# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:00:14 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2,3-dimethylnaphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C)C(=O)c2ccccc2C1=O
#
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
 DMW  DMW  2,3-dimethylnaphthalene-1,4-dione  ligand  24  14  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DMW
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
 DMW  C5    C  CR6   0  -0.047   0.6739   0.0186   1.7359
 DMW  C5M   C  CH3   0  -0.738   1.4429   0.0289   3.0176
 DMW  C4    C  CR6   0   0.359   1.4460   0.0017   0.4680
 DMW  O4    O  O     0  -0.376   2.6604  -0.0117   0.4798
 DMW  C3    C  CR66  0  -0.026   0.7044   0.0014  -0.8144
 DMW  C2    C  CR66  0  -0.025  -0.6898   0.0053  -0.8186
 DMW  C1    C  CR6   0   0.359  -1.4389   0.0124   0.4592
 DMW  O1    O  O     0  -0.376  -2.6536   0.0131   0.4637
 DMW  C6    C  CR6   0  -0.046  -0.6745   0.0183   1.7318
 DMW  C3A   C  CR16  0  -0.271   1.4013  -0.0029  -2.0176
 DMW  C3B   C  CR16  0  -0.235   0.7094  -0.0041  -3.2187
 DMW  C3C   C  CR16  0  -0.234  -0.6799  -0.0018  -3.2230
 DMW  C3D   C  CR16  0  -0.271  -1.3792   0.0030  -2.0261
 DMW  C6M   C  CH3   0  -0.738  -1.4511   0.0285   3.0090
 DMW  H5M1  H  HCH3  0   0.267   2.5146   0.0867   2.8524
 DMW  H5M2  H  HCH3  0   0.257   1.1501   0.8760   3.6399
 DMW  H5M3  H  HCH3  0   0.260   1.2399  -0.8731   3.5988
 DMW  H3A   H  HCR6  0   0.272   2.4825  -0.0056  -2.0178
 DMW  H3B   H  HCR6  0   0.275   1.2547  -0.0069  -4.1530
 DMW  H3C   H  HCR6  0   0.275  -1.2200  -0.0037  -4.1603
 DMW  H3D   H  HCR6  0   0.272  -2.4605   0.0051  -2.0328
 DMW  H6M1  H  HCH3  0   0.268  -2.5224  -0.0147   2.8374
 DMW  H6M2  H  HCH3  0   0.258  -1.1747  -0.8181   3.6396
 DMW  H6M3  H  HCH3  0   0.260  -1.2395   0.9326   3.5837

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
 DMW  C5   C5M   single    1.495  0.020  1.495
 DMW  C5   C4    single    1.485  0.020  1.485
 DMW  C5   C6    double    1.348  0.020  1.348
 DMW  C5M  H5M1  single    0.970  0.020  1.090
 DMW  C5M  H5M2  single    0.970  0.020  1.090
 DMW  C5M  H5M3  single    0.970  0.020  1.090
 DMW  C4   O4    double    1.215  0.020  1.215
 DMW  C4   C3    single    1.481  0.020  1.481
 DMW  C3   C2    aromatic  1.394  0.020  1.394
 DMW  C3   C3A   aromatic  1.390  0.020  1.390
 DMW  C2   C1    single    1.481  0.020  1.481
 DMW  C2   C3D   aromatic  1.390  0.020  1.390
 DMW  C1   O1    double    1.215  0.020  1.215
 DMW  C1   C6    single    1.485  0.020  1.485
 DMW  C6   C6M   single    1.495  0.020  1.495
 DMW  C3A  C3B   aromatic  1.386  0.020  1.386
 DMW  C3A  H3A   single    0.930  0.020  1.080
 DMW  C3B  C3C   aromatic  1.389  0.020  1.389
 DMW  C3B  H3B   single    0.930  0.020  1.080
 DMW  C3C  C3D   aromatic  1.386  0.020  1.386
 DMW  C3C  H3C   single    0.930  0.020  1.080
 DMW  C3D  H3D   single    0.930  0.020  1.080
 DMW  C6M  H6M1  single    0.970  0.020  1.090
 DMW  C6M  H6M2  single    0.970  0.020  1.090
 DMW  C6M  H6M3  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
 DMW  C6    C5   C4    121.16  3.000
 DMW  C6    C5   C5M   121.13  3.000
 DMW  C4    C5   C5M   117.70  3.000
 DMW  H5M3  C5M  H5M2  106.73  3.000
 DMW  H5M3  C5M  H5M1  107.97  3.000
 DMW  H5M2  C5M  H5M1  108.08  3.000
 DMW  H5M3  C5M  C5    110.79  3.000
 DMW  H5M2  C5M  C5    110.87  3.000
 DMW  H5M1  C5M  C5    112.19  3.000
 DMW  C3    C4   O4    120.60  3.000
 DMW  C3    C4   C5    118.62  3.000
 DMW  O4    C4   C5    120.78  3.000
 DMW  C3A   C3   C2    119.91  3.000
 DMW  C3A   C3   C4    119.88  3.000
 DMW  C2    C3   C4    120.21  3.000
 DMW  C3D   C2   C1    119.89  3.000
 DMW  C3D   C2   C3    119.90  3.000
 DMW  C1    C2   C3    120.21  3.000
 DMW  C6    C1   O1    120.78  3.000
 DMW  C6    C1   C2    118.63  3.000
 DMW  O1    C1   C2    120.59  3.000
 DMW  C6M   C6   C1    117.71  3.000
 DMW  C6M   C6   C5    121.13  3.000
 DMW  C1    C6   C5    121.16  3.000
 DMW  H3A   C3A  C3B   119.93  3.000
 DMW  H3A   C3A  C3    120.09  3.000
 DMW  C3B   C3A  C3    119.98  3.000
 DMW  H3B   C3B  C3C   120.09  3.000
 DMW  H3B   C3B  C3A   119.79  3.000
 DMW  C3C   C3B  C3A   120.12  3.000
 DMW  H3C   C3C  C3D   119.75  3.000
 DMW  H3C   C3C  C3B   120.13  3.000
 DMW  C3D   C3C  C3B   120.12  3.000
 DMW  H3D   C3D  C3C   119.94  3.000
 DMW  H3D   C3D  C2    120.08  3.000
 DMW  C3C   C3D  C2    119.98  3.000
 DMW  H6M3  C6M  H6M2  106.80  3.000
 DMW  H6M3  C6M  H6M1  107.90  3.000
 DMW  H6M2  C6M  H6M1  108.08  3.000
 DMW  H6M3  C6M  C6    110.77  3.000
 DMW  H6M2  C6M  C6    110.90  3.000
 DMW  H6M1  C6M  C6    112.17  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
 DMW  CONST_01  C3C   C3D  C2   C3      0.00   0.0  0
 DMW  CONST_02  C3C   C3B  C3A  C3      0.00   0.0  0
 DMW  CONST_03  C3B   C3A  C3   C2      0.00   0.0  0
 DMW  CONST_04  C3B   C3C  C3D  C2      0.00   0.0  0
 DMW  CONST_05  C3D   C2   C3   C3A     0.00   0.0  0
 DMW  CONST_06  C3D   C3C  C3B  C3A     0.00   0.0  0
 DMW  CONST_07  H3A   C3A  C3   C4      0.00   0.0  0
 DMW  CONST_08  H3D   C3D  C2   C3    180.00   0.0  0
 DMW  CONST_09  H3B   C3B  C3A  C3    180.00   0.0  0
 DMW  CONST_10  H3C   C3C  C3D  C2    180.00   0.0  0
 DMW  Var_01    H6M1  C6M  C6   C5   -177.63  30.0  3
 DMW  Var_02    H5M1  C5M  C5   C4      3.67  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
 DMW  plan-1  C5   0.020
 DMW  plan-1  C5M  0.020
 DMW  plan-1  C4   0.020
 DMW  plan-1  O4   0.020
 DMW  plan-1  C3   0.020
 DMW  plan-1  C2   0.020
 DMW  plan-1  C1   0.020
 DMW  plan-1  O1   0.020
 DMW  plan-1  C6   0.020
 DMW  plan-1  C3A  0.020
 DMW  plan-1  C3B  0.020
 DMW  plan-1  C3C  0.020
 DMW  plan-1  C3D  0.020
 DMW  plan-1  C6M  0.020
 DMW  plan-1  H3A  0.020
 DMW  plan-1  H3B  0.020
 DMW  plan-1  H3C  0.020
 DMW  plan-1  H3D  0.020

