# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:23:45 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-ethyl-1-[(1~{R},8~{S},9~{S},10~{S})-10-oxidanyl-11-oxatricyclo[6.2.1.0^{2,7}]undeca-2(7),3,5-trien-9-yl]imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)CN([C@H]2[C@H](O)[C@@H]3O[C@H]2c4ccccc34)C1=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
 LXS  LXS  3-ethyl-1-[(1~{R},8~{S},9~{S},10~{S})-10-oxidanyl-11-oxatricyclo[6.2.1.0^{2,7}]undeca-2(7),3,5-trien-9-yl]imidazolidine-2,4-dione  ligand  37  21  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LXS
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
 LXS  N1   N  NR5   0  -0.528  -3.8474  -32.6244  -16.2760
 LXS  C4   C  CH1   0  -0.145  -4.7096  -33.6942  -16.7208
 LXS  C5   C  CH1   0   0.087  -6.2130  -33.5303  -16.3482
 LXS  C6   C  CH1   0  -0.143  -6.8441  -33.5152  -17.7545
 LXS  C7   C  CH1   0  -0.077  -4.7915  -33.8109  -18.2754
 LXS  C8   C  CR6   0   0.124  -5.0983  -32.4231  -18.7726
 LXS  C10  C  CR16  0  -0.252  -4.9685  -30.1861  -19.5548
 LXS  C13  C  CR6   0   0.117  -6.4286  -32.2243  -18.4156
 LXS  N    N  NR5   0  -0.553  -1.9712  -31.4569  -16.0870
 LXS  C    C  CH3   0  -0.663  -0.1780  -30.6847  -17.5976
 LXS  C1   C  CH2   0  -0.321  -0.5600  -31.1422  -16.2004
 LXS  C11  C  CR16  0  -0.256  -6.2982  -29.9868  -19.2020
 LXS  C12  C  CR16  0  -0.330  -7.0473  -31.0080  -18.6136
 LXS  C14  C  CR5   0   0.778  -2.5102  -32.6874  -16.4607
 LXS  C2   C  CR5   0   0.527  -2.9414  -30.5793  -15.7090
 LXS  C3   C  CH2   0  -0.414  -4.2525  -31.3236  -15.8013
 LXS  C9   C  CR16  0  -0.337  -4.3437  -31.4144  -19.3317
 LXS  O1   O  OH1   0  -0.664  -6.7233  -34.6338  -15.6525
 LXS  O2   O  O2    0  -0.473  -6.0374  -34.4683  -18.4419
 LXS  O3   O  O     0  -0.484  -1.8690  -33.6268  -16.8794
 LXS  H1   H  HCH1  0   0.298  -4.3439  -34.6354  -16.3056
 LXS  H2   H  HCH1  0   0.254  -6.4225  -32.5992  -15.8124
 LXS  H3   H  HCH1  0   0.274  -7.9013  -33.7752  -17.7836
 LXS  H4   H  HCH1  0   0.273  -3.9784  -34.3584  -18.7469
 LXS  H5   H  HCR6  0   0.262  -4.4111  -29.3766  -20.0079
 LXS  H6   H  HCH3  0   0.243   0.8813  -30.4310  -17.6253
 LXS  H7   H  HCH3  0   0.235  -0.3531  -31.4687  -18.3339
 LXS  H8   H  HCH3  0   0.234  -0.7426  -29.8003  -17.8925
 LXS  H9   H  HCH2  0   0.266   0.0056  -32.0274  -15.9135
 LXS  H10  H  HCH2  0   0.266  -0.3386  -30.3685  -15.4670
 LXS  H11  H  HCR6  0   0.262  -6.7583  -29.0245  -19.3856
 LXS  H12  H  HCR6  0   0.260  -8.0760  -30.8382  -18.3217
 LXS  H13  H  HCH2  0   0.295  -4.9280  -30.8009  -16.4848
 LXS  H14  H  HCH2  0   0.309  -4.7272  -31.3628  -14.8175
 LXS  H15  H  HCR6  0   0.257  -3.3036  -31.5617  -19.5958
 LXS  H16  H  HOH1  0   0.459  -6.3375  -34.6483  -14.7706
 LXS  O    O  O     0  -0.440  -2.7785  -29.4324  -15.3653

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
 LXS  C10  C9   aromatic  1.396  0.020  1.396
 LXS  C10  C11  aromatic  1.390  0.020  1.390
 LXS  C9   C8   aromatic  1.378  0.020  1.378
 LXS  C11  C12  aromatic  1.396  0.020  1.396
 LXS  C8   C13  aromatic  1.392  0.020  1.392
 LXS  C8   C7   single    1.506  0.020  1.506
 LXS  C12  C13  aromatic  1.379  0.020  1.379
 LXS  C13  C6   single    1.509  0.020  1.509
 LXS  O2   C7   single    1.419  0.020  1.419
 LXS  O2   C6   single    1.425  0.020  1.425
 LXS  C7   C4   single    1.561  0.020  1.561
 LXS  C6   C5   single    1.541  0.020  1.541
 LXS  C    C1   single    1.519  0.020  1.519
 LXS  O3   C14  double    1.212  0.020  1.212
 LXS  C4   C5   single    1.558  0.020  1.558
 LXS  C4   N1   single    1.444  0.020  1.444
 LXS  C14  N    single    1.394  0.020  1.394
 LXS  C14  N1   single    1.351  0.020  1.351
 LXS  C1   N    single    1.450  0.020  1.450
 LXS  C5   O1   single    1.401  0.020  1.401
 LXS  N    C2   single    1.362  0.020  1.362
 LXS  N1   C3   single    1.443  0.020  1.443
 LXS  C2   C3   single    1.510  0.020  1.510
 LXS  C2   O    double    1.208  0.020  1.208
 LXS  C4   H1   single    0.970  0.020  1.090
 LXS  C5   H2   single    0.970  0.020  1.090
 LXS  C6   H3   single    0.970  0.020  1.090
 LXS  C7   H4   single    0.970  0.020  1.090
 LXS  C10  H5   single    0.930  0.020  1.080
 LXS  C    H6   single    0.970  0.020  1.090
 LXS  C    H7   single    0.970  0.020  1.090
 LXS  C    H8   single    0.970  0.020  1.090
 LXS  C1   H9   single    0.970  0.020  1.090
 LXS  C1   H10  single    0.970  0.020  1.090
 LXS  C11  H11  single    0.930  0.020  1.080
 LXS  C12  H12  single    0.930  0.020  1.080
 LXS  C3   H13  single    0.970  0.020  1.090
 LXS  C3   H14  single    0.970  0.020  1.090
 LXS  C9   H15  single    0.930  0.020  1.080
 LXS  O1   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
 LXS  C3   N1   C14  111.40  3.000
 LXS  C3   N1   C4   126.98  3.000
 LXS  C14  N1   C4   120.94  3.000
 LXS  H1   C4   C7   109.38  3.000
 LXS  H1   C4   C5   108.85  3.000
 LXS  C7   C4   C5   101.27  3.000
 LXS  H1   C4   N1   108.76  3.000
 LXS  C5   C4   N1   115.13  3.000
 LXS  C7   C4   N1   113.16  3.000
 LXS  H2   C5   O1   110.94  3.000
 LXS  H2   C5   C6   111.10  3.000
 LXS  O1   C5   C6   108.16  3.000
 LXS  H2   C5   C4   113.04  3.000
 LXS  O1   C5   C4   112.80  3.000
 LXS  C6   C5   C4   100.25  3.000
 LXS  H3   C6   O2   112.14  3.000
 LXS  H3   C6   C13  117.38  3.000
 LXS  O2   C6   C13  101.83  3.000
 LXS  H3   C6   C5   114.80  3.000
 LXS  O2   C6   C5   101.64  3.000
 LXS  C13  C6   C5   107.18  3.000
 LXS  H4   C7   O2   111.86  3.000
 LXS  H4   C7   C8   118.24  3.000
 LXS  O2   C7   C8   102.09  3.000
 LXS  H4   C7   C4   115.47  3.000
 LXS  O2   C7   C4   101.39  3.000
 LXS  C8   C7   C4   105.70  3.000
 LXS  C9   C8   C13  121.53  3.000
 LXS  C13  C8   C7   103.99  3.000
 LXS  C9   C8   C7   134.18  3.000
 LXS  H5   C10  C9   119.64  3.000
 LXS  H5   C10  C11  119.45  3.000
 LXS  C9   C10  C11  120.91  3.000
 LXS  C12  C13  C8   121.20  3.000
 LXS  C12  C13  C6   133.95  3.000
 LXS  C8   C13  C6   104.68  3.000
 LXS  C2   N    C14  111.57  3.000
 LXS  C2   N    C1   125.11  3.000
 LXS  C14  N    C1   123.14  3.000
 LXS  H8   C    H7   108.53  3.000
 LXS  H8   C    H6   107.92  3.000
 LXS  H7   C    H6   107.85  3.000
 LXS  H8   C    C1   111.29  3.000
 LXS  H7   C    C1   111.38  3.000
 LXS  H6   C    C1   109.75  3.000
 LXS  H10  C1   H9   107.13  3.000
 LXS  H10  C1   C    110.76  3.000
 LXS  H9   C1   C    110.89  3.000
 LXS  H10  C1   N    107.42  3.000
 LXS  H9   C1   N    107.96  3.000
 LXS  C    C1   N    112.46  3.000
 LXS  H11  C11  C12  119.58  3.000
 LXS  H11  C11  C10  119.41  3.000
 LXS  C12  C11  C10  121.01  3.000
 LXS  H12  C12  C11  120.57  3.000
 LXS  H12  C12  C13  121.73  3.000
 LXS  C11  C12  C13  117.70  3.000
 LXS  O3   C14  N    124.89  3.000
 LXS  N    C14  N1   107.74  3.000
 LXS  O3   C14  N1   127.36  3.000
 LXS  C3   C2   O    127.02  3.000
 LXS  O    C2   N    126.49  3.000
 LXS  C3   C2   N    106.49  3.000
 LXS  H14  C3   H13  108.14  3.000
 LXS  H14  C3   C2   109.86  3.000
 LXS  H13  C3   C2   109.80  3.000
 LXS  H14  C3   N1   112.69  3.000
 LXS  H13  C3   N1   113.49  3.000
 LXS  C2   C3   N1   102.74  3.000
 LXS  H15  C9   C10  120.70  3.000
 LXS  H15  C9   C8   121.67  3.000
 LXS  C10  C9   C8   117.63  3.000
 LXS  H16  O1   C5   108.71  3.000
 LXS  C7   O2   C6    97.50  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
 LXS  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 LXS  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 LXS  CONST_03  C13  C8   C9   C10    0.00   0.0  0
 LXS  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 LXS  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 LXS  CONST_06  C9   C8   C13  C12    0.00   0.0  0
 LXS  CONST_07  C2   N    C14  N1     0.00   0.0  0
 LXS  CONST_08  N    C2   C3   N1     0.00   0.0  0
 LXS  CONST_09  N    C14  N1   C4   180.00   0.0  0
 LXS  CONST_10  C2   C3   N1   C4   180.00   0.0  0
 LXS  CONST_11  C3   N1   C14  N      0.00   0.0  0
 LXS  CONST_12  C3   C2   N    C14    0.00   0.0  0
 LXS  CONST_13  C2   C3   N1   C14    0.00   0.0  0
 LXS  CONST_14  C1   N    C14  N1   180.00   0.0  0
 LXS  CONST_15  O3   C14  N1   C4     0.00   0.0  0
 LXS  CONST_16  C14  N    C2   O    180.00   0.0  0
 LXS  CONST_17  C3   C2   N    C1   180.00   0.0  0
 LXS  CONST_18  O3   C14  N    C2   180.00   0.0  0
 LXS  CONST_19  O3   C14  N1   C3   180.00   0.0  0
 LXS  CONST_20  H12  C12  C13  C6     0.00   0.0  0
 LXS  CONST_21  H15  C9   C8   C7     0.00   0.0  0
 LXS  CONST_22  H5   C10  C9   C8   180.00   0.0  0
 LXS  CONST_23  H11  C11  C12  C13  180.00   0.0  0
 LXS  CONST_24  C1   N    C2   O      0.00   0.0  0
 LXS  CONST_25  O3   C14  N    C1     0.00   0.0  0
 LXS  Var_01    H13  C3   N1   C4   -52.41  30.0  1
 LXS  Var_02    C14  N    C1   C     83.15  30.0  3
 LXS  Var_03    H6   C    C1   N    178.25  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
 LXS  chir_01  C4  C7  C5  N1   positiv
 LXS  chir_02  C5  O1  C6  C4   positiv
 LXS  chir_03  C6  O2  C5  C13  negativ
 LXS  chir_04  C7  O2  C8  C4   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
 LXS  plan-1  N1   0.020
 LXS  plan-1  C4   0.020
 LXS  plan-1  N    0.020
 LXS  plan-1  C1   0.020
 LXS  plan-1  C14  0.020
 LXS  plan-1  C2   0.020
 LXS  plan-1  C3   0.020
 LXS  plan-1  O3   0.020
 LXS  plan-1  O    0.020
 LXS  plan-2  C6   0.020
 LXS  plan-2  C7   0.020
 LXS  plan-2  C8   0.020
 LXS  plan-2  C10  0.020
 LXS  plan-2  C13  0.020
 LXS  plan-2  C11  0.020
 LXS  plan-2  C12  0.020
 LXS  plan-2  C9   0.020
 LXS  plan-2  H5   0.020
 LXS  plan-2  H11  0.020
 LXS  plan-2  H12  0.020
 LXS  plan-2  H15  0.020

