# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 00:33:29 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: 6,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)C2=COc3cc(O)c(O)cc3C2=O
#
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
 674  674  "6,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one"
  ligand  30  20  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_674
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
 674  C8A  C  CR66  0   0.363  16.0062  23.1158  45.1025
 674  C4A  C  CR66  0  -0.119  14.9949  22.9627  44.1637
 674  C4   C  CR6   0   0.418  15.2447  23.2587  42.7525
 674  C3   C  CR6   0  -0.227  16.6112  23.6875  42.4586
 674  C2   C  CR16  0   0.036  17.5016  23.7871  43.4662
 674  O1   O  O     0  -0.425  17.2421  23.5306  44.7471
 674  C8   C  CR16  0  -0.460  15.7983  22.8484  46.4520
 674  C7   C  CR6   0   0.289  14.5555  22.4201  46.8658
 674  C6   C  CR6   0   0.317  13.5058  22.2506  45.9301
 674  C5   C  CR16  0  -0.405  13.7377  22.5235  44.6050
 674  O4   O  OH1   0  -0.626  14.2446  22.1362  48.1380
 674  O3   O  OH1   0  -0.625  12.2878  21.8326  46.3218
 674  C1'  C  CR6   0   0.070  17.0192  24.0455  41.0885
 674  C2'  C  CR16  0  -0.289  17.6796  25.2474  40.8346
 674  C3'  C  CR16  0  -0.323  18.1083  25.5840  39.5615
 674  C4'  C  CR6   0   0.346  17.8739  24.7170  38.4977
 674  C5'  C  CR16  0  -0.369  17.2057  23.5166  38.7328
 674  C6'  C  CR16  0  -0.274  16.7861  23.1910  40.0116
 674  O5   O  OH1   0  -0.627  18.3070  25.0852  37.2773
 674  O2   O  O     0  -0.423  14.3738  23.1647  41.8987
 674  H2   H  HCR6  0   0.303  18.5315  24.0880  43.3207
 674  H8   H  HCR6  0   0.301  16.6052  22.9784  47.1639
 674  H5   H  HCR6  0   0.275  12.9382  22.3950  43.8866
 674  HO4  H  HOH1  0   0.491  15.0055  22.2332  48.7237
 674  HO3  H  HOH1  0   0.474  12.2859  21.6074  47.2598
 674  H2'  H  HCR6  0   0.253  17.8571  25.9442  41.6450
 674  H3'  H  HCR6  0   0.262  18.6186  26.5233  39.3891
 674  H5'  H  HCR6  0   0.270  17.0158  22.8285  37.9163
 674  H6'  H  HCR6  0   0.252  16.2873  22.2439  40.1677
 674  HO5  H  HOH1  0   0.473  18.0965  24.4080  36.6241

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
 674  O5   C4'  single    1.346  0.020  1.346
 674  C4'  C5'  aromatic  1.394  0.020  1.394
 674  C4'  C3'  aromatic  1.392  0.020  1.392
 674  C5'  C6'  aromatic  1.385  0.020  1.385
 674  C3'  C2'  aromatic  1.385  0.020  1.385
 674  C6'  C1'  aromatic  1.394  0.020  1.394
 674  C2'  C1'  aromatic  1.395  0.020  1.395
 674  C1'  C3   single    1.474  0.020  1.474
 674  O2   C4   double    1.223  0.020  1.223
 674  C3   C4   single    1.462  0.020  1.462
 674  C3   C2   double    1.348  0.020  1.348
 674  C4   C4A  single    1.463  0.020  1.463
 674  C2   O1   single    1.332  0.020  1.332
 674  C4A  C5   aromatic  1.403  0.020  1.403
 674  C4A  C8A  aromatic  1.388  0.020  1.388
 674  C5   C6   aromatic  1.373  0.020  1.373
 674  O1   C8A  single    1.351  0.020  1.351
 674  C8A  C8   aromatic  1.391  0.020  1.391
 674  C6   O3   single    1.346  0.020  1.346
 674  C6   C7   aromatic  1.416  0.020  1.416
 674  C8   C7   aromatic  1.378  0.020  1.378
 674  C7   O4   single    1.340  0.020  1.340
 674  C2   H2   single    0.930  0.020  1.080
 674  C8   H8   single    0.930  0.020  1.080
 674  C5   H5   single    0.930  0.020  1.080
 674  O4   HO4  single    0.850  0.020  0.980
 674  O3   HO3  single    0.850  0.020  0.980
 674  C2'  H2'  single    0.930  0.020  1.080
 674  C3'  H3'  single    0.930  0.020  1.080
 674  C5'  H5'  single    0.930  0.020  1.080
 674  C6'  H6'  single    0.930  0.020  1.080
 674  O5   HO5  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
 674  C8   C8A  O1   116.80  3.000
 674  C8   C8A  C4A  121.72  3.000
 674  O1   C8A  C4A  121.49  3.000
 674  C5   C4A  C4   121.31  3.000
 674  C5   C4A  C8A  118.33  3.000
 674  C4   C4A  C8A  120.36  3.000
 674  O2   C4   C3   123.21  3.000
 674  C3   C4   C4A  114.38  3.000
 674  O2   C4   C4A  122.41  3.000
 674  C1'  C3   C2   119.60  3.000
 674  C2   C3   C4   119.25  3.000
 674  C1'  C3   C4   121.13  3.000
 674  H2   C2   O1   111.60  3.000
 674  H2   C2   C3   123.25  3.000
 674  O1   C2   C3   125.16  3.000
 674  C2   O1   C8A  119.36  3.000
 674  H8   C8   C7   120.76  3.000
 674  H8   C8   C8A  120.18  3.000
 674  C7   C8   C8A  119.06  3.000
 674  O4   C7   C6   115.46  3.000
 674  O4   C7   C8   124.06  3.000
 674  C6   C7   C8   120.48  3.000
 674  O3   C6   C5   119.70  3.000
 674  O3   C6   C7   121.04  3.000
 674  C5   C6   C7   119.26  3.000
 674  H5   C5   C6   119.50  3.000
 674  H5   C5   C4A  119.35  3.000
 674  C6   C5   C4A  121.15  3.000
 674  HO4  O4   C7   111.83  3.000
 674  HO3  O3   C6   110.93  3.000
 674  C6'  C1'  C2'  117.82  3.000
 674  C2'  C1'  C3   120.64  3.000
 674  C6'  C1'  C3   121.52  3.000
 674  H2'  C2'  C3'  118.73  3.000
 674  H2'  C2'  C1'  119.71  3.000
 674  C3'  C2'  C1'  121.56  3.000
 674  H3'  C3'  C4'  119.86  3.000
 674  H3'  C3'  C2'  120.20  3.000
 674  C4'  C3'  C2'  119.94  3.000
 674  O5   C4'  C5'  122.86  3.000
 674  C5'  C4'  C3'  119.22  3.000
 674  O5   C4'  C3'  117.92  3.000
 674  H5'  C5'  C6'  119.54  3.000
 674  H5'  C5'  C4'  120.23  3.000
 674  C6'  C5'  C4'  120.23  3.000
 674  H6'  C6'  C5'  118.61  3.000
 674  H6'  C6'  C1'  120.14  3.000
 674  C5'  C6'  C1'  121.23  3.000
 674  HO5  O5   C4'  110.60  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
 674  CONST_01  C6   C5   C4A  C8A     0.00   0.0  0
 674  CONST_02  C6   C7   C8   C8A     0.00   0.0  0
 674  CONST_03  C1'  C3   C4   C4A   180.00   0.0  0
 674  CONST_04  C7   C6   C5   C4A     0.00   0.0  0
 674  CONST_05  C7   C8   C8A  C4A     0.00   0.0  0
 674  CONST_06  C5   C4A  C8A  C8      0.00   0.0  0
 674  CONST_07  C5   C6   C7   C8      0.00   0.0  0
 674  CONST_08  C4'  C5'  C6'  C1'     0.00   0.0  0
 674  CONST_09  C4'  C3'  C2'  C1'     0.00   0.0  0
 674  CONST_10  C5'  C4'  C3'  C2'     0.00   0.0  0
 674  CONST_11  C5'  C6'  C1'  C2'     0.00   0.0  0
 674  CONST_12  C6'  C5'  C4'  C3'     0.00   0.0  0
 674  CONST_13  C6'  C1'  C2'  C3'     0.00   0.0  0
 674  CONST_14  C5'  C6'  C1'  C3    180.00   0.0  0
 674  CONST_15  C3'  C2'  C1'  C3    180.00   0.0  0
 674  CONST_16  O4   C7   C8   C8A   180.00   0.0  0
 674  CONST_17  O3   C6   C5   C4A   180.00   0.0  0
 674  CONST_18  O2   C4   C3   C2    180.00   0.0  0
 674  CONST_19  O3   C6   C7   C8    180.00   0.0  0
 674  CONST_20  O4   C7   C6   C5    180.00   0.0  0
 674  CONST_21  O2   C4   C3   C1'     0.00   0.0  0
 674  CONST_22  O5   C4'  C3'  C2'   180.00   0.0  0
 674  CONST_23  O5   C4'  C5'  C6'   180.00   0.0  0
 674  CONST_24  H5   C5   C4A  C8A   180.00   0.0  0
 674  CONST_25  H8   C8   C8A  C4A   180.00   0.0  0
 674  CONST_26  H5   C5   C4A  C4      0.00   0.0  0
 674  CONST_27  H6'  C6'  C1'  C3      0.00   0.0  0
 674  CONST_28  H2'  C2'  C1'  C3      0.00   0.0  0
 674  CONST_29  H8   C8   C8A  O1      0.00   0.0  0
 674  CONST_30  H5   C5   C6   C7    180.00   0.0  0
 674  CONST_31  H8   C8   C7   C6    180.00   0.0  0
 674  CONST_32  H5'  C5'  C6'  C1'   180.00   0.0  0
 674  CONST_33  H3'  C3'  C2'  C1'   180.00   0.0  0
 674  CONST_34  H6'  C6'  C1'  C2'   180.00   0.0  0
 674  CONST_35  H5'  C5'  C4'  C3'   180.00   0.0  0
 674  CONST_36  H6'  C6'  C5'  C4'   180.00   0.0  0
 674  CONST_37  H2'  C2'  C3'  C4'   180.00   0.0  0
 674  CONST_38  H3'  C3'  C4'  C5'   180.00   0.0  0
 674  CONST_39  H2'  C2'  C1'  C6'   180.00   0.0  0
 674  Var_01    C3   C4   C4A  C8A     0.96  30.0  1
 674  Var_02    C3   C2   O1   C8A     1.08  30.0  1
 674  Var_03    C2   C3   C4   C4A    -0.57  30.0  1
 674  Var_04    C2   O1   C8A  C4A    -0.63  30.0  1
 674  Var_05    C6'  C1'  C3   C4    -51.82  30.0  3
 674  Var_06    C2'  C1'  C3   C4    129.50  30.0  3
 674  Var_07    O1   C2   C3   C4     -0.44  30.0  1
 674  Var_08    C5   C4A  C4   C3   -179.22  30.0  1
 674  Var_09    C6'  C1'  C3   C2    129.81  30.0  3
 674  Var_10    C2'  C1'  C3   C2    -48.87  30.0  3
 674  Var_11    C8   C8A  O1   C2    179.27  30.0  1
 674  Var_12    C1'  C3   C2   O1    177.96  30.0  1
 674  Var_13    O2   C4   C4A  C8A  -178.38  30.0  1
 674  Var_14    O2   C4   C4A  C5      1.44  30.0  1
 674  Var_15    H2   C2   O1   C8A  -178.73  30.0  1
 674  Var_16    H2   C2   C3   C4    179.35  30.0  1
 674  Var_17    H2   C2   C3   C1'    -2.25  30.0  1

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
 674  plan-1  C3   0.020
 674  plan-1  C1'  0.020
 674  plan-1  C2'  0.020
 674  plan-1  C3'  0.020
 674  plan-1  C4'  0.020
 674  plan-1  C5'  0.020
 674  plan-1  C6'  0.020
 674  plan-1  O5   0.020
 674  plan-1  H2'  0.020
 674  plan-1  H3'  0.020
 674  plan-1  H5'  0.020
 674  plan-1  H6'  0.020
 674  plan-2  C8A  0.020
 674  plan-2  C4A  0.020
 674  plan-2  C4   0.020
 674  plan-2  O1   0.020
 674  plan-2  C8   0.020
 674  plan-2  C7   0.020
 674  plan-2  C6   0.020
 674  plan-2  C5   0.020
 674  plan-2  O4   0.020
 674  plan-2  O3   0.020
 674  plan-2  H8   0.020
 674  plan-2  H5   0.020
 674  plan-3  C4A  0.020
 674  plan-3  C4   0.020
 674  plan-3  C3   0.020
 674  plan-3  O2   0.020

