# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 06:20:39 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (6aR,12aR)-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromene-3,6a(12aH)-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2[C@H]3Oc4cc5OCOc5cc4[C@@]3(O)COc2c1
#
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
 HMK  HMK  (6aR,12aR)-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromene-3,6a(12aH)-diol  ligand  34  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HMK
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
 HMK  C1    C  CH2   0  -0.211   0.5883  -1.5288  -0.8855
 HMK  O1    O  O2    0  -0.475   1.9852  -1.7437  -0.8221
 HMK  C2    C  CR6   0   0.383   2.7134  -0.6952  -0.3846
 HMK  C3    C  CR6   0  -0.070   2.1592   0.3223   0.3947
 HMK  C4    C  CR15  0   0.013   0.7392   0.2588   0.8458
 HMK  C5    C  CR5   0   0.102   0.0287  -1.0469   0.4497
 HMK  C6    C  CR16  0  -0.449   4.0605  -0.6823  -0.7295
 HMK  C7    C  CR6   0   0.366   4.8712   0.3606  -0.3026
 HMK  C8    C  CR16  0  -0.396   4.3343   1.3942   0.4687
 HMK  C9    C  CR16  0  -0.270   2.9970   1.3530   0.8112
 HMK  O2    O  O     0  -0.484  -0.0471   1.3158   0.2618
 HMK  O5    O  OH1   0  -0.655   0.2232  -1.9763   1.4752
 HMK  O6    O  OH1   0  -0.628   6.1658   0.3295  -0.6642
 HMK  C10   C  CR56  0   0.393  -1.3078   0.8337   0.1290
 HMK  C11   C  CR56  0  -0.034  -1.3752  -0.5418   0.2555
 HMK  C12   C  CR16  0  -0.439  -2.4245   1.6338  -0.1018
 HMK  C13   C  CR56  0   0.306  -3.6072   0.9345  -0.2074
 HMK  C14   C  CR56  0   0.284  -3.6883  -0.4469  -0.0841
 HMK  C15   C  CR16  0  -0.403  -2.5818  -1.2297   0.1472
 HMK  O3    O  O     0  -0.484  -4.8417   1.4342  -0.4453
 HMK  C16   C  CH2   0   0.066  -5.7456   0.3601  -0.2114
 HMK  O4    O  O     0  -0.490  -4.9826  -0.8334  -0.2545
 HMK  H11   H  HCH2  0   0.273   0.1371  -2.4787  -1.1780
 HMK  H12A  H  HCH2  0   0.245   0.3604  -0.7947  -1.6666
 HMK  H4    H  HCR5  0   0.271   0.6806   0.3664   1.9365
 HMK  H6    H  HCR6  0   0.272   4.4720  -1.4843  -1.3301
 HMK  H8    H  HCR6  0   0.272   4.9592   2.2109   0.8097
 HMK  H9    H  HCR6  0   0.266   2.5910   2.1445   1.4300
 HMK  HO5   H  HOH1  0   0.460  -0.0827  -2.8432   1.1873
 HMK  HO6   H  HOH1  0   0.477   6.6323   1.0948  -0.3103
 HMK  H12   H  HCR6  0   0.284  -2.3688   2.7101  -0.1905
 HMK  H15   H  HCR6  0   0.276  -2.6493  -2.3064   0.2374
 HMK  H161  H  HCH2  0   0.231  -6.2068   0.4777   0.7762
 HMK  H162  H  HCH2  0   0.248  -6.5062   0.3432  -0.9902

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
 HMK  C1   O1    single    1.415  0.020  1.415
 HMK  C1   C5    single    1.526  0.020  1.526
 HMK  C1   H11   single    0.970  0.020  1.090
 HMK  C1   H12A  single    0.970  0.020  1.090
 HMK  O1   C2    single    1.349  0.020  1.349
 HMK  C2   C3    aromatic  1.396  0.020  1.396
 HMK  C2   C6    aromatic  1.391  0.020  1.391
 HMK  C3   C4    single    1.491  0.020  1.491
 HMK  C3   C9    aromatic  1.392  0.020  1.392
 HMK  C4   C5    single    1.538  0.020  1.538
 HMK  C4   O2    single    1.441  0.020  1.441
 HMK  C4   H4    single    0.970  0.020  1.090
 HMK  C5   O5    single    1.398  0.020  1.398
 HMK  C5   C11   single    1.505  0.020  1.505
 HMK  C6   C7    aromatic  1.388  0.020  1.388
 HMK  C6   H6    single    0.930  0.020  1.080
 HMK  C7   C8    aromatic  1.397  0.020  1.397
 HMK  C7   O6    single    1.345  0.020  1.345
 HMK  C8   C9    aromatic  1.381  0.020  1.381
 HMK  C8   H8    single    0.930  0.020  1.080
 HMK  C9   H9    single    0.930  0.020  1.080
 HMK  O2   C10   single    1.356  0.020  1.356
 HMK  O5   HO5   single    0.850  0.020  0.980
 HMK  O6   HO6   single    0.850  0.020  0.980
 HMK  C10  C11   aromatic  1.383  0.020  1.383
 HMK  C10  C12   aromatic  1.393  0.020  1.393
 HMK  C11  C15   aromatic  1.393  0.020  1.393
 HMK  C12  C13   aromatic  1.378  0.020  1.378
 HMK  C12  H12   single    0.930  0.020  1.080
 HMK  C13  C14   aromatic  1.389  0.020  1.389
 HMK  C13  O3    single    1.353  0.020  1.353
 HMK  C14  C15   aromatic  1.375  0.020  1.375
 HMK  C14  O4    single    1.361  0.020  1.361
 HMK  C15  H15   single    0.930  0.020  1.080
 HMK  O3   C16   single    1.423  0.020  1.423
 HMK  C16  O4    single    1.417  0.020  1.417
 HMK  C16  H161  single    0.970  0.020  1.090
 HMK  C16  H162  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
 HMK  H12A  C1   H11   107.81  3.000
 HMK  H12A  C1   C5    109.63  3.000
 HMK  H11   C1   C5    110.96  3.000
 HMK  H12A  C1   O1    109.82  3.000
 HMK  H11   C1   O1    106.74  3.000
 HMK  C5    C1   O1    111.77  3.000
 HMK  C2    O1   C1    115.43  3.000
 HMK  C6    C2   C3    121.07  3.000
 HMK  C6    C2   O1    116.72  3.000
 HMK  C3    C2   O1    122.20  3.000
 HMK  C9    C3   C4    120.94  3.000
 HMK  C9    C3   C2    117.88  3.000
 HMK  C4    C3   C2    121.05  3.000
 HMK  H4    C4   O2    107.56  3.000
 HMK  H4    C4   C5    108.33  3.000
 HMK  O2    C4   C5    105.44  3.000
 HMK  H4    C4   C3    110.32  3.000
 HMK  O2    C4   C3    111.45  3.000
 HMK  C5    C4   C3    113.46  3.000
 HMK  C11   C5   O5    116.60  3.000
 HMK  C11   C5   C4    100.33  3.000
 HMK  O5    C5   C4    108.14  3.000
 HMK  C11   C5   C1    109.59  3.000
 HMK  O5    C5   C1    112.40  3.000
 HMK  C4    C5   C1    108.90  3.000
 HMK  H6    C6   C7    120.33  3.000
 HMK  H6    C6   C2    119.91  3.000
 HMK  C7    C6   C2    119.76  3.000
 HMK  O6    C7   C8    122.39  3.000
 HMK  O6    C7   C6    117.53  3.000
 HMK  C8    C7   C6    120.08  3.000
 HMK  H8    C8   C9    120.19  3.000
 HMK  H8    C8   C7    120.65  3.000
 HMK  C9    C8   C7    119.15  3.000
 HMK  H9    C9   C8    118.86  3.000
 HMK  H9    C9   C3    119.09  3.000
 HMK  C8    C9   C3    122.05  3.000
 HMK  C10   O2   C4    106.62  3.000
 HMK  HO5   O5   C5    109.57  3.000
 HMK  HO6   O6   C7    110.42  3.000
 HMK  C12   C10  C11   123.19  3.000
 HMK  C12   C10  O2    123.86  3.000
 HMK  C11   C10  O2    112.95  3.000
 HMK  C15   C11  C10   121.75  3.000
 HMK  C15   C11  C5    130.73  3.000
 HMK  C10   C11  C5    107.47  3.000
 HMK  H12   C12  C13   122.89  3.000
 HMK  H12   C12  C10   122.95  3.000
 HMK  C13   C12  C10   114.16  3.000
 HMK  O3    C13  C14   109.24  3.000
 HMK  O3    C13  C12   127.53  3.000
 HMK  C14   C13  C12   123.23  3.000
 HMK  O4    C14  C15   128.65  3.000
 HMK  O4    C14  C13   109.07  3.000
 HMK  C15   C14  C13   122.27  3.000
 HMK  H15   C15  C14   122.01  3.000
 HMK  H15   C15  C11   122.59  3.000
 HMK  C14   C15  C11   115.40  3.000
 HMK  C16   O3   C13   105.77  3.000
 HMK  H162  C16  H161  110.62  3.000
 HMK  H162  C16  O4    109.95  3.000
 HMK  H161  C16  O4    110.13  3.000
 HMK  H162  C16  O3    109.75  3.000
 HMK  H161  C16  O3    109.53  3.000
 HMK  O4    C16  O3    106.78  3.000
 HMK  C16   O4   C14   105.60  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
 HMK  CONST_01  C8   C9   C3   C2     0.00   0.0  0
 HMK  CONST_02  C8   C7   C6   C2     0.00   0.0  0
 HMK  CONST_03  C7   C6   C2   C3     0.00   0.0  0
 HMK  CONST_04  C7   C8   C9   C3     0.00   0.0  0
 HMK  CONST_05  C9   C3   C2   C6     0.00   0.0  0
 HMK  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 HMK  CONST_07  C14  C15  C11  C10    0.00   0.0  0
 HMK  CONST_08  C14  C13  C12  C10    0.00   0.0  0
 HMK  CONST_09  C13  C12  C10  C11    0.00   0.0  0
 HMK  CONST_10  C13  C14  C15  C11    0.00   0.0  0
 HMK  CONST_11  C15  C11  C10  C12    0.00   0.0  0
 HMK  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 HMK  CONST_13  O6   C7   C6   C2   180.00   0.0  0
 HMK  CONST_14  O6   C7   C8   C9   180.00   0.0  0
 HMK  CONST_15  H6   C6   C2   O1     0.00   0.0  0
 HMK  CONST_16  H9   C9   C3   C2   180.00   0.0  0
 HMK  CONST_17  H8   C8   C9   C3   180.00   0.0  0
 HMK  CONST_18  H15  C15  C11  C5     0.00   0.0  0
 HMK  CONST_19  H12  C12  C10  O2     0.00   0.0  0
 HMK  Var_01    C3   C2   O1   C1    22.43  30.0  1
 HMK  Var_02    C5   C1   O1   C2   -54.22  30.0  1
 HMK  Var_03    C11  C10  O2   C4   -15.17  30.0  1
 HMK  Var_04    O4   C16  O3   C13  -18.16  30.0  1
 HMK  Var_05    O3   C16  O4   C14   18.39  30.0  1

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
 HMK  chir_01  C4  C3  C5  O2   positiv
 HMK  chir_02  C5  C1  C4  C11  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
 HMK  plan-1  O1   0.020
 HMK  plan-1  C2   0.020
 HMK  plan-1  C3   0.020
 HMK  plan-1  C4   0.020
 HMK  plan-1  C6   0.020
 HMK  plan-1  C7   0.020
 HMK  plan-1  C8   0.020
 HMK  plan-1  C9   0.020
 HMK  plan-1  O6   0.020
 HMK  plan-1  H6   0.020
 HMK  plan-1  H8   0.020
 HMK  plan-1  H9   0.020
 HMK  plan-2  C5   0.020
 HMK  plan-2  O2   0.020
 HMK  plan-2  C10  0.020
 HMK  plan-2  C11  0.020
 HMK  plan-2  C12  0.020
 HMK  plan-2  C13  0.020
 HMK  plan-2  C14  0.020
 HMK  plan-2  C15  0.020
 HMK  plan-2  O3   0.020
 HMK  plan-2  O4   0.020
 HMK  plan-2  H12  0.020
 HMK  plan-2  H15  0.020

