# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:25:03 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: methyl (1R,2R,4S)-2-ethyl-2,4,5,7-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@]1(O)C[C@H](O)c2c(O)c3C(=O)c4c(O)cccc4C(=O)c3cc2[C@H]1C(=O)OC
#
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
 VAK  VAK  'methyl (1R,2R,4S)-2-ethyl-2,4,5,7-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate'  ligand  50  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VAK
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
 VAK  C1    C  CR16  0  -0.306  -4.5977   2.0533  -0.7939
 VAK  C2    C  CR16  0  -0.217  -5.9197   1.6353  -0.6449
 VAK  C3    C  CR16  0  -0.330  -6.2155   0.3672  -0.1984
 VAK  C4    C  CR6   0   0.388  -5.1868  -0.5294   0.1155
 VAK  C5    C  CR6   0   0.476  -2.7646  -1.0388   0.2969
 VAK  C6    C  CR6   0   0.383  -0.3286  -1.4750   0.4576
 VAK  C7    C  CH1   0  -0.027   2.1007  -2.0724   0.6272
 VAK  C8    C  CH2   0  -0.519   3.4944  -1.4616   0.5998
 VAK  C9    C  CT    0   0.234   3.6899  -0.4164  -0.4934
 VAK  C10   C  CH1   0  -0.480   2.6794   0.7321  -0.2816
 VAK  C11   C  CR16  0  -0.349   0.2250   1.0864  -0.4503
 VAK  C12   C  CR6   0   0.319  -2.1696   1.6422  -0.6523
 VAK  C13   C  CH2   0  -0.439   5.1308   0.1133  -0.5128
 VAK  C14   C  C     0   0.615   3.0082   1.5824   0.9322
 VAK  C15   C  CH3   0  -0.429   4.0424   3.5664   1.6610
 VAK  C16   C  CR66  0  -0.177  -3.8470  -0.1193  -0.0282
 VAK  O16   O  O2    0  -0.443   3.6444   2.6925   0.6016
 VAK  C17   C  CR66  0  -0.178  -1.3843  -0.6020   0.1503
 VAK  O17   O  O     0  -0.430   2.7161   1.2878   2.0638
 VAK  C18   C  CR66  0  -0.029  -1.0851   0.6914  -0.3109
 VAK  O18   O  O     0  -0.369  -1.9192   2.7599  -1.0524
 VAK  C19   C  CR6   0   0.176   1.2720   0.2144  -0.1352
 VAK  O19   O  OH1   0  -0.611  -5.5352  -1.7376   0.5370
 VAK  C20   C  CR6   0  -0.045   1.0117  -1.0646   0.3192
 VAK  O20   O  O     0  -0.527  -3.0196  -2.1893   0.6959
 VAK  C21   C  CR66  0  -0.033  -3.5710   1.1830  -0.4879
 VAK  O21   O  OH1   0  -0.620  -0.5350  -2.7123   0.8946
 VAK  C22   C  CH3   0  -0.684   6.1642  -0.9110  -0.9642
 VAK  O22   O  OH1   0  -0.667   2.0648  -3.1428  -0.3004
 VAK  O23   O  OH1   0  -0.673   3.3351  -0.9303  -1.7628
 VAK  H1    H  HCR6  0   0.274  -4.3800   3.0515  -1.1456
 VAK  H2    H  HCR6  0   0.281  -6.7264   2.3156  -0.8830
 VAK  H3    H  HCR6  0   0.287  -7.2428   0.0463  -0.0845
 VAK  H7    H  HCH1  0   0.244   1.9340  -2.4507   1.6426
 VAK  H8    H  HCH2  0   0.266   3.7131  -1.0159   1.5702
 VAK  H8A   H  HCH2  0   0.267   4.2141  -2.2771   0.4840
 VAK  H10   H  HCH1  0   0.309   2.7263   1.3707  -1.1684
 VAK  H11   H  HCR6  0   0.269   0.4543   2.0808  -0.8111
 VAK  H13   H  HCH2  0   0.238   5.1743   0.9804  -1.1780
 VAK  H13A  H  HCH2  0   0.227   5.4016   0.4714   0.4844
 VAK  H15   H  HCH3  0   0.256   4.5817   4.3807   1.1873
 VAK  H15A  H  HCH3  0   0.244   3.1769   3.9627   2.1909
 VAK  H15B  H  HCH3  0   0.242   4.6984   3.0605   2.3687
 VAK  HO19  H  HOH1  0   0.490  -4.7180  -2.2503   0.7153
 VAK  HO21  H  HOH1  0   0.495  -1.5047  -2.8723   0.9381
 VAK  H22   H  HCH3  0   0.227   6.2188  -1.7693  -0.2940
 VAK  H22A  H  HCH3  0   0.225   5.9575  -1.2804  -1.9688
 VAK  H22B  H  HCH3  0   0.241   7.1546  -0.4567  -0.9844
 VAK  HO22  H  HOH1  0   0.457   1.3056  -3.6984  -0.0970
 VAK  HO23  H  HOH1  0   0.451   3.6031  -1.8529  -1.8205

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
 VAK  C21  C1    aromatic  1.380  0.020  1.380
 VAK  C1   C2    aromatic  1.394  0.020  1.394
 VAK  C1   H1    single    0.930  0.020  1.080
 VAK  C3   C2    aromatic  1.377  0.020  1.377
 VAK  C2   H2    single    0.930  0.020  1.080
 VAK  C4   C3    aromatic  1.400  0.020  1.400
 VAK  C3   H3    single    0.930  0.020  1.080
 VAK  C16  C4    aromatic  1.408  0.020  1.408
 VAK  O19  C4    single    1.326  0.020  1.326
 VAK  C17  C5    single    1.455  0.020  1.455
 VAK  O20  C5    double    1.244  0.020  1.244
 VAK  C5   C16   single    1.457  0.020  1.457
 VAK  C20  C6    aromatic  1.409  0.020  1.409
 VAK  O21  C6    single    1.328  0.020  1.328
 VAK  C6   C17   aromatic  1.404  0.020  1.404
 VAK  C8   C7    single    1.522  0.020  1.522
 VAK  C7   O22   single    1.417  0.020  1.417
 VAK  C7   C20   single    1.515  0.020  1.515
 VAK  C7   H7    single    0.970  0.020  1.090
 VAK  C8   C9    single    1.525  0.020  1.525
 VAK  C8   H8    single    0.970  0.020  1.090
 VAK  C8   H8A   single    0.970  0.020  1.090
 VAK  C13  C9    single    1.535  0.020  1.535
 VAK  C9   O23   single    1.415  0.020  1.415
 VAK  C9   C10   single    1.544  0.020  1.544
 VAK  C14  C10   single    1.518  0.020  1.518
 VAK  C10  C19   single    1.507  0.020  1.507
 VAK  C10  H10   single    0.970  0.020  1.090
 VAK  C19  C11   aromatic  1.398  0.020  1.398
 VAK  C11  C18   aromatic  1.375  0.020  1.375
 VAK  C11  H11   single    0.930  0.020  1.080
 VAK  C18  C12   single    1.482  0.020  1.482
 VAK  C12  O18   double    1.213  0.020  1.213
 VAK  C12  C21   single    1.484  0.020  1.484
 VAK  C22  C13   single    1.523  0.020  1.523
 VAK  C13  H13   single    0.970  0.020  1.090
 VAK  C13  H13A  single    0.970  0.020  1.090
 VAK  O17  C14   double    1.205  0.020  1.205
 VAK  C14  O16   single    1.322  0.020  1.322
 VAK  C15  O16   single    1.430  0.020  1.430
 VAK  C15  H15   single    0.970  0.020  1.090
 VAK  C15  H15A  single    0.970  0.020  1.090
 VAK  C15  H15B  single    0.970  0.020  1.090
 VAK  C16  C21   aromatic  1.408  0.020  1.408
 VAK  C17  C18   aromatic  1.405  0.020  1.405
 VAK  C20  C19   aromatic  1.382  0.020  1.382
 VAK  O19  HO19  single    0.850  0.020  0.980
 VAK  O21  HO21  single    0.850  0.020  0.980
 VAK  C22  H22   single    0.970  0.020  1.090
 VAK  C22  H22A  single    0.970  0.020  1.090
 VAK  C22  H22B  single    0.970  0.020  1.090
 VAK  O22  HO22  single    0.850  0.020  0.980
 VAK  O23  HO23  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
 VAK  H1    C1   C21   120.31  3.000
 VAK  H1    C1   C2    120.18  3.000
 VAK  C21   C1   C2    119.51  3.000
 VAK  H2    C2   C3    119.37  3.000
 VAK  H2    C2   C1    119.67  3.000
 VAK  C3    C2   C1    120.96  3.000
 VAK  H3    C3   C4    118.94  3.000
 VAK  H3    C3   C2    120.75  3.000
 VAK  C4    C3   C2    120.31  3.000
 VAK  O19   C4   C16   123.20  3.000
 VAK  O19   C4   C3    117.49  3.000
 VAK  C16   C4   C3    119.31  3.000
 VAK  O20   C5   C17   120.28  3.000
 VAK  O20   C5   C16   120.20  3.000
 VAK  C17   C5   C16   119.52  3.000
 VAK  O21   C6   C20   116.84  3.000
 VAK  O21   C6   C17   122.30  3.000
 VAK  C20   C6   C17   120.85  3.000
 VAK  H7    C7   O22   109.99  3.000
 VAK  H7    C7   C20   107.96  3.000
 VAK  O22   C7   C20   110.56  3.000
 VAK  H7    C7   C8    107.12  3.000
 VAK  C20   C7   C8    112.80  3.000
 VAK  O22   C7   C8    108.34  3.000
 VAK  H8A   C8   H8    105.49  3.000
 VAK  H8A   C8   C9    110.54  3.000
 VAK  H8    C8   C9    109.40  3.000
 VAK  H8A   C8   C7    107.77  3.000
 VAK  H8    C8   C7    109.38  3.000
 VAK  C9    C8   C7    113.91  3.000
 VAK  O23   C9   C13   110.44  3.000
 VAK  O23   C9   C10   103.25  3.000
 VAK  C13   C9   C10   111.05  3.000
 VAK  C10   C9   C8    109.12  3.000
 VAK  O23   C9   C8    111.23  3.000
 VAK  C13   C9   C8    111.46  3.000
 VAK  H10   C10  C19   108.63  3.000
 VAK  H10   C10  C14   108.18  3.000
 VAK  C19   C10  C14   108.49  3.000
 VAK  H10   C10  C9    107.15  3.000
 VAK  C19   C10  C9    111.65  3.000
 VAK  C14   C10  C9    112.61  3.000
 VAK  H11   C11  C19   119.30  3.000
 VAK  H11   C11  C18   119.96  3.000
 VAK  C19   C11  C18   120.74  3.000
 VAK  C21   C12  O18   121.09  3.000
 VAK  C21   C12  C18   117.84  3.000
 VAK  O18   C12  C18   121.07  3.000
 VAK  H13A  C13  H13   106.57  3.000
 VAK  H13A  C13  C22   108.80  3.000
 VAK  H13   C13  C22   109.02  3.000
 VAK  H13A  C13  C9    109.50  3.000
 VAK  H13   C13  C9    108.58  3.000
 VAK  C22   C13  C9    114.10  3.000
 VAK  O17   C14  O16   123.84  3.000
 VAK  O16   C14  C10   112.01  3.000
 VAK  O17   C14  C10   124.14  3.000
 VAK  H15B  C15  H15A  109.34  3.000
 VAK  H15B  C15  H15   109.43  3.000
 VAK  H15A  C15  H15   109.51  3.000
 VAK  H15B  C15  O16   111.41  3.000
 VAK  H15A  C15  O16   111.20  3.000
 VAK  H15   C15  O16   105.87  3.000
 VAK  C21   C16  C5    120.72  3.000
 VAK  C21   C16  C4    119.27  3.000
 VAK  C5    C16  C4    120.01  3.000
 VAK  C15   O16  C14   117.52  3.000
 VAK  C18   C17  C6    118.95  3.000
 VAK  C18   C17  C5    120.75  3.000
 VAK  C6    C17  C5    120.30  3.000
 VAK  C17   C18  C12   120.68  3.000
 VAK  C17   C18  C11   120.02  3.000
 VAK  C12   C18  C11   119.30  3.000
 VAK  C20   C19  C11   120.67  3.000
 VAK  C20   C19  C10   121.72  3.000
 VAK  C11   C19  C10   117.59  3.000
 VAK  HO19  O19  C4    108.36  3.000
 VAK  C19   C20  C7    123.16  3.000
 VAK  C19   C20  C6    118.76  3.000
 VAK  C7    C20  C6    118.04  3.000
 VAK  C16   C21  C12   120.49  3.000
 VAK  C16   C21  C1    120.64  3.000
 VAK  C12   C21  C1    118.87  3.000
 VAK  HO21  O21  C6    108.62  3.000
 VAK  H22B  C22  H22A  107.25  3.000
 VAK  H22B  C22  H22   107.10  3.000
 VAK  H22A  C22  H22   108.01  3.000
 VAK  H22B  C22  C13   109.98  3.000
 VAK  H22A  C22  C13   111.85  3.000
 VAK  H22   C22  C13   112.41  3.000
 VAK  HO22  O22  C7    108.53  3.000
 VAK  HO23  O23  C9    109.40  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
 VAK  CONST_01  C4   C16  C21  C1     0.00   0.0  0
 VAK  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 VAK  CONST_03  C16  C21  C1   C2     0.00   0.0  0
 VAK  CONST_04  C16  C4   C3   C2     0.00   0.0  0
 VAK  CONST_05  C21  C1   C2   C3     0.00   0.0  0
 VAK  CONST_06  C21  C16  C4   C3     0.00   0.0  0
 VAK  CONST_07  C11  C19  C20  C6     0.00   0.0  0
 VAK  CONST_08  C11  C18  C17  C6     0.00   0.0  0
 VAK  CONST_09  C19  C20  C6   C17    0.00   0.0  0
 VAK  CONST_10  C19  C11  C18  C17    0.00   0.0  0
 VAK  CONST_11  C20  C19  C11  C18    0.00   0.0  0
 VAK  CONST_12  C20  C6   C17  C18    0.00   0.0  0
 VAK  CONST_13  O19  C4   C3   C2   180.00   0.0  0
 VAK  CONST_14  O21  C6   C17  C5     0.00   0.0  0
 VAK  CONST_15  O19  C4   C16  C5     0.00   0.0  0
 VAK  CONST_16  O21  C6   C20  C7     0.00   0.0  0
 VAK  CONST_17  O21  C6   C17  C18  180.00   0.0  0
 VAK  CONST_18  O21  C6   C20  C19  180.00   0.0  0
 VAK  CONST_19  C21  C16  C4   O19  180.00   0.0  0
 VAK  CONST_20  H3   C3   C2   C1   180.00   0.0  0
 VAK  CONST_21  H1   C1   C2   C3   180.00   0.0  0
 VAK  CONST_22  H2   C2   C3   C4   180.00   0.0  0
 VAK  CONST_23  H11  C11  C19  C10    0.00   0.0  0
 VAK  Var_01    H22  C22  C13  C9   -62.62  30.0  3
 VAK  Var_02    O17  C14  O16  C15    2.10  30.0  2
 VAK  Var_03    H15  C15  O16  C14  177.38  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
 VAK  chir_01  C7   C8  O22  C20  positiv
 VAK  chir_02  C9   C8  C13  C10  positiv
 VAK  chir_03  C10  C9  C14  C19  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
 VAK  plan-1  C1   0.020
 VAK  plan-1  C2   0.020
 VAK  plan-1  C3   0.020
 VAK  plan-1  C4   0.020
 VAK  plan-1  C5   0.020
 VAK  plan-1  C6   0.020
 VAK  plan-1  C7   0.020
 VAK  plan-1  C10  0.020
 VAK  plan-1  C11  0.020
 VAK  plan-1  C12  0.020
 VAK  plan-1  C16  0.020
 VAK  plan-1  C17  0.020
 VAK  plan-1  C18  0.020
 VAK  plan-1  O18  0.020
 VAK  plan-1  C19  0.020
 VAK  plan-1  O19  0.020
 VAK  plan-1  C20  0.020
 VAK  plan-1  O20  0.020
 VAK  plan-1  C21  0.020
 VAK  plan-1  O21  0.020
 VAK  plan-1  H1   0.020
 VAK  plan-1  H2   0.020
 VAK  plan-1  H3   0.020
 VAK  plan-1  H11  0.020
 VAK  plan-2  C10  0.020
 VAK  plan-2  C14  0.020
 VAK  plan-2  O16  0.020
 VAK  plan-2  O17  0.020

