# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:22:18 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  40  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  -4.8214   2.1700   1.5787
 8U8  C13  C  C      0   0.272  -4.4846   0.9741   0.7539
 8U8  C14  C  C1     0  -0.557  -5.4298   0.3191   0.0438
 8U8  C16  C  C      0   0.548  -5.1247  -0.8375  -0.7623
 8U8  O9   O  O      0  -0.440  -5.9116  -1.4739  -1.4205
 8U8  O8   O  O2     0  -0.470  -3.8287  -1.2492  -0.7820
 8U8  C11  C  C      0   0.399  -2.8487  -0.6251  -0.0893
 8U8  C10  C  C1     0  -0.439  -1.5751  -1.1497  -0.1992
 8U8  C12  C  C      0  -0.054  -3.1248   0.4945   0.6997
 8U8  C7   C  C1     0  -0.317  -2.0530   1.0760   1.3819
 8U8  C8   C  C1     0  -0.352  -0.7705   0.5777   1.2879
 8U8  C9   C  C      0   0.406  -0.5277  -0.5517   0.4944
 8U8  O2   O  O2     0  -0.489   0.6682  -1.1405   0.3404
 8U8  C5   C  CH1    0   0.218   1.8001  -0.6726   1.0524
 8U8  O1   O  O2     0  -0.498   2.1906   0.5864   0.6392
 8U8  C1   C  CH1    0  -0.148   2.6687   0.6702  -0.7052
 8U8  C6   C  C      0   0.444   2.9629   2.1703  -0.9377
 8U8  O7   O  OC    -1  -0.608   4.0431   2.5997  -0.4533
 8U8  O6   O  O      0  -0.567   2.1226   2.8303  -1.5572
 8U8  C2   C  CH1    0   0.028   3.8937  -0.2234  -0.8986
 8U8  O5   O  OH1    0  -0.705   4.9965   0.2098  -0.1545
 8U8  C3   C  CH1    0   0.003   3.5589  -1.6611  -0.5007
 8U8  O4   O  OH1    0  -0.667   2.7124  -2.1664  -1.5055
 8U8  C4   C  CH1    0  -0.021   2.8934  -1.7363   0.8816
 8U8  O3   O  OH1    0  -0.661   3.8818  -1.5586   1.8630
 8U8  H1   H  HCH3   0   0.269  -5.8812   2.4056   1.5162
 8U8  H2   H  HCH3   0   0.265  -4.5687   2.0050   2.6271
 8U8  H3   H  HCH3   0   0.265  -4.2553   3.0416   1.2460
 8U8  H4   H  H      0   0.279  -6.4623   0.6409   0.0527
 8U8  H5   H  H      0   0.287  -1.3938  -2.0216  -0.8149
 8U8  H6   H  H      0   0.276  -2.2216   1.9489   1.9982
 8U8  H7   H  H      0   0.292   0.0209   1.0820   1.8209
 8U8  H8   H  HCH1   0   0.257   1.5471  -0.5784   2.1161
 8U8  H9   H  HCH1   0   0.225   1.8884   0.3540  -1.4040
 8U8  H11  H  HCH1   0   0.204   4.1156  -0.2245  -1.9796
 8U8  H12  H  HOH1   0   0.438   4.8969   1.1906  -0.1305
 8U8  H13  H  HCH1   0   0.226   4.4937  -2.2383  -0.4451
 8U8  H14  H  HOH1   0   0.452   2.3982  -3.0366  -1.2419
 8U8  H15  H  HCH1   0   0.237   2.4224  -2.7245   0.9846
 8U8  H16  H  HOH1   0   0.455   3.5388  -1.8906   2.6985

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   deloc     1.235  0.020  1.235
 8U8  O5   C2   single    1.399  0.020  1.399
 8U8  C6   O7   deloc     1.259  0.020  1.259
 8U8  C6   C1   single    1.546  0.020  1.546
 8U8  O1   C5   single    1.381  0.020  1.381
 8U8  O1   C1   single    1.429  0.020  1.429
 8U8  O2   C5   single    1.417  0.020  1.417
 8U8  O2   C9   single    1.342  0.020  1.342
 8U8  C5   C4   single    1.535  0.020  1.535
 8U8  C2   C1   single    1.529  0.020  1.529
 8U8  C2   C3   single    1.529  0.020  1.529
 8U8  C10  C9   aromatic  1.391  0.020  1.391
 8U8  C10  C11  aromatic  1.382  0.020  1.382
 8U8  O8   C11  single    1.353  0.020  1.353
 8U8  O8   C16  single    1.360  0.020  1.360
 8U8  C9   C8   aromatic  1.401  0.020  1.401
 8U8  C3   C4   single    1.536  0.020  1.536
 8U8  C3   O4   single    1.408  0.020  1.408
 8U8  O9   C16  double    1.207  0.020  1.207
 8U8  C11  C12  aromatic  1.397  0.020  1.397
 8U8  C4   O3   single    1.404  0.020  1.404
 8U8  C16  C14  single    1.442  0.020  1.442
 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    1.352  0.020  1.352
 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  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   107.08  3.000
 8U8  H3   C15  H1   108.36  3.000
 8U8  H2   C15  H1   108.29  3.000
 8U8  H3   C15  C13  110.77  3.000
 8U8  H2   C15  C13  110.97  3.000
 8U8  H1   C15  C13  111.23  3.000
 8U8  C12  C13  C14  118.57  3.000
 8U8  C14  C13  C15  121.42  3.000
 8U8  C12  C13  C15  120.01  3.000
 8U8  H4   C14  C16  116.44  3.000
 8U8  H4   C14  C13  121.27  3.000
 8U8  C16  C14  C13  122.29  3.000
 8U8  O8   C16  O9   116.98  3.000
 8U8  O9   C16  C14  126.12  3.000
 8U8  O8   C16  C14  116.90  3.000
 8U8  C11  O8   C16  122.91  3.000
 8U8  C12  C11  C10  122.09  3.000
 8U8  C12  C11  O8   121.05  3.000
 8U8  C10  C11  O8   116.87  3.000
 8U8  H5   C10  C9   120.23  3.000
 8U8  H5   C10  C11  120.36  3.000
 8U8  C9   C10  C11  119.41  3.000
 8U8  C7   C12  C11  117.24  3.000
 8U8  C7   C12  C13  124.48  3.000
 8U8  C11  C12  C13  118.28  3.000
 8U8  H6   C7   C8   118.38  3.000
 8U8  H6   C7   C12  119.63  3.000
 8U8  C8   C7   C12  121.98  3.000
 8U8  H7   C8   C9   121.94  3.000
 8U8  H7   C8   C7   118.65  3.000
 8U8  C9   C8   C7   119.40  3.000
 8U8  O2   C9   C8   124.96  3.000
 8U8  C8   C9   C10  119.88  3.000
 8U8  O2   C9   C10  115.16  3.000
 8U8  C5   O2   C9   120.63  3.000
 8U8  H8   C5   C4   109.36  3.000
 8U8  H8   C5   O1   106.07  3.000
 8U8  C4   C5   O1   113.39  3.000
 8U8  H8   C5   O2   109.35  3.000
 8U8  C4   C5   O2   106.51  3.000
 8U8  O1   C5   O2   112.12  3.000
 8U8  C1   O1   C5   115.43  3.000
 8U8  H9   C1   C2   108.77  3.000
 8U8  H9   C1   C6   108.67  3.000
 8U8  C2   C1   C6   113.30  3.000
 8U8  H9   C1   O1   110.20  3.000
 8U8  C2   C1   O1   110.66  3.000
 8U8  C6   C1   O1   105.19  3.000
 8U8  O6   C6   O7   126.46  3.000
 8U8  O7   C6   C1   115.86  3.000
 8U8  O6   C6   C1   117.67  3.000
 8U8  H11  C2   C3   107.34  3.000
 8U8  H11  C2   O5   111.27  3.000
 8U8  C3   C2   O5   108.99  3.000
 8U8  H11  C2   C1   106.60  3.000
 8U8  C3   C2   C1   109.95  3.000
 8U8  O5   C2   C1   112.55  3.000
 8U8  H12  O5   C2   103.96  3.000
 8U8  H13  C3   C4   107.28  3.000
 8U8  H13  C3   O4   111.03  3.000
 8U8  C4   C3   O4   111.36  3.000
 8U8  H13  C3   C2   108.69  3.000
 8U8  O4   C3   C2   106.47  3.000
 8U8  C4   C3   C2   112.03  3.000
 8U8  H14  O4   C3   109.00  3.000
 8U8  H15  C4   O3   110.47  3.000
 8U8  H15  C4   C3   108.29  3.000
 8U8  O3   C4   C3   108.53  3.000
 8U8  H15  C4   C5   107.90  3.000
 8U8  O3   C4   C5   109.63  3.000
 8U8  C3   C4   C5   112.02  3.000
 8U8  H16  O3   C4   108.20  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  Var_01    O8   C16  C14  C13   -0.08  30.0  1
 8U8  Var_02    C11  C12  C13  C14    0.17  30.0  1
 8U8  Var_03    C10  C11  O8   C16  179.99  30.0  1
 8U8  Var_04    C12  C13  C14  C16   -0.01  30.0  1
 8U8  Var_05    H1   C15  C13  C14    0.10  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-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

