# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:01:28 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one
#   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(=NC(=O)N=C3O)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
 53M  53M  (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one  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_53M
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
 53M  C2    C  CR16   0  -0.015  -1.2028   0.7573  -0.6806
 53M  C3    C  CH1    0   0.064  -2.3140   1.3831   0.1958
 53M  C5    C  CH3    0  -0.717  -3.6930   0.8079  -0.0619
 53M  O6    O  O2     0  -0.493  -2.3973   2.7643  -0.0770
 53M  C7    C  CH1    0   0.033  -1.2052   3.4694   0.2098
 53M  C9    C  CH3    0  -0.691  -1.4382   4.9348  -0.0840
 53M  C10   C  CH2    0  -0.318  -0.0792   2.8953  -0.6296
 53M  N11   N  NR6    0  -0.564   0.0480   1.4641  -0.4163
 53M  C12   C  CR66   0   0.452   1.2364   0.8684  -0.1409
 53M  C13   C  CR16   0  -0.352   2.3168   1.5628   0.4372
 53M  C14   C  CR16   0  -0.266   3.4988   0.9214   0.7253
 53M  C15   C  CR6    0   0.229   3.6382  -0.4355   0.4511
 53M  C16   C  CR16   0  -0.357   2.5857  -1.1426  -0.1256
 53M  C17   C  CR66   0   0.053   1.4121  -0.5002  -0.4351
 53M  C18   C  C      0  -0.455   0.3004  -1.2046  -1.1321
 53M  C19   C  CR6    0  -0.463  -1.0750  -0.7775  -0.5424
 53M  C20   C  C      0   0.591  -1.1610  -1.2903   0.8717
 53M  O21   O  OH1    0  -0.551  -0.4501  -0.6037   1.7292
 53M  N22   N  N      0  -0.482  -1.8081  -2.3218   1.2484
 53M  C23   C  C      0   0.499  -2.5570  -3.0370   0.3233
 53M  O24   O  O      0  -0.425  -3.0678  -4.0832   0.6494
 53M  N25   N  N      0  -0.478  -2.7484  -2.5543  -0.9658
 53M  C26   C  C      0   0.571  -2.1163  -1.5169  -1.3478
 53M  O27   O  OH1    0  -0.560  -2.2759  -1.0502  -2.5611
 53M  N28   N  N      1   0.319   4.8641  -1.1078   0.7589
 53M  O29   O  O      0  -0.405   4.9457  -2.2975   0.5289
 53M  O30   O  O     -1  -0.404   5.7742  -0.4626   1.2383
 53M  H2    H  HCR6   0   0.286  -1.4739   0.9581  -1.7237
 53M  H3    H  HCH1   0   0.228  -2.0505   1.2427   1.2527
 53M  H51   H  HCH3   0   0.232  -3.7850  -0.2199   0.2855
 53M  H52   H  HCH3   0   0.269  -4.4323   1.3849   0.4931
 53M  H53   H  HCH3   0   0.242  -3.9605   0.8454  -1.1186
 53M  H7    H  HCH1   0   0.219  -0.9478   3.3431   1.2723
 53M  H91   H  HCH3   0   0.247  -2.2571   5.3261   0.5193
 53M  H92   H  HCH3   0   0.238  -0.5448   5.5120   0.1530
 53M  H93   H  HCH3   0   0.232  -1.6778   5.0948  -1.1363
 53M  H102  H  HCH2   0   0.255  -0.2901   3.0755  -1.6917
 53M  H103  H  HCH2   0   0.277   0.8532   3.4027  -0.4007
 53M  H13   H  HCR6   0   0.282   2.2309   2.6063   0.7014
 53M  H14   H  HCR6   0   0.292   4.3011   1.4818   1.1829
 53M  H16   H  HCR6   0   0.286   2.6878  -2.1934  -0.3607
 53M  H182  H  H      0   0.310   0.2988  -0.9403  -2.1931
 53M  H183  H  H      0   0.298   0.4196  -2.2873  -1.0710
 53M  H21   H  HOH1   0   0.494  -0.5137  -1.0092   2.6093
 53M  H27   H  HOH1   0   0.497  -2.9141  -1.5982  -3.0451

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
 53M  C9   C7    single    1.513  0.020  1.513
 53M  C10  C7    single    1.517  0.020  1.517
 53M  C10  N11   single    1.453  0.020  1.453
 53M  C7   O6    single    1.414  0.020  1.414
 53M  C13  C14   aromatic  1.375  0.020  1.375
 53M  C13  C12   aromatic  1.408  0.020  1.408
 53M  C14  C15   aromatic  1.391  0.020  1.391
 53M  O29  N28   double    1.215  0.020  1.215
 53M  O6   C3    single    1.410  0.020  1.410
 53M  N11  C12   single    1.358  0.020  1.358
 53M  N11  C2    single    1.461  0.020  1.461
 53M  C12  C17   aromatic  1.411  0.020  1.411
 53M  C15  N28   single    1.432  0.020  1.432
 53M  C15  C16   aromatic  1.393  0.020  1.393
 53M  N28  O30   single    1.214  0.020  1.214
 53M  C3   C2    single    1.547  0.020  1.547
 53M  C3   C5    single    1.516  0.020  1.516
 53M  C2   C19   single    1.546  0.020  1.546
 53M  C17  C16   aromatic  1.373  0.020  1.373
 53M  C17  C18   single    1.489  0.020  1.489
 53M  O21  C20   single    1.308  0.020  1.308
 53M  C19  C18   single    1.556  0.020  1.556
 53M  C19  C20   single    1.507  0.020  1.507
 53M  C19  C26   single    1.510  0.020  1.510
 53M  C20  N22   double    1.275  0.020  1.275
 53M  O27  C26   single    1.310  0.020  1.310
 53M  C26  N25   double    1.273  0.020  1.273
 53M  N22  C23   single    1.389  0.020  1.389
 53M  N25  C23   single    1.390  0.020  1.390
 53M  C23  O24   double    1.209  0.020  1.209
 53M  C2   H2    single    0.970  0.020  1.090
 53M  C3   H3    single    0.970  0.020  1.090
 53M  C5   H51   single    0.970  0.020  1.090
 53M  C5   H52   single    0.970  0.020  1.090
 53M  C5   H53   single    0.970  0.020  1.090
 53M  C7   H7    single    0.970  0.020  1.090
 53M  C9   H91   single    0.970  0.020  1.090
 53M  C9   H92   single    0.970  0.020  1.090
 53M  C9   H93   single    0.970  0.020  1.090
 53M  C10  H102  single    0.970  0.020  1.090
 53M  C10  H103  single    0.970  0.020  1.090
 53M  C13  H13   single    0.930  0.020  1.080
 53M  C14  H14   single    0.930  0.020  1.080
 53M  C16  H16   single    0.930  0.020  1.080
 53M  C18  H182  single    0.970  0.020  1.090
 53M  C18  H183  single    0.970  0.020  1.090
 53M  O21  H21   single    0.850  0.020  0.980
 53M  O27  H27   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
 53M  H2    C2   C19   106.69  3.000
 53M  H2    C2   N11   107.17  3.000
 53M  C19   C2   N11   113.16  3.000
 53M  H2    C2   C3    106.70  3.000
 53M  C19   C2   C3    114.21  3.000
 53M  N11   C2   C3    108.46  3.000
 53M  H3    C3   O6    109.00  3.000
 53M  H3    C3   C5    109.46  3.000
 53M  O6    C3   C5    106.55  3.000
 53M  H3    C3   C2    108.73  3.000
 53M  C5    C3   C2    113.79  3.000
 53M  O6    C3   C2    109.20  3.000
 53M  H53   C5   H52   107.98  3.000
 53M  H53   C5   H51   108.71  3.000
 53M  H52   C5   H51   106.26  3.000
 53M  H53   C5   C3    112.01  3.000
 53M  H52   C5   C3    109.25  3.000
 53M  H51   C5   C3    112.38  3.000
 53M  C7    O6   C3    113.53  3.000
 53M  H7    C7   C10   108.49  3.000
 53M  H7    C7   C9    109.56  3.000
 53M  C10   C7   C9    111.93  3.000
 53M  H7    C7   O6    109.61  3.000
 53M  C10   C7   O6    108.95  3.000
 53M  C9    C7   O6    108.29  3.000
 53M  H93   C9   H92   108.19  3.000
 53M  H93   C9   H91   108.44  3.000
 53M  H92   C9   H91   107.78  3.000
 53M  H93   C9   C7    111.30  3.000
 53M  H92   C9   C7    110.16  3.000
 53M  H91   C9   C7    110.86  3.000
 53M  H103  C10  H102  106.99  3.000
 53M  H103  C10  N11   110.75  3.000
 53M  H102  C10  N11   108.71  3.000
 53M  H103  C10  C7    110.11  3.000
 53M  H102  C10  C7    109.30  3.000
 53M  N11   C10  C7    110.89  3.000
 53M  C12   N11  C10   122.60  3.000
 53M  C12   N11  C2    125.03  3.000
 53M  C10   N11  C2    112.03  3.000
 53M  C17   C12  C13   117.93  3.000
 53M  C17   C12  N11   119.49  3.000
 53M  C13   C12  N11   122.58  3.000
 53M  H13   C13  C14   117.89  3.000
 53M  H13   C13  C12   121.05  3.000
 53M  C14   C13  C12   121.02  3.000
 53M  H14   C14  C15   120.99  3.000
 53M  H14   C14  C13   119.02  3.000
 53M  C15   C14  C13   119.98  3.000
 53M  N28   C15  C16   119.84  3.000
 53M  C16   C15  C14   120.06  3.000
 53M  N28   C15  C14   120.09  3.000
 53M  H16   C16  C17   119.09  3.000
 53M  H16   C16  C15   120.78  3.000
 53M  C17   C16  C15   120.10  3.000
 53M  C18   C17  C16   121.47  3.000
 53M  C18   C17  C12   117.61  3.000
 53M  C16   C17  C12   120.88  3.000
 53M  H183  C18  H182  107.12  3.000
 53M  H183  C18  C19   110.34  3.000
 53M  H182  C18  C19   107.46  3.000
 53M  H183  C18  C17   111.21  3.000
 53M  H182  C18  C17   109.93  3.000
 53M  C19   C18  C17   110.64  3.000
 53M  C26   C19  C20   107.14  3.000
 53M  C26   C19  C18   105.84  3.000
 53M  C20   C19  C18   108.22  3.000
 53M  C26   C19  C2    112.42  3.000
 53M  C20   C19  C2    114.64  3.000
 53M  C18   C19  C2    108.15  3.000
 53M  N22   C20  O21   120.45  3.000
 53M  N22   C20  C19   125.57  3.000
 53M  O21   C20  C19   113.92  3.000
 53M  H21   O21  C20   109.83  3.000
 53M  C23   N22  C20   119.59  3.000
 53M  N25   C23  O24   119.51  3.000
 53M  O24   C23  N22   119.59  3.000
 53M  N25   C23  N22   120.88  3.000
 53M  C26   N25  C23   119.53  3.000
 53M  O27   C26  N25   120.51  3.000
 53M  N25   C26  C19   125.53  3.000
 53M  O27   C26  C19   113.81  3.000
 53M  H27   O27  C26   109.93  3.000
 53M  O30   N28  O29   123.02  3.000
 53M  O30   N28  C15   118.50  3.000
 53M  O29   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
 53M  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 53M  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 53M  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 53M  CONST_04  C16  C17  C12  C13     0.00   0.0  0
 53M  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 53M  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 53M  CONST_07  N25  C23  N22  C20     0.00   0.0  0
 53M  CONST_08  C26  N25  C23  N22     0.00   0.0  0
 53M  CONST_09  N28  C15  C14  C13   180.00   0.0  0
 53M  CONST_10  N28  C15  C16  C17   180.00   0.0  0
 53M  CONST_11  O24  C23  N22  C20   180.00   0.0  0
 53M  CONST_12  C26  N25  C23  O24   180.00   0.0  0
 53M  CONST_13  H13  C13  C12  N11     0.00   0.0  0
 53M  CONST_14  H14  C14  C13  C12   180.00   0.0  0
 53M  CONST_15  H16  C16  C17  C12   180.00   0.0  0
 53M  CONST_16  O29  N28  C15  C14   180.00   0.0  0
 53M  CONST_17  O30  N28  C15  C14     0.00   0.0  0
 53M  CONST_18  O29  N28  C15  C16     0.00   0.0  0
 53M  CONST_19  O30  N28  C15  C16   180.00   0.0  0
 53M  Var_01    C7   C10  N11  C2     55.86  30.0  1
 53M  Var_02    C13  C12  N11  C2   -163.21  30.0  1
 53M  Var_03    C17  C18  C19  C2     57.65  30.0  1
 53M  Var_04    N22  C20  C19  C2    137.51  30.0  3
 53M  Var_05    N25  C26  C19  C2   -139.59  30.0  3
 53M  Var_06    C19  C18  C17  C12   -41.74  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
 53M  chir_01  C2  N11  C3   C19  positiv
 53M  chir_02  C3  O6   C2   C5   positiv
 53M  chir_03  C7  O6   C10  C9   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
 53M  plan-1  N11  0.020
 53M  plan-1  C12  0.020
 53M  plan-1  C13  0.020
 53M  plan-1  C14  0.020
 53M  plan-1  C15  0.020
 53M  plan-1  C16  0.020
 53M  plan-1  C17  0.020
 53M  plan-1  C18  0.020
 53M  plan-1  N28  0.020
 53M  plan-1  H13  0.020
 53M  plan-1  H14  0.020
 53M  plan-1  H16  0.020
 53M  plan-2  C15  0.020
 53M  plan-2  N28  0.020
 53M  plan-2  O29  0.020
 53M  plan-2  O30  0.020
 53M  plan-3  C20  0.020
 53M  plan-3  N22  0.020
 53M  plan-3  C23  0.020
 53M  plan-3  O24  0.020
 53M  plan-3  N25  0.020
 53M  plan-3  C26  0.020

