9482  12.1356  54.9928
 H9R  H9   H  HCR6  0   0.275  92.9637   7.3104  55.2638
 H9R  H10  H  HCR6  0   0.263  91.0177   8.0581  53.9785
 H9R  H11  H  HCR6  0   0.282  90.0541   8.9981  52.2252
 H9R  H12  H  HCR6  0   0.291  88.8582  14.1189  54.6425
 H9R  H13  H  HOH1  0   0.458  87.6400  15.4004  50.1454
 H9R  H14  H  HOH1  0   0.446  85.5392  16.6214  48.1411
 H9R  H15  H  HOH1  0   0.456  81.5628  14.9788  48.7086
 H9R  H16  H  HOH1  0   0.453  81.0322  12.2958  52.4453
 H9R  H17  H  HOH1  0   0.484  93.8220  12.3927  56.3429
 H9R  H18  H  HOH1  0   0.476  95.0951   9.5607  56.9414
 H9R  H19  H  HOH1  0   0.476  86.8431  11.0190  50.4693
 H9R  H20  H  HOH1  0   0.487  87.3775  15.7972  54.3587
 H9R  OAM  O  O     0  -0.508  87.9869   9.9110  50.8727
 H9R  OAC  O  OH1   0  -0.640  94.0871  11.4704  56.4363

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
 H9R  O3   C3   single    1.405  0.020  1.405
 H9R  O4   C4   single    1.409  0.020  1.409
 H9R  C4   C3   single    1.522  0.020  1.522
 H9R  C4   C5   single    1.537  0.020  1.537
 H9R  C3   C2   single    1.523  0.020  1.523
 H9R  O2   C2   single    1.408  0.020  1.408
 H9R  C2   C1   single    1.534  0.020  1.534
 H9R  OAP  CAO  single    1.325  0.020  1.325
 H9R  C6   C5   single    1.514  0.020  1.514
 H9R  C6   O6   single    1.408  0.020  1.408
 H9R  OAM  CAL  double    1.243  0.020  1.243
 H9R  C5   O5   single    1.410  0.020  1.410
 H9R  C1   O5   single    1.408  0.020  1.408
 H9R  C1   CAU  single    1.506  0.020  1.506
 H9R  CAO  CAU  aromatic  1.394  0.020  1.394
 H9R  CAO  CAN  aromatic  1.417  0.020  1.417
 H9R  CAL  CAN  single    1.446  0.020  1.446
 H9R  CAL  CAK  single    1.437  0.020  1.437
 H9R  CAU  CAS  aromatic  1.407  0.020  1.407
 H9R  CAN  CAQ  aromatic  1.392  0.020  1.392
 H9R  CAK  CAI  double    1.354  0.020  1.354
 H9R  CAS  OAT  single    1.337  0.020  1.337
 H9R  CAS  CAR  aromatic  1.393  0.020  1.393
 H9R  CAQ  CAR  aromatic  1.379  0.020  1.379
 H9R  CAQ  OAJ  single    1.349  0.020  1.349
 H9R  CAI  OAJ  single    1.341  0.020  1.341
 H9R  CAI  CAH  single    1.461  0.020  1.461
 H9R  CAH  CAG  aromatic  1.393  0.020  1.393
 H9R  CAH  CAA  aromatic  1.400  0.020  1.400
 H9R  CAG  CAF  aromatic  1.384  0.020  1.384
 H9R  CAA  CAB  aromatic  1.381  0.020  1.381
 H9R  CAF  CAD  aromatic  1.387  0.020  1.387
 H9R  CAB  CAD  aromatic  1.405  0.020  1.405
 H9R  CAB  OAC  single    1.350  0.020  1.350
 H9R  CAD  OAE  single    1.341  0.020  1.341
 H9R  C4   H1   single    0.970  0.020  1.090
 H9R  C5   H2   single    0.970  0.020  1.090
 H9R  C6   H3   single    0.970  0.020  1.090
 H9R  C6   H4   single    0.970  0.020  1.090
 H9R  C3   H5   single    0.970  0.020  1.090
 H9R  C1   H6   single    0.970  0.020  1.090
 H9R  C2   H7   single    0.970  0.020  1.090
 H9R  CAA  H8   single    0.930  0.020  1.080
 H9R  CAF  H9   single    0.930  0.020  1.080
 H9R  CAG  H10  single    0.930  0.020  1.080
 H9R  CAK  H11  single    0.930  0.020  1.080
 H9R  CAR  H12  single    0.930  0.020  1.080
 H9R  O2   H13  single    0.850  0.020  0.980
 H9R  O3   H14  single    0.850  0.020  0.980
 H9R  O4   H15  single    0.850  0.020  0.980
 H9R  O6   H16  single    0.850  0.020  0.980
 H9R  OAC  H17  single    0.850  0.020  0.980
 H9R  OAE  H18  single    0.850  0.020  0.980
 H9R  OAP  H19  single    0.850  0.020  0.980
 H9R  OAT  H20  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
 H9R  H1   C4   O4   111.22  3.000
 H9R  H1   C4   C3   108.33  3.000
 H9R  O4   C4   C3   108.01  3.000
 H9R  H1   C4   C5   108.62  3.000
 H9R  C3   C4   C5   109.73  3.000
 H9R  O4   C4   C5   110.89  3.000
 H9R  H2   C5   O5   110.07  3.000
 H9R  H2   C5   C6   108.72  3.000
 H9R  O5   C5   C6   107.49  3.000
 H9R  H2   C5   C4   107.90  3.000
 H9R  O5   C5   C4   110.82  3.000
 H9R  C6   C5   C4   111.84  3.000
 H9R  H4   C6   H3   107.14  3.000
 H9R  H4   C6   O6   111.93  3.000
 H9R  H3   C6   O6   111.35  3.000
 H9R  H4   C6   C5   108.82  3.000
 H9R  H3   C6   C5   108.53  3.000
 H9R  O6   C6   C5   108.99  3.000
 H9R  H5   C3   O3   110.88  3.000
 H9R  H5   C3   C2   107.72  3.000
 H9R  O3   C3   C2   111.72  3.000
 H9R  H5   C3   C4   107.67  3.000
 H9R  C2   C3   C4   110.25  3.000
 H9R  O3   C3   C4   108.53  3.000
 H9R  H6   C1   O5   108.98  3.000
 H9R  H6   C1   CAU  108.69  3.000
 H9R  O5   C1   CAU  109.58  3.000
 H9R  H6   C1   C2   106.61  3.000
 H9R  CAU  C1   C2   112.80  3.000
 H9R  O5   C1   C2   110.08  3.000
 H9R  H7   C2   O2   111.13  3.000
 H9R  H7   C2   C1   109.53  3.000
 H9R  O2   C2   C1   111.14  3.000
 H9R  H7   C2   C3   108.36  3.000
 H9R  C1   C2   C3   109.26  3.000
 H9R  O2   C2   C3   107.33  3.000
 H9R  H8   CAA  CAH  120.69  3.000
 H9R  H8   CAA  CAB  118.68  3.000
 H9R  CAH  CAA  CAB  120.62  3.000
 H9R  OAC  CAB  CAD  115.70  3.000
 H9R  OAC  CAB  CAA  124.22  3.000
 H9R  CAD  CAB  CAA  120.08  3.000
 H9R  OAE  CAD  CAF  119.15  3.000
 H9R  OAE  CAD  CAB  121.68  3.000
 H9R  CAF  CAD  CAB  119.16  3.000
 H9R  H9   CAF  CAG  120.15  3.000
 H9R  H9   CAF  CAD  119.15  3.000
 H9R  CAG  CAF  CAD  120.70  3.000
 H9R  H10  CAG  CAH  120.76  3.000
 H9R  H10  CAG  CAF  118.81  3.000
 H9R  CAH  CAG  CAF  120.41  3.000
 H9R  CAI  CAH  CAG  120.60  3.000
 H9R  CAG  CAH  CAA  119.02  3.000
 H9R  CAI  CAH  CAA  120.39  3.000
 H9R  OAJ  CAI  CAK  121.68  3.000
 H9R  OAJ  CAI  CAH  112.66  3.000
 H9R  CAK  CAI  CAH  125.65  3.000
 H9R  H11  CAK  CAL  118.91  3.000
 H9R  H11  CAK  CAI  120.03  3.000
 H9R  CAL  CAK  CAI  121.03  3.000
 H9R  OAM  CAL  CAN  121.86  3.000
 H9R  CAN  CAL  CAK  115.38  3.000
 H9R  OAM  CAL  CAK  122.75  3.000
 H9R  CAQ  CAN  CAO  118.49  3.000
 H9R  CAQ  CAN  CAL  119.85  3.000
 H9R  CAO  CAN  CAL  121.65  3.000
 H9R  OAP  CAO  CAU  120.06  3.000
 H9R  CAU  CAO  CAN  121.01  3.000
 H9R  OAP  CAO  CAN  118.94  3.000
 H9R  OAJ  CAQ  CAR  117.27  3.000
 H9R  OAJ  CAQ  CAN  120.57  3.000
 H9R  CAR  CAQ  CAN  122.15  3.000
 H9R  H12  CAR  CAS  121.16  3.000
 H9R  H12  CAR  CAQ  120.63  3.000
 H9R  CAS  CAR  CAQ  118.21  3.000
 H9R  OAT  CAS  CAU  117.18  3.000
 H9R  OAT  CAS  CAR  120.41  3.000
 H9R  CAU  CAS  CAR  122.41  3.000
 H9R  CAS  CAU  CAO  117.73  3.000
 H9R  CAS  CAU  C1   120.58  3.000
 H9R  CAO  CAU  C1   121.69  3.000
 H9R  H13  O2   C2   108.72  3.000
 H9R  H14  O3   C3   107.73  3.000
 H9R  H15  O4   C4   109.16  3.000
 H9R  C1   O5   C5   112.87  3.000
 H9R  H16  O6   C6   108.03  3.000
 H9R  H18  OAE  CAD  110.86  3.000
 H9R  CAQ  OAJ  CAI  121.47  3.000
 H9R  H19  OAP  CAO  107.33  3.000
 H9R  H20  OAT  CAS  111.18  3.000
 H9R  H17  OAC  CAB  111.42  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
 H9R  CONST_01  CAF  CAG  CAH  CAA     0.00   0.0  0
 H9R  CONST_02  CAF  CAD  CAB  CAA     0.00   0.0  0
 H9R  CONST_03  CAG  CAH  CAA  CAB     0.00   0.0  0
 H9R  CONST_04  CAG  CAF  CAD  CAB     0.00   0.0  0
 H9R  CONST_05  CAH  CAG  CAF  CAD     0.00   0.0  0
 H9R  CONST_06  CAH  CAA  CAB  CAD     0.00   0.0  0
 H9R  CONST_07  CAQ  OAJ  CAI  CAH   180.00   0.0  0
 H9R  CONST_08  CAS  CAU  CAO  CAN     0.00   0.0  0
 H9R  CONST_09  CAS  CAR  CAQ  CAN     0.00   0.0  0
 H9R  CONST_10  CAR  CAS  CAU  CAO     0.00   0.0  0
 H9R  CONST_11  CAR  CAQ  CAN  CAO     0.00   0.0  0
 H9R  CONST_12  CAU  CAO  CAN  CAQ     0.00   0.0  0
 H9R  CONST_13  CAU  CAS  CAR  CAQ     0.00   0.0  0
 H9R  CONST_14  CAN  CAO  CAU  C1    180.00   0.0  0
 H9R  CONST_15  CAR  CAS  CAU  C1    180.00   0.0  0
 H9R  CONST_16  CAI  CAH  CAA  CAB   180.00   0.0  0
 H9R  CONST_17  CAI  CAH  CAG  CAF   180.00   0.0  0
 H9R  CONST_18  OAP  CAO  CAU  C1      0.00   0.0  0
 H9R  CONST_19  OAT  CAS  CAU  C1      0.00   0.0  0
 H9R  CONST_20  OAE  CAD  CAB  CAA   180.00   0.0  0
 H9R  CONST_21  OAC  CAB  CAD  CAF   180.00   0.0  0
 H9R  CONST_22  OAE  CAD  CAF  CAG   180.00   0.0  0
 H9R  CONST_23  OAC  CAB  CAA  CAH   180.00   0.0  0
 H9R  CONST_24  OAP  CAO  CAN  CAL     0.00   0.0  0
 H9R  CONST_25  OAT  CAS  CAU  CAO   180.00   0.0  0
 H9R  CONST_26  OAP  CAO  CAN  CAQ   180.00   0.0  0
 H9R  CONST_27  OAT  CAS  CAR  CAQ   180.00   0.0  0
 H9R  CONST_28  OAP  CAO  CAU  CAS   180.00   0.0  0
 H9R  CONST_29  H10  CAG  CAH  CAA   180.00   0.0  0
 H9R  CONST_30  H9   CAF  CAD  CAB   180.00   0.0  0
 H9R  CONST_31  H10  CAG  CAF  CAD   180.00   0.0  0
 H9R  CONST_32  H8   CAA  CAB  CAD   180.00   0.0  0
 H9R  CONST_33  H8   CAA  CAH  CAG   180.00   0.0  0
 H9R  CONST_34  H9   CAF  CAG  CAH   180.00   0.0  0
 H9R  CONST_35  H10  CAG  CAH  CAI     0.00   0.0  0
 H9R  CONST_36  H8   CAA  CAH  CAI     0.00   0.0  0
 H9R  CONST_37  H12  CAR  CAQ  CAN   180.00   0.0  0
 H9R  CONST_38  H12  CAR  CAS  CAU   180.00   0.0  0
 H9R  CONST_39  H12  CAR  CAQ  OAJ     0.00   0.0  0
 H9R  Var_01    CAK  CAI  CAH  CAA   155.41  30.0  2
 H9R  Var_02    OAJ  CAI  CAH  CAA   -23.69  30.0  2
 H9R  Var_03    CAK  CAI  CAH  CAG   -24.15  30.0  2
 H9R  Var_04    OAJ  CAI  CAH  CAG   156.75  30.0  2
 H9R  Var_05    CAL  CAK  CAI  CAH  -179.70  30.0  1
 H9R  Var_06    CAN  CAL  CAK  CAI     0.92  30.0  1
 H9R  Var_07    CAN  CAQ  OAJ  CAI     0.99  30.0  1
 H9R  Var_08    CAR  CAQ  OAJ  CAI  -179.18  30.0  1
 H9R  Var_09    CAO  CAN  CAL  CAK   179.22  30.0  1
 H9R  Var_10    CAQ  CAN  CAL  CAK    -0.27  30.0  1
 H9R  Var_11    CAQ  OAJ  CAI  CAK    -0.33  30.0  1
 H9R  Var_12    OAJ  CAI  CAK  CAL    -0.66  30.0  1
 H9R  Var_13    OAM  CAL  CAK  CAI  -179.87  30.0  1
 H9R  Var_14    OAM  CAL  CAN  CAO     0.00  30.0  1
 H9R  Var_15    OAM  CAL  CAN  CAQ  -179.49  30.0  1
 H9R  Var_16    H11  CAK  CAI  CAH    -1.33  30.0  1
 H9R  Var_17    H11  CAK  CAL  CAN  -177.46  30.0  1
 H9R  Var_18    H11  CAK  CAI  OAJ   177.70  30.0  1
 H9R  Var_19    H11  CAK  CAL  OAM     1.75  30.0  1

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
 H9R  chir_01  C4  O4  C3   C5  negativ
 H9R  chir_02  C5  O5  C4   C6  negativ
 H9R  chir_03  C3  O3  C4   C2  negativ
 H9R  chir_04  C1  O5  CAU  C2  negativ
 H9R  chir_05  C2  O2  C1   C3  negativ

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
 H9R  plan-1  CAA  0.020
 H9R  plan-1  CAB  0.020
 H9R  plan-1  CAD  0.020
 H9R  plan-1  CAF  0.020
 H9R  plan-1  CAG  0.020
 H9R  plan-1  CAH  0.020
 H9R  plan-1  CAI  0.020
 H9R  plan-1  OAE  0.020
 H9R  plan-1  H8   0.020
 H9R  plan-1  H9   0.020
 H9R  plan-1  H10  0.020
 H9R  plan-1  OAC  0.020
 H9R  plan-2  C1   0.020
 H9R  plan-2  CAL  0.020
 H9R  plan-2  CAN  0.020
 H9R  plan-2  CAO  0.020
 H9R  plan-2  CAQ  0.020
 H9R  plan-2  CAR  0.020
 H9R  plan-2  CAS  0.020
 H9R  plan-2  CAU  0.020
 H9R  plan-2  OAJ  0.020
 H9R  plan-2  OAP  0.020
 H9R  plan-2  OAT  0.020
 H9R  plan-2  H12  0.020
 H9R  plan-3  CAK  0.020
 H9R  plan-3  CAL  0.020
 H9R  plan-3  CAN  0.020
 H9R  plan-3  OAM  0.020

