# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:09:01 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (2S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)C[C@H](Oc2c1)c3ccc(O)c(O)c3
#
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
 ERD  ERD  (2S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-2,3-dihydro-4H-chromen-4-one  ligand  33  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ERD
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
 ERD  O13   O  O     0  -0.407   2.8636   -4.8750   2.5462
 ERD  C9    C  C     0   0.405   2.0140   -4.7344   1.6874
 ERD  C10   C  CH2   0  -0.597   1.3882   -5.9383   1.0224
 ERD  C11   C  CH1   0  -0.054   0.9678   -5.6283  -0.4004
 ERD  C14   C  CR6   0   0.103   0.2664   -6.7724  -1.0698
 ERD  C15   C  CR16  0  -0.333   0.8910   -7.4757  -2.0864
 ERD  C16   C  CR16  0  -0.330   0.2652   -8.5677  -2.6778
 ERD  C17   C  CR6   0   0.286  -0.9961   -8.9623  -2.2665
 ERD  O24   O  OH1   0  -0.631  -1.5828  -10.0206  -2.8608
 ERD  C18   C  CR6   0   0.278  -1.6354   -8.2483  -1.2407
 ERD  O23   O  OH1   0  -0.644  -2.8660   -8.6877  -0.8942
 ERD  C19   C  CR16  0  -0.418  -1.0044   -7.1687  -0.6504
 ERD  O12   O  O2    0  -0.479   0.0864   -4.5054  -0.4062
 ERD  C4    C  CR6   0   0.439   0.4947   -3.4021   0.2386
 ERD  C3    C  CR6   0  -0.289   1.4817   -3.4449   1.2491
 ERD  C5    C  CR16  0  -0.485  -0.1193   -2.2231  -0.1448
 ERD  C6    C  CR6   0   0.407   0.2497   -1.0379   0.4815
 ERD  O29   O  OH1   0  -0.617  -0.3623    0.0809   0.0839
 ERD  C1    C  CR16  0  -0.552   1.2313   -1.0282   1.4695
 ERD  C2    C  CR6   0   0.395   1.8411   -2.2146   1.8480
 ERD  O30   O  OH1   0  -0.595   2.7746   -2.2190   2.8005
 ERD  H101  H  HCH2  0   0.285   2.0964   -6.7675   1.0307
 ERD  H102  H  HCH2  0   0.286   0.5206   -6.2466   1.6173
 ERD  H11   H  HCH1  0   0.266   1.8603   -5.3648  -0.9820
 ERD  H15   H  HCR6  0   0.255   1.8754   -7.1803  -2.4271
 ERD  H16   H  HCR6  0   0.266   0.7575   -9.1172  -3.4706
 ERD  HO24  H  HOH1  0   0.473  -2.4547  -10.1833  -2.4822
 ERD  HO23  H  HOH1  0   0.483  -3.2426   -8.1456  -0.1925
 ERD  H19   H  HCR6  0   0.273  -1.5154   -6.6294   0.1411
 ERD  H5    H  HCR6  0   0.277  -0.8664   -2.2259  -0.9275
 ERD  HO29  H  HOH1  0   0.483  -0.0281    0.8466   0.5658
 ERD  H1    H  HCR6  0   0.289   1.5185   -0.0968   1.9467
 ERD  HO30  H  HOH1  0   0.481   2.8978   -1.3251   3.1428

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
 ERD  O13  C9    double    1.216  0.020  1.216
 ERD  C9   C3    single    1.462  0.020  1.462
 ERD  C9   C10   single    1.511  0.020  1.511
 ERD  C10  C11   single    1.516  0.020  1.516
 ERD  C10  H101  single    0.970  0.020  1.090
 ERD  C10  H102  single    0.970  0.020  1.090
 ERD  C11  O12   single    1.427  0.020  1.427
 ERD  C11  C14   single    1.500  0.020  1.500
 ERD  C11  H11   single    0.970  0.020  1.090
 ERD  C14  C15   aromatic  1.385  0.020  1.385
 ERD  C14  C19   aromatic  1.396  0.020  1.396
 ERD  C15  C16   aromatic  1.391  0.020  1.391
 ERD  C15  H15   single    0.930  0.020  1.080
 ERD  C16  C17   aromatic  1.384  0.020  1.384
 ERD  C16  H16   single    0.930  0.020  1.080
 ERD  C17  C18   aromatic  1.404  0.020  1.404
 ERD  C17  O24   single    1.348  0.020  1.348
 ERD  O24  HO24  single    0.850  0.020  0.980
 ERD  C18  C19   aromatic  1.383  0.020  1.383
 ERD  C18  O23   single    1.352  0.020  1.352
 ERD  O23  HO23  single    0.850  0.020  0.980
 ERD  C19  H19   single    0.930  0.020  1.080
 ERD  O12  C4    single    1.342  0.020  1.342
 ERD  C4   C3    aromatic  1.413  0.020  1.413
 ERD  C4   C5    aromatic  1.383  0.020  1.383
 ERD  C3   C2    aromatic  1.415  0.020  1.415
 ERD  C5   C6    aromatic  1.390  0.020  1.390
 ERD  C5   H5    single    0.930  0.020  1.080
 ERD  C6   C1    aromatic  1.393  0.020  1.393
 ERD  C6   O29   single    1.336  0.020  1.336
 ERD  O29  HO29  single    0.850  0.020  0.980
 ERD  C1   C2    aromatic  1.387  0.020  1.387
 ERD  C1   H1    single    0.930  0.020  1.080
 ERD  C2   O30   single    1.334  0.020  1.334
 ERD  O30  HO30  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
 ERD  C3    C9   C10   114.83  3.000
 ERD  C10   C9   O13   120.53  3.000
 ERD  C3    C9   O13   124.61  3.000
 ERD  H102  C10  H101  107.22  3.000
 ERD  H102  C10  C11   110.33  3.000
 ERD  H101  C10  C11   110.05  3.000
 ERD  H102  C10  C9    108.24  3.000
 ERD  H101  C10  C9    109.48  3.000
 ERD  C11   C10  C9    111.41  3.000
 ERD  H11   C11  O12   108.12  3.000
 ERD  H11   C11  C14   109.09  3.000
 ERD  O12   C11  C14   108.03  3.000
 ERD  H11   C11  C10   108.73  3.000
 ERD  C14   C11  C10   113.12  3.000
 ERD  O12   C11  C10   109.63  3.000
 ERD  C19   C14  C15   119.15  3.000
 ERD  C19   C14  C11   120.55  3.000
 ERD  C15   C14  C11   120.27  3.000
 ERD  H15   C15  C16   119.31  3.000
 ERD  H15   C15  C14   120.16  3.000
 ERD  C16   C15  C14   120.53  3.000
 ERD  H16   C16  C17   119.16  3.000
 ERD  H16   C16  C15   120.34  3.000
 ERD  C17   C16  C15   120.50  3.000
 ERD  C18   C17  O24   121.55  3.000
 ERD  O24   C17  C16   119.30  3.000
 ERD  C18   C17  C16   119.15  3.000
 ERD  HO24  O24  C17   110.66  3.000
 ERD  C19   C18  O23   124.04  3.000
 ERD  O23   C18  C17   115.88  3.000
 ERD  C19   C18  C17   120.08  3.000
 ERD  HO23  O23  C18   111.07  3.000
 ERD  H19   C19  C18   118.97  3.000
 ERD  H19   C19  C14   120.44  3.000
 ERD  C18   C19  C14   120.59  3.000
 ERD  C4    O12  C11   117.20  3.000
 ERD  C5    C4   C3    122.27  3.000
 ERD  C5    C4   O12   115.63  3.000
 ERD  C3    C4   O12   122.09  3.000
 ERD  C2    C3   C4    116.98  3.000
 ERD  C2    C3   C9    123.20  3.000
 ERD  C4    C3   C9    119.69  3.000
 ERD  H5    C5   C6    120.75  3.000
 ERD  H5    C5   C4    120.32  3.000
 ERD  C6    C5   C4    118.93  3.000
 ERD  C1    C6   O29   121.88  3.000
 ERD  O29   C6   C5    117.28  3.000
 ERD  C1    C6   C5    120.83  3.000
 ERD  HO29  O29  C6    110.94  3.000
 ERD  H1    C1   C2    119.86  3.000
 ERD  H1    C1   C6    120.29  3.000
 ERD  C2    C1   C6    119.84  3.000
 ERD  O30   C2   C1    120.37  3.000
 ERD  O30   C2   C3    118.50  3.000
 ERD  C1    C2   C3    121.12  3.000
 ERD  HO30  O30  C2    109.85  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
 ERD  CONST_01  C17  C16  C15  C14    0.00   0.0  0
 ERD  CONST_02  C17  C18  C19  C14    0.00   0.0  0
 ERD  CONST_03  C18  C19  C14  C15    0.00   0.0  0
 ERD  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 ERD  CONST_05  C19  C14  C15  C16    0.00   0.0  0
 ERD  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 ERD  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 ERD  CONST_08  C1   C6   C5   C4     0.00   0.0  0
 ERD  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 ERD  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 ERD  CONST_11  C2   C3   C4   C5     0.00   0.0  0
 ERD  CONST_12  C2   C1   C6   C5     0.00   0.0  0
 ERD  CONST_13  C16  C15  C14  C11  180.00   0.0  0
 ERD  CONST_14  C18  C19  C14  C11  180.00   0.0  0
 ERD  CONST_15  O30  C2   C3   C9     0.00   0.0  0
 ERD  CONST_16  O23  C18  C19  C14  180.00   0.0  0
 ERD  CONST_17  O24  C17  C16  C15  180.00   0.0  0
 ERD  CONST_18  O23  C18  C17  C16  180.00   0.0  0
 ERD  CONST_19  C19  C18  C17  O24  180.00   0.0  0
 ERD  CONST_20  O30  C2   C3   C4   180.00   0.0  0
 ERD  CONST_21  O29  C6   C5   C4   180.00   0.0  0
 ERD  CONST_22  O30  C2   C1   C6   180.00   0.0  0
 ERD  CONST_23  C2   C1   C6   O29  180.00   0.0  0
 ERD  CONST_24  H15  C15  C14  C11    0.00   0.0  0
 ERD  CONST_25  H19  C19  C14  C11    0.00   0.0  0
 ERD  CONST_26  H16  C16  C15  C14  180.00   0.0  0
 ERD  CONST_27  H5   C5   C4   O12    0.00   0.0  0
 ERD  CONST_28  H1   C1   C2   C3   180.00   0.0  0
 ERD  Var_01    C4   C3   C9   C10   -2.30  30.0  1
 ERD  Var_02    C3   C9   C10  C11   32.06  30.0  1
 ERD  Var_03    C3   C4   O12  C11  -21.55  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
 ERD  chir_01  C11  C10  O12  C14  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
 ERD  plan-1  C11  0.020
 ERD  plan-1  C14  0.020
 ERD  plan-1  C15  0.020
 ERD  plan-1  C16  0.020
 ERD  plan-1  C17  0.020
 ERD  plan-1  O24  0.020
 ERD  plan-1  C18  0.020
 ERD  plan-1  O23  0.020
 ERD  plan-1  C19  0.020
 ERD  plan-1  H15  0.020
 ERD  plan-1  H16  0.020
 ERD  plan-1  H19  0.020
 ERD  plan-2  C9   0.020
 ERD  plan-2  O12  0.020
 ERD  plan-2  C4   0.020
 ERD  plan-2  C3   0.020
 ERD  plan-2  C5   0.020
 ERD  plan-2  C6   0.020
 ERD  plan-2  O29  0.020
 ERD  plan-2  C1   0.020
 ERD  plan-2  C2   0.020
 ERD  plan-2  O30  0.020
 ERD  plan-2  H5   0.020
 ERD  plan-2  H1   0.020
 ERD  plan-3  O13  0.020
 ERD  plan-3  C9   0.020
 ERD  plan-3  C10  0.020
 ERD  plan-3  C3   0.020

