# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:31:57 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 2-methylnaphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=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
 VK3  VK3  2-methylnaphthalene-1,4-dione  ligand  21  13  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VK3
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
 VK3  C1K   C  CR6   0   0.378   1.7026   0.0120   0.2391
 VK3  O1K   O  O     0  -0.384   2.8820   0.0183  -0.0540
 VK3  C2K   C  CR16  0  -0.394   1.2836   0.0083   1.6482
 VK3  C3K   C  CR6   0   0.005   0.0024  -0.0006   2.0376
 VK3  C4K   C  CR6   0   0.352  -1.0823  -0.0073   1.0176
 VK3  O4K   O  O     0  -0.361  -2.2442  -0.0178   1.3652
 VK3  C5K   C  CR66  0  -0.011  -0.7033  -0.0010  -0.4160
 VK3  C6K   C  CR16  0  -0.269  -1.6955  -0.0044  -1.3901
 VK3  C7K   C  CR16  0  -0.234  -1.3491   0.0012  -2.7326
 VK3  C8K   C  CR16  0  -0.233  -0.0120   0.0102  -3.1088
 VK3  C9K   C  CR16  0  -0.266   0.9824   0.0136  -2.1426
 VK3  C10   C  CR66  0  -0.034   0.6416   0.0081  -0.7955
 VK3  C11   C  CH3   0  -0.711  -0.4112  -0.0055   3.4688
 VK3  H2K1  H  HCR6  0   0.284   2.0826   0.0125   2.3808
 VK3  H6K1  H  HCR6  0   0.273  -2.7378  -0.0112  -1.1014
 VK3  H7K1  H  HCR6  0   0.277  -2.1243  -0.0013  -3.4868
 VK3  H8K1  H  HCR6  0   0.276   0.2552   0.0147  -4.1571
 VK3  H9K1  H  HCR6  0   0.273   2.0234   0.0212  -2.4367
 VK3  H111  H  HCH3  0   0.257   0.4568   0.0083   4.1238
 VK3  H112  H  HCH3  0   0.261  -1.0323   0.8612   3.6998
 VK3  H113  H  HCH3  0   0.261  -1.0038  -0.8914   3.7013

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
 VK3  C1K  O1K   double    1.215  0.020  1.215
 VK3  C1K  C2K   single    1.470  0.020  1.470
 VK3  C1K  C10   single    1.482  0.020  1.482
 VK3  C2K  C3K   double    1.339  0.020  1.339
 VK3  C2K  H2K1  single    0.930  0.020  1.080
 VK3  C3K  C4K   single    1.489  0.020  1.489
 VK3  C3K  C11   single    1.490  0.020  1.490
 VK3  C4K  O4K   double    1.213  0.020  1.213
 VK3  C4K  C5K   single    1.483  0.020  1.483
 VK3  C5K  C6K   aromatic  1.390  0.020  1.390
 VK3  C5K  C10   aromatic  1.397  0.020  1.397
 VK3  C6K  C7K   aromatic  1.387  0.020  1.387
 VK3  C6K  H6K1  single    0.930  0.020  1.080
 VK3  C7K  C8K   aromatic  1.389  0.020  1.389
 VK3  C7K  H7K1  single    0.930  0.020  1.080
 VK3  C8K  C9K   aromatic  1.387  0.020  1.387
 VK3  C8K  H8K1  single    0.930  0.020  1.080
 VK3  C9K  C10   aromatic  1.390  0.020  1.390
 VK3  C9K  H9K1  single    0.930  0.020  1.080
 VK3  C11  H111  single    0.970  0.020  1.090
 VK3  C11  H112  single    0.970  0.020  1.090
 VK3  C11  H113  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
 VK3  C10   C1K  C2K   117.72  3.000
 VK3  C10   C1K  O1K   121.77  3.000
 VK3  C2K   C1K  O1K   120.51  3.000
 VK3  H2K1  C2K  C3K   120.58  3.000
 VK3  H2K1  C2K  C1K   115.96  3.000
 VK3  C3K   C2K  C1K   123.46  3.000
 VK3  C11   C3K  C4K   117.12  3.000
 VK3  C11   C3K  C2K   123.03  3.000
 VK3  C4K   C3K  C2K   119.86  3.000
 VK3  C5K   C4K  O4K   121.47  3.000
 VK3  C5K   C4K  C3K   118.43  3.000
 VK3  O4K   C4K  C3K   120.11  3.000
 VK3  C10   C5K  C6K   119.77  3.000
 VK3  C10   C5K  C4K   120.56  3.000
 VK3  C6K   C5K  C4K   119.66  3.000
 VK3  H6K1  C6K  C7K   119.95  3.000
 VK3  H6K1  C6K  C5K   120.05  3.000
 VK3  C7K   C6K  C5K   120.01  3.000
 VK3  H7K1  C7K  C8K   120.07  3.000
 VK3  H7K1  C7K  C6K   119.75  3.000
 VK3  C8K   C7K  C6K   120.18  3.000
 VK3  H8K1  C8K  C9K   119.88  3.000
 VK3  H8K1  C8K  C7K   120.01  3.000
 VK3  C9K   C8K  C7K   120.11  3.000
 VK3  H9K1  C9K  C10   119.98  3.000
 VK3  H9K1  C9K  C8K   120.05  3.000
 VK3  C10   C9K  C8K   119.98  3.000
 VK3  C9K   C10  C5K   119.95  3.000
 VK3  C9K   C10  C1K   120.08  3.000
 VK3  C5K   C10  C1K   119.97  3.000
 VK3  H113  C11  H112  106.90  3.000
 VK3  H113  C11  H111  108.39  3.000
 VK3  H112  C11  H111  108.47  3.000
 VK3  H113  C11  C3K   110.99  3.000
 VK3  H112  C11  C3K   111.03  3.000
 VK3  H111  C11  C3K   110.91  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
 VK3  CONST_01  C8K   C7K  C6K  C5K    0.00   0.0  0
 VK3  CONST_02  C8K   C9K  C10  C5K    0.00   0.0  0
 VK3  CONST_03  C9K   C10  C5K  C6K    0.00   0.0  0
 VK3  CONST_04  C9K   C8K  C7K  C6K    0.00   0.0  0
 VK3  CONST_05  C10   C5K  C6K  C7K    0.00   0.0  0
 VK3  CONST_06  C10   C9K  C8K  C7K    0.00   0.0  0
 VK3  CONST_07  H9K1  C9K  C10  C1K    0.00   0.0  0
 VK3  CONST_08  H6K1  C6K  C5K  C4K    0.00   0.0  0
 VK3  CONST_09  H7K1  C7K  C6K  C5K  180.00   0.0  0
 VK3  CONST_10  H8K1  C8K  C7K  C6K  180.00   0.0  0
 VK3  Var_01    H111  C11  C3K  C2K    0.52  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
 VK3  plan-1  C1K   0.020
 VK3  plan-1  O1K   0.020
 VK3  plan-1  C2K   0.020
 VK3  plan-1  C3K   0.020
 VK3  plan-1  C4K   0.020
 VK3  plan-1  O4K   0.020
 VK3  plan-1  C5K   0.020
 VK3  plan-1  C6K   0.020
 VK3  plan-1  C7K   0.020
 VK3  plan-1  C8K   0.020
 VK3  plan-1  C9K   0.020
 VK3  plan-1  C10   0.020
 VK3  plan-1  C11   0.020
 VK3  plan-1  H2K1  0.020
 VK3  plan-1  H6K1  0.020
 VK3  plan-1  H7K1  0.020
 VK3  plan-1  H8K1  0.020
 VK3  plan-1  H9K1  0.020

