# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:00:47 2022
#   Inital geometry file: a 154 line input string
#   Ligand name: 5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](OC2=C(Oc3cc(O)cc(O)c3C2=O)c4ccc(O)cc4)[C@H](O)[C@H](OC(C)=O)[C@H]1OC(C)=O
#
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
 SL0  SL0  '5,7-dihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-3-yl 3,4-di-O-acetyl-6-deoxy-alpha-L-mannopyranoside'  ligand  61  37  .  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_SL0
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
 SL0  C1    C  CH3   0  -0.771   5.2514   3.5334   1.4752
 SL0  C2    C  C     0   0.568   3.9487   2.7942   1.4500
 SL0  O1    O  O     0  -0.447   3.1340   2.7860   2.3371
 SL0  O2    O  O2    0  -0.464   3.7829   2.1477   0.2951
 SL0  C3    C  CH1   0  -0.000   2.5974   1.3871   0.0913
 SL0  C4    C  CH1   0  -0.039   1.4382   2.2624  -0.3676
 SL0  O3    O  OH1   0  -0.665   1.8641   2.9812  -1.4937
 SL0  C5    C  CH1   0   0.012   2.9196   0.3561  -0.9782
 SL0  O4    O  O2    0  -0.466   3.9081  -0.5242  -0.4545
 SL0  C6    C  C     0   0.564   5.1532  -0.5068  -0.9387
 SL0  O5    O  O     0  -0.442   5.5062   0.1722  -1.8668
 SL0  C7    C  CH3   0  -0.776   6.0381  -1.4294  -0.1572
 SL0  C8    C  CH1   0   0.013   1.6775  -0.4838  -1.2846
 SL0  C9    C  CH3   0  -0.689   1.8868  -1.4270  -2.4490
 SL0  O6    O  O2    0  -0.482   0.5871   0.3642  -1.6254
 SL0  C10   C  CH1   0   0.239   0.2506   1.3645  -0.7273
 SL0  O7    O  O2    0  -0.505  -0.2479   0.8454   0.4933
 SL0  C11   C  CR6   0   0.114  -1.5242   0.3806   0.4488
 SL0  C12   C  CR6   0   0.431  -2.6048   1.3655   0.3857
 SL0  O8    O  O     0  -0.433  -2.3572   2.5632   0.4057
 SL0  C13   C  CR6   0   0.247  -1.7719  -0.9432   0.5089
 SL0  C14   C  CR6   0  -0.023  -0.7723  -2.0029   0.6538
 SL0  C15   C  CR16  0  -0.250   0.2004  -1.9440   1.6497
 SL0  C16   C  CR16  0  -0.370   1.1534  -2.9404   1.7689
 SL0  C17   C  CR6   0   0.364   1.1505  -4.0162   0.8828
 SL0  O9    O  OH1   0  -0.622   2.0566  -5.0046   0.9369
 SL0  C18   C  CR16  0  -0.325   0.1714  -4.0906  -0.1081
 SL0  C19   C  CR16  0  -0.251  -0.7818  -3.0965  -0.2129
 SL0  O10   O  O     0  -0.459  -3.0263  -1.4214   0.4429
 SL0  C20   C  CR66  0   0.404  -4.0906  -0.6076   0.2981
 SL0  C21   C  CR16  0  -0.472  -5.3116  -1.2488   0.1861
 SL0  C22   C  CR6   0   0.400  -6.4486  -0.4660   0.0544
 SL0  O11   O  OH1   0  -0.617  -7.6216  -1.0951  -0.0577
 SL0  C23   C  CR16  0  -0.538  -6.3559   0.9272   0.0418
 SL0  C24   C  CR6   0   0.388  -5.1248   1.5488   0.1559
 SL0  C25   C  CR66  0  -0.276  -3.9389   0.7854   0.2816
 SL0  O12   O  OH1   0  -0.595  -5.0232   2.8784   0.1438
 SL0  H733  H  HCH3  0   0.280   5.1823   4.4129   0.8322
 SL0  H731  H  HCH3  0   0.265   5.4814   3.8617   2.4847
 SL0  H732  H  HCH3  0   0.267   6.0662   2.9183   1.0962
 SL0  H23   H  HCH1  0   0.272   2.3150   0.8751   1.0165
 SL0  H22   H  HCH1  0   0.261   1.1293   2.9299   0.4445
 SL0  H1    H  HOH1  0   0.464   1.2347   3.6880  -1.6666
 SL0  H24   H  HCH1  0   0.270   3.2777   0.8437  -1.8876
 SL0  H643  H  HCH3  0   0.268   5.5473  -2.3808   0.0413
 SL0  H642  H  HCH3  0   0.265   6.9702  -1.6032  -0.6871
 SL0  H641  H  HCH3  0   0.277   6.2696  -0.9767   0.8088
 SL0  H25   H  HCH1  0   0.252   1.4328  -1.0698  -0.3935
 SL0  H512  H  HCH3  0   0.238   2.6911  -2.1304  -2.2377
 SL0  H513  H  HCH3  0   0.249   0.9850  -2.0127  -2.6268
 SL0  H511  H  HCH3  0   0.234   2.1351  -0.8844  -3.3625
 SL0  H21   H  HCH1  0   0.263  -0.5150   1.9599  -1.2328
 SL0  H12   H  HCR6  0   0.266   0.2170  -1.1164   2.3457
 SL0  H13   H  HCR6  0   0.280   1.9005  -2.8753   2.5512
 SL0  H15   H  HCR6  0   0.271   0.1681  -4.9252  -0.7974
 SL0  H16   H  HCR6  0   0.267  -1.5236  -3.1647  -0.9983
 SL0  H8    H  HCR6  0   0.287  -5.3723  -2.3288   0.2050
 SL0  H6    H  HCR6  0   0.294  -7.2536   1.5283  -0.0603
 SL0  H221  H  HOH1  0   0.478   2.6746  -4.8647   1.6635
 SL0  H231  H  HOH1  0   0.484  -8.3463  -0.4642  -0.1409
 SL0  H241  H  HOH1  0   0.483  -5.8969   3.2748   0.0410

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
 SL0  C1   C2    single    1.498  0.020  1.498
 SL0  C1   H733  single    0.970  0.020  1.090
 SL0  C1   H731  single    0.970  0.020  1.090
 SL0  C1   H732  single    0.970  0.020  1.090
 SL0  C2   O2    single    1.334  0.020  1.334
 SL0  C2   O1    double    1.204  0.020  1.204
 SL0  O2   C3    single    1.423  0.020  1.423
 SL0  C3   C5    single    1.520  0.020  1.520
 SL0  C3   H23   single    0.970  0.020  1.090
 SL0  C4   C3    single    1.523  0.020  1.523
 SL0  C4   C10   single    1.532  0.020  1.532
 SL0  C4   H22   single    0.970  0.020  1.090
 SL0  O3   C4    single    1.402  0.020  1.402
 SL0  O3   H1    single    0.850  0.020  0.980
 SL0  C5   O4    single    1.423  0.020  1.423
 SL0  C5   C8    single    1.530  0.020  1.530
 SL0  C5   H24   single    0.970  0.020  1.090
 SL0  C6   C7    single    1.498  0.020  1.498
 SL0  C6   O4    single    1.336  0.020  1.336
 SL0  O5   C6    double    1.203  0.020  1.203
 SL0  C7   H643  single    0.970  0.020  1.090
 SL0  C7   H642  single    0.970  0.020  1.090
 SL0  C7   H641  single    0.970  0.020  1.090
 SL0  C8   C9    single    1.513  0.020  1.513
 SL0  C8   H25   single    0.970  0.020  1.090
 SL0  C9   H512  single    0.970  0.020  1.090
 SL0  C9   H513  single    0.970  0.020  1.090
 SL0  C9   H511  single    0.970  0.020  1.090
 SL0  O6   C8    single    1.423  0.020  1.423
 SL0  C10  O6    single    1.386  0.020  1.386
 SL0  C10  O7    single    1.417  0.020  1.417
 SL0  C10  H21   single    0.970  0.020  1.090
 SL0  O7   C11   single    1.359  0.020  1.359
 SL0  C11  C12   single    1.463  0.020  1.463
 SL0  C11  C13   double    1.348  0.020  1.348
 SL0  C12  C25   single    1.459  0.020  1.459
 SL0  O8   C12   double    1.223  0.020  1.223
 SL0  C13  C14   single    1.464  0.020  1.464
 SL0  C13  O10   single    1.344  0.020  1.344
 SL0  C14  C19   aromatic  1.395  0.020  1.395
 SL0  C15  C16   aromatic  1.384  0.020  1.384
 SL0  C15  C14   aromatic  1.393  0.020  1.393
 SL0  C15  H12   single    0.930  0.020  1.080
 SL0  C16  C17   aromatic  1.394  0.020  1.394
 SL0  C16  H13   single    0.930  0.020  1.080
 SL0  C17  O9    single    1.342  0.020  1.342
 SL0  C17  C18   aromatic  1.395  0.020  1.395
 SL0  C18  H15   single    0.930  0.020  1.080
 SL0  C19  C18   aromatic  1.381  0.020  1.381
 SL0  C19  H16   single    0.930  0.020  1.080
 SL0  O10  C20   single    1.348  0.020  1.348
 SL0  C20  C21   aromatic  1.384  0.020  1.384
 SL0  C21  C22   aromatic  1.387  0.020  1.387
 SL0  C21  H8    single    0.930  0.020  1.080
 SL0  C22  O11   single    1.336  0.020  1.336
 SL0  C23  C22   aromatic  1.396  0.020  1.396
 SL0  C23  H6    single    0.930  0.020  1.080
 SL0  C24  C23   aromatic  1.384  0.020  1.384
 SL0  C25  C24   aromatic  1.416  0.020  1.416
 SL0  C25  C20   aromatic  1.401  0.020  1.401
 SL0  O12  C24   single    1.333  0.020  1.333
 SL0  O9   H221  single    0.850  0.020  0.980
 SL0  O11  H231  single    0.850  0.020  0.980
 SL0  O12  H241  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
 SL0  H732  C1   H731  109.62  3.000
 SL0  H732  C1   H733  107.30  3.000
 SL0  H731  C1   H733  108.50  3.000
 SL0  H732  C1   C2    111.48  3.000
 SL0  H731  C1   C2    110.42  3.000
 SL0  H733  C1   C2    109.43  3.000
 SL0  O2    C2   O1    123.39  3.000
 SL0  O1    C2   C1    125.39  3.000
 SL0  O2    C2   C1    111.21  3.000
 SL0  C3    O2   C2    119.11  3.000
 SL0  H23   C3   C5    109.39  3.000
 SL0  H23   C3   C4    109.09  3.000
 SL0  C5    C3   C4    109.82  3.000
 SL0  C4    C3   O2    111.72  3.000
 SL0  H23   C3   O2    110.11  3.000
 SL0  C5    C3   O2    106.66  3.000
 SL0  H22   C4   C10   108.22  3.000
 SL0  H22   C4   O3    111.63  3.000
 SL0  C10   C4   O3    110.33  3.000
 SL0  O3    C4   C3    107.78  3.000
 SL0  H22   C4   C3    109.96  3.000
 SL0  C10   C4   C3    108.90  3.000
 SL0  H1    O3   C4    108.79  3.000
 SL0  H24   C5   C8    110.15  3.000
 SL0  H24   C5   O4    110.78  3.000
 SL0  C8    C5   O4    107.33  3.000
 SL0  H24   C5   C3    110.64  3.000
 SL0  C8    C5   C3    109.94  3.000
 SL0  O4    C5   C3    107.93  3.000
 SL0  C6    O4   C5    120.38  3.000
 SL0  C7    C6   O5    125.21  3.000
 SL0  O5    C6   O4    124.09  3.000
 SL0  C7    C6   O4    110.69  3.000
 SL0  H641  C7   H642  108.43  3.000
 SL0  H641  C7   H643  107.25  3.000
 SL0  H642  C7   H643  109.63  3.000
 SL0  H641  C7   C6    109.35  3.000
 SL0  H642  C7   C6    110.54  3.000
 SL0  H643  C7   C6    111.53  3.000
 SL0  H25   C8   O6    110.06  3.000
 SL0  O6    C8   C9    107.05  3.000
 SL0  H25   C8   C9    108.90  3.000
 SL0  O6    C8   C5    110.05  3.000
 SL0  H25   C8   C5    108.20  3.000
 SL0  C9    C8   C5    112.57  3.000
 SL0  H511  C9   H513  108.60  3.000
 SL0  H511  C9   H512  108.39  3.000
 SL0  H513  C9   H512  107.20  3.000
 SL0  H511  C9   C8    111.46  3.000
 SL0  H513  C9   C8    110.25  3.000
 SL0  H512  C9   C8    110.82  3.000
 SL0  C10   O6   C8    117.46  3.000
 SL0  H21   C10  O7    110.57  3.000
 SL0  H21   C10  O6    105.27  3.000
 SL0  O7    C10  O6    112.29  3.000
 SL0  H21   C10  C4    109.40  3.000
 SL0  O7    C10  C4    106.58  3.000
 SL0  O6    C10  C4    112.77  3.000
 SL0  C11   O7   C10   115.31  3.000
 SL0  C13   C11  C12   121.82  3.000
 SL0  C13   C11  O7    120.46  3.000
 SL0  C12   C11  O7    117.69  3.000
 SL0  C25   C12  O8    125.15  3.000
 SL0  O8    C12  C11   120.59  3.000
 SL0  C25   C12  C11   114.25  3.000
 SL0  O10   C13  C14   112.61  3.000
 SL0  O10   C13  C11   121.24  3.000
 SL0  C14   C13  C11   126.14  3.000
 SL0  C19   C14  C15   118.80  3.000
 SL0  C15   C14  C13   121.12  3.000
 SL0  C19   C14  C13   120.08  3.000
 SL0  H12   C15  C16   119.01  3.000
 SL0  H12   C15  C14   120.20  3.000
 SL0  C16   C15  C14   120.79  3.000
 SL0  H13   C16  C17   120.45  3.000
 SL0  H13   C16  C15   119.58  3.000
 SL0  C17   C16  C15   119.97  3.000
 SL0  C18   C17  O9    117.60  3.000
 SL0  C18   C17  C16   119.62  3.000
 SL0  O9    C17  C16   122.78  3.000
 SL0  H221  O9   C17   110.87  3.000
 SL0  H15   C18  C19   120.30  3.000
 SL0  C19   C18  C17   119.99  3.000
 SL0  H15   C18  C17   119.71  3.000
 SL0  H16   C19  C18   118.86  3.000
 SL0  H16   C19  C14   120.31  3.000
 SL0  C18   C19  C14   120.81  3.000
 SL0  C20   O10  C13   121.83  3.000
 SL0  C25   C20  C21   123.72  3.000
 SL0  C25   C20  O10   121.07  3.000
 SL0  C21   C20  O10   115.20  3.000
 SL0  H8    C21  C22   121.27  3.000
 SL0  H8    C21  C20   120.71  3.000
 SL0  C22   C21  C20   118.01  3.000
 SL0  C23   C22  O11   121.83  3.000
 SL0  C23   C22  C21   120.64  3.000
 SL0  O11   C22  C21   117.53  3.000
 SL0  H231  O11  C22   111.04  3.000
 SL0  H6    C23  C24   119.66  3.000
 SL0  C24   C23  C22   120.43  3.000
 SL0  H6    C23  C22   119.91  3.000
 SL0  O12   C24  C25   118.33  3.000
 SL0  O12   C24  C23   120.99  3.000
 SL0  C25   C24  C23   120.68  3.000
 SL0  C24   C25  C20   116.51  3.000
 SL0  C20   C25  C12   119.57  3.000
 SL0  C24   C25  C12   123.91  3.000
 SL0  H241  O12  C24   109.97  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
 SL0  CONST_01  C17   C18  C19  C14     0.00   0.0  0
 SL0  CONST_02  C17   C16  C15  C14     0.00   0.0  0
 SL0  CONST_03  C18   C17  C16  C15     0.00   0.0  0
 SL0  CONST_04  C18   C19  C14  C15     0.00   0.0  0
 SL0  CONST_05  C19   C14  C15  C16     0.00   0.0  0
 SL0  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 SL0  CONST_07  C23   C22  C21  C20     0.00   0.0  0
 SL0  CONST_08  C23   C24  C25  C20     0.00   0.0  0
 SL0  CONST_09  C24   C25  C20  C21     0.00   0.0  0
 SL0  CONST_10  C24   C23  C22  C21     0.00   0.0  0
 SL0  CONST_11  C25   C20  C21  C22     0.00   0.0  0
 SL0  CONST_12  C25   C24  C23  C22     0.00   0.0  0
 SL0  CONST_13  C18   C19  C14  C13   180.00   0.0  0
 SL0  CONST_14  C16   C15  C14  C13   180.00   0.0  0
 SL0  CONST_15  O12   C24  C25  C12     0.00   0.0  0
 SL0  CONST_16  O9    C17  C16  C15   180.00   0.0  0
 SL0  CONST_17  C19   C18  C17  O9    180.00   0.0  0
 SL0  CONST_18  O11   C22  C21  C20   180.00   0.0  0
 SL0  CONST_19  O12   C24  C25  C20   180.00   0.0  0
 SL0  CONST_20  O12   C24  C23  C22   180.00   0.0  0
 SL0  CONST_21  C24   C23  C22  O11   180.00   0.0  0
 SL0  CONST_22  H16   C19  C14  C13     0.00   0.0  0
 SL0  CONST_23  H12   C15  C14  C13     0.00   0.0  0
 SL0  CONST_24  H15   C18  C19  C14   180.00   0.0  0
 SL0  CONST_25  H13   C16  C15  C14   180.00   0.0  0
 SL0  CONST_26  H8    C21  C20  O10     0.00   0.0  0
 SL0  CONST_27  H6    C23  C22  C21   180.00   0.0  0
 SL0  Var_01    C24   C25  C12  C11  -177.48  30.0  1
 SL0  Var_02    C19   C14  C13  C11  -129.82  30.0  2
 SL0  Var_03    C14   C13  C11  C12  -176.15  30.0  1
 SL0  Var_04    C25   C12  C11  C13    -4.85  30.0  1
 SL0  Var_05    C21   C20  O10  C13   177.24  30.0  1
 SL0  Var_06    C12   C11  O7   C10   -73.85  30.0  3
 SL0  Var_07    C7    C6   O4   C5    175.11  30.0  2
 SL0  Var_08    H733  C1   C2   O1   -105.38  30.0  3
 SL0  Var_09    H643  C7   C6   O4     43.88  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
 SL0  chir_01  C3   O2  C5  C4   positiv
 SL0  chir_02  C4   O3  C3  C10  positiv
 SL0  chir_03  C5   O4  C8  C3   negativ
 SL0  chir_04  C8   O6  C5  C9   positiv
 SL0  chir_05  C10  O7  O6  C4   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
 SL0  plan-1  C13  0.020
 SL0  plan-1  C14  0.020
 SL0  plan-1  C15  0.020
 SL0  plan-1  C16  0.020
 SL0  plan-1  C17  0.020
 SL0  plan-1  O9   0.020
 SL0  plan-1  C18  0.020
 SL0  plan-1  C19  0.020
 SL0  plan-1  H12  0.020
 SL0  plan-1  H13  0.020
 SL0  plan-1  H15  0.020
 SL0  plan-1  H16  0.020
 SL0  plan-2  C12  0.020
 SL0  plan-2  O10  0.020
 SL0  plan-2  C20  0.020
 SL0  plan-2  C21  0.020
 SL0  plan-2  C22  0.020
 SL0  plan-2  O11  0.020
 SL0  plan-2  C23  0.020
 SL0  plan-2  C24  0.020
 SL0  plan-2  C25  0.020
 SL0  plan-2  O12  0.020
 SL0  plan-2  H8   0.020
 SL0  plan-2  H6   0.020
 SL0  plan-3  C11  0.020
 SL0  plan-3  C12  0.020
 SL0  plan-3  O8   0.020
 SL0  plan-3  C25  0.020
 SL0  plan-4  C1   0.020
 SL0  plan-4  C2   0.020
 SL0  plan-4  O1   0.020
 SL0  plan-4  O2   0.020
 SL0  plan-5  O4   0.020
 SL0  plan-5  C6   0.020
 SL0  plan-5  O5   0.020
 SL0  plan-5  C7   0.020

