# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 02:22:46 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2R,4S,4aS,5S)-6'-hydroxy-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'(3'H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN2[C@H]([C@H](C)O1)[C@]3(Cc4cc(ccc24)[N](=O)=O)C(=O)NC(=O)N=C3O
#
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
 53L  53L  (2R,4S,4aS,5S)-6'-hydroxy-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'(3'H)-dione  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_53L
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
 53L  C2    C  CR16   0  -0.007  -1.2023   0.7963  -0.6894
 53L  C3    C  CH1    0   0.063  -2.2986   1.4345   0.1958
 53L  C5    C  CH3    0  -0.715  -3.6844   0.8697  -0.0470
 53L  O6    O  O2     0  -0.493  -2.3726   2.8162  -0.0779
 53L  C7    C  CH1    0   0.033  -1.1711   3.5087   0.2001
 53L  C9    C  CH3    0  -0.691  -1.3914   4.9771  -0.0884
 53L  C10   C  CH2    0  -0.317  -0.0575   2.9249  -0.6500
 53L  N11   N  NR6    0  -0.564   0.0577   1.4923  -0.4417
 53L  C12   C  CR66   0   0.450   1.2380   0.8842  -0.1618
 53L  C13   C  CR16   0  -0.352   2.3276   1.5662   0.4141
 53L  C14   C  CR16   0  -0.267   3.5002   0.9098   0.7058
 53L  C15   C  CR6    0   0.229   3.6217  -0.4500   0.4364
 53L  C16   C  CR16   0  -0.357   2.5602  -1.1447  -0.1392
 53L  C17   C  CR66   0   0.052   1.3953  -0.4880  -0.4515
 53L  C18   C  C      0  -0.458   0.2737  -1.1782  -1.1463
 53L  C19   C  CR6    0  -0.488  -1.0955  -0.7362  -0.5547
 53L  C20   C  C      0   0.600  -1.1728  -1.2564   0.8560
 53L  O21   O  OH1    0  -0.543  -0.4649  -0.5682   1.7103
 53L  N22   N  N      0  -0.490  -1.7982  -2.3001   1.2475
 53L  C23   C  C      0   0.600  -2.5642  -3.0241   0.3663
 53L  O24   O  O      0  -0.429  -3.1087  -4.0521   0.6882
 53L  N25   N  NH1    0  -0.703  -2.7214  -2.5270  -0.9194
 53L  C26   C  C      0   0.639  -2.1389  -1.4123  -1.4382
 53L  O27   O  O      0  -0.409  -2.3751  -1.0334  -2.5609
 53L  N28   N  N      1   0.318   4.8376  -1.1377   0.7482
 53L  O29   O  O     -1  -0.405   5.7555  -0.5038   1.2280
 53L  O30   O  O      0  -0.405   4.9038  -2.3291   0.5211
 53L  H2    H  HCR6   0   0.282  -1.4839   0.9844  -1.7329
 53L  H3    H  HCH1   0   0.227  -2.0264   1.2946   1.2504
 53L  H51   H  HCH3   0   0.228  -3.7743  -0.1659   0.2795
 53L  H52   H  HCH3   0   0.268  -4.4120   1.4360   0.5340
 53L  H53   H  HCH3   0   0.245  -3.9699   0.9288  -1.0977
 53L  H7    H  HCH1   0   0.219  -0.9061   3.3778   1.2602
 53L  H91   H  HCH3   0   0.247  -2.2027   5.3747   0.5209
 53L  H92   H  HCH3   0   0.238  -0.4910   5.5451   0.1447
 53L  H93   H  HCH3   0   0.232  -1.6358   5.1424  -1.1387
 53L  H102  H  HCH2   0   0.255  -0.2755   3.1096  -1.7096
 53L  H103  H  HCH2   0   0.276   0.8816   3.4225  -0.4273
 53L  H13   H  HCR6   0   0.281   2.2554   2.6117   0.6745
 53L  H14   H  HCR6   0   0.291   4.3096   1.4605   1.1627
 53L  H16   H  HCR6   0   0.286   2.6486  -2.1975  -0.3706
 53L  H182  H  H      0   0.308   0.2642  -0.9065  -2.2056
 53L  H183  H  H      0   0.299   0.3827  -2.2625  -1.0924
 53L  H21   H  HOH1   0   0.497  -0.5151  -0.9763   2.5904
 53L  H25   H  HNH1   0   0.431  -3.3483  -3.0398  -1.5285

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
 53L  O24  C23   double    1.207  0.020  1.207
 53L  C23  N25   single    1.387  0.020  1.387
 53L  C23  N22   single    1.374  0.020  1.374
 53L  N25  C26   single    1.361  0.020  1.361
 53L  N22  C20   double    1.278  0.020  1.278
 53L  C26  O27   double    1.208  0.020  1.208
 53L  C26  C19   single    1.525  0.020  1.525
 53L  C20  C19   single    1.506  0.020  1.506
 53L  C20  O21   single    1.306  0.020  1.306
 53L  C19  C18   single    1.556  0.020  1.556
 53L  C19  C2    single    1.542  0.020  1.542
 53L  C18  C17   single    1.489  0.020  1.489
 53L  C5   C3    single    1.516  0.020  1.516
 53L  C2   C3    single    1.547  0.020  1.547
 53L  C2   N11   single    1.461  0.020  1.461
 53L  C16  C17   aromatic  1.373  0.020  1.373
 53L  C16  C15   aromatic  1.393  0.020  1.393
 53L  C17  C12   aromatic  1.411  0.020  1.411
 53L  C3   O6    single    1.410  0.020  1.410
 53L  O30  N28   double    1.215  0.020  1.215
 53L  C15  N28   single    1.431  0.020  1.431
 53L  C15  C14   aromatic  1.392  0.020  1.392
 53L  N28  O29   single    1.214  0.020  1.214
 53L  N11  C12   single    1.357  0.020  1.357
 53L  N11  C10   single    1.452  0.020  1.452
 53L  C12  C13   aromatic  1.409  0.020  1.409
 53L  O6   C7    single    1.414  0.020  1.414
 53L  C14  C13   aromatic  1.375  0.020  1.375
 53L  C7   C10   single    1.518  0.020  1.518
 53L  C7   C9    single    1.513  0.020  1.513
 53L  C2   H2    single    0.970  0.020  1.090
 53L  C3   H3    single    0.970  0.020  1.090
 53L  C5   H51   single    0.970  0.020  1.090
 53L  C5   H52   single    0.970  0.020  1.090
 53L  C5   H53   single    0.970  0.020  1.090
 53L  C7   H7    single    0.970  0.020  1.090
 53L  C9   H91   single    0.970  0.020  1.090
 53L  C9   H92   single    0.970  0.020  1.090
 53L  C9   H93   single    0.970  0.020  1.090
 53L  C10  H102  single    0.970  0.020  1.090
 53L  C10  H103  single    0.970  0.020  1.090
 53L  C13  H13   single    0.930  0.020  1.080
 53L  C14  H14   single    0.930  0.020  1.080
 53L  C16  H16   single    0.930  0.020  1.080
 53L  C18  H182  single    0.970  0.020  1.090
 53L  C18  H183  single    0.970  0.020  1.090
 53L  O21  H21   single    0.850  0.020  0.980
 53L  N25  H25   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
 53L  H2    C2   C19   105.74  3.000
 53L  H2    C2   N11   107.52  3.000
 53L  C19   C2   N11   113.52  3.000
 53L  H2    C2   C3    106.96  3.000
 53L  N11   C2   C3    108.53  3.000
 53L  C19   C2   C3    114.15  3.000
 53L  H3    C3   O6    108.91  3.000
 53L  H3    C3   C5    109.44  3.000
 53L  O6    C3   C5    106.61  3.000
 53L  H3    C3   C2    108.75  3.000
 53L  O6    C3   C2    109.29  3.000
 53L  C5    C3   C2    113.73  3.000
 53L  H53   C5   H52   108.10  3.000
 53L  H53   C5   H51   108.59  3.000
 53L  H52   C5   H51   106.20  3.000
 53L  H53   C5   C3    111.93  3.000
 53L  H52   C5   C3    109.35  3.000
 53L  H51   C5   C3    112.43  3.000
 53L  C7    O6   C3    113.39  3.000
 53L  H7    C7   C10   108.49  3.000
 53L  H7    C7   C9    109.53  3.000
 53L  C10   C7   C9    111.93  3.000
 53L  H7    C7   O6    109.61  3.000
 53L  C9    C7   O6    108.31  3.000
 53L  C10   C7   O6    108.95  3.000
 53L  H93   C9   H92   108.18  3.000
 53L  H93   C9   H91   108.43  3.000
 53L  H92   C9   H91   107.78  3.000
 53L  H93   C9   C7    111.31  3.000
 53L  H92   C9   C7    110.17  3.000
 53L  H91   C9   C7    110.85  3.000
 53L  H103  C10  H102  107.02  3.000
 53L  H103  C10  N11   110.73  3.000
 53L  H102  C10  N11   108.68  3.000
 53L  H103  C10  C7    110.09  3.000
 53L  H102  C10  C7    109.29  3.000
 53L  N11   C10  C7    110.94  3.000
 53L  C12   N11  C10   122.73  3.000
 53L  C10   N11  C2    112.17  3.000
 53L  C12   N11  C2    124.88  3.000
 53L  C17   C12  C13   117.93  3.000
 53L  C13   C12  N11   122.70  3.000
 53L  C17   C12  N11   119.37  3.000
 53L  H13   C13  C14   117.90  3.000
 53L  H13   C13  C12   121.04  3.000
 53L  C14   C13  C12   121.01  3.000
 53L  H14   C14  C15   120.97  3.000
 53L  H14   C14  C13   119.03  3.000
 53L  C15   C14  C13   119.99  3.000
 53L  N28   C15  C16   119.85  3.000
 53L  N28   C15  C14   120.10  3.000
 53L  C16   C15  C14   120.06  3.000
 53L  H16   C16  C17   119.09  3.000
 53L  H16   C16  C15   120.77  3.000
 53L  C17   C16  C15   120.12  3.000
 53L  C18   C17  C16   121.57  3.000
 53L  C16   C17  C12   120.85  3.000
 53L  C18   C17  C12   117.55  3.000
 53L  H183  C18  H182  107.19  3.000
 53L  H183  C18  C19   110.58  3.000
 53L  H182  C18  C19   106.87  3.000
 53L  H183  C18  C17   111.24  3.000
 53L  H182  C18  C17   110.08  3.000
 53L  C19   C18  C17   110.72  3.000
 53L  C26   C19  C20   110.76  3.000
 53L  C20   C19  C18   107.66  3.000
 53L  C26   C19  C18   104.83  3.000
 53L  C18   C19  C2    108.06  3.000
 53L  C20   C19  C2    114.94  3.000
 53L  C26   C19  C2    110.04  3.000
 53L  N22   C20  O21   119.69  3.000
 53L  O21   C20  C19   113.78  3.000
 53L  N22   C20  C19   126.46  3.000
 53L  H21   O21  C20   110.08  3.000
 53L  C23   N22  C20   120.44  3.000
 53L  N25   C23  O24   120.08  3.000
 53L  N25   C23  N22   117.95  3.000
 53L  O24   C23  N22   121.96  3.000
 53L  H25   N25  C26   116.76  3.000
 53L  H25   N25  C23   116.48  3.000
 53L  C26   N25  C23   126.76  3.000
 53L  O27   C26  N25   121.84  3.000
 53L  O27   C26  C19   122.20  3.000
 53L  N25   C26  C19   115.80  3.000
 53L  O30   N28  O29   123.00  3.000
 53L  O29   N28  C15   118.51  3.000
 53L  O30   N28  C15   118.48  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
 53L  CONST_01  C15  C16  C17  C12    0.00   0.0  0
 53L  CONST_02  C15  C14  C13  C12    0.00   0.0  0
 53L  CONST_03  C16  C17  C12  C13    0.00   0.0  0
 53L  CONST_04  C16  C15  C14  C13    0.00   0.0  0
 53L  CONST_05  C17  C16  C15  C14    0.00   0.0  0
 53L  CONST_06  C17  C12  C13  C14    0.00   0.0  0
 53L  CONST_07  N25  C23  N22  C20    0.00   0.0  0
 53L  CONST_08  C26  N25  C23  N22    0.00   0.0  0
 53L  CONST_09  N28  C15  C14  C13  180.00   0.0  0
 53L  CONST_10  N28  C15  C16  C17  180.00   0.0  0
 53L  CONST_11  O24  C23  N22  C20  180.00   0.0  0
 53L  CONST_12  C26  N25  C23  O24  180.00   0.0  0
 53L  CONST_13  H13  C13  C12  N11    0.00   0.0  0
 53L  CONST_14  H16  C16  C17  C12  180.00   0.0  0
 53L  CONST_15  H14  C14  C13  C12  180.00   0.0  0
 53L  CONST_16  H25  N25  C23  N22  180.00   0.0  0
 53L  CONST_17  O30  N28  C15  C14  180.00   0.0  0
 53L  CONST_18  O29  N28  C15  C14    0.00   0.0  0
 53L  CONST_19  O30  N28  C15  C16    0.00   0.0  0
 53L  CONST_20  O29  N28  C15  C16  180.00   0.0  0
 53L  Var_01    C17  C12  N11  C2    17.37  30.0  1
 53L  Var_02    C7   C10  N11  C2    55.53  30.0  1
 53L  Var_03    C19  C18  C17  C12  -42.02  30.0  1
 53L  Var_04    C23  N25  C26  C19    7.03  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
 53L  chir_01  C2   C19  C3   N11  negativ
 53L  chir_02  C3   O6   C2   C5   positiv
 53L  chir_03  C7   O6   C10  C9   negativ
 53L  chir_04  C19  C20  C18  C2   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
 53L  plan-1  N11  0.020
 53L  plan-1  C12  0.020
 53L  plan-1  C13  0.020
 53L  plan-1  C14  0.020
 53L  plan-1  C15  0.020
 53L  plan-1  C16  0.020
 53L  plan-1  C17  0.020
 53L  plan-1  C18  0.020
 53L  plan-1  N28  0.020
 53L  plan-1  H13  0.020
 53L  plan-1  H14  0.020
 53L  plan-1  H16  0.020
 53L  plan-2  C15  0.020
 53L  plan-2  N28  0.020
 53L  plan-2  O29  0.020
 53L  plan-2  O30  0.020
 53L  plan-3  C19  0.020
 53L  plan-3  N25  0.020
 53L  plan-3  C26  0.020
 53L  plan-3  O27  0.020
 53L  plan-4  C20  0.020
 53L  plan-4  N22  0.020
 53L  plan-4  C23  0.020
 53L  plan-4  O24  0.020
 53L  plan-4  N25  0.020
 53L  plan-4  C26  0.020
 53L  plan-4  H25  0.020

