# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 03:28:57 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[C@@H]2CC(=O)c3c(O)cc(O)cc3O2
#
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
 NAR  NAR  (2S)-5,7-dihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one  ligand  32  20  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NAR
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
 NAR  C1    C  CR16  0  -0.380   1.8335   0.2551  -2.1254
 NAR  C2    C  CR6   0   0.301   1.7858   0.2224  -3.5108
 NAR  C3    C  CR16  0  -0.377   0.5789   0.0807  -4.1877
 NAR  C4    C  CR6   0   0.273  -0.5938  -0.0753  -3.4679
 NAR  C5    C  CR6   0  -0.375  -0.5862  -0.0383  -2.0539
 NAR  C6    C  CR6   0   0.456   0.6525   0.1358  -1.4064
 NAR  C7    C  C     0   0.421  -1.7868  -0.2971  -1.2629
 NAR  C8    C  CH2   0  -0.593  -1.5519  -0.4509   0.2163
 NAR  C9    C  CH1   0  -0.049  -0.4214   0.4451   0.6878
 NAR  O1    O  O2    0  -0.512   0.7641   0.1935  -0.0727
 NAR  O2    O  O     0  -0.280  -2.8978  -0.4296  -1.7487
 NAR  C10   C  CR6   0   0.044  -0.0825   0.2446   2.1342
 NAR  C11   C  CR16  0  -0.267   0.4586  -0.9601   2.5819
 NAR  C12   C  CR16  0  -0.356   0.7532  -1.1558   3.9181
 NAR  C13   C  CR6   0   0.362   0.5013  -0.1414   4.8433
 NAR  C14   C  CR16  0  -0.263  -0.0480   1.0607   4.4103
 NAR  C15   C  CR16  0  -0.298  -0.3269   1.2462   3.0630
 NAR  O3    O  OH1   0  -0.702   0.8113  -0.3820   6.1313
 NAR  O4    O  OH1   0  -0.677   2.9431   0.3044  -4.2207
 NAR  O5    O  OH1   0  -0.596  -1.7106  -0.3289  -4.1652
 NAR  H11   H  HCR6  0   0.282   2.7754   0.3779  -1.6066
 NAR  H31   H  HCR6  0   0.274   0.5543   0.0596  -5.2695
 NAR  H81   H  HCH2  0   0.315  -1.3204  -1.5041   0.4137
 NAR  H82   H  HCH2  0   0.218  -2.4616  -0.2086   0.7664
 NAR  H9    H  HCH1  0   0.289  -0.7067   1.4916   0.5218
 NAR  H111  H  HCR6  0   0.267   0.6582  -1.7619   1.8812
 NAR  H121  H  HCR6  0   0.262   1.1810  -2.0924   4.2528
 NAR  H141  H  HCR6  0   0.290  -0.2576   1.8549   5.1178
 NAR  H151  H  HCR6  0   0.271  -0.7413   2.1928   2.7372
 NAR  HO3   H  HOH1  0   0.448   0.5765   0.3736   6.6815
 NAR  H41   H  HOH1  0   0.471   3.1536   1.2248  -4.4174
 NAR  H51   H  HOH1  0   0.482  -2.4765   0.0897  -3.7508

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
 NAR  C1   C2    aromatic  1.387  0.020  1.387
 NAR  C1   C6    aromatic  1.388  0.020  1.388
 NAR  C1   H11   single    0.930  0.020  1.080
 NAR  C2   C3    aromatic  1.391  0.020  1.391
 NAR  C2   O4    single    1.360  0.020  1.360
 NAR  C3   C4    aromatic  1.385  0.020  1.385
 NAR  C3   H31   single    0.930  0.020  1.080
 NAR  C4   C5    aromatic  1.415  0.020  1.415
 NAR  C4   O5    single    1.341  0.020  1.341
 NAR  C5   C6    aromatic  1.408  0.020  1.408
 NAR  C5   C7    single    1.461  0.020  1.461
 NAR  C6   O1    single    1.340  0.020  1.340
 NAR  C7   C8    single    1.506  0.020  1.506
 NAR  C7   O2    double    1.220  0.020  1.220
 NAR  C8   C9    single    1.518  0.020  1.518
 NAR  C8   H81   single    0.970  0.020  1.090
 NAR  C8   H82   single    0.970  0.020  1.090
 NAR  C9   O1    single    1.431  0.020  1.431
 NAR  C9   C10   single    1.499  0.020  1.499
 NAR  C9   H9    single    0.970  0.020  1.090
 NAR  C10  C11   aromatic  1.394  0.020  1.394
 NAR  C10  C15   aromatic  1.388  0.020  1.388
 NAR  C11  C12   aromatic  1.382  0.020  1.382
 NAR  C11  H111  single    0.930  0.020  1.080
 NAR  C12  C13   aromatic  1.396  0.020  1.396
 NAR  C12  H121  single    0.930  0.020  1.080
 NAR  C13  C14   aromatic  1.391  0.020  1.391
 NAR  C13  O3    single    1.346  0.020  1.346
 NAR  C14  C15   aromatic  1.388  0.020  1.388
 NAR  C14  H141  single    0.930  0.020  1.080
 NAR  C15  H151  single    0.930  0.020  1.080
 NAR  O3   HO3   single    0.850  0.020  0.980
 NAR  O4   H41   single    0.850  0.020  0.980
 NAR  O5   H51   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
 NAR  H11   C1   C6   120.13  3.000
 NAR  H11   C1   C2   120.77  3.000
 NAR  C6    C1   C2   119.10  3.000
 NAR  O4    C2   C3   119.37  3.000
 NAR  O4    C2   C1   119.39  3.000
 NAR  C3    C2   C1   121.23  3.000
 NAR  H31   C3   C4   119.88  3.000
 NAR  H31   C3   C2   120.54  3.000
 NAR  C4    C3   C2   119.55  3.000
 NAR  O5    C4   C5   121.96  3.000
 NAR  O5    C4   C3   117.15  3.000
 NAR  C5    C4   C3   120.80  3.000
 NAR  C7    C5   C6   119.72  3.000
 NAR  C7    C5   C4   122.15  3.000
 NAR  C6    C5   C4   117.88  3.000
 NAR  O1    C6   C5   122.43  3.000
 NAR  O1    C6   C1   116.18  3.000
 NAR  C5    C6   C1   121.39  3.000
 NAR  O2    C7   C8   121.49  3.000
 NAR  O2    C7   C5   123.52  3.000
 NAR  C8    C7   C5   114.95  3.000
 NAR  H82   C8   H81  107.39  3.000
 NAR  H82   C8   C9   109.48  3.000
 NAR  H81   C8   C9   110.73  3.000
 NAR  H82   C8   C7   110.05  3.000
 NAR  H81   C8   C7   107.94  3.000
 NAR  C9    C8   C7   111.17  3.000
 NAR  H9    C9   C10  109.41  3.000
 NAR  H9    C9   O1   107.62  3.000
 NAR  C10   C9   O1   107.58  3.000
 NAR  H9    C9   C8   108.81  3.000
 NAR  C10   C9   C8   112.91  3.000
 NAR  O1    C9   C8   110.38  3.000
 NAR  C9    O1   C6   117.89  3.000
 NAR  C15   C10  C11  118.49  3.000
 NAR  C15   C10  C9   120.63  3.000
 NAR  C11   C10  C9   120.87  3.000
 NAR  H111  C11  C12  118.76  3.000
 NAR  H111  C11  C10  120.21  3.000
 NAR  C12   C11  C10  121.02  3.000
 NAR  H121  C12  C13  119.67  3.000
 NAR  H121  C12  C11  120.36  3.000
 NAR  C13   C12  C11  119.96  3.000
 NAR  O3    C13  C14  122.90  3.000
 NAR  O3    C13  C12  117.56  3.000
 NAR  C14   C13  C12  119.54  3.000
 NAR  H141  C14  C15  119.78  3.000
 NAR  H141  C14  C13  120.42  3.000
 NAR  C15   C14  C13  119.80  3.000
 NAR  H151  C15  C14  119.03  3.000
 NAR  H151  C15  C10  119.78  3.000
 NAR  C14   C15  C10  121.18  3.000
 NAR  HO3   O3   C13  110.48  3.000
 NAR  H41   O4   C2   110.47  3.000
 NAR  H51   O5   C4   110.81  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
 NAR  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 NAR  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 NAR  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 NAR  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 NAR  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 NAR  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 NAR  CONST_07  C13   C12  C11  C10    0.00   0.0  0
 NAR  CONST_08  C13   C14  C15  C10    0.00   0.0  0
 NAR  CONST_09  C14   C15  C10  C11    0.00   0.0  0
 NAR  CONST_10  C14   C13  C12  C11    0.00   0.0  0
 NAR  CONST_11  C15   C10  C11  C12    0.00   0.0  0
 NAR  CONST_12  C15   C14  C13  C12    0.00   0.0  0
 NAR  CONST_13  C12   C11  C10  C9   180.00   0.0  0
 NAR  CONST_14  C14   C15  C10  C9   180.00   0.0  0
 NAR  CONST_15  O5    C4   C3   C2   180.00   0.0  0
 NAR  CONST_16  O4    C2   C3   C4   180.00   0.0  0
 NAR  CONST_17  O4    C2   C1   C6   180.00   0.0  0
 NAR  CONST_18  O5    C4   C5   C6   180.00   0.0  0
 NAR  CONST_19  O5    C4   C5   C7     0.00   0.0  0
 NAR  CONST_20  O3    C13  C12  C11  180.00   0.0  0
 NAR  CONST_21  O3    C13  C14  C15  180.00   0.0  0
 NAR  CONST_22  H31   C3   C2   C1   180.00   0.0  0
 NAR  CONST_23  H11   C1   C2   C3   180.00   0.0  0
 NAR  CONST_24  H111  C11  C10  C9     0.00   0.0  0
 NAR  CONST_25  H151  C15  C10  C9     0.00   0.0  0
 NAR  CONST_26  H121  C12  C11  C10  180.00   0.0  0
 NAR  CONST_27  H141  C14  C15  C10  180.00   0.0  0
 NAR  Var_01    C8    C7   C5   C4   169.93  30.0  1
 NAR  Var_02    C9    C8   C7   C5    34.00  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
 NAR  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
 NAR  plan-1  C9    0.020
 NAR  plan-1  C10   0.020
 NAR  plan-1  C11   0.020
 NAR  plan-1  C12   0.020
 NAR  plan-1  C13   0.020
 NAR  plan-1  C14   0.020
 NAR  plan-1  C15   0.020
 NAR  plan-1  O3    0.020
 NAR  plan-1  H111  0.020
 NAR  plan-1  H121  0.020
 NAR  plan-1  H141  0.020
 NAR  plan-1  H151  0.020
 NAR  plan-2  C1    0.020
 NAR  plan-2  C2    0.020
 NAR  plan-2  C3    0.020
 NAR  plan-2  C4    0.020
 NAR  plan-2  C5    0.020
 NAR  plan-2  C6    0.020
 NAR  plan-2  C7    0.020
 NAR  plan-2  O1    0.020
 NAR  plan-2  O4    0.020
 NAR  plan-2  O5    0.020
 NAR  plan-2  H11   0.020
 NAR  plan-2  H31   0.020
 NAR  plan-3  C5    0.020
 NAR  plan-3  C7    0.020
 NAR  plan-3  C8    0.020
 NAR  plan-3  O2    0.020

