# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:55:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2R,4S,4aS,5R)-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(=NC(=O)NC3=O)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
 50M  50M  (2R,4S,4aS,5R)-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_50M
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
 50M  C2    C  CR16   0  -0.008  -1.2020   0.7999  -0.6826
 50M  C3    C  CR16   0   0.064  -2.2757   1.4342   0.2320
 50M  C5    C  CH3    0  -0.717  -3.6642   0.8611   0.0266
 50M  C7    C  CR16   0   0.033  -1.1555   3.5125   0.2031
 50M  C13   C  CR16   0  -0.355   2.3200   1.5734   0.4303
 50M  C15   C  CR6    0   0.228   3.6141  -0.4428   0.4725
 50M  C16   C  CR16   0  -0.358   2.5583  -1.1405  -0.1118
 50M  C17   C  CR6    0   0.054   1.3973  -0.4848  -0.4379
 50M  C18   C  CH2    0  -0.459   0.2846  -1.1715  -1.1510
 50M  C19   C  CT     0  -0.493  -1.0862  -0.7346  -0.5551
 50M  C20   C  C      0   0.577  -2.1310  -1.4603  -1.3671
 50M  C23   C  C      0   0.601  -2.5894  -3.0497   0.2353
 50M  C26   C  C      0   0.657  -1.0991  -1.2078   0.8872
 50M  O6    O  O      0  -0.494  -2.3609   2.8149  -0.0459
 50M  C9    C  CH3    0  -0.692  -1.3854   4.9779  -0.0926
 50M  C10   C  C      0  -0.319  -0.0564   2.9256  -0.6647
 50M  N11   N  NR6    0  -0.561   0.0626   1.4938  -0.4558
 50M  C12   C  CR6    0   0.453   1.2366   0.8880  -0.1523
 50M  C14   C  CR16   0  -0.266   3.4901   0.9181   0.7351
 50M  O21   O  OH1    0  -0.552  -2.3090  -0.9636  -2.5629
 50M  N22   N  N      0  -0.486  -2.7580  -2.5178  -1.0218
 50M  O24   O  O      0  -0.429  -3.1304  -4.0756   0.5700
 50M  N25   N  NH1    0  -0.703  -1.7885  -2.3584   1.1305
 50M  O27   O  O      0  -0.400  -0.4849  -0.6383   1.7579
 50M  N28   N  N      1   0.318   4.8271  -1.1284   0.7978
 50M  O29   O  O     -1  -0.406   4.8959  -2.3209   0.5768
 50M  O30   O  O      0  -0.406   5.7411  -0.4922   1.2826
 50M  H2    H  HCR6   0   0.284  -1.5033   1.0147  -1.7142
 50M  H3    H  HCR6   0   0.229  -1.9711   1.2976   1.2774
 50M  H51   H  HCH3   0   0.228  -3.7423  -0.1701   0.3696
 50M  H52   H  HCH3   0   0.269  -4.3833   1.4317   0.6137
 50M  H53   H  HCH3   0   0.243  -3.9730   0.9041  -1.0188
 50M  H7    H  HCR6   0   0.219  -0.8699   3.3903   1.2589
 50M  H13   H  HCR6   0   0.281   2.2444   2.6202   0.6849
 50M  H16   H  HCR6   0   0.285   2.6504  -2.1935  -0.3406
 50M  H182  H  HCH2   0   0.310   0.2921  -0.8946  -2.2088
 50M  H183  H  HCH2   0   0.299   0.3948  -2.2559  -1.1009
 50M  H91   H  HCH3   0   0.247  -2.1887   5.3776   0.5261
 50M  H92   H  HCH3   0   0.238  -0.4836   5.5508   0.1222
 50M  H93   H  HCH3   0   0.232  -1.6465   5.1346  -1.1403
 50M  H102  H  H      0   0.256  -0.2950   3.1056  -1.7207
 50M  H103  H  H      0   0.276   0.8874   3.4234  -0.4626
 50M  H14   H  HCR6   0   0.291   4.2955   1.4707   1.1968
 50M  H21   H  HOH1   0   0.500  -2.9477  -1.5031  -3.0567
 50M  H25   H  HNH1   0   0.429  -1.7386  -2.7291   2.0724

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
 50M  C9   C7    single    1.513  0.020  1.513
 50M  C10  C7    single    1.518  0.020  1.518
 50M  C10  N11   single    1.452  0.020  1.452
 50M  C7   O6    single    1.415  0.020  1.415
 50M  C13  C14   aromatic  1.375  0.020  1.375
 50M  C13  C12   aromatic  1.408  0.020  1.408
 50M  C14  C15   aromatic  1.392  0.020  1.392
 50M  O30  N28   double    1.215  0.020  1.215
 50M  O6   C3    single    1.411  0.020  1.411
 50M  N11  C12   single    1.356  0.020  1.356
 50M  N11  C2    single    1.460  0.020  1.460
 50M  C12  C17   aromatic  1.411  0.020  1.411
 50M  N28  C15   single    1.431  0.020  1.431
 50M  N28  O29   single    1.215  0.020  1.215
 50M  C15  C16   aromatic  1.394  0.020  1.394
 50M  C3   C2    single    1.546  0.020  1.546
 50M  C3   C5    single    1.516  0.020  1.516
 50M  C17  C16   aromatic  1.373  0.020  1.373
 50M  C17  C18   single    1.489  0.020  1.489
 50M  C2   C19   single    1.544  0.020  1.544
 50M  O27  C26   double    1.208  0.020  1.208
 50M  C19  C18   single    1.557  0.020  1.557
 50M  C19  C26   single    1.518  0.020  1.518
 50M  C19  C20   single    1.509  0.020  1.509
 50M  C26  N25   single    1.363  0.020  1.363
 50M  O21  C20   single    1.307  0.020  1.307
 50M  C20  N22   double    1.277  0.020  1.277
 50M  N25  C23   single    1.386  0.020  1.386
 50M  N22  C23   single    1.375  0.020  1.375
 50M  C23  O24   double    1.207  0.020  1.207
 50M  C2   H2    single    0.970  0.020  1.090
 50M  C3   H3    single    0.970  0.020  1.090
 50M  C5   H51   single    0.970  0.020  1.090
 50M  C5   H52   single    0.970  0.020  1.090
 50M  C5   H53   single    0.970  0.020  1.090
 50M  C7   H7    single    0.970  0.020  1.090
 50M  C13  H13   single    0.930  0.020  1.080
 50M  C16  H16   single    0.930  0.020  1.080
 50M  C18  H182  single    0.970  0.020  1.090
 50M  C18  H183  single    0.970  0.020  1.090
 50M  C9   H91   single    0.970  0.020  1.090
 50M  C9   H92   single    0.970  0.020  1.090
 50M  C9   H93   single    0.970  0.020  1.090
 50M  C10  H102  single    0.970  0.020  1.090
 50M  C10  H103  single    0.970  0.020  1.090
 50M  C14  H14   single    0.930  0.020  1.080
 50M  O21  H21   single    0.850  0.020  0.980
 50M  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
 50M  H2    C2   N11   106.93  3.000
 50M  H2    C2   C19   107.04  3.000
 50M  N11   C2   C19   113.23  3.000
 50M  H2    C2   C3    106.58  3.000
 50M  C19   C2   C3    114.26  3.000
 50M  N11   C2   C3    108.33  3.000
 50M  H3    C3   O6    109.04  3.000
 50M  H3    C3   C5    109.65  3.000
 50M  O6    C3   C5    106.73  3.000
 50M  H3    C3   C2    108.63  3.000
 50M  C5    C3   C2    113.62  3.000
 50M  O6    C3   C2    109.07  3.000
 50M  H53   C5   H52   107.99  3.000
 50M  H53   C5   H51   108.58  3.000
 50M  H52   C5   H51   106.18  3.000
 50M  H53   C5   C3    111.98  3.000
 50M  H52   C5   C3    109.48  3.000
 50M  H51   C5   C3    112.38  3.000
 50M  H7    C7   C10   108.51  3.000
 50M  H7    C7   C9    109.55  3.000
 50M  C10   C7   C9    111.88  3.000
 50M  H7    C7   O6    109.59  3.000
 50M  C10   C7   O6    109.00  3.000
 50M  C9    C7   O6    108.29  3.000
 50M  H13   C13  C14   117.98  3.000
 50M  H13   C13  C12   121.03  3.000
 50M  C14   C13  C12   120.95  3.000
 50M  N28   C15  C14   120.08  3.000
 50M  N28   C15  C16   119.84  3.000
 50M  C14   C15  C16   120.08  3.000
 50M  H16   C16  C17   119.13  3.000
 50M  H16   C16  C15   120.77  3.000
 50M  C17   C16  C15   120.08  3.000
 50M  C12   C17  C18   117.41  3.000
 50M  C18   C17  C16   121.70  3.000
 50M  C12   C17  C16   120.85  3.000
 50M  H183  C18  H182  107.18  3.000
 50M  H183  C18  C19   110.50  3.000
 50M  H182  C18  C19   107.77  3.000
 50M  H183  C18  C17   111.15  3.000
 50M  H182  C18  C17   109.96  3.000
 50M  C19   C18  C17   110.18  3.000
 50M  C26   C19  C20   110.82  3.000
 50M  C20   C19  C18   105.58  3.000
 50M  C26   C19  C18   106.48  3.000
 50M  C20   C19  C2    112.43  3.000
 50M  C26   C19  C2    112.81  3.000
 50M  C18   C19  C2    108.26  3.000
 50M  N22   C20  O21   119.69  3.000
 50M  N22   C20  C19   126.35  3.000
 50M  O21   C20  C19   113.81  3.000
 50M  N25   C23  O24   120.25  3.000
 50M  O24   C23  N22   121.82  3.000
 50M  N25   C23  N22   117.92  3.000
 50M  O27   C26  N25   121.76  3.000
 50M  N25   C26  C19   115.91  3.000
 50M  O27   C26  C19   122.24  3.000
 50M  C7    O6   C3    113.35  3.000
 50M  H93   C9   H92   108.17  3.000
 50M  H93   C9   H91   108.43  3.000
 50M  H92   C9   H91   107.78  3.000
 50M  H93   C9   C7    111.30  3.000
 50M  H92   C9   C7    110.18  3.000
 50M  H91   C9   C7    110.87  3.000
 50M  H103  C10  H102  107.03  3.000
 50M  H103  C10  N11   110.74  3.000
 50M  H102  C10  N11   108.54  3.000
 50M  H103  C10  C7    110.22  3.000
 50M  H102  C10  C7    109.22  3.000
 50M  N11   C10  C7    110.99  3.000
 50M  C12   N11  C10   122.95  3.000
 50M  C12   N11  C2    124.92  3.000
 50M  C10   N11  C2    112.05  3.000
 50M  N11   C12  C17   119.21  3.000
 50M  C17   C12  C13   118.01  3.000
 50M  N11   C12  C13   122.78  3.000
 50M  H14   C14  C15   120.96  3.000
 50M  H14   C14  C13   119.03  3.000
 50M  C15   C14  C13   120.00  3.000
 50M  H21   O21  C20   110.10  3.000
 50M  C23   N22  C20   120.48  3.000
 50M  H25   N25  C26   116.72  3.000
 50M  H25   N25  C23   116.51  3.000
 50M  C26   N25  C23   126.73  3.000
 50M  O30   N28  O29   122.97  3.000
 50M  O29   N28  C15   118.49  3.000
 50M  O30   N28  C15   118.54  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
 50M  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 50M  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 50M  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 50M  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 50M  CONST_05  C14  C13  C12  C17     0.00   0.0  0
 50M  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 50M  CONST_07  N25  C23  N22  C20     0.00   0.0  0
 50M  CONST_08  N22  C23  N25  C26     0.00   0.0  0
 50M  CONST_09  N28  C15  C14  C13   180.00   0.0  0
 50M  CONST_10  N28  C15  C16  C17   180.00   0.0  0
 50M  CONST_11  O24  C23  N22  C20   180.00   0.0  0
 50M  CONST_12  O24  C23  N25  C26   180.00   0.0  0
 50M  CONST_13  H13  C13  C14  C15   180.00   0.0  0
 50M  CONST_14  H14  C14  C15  C16   180.00   0.0  0
 50M  CONST_15  H16  C16  C17  C18     0.00   0.0  0
 50M  CONST_16  H25  N25  C23  N22   180.00   0.0  0
 50M  CONST_17  O30  N28  C15  C16   180.00   0.0  0
 50M  CONST_18  O29  N28  C15  C16     0.00   0.0  0
 50M  CONST_19  O30  N28  C15  C14     0.00   0.0  0
 50M  CONST_20  O29  N28  C15  C14   180.00   0.0  0
 50M  Var_01    C7   C10  N11  C2     55.60  30.0  1
 50M  Var_02    C13  C12  N11  C2   -161.04  30.0  1
 50M  Var_03    C19  C18  C17  C16   139.40  30.0  1
 50M  Var_04    C23  N25  C26  C19    -7.59  30.0  1
 50M  Var_05    O21  C20  N22  C23  -179.59  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
 50M  chir_01  C2   N11  C3   C19  positiv
 50M  chir_02  C3   O6   C2   C5   positiv
 50M  chir_03  C7   O6   C10  C9   negativ
 50M  chir_04  C19  C26  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
 50M  plan-1  C13  0.020
 50M  plan-1  C15  0.020
 50M  plan-1  C16  0.020
 50M  plan-1  C17  0.020
 50M  plan-1  C18  0.020
 50M  plan-1  N11  0.020
 50M  plan-1  C12  0.020
 50M  plan-1  C14  0.020
 50M  plan-1  N28  0.020
 50M  plan-1  H13  0.020
 50M  plan-1  H16  0.020
 50M  plan-1  H14  0.020
 50M  plan-2  C15  0.020
 50M  plan-2  N28  0.020
 50M  plan-2  O29  0.020
 50M  plan-2  O30  0.020
 50M  plan-3  C19  0.020
 50M  plan-3  C26  0.020
 50M  plan-3  N25  0.020
 50M  plan-3  O27  0.020
 50M  plan-4  C20  0.020
 50M  plan-4  C23  0.020
 50M  plan-4  C26  0.020
 50M  plan-4  N22  0.020
 50M  plan-4  O24  0.020
 50M  plan-4  N25  0.020
 50M  plan-4  H25  0.020

