# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:29:59 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC(=O)c2c(O)cccc2C1=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
 F2X  F2X  (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione  ligand  24  14  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F2X
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
 F2X  O2   O  O     0  -0.380  -51.6487  37.9077  -25.8639
 F2X  C4   C  C     0   0.388  -50.7223  38.3806  -25.2462
 F2X  C3   C  CH1   0  -0.406  -49.3209  37.8319  -25.3171
 F2X  C11  C  CH3   0  -0.657  -49.2341  36.4975  -26.0359
 F2X  C7   C  CH2   0  -0.564  -48.7292  37.7628  -23.9073
 F2X  C5   C  C     0   0.433  -48.7939  39.0657  -23.1696
 F2X  O3   O  O     0  -0.449  -47.9366  39.3683  -22.3460
 F2X  C1   C  CR6   0  -0.004  -50.9052  39.5927  -24.3961
 F2X  C2   C  CR6   0  -0.177  -49.9382  39.9405  -23.4324
 F2X  C8   C  CR16  0  -0.311  -52.0186  40.3868  -24.5911
 F2X  C10  C  CR16  0  -0.220  -52.1700  41.5504  -23.8394
 F2X  C9   C  CR16  0  -0.333  -51.2323  41.9186  -22.8981
 F2X  C6   C  CR6   0   0.386  -50.1063  41.1193  -22.6796
 F2X  O1   O  OH1   0  -0.617  -49.2361  41.5044  -21.7539
 F2X  H1   H  HCH1  0   0.297  -48.7427  38.5773  -25.8801
 F2X  H2   H  HCH3  0   0.242  -48.1970  36.1648  -26.0742
 F2X  H3   H  HCH3  0   0.232  -49.8141  35.7291  -25.5238
 F2X  H4   H  HCH3  0   0.246  -49.5965  36.5715  -27.0599
 F2X  H5   H  HCH2  0   0.294  -49.2844  37.0265  -23.3132
 F2X  H6   H  HCH2  0   0.291  -47.6937  37.4235  -23.9449
 F2X  H7   H  HCR6  0   0.269  -52.7580  40.1207  -25.3334
 F2X  H8   H  HCR6  0   0.278  -53.0344  42.1816  -23.9975
 F2X  H9   H  HCR6  0   0.283  -51.3560  42.8247  -22.3190
 F2X  H10  H  HOH1  0   0.480  -48.5149  40.8359  -21.7183

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
 F2X  O2   C4   double    1.210  0.020  1.210
 F2X  C11  C3   single    1.518  0.020  1.518
 F2X  C4   C3   single    1.507  0.020  1.507
 F2X  C4   C1   single    1.492  0.020  1.492
 F2X  C3   C7   single    1.531  0.020  1.531
 F2X  C8   C1   aromatic  1.381  0.020  1.381
 F2X  C8   C10  aromatic  1.394  0.020  1.394
 F2X  C1   C2   aromatic  1.409  0.020  1.409
 F2X  C7   C5   single    1.499  0.020  1.499
 F2X  C10  C9   aromatic  1.379  0.020  1.379
 F2X  C2   C5   single    1.464  0.020  1.464
 F2X  C2   C6   aromatic  1.409  0.020  1.409
 F2X  C5   O3   double    1.227  0.020  1.227
 F2X  C9   C6   aromatic  1.398  0.020  1.398
 F2X  C6   O1   single    1.327  0.020  1.327
 F2X  C3   H1   single    0.970  0.020  1.090
 F2X  C11  H2   single    0.970  0.020  1.090
 F2X  C11  H3   single    0.970  0.020  1.090
 F2X  C11  H4   single    0.970  0.020  1.090
 F2X  C7   H5   single    0.970  0.020  1.090
 F2X  C7   H6   single    0.970  0.020  1.090
 F2X  C8   H7   single    0.930  0.020  1.080
 F2X  C10  H8   single    0.930  0.020  1.080
 F2X  C9   H9   single    0.930  0.020  1.080
 F2X  O1   H10  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
 F2X  C1   C4   C3   115.90  3.000
 F2X  C1   C4   O2   120.98  3.000
 F2X  C3   C4   O2   123.09  3.000
 F2X  H1   C3   C7   107.41  3.000
 F2X  H1   C3   C11  108.89  3.000
 F2X  C7   C3   C11  111.98  3.000
 F2X  H1   C3   C4   105.46  3.000
 F2X  C7   C3   C4   109.43  3.000
 F2X  C11  C3   C4   113.30  3.000
 F2X  H4   C11  H3   108.21  3.000
 F2X  H4   C11  H2   107.73  3.000
 F2X  H3   C11  H2   107.91  3.000
 F2X  H4   C11  C3   111.50  3.000
 F2X  H3   C11  C3   111.50  3.000
 F2X  H2   C11  C3   109.84  3.000
 F2X  H6   C7   H5   106.89  3.000
 F2X  H6   C7   C5   109.18  3.000
 F2X  H5   C7   C5   107.17  3.000
 F2X  H6   C7   C3   110.45  3.000
 F2X  H5   C7   C3   109.48  3.000
 F2X  C5   C7   C3   113.42  3.000
 F2X  C2   C5   O3   121.29  3.000
 F2X  O3   C5   C7   120.98  3.000
 F2X  C2   C5   C7   117.70  3.000
 F2X  C8   C1   C2   120.52  3.000
 F2X  C2   C1   C4   120.42  3.000
 F2X  C8   C1   C4   119.04  3.000
 F2X  C6   C2   C1   119.36  3.000
 F2X  C6   C2   C5   119.82  3.000
 F2X  C1   C2   C5   120.78  3.000
 F2X  H7   C8   C10  120.11  3.000
 F2X  H7   C8   C1   120.44  3.000
 F2X  C10  C8   C1   119.43  3.000
 F2X  H8   C10  C9   119.17  3.000
 F2X  H8   C10  C8   119.67  3.000
 F2X  C9   C10  C8   121.16  3.000
 F2X  H9   C9   C6   119.15  3.000
 F2X  H9   C9   C10  120.73  3.000
 F2X  C6   C9   C10  120.12  3.000
 F2X  O1   C6   C9   118.11  3.000
 F2X  O1   C6   C2   122.49  3.000
 F2X  C9   C6   C2   119.41  3.000
 F2X  H10  O1   C6   107.98  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
 F2X  CONST_01  C9   C10  C8   C1     0.00   0.0  0
 F2X  CONST_02  C9   C6   C2   C1     0.00   0.0  0
 F2X  CONST_03  C10  C8   C1   C2     0.00   0.0  0
 F2X  CONST_04  C10  C9   C6   C2     0.00   0.0  0
 F2X  CONST_05  C6   C2   C1   C8     0.00   0.0  0
 F2X  CONST_06  C6   C9   C10  C8     0.00   0.0  0
 F2X  CONST_07  O1   C6   C2   C5     0.00   0.0  0
 F2X  CONST_08  O1   C6   C2   C1   180.00   0.0  0
 F2X  CONST_09  O1   C6   C9   C10  180.00   0.0  0
 F2X  CONST_10  H7   C8   C1   C4     0.00   0.0  0
 F2X  CONST_11  H8   C10  C8   C1   180.00   0.0  0
 F2X  CONST_12  H9   C9   C6   C2   180.00   0.0  0
 F2X  Var_01    C8   C1   C4   C3   160.28  30.0  1
 F2X  Var_02    C2   C5   C7   C3    33.28  30.0  1
 F2X  Var_03    C1   C2   C5   C7    -3.11  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
 F2X  chir_01  C3  C11  C4  C7  negativ

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
 F2X  plan-1  O2   0.020
 F2X  plan-1  C4   0.020
 F2X  plan-1  C3   0.020
 F2X  plan-1  C1   0.020
 F2X  plan-2  C4   0.020
 F2X  plan-2  C5   0.020
 F2X  plan-2  C1   0.020
 F2X  plan-2  C2   0.020
 F2X  plan-2  C8   0.020
 F2X  plan-2  C10  0.020
 F2X  plan-2  C9   0.020
 F2X  plan-2  C6   0.020
 F2X  plan-2  O1   0.020
 F2X  plan-2  H7   0.020
 F2X  plan-2  H8   0.020
 F2X  plan-2  H9   0.020
 F2X  plan-3  C7   0.020
 F2X  plan-3  C5   0.020
 F2X  plan-3  O3   0.020
 F2X  plan-3  C2   0.020

