# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 21:27:09 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2R,4S,4aS)-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4',6'(1'H,3'H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN2[C@H]([C@H](C)O1)C3(Cc4cc(ccc24)[N+]([O-])=O)C(=O)NC(=O)NC3=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
 54Q  54Q  (2R,4S,4aS)-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4',6'(1'H,3'H)-trione  ligand  45  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_54Q
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
 54Q  O5   O  O      0  -0.406   5.6839  -0.5546   1.3067
 54Q  N3   N  N      1   0.318   4.7614  -1.1756   0.8181
 54Q  O4   O  O     -1  -0.407   4.8105  -2.3699   0.6006
 54Q  C9   C  CR6    0   0.228   3.5630  -0.4695   0.4837
 54Q  C8   C  CR16   0  -0.267   3.4627   0.8949   0.7393
 54Q  C7   C  CR16   0  -0.354   2.3068   1.5702   0.4245
 54Q  C10  C  CR16   0  -0.358   2.4977  -1.1507  -0.1032
 54Q  C11  C  CR6    0   0.053   1.3503  -0.4760  -0.4383
 54Q  C6   C  CR6    0   0.451   1.2138   0.9017  -0.1605
 54Q  N    N  NT     0  -0.560   0.0532   1.5257  -0.4760
 54Q  C5   C  CH2    0  -0.318  -0.0441   2.9587  -0.6860
 54Q  C3   C  CH1    0   0.033  -1.1327   3.5647   0.1827
 54Q  C4   C  CH3    0  -0.692  -1.3398   5.0333  -0.1146
 54Q  O    O  O2     0  -0.495  -2.3493   2.8859  -0.0623
 54Q  C1   C  CH1    0   0.062  -2.2824   1.5056   0.2236
 54Q  C2   C  CH3    0  -0.715  -3.6792   0.9490   0.0306
 54Q  C12  C  CH2    0  -0.461   0.2272  -1.1438  -1.1532
 54Q  C13  C  CT     0  -0.514  -1.1364  -0.6822  -0.5622
 54Q  C    C  CH1    0  -0.002  -1.2228   0.8495  -0.6914
 54Q  C16  C  C      0   0.656  -1.1503  -1.1574   0.8781
 54Q  O3   O  O      0  -0.390  -0.5611  -0.5754   1.7555
 54Q  N2   N  NH1    0  -0.707  -1.7953  -2.3390   1.1299
 54Q  C15  C  C      0   0.697  -2.5927  -3.0518   0.2688
 54Q  O2   O  O      0  -0.431  -3.1305  -4.0829   0.5850
 54Q  N1   N  NH1    0  -0.708  -2.7479  -2.4933  -0.9781
 54Q  C14  C  C      0   0.635  -2.1869  -1.3394  -1.4494
 54Q  O1   O  O      0  -0.399  -2.4581  -0.9235  -2.5493
 54Q  H12  H  HCR6   0   0.291   4.2758   1.4345   1.2027
 54Q  H11  H  HCR6   0   0.281   2.2488   2.6197   0.6724
 54Q  H13  H  HCR6   0   0.284   2.5725  -2.2063  -0.3267
 54Q  H9   H  HCH2   0   0.275   0.9078   3.4418  -0.4857
 54Q  H10  H  HCH2   0   0.255  -0.2818   3.1405  -1.7418
 54Q  H2   H  HCH1   0   0.218  -0.8467   3.4399   1.2382
 54Q  H7   H  HCH3   0   0.232  -1.5985   5.1931  -1.1624
 54Q  H8   H  HCH3   0   0.247  -2.1371   5.4455   0.5036
 54Q  H6   H  HCH3   0   0.237  -0.4295   5.5928   0.0999
 54Q  H1   H  HCH1   0   0.229  -1.9742   1.3733   1.2683
 54Q  H3   H  HCH3   0   0.245  -4.0016   1.0115  -1.0092
 54Q  H5   H  HCH3   0   0.226  -3.7599  -0.0886   0.3554
 54Q  H4   H  HCH3   0   0.268  -4.3851   1.5141   0.6390
 54Q  H14  H  HCH2   0   0.308   0.2345  -0.8626  -2.2102
 54Q  H15  H  HCH2   0   0.297   0.3222  -2.2301  -1.1087
 54Q  H    H  HCH1   0   0.280  -1.5274   1.0506  -1.7255
 54Q  H17  H  HNH1   0   0.439  -1.7238  -2.7072   2.0715
 54Q  H16  H  HNH1   0   0.441  -3.3745  -2.9851  -1.6046

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
 54Q  O2   C15  double    1.205  0.020  1.205
 54Q  C15  N1   single    1.375  0.020  1.375
 54Q  C15  N2   single    1.373  0.020  1.373
 54Q  N1   C14  single    1.367  0.020  1.367
 54Q  O1   C14  double    1.207  0.020  1.207
 54Q  C14  C13  single    1.524  0.020  1.524
 54Q  N2   C16  single    1.370  0.020  1.370
 54Q  C16  C13  single    1.517  0.020  1.517
 54Q  C16  O3   double    1.207  0.020  1.207
 54Q  C13  C12  single    1.556  0.020  1.556
 54Q  C13  C    single    1.540  0.020  1.540
 54Q  C12  C11  single    1.489  0.020  1.489
 54Q  C2   C1   single    1.516  0.020  1.516
 54Q  C    C1   single    1.546  0.020  1.546
 54Q  C    N    single    1.460  0.020  1.460
 54Q  C10  C11  aromatic  1.373  0.020  1.373
 54Q  C10  C9   aromatic  1.394  0.020  1.394
 54Q  C11  C6   aromatic  1.412  0.020  1.412
 54Q  O4   N3   single    1.215  0.020  1.215
 54Q  C1   O    single    1.411  0.020  1.411
 54Q  N3   C9   single    1.431  0.020  1.431
 54Q  N3   O5   double    1.215  0.020  1.215
 54Q  N    C6   single    1.355  0.020  1.355
 54Q  N    C5   single    1.452  0.020  1.452
 54Q  C9   C8   aromatic  1.392  0.020  1.392
 54Q  C6   C7   aromatic  1.409  0.020  1.409
 54Q  O    C3   single    1.415  0.020  1.415
 54Q  C8   C7   aromatic  1.375  0.020  1.375
 54Q  C5   C3   single    1.519  0.020  1.519
 54Q  C3   C4   single    1.513  0.020  1.513
 54Q  C8   H12  single    0.930  0.020  1.080
 54Q  C7   H11  single    0.930  0.020  1.080
 54Q  C10  H13  single    0.930  0.020  1.080
 54Q  C5   H9   single    0.970  0.020  1.090
 54Q  C5   H10  single    0.970  0.020  1.090
 54Q  C3   H2   single    0.970  0.020  1.090
 54Q  C4   H7   single    0.970  0.020  1.090
 54Q  C4   H8   single    0.970  0.020  1.090
 54Q  C4   H6   single    0.970  0.020  1.090
 54Q  C1   H1   single    0.970  0.020  1.090
 54Q  C2   H3   single    0.970  0.020  1.090
 54Q  C2   H5   single    0.970  0.020  1.090
 54Q  C2   H4   single    0.970  0.020  1.090
 54Q  C12  H14  single    0.970  0.020  1.090
 54Q  C12  H15  single    0.970  0.020  1.090
 54Q  C    H    single    0.970  0.020  1.090
 54Q  N2   H17  single    0.860  0.020  1.020
 54Q  N1   H16  single    0.860  0.020  1.020

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
 54Q  C9   N3   O4   118.50  3.000
 54Q  C9   N3   O5   118.55  3.000
 54Q  O4   N3   O5   122.95  3.000
 54Q  C10  C9   C8   120.09  3.000
 54Q  C8   C9   N3   120.09  3.000
 54Q  C10  C9   N3   119.83  3.000
 54Q  H12  C8   C7   119.04  3.000
 54Q  H12  C8   C9   120.95  3.000
 54Q  C7   C8   C9   120.00  3.000
 54Q  H11  C7   C6   120.99  3.000
 54Q  H11  C7   C8   118.03  3.000
 54Q  C6   C7   C8   120.94  3.000
 54Q  H13  C10  C11  119.15  3.000
 54Q  H13  C10  C9   120.74  3.000
 54Q  C11  C10  C9   120.09  3.000
 54Q  C12  C11  C6   117.32  3.000
 54Q  C6   C11  C10  120.82  3.000
 54Q  C12  C11  C10  121.81  3.000
 54Q  N    C6   C11  119.10  3.000
 54Q  N    C6   C7   122.88  3.000
 54Q  C11  C6   C7   118.02  3.000
 54Q  C    N    C5   112.16  3.000
 54Q  C5   N    C6   123.08  3.000
 54Q  C    N    C6   124.72  3.000
 54Q  H10  C5   H9   107.07  3.000
 54Q  H10  C5   C3   109.21  3.000
 54Q  H9   C5   C3   110.19  3.000
 54Q  H10  C5   N    108.50  3.000
 54Q  H9   C5   N    110.71  3.000
 54Q  C3   C5   N    111.05  3.000
 54Q  H2   C3   O    109.58  3.000
 54Q  H2   C3   C4   109.53  3.000
 54Q  O    C3   C4   108.31  3.000
 54Q  H2   C3   C5   108.48  3.000
 54Q  C4   C3   C5   111.90  3.000
 54Q  O    C3   C5   109.02  3.000
 54Q  H6   C4   H8   107.78  3.000
 54Q  H6   C4   H7   108.18  3.000
 54Q  H8   C4   H7   108.41  3.000
 54Q  H6   C4   C3   110.20  3.000
 54Q  H8   C4   C3   110.84  3.000
 54Q  H7   C4   C3   111.31  3.000
 54Q  C1   O    C3   113.17  3.000
 54Q  H1   C1   C    108.65  3.000
 54Q  H1   C1   C2   109.62  3.000
 54Q  C    C1   C2   113.60  3.000
 54Q  H1   C1   O    108.92  3.000
 54Q  C    C1   O    109.13  3.000
 54Q  C2   C1   O    106.84  3.000
 54Q  H4   C2   H5   106.21  3.000
 54Q  H4   C2   H3   108.13  3.000
 54Q  H5   C2   H3   108.46  3.000
 54Q  H4   C2   C1   109.60  3.000
 54Q  H5   C2   C1   112.32  3.000
 54Q  H3   C2   C1   111.89  3.000
 54Q  H15  C12  H14  107.14  3.000
 54Q  H15  C12  C13  110.85  3.000
 54Q  H14  C12  C13  107.26  3.000
 54Q  H15  C12  C11  111.17  3.000
 54Q  H14  C12  C11  110.10  3.000
 54Q  C13  C12  C11  110.21  3.000
 54Q  C14  C13  C16  114.29  3.000
 54Q  C16  C13  C    113.01  3.000
 54Q  C14  C13  C    109.97  3.000
 54Q  C    C13  C12  108.20  3.000
 54Q  C16  C13  C12  106.01  3.000
 54Q  C14  C13  C12  104.78  3.000
 54Q  H    C    C13  106.09  3.000
 54Q  H    C    C1   106.85  3.000
 54Q  C13  C    C1   114.27  3.000
 54Q  H    C    N    107.27  3.000
 54Q  C1   C    N    108.37  3.000
 54Q  C13  C    N    113.54  3.000
 54Q  N2   C16  O3   120.83  3.000
 54Q  O3   C16  C13  122.34  3.000
 54Q  N2   C16  C13  116.69  3.000
 54Q  H17  N2   C15  115.78  3.000
 54Q  H17  N2   C16  116.81  3.000
 54Q  C15  N2   C16  127.31  3.000
 54Q  N1   C15  O2   122.35  3.000
 54Q  N1   C15  N2   115.04  3.000
 54Q  O2   C15  N2   122.60  3.000
 54Q  H16  N1   C14  116.76  3.000
 54Q  H16  N1   C15  115.67  3.000
 54Q  C14  N1   C15  127.53  3.000
 54Q  O1   C14  N1   120.86  3.000
 54Q  O1   C14  C13  122.47  3.000
 54Q  N1   C14  C13  116.50  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
 54Q  CONST_01  C6   C11  C10  C9      0.00   0.0  0
 54Q  CONST_02  C6   C7   C8   C9      0.00   0.0  0
 54Q  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 54Q  CONST_04  C11  C6   C7   C8      0.00   0.0  0
 54Q  CONST_05  C10  C11  C6   C7      0.00   0.0  0
 54Q  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 54Q  CONST_07  C15  N2   C16  C13     0.00   0.0  0
 54Q  CONST_08  N1   C15  N2   C16     0.00   0.0  0
 54Q  CONST_09  C14  N1   C15  N2      0.00   0.0  0
 54Q  CONST_10  C11  C10  C9   N3    180.00   0.0  0
 54Q  CONST_11  C7   C8   C9   N3    180.00   0.0  0
 54Q  CONST_12  O2   C15  N2   C16   180.00   0.0  0
 54Q  CONST_13  C15  N2   C16  O3    180.00   0.0  0
 54Q  CONST_14  C14  N1   C15  O2    180.00   0.0  0
 54Q  CONST_15  H11  C7   C8   C9    180.00   0.0  0
 54Q  CONST_16  H13  C10  C9   C8    180.00   0.0  0
 54Q  CONST_17  H12  C8   C9   C10   180.00   0.0  0
 54Q  CONST_18  H17  N2   C16  C13   180.00   0.0  0
 54Q  CONST_19  H16  N1   C15  N2    180.00   0.0  0
 54Q  CONST_20  C10  C9   N3   O5    180.00   0.0  0
 54Q  CONST_21  C8   C9   N3   O5      0.00   0.0  0
 54Q  CONST_22  C10  C9   N3   O4      0.00   0.0  0
 54Q  CONST_23  C8   C9   N3   O4    180.00   0.0  0
 54Q  Var_01    C    N    C6   C7   -160.35  30.0  1
 54Q  Var_02    C13  C12  C11  C10   139.17  30.0  1
 54Q  Var_03    C14  C13  C12  C11   175.37  30.0  1
 54Q  Var_04    C3   C5   N    C6   -126.80  30.0  1
 54Q  Var_05    N1   C14  C13  C12    98.40  30.0  3
 54Q  Var_06    N2   C16  C13  C12   -96.87  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
 54Q  chir_01  C3  O  C5  C4   negativ
 54Q  chir_02  C1  O  C2  C    negativ
 54Q  chir_03  C   N  C1  C13  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
 54Q  plan-1  N3   0.020
 54Q  plan-1  C9   0.020
 54Q  plan-1  C8   0.020
 54Q  plan-1  C7   0.020
 54Q  plan-1  C10  0.020
 54Q  plan-1  C11  0.020
 54Q  plan-1  C6   0.020
 54Q  plan-1  N    0.020
 54Q  plan-1  C12  0.020
 54Q  plan-1  H12  0.020
 54Q  plan-1  H11  0.020
 54Q  plan-1  H13  0.020
 54Q  plan-2  O5   0.020
 54Q  plan-2  N3   0.020
 54Q  plan-2  O4   0.020
 54Q  plan-2  C9   0.020
 54Q  plan-3  C13  0.020
 54Q  plan-3  N1   0.020
 54Q  plan-3  C14  0.020
 54Q  plan-3  O1   0.020
 54Q  plan-4  C13  0.020
 54Q  plan-4  C16  0.020
 54Q  plan-4  O3   0.020
 54Q  plan-4  N2   0.020
 54Q  plan-4  C15  0.020
 54Q  plan-4  O2   0.020
 54Q  plan-4  N1   0.020
 54Q  plan-4  C14  0.020
 54Q  plan-4  H17  0.020
 54Q  plan-4  H16  0.020

