# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 03:04:47 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC2=C(O)C(=O)c3ccccc3C2=O)cc1
#
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
 0VJ  0VJ  2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione  ligand  36  22  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0VJ
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
 0VJ  C01  C  CR16  0  -0.229   4.1909  -2.0369  -1.0731
 0VJ  C02  C  CR16  0  -0.237   4.7474  -0.8529  -1.5384
 0VJ  C03  C  CR16  0  -0.262   4.1525   0.3603  -1.2285
 0VJ  C04  C  CR66  0  -0.028   3.0001   0.3843  -0.4517
 0VJ  C05  C  CR66  0  -0.023   2.4376  -0.8045   0.0174
 0VJ  C06  C  CR16  0  -0.274   3.0394  -2.0146  -0.2979
 0VJ  C07  C  CR6   0   0.303   2.3631   1.6639  -0.1187
 0VJ  C08  C  CR6   0   0.259   1.1279   1.6425   0.7160
 0VJ  C09  C  CR6   0  -0.133   0.5779   0.5010   1.1764
 0VJ  C10  C  CR6   0   0.376   1.2069  -0.7853   0.8579
 0VJ  C11  C  CH2   0  -0.582  -0.6856   0.4804   1.9879
 0VJ  C12  C  CR6   0   0.118  -1.8852   0.1063   1.1482
 0VJ  C13  C  CR16  0  -0.293  -2.5100  -1.1307   1.2910
 0VJ  C14  C  CR16  0  -0.331  -3.6074  -1.4781   0.5230
 0VJ  C15  C  CR6   0   0.367  -4.1125  -0.5866  -0.4240
 0VJ  C16  C  CR16  0  -0.368  -3.4977   0.6535  -0.5819
 0VJ  C17  C  CR16  0  -0.281  -2.3982   0.9841   0.2014
 0VJ  O01  O  O2    0  -0.473  -5.1838  -1.0024  -1.1293
 0VJ  O02  O  O     0  -0.382   0.7387  -1.8266   1.2774
 0VJ  O03  O  O     0  -0.381   2.7859   2.7407  -0.4882
 0VJ  O    O  OH1   0  -0.595   0.6007   2.8321   0.9672
 0VJ  C    C  CH3   0  -0.436  -5.7278  -0.1335  -2.1020
 0VJ  H1   H  HCR6  0   0.278   4.6557  -2.9838  -1.3127
 0VJ  H2   H  HCR6  0   0.277   5.6444  -0.8750  -2.1421
 0VJ  H3   H  HCR6  0   0.277   4.5843   1.2845  -1.5882
 0VJ  H4   H  HCR6  0   0.274   2.6119  -2.9413   0.0595
 0VJ  H5   H  HCH2  0   0.274  -0.5808  -0.2340   2.8053
 0VJ  H6   H  HCH2  0   0.276  -0.8469   1.4559   2.4474
 0VJ  H7   H  HCR6  0   0.247  -2.1302  -1.8385   2.0172
 0VJ  H8   H  HCR6  0   0.258  -4.0779  -2.4451   0.6515
 0VJ  H9   H  HCR6  0   0.276  -3.8607   1.3759  -1.3002
 0VJ  H10  H  HCR6  0   0.252  -1.9425   1.9576   0.0618
 0VJ  H11  H  HOH1  0   0.482   1.1527   3.5186   0.5584
 0VJ  H12  H  HCH3  0   0.227  -6.0760   0.8059  -1.6643
 0VJ  H13  H  HCH3  0   0.227  -5.0099   0.0935  -2.8949
 0VJ  H14  H  HCH3  0   0.258  -6.5784  -0.6513  -2.5380

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
 0VJ  C01  C06  aromatic  1.388  0.020  1.388
 0VJ  C01  C02  aromatic  1.389  0.020  1.389
 0VJ  C06  C05  aromatic  1.388  0.020  1.388
 0VJ  C02  C03  aromatic  1.386  0.020  1.386
 0VJ  O02  C10  double    1.216  0.020  1.216
 0VJ  C05  C10  single    1.490  0.020  1.490
 0VJ  C05  C04  aromatic  1.396  0.020  1.396
 0VJ  C03  C04  aromatic  1.390  0.020  1.390
 0VJ  C10  C09  single    1.467  0.020  1.467
 0VJ  C04  C07  single    1.468  0.020  1.468
 0VJ  C17  C16  aromatic  1.390  0.020  1.390
 0VJ  C17  C12  aromatic  1.389  0.020  1.389
 0VJ  C09  C11  single    1.502  0.020  1.502
 0VJ  C09  C08  double    1.348  0.020  1.348
 0VJ  C16  C15  aromatic  1.393  0.020  1.393
 0VJ  C07  C08  single    1.491  0.020  1.491
 0VJ  C07  O03  double    1.214  0.020  1.214
 0VJ  C11  C12  single    1.511  0.020  1.511
 0VJ  C12  C13  aromatic  1.393  0.020  1.393
 0VJ  C08  O    single    1.325  0.020  1.325
 0VJ  C15  O01  single    1.348  0.020  1.348
 0VJ  C15  C14  aromatic  1.395  0.020  1.395
 0VJ  C13  C14  aromatic  1.384  0.020  1.384
 0VJ  O01  C    single    1.413  0.020  1.413
 0VJ  C01  H1   single    0.930  0.020  1.080
 0VJ  C02  H2   single    0.930  0.020  1.080
 0VJ  C03  H3   single    0.930  0.020  1.080
 0VJ  C06  H4   single    0.930  0.020  1.080
 0VJ  C11  H5   single    0.970  0.020  1.090
 0VJ  C11  H6   single    0.970  0.020  1.090
 0VJ  C13  H7   single    0.930  0.020  1.080
 0VJ  C14  H8   single    0.930  0.020  1.080
 0VJ  C16  H9   single    0.930  0.020  1.080
 0VJ  C17  H10  single    0.930  0.020  1.080
 0VJ  O    H11  single    0.850  0.020  0.980
 0VJ  C    H12  single    0.970  0.020  1.090
 0VJ  C    H13  single    0.970  0.020  1.090
 0VJ  C    H14  single    0.970  0.020  1.090

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
 0VJ  H1   C01  C06  119.62  3.000
 0VJ  H1   C01  C02  119.99  3.000
 0VJ  C06  C01  C02  120.39  3.000
 0VJ  H2   C02  C03  119.91  3.000
 0VJ  H2   C02  C01  120.14  3.000
 0VJ  C03  C02  C01  119.95  3.000
 0VJ  H3   C03  C04  120.14  3.000
 0VJ  H3   C03  C02  120.14  3.000
 0VJ  C04  C03  C02  119.73  3.000
 0VJ  C07  C04  C05  119.42  3.000
 0VJ  C07  C04  C03  120.12  3.000
 0VJ  C05  C04  C03  120.47  3.000
 0VJ  C10  C05  C06  119.83  3.000
 0VJ  C10  C05  C04  120.74  3.000
 0VJ  C06  C05  C04  119.43  3.000
 0VJ  H4   C06  C05  120.05  3.000
 0VJ  H4   C06  C01  119.92  3.000
 0VJ  C05  C06  C01  120.04  3.000
 0VJ  O03  C07  C08  118.13  3.000
 0VJ  O03  C07  C04  123.57  3.000
 0VJ  C08  C07  C04  118.30  3.000
 0VJ  O    C08  C09  122.21  3.000
 0VJ  O    C08  C07  115.02  3.000
 0VJ  C09  C08  C07  122.77  3.000
 0VJ  C11  C09  C10  117.78  3.000
 0VJ  C11  C09  C08  122.64  3.000
 0VJ  C10  C09  C08  119.56  3.000
 0VJ  O02  C10  C09  120.72  3.000
 0VJ  C09  C10  C05  119.20  3.000
 0VJ  O02  C10  C05  120.08  3.000
 0VJ  H6   C11  H5   106.52  3.000
 0VJ  H6   C11  C12  109.77  3.000
 0VJ  H5   C11  C12  109.31  3.000
 0VJ  H6   C11  C09  109.87  3.000
 0VJ  H5   C11  C09  109.46  3.000
 0VJ  C12  C11  C09  111.78  3.000
 0VJ  C17  C12  C13  117.72  3.000
 0VJ  C13  C12  C11  121.25  3.000
 0VJ  C17  C12  C11  121.02  3.000
 0VJ  H7   C13  C14  119.09  3.000
 0VJ  H7   C13  C12  119.46  3.000
 0VJ  C14  C13  C12  121.44  3.000
 0VJ  H8   C14  C15  119.59  3.000
 0VJ  H8   C14  C13  120.18  3.000
 0VJ  C15  C14  C13  120.23  3.000
 0VJ  O01  C15  C16  124.46  3.000
 0VJ  O01  C15  C14  116.46  3.000
 0VJ  C16  C15  C14  119.08  3.000
 0VJ  H9   C16  C17  118.75  3.000
 0VJ  H9   C16  C15  121.46  3.000
 0VJ  C17  C16  C15  119.80  3.000
 0VJ  H10  C17  C16  118.27  3.000
 0VJ  H10  C17  C12  120.00  3.000
 0VJ  C16  C17  C12  121.73  3.000
 0VJ  C    O01  C15  118.44  3.000
 0VJ  H11  O    C08  109.19  3.000
 0VJ  H14  C    H13  108.76  3.000
 0VJ  H14  C    H12  108.70  3.000
 0VJ  H13  C    H12  108.73  3.000
 0VJ  H14  C    O01  106.52  3.000
 0VJ  H13  C    O01  111.97  3.000
 0VJ  H12  C    O01  112.05  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
 0VJ  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 0VJ  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 0VJ  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 0VJ  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 0VJ  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 0VJ  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 0VJ  CONST_07  C15  C16  C17  C12    0.00   0.0  0
 0VJ  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 0VJ  CONST_09  C16  C17  C12  C13    0.00   0.0  0
 0VJ  CONST_10  C16  C15  C14  C13    0.00   0.0  0
 0VJ  CONST_11  C17  C16  C15  C14    0.00   0.0  0
 0VJ  CONST_12  C17  C12  C13  C14    0.00   0.0  0
 0VJ  CONST_13  C16  C17  C12  C11  180.00   0.0  0
 0VJ  CONST_14  C14  C13  C12  C11  180.00   0.0  0
 0VJ  CONST_15  O01  C15  C14  C13  180.00   0.0  0
 0VJ  CONST_16  O01  C15  C16  C17  180.00   0.0  0
 0VJ  CONST_17  H3   C03  C02  C01  180.00   0.0  0
 0VJ  CONST_18  H4   C06  C01  C02  180.00   0.0  0
 0VJ  CONST_19  H1   C01  C02  C03  180.00   0.0  0
 0VJ  CONST_20  H2   C02  C03  C04  180.00   0.0  0
 0VJ  CONST_21  H9   C16  C17  C12  180.00   0.0  0
 0VJ  CONST_22  H8   C14  C13  C12  180.00   0.0  0
 0VJ  CONST_23  H10  C17  C12  C13  180.00   0.0  0
 0VJ  CONST_24  H7   C13  C14  C15  180.00   0.0  0
 0VJ  Var_01    C12  C11  C09  C08  100.57  30.0  3
 0VJ  Var_02    C17  C12  C11  C09  -71.13  30.0  2
 0VJ  Var_03    H12  C    O01  C15  -60.60  30.0  3

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
 0VJ  plan-1  C11  0.020
 0VJ  plan-1  C12  0.020
 0VJ  plan-1  C13  0.020
 0VJ  plan-1  C14  0.020
 0VJ  plan-1  C15  0.020
 0VJ  plan-1  C16  0.020
 0VJ  plan-1  C17  0.020
 0VJ  plan-1  O01  0.020
 0VJ  plan-1  H7   0.020
 0VJ  plan-1  H8   0.020
 0VJ  plan-1  H9   0.020
 0VJ  plan-1  H10  0.020
 0VJ  plan-2  C01  0.020
 0VJ  plan-2  C02  0.020
 0VJ  plan-2  C03  0.020
 0VJ  plan-2  C04  0.020
 0VJ  plan-2  C05  0.020
 0VJ  plan-2  C06  0.020
 0VJ  plan-2  C07  0.020
 0VJ  plan-2  C08  0.020
 0VJ  plan-2  C09  0.020
 0VJ  plan-2  C10  0.020
 0VJ  plan-2  C11  0.020
 0VJ  plan-2  O02  0.020
 0VJ  plan-2  O03  0.020
 0VJ  plan-2  O    0.020
 0VJ  plan-2  H1   0.020
 0VJ  plan-2  H2   0.020
 0VJ  plan-2  H3   0.020
 0VJ  plan-2  H4   0.020

