# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:07:18 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: methyl {3-[(1R,3S)-1,3-dihydroxypentyl]-4,5-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl}acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](O)C[C@@H](O)c1c(O)c2C(=O)c3c(O)cccc3C(=O)c2cc1CC(=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
 AKV  AKV  'methyl {3-[(1R,3S)-1,3-dihydroxypentyl]-4,5-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl}acetate'  ligand  52  30  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AKV
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
 AKV  O20   O  O     0  -0.400  -2.5249   2.2619   0.8554
 AKV  C5    C  CR6   0   0.273  -2.6201   1.1482   0.3065
 AKV  C17   C  CR66  0   0.011  -1.4243   0.3775  -0.0029
 AKV  C6    C  CR6   0   0.328  -0.1548   0.8740   0.3372
 AKV  O21   O  OH1   0  -0.691  -0.0037   2.0654   0.9113
 AKV  C16   C  CR66  0   0.043  -3.9303   0.6046  -0.0246
 AKV  C4    C  CR6   0   0.237  -5.0954   1.3286   0.2970
 AKV  O19   O  OH1   0  -0.617  -5.0740   2.5091   0.8986
 AKV  C3    C  CR16  0  -0.241  -6.3472   0.7891  -0.0252
 AKV  C2    C  CR16  0  -0.241  -6.4359  -0.4333  -0.6495
 AKV  C1    C  CR16  0  -0.282  -5.2907  -1.1579  -0.9762
 AKV  C21   C  CR66  0   0.004  -4.0490  -0.6439  -0.6651
 AKV  C12   C  CR6   0   0.320  -2.8389  -1.4285  -1.0151
 AKV  O18   O  O     0  -0.312  -2.9299  -2.4942  -1.5907
 AKV  C18   C  CR66  0  -0.180  -1.5208  -0.8713  -0.6359
 AKV  C11   C  CR16  0  -0.307  -0.3785  -1.5856  -0.9193
 AKV  C19   C  CR6   0  -0.007   0.8817  -1.0933  -0.5751
 AKV  C10   C  CH2   0  -0.675   2.0833  -1.9311  -0.9063
 AKV  C14   C  C     0   0.619   2.5587  -2.7126   0.3011
 AKV  O16   O  O2    0  -0.431   3.8184  -3.1109   0.1496
 AKV  C15   C  CH3   0  -0.468   4.3775  -3.8829   1.2070
 AKV  O17   O  O     0  -0.412   1.8819  -2.9623   1.2572
 AKV  C20   C  CR6   0  -0.001   1.0093   0.1307   0.0695
 AKV  C7    C  CH1   0  -0.022   2.3658   0.6879   0.4691
 AKV  O22   O  OH1   0  -0.630   2.4228   1.1152   1.8022
 AKV  C8    C  CH2   0  -0.495   2.8205   1.7662  -0.5224
 AKV  C9    C  CH1   0  -0.014   4.3049   2.0954  -0.3845
 AKV  O23   O  OH1   0  -0.634   5.1029   0.9657  -0.6813
 AKV  C13   C  CH2   0  -0.448   4.6910   3.3079  -1.2258
 AKV  C22   C  CH3   0  -0.673   6.1526   3.7058  -1.0820
 AKV  H21   H  HOH1  0   0.476  -0.8959   2.4608   1.0493
 AKV  H19   H  HOH1  0   0.461  -4.1387   2.7612   1.0515
 AKV  H3    H  HCR6  0   0.290  -7.2392   1.3483   0.2240
 AKV  H2    H  HCR6  0   0.272  -7.4096  -0.8369  -0.8893
 AKV  H1    H  HCR6  0   0.287  -5.3781  -2.1173  -1.4645
 AKV  H11   H  HCR6  0   0.259  -0.4573  -2.5449  -1.4120
 AKV  H101  H  HCH2  0   0.320   1.8299  -2.6586  -1.6818
 AKV  H102  H  HCH2  0   0.299   2.9006  -1.3425  -1.3233
 AKV  H151  H  HCH3  0   0.252   5.3894  -4.1272   0.8960
 AKV  H152  H  HCH3  0   0.223   4.4110  -3.3162   2.1372
 AKV  H153  H  HCH3  0   0.259   3.8170  -4.8023   1.3744
 AKV  H7    H  HCH1  0   0.208   3.0977  -0.1183   0.4207
 AKV  H22   H  HOH1  0   0.443   1.7979   1.8363   1.9210
 AKV  H81   H  HCH2  0   0.246   2.2221   2.6716  -0.3863
 AKV  H82   H  HCH2  0   0.245   2.6183   1.4319  -1.5480
 AKV  H9    H  HCH1  0   0.207   4.5151   2.3213   0.6651
 AKV  H23   H  HOH1  0   0.450   5.0513   0.8046  -1.6280
 AKV  H131  H  HCH2  0   0.225   4.0535   4.1473  -0.9347
 AKV  H132  H  HCH2  0   0.257   4.4562   3.1124  -2.2800
 AKV  H221  H  HCH3  0   0.232   6.3921   3.9461  -0.0453
 AKV  H222  H  HCH3  0   0.208   6.8224   2.9052  -1.3929
 AKV  H223  H  HCH3  0   0.227   6.3821   4.5832  -1.6863

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
 AKV  O20  C5    double    1.245  0.020  1.245
 AKV  C5   C17   single    1.456  0.020  1.456
 AKV  C5   C16   single    1.457  0.020  1.457
 AKV  C17  C6    aromatic  1.405  0.020  1.405
 AKV  C17  C18   aromatic  1.403  0.020  1.403
 AKV  C6   O21   single    1.331  0.020  1.331
 AKV  C6   C20   aromatic  1.407  0.020  1.407
 AKV  O21  H21   single    0.850  0.020  0.980
 AKV  C16  C4    aromatic  1.409  0.020  1.409
 AKV  C16  C21   aromatic  1.408  0.020  1.408
 AKV  C4   O19   single    1.325  0.020  1.325
 AKV  C4   C3    aromatic  1.401  0.020  1.401
 AKV  O19  H19   single    0.850  0.020  0.980
 AKV  C3   C2    aromatic  1.375  0.020  1.375
 AKV  C3   H3    single    0.930  0.020  1.080
 AKV  C2   C1    aromatic  1.394  0.020  1.394
 AKV  C2   H2    single    0.930  0.020  1.080
 AKV  C1   C21   aromatic  1.379  0.020  1.379
 AKV  C1   H1    single    0.930  0.020  1.080
 AKV  C21  C12   single    1.484  0.020  1.484
 AKV  C12  O18   double    1.215  0.020  1.215
 AKV  C12  C18   single    1.480  0.020  1.480
 AKV  C18  C11   aromatic  1.377  0.020  1.377
 AKV  C11  C19   aromatic  1.396  0.020  1.396
 AKV  C11  H11   single    0.930  0.020  1.080
 AKV  C19  C10   single    1.502  0.020  1.502
 AKV  C19  C20   aromatic  1.389  0.020  1.389
 AKV  C10  C14   single    1.515  0.020  1.515
 AKV  C10  H101  single    0.970  0.020  1.090
 AKV  C10  H102  single    0.970  0.020  1.090
 AKV  C14  O16   single    1.330  0.020  1.330
 AKV  C14  O17   double    1.198  0.020  1.198
 AKV  O16  C15   single    1.424  0.020  1.424
 AKV  C15  H151  single    0.970  0.020  1.090
 AKV  C15  H152  single    0.970  0.020  1.090
 AKV  C15  H153  single    0.970  0.020  1.090
 AKV  C20  C7    single    1.520  0.020  1.520
 AKV  C7   O22   single    1.401  0.020  1.401
 AKV  C7   C8    single    1.534  0.020  1.534
 AKV  C7   H7    single    0.970  0.020  1.090
 AKV  O22  H22   single    0.850  0.020  0.980
 AKV  C8   C9    single    1.527  0.020  1.527
 AKV  C8   H81   single    0.970  0.020  1.090
 AKV  C8   H82   single    0.970  0.020  1.090
 AKV  C9   O23   single    1.415  0.020  1.415
 AKV  C9   C13   single    1.525  0.020  1.525
 AKV  C9   H9    single    0.970  0.020  1.090
 AKV  O23  H23   single    0.850  0.020  0.980
 AKV  C13  C22   single    1.522  0.020  1.522
 AKV  C13  H131  single    0.970  0.020  1.090
 AKV  C13  H132  single    0.970  0.020  1.090
 AKV  C22  H221  single    0.970  0.020  1.090
 AKV  C22  H222  single    0.970  0.020  1.090
 AKV  C22  H223  single    0.970  0.020  1.090

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
 AKV  C16   C5   C17   119.54  3.000
 AKV  C16   C5   O20   120.18  3.000
 AKV  C17   C5   O20   120.28  3.000
 AKV  C18   C17  C6    119.07  3.000
 AKV  C18   C17  C5    120.69  3.000
 AKV  C6    C17  C5    120.24  3.000
 AKV  C20   C6   O21   117.45  3.000
 AKV  C20   C6   C17   120.99  3.000
 AKV  O21   C6   C17   121.56  3.000
 AKV  H21   O21  C6    108.47  3.000
 AKV  C21   C16  C4    119.32  3.000
 AKV  C21   C16  C5    120.67  3.000
 AKV  C4    C16  C5    120.02  3.000
 AKV  C3    C4   O19   117.51  3.000
 AKV  C3    C4   C16   119.26  3.000
 AKV  O19   C4   C16   123.23  3.000
 AKV  H19   O19  C4    108.37  3.000
 AKV  H3    C3   C2    120.72  3.000
 AKV  H3    C3   C4    119.00  3.000
 AKV  C2    C3   C4    120.28  3.000
 AKV  H2    C2   C1    119.60  3.000
 AKV  H2    C2   C3    119.37  3.000
 AKV  C1    C2   C3    121.02  3.000
 AKV  H1    C1   C21   120.39  3.000
 AKV  H1    C1   C2    120.08  3.000
 AKV  C21   C1   C2    119.54  3.000
 AKV  C12   C21  C1    118.93  3.000
 AKV  C12   C21  C16   120.48  3.000
 AKV  C1    C21  C16   120.59  3.000
 AKV  C18   C12  O18   121.21  3.000
 AKV  C18   C12  C21   117.82  3.000
 AKV  O18   C12  C21   120.97  3.000
 AKV  C11   C18  C12   119.39  3.000
 AKV  C11   C18  C17   119.83  3.000
 AKV  C12   C18  C17   120.77  3.000
 AKV  H11   C11  C19   119.41  3.000
 AKV  H11   C11  C18   119.58  3.000
 AKV  C19   C11  C18   121.01  3.000
 AKV  C20   C19  C10   121.36  3.000
 AKV  C20   C19  C11   120.53  3.000
 AKV  C10   C19  C11   118.11  3.000
 AKV  H102  C10  H101  105.17  3.000
 AKV  H102  C10  C14   110.38  3.000
 AKV  H101  C10  C14   107.15  3.000
 AKV  H102  C10  C19   112.52  3.000
 AKV  H101  C10  C19   110.01  3.000
 AKV  C14   C10  C19   111.30  3.000
 AKV  O17   C14  O16   124.32  3.000
 AKV  O17   C14  C10   124.50  3.000
 AKV  O16   C14  C10   111.16  3.000
 AKV  C15   O16  C14   116.73  3.000
 AKV  H153  C15  H152  108.86  3.000
 AKV  H153  C15  H151  109.47  3.000
 AKV  H152  C15  H151  109.43  3.000
 AKV  H153  C15  O16   111.70  3.000
 AKV  H152  C15  O16   111.35  3.000
 AKV  H151  C15  O16   105.97  3.000
 AKV  C7    C20  C19   121.80  3.000
 AKV  C7    C20  C6    119.66  3.000
 AKV  C19   C20  C6    118.54  3.000
 AKV  H7    C7   C8    106.99  3.000
 AKV  H7    C7   O22   103.92  3.000
 AKV  C8    C7   O22   112.87  3.000
 AKV  H7    C7   C20   108.45  3.000
 AKV  C8    C7   C20   110.63  3.000
 AKV  O22   C7   C20   113.47  3.000
 AKV  H22   O22  C7    108.65  3.000
 AKV  H82   C8   H81   105.52  3.000
 AKV  H82   C8   C9    109.22  3.000
 AKV  H81   C8   C9    110.01  3.000
 AKV  H82   C8   C7    109.59  3.000
 AKV  H81   C8   C7    109.84  3.000
 AKV  C9    C8   C7    112.42  3.000
 AKV  H9    C9   C13   108.44  3.000
 AKV  H9    C9   O23   104.94  3.000
 AKV  C13   C9   O23   112.10  3.000
 AKV  H9    C9   C8    108.54  3.000
 AKV  C13   C9   C8    111.57  3.000
 AKV  O23   C9   C8    110.94  3.000
 AKV  H23   O23  C9    108.06  3.000
 AKV  H132  C13  H131  105.53  3.000
 AKV  H132  C13  C22   110.05  3.000
 AKV  H131  C13  C22   109.52  3.000
 AKV  H132  C13  C9    109.51  3.000
 AKV  H131  C13  C9    108.41  3.000
 AKV  C22   C13  C9    113.51  3.000
 AKV  H223  C22  H222  107.70  3.000
 AKV  H223  C22  H221  107.66  3.000
 AKV  H222  C22  H221  107.35  3.000
 AKV  H223  C22  C13   111.13  3.000
 AKV  H222  C22  C13   111.81  3.000
 AKV  H221  C22  C13   111.00  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
 AKV  CONST_01  C19   C20  C6   C17     0.00   0.0  0
 AKV  CONST_02  C19   C11  C18  C17     0.00   0.0  0
 AKV  CONST_03  C11   C18  C17  C6      0.00   0.0  0
 AKV  CONST_04  C11   C19  C20  C6      0.00   0.0  0
 AKV  CONST_05  C2    C3   C4   C16     0.00   0.0  0
 AKV  CONST_06  C2    C1   C21  C16     0.00   0.0  0
 AKV  CONST_07  C1    C21  C16  C4      0.00   0.0  0
 AKV  CONST_08  C1    C2   C3   C4      0.00   0.0  0
 AKV  CONST_09  C21   C16  C4   C3      0.00   0.0  0
 AKV  CONST_10  C21   C1   C2   C3      0.00   0.0  0
 AKV  CONST_11  C20   C6   C17  C18     0.00   0.0  0
 AKV  CONST_12  C20   C19  C11  C18     0.00   0.0  0
 AKV  CONST_13  O21   C6   C17  C5      0.00   0.0  0
 AKV  CONST_14  O19   C4   C16  C5      0.00   0.0  0
 AKV  CONST_15  C7    C20  C6   C17   180.00   0.0  0
 AKV  CONST_16  C10   C19  C20  C6    180.00   0.0  0
 AKV  CONST_17  C18   C17  C6   O21   180.00   0.0  0
 AKV  CONST_18  C19   C20  C6   O21   180.00   0.0  0
 AKV  CONST_19  C21   C16  C4   O19   180.00   0.0  0
 AKV  CONST_20  C2    C3   C4   O19   180.00   0.0  0
 AKV  CONST_21  C10   C19  C11  C18   180.00   0.0  0
 AKV  CONST_22  C7    C20  C19  C11   180.00   0.0  0
 AKV  CONST_23  H11   C11  C18  C17   180.00   0.0  0
 AKV  CONST_24  H3    C3   C4   C16   180.00   0.0  0
 AKV  CONST_25  H1    C1   C21  C16   180.00   0.0  0
 AKV  CONST_26  H2    C2   C3   C4    180.00   0.0  0
 AKV  Var_01    C14   C10  C19  C11   -98.88  30.0  2
 AKV  Var_02    O16   C14  C10  C19  -160.49  30.0  3
 AKV  Var_03    H151  C15  O16  C14   178.87  30.0  3
 AKV  Var_04    H221  C22  C13  C9    -59.35  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
 AKV  chir_01  C7  C20  O22  C8  positiv
 AKV  chir_02  C9  O23  C13  C8  negativ

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
 AKV  plan-1  O20  0.020
 AKV  plan-1  C5   0.020
 AKV  plan-1  C17  0.020
 AKV  plan-1  C6   0.020
 AKV  plan-1  O21  0.020
 AKV  plan-1  C16  0.020
 AKV  plan-1  C4   0.020
 AKV  plan-1  O19  0.020
 AKV  plan-1  C3   0.020
 AKV  plan-1  C2   0.020
 AKV  plan-1  C1   0.020
 AKV  plan-1  C21  0.020
 AKV  plan-1  C12  0.020
 AKV  plan-1  O18  0.020
 AKV  plan-1  C18  0.020
 AKV  plan-1  C11  0.020
 AKV  plan-1  C19  0.020
 AKV  plan-1  C10  0.020
 AKV  plan-1  C20  0.020
 AKV  plan-1  C7   0.020
 AKV  plan-1  H3   0.020
 AKV  plan-1  H2   0.020
 AKV  plan-1  H1   0.020
 AKV  plan-1  H11  0.020
 AKV  plan-2  C10  0.020
 AKV  plan-2  C14  0.020
 AKV  plan-2  O16  0.020
 AKV  plan-2  O17  0.020

