# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:22:28 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: methyl 3-[3-chloranyl-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-phenyl]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cccc(c1)c2ccc(O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)c(Cl)c2
#
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
 SBQ  SBQ  'methyl 3-[3-chloranyl-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-phenyl]benzoate'  ligand  50  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SBQ
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
 SBQ  C12  C   CR16  0  -0.226  -0.7691   3.2087  18.5893
 SBQ  C10  C   CR6   0   0.114  -1.9445   3.0895  16.4791
 SBQ  C4   C   CH2   0  -0.197  -4.3389   3.9782   9.3184
 SBQ  C6   C   CR6   0   0.468  -2.4392   1.3804  12.5707
 SBQ  C7   C   CR16  0  -0.359  -3.5468   1.7292  13.3373
 SBQ  C2   C   CR16  0   0.021  -3.2978   1.9591   8.1490
 SBQ  O1   O   OH1   0  -0.666  -2.3624  -0.0234   7.2283
 SBQ  C    C   CR16  0  -0.038  -3.3851  -0.1815   9.4288
 SBQ  O    O   OH1   0  -0.663  -4.5797  -0.5709   8.8042
 SBQ  C1   C   CR16  0   0.027  -2.5696   0.6544   8.4391
 SBQ  C11  C   CR16  0  -0.301  -0.9232   2.6574  17.3264
 SBQ  C13  C   CR16  0  -0.270  -1.6318   4.1985  19.0297
 SBQ  C14  C   CR6   0  -0.061  -2.6558   4.6424  18.1968
 SBQ  C15  C   C     0   0.599  -3.5562   5.7123  18.7007
 SBQ  C16  C   CH3   0  -0.423  -5.4020   7.0832  18.2028
 SBQ  C17  C   CR16  0  -0.338  -2.8051   4.0887  16.9283
 SBQ  C18  C   CR16  0  -0.260  -1.0067   2.1646  14.3619
 SBQ  C19  C   CR6   0  -0.154  -1.1704   1.6182  13.1044
 SBQ  C3   C   CR16  0  -0.021  -3.5688   2.6858   9.4756
 SBQ  C5   C   CR16  0   0.205  -3.7050   0.6467  10.6760
 SBQ  C8   C   CR16  0  -0.293  -3.3802   2.2761  14.5998
 SBQ  C9   C   CR6   0   0.061  -2.1156   2.5039  15.1356
 SBQ  O2   O   OH1   0  -0.673  -2.4813   2.7559   7.3240
 SBQ  O4   O   O     0  -0.486  -4.3015   1.8544  10.3697
 SBQ  O6   O   O2    0  -0.456  -4.4777   6.0644  17.8205
 SBQ  O7   O   O     0  -0.448  -3.4572   6.2075  19.7977
 SBQ  CL   CL  CL    0  -0.105   0.2196   1.2248  12.1549
 SBQ  H14  H   HCR6  0   0.267   0.0222   2.8548  19.2362
 SBQ  H8   H   HCH2  0   0.210  -3.6976   4.6899   8.7853
 SBQ  H9   H   HCH2  0   0.221  -4.5077   4.4017  10.3173
 SBQ  H11  H   HCR6  0   0.293  -4.5519   1.5749  12.9728
 SBQ  H2   H   HCR6  0   0.232  -4.2508   1.7302   7.6589
 SBQ  H6   H   HOH1  0   0.452  -1.8143  -0.7952   7.4024
 SBQ  H    H   HCR6  0   0.246  -2.7949  -1.0555   9.7385
 SBQ  H5   H   HOH1  0   0.459  -4.9968  -1.2548   9.3372
 SBQ  H1   H   HCR6  0   0.222  -1.6101   0.8964   8.9200
 SBQ  H13  H   HCR6  0   0.266  -0.2527   1.8693  17.0070
 SBQ  H15  H   HCR6  0   0.266  -1.5095   4.6220  20.0171
 SBQ  H18  H   HCH3  0   0.255  -6.0726   7.2076  17.3580
 SBQ  H17  H   HCH3  0   0.242  -5.9753   6.7896  19.0813
 SBQ  H16  H   HCH3  0   0.242  -4.8928   8.0256  18.4021
 SBQ  H19  H   HCR6  0   0.265  -3.5839   4.4478  16.2691
 SBQ  H20  H   HCR6  0   0.279  -0.0054   2.3482  14.7286
 SBQ  H3   H   HCR6  0   0.235  -2.6011   2.9593   9.9192
 SBQ  H4   H   HCR6  0   0.265  -4.4127   0.1046  11.3150
 SBQ  H12  H   HCR6  0   0.267  -4.2649   2.5130  15.1768
 SBQ  H7   H   HOH1  0   0.457  -3.0439   3.3393   6.8073
 SBQ  H10  H   HOH1  0   0.460  -5.9618   4.5898   8.4599
 SBQ  O5   O   O2    0  -0.486  -2.4748   0.8178  11.3513
 SBQ  O3   O   OH1   0  -0.670  -5.5467   3.7412   8.6369

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
 SBQ  O1   C1   single    1.403  0.020  1.403
 SBQ  O2   C2   single    1.408  0.020  1.408
 SBQ  C2   C1   single    1.522  0.020  1.522
 SBQ  C2   C3   single    1.537  0.020  1.537
 SBQ  C1   C    single    1.531  0.020  1.531
 SBQ  O    C    single    1.403  0.020  1.403
 SBQ  O3   C4   single    1.407  0.020  1.407
 SBQ  C    C5   single    1.531  0.020  1.531
 SBQ  C3   C4   single    1.513  0.020  1.513
 SBQ  C3   O4   single    1.424  0.020  1.424
 SBQ  O4   C5   single    1.381  0.020  1.381
 SBQ  C5   O5   single    1.414  0.020  1.414
 SBQ  O5   C6   single    1.343  0.020  1.343
 SBQ  CL   C19  single    1.729  0.020  1.729
 SBQ  C6   C19  aromatic  1.397  0.020  1.397
 SBQ  C6   C7   aromatic  1.391  0.020  1.391
 SBQ  C19  C18  aromatic  1.381  0.020  1.381
 SBQ  C7   C8   aromatic  1.386  0.020  1.386
 SBQ  C18  C9   aromatic  1.394  0.020  1.394
 SBQ  C8   C9   aromatic  1.392  0.020  1.392
 SBQ  C9   C10  single    1.476  0.020  1.476
 SBQ  C10  C17  aromatic  1.393  0.020  1.393
 SBQ  C10  C11  aromatic  1.396  0.020  1.396
 SBQ  C17  C14  aromatic  1.392  0.020  1.392
 SBQ  C11  C12  aromatic  1.387  0.020  1.387
 SBQ  O6   C16  single    1.428  0.020  1.428
 SBQ  O6   C15  single    1.322  0.020  1.322
 SBQ  C14  C15  single    1.486  0.020  1.486
 SBQ  C14  C13  aromatic  1.393  0.020  1.393
 SBQ  C15  O7   double    1.208  0.020  1.208
 SBQ  C12  C13  aromatic  1.385  0.020  1.385
 SBQ  C12  H14  single    0.930  0.020  1.080
 SBQ  C4   H8   single    0.970  0.020  1.090
 SBQ  C4   H9   single    0.970  0.020  1.090
 SBQ  C7   H11  single    0.930  0.020  1.080
 SBQ  C2   H2   single    0.970  0.020  1.090
 SBQ  O1   H6   single    0.850  0.020  0.980
 SBQ  C    H    single    0.970  0.020  1.090
 SBQ  O    H5   single    0.850  0.020  0.980
 SBQ  C1   H1   single    0.970  0.020  1.090
 SBQ  C11  H13  single    0.930  0.020  1.080
 SBQ  C13  H15  single    0.930  0.020  1.080
 SBQ  C16  H18  single    0.970  0.020  1.090
 SBQ  C16  H17  single    0.970  0.020  1.090
 SBQ  C16  H16  single    0.970  0.020  1.090
 SBQ  C17  H19  single    0.930  0.020  1.080
 SBQ  C18  H20  single    0.930  0.020  1.080
 SBQ  C3   H3   single    0.970  0.020  1.090
 SBQ  C5   H4   single    0.970  0.020  1.090
 SBQ  C8   H12  single    0.930  0.020  1.080
 SBQ  O2   H7   single    0.850  0.020  0.980
 SBQ  O3   H10  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
 SBQ  H14  C12  C13  119.96  3.000
 SBQ  H14  C12  C11  119.73  3.000
 SBQ  C13  C12  C11  120.31  3.000
 SBQ  C9   C10  C17  120.44  3.000
 SBQ  C17  C10  C11  118.58  3.000
 SBQ  C9   C10  C11  120.98  3.000
 SBQ  H9   C4   H8   106.37  3.000
 SBQ  H9   C4   O3   111.94  3.000
 SBQ  H8   C4   O3   112.08  3.000
 SBQ  H9   C4   C3   108.26  3.000
 SBQ  H8   C4   C3   107.91  3.000
 SBQ  O3   C4   C3   110.09  3.000
 SBQ  O5   C6   C19  116.24  3.000
 SBQ  C19  C6   C7   118.03  3.000
 SBQ  O5   C6   C7   125.73  3.000
 SBQ  H11  C7   C8   118.39  3.000
 SBQ  H11  C7   C6   121.27  3.000
 SBQ  C8   C7   C6   120.34  3.000
 SBQ  H2   C2   O2   111.13  3.000
 SBQ  H2   C2   C3   109.37  3.000
 SBQ  O2   C2   C3   109.91  3.000
 SBQ  H2   C2   C1   108.80  3.000
 SBQ  C3   C2   C1   108.98  3.000
 SBQ  O2   C2   C1   108.62  3.000
 SBQ  H6   O1   C1   108.38  3.000
 SBQ  H    C    C5   108.23  3.000
 SBQ  H    C    C1   109.29  3.000
 SBQ  C5   C    C1   110.04  3.000
 SBQ  H    C    O    111.22  3.000
 SBQ  C5   C    O    109.56  3.000
 SBQ  C1   C    O    108.50  3.000
 SBQ  H5   O    C    108.65  3.000
 SBQ  H1   C1   C    107.59  3.000
 SBQ  H1   C1   O1   110.78  3.000
 SBQ  C    C1   O1   111.89  3.000
 SBQ  H1   C1   C2   108.18  3.000
 SBQ  C    C1   C2   109.66  3.000
 SBQ  O1   C1   C2   108.68  3.000
 SBQ  H13  C11  C10  119.96  3.000
 SBQ  H13  C11  C12  119.29  3.000
 SBQ  C10  C11  C12  120.74  3.000
 SBQ  H15  C13  C14  120.30  3.000
 SBQ  H15  C13  C12  119.99  3.000
 SBQ  C14  C13  C12  119.71  3.000
 SBQ  C17  C14  C15  122.02  3.000
 SBQ  C15  C14  C13  118.17  3.000
 SBQ  C17  C14  C13  119.81  3.000
 SBQ  O7   C15  O6   123.56  3.000
 SBQ  O7   C15  C14  123.60  3.000
 SBQ  O6   C15  C14  112.84  3.000
 SBQ  H16  C16  H17  109.36  3.000
 SBQ  H16  C16  H18  109.39  3.000
 SBQ  H17  C16  H18  109.46  3.000
 SBQ  H16  C16  O6   111.33  3.000
 SBQ  H17  C16  O6   111.36  3.000
 SBQ  H18  C16  O6   105.86  3.000
 SBQ  H19  C17  C14  120.03  3.000
 SBQ  H19  C17  C10  119.10  3.000
 SBQ  C14  C17  C10  120.85  3.000
 SBQ  H20  C18  C9   120.45  3.000
 SBQ  H20  C18  C19  119.04  3.000
 SBQ  C9   C18  C19  120.50  3.000
 SBQ  CL   C19  C18  119.67  3.000
 SBQ  C18  C19  C6   121.53  3.000
 SBQ  CL   C19  C6   118.80  3.000
 SBQ  H3   C3   O4   110.18  3.000
 SBQ  H3   C3   C2   108.11  3.000
 SBQ  O4   C3   C2   110.90  3.000
 SBQ  H3   C3   C4   106.12  3.000
 SBQ  O4   C3   C4   107.59  3.000
 SBQ  C2   C3   C4   113.83  3.000
 SBQ  H4   C5   O5   110.06  3.000
 SBQ  H4   C5   O4   106.42  3.000
 SBQ  O5   C5   O4   112.08  3.000
 SBQ  H4   C5   C    110.00  3.000
 SBQ  O5   C5   C    105.83  3.000
 SBQ  O4   C5   C    112.49  3.000
 SBQ  H12  C8   C9   120.10  3.000
 SBQ  H12  C8   C7   118.27  3.000
 SBQ  C9   C8   C7   121.63  3.000
 SBQ  C8   C9   C18  117.98  3.000
 SBQ  C8   C9   C10  121.38  3.000
 SBQ  C18  C9   C10  120.64  3.000
 SBQ  H7   O2   C2   108.61  3.000
 SBQ  C5   O4   C3   115.31  3.000
 SBQ  C16  O6   C15  117.58  3.000
 SBQ  C5   O5   C6   120.49  3.000
 SBQ  H10  O3   C4   108.14  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
 SBQ  CONST_01  C9   C10  C11  C12   180.00   0.0  0
 SBQ  CONST_02  C17  C10  C11  C12     0.00   0.0  0
 SBQ  CONST_03  C17  C14  C13  C12     0.00   0.0  0
 SBQ  CONST_04  C19  C18  C9   C10   180.00   0.0  0
 SBQ  CONST_05  C7   C8   C9   C10   180.00   0.0  0
 SBQ  CONST_06  C13  C14  C17  C10     0.00   0.0  0
 SBQ  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 SBQ  CONST_08  C9   C18  C19  C6      0.00   0.0  0
 SBQ  CONST_09  C9   C8   C7   C6      0.00   0.0  0
 SBQ  CONST_10  C18  C19  C6   C7      0.00   0.0  0
 SBQ  CONST_11  C18  C9   C8   C7      0.00   0.0  0
 SBQ  CONST_14  C14  C17  C10  C11     0.00   0.0  0
 SBQ  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 SBQ  CONST_16  C9   C10  C17  C14   180.00   0.0  0
 SBQ  CONST_19  C8   C7   C6   C19     0.00   0.0  0
 SBQ  CONST_20  C8   C9   C18  C19     0.00   0.0  0
 SBQ  CONST_21  C15  C14  C13  C12   180.00   0.0  0
 SBQ  CONST_22  C15  C14  C17  C10   180.00   0.0  0
 SBQ  CONST_23  CL   C19  C6   C7    180.00   0.0  0
 SBQ  CONST_24  O5   C6   C19  C18   180.00   0.0  0
 SBQ  CONST_25  O5   C6   C7   C8    180.00   0.0  0
 SBQ  CONST_26  CL   C19  C18  C9    180.00   0.0  0
 SBQ  CONST_27  H20  C18  C9   C10     0.00   0.0  0
 SBQ  CONST_28  H12  C8   C9   C10     0.00   0.0  0
 SBQ  CONST_29  H14  C12  C11  C10   180.00   0.0  0
 SBQ  CONST_30  H19  C17  C10  C11   180.00   0.0  0
 SBQ  CONST_31  H15  C13  C12  C11   180.00   0.0  0
 SBQ  CONST_32  H13  C11  C12  C13   180.00   0.0  0
 SBQ  CONST_33  H11  C7   C6   C19   180.00   0.0  0
 SBQ  Var_01    O6   C15  C14  C13   179.20  30.0  2
 SBQ  Var_02    H18  C16  O6   C15  -179.06  30.0  3

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
 SBQ  chir_01  C2  O2  C1  C3  negativ
 SBQ  chir_02  C   O   C5  C1  positiv
 SBQ  chir_03  C1  O1  C   C2  positiv
 SBQ  chir_04  C3  O4  C2  C4  negativ
 SBQ  chir_05  C5  O4  O5  C   positiv

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
 SBQ  plan-1  C12  0.020
 SBQ  plan-1  C10  0.020
 SBQ  plan-1  C11  0.020
 SBQ  plan-1  C13  0.020
 SBQ  plan-1  C14  0.020
 SBQ  plan-1  C15  0.020
 SBQ  plan-1  C17  0.020
 SBQ  plan-1  C9   0.020
 SBQ  plan-1  H14  0.020
 SBQ  plan-1  H13  0.020
 SBQ  plan-1  H15  0.020
 SBQ  plan-1  H19  0.020
 SBQ  plan-2  C10  0.020
 SBQ  plan-2  C6   0.020
 SBQ  plan-2  C7   0.020
 SBQ  plan-2  C18  0.020
 SBQ  plan-2  C19  0.020
 SBQ  plan-2  C8   0.020
 SBQ  plan-2  C9   0.020
 SBQ  plan-2  CL   0.020
 SBQ  plan-2  H11  0.020
 SBQ  plan-2  H20  0.020
 SBQ  plan-2  H12  0.020
 SBQ  plan-2  O5   0.020
 SBQ  plan-3  C14  0.020
 SBQ  plan-3  C15  0.020
 SBQ  plan-3  O6   0.020
 SBQ  plan-3  O7   0.020

