# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:58:19 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 5,7-dihydroxy-2-phenyl-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)C=C(Oc2c1)c3ccccc3
#
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
 57D  57D  5,7-dihydroxy-2-phenyl-4H-chromen-4-one  ligand  29  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_57D
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
 57D  C2   C  CR6   0   0.411  -1.0990  -0.3165  -0.0549
 57D  C3   C  CR16  0  -0.513  -0.6252  -1.5755  -0.1827
 57D  C4   C  CR6   0   0.532   0.7903  -1.8365  -0.2083
 57D  C5   C  CR66  0  -0.351   1.6329  -0.6659  -0.1204
 57D  C6   C  CR6   0   0.403   3.0455  -0.7565  -0.1548
 57D  C7   C  CR16  0  -0.454   3.8174   0.3874  -0.0765
 57D  C8   C  CR6   0   0.398   3.1980   1.6349   0.0374
 57D  C9   C  CR16  0  -0.514   1.8111   1.7582   0.0746
 57D  C10  C  CR66  0   0.421   1.0599   0.6010  -0.0059
 57D  O1   O  O     0  -0.467  -0.2820   0.7412   0.0378
 57D  O4   O  O     0  -0.506   1.2612  -2.9805  -0.3097
 57D  O5   O  OH1   0  -0.629   3.6389  -1.9404  -0.2643
 57D  O7   O  OH1   0  -0.615   4.0024   2.6991   0.1092
 57D  C2'  C  CR16  0  -0.275  -2.9185   1.3602  -0.3334
 57D  C3'  C  CR16  0  -0.238  -4.2631   1.6972  -0.3173
 57D  C4'  C  CR16  0  -0.250  -5.2200   0.7494   0.0180
 57D  C5'  C  CR16  0  -0.236  -4.8261  -0.5431   0.3412
 57D  C6'  C  CR16  0  -0.303  -3.4849  -0.8862   0.3247
 57D  C1'  C  CR6   0   0.026  -2.5167   0.0598  -0.0189
 57D  H3   H  HCR6  0   0.286  -1.3088  -2.4055  -0.2843
 57D  H7   H  HCR6  0   0.281   4.8975   0.3186  -0.1025
 57D  H9   H  HCR6  0   0.295   1.3278   2.7231   0.1664
 57D  HO5  H  HOH1  0   0.476   2.9293  -2.6261  -0.3069
 57D  HO7  H  HOH1  0   0.484   3.4916   3.5146   0.1741
 57D  H3'  H  HCR6  0   0.268  -4.5622   2.7051  -0.5719
 57D  H4'  H  HCR6  0   0.268  -6.2685   1.0164   0.0308
 57D  H5'  H  HCR6  0   0.268  -5.5644  -1.2852   0.6145
 57D  H6'  H  HCR6  0   0.266  -3.1957  -1.8908   0.6031
 57D  H2'  H  HCR6  0   0.266  -2.1918   2.1134  -0.6052

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
 57D  C2   C3   double    1.351  0.020  1.351
 57D  C2   O1   single    1.340  0.020  1.340
 57D  C2   C1'  single    1.467  0.020  1.467
 57D  C3   C4   single    1.440  0.020  1.440
 57D  C4   C5   single    1.445  0.020  1.445
 57D  C4   O4   double    1.241  0.020  1.241
 57D  C5   C6   aromatic  1.416  0.020  1.416
 57D  C5   C10  aromatic  1.395  0.020  1.395
 57D  C6   C7   aromatic  1.382  0.020  1.382
 57D  C6   O5   single    1.329  0.020  1.329
 57D  C7   C8   aromatic  1.397  0.020  1.397
 57D  C8   C9   aromatic  1.393  0.020  1.393
 57D  C8   O7   single    1.336  0.020  1.336
 57D  C9   C10  aromatic  1.382  0.020  1.382
 57D  C10  O1   single    1.350  0.020  1.350
 57D  C2'  C3'  aromatic  1.386  0.020  1.386
 57D  C2'  C1'  aromatic  1.397  0.020  1.397
 57D  C3'  C4'  aromatic  1.388  0.020  1.388
 57D  C4'  C5'  aromatic  1.389  0.020  1.389
 57D  C5'  C6'  aromatic  1.384  0.020  1.384
 57D  C6'  C1'  aromatic  1.397  0.020  1.397
 57D  C3   H3   single    0.930  0.020  1.080
 57D  C7   H7   single    0.930  0.020  1.080
 57D  C9   H9   single    0.930  0.020  1.080
 57D  O5   HO5  single    0.850  0.020  0.980
 57D  O7   HO7  single    0.850  0.020  0.980
 57D  C2'  H2'  single    0.930  0.020  1.080
 57D  C3'  H3'  single    0.930  0.020  1.080
 57D  C4'  H4'  single    0.930  0.020  1.080
 57D  C5'  H5'  single    0.930  0.020  1.080
 57D  C6'  H6'  single    0.930  0.020  1.080

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
 57D  C1'  C2   O1   112.65  3.000
 57D  C1'  C2   C3   125.46  3.000
 57D  O1   C2   C3   121.89  3.000
 57D  H3   C3   C4   118.77  3.000
 57D  H3   C3   C2   120.19  3.000
 57D  C4   C3   C2   121.02  3.000
 57D  O4   C4   C5   122.04  3.000
 57D  O4   C4   C3   122.79  3.000
 57D  C5   C4   C3   115.17  3.000
 57D  C10  C5   C6   118.03  3.000
 57D  C10  C5   C4   120.07  3.000
 57D  C6   C5   C4   121.90  3.000
 57D  O5   C6   C7   119.51  3.000
 57D  O5   C6   C5   120.30  3.000
 57D  C7   C6   C5   120.19  3.000
 57D  H7   C7   C8   120.06  3.000
 57D  H7   C7   C6   120.21  3.000
 57D  C8   C7   C6   119.73  3.000
 57D  O7   C8   C9   121.84  3.000
 57D  O7   C8   C7   116.66  3.000
 57D  C9   C8   C7   121.51  3.000
 57D  H9   C9   C10  120.55  3.000
 57D  H9   C9   C8   121.70  3.000
 57D  C10  C9   C8   117.74  3.000
 57D  O1   C10  C9   116.84  3.000
 57D  O1   C10  C5   120.35  3.000
 57D  C9   C10  C5   122.81  3.000
 57D  C10  O1   C2   121.46  3.000
 57D  HO5  O5   C6   107.53  3.000
 57D  HO7  O7   C8   111.00  3.000
 57D  H2'  C2'  C1'  120.77  3.000
 57D  H2'  C2'  C3'  119.04  3.000
 57D  C1'  C2'  C3'  120.18  3.000
 57D  H3'  C3'  C4'  120.16  3.000
 57D  H3'  C3'  C2'  119.47  3.000
 57D  C4'  C3'  C2'  120.36  3.000
 57D  H4'  C4'  C5'  120.11  3.000
 57D  H4'  C4'  C3'  120.16  3.000
 57D  C5'  C4'  C3'  119.73  3.000
 57D  H5'  C5'  C6'  119.61  3.000
 57D  H5'  C5'  C4'  120.22  3.000
 57D  C6'  C5'  C4'  120.16  3.000
 57D  H6'  C6'  C1'  120.46  3.000
 57D  H6'  C6'  C5'  119.08  3.000
 57D  C1'  C6'  C5'  120.44  3.000
 57D  C6'  C1'  C2'  119.11  3.000
 57D  C6'  C1'  C2   120.15  3.000
 57D  C2'  C1'  C2   120.74  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
 57D  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 57D  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 57D  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 57D  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 57D  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 57D  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 57D  CONST_07  C5'  C4'  C3'  C2'     0.00   0.0  0
 57D  CONST_08  C5'  C6'  C1'  C2'     0.00   0.0  0
 57D  CONST_09  C6'  C1'  C2'  C3'     0.00   0.0  0
 57D  CONST_10  C6'  C5'  C4'  C3'     0.00   0.0  0
 57D  CONST_11  C1'  C2'  C3'  C4'     0.00   0.0  0
 57D  CONST_12  C1'  C6'  C5'  C4'     0.00   0.0  0
 57D  CONST_13  C3'  C2'  C1'  C2    180.00   0.0  0
 57D  CONST_14  C5'  C6'  C1'  C2    180.00   0.0  0
 57D  CONST_15  O5   C6   C5   C4      0.00   0.0  0
 57D  CONST_16  O7   C8   C7   C6    180.00   0.0  0
 57D  CONST_17  O5   C6   C7   C8    180.00   0.0  0
 57D  CONST_18  O5   C6   C5   C10   180.00   0.0  0
 57D  CONST_19  O7   C8   C9   C10   180.00   0.0  0
 57D  CONST_20  H2'  C2'  C1'  C2      0.00   0.0  0
 57D  CONST_21  H6'  C6'  C1'  C2      0.00   0.0  0
 57D  CONST_22  H7   C7   C6   C5    180.00   0.0  0
 57D  CONST_23  H9   C9   C10  C5    180.00   0.0  0
 57D  CONST_24  H4'  C4'  C3'  C2'   180.00   0.0  0
 57D  CONST_25  H5'  C5'  C4'  C3'   180.00   0.0  0
 57D  CONST_26  H3'  C3'  C4'  C5'   180.00   0.0  0
 57D  Var_01    C5   C4   C3   C2     -1.38  30.0  1
 57D  Var_02    C5   C10  O1   C2     -1.43  30.0  1
 57D  Var_03    C2'  C1'  C2   C3   -158.28  30.0  2
 57D  Var_04    C6   C5   C4   C3   -178.95  30.0  1
 57D  Var_05    O1   C2   C3   C4      0.77  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
 57D  plan-1  C2   0.020
 57D  plan-1  C2'  0.020
 57D  plan-1  C3'  0.020
 57D  plan-1  C4'  0.020
 57D  plan-1  C5'  0.020
 57D  plan-1  C6'  0.020
 57D  plan-1  C1'  0.020
 57D  plan-1  H3'  0.020
 57D  plan-1  H4'  0.020
 57D  plan-1  H5'  0.020
 57D  plan-1  H6'  0.020
 57D  plan-1  H2'  0.020
 57D  plan-2  C4   0.020
 57D  plan-2  C5   0.020
 57D  plan-2  C6   0.020
 57D  plan-2  C7   0.020
 57D  plan-2  C8   0.020
 57D  plan-2  C9   0.020
 57D  plan-2  C10  0.020
 57D  plan-2  O1   0.020
 57D  plan-2  O5   0.020
 57D  plan-2  O7   0.020
 57D  plan-2  H7   0.020
 57D  plan-2  H9   0.020
 57D  plan-3  C3   0.020
 57D  plan-3  C4   0.020
 57D  plan-3  C5   0.020
 57D  plan-3  O4   0.020

