# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:47:43 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-hydroxy-6,7-dimethyl-3-(naphthalen-1-ylmethyl)-2H-chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2OC(=O)C(=C(O)c2cc1C)Cc3cccc4ccccc34
#
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
 CC2  CC2  4-hydroxy-6,7-dimethyl-3-(naphthalen-1-ylmethyl)-2H-chromen-2-one  ligand  43  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CC2
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
 CC2  C1    C  CR6   0   0.066  -5.1265  -0.1699   0.3247
 CC2  O1    O  OH1   0  -0.583  -0.6612   1.7874  -1.1837
 CC2  C2    C  CR16  0  -0.374  -4.1530  -1.1516   0.3868
 CC2  O2    O  O     0  -0.467  -1.9428  -1.8650   0.1159
 CC2  C3    C  CR66  0   0.355  -2.8446  -0.8661   0.0240
 CC2  C4    C  CR66  0  -0.060  -2.4812   0.4023  -0.4125
 CC2  C5    C  CR16  0  -0.377  -3.4749   1.3875  -0.4678
 CC2  C6    C  CR6   0   0.087  -4.7825   1.1269  -0.1100
 CC2  O7    O  O     0  -0.438   0.0819  -2.6731  -0.0450
 CC2  C8    C  CR6   0   0.531  -0.6284  -1.7061  -0.1979
 CC2  C9    C  CR6   0  -0.314  -0.2010  -0.4191  -0.6803
 CC2  C10   C  CR6   0   0.467  -1.0952   0.6041  -0.7713
 CC2  C11   C  CH3   0  -0.738  -6.5358  -0.4868   0.7173
 CC2  C12   C  CH3   0  -0.734  -5.8224   2.2049  -0.1751
 CC2  C13   C  CH2   0  -0.553   1.2431  -0.2712  -1.0448
 CC2  C14   C  CR6   0   0.105   2.1630   0.0690   0.1072
 CC2  C15   C  CR66  0   0.087   3.5719   0.1177  -0.1211
 CC2  C16   C  CR66  0   0.110   4.4444   0.4357   0.9549
 CC2  C17   C  CR16  0  -0.331   3.9040   0.7036   2.2349
 CC2  C18   C  CR16  0  -0.245   2.5544   0.6580   2.4302
 CC2  C19   C  CR16  0  -0.316   1.6878   0.3397   1.3636
 CC2  C20   C  CR16  0  -0.329   4.1449  -0.1378  -1.3911
 CC2  C21   C  CR16  0  -0.247   5.5001  -0.0836  -1.5815
 CC2  C22   C  CR16  0  -0.262   6.3604   0.2283  -0.5110
 CC2  C23   C  CR16  0  -0.311   5.8398   0.4817   0.7285
 CC2  HO1   H  HOH1  0   0.497  -1.3664   2.4400  -1.2603
 CC2  H2    H  HCR6  0   0.277  -4.4051  -2.1512   0.7192
 CC2  H5    H  HCR6  0   0.253  -3.2377   2.3934  -0.7955
 CC2  H11   H  HCH3  0   0.253  -6.8766   0.1575   1.5300
 CC2  H11A  H  HCH3  0   0.254  -7.2226  -0.3312  -0.1170
 CC2  H11B  H  HCH3  0   0.260  -6.6349  -1.5202   1.0435
 CC2  H12   H  HCH3  0   0.250  -6.2226   2.4326   0.8152
 CC2  H12A  H  HCH3  0   0.256  -5.4142   3.1262  -0.5871
 CC2  H12B  H  HCH3  0   0.248  -6.6690   1.9076  -0.7965
 CC2  H13   H  HCH2  0   0.269   1.5793  -1.2062  -1.4989
 CC2  H13A  H  HCH2  0   0.274   1.3563   0.4850  -1.8252
 CC2  H17   H  HCR6  0   0.253   4.5742   0.9456   3.0509
 CC2  H18   H  HCR6  0   0.256   2.1372   0.8658   3.4071
 CC2  H19   H  HCR6  0   0.241   0.6228   0.3165   1.5563
 CC2  H20   H  HCR6  0   0.258   3.5101  -0.3784  -2.2332
 CC2  H21   H  HCR6  0   0.258   5.9137  -0.2830  -2.5616
 CC2  H22   H  HCR6  0   0.258   7.4298   0.2669  -0.6721
 CC2  H23   H  HCR6  0   0.255   6.4940   0.7219   1.5583

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
 CC2  C1   C2    aromatic  1.384  0.020  1.384
 CC2  C1   C6    aromatic  1.410  0.020  1.410
 CC2  C1   C11   single    1.497  0.020  1.497
 CC2  O1   C10   single    1.326  0.020  1.326
 CC2  C2   C3    aromatic  1.388  0.020  1.388
 CC2  O2   C3    single    1.349  0.020  1.349
 CC2  O2   C8    single    1.361  0.020  1.361
 CC2  C3   C4    aromatic  1.390  0.020  1.390
 CC2  C4   C5    aromatic  1.400  0.020  1.400
 CC2  C4   C10   single    1.446  0.020  1.446
 CC2  C5   C6    aromatic  1.381  0.020  1.381
 CC2  C6   C12   single    1.499  0.020  1.499
 CC2  O7   C8    double    1.209  0.020  1.209
 CC2  C8   C9    single    1.439  0.020  1.439
 CC2  C9   C10   double    1.362  0.020  1.362
 CC2  C9   C13   single    1.497  0.020  1.497
 CC2  C13  C14   single    1.513  0.020  1.513
 CC2  C14  C15   aromatic  1.428  0.020  1.428
 CC2  C14  C19   aromatic  1.370  0.020  1.370
 CC2  C15  C16   aromatic  1.421  0.020  1.421
 CC2  C15  C20   aromatic  1.416  0.020  1.416
 CC2  C16  C17   aromatic  1.415  0.020  1.415
 CC2  C16  C23   aromatic  1.414  0.020  1.414
 CC2  C17  C18   aromatic  1.364  0.020  1.364
 CC2  C18  C19   aromatic  1.411  0.020  1.411
 CC2  C20  C21   aromatic  1.370  0.020  1.370
 CC2  C21  C22   aromatic  1.408  0.020  1.408
 CC2  C22  C23   aromatic  1.368  0.020  1.368
 CC2  O1   HO1   single    0.850  0.020  0.980
 CC2  C2   H2    single    0.930  0.020  1.080
 CC2  C5   H5    single    0.930  0.020  1.080
 CC2  C11  H11   single    0.970  0.020  1.090
 CC2  C11  H11A  single    0.970  0.020  1.090
 CC2  C11  H11B  single    0.970  0.020  1.090
 CC2  C12  H12   single    0.970  0.020  1.090
 CC2  C12  H12A  single    0.970  0.020  1.090
 CC2  C12  H12B  single    0.970  0.020  1.090
 CC2  C13  H13   single    0.970  0.020  1.090
 CC2  C13  H13A  single    0.970  0.020  1.090
 CC2  C17  H17   single    0.930  0.020  1.080
 CC2  C18  H18   single    0.930  0.020  1.080
 CC2  C19  H19   single    0.930  0.020  1.080
 CC2  C20  H20   single    0.930  0.020  1.080
 CC2  C21  H21   single    0.930  0.020  1.080
 CC2  C22  H22   single    0.930  0.020  1.080
 CC2  C23  H23   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
 CC2  C11   C1   C6    120.34  3.000
 CC2  C11   C1   C2    120.02  3.000
 CC2  C6    C1   C2    119.64  3.000
 CC2  HO1   O1   C10   112.92  3.000
 CC2  H2    C2   C3    119.32  3.000
 CC2  H2    C2   C1    120.31  3.000
 CC2  C3    C2   C1    120.37  3.000
 CC2  C8    O2   C3    122.93  3.000
 CC2  C4    C3   O2    121.50  3.000
 CC2  C4    C3   C2    121.10  3.000
 CC2  O2    C3   C2    117.40  3.000
 CC2  C10   C4   C5    124.90  3.000
 CC2  C10   C4   C3    117.13  3.000
 CC2  C5    C4   C3    117.97  3.000
 CC2  H5    C5   C6    117.43  3.000
 CC2  H5    C5   C4    120.62  3.000
 CC2  C6    C5   C4    121.94  3.000
 CC2  C12   C6   C5    120.67  3.000
 CC2  C12   C6   C1    120.36  3.000
 CC2  C5    C6   C1    118.98  3.000
 CC2  C9    C8   O7    125.65  3.000
 CC2  C9    C8   O2    117.94  3.000
 CC2  O7    C8   O2    116.41  3.000
 CC2  C13   C9   C10   122.89  3.000
 CC2  C13   C9   C8    117.16  3.000
 CC2  C10   C9   C8    119.95  3.000
 CC2  C9    C10  C4    120.53  3.000
 CC2  C9    C10  O1    118.44  3.000
 CC2  C4    C10  O1    121.03  3.000
 CC2  H11B  C11  H11A  107.89  3.000
 CC2  H11B  C11  H11   107.99  3.000
 CC2  H11A  C11  H11   106.76  3.000
 CC2  H11B  C11  C1    111.43  3.000
 CC2  H11A  C11  C1    111.21  3.000
 CC2  H11   C11  C1    111.36  3.000
 CC2  H12B  C12  H12A  107.81  3.000
 CC2  H12B  C12  H12   106.79  3.000
 CC2  H12A  C12  H12   107.71  3.000
 CC2  H12B  C12  C6    111.52  3.000
 CC2  H12A  C12  C6    111.40  3.000
 CC2  H12   C12  C6    111.39  3.000
 CC2  H13A  C13  H13   105.28  3.000
 CC2  H13A  C13  C14   108.98  3.000
 CC2  H13   C13  C14   108.77  3.000
 CC2  H13A  C13  C9    110.02  3.000
 CC2  H13   C13  C9    108.28  3.000
 CC2  C14   C13  C9    115.06  3.000
 CC2  C19   C14  C15   118.82  3.000
 CC2  C19   C14  C13   122.12  3.000
 CC2  C15   C14  C13   119.07  3.000
 CC2  C20   C15  C16   118.09  3.000
 CC2  C20   C15  C14   122.43  3.000
 CC2  C16   C15  C14   119.49  3.000
 CC2  C23   C16  C17   121.03  3.000
 CC2  C23   C16  C15   119.45  3.000
 CC2  C17   C16  C15   119.52  3.000
 CC2  H17   C17  C18   120.77  3.000
 CC2  H17   C17  C16   119.17  3.000
 CC2  C18   C17  C16   120.06  3.000
 CC2  H18   C18  C19   119.27  3.000
 CC2  H18   C18  C17   120.27  3.000
 CC2  C19   C18  C17   120.46  3.000
 CC2  H19   C19  C18   118.33  3.000
 CC2  H19   C19  C14   120.02  3.000
 CC2  C18   C19  C14   121.65  3.000
 CC2  H20   C20  C21   118.77  3.000
 CC2  H20   C20  C15   120.05  3.000
 CC2  C21   C20  C15   121.18  3.000
 CC2  H21   C21  C22   119.72  3.000
 CC2  H21   C21  C20   119.78  3.000
 CC2  C22   C21  C20   120.50  3.000
 CC2  H22   C22  C23   120.29  3.000
 CC2  H22   C22  C21   119.89  3.000
 CC2  C23   C22  C21   119.82  3.000
 CC2  H23   C23  C22   120.34  3.000
 CC2  H23   C23  C16   118.70  3.000
 CC2  C22   C23  C16   120.96  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
 CC2  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 CC2  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 CC2  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 CC2  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 CC2  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 CC2  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 CC2  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 CC2  CONST_08  C23  C16  C15  C14  180.00   0.0  0
 CC2  CONST_09  C21  C20  C15  C14  180.00   0.0  0
 CC2  CONST_10  C17  C18  C19  C14    0.00   0.0  0
 CC2  CONST_11  C18  C19  C14  C15    0.00   0.0  0
 CC2  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 CC2  CONST_13  C22  C23  C16  C15    0.00   0.0  0
 CC2  CONST_14  C22  C21  C20  C15    0.00   0.0  0
 CC2  CONST_15  C19  C14  C15  C16    0.00   0.0  0
 CC2  CONST_16  C21  C20  C15  C16    0.00   0.0  0
 CC2  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 CC2  CONST_18  C21  C22  C23  C16    0.00   0.0  0
 CC2  CONST_19  C20  C15  C16  C17  180.00   0.0  0
 CC2  CONST_20  C22  C23  C16  C17  180.00   0.0  0
 CC2  CONST_21  C23  C16  C17  C18  180.00   0.0  0
 CC2  CONST_22  C20  C15  C14  C19  180.00   0.0  0
 CC2  CONST_23  C23  C16  C15  C20    0.00   0.0  0
 CC2  CONST_24  C23  C22  C21  C20    0.00   0.0  0
 CC2  CONST_25  C12  C6   C1   C2   180.00   0.0  0
 CC2  CONST_26  C11  C1   C2   C3   180.00   0.0  0
 CC2  CONST_27  C12  C6   C5   C4   180.00   0.0  0
 CC2  CONST_28  C11  C1   C6   C5   180.00   0.0  0
 CC2  CONST_29  C16  C15  C14  C13  180.00   0.0  0
 CC2  CONST_30  C20  C15  C14  C13    0.00   0.0  0
 CC2  CONST_31  C18  C19  C14  C13  180.00   0.0  0
 CC2  CONST_32  H5   C5   C6   C1   180.00   0.0  0
 CC2  CONST_33  H2   C2   C3   O2     0.00   0.0  0
 CC2  CONST_34  H20  C20  C15  C14    0.00   0.0  0
 CC2  CONST_35  H18  C18  C19  C14  180.00   0.0  0
 CC2  CONST_36  H19  C19  C14  C15  180.00   0.0  0
 CC2  CONST_37  H17  C17  C16  C15  180.00   0.0  0
 CC2  CONST_38  H23  C23  C16  C15  180.00   0.0  0
 CC2  CONST_39  H21  C21  C20  C15  180.00   0.0  0
 CC2  CONST_40  H22  C22  C23  C16  180.00   0.0  0
 CC2  Var_01    C10  C9   C8   O2     2.00  30.0  1
 CC2  Var_02    C9   C8   O2   C3    -1.61  30.0  1
 CC2  Var_03    C9   C10  C4   C3     0.11  30.0  1
 CC2  Var_04    C8   C9   C10  C4    -1.27  30.0  1
 CC2  Var_05    C14  C13  C9   C8   -85.24  30.0  3
 CC2  Var_06    C15  C14  C13  C9   174.70  30.0  2
 CC2  Var_07    H12  C12  C6   C1    63.26  30.0  2
 CC2  Var_08    H11  C11  C1   C2   121.61  30.0  2

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
 CC2  plan-1  C13  0.020
 CC2  plan-1  C14  0.020
 CC2  plan-1  C15  0.020
 CC2  plan-1  C16  0.020
 CC2  plan-1  C17  0.020
 CC2  plan-1  C18  0.020
 CC2  plan-1  C19  0.020
 CC2  plan-1  C20  0.020
 CC2  plan-1  C21  0.020
 CC2  plan-1  C22  0.020
 CC2  plan-1  C23  0.020
 CC2  plan-1  H17  0.020
 CC2  plan-1  H18  0.020
 CC2  plan-1  H19  0.020
 CC2  plan-1  H20  0.020
 CC2  plan-1  H21  0.020
 CC2  plan-1  H22  0.020
 CC2  plan-1  H23  0.020
 CC2  plan-2  C1   0.020
 CC2  plan-2  C2   0.020
 CC2  plan-2  O2   0.020
 CC2  plan-2  C3   0.020
 CC2  plan-2  C4   0.020
 CC2  plan-2  C5   0.020
 CC2  plan-2  C6   0.020
 CC2  plan-2  C10  0.020
 CC2  plan-2  C11  0.020
 CC2  plan-2  C12  0.020
 CC2  plan-2  H2   0.020
 CC2  plan-2  H5   0.020
 CC2  plan-3  O2   0.020
 CC2  plan-3  O7   0.020
 CC2  plan-3  C8   0.020
 CC2  plan-3  C9   0.020

