# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:18:02 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (2S)-7-hydroxy-2-phenyl-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2C(=O)C[C@H](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
 DDC  DDC  (2S)-7-hydroxy-2-phenyl-2,3-dihydro-4H-chromen-4-one  ligand  30  18  .  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_DDC
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
 DDC  C1   C  CR6   0   0.391   1.2328  -0.3010   3.5498
 DDC  C2   C  CR16  0  -0.346  -0.0594  -0.0957   4.0580
 DDC  C3   C  CR16  0  -0.260  -1.0969   0.1043   3.1822
 DDC  C4   C  CR6   0  -0.170  -0.9012   0.1042   1.7945
 DDC  C5   C  CR6   0   0.424   0.3933  -0.1247   1.3068
 DDC  C6   C  CR16  0  -0.497   1.4570  -0.3224   2.1796
 DDC  C7   C  C     0   0.394  -1.9937   0.4175   0.8741
 DDC  C8   C  CH2   0  -0.603  -1.5840   0.5247  -0.5729
 DDC  C9   C  CH1   0  -0.047  -0.4244  -0.4071  -0.8861
 DDC  O1   O  O2    0  -0.476   0.6730  -0.1599  -0.0052
 DDC  O2   O  OH1   0  -0.615   2.2157  -0.4849   4.4369
 DDC  C10  C  CR6   0   0.110   0.0695  -0.2448  -2.2949
 DDC  C11  C  CR16  0  -0.295   0.7486   0.9087  -2.6819
 DDC  C12  C  CR16  0  -0.240   1.1613   1.0688  -3.9959
 DDC  C13  C  CR16  0  -0.262   0.8940   0.0819  -4.9379
 DDC  C14  C  CR16  0  -0.239   0.2156  -1.0672  -4.5583
 DDC  C15  C  CR16  0  -0.316  -0.1903  -1.2304  -3.2394
 DDC  O3   O  O     0  -0.408  -3.1337   0.6259   1.2419
 DDC  H2   H  HCR6  0   0.272  -0.2217  -0.0875   5.1276
 DDC  H3   H  HCR6  0   0.270  -2.0925   0.2810   3.5681
 DDC  H6   H  HCR6  0   0.287   2.4492  -0.5016   1.7809
 DDC  H81  H  HCH2  0   0.291  -2.4297   0.2990  -1.2235
 DDC  H82  H  HCH2  0   0.291  -1.2962   1.5652  -0.7652
 DDC  H9   H  HCH1  0   0.269  -0.7536  -1.4431  -0.7349
 DDC  HO2  H  HOH1  0   0.483   3.0643  -0.6026   3.9936
 DDC  H11  H  HCR6  0   0.257   0.9563   1.6873  -1.9579
 DDC  H12  H  HCR6  0   0.259   1.6897   1.9672  -4.2876
 DDC  H13  H  HCR6  0   0.259   1.2150   0.2098  -5.9636
 DDC  H14  H  HCR6  0   0.259   0.0053  -1.8398  -5.2863
 DDC  H15  H  HCR6  0   0.257  -0.7139  -2.1321  -2.9440

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
 DDC  C1   C2   aromatic  1.404  0.020  1.404
 DDC  C1   C6   aromatic  1.389  0.020  1.389
 DDC  C1   O2   single    1.337  0.020  1.337
 DDC  C2   C3   aromatic  1.372  0.020  1.372
 DDC  C2   H2   single    0.930  0.020  1.080
 DDC  C3   C4   aromatic  1.401  0.020  1.401
 DDC  C3   H3   single    0.930  0.020  1.080
 DDC  C4   C5   aromatic  1.402  0.020  1.402
 DDC  C4   C7   single    1.462  0.020  1.462
 DDC  C5   C6   aromatic  1.390  0.020  1.390
 DDC  C5   O1   single    1.342  0.020  1.342
 DDC  C6   H6   single    0.930  0.020  1.080
 DDC  C7   C8   single    1.508  0.020  1.508
 DDC  C7   O3   double    1.216  0.020  1.216
 DDC  C8   C9   single    1.520  0.020  1.520
 DDC  C8   H81  single    0.970  0.020  1.090
 DDC  C8   H82  single    0.970  0.020  1.090
 DDC  C9   O1   single    1.429  0.020  1.429
 DDC  C9   C10  single    1.502  0.020  1.502
 DDC  C9   H9   single    0.970  0.020  1.090
 DDC  O2   HO2  single    0.850  0.020  0.980
 DDC  C10  C11  aromatic  1.393  0.020  1.393
 DDC  C10  C15  aromatic  1.390  0.020  1.390
 DDC  C11  C12  aromatic  1.387  0.020  1.387
 DDC  C11  H11  single    0.930  0.020  1.080
 DDC  C12  C13  aromatic  1.390  0.020  1.390
 DDC  C12  H12  single    0.930  0.020  1.080
 DDC  C13  C14  aromatic  1.387  0.020  1.387
 DDC  C13  H13  single    0.930  0.020  1.080
 DDC  C14  C15  aromatic  1.390  0.020  1.390
 DDC  C14  H14  single    0.930  0.020  1.080
 DDC  C15  H15  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
 DDC  O2   C1   C6   122.27  3.000
 DDC  O2   C1   C2   117.18  3.000
 DDC  C6   C1   C2   120.54  3.000
 DDC  H2   C2   C3   121.09  3.000
 DDC  H2   C2   C1   119.81  3.000
 DDC  C3   C2   C1   119.10  3.000
 DDC  H3   C3   C4   118.79  3.000
 DDC  H3   C3   C2   119.45  3.000
 DDC  C4   C3   C2   121.76  3.000
 DDC  C7   C4   C5   120.38  3.000
 DDC  C7   C4   C3   121.25  3.000
 DDC  C5   C4   C3   118.25  3.000
 DDC  O1   C5   C6   116.79  3.000
 DDC  O1   C5   C4   122.46  3.000
 DDC  C6   C5   C4   120.75  3.000
 DDC  H6   C6   C5   119.53  3.000
 DDC  H6   C6   C1   120.88  3.000
 DDC  C5   C6   C1   119.59  3.000
 DDC  O3   C7   C8   122.21  3.000
 DDC  O3   C7   C4   123.15  3.000
 DDC  C8   C7   C4   114.59  3.000
 DDC  H82  C8   H81  107.17  3.000
 DDC  H82  C8   C9   110.20  3.000
 DDC  H81  C8   C9   109.98  3.000
 DDC  H82  C8   C7   107.88  3.000
 DDC  H81  C8   C7   110.31  3.000
 DDC  C9   C8   C7   111.19  3.000
 DDC  H9   C9   C10  109.26  3.000
 DDC  H9   C9   O1   107.98  3.000
 DDC  C10  C9   O1   107.88  3.000
 DDC  H9   C9   C8   108.75  3.000
 DDC  C10  C9   C8   112.21  3.000
 DDC  O1   C9   C8   110.66  3.000
 DDC  C9   O1   C5   116.57  3.000
 DDC  HO2  O2   C1   111.02  3.000
 DDC  C15  C10  C11  119.31  3.000
 DDC  C15  C10  C9   119.97  3.000
 DDC  C11  C10  C9   120.68  3.000
 DDC  H11  C11  C12  119.56  3.000
 DDC  H11  C11  C10  120.19  3.000
 DDC  C12  C11  C10  120.25  3.000
 DDC  H12  C12  C13  120.03  3.000
 DDC  H12  C12  C11  119.77  3.000
 DDC  C13  C12  C11  120.20  3.000
 DDC  H13  C13  C14  120.15  3.000
 DDC  H13  C13  C12  120.08  3.000
 DDC  C14  C13  C12  119.77  3.000
 DDC  H14  C14  C15  119.86  3.000
 DDC  H14  C14  C13  120.14  3.000
 DDC  C15  C14  C13  119.99  3.000
 DDC  H15  C15  C14  119.83  3.000
 DDC  H15  C15  C10  119.69  3.000
 DDC  C14  C15  C10  120.48  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
 DDC  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 DDC  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 DDC  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 DDC  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 DDC  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 DDC  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 DDC  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 DDC  CONST_08  C13  C14  C15  C10    0.00   0.0  0
 DDC  CONST_09  C14  C15  C10  C11    0.00   0.0  0
 DDC  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 DDC  CONST_11  C15  C10  C11  C12    0.00   0.0  0
 DDC  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 DDC  CONST_13  C12  C11  C10  C9   180.00   0.0  0
 DDC  CONST_14  C14  C15  C10  C9   180.00   0.0  0
 DDC  CONST_15  O2   C1   C2   C3   180.00   0.0  0
 DDC  CONST_16  O2   C1   C6   C5   180.00   0.0  0
 DDC  CONST_17  H3   C3   C2   C1   180.00   0.0  0
 DDC  CONST_18  H6   C6   C1   C2   180.00   0.0  0
 DDC  CONST_19  H2   C2   C3   C4   180.00   0.0  0
 DDC  CONST_20  H11  C11  C10  C9     0.00   0.0  0
 DDC  CONST_21  H15  C15  C10  C9     0.00   0.0  0
 DDC  CONST_22  H12  C12  C11  C10  180.00   0.0  0
 DDC  CONST_23  H14  C14  C15  C10  180.00   0.0  0
 DDC  CONST_24  H13  C13  C12  C11  180.00   0.0  0
 DDC  Var_01    C8   C7   C4   C3   173.51  30.0  1
 DDC  Var_02    C9   C8   C7   C4    31.62  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
 DDC  chir_01  C9  C8  O1  C10  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
 DDC  plan-1  C9   0.020
 DDC  plan-1  C10  0.020
 DDC  plan-1  C11  0.020
 DDC  plan-1  C12  0.020
 DDC  plan-1  C13  0.020
 DDC  plan-1  C14  0.020
 DDC  plan-1  C15  0.020
 DDC  plan-1  H11  0.020
 DDC  plan-1  H12  0.020
 DDC  plan-1  H13  0.020
 DDC  plan-1  H14  0.020
 DDC  plan-1  H15  0.020
 DDC  plan-2  C1   0.020
 DDC  plan-2  C2   0.020
 DDC  plan-2  C3   0.020
 DDC  plan-2  C4   0.020
 DDC  plan-2  C5   0.020
 DDC  plan-2  C6   0.020
 DDC  plan-2  C7   0.020
 DDC  plan-2  O1   0.020
 DDC  plan-2  O2   0.020
 DDC  plan-2  H2   0.020
 DDC  plan-2  H3   0.020
 DDC  plan-2  H6   0.020
 DDC  plan-3  C4   0.020
 DDC  plan-3  C7   0.020
 DDC  plan-3  C8   0.020
 DDC  plan-3  O3   0.020

