# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 00:04:07 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-[(1~{R})-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CC[C@@H](O)C1=CC(=O)c2c(O)ccc(O)c2C1=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
 FNO  FNO  2-[(1~{R})-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione  ligand  37  21  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FNO
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
 FNO  C10  C  CR6   0   0.409  -22.6032  -3.1231  -29.1386
 FNO  C13  C  CR6   0   0.442  -22.4384  -0.2889  -29.5991
 FNO  C15  C  CR6   0   0.361  -22.9182  -2.6783  -26.7329
 FNO  C17  C  C     0   0.096  -20.1669  -4.6012  -34.0993
 FNO  C20  C  CH3   0  -0.720  -19.6451  -3.2186  -34.3545
 FNO  C21  C  CH3   0  -0.703  -20.0656  -5.5309  -35.2725
 FNO  C06  C  CH1   0  -0.020  -22.2846  -3.5406  -31.6706
 FNO  C07  C  CR6   0   0.050  -22.4188  -2.5844  -30.5052
 FNO  C08  C  CH2   0  -0.555  -20.8870  -4.1803  -31.7080
 FNO  C09  C  CR66  0  -0.166  -22.7228  -2.1913  -28.0251
 FNO  C11  C  CR66  0  -0.208  -22.6425  -0.7934  -28.2491
 FNO  C12  C  CR16  0  -0.408  -22.3436  -1.2610  -30.6918
 FNO  C14  C  C1    0  -0.260  -20.6971  -5.0084  -32.9431
 FNO  C16  C  CR6   0   0.369  -22.7579   0.0986  -27.1865
 FNO  C18  C  CR16  0  -0.312  -23.0391  -1.7586  -25.6686
 FNO  C19  C  CR16  0  -0.310  -22.9618  -0.4134  -25.8871
 FNO  O01  O  OH1   0  -0.655  -23.3243  -4.4820  -31.7184
 FNO  O02  O  O     0  -0.454  -22.6467  -4.3416  -28.9587
 FNO  O03  O  OH1   0  -0.606  -22.9985  -3.9679  -26.4336
 FNO  O04  O  O     0  -0.449  -22.3532   0.9155  -29.8400
 FNO  O05  O  OH1   0  -0.609  -22.6879   1.4162  -27.3263
 FNO  H1   H  HCH3  0   0.239  -19.6791  -2.5701  -33.4814
 FNO  H2   H  HCH3  0   0.236  -18.6111  -3.2574  -34.7055
 FNO  H3   H  HCH3  0   0.238  -20.2223  -2.7361  -35.1472
 FNO  H4   H  HCH3  0   0.236  -20.4597  -6.5215  -35.0472
 FNO  H5   H  HCH3  0   0.231  -20.6133  -5.1357  -36.1319
 FNO  H6   H  HCH3  0   0.231  -19.0268  -5.6433  -35.5935
 FNO  H7   H  HCH1  0   0.267  -22.3876  -2.9413  -32.5798
 FNO  H8   H  HCH2  0   0.254  -20.7448  -4.8059  -30.8227
 FNO  H9   H  HCH2  0   0.259  -20.1450  -3.3827  -31.6405
 FNO  H10  H  HCR6  0   0.289  -22.2092  -0.8504  -31.6870
 FNO  H11  H  H     0   0.226  -21.0551  -6.0318  -32.8854
 FNO  H12  H  HCR6  0   0.293  -23.1939  -2.1382  -24.6666
 FNO  H13  H  HCR6  0   0.293  -23.0554   0.2781  -25.0594
 FNO  H14  H  HOH1  0   0.449  -23.2035  -5.1055  -30.9934
 FNO  H15  H  HOH1  0   0.485  -22.8882  -4.4816  -27.2633
 FNO  H16  H  HOH1  0   0.481  -22.5416   1.6114  -28.2789

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
 FNO  C21  C17  single    1.500  0.020  1.500
 FNO  C17  C20  single    1.500  0.020  1.500
 FNO  C17  C14  double    1.336  0.020  1.336
 FNO  C14  C08  single    1.499  0.020  1.499
 FNO  C06  O01  single    1.403  0.020  1.403
 FNO  C06  C08  single    1.537  0.020  1.537
 FNO  C06  C07  single    1.514  0.020  1.514
 FNO  C12  C07  double    1.339  0.020  1.339
 FNO  C12  C13  single    1.466  0.020  1.466
 FNO  C07  C10  single    1.480  0.020  1.480
 FNO  O04  C13  double    1.231  0.020  1.231
 FNO  C13  C11  single    1.455  0.020  1.455
 FNO  C10  O02  double    1.233  0.020  1.233
 FNO  C10  C09  single    1.457  0.020  1.457
 FNO  C11  C09  aromatic  1.418  0.020  1.418
 FNO  C11  C16  aromatic  1.392  0.020  1.392
 FNO  C09  C15  aromatic  1.395  0.020  1.395
 FNO  O05  C16  single    1.327  0.020  1.327
 FNO  C16  C19  aromatic  1.412  0.020  1.412
 FNO  C15  O03  single    1.326  0.020  1.326
 FNO  C15  C18  aromatic  1.412  0.020  1.412
 FNO  C19  C18  aromatic  1.365  0.020  1.365
 FNO  C20  H1   single    0.970  0.020  1.090
 FNO  C20  H2   single    0.970  0.020  1.090
 FNO  C20  H3   single    0.970  0.020  1.090
 FNO  C21  H4   single    0.970  0.020  1.090
 FNO  C21  H5   single    0.970  0.020  1.090
 FNO  C21  H6   single    0.970  0.020  1.090
 FNO  C06  H7   single    0.970  0.020  1.090
 FNO  C08  H8   single    0.970  0.020  1.090
 FNO  C08  H9   single    0.970  0.020  1.090
 FNO  C12  H10  single    0.930  0.020  1.080
 FNO  C14  H11  single    0.930  0.020  1.080
 FNO  C18  H12  single    0.930  0.020  1.080
 FNO  C19  H13  single    0.930  0.020  1.080
 FNO  O01  H14  single    0.850  0.020  0.980
 FNO  O03  H15  single    0.850  0.020  0.980
 FNO  O05  H16  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
 FNO  O02  C10  C09  121.19  3.000
 FNO  C09  C10  C07  118.88  3.000
 FNO  O02  C10  C07  119.92  3.000
 FNO  O04  C13  C12  119.90  3.000
 FNO  O04  C13  C11  122.02  3.000
 FNO  C12  C13  C11  118.08  3.000
 FNO  O03  C15  C18  117.27  3.000
 FNO  C18  C15  C09  118.88  3.000
 FNO  O03  C15  C09  123.85  3.000
 FNO  C14  C17  C21  120.99  3.000
 FNO  C14  C17  C20  124.50  3.000
 FNO  C21  C17  C20  114.50  3.000
 FNO  H3   C20  H2   106.40  3.000
 FNO  H3   C20  H1   107.60  3.000
 FNO  H2   C20  H1   107.96  3.000
 FNO  H3   C20  C17  110.29  3.000
 FNO  H2   C20  C17  110.56  3.000
 FNO  H1   C20  C17  113.71  3.000
 FNO  H6   C21  H5   106.41  3.000
 FNO  H6   C21  H4   108.12  3.000
 FNO  H5   C21  H4   108.06  3.000
 FNO  H6   C21  C17  110.95  3.000
 FNO  H5   C21  C17  110.91  3.000
 FNO  H4   C21  C17  112.16  3.000
 FNO  H7   C06  O01  105.63  3.000
 FNO  H7   C06  C08  107.06  3.000
 FNO  O01  C06  C08  113.18  3.000
 FNO  H7   C06  C07  106.59  3.000
 FNO  C08  C06  C07  111.24  3.000
 FNO  O01  C06  C07  112.60  3.000
 FNO  C12  C07  C06  120.82  3.000
 FNO  C12  C07  C10  119.70  3.000
 FNO  C06  C07  C10  119.47  3.000
 FNO  H9   C08  H8   106.24  3.000
 FNO  H9   C08  C14  111.62  3.000
 FNO  H8   C08  C14  109.54  3.000
 FNO  H9   C08  C06  108.20  3.000
 FNO  H8   C08  C06  109.67  3.000
 FNO  C14  C08  C06  111.41  3.000
 FNO  C11  C09  C15  119.90  3.000
 FNO  C15  C09  C10  119.76  3.000
 FNO  C11  C09  C10  120.34  3.000
 FNO  C16  C11  C09  120.42  3.000
 FNO  C16  C11  C13  119.83  3.000
 FNO  C09  C11  C13  119.74  3.000
 FNO  H10  C12  C07  120.60  3.000
 FNO  H10  C12  C13  116.16  3.000
 FNO  C07  C12  C13  123.24  3.000
 FNO  H11  C14  C08  115.80  3.000
 FNO  H11  C14  C17  117.66  3.000
 FNO  C08  C14  C17  126.53  3.000
 FNO  O05  C16  C19  117.70  3.000
 FNO  C19  C16  C11  118.83  3.000
 FNO  O05  C16  C11  123.47  3.000
 FNO  H12  C18  C19  120.12  3.000
 FNO  H12  C18  C15  118.79  3.000
 FNO  C19  C18  C15  121.09  3.000
 FNO  H13  C19  C18  120.15  3.000
 FNO  H13  C19  C16  118.99  3.000
 FNO  C18  C19  C16  120.86  3.000
 FNO  H14  O01  C06  108.39  3.000
 FNO  H15  O03  C15  108.14  3.000
 FNO  H16  O05  C16  107.88  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
 FNO  CONST_01  C16  C11  C09  C15     0.00   0.0  0
 FNO  CONST_02  C16  C19  C18  C15     0.00   0.0  0
 FNO  CONST_03  C19  C16  C11  C09     0.00   0.0  0
 FNO  CONST_04  C19  C18  C15  C09     0.00   0.0  0
 FNO  CONST_05  C18  C15  C09  C11     0.00   0.0  0
 FNO  CONST_06  C18  C19  C16  C11     0.00   0.0  0
 FNO  CONST_07  O03  C15  C09  C10     0.00   0.0  0
 FNO  CONST_08  O05  C16  C11  C13     0.00   0.0  0
 FNO  CONST_09  O05  C16  C11  C09   180.00   0.0  0
 FNO  CONST_10  O03  C15  C09  C11   180.00   0.0  0
 FNO  CONST_11  O05  C16  C19  C18   180.00   0.0  0
 FNO  CONST_12  O03  C15  C18  C19   180.00   0.0  0
 FNO  CONST_13  H13  C19  C18  C15   180.00   0.0  0
 FNO  CONST_14  H12  C18  C15  C09   180.00   0.0  0
 FNO  Var_01    C08  C14  C17  C20     0.82   0.0  2
 FNO  Var_02    C06  C08  C14  C17    92.90  30.0  3
 FNO  Var_03    H4   C21  C17  C20  -179.69  30.0  3
 FNO  Var_04    H1   C20  C17  C21  -177.12  30.0  3

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
 FNO  chir_01  C06  O01  C08  C07  positiv

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
 FNO  plan-1  C10  0.020
 FNO  plan-1  C13  0.020
 FNO  plan-1  C15  0.020
 FNO  plan-1  C06  0.020
 FNO  plan-1  C07  0.020
 FNO  plan-1  C09  0.020
 FNO  plan-1  C11  0.020
 FNO  plan-1  C12  0.020
 FNO  plan-1  C16  0.020
 FNO  plan-1  C18  0.020
 FNO  plan-1  C19  0.020
 FNO  plan-1  O02  0.020
 FNO  plan-1  O03  0.020
 FNO  plan-1  O04  0.020
 FNO  plan-1  O05  0.020
 FNO  plan-1  H10  0.020
 FNO  plan-1  H12  0.020
 FNO  plan-1  H13  0.020
 FNO  plan-2  C17  0.020
 FNO  plan-2  C20  0.020
 FNO  plan-2  C21  0.020
 FNO  plan-2  C08  0.020
 FNO  plan-2  C14  0.020
 FNO  plan-2  H11  0.020

