# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:30:05 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)Oc2cc(O[C@@H]3O[C@H]([C@@H](O)[C@H](O)[C@H]3O)C(O)=O)ccc12
#
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
 8U8  8U8  '(2~{R},3~{S},4~{S},5~{R},6~{S})-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid'  ligand  41  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8U8
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
 8U8  C15  C  CH3   0  -0.749  -4.8769   2.1549   1.5807
 8U8  C13  C  CR6   0   0.273  -4.5173   0.9813   0.7339
 8U8  C14  C  CR16  0  -0.556  -5.4397   0.3512  -0.0266
 8U8  C16  C  CR6   0   0.549  -5.1107  -0.7822  -0.8564
 8U8  O9   O  O     0  -0.439  -5.8767  -1.3951  -1.5596
 8U8  O8   O  O     0  -0.470  -3.8160  -1.1982  -0.8450
 8U8  C11  C  CR66  0   0.400  -2.8587  -0.5993  -0.1011
 8U8  C10  C  CR16  0  -0.436  -1.5830  -1.1244  -0.1851
 8U8  C12  C  CR66  0  -0.053  -3.1575   0.4974   0.7112
 8U8  C7   C  CR16  0  -0.318  -2.1083   1.0541   1.4466
 8U8  C8   C  CR16  0  -0.349  -0.8245   0.5538   1.3806
 8U8  C9   C  CR6   0   0.403  -0.5595  -0.5499   0.5603
 8U8  O2   O  O2    0  -0.488   0.6426  -1.1376   0.4258
 8U8  C5   C  CH1   0   0.207   1.7679  -0.6389   1.1154
 8U8  O1   O  O2    0  -0.484   2.1251   0.6280   0.6804
 8U8  C1   C  CH1   0  -0.088   2.5581   0.7119  -0.6579
 8U8  C6   C  C     0   0.514   2.8779   2.1696  -0.9078
 8U8  O7   O  OH1   0  -0.594   3.2297   2.3578  -2.1717
 8U8  O6   O  O     0  -0.420   2.8138   3.0425  -0.0858
 8U8  C2   C  CH1   0  -0.003   3.7928  -0.1579  -0.9085
 8U8  O5   O  OH1   0  -0.666   4.8932   0.3706  -0.2099
 8U8  C3   C  CH1   0   0.004   3.5005  -1.5964  -0.4705
 8U8  O4   O  OH1   0  -0.664   2.6185  -2.1125  -1.4362
 8U8  C4   C  CH1   0  -0.023   2.8957  -1.6632   0.9374
 8U8  O3   O  OH1   0  -0.658   3.9181  -1.3982   1.8608
 8U8  H1   H  HCH3  0   0.269  -5.9353   2.3905   1.4981
 8U8  H2   H  HCH3  0   0.265  -4.6490   1.9642   2.6304
 8U8  H3   H  HCH3  0   0.266  -4.3048   3.0352   1.2829
 8U8  H4   H  HCR6  0   0.280  -6.4708   0.6767  -0.0433
 8U8  H5   H  HCR6  0   0.289  -1.3829  -1.9769  -0.8217
 8U8  H6   H  HCR6  0   0.277  -2.2944   1.9080   2.0840
 8U8  H7   H  HCR6  0   0.293  -0.0520   1.0362   1.9599
 8U8  H8   H  HCH1  0   0.268   1.5347  -0.5321   2.1815
 8U8  H9   H  HCH1  0   0.284   1.7621   0.4176  -1.3549
 8U8  H10  H  HOH1  0   0.489   3.4377   3.2913  -2.3280
 8U8  H11  H  HCH1  0   0.263   3.9812  -0.1819  -1.9864
 8U8  H12  H  HOH1  0   0.463   5.5659   0.6231  -0.8470
 8U8  H13  H  HCH1  0   0.241   4.4480  -2.1533  -0.4571
 8U8  H14  H  HOH1  0   0.456   2.3074  -2.9776  -1.1512
 8U8  H15  H  HCH1  0   0.248   2.4765  -2.6673   1.0934
 8U8  H16  H  HOH1  0   0.458   3.6228  -1.6824   2.7316

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
 8U8  O6   C6   double    1.201  0.020  1.201
 8U8  O5   C2   single    1.406  0.020  1.406
 8U8  C6   O7   single    1.325  0.020  1.325
 8U8  C6   C1   single    1.513  0.020  1.513
 8U8  O1   C5   single    1.386  0.020  1.386
 8U8  O1   C1   single    1.409  0.020  1.409
 8U8  O2   C5   single    1.411  0.020  1.411
 8U8  O2   C9   single    1.345  0.020  1.345
 8U8  C5   C4   single    1.534  0.020  1.534
 8U8  C2   C1   single    1.531  0.020  1.531
 8U8  C2   C3   single    1.532  0.020  1.532
 8U8  C10  C9   aromatic  1.390  0.020  1.390
 8U8  C10  C11  aromatic  1.382  0.020  1.382
 8U8  O8   C11  single    1.352  0.020  1.352
 8U8  O8   C16  single    1.360  0.020  1.360
 8U8  C9   C8   aromatic  1.400  0.020  1.400
 8U8  C3   C4   single    1.534  0.020  1.534
 8U8  C3   O4   single    1.406  0.020  1.406
 8U8  O9   C16  double    1.207  0.020  1.207
 8U8  C11  C12  aromatic  1.397  0.020  1.397
 8U8  C4   O3   single    1.403  0.020  1.403
 8U8  C16  C14  single    1.443  0.020  1.443
 8U8  C8   C7   aromatic  1.379  0.020  1.379
 8U8  C12  C7   aromatic  1.397  0.020  1.397
 8U8  C12  C13  single    1.443  0.020  1.443
 8U8  C14  C13  double    1.351  0.020  1.351
 8U8  C13  C15  single    1.491  0.020  1.491
 8U8  C15  H1   single    0.970  0.020  1.090
 8U8  C15  H2   single    0.970  0.020  1.090
 8U8  C15  H3   single    0.970  0.020  1.090
 8U8  C14  H4   single    0.930  0.020  1.080
 8U8  C10  H5   single    0.930  0.020  1.080
 8U8  C7   H6   single    0.930  0.020  1.080
 8U8  C8   H7   single    0.930  0.020  1.080
 8U8  C5   H8   single    0.970  0.020  1.090
 8U8  C1   H9   single    0.970  0.020  1.090
 8U8  O7   H10  single    0.850  0.020  0.980
 8U8  C2   H11  single    0.970  0.020  1.090
 8U8  O5   H12  single    0.850  0.020  0.980
 8U8  C3   H13  single    0.970  0.020  1.090
 8U8  O4   H14  single    0.850  0.020  0.980
 8U8  C4   H15  single    0.970  0.020  1.090
 8U8  O3   H16  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
 8U8  H3   C15  H2   107.10  3.000
 8U8  H3   C15  H1   108.34  3.000
 8U8  H2   C15  H1   108.32  3.000
 8U8  H3   C15  C13  110.70  3.000
 8U8  H2   C15  C13  111.01  3.000
 8U8  H1   C15  C13  111.23  3.000
 8U8  C12  C13  C14  118.54  3.000
 8U8  C14  C13  C15  121.46  3.000
 8U8  C12  C13  C15  119.99  3.000
 8U8  H4   C14  C16  116.42  3.000
 8U8  H4   C14  C13  121.27  3.000
 8U8  C16  C14  C13  122.30  3.000
 8U8  O8   C16  O9   116.98  3.000
 8U8  O9   C16  C14  126.11  3.000
 8U8  O8   C16  C14  116.91  3.000
 8U8  C11  O8   C16  122.89  3.000
 8U8  C12  C11  C10  122.07  3.000
 8U8  C12  C11  O8   121.07  3.000
 8U8  C10  C11  O8   116.85  3.000
 8U8  H5   C10  C9   120.30  3.000
 8U8  H5   C10  C11  120.37  3.000
 8U8  C9   C10  C11  119.33  3.000
 8U8  C7   C12  C11  117.28  3.000
 8U8  C7   C12  C13  124.45  3.000
 8U8  C11  C12  C13  118.28  3.000
 8U8  H6   C7   C8   118.34  3.000
 8U8  H6   C7   C12  119.71  3.000
 8U8  C8   C7   C12  121.95  3.000
 8U8  H7   C8   C9   122.08  3.000
 8U8  H7   C8   C7   118.57  3.000
 8U8  C9   C8   C7   119.34  3.000
 8U8  O2   C9   C8   124.90  3.000
 8U8  C8   C9   C10  120.02  3.000
 8U8  O2   C9   C10  115.07  3.000
 8U8  C5   O2   C9   120.63  3.000
 8U8  H8   C5   C4   109.53  3.000
 8U8  H8   C5   O1   105.72  3.000
 8U8  C4   C5   O1   112.60  3.000
 8U8  H8   C5   O2   109.88  3.000
 8U8  C4   C5   O2   107.08  3.000
 8U8  O1   C5   O2   112.03  3.000
 8U8  C1   O1   C5   115.57  3.000
 8U8  H9   C1   C2   109.17  3.000
 8U8  H9   C1   C6   107.85  3.000
 8U8  C2   C1   C6   110.48  3.000
 8U8  H9   C1   O1   111.35  3.000
 8U8  C2   C1   O1   111.68  3.000
 8U8  C6   C1   O1   106.21  3.000
 8U8  O6   C6   O7   124.32  3.000
 8U8  O7   C6   C1   110.51  3.000
 8U8  O6   C6   C1   125.17  3.000
 8U8  H10  O7   C6   110.34  3.000
 8U8  H11  C2   C3   107.09  3.000
 8U8  H11  C2   O5   111.27  3.000
 8U8  C3   C2   O5   111.11  3.000
 8U8  H11  C2   C1   108.21  3.000
 8U8  C3   C2   C1   109.44  3.000
 8U8  O5   C2   C1   109.64  3.000
 8U8  H12  O5   C2   108.50  3.000
 8U8  H13  C3   C4   107.86  3.000
 8U8  H13  C3   O4   111.29  3.000
 8U8  C4   C3   O4   111.54  3.000
 8U8  H13  C3   C2   108.35  3.000
 8U8  O4   C3   C2   105.55  3.000
 8U8  C4   C3   C2   112.25  3.000
 8U8  H14  O4   C3   109.23  3.000
 8U8  H15  C4   O3   110.92  3.000
 8U8  H15  C4   C3   108.69  3.000
 8U8  O3   C4   C3   107.97  3.000
 8U8  H15  C4   C5   108.25  3.000
 8U8  O3   C4   C5   109.47  3.000
 8U8  C3   C4   C5   111.55  3.000
 8U8  H16  O3   C4   108.43  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
 8U8  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 8U8  CONST_02  C8   C7   C12  C11     0.00   0.0  0
 8U8  CONST_03  C7   C8   C9   C10     0.00   0.0  0
 8U8  CONST_04  C7   C12  C11  C10     0.00   0.0  0
 8U8  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 8U8  CONST_06  C9   C8   C7   C12     0.00   0.0  0
 8U8  CONST_07  O2   C9   C10  C11   180.00   0.0  0
 8U8  CONST_08  O2   C9   C8   C7    180.00   0.0  0
 8U8  CONST_09  H6   C7   C12  C13     0.00   0.0  0
 8U8  CONST_10  H5   C10  C11  O8      0.00   0.0  0
 8U8  CONST_11  H7   C8   C9   C10   180.00   0.0  0
 8U8  CONST_12  H10  O7   C6   C1    180.00   0.0  0
 8U8  Var_01    O8   C16  C14  C13    -0.06  30.0  1
 8U8  Var_02    C11  C12  C13  C14     0.20  30.0  1
 8U8  Var_03    C10  C11  O8   C16  -179.94  30.0  1
 8U8  Var_04    C12  C13  C14  C16    -0.05  30.0  1
 8U8  Var_05    H1   C15  C13  C14     0.76  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
 8U8  chir_01  C5  O1  O2  C4  negativ
 8U8  chir_02  C1  O1  C6  C2  negativ
 8U8  chir_03  C2  O5  C1  C3  positiv
 8U8  chir_04  C3  O4  C4  C2  positiv
 8U8  chir_05  C4  O3  C3  C5  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
 8U8  plan-1  C1   0.020
 8U8  plan-1  C6   0.020
 8U8  plan-1  O7   0.020
 8U8  plan-1  O6   0.020
 8U8  plan-1  H10  0.020
 8U8  plan-2  C13  0.020
 8U8  plan-2  O8   0.020
 8U8  plan-2  C11  0.020
 8U8  plan-2  C10  0.020
 8U8  plan-2  C12  0.020
 8U8  plan-2  C7   0.020
 8U8  plan-2  C8   0.020
 8U8  plan-2  C9   0.020
 8U8  plan-2  O2   0.020
 8U8  plan-2  H5   0.020
 8U8  plan-2  H6   0.020
 8U8  plan-2  H7   0.020
 8U8  plan-3  C14  0.020
 8U8  plan-3  C16  0.020
 8U8  plan-3  O9   0.020
 8U8  plan-3  O8   0.020

