# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:58:46 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: (3S,4S)-8-{6-amino-5-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1OCC2(CCN(CC2)c3cnc(Sc4ccnc(N)c4Cl)c(N)n3)[C@@H]1N
#
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
 VKS  VKS  (3S,4S)-8-{6-amino-5-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine  ligand  52  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VKS
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
 VKS  C1   C   CR16  0  -0.050  17.5072  39.4917  4.1125
 VKS  C2   C   CR6   0   0.515  16.3766  39.4904  6.0993
 VKS  C3   C   CR6   0  -0.213  17.4871  40.0793  6.7333
 VKS  O1   O   O2    0  -0.508  29.0267  41.4853  1.7339
 VKS  C11  C   CH2   0  -0.336  25.1908  40.2998  2.7641
 VKS  C12  C   CH2   0  -0.432  26.4865  40.7052  3.4586
 VKS  C13  C   CT    0  -0.161  27.0489  42.0395  2.9344
 VKS  C14  C   CH2   0  -0.410  25.9381  43.0896  2.9597
 VKS  C15  C   CH2   0  -0.134  27.6730  41.8625  1.5407
 VKS  C16  C   CH1   0   0.062  29.3602  41.5323  3.1190
 VKS  C17  C   CH1   0  -0.105  28.2946  42.4389  3.7524
 VKS  C18  C   CH3   0  -0.695  30.7956  41.9752  3.2925
 VKS  N1   N   N     0  -0.463  16.4099  39.2034  4.7999
 VKS  C4   C   CR6   0   0.060  18.6302  40.3715  6.0104
 VKS  C5   C   CR16  0  -0.366  18.6394  40.0704  4.6479
 VKS  S1   S   S2    0   0.102  19.9891  41.1102  6.8582
 VKS  C6   C   CR6   0  -0.142  21.2362  41.1777  5.6204
 VKS  N2   N   N     0  -0.305  21.4378  42.3242  4.9911
 VKS  C7   C   CR16  0  -0.215  22.3958  42.4312  4.1042
 VKS  C8   C   CR6   0   0.501  23.2293  41.3168  3.8074
 VKS  N3   N   N     0  -0.485  23.0399  40.1684  4.4511
 VKS  C9   C   CR6   0   0.481  22.0623  40.0665  5.3447
 VKS  N4   N   NH2   0  -0.824  21.8767  38.8671  5.9264
 VKS  CL1  CL  CL    0  -0.110  17.4138  40.4419  8.4253
 VKS  C10  C   CH2   0  -0.348  24.6710  42.5952  2.2693
 VKS  N5   N   NT    0  -0.477  24.2035  41.3597  2.8706
 VKS  N6   N   NH2   0  -0.791  28.5528  43.8653  3.6836
 VKS  N7   N   NH2   0  -0.827  15.2275  39.2317  6.7677
 VKS  H1   H   HCR6  0   0.268  17.4847  39.2445  3.0569
 VKS  H2   H   HCH2  0   0.277  24.7968  39.3844  3.1942
 VKS  H3   H   HCH2  0   0.246  25.3659  40.1091  1.7016
 VKS  H4   H   HCH2  0   0.239  26.2922  40.7974  4.5319
 VKS  H5   H   HCH2  0   0.250  27.2116  39.8961  3.3415
 VKS  H6   H   HCH2  0   0.240  26.2655  44.0131  2.4805
 VKS  H7   H   HCH2  0   0.235  25.6992  43.3415  3.9974
 VKS  H8   H   HCH2  0   0.210  27.6274  42.7992  0.9691
 VKS  H9   H   HCH2  0   0.220  27.1658  41.1006  0.9399
 VKS  H10  H   HCH1  0   0.203  29.2625  40.5259  3.5502
 VKS  H11  H   HCH1  0   0.244  28.1606  42.1813  4.8066
 VKS  H12  H   HCH3  0   0.230  31.0507  42.0015  4.3532
 VKS  H13  H   HCH3  0   0.240  31.4804  41.2773  2.8096
 VKS  H14  H   HCH3  0   0.220  30.9752  42.9667  2.8757
 VKS  H15  H   HCR6  0   0.272  19.4936  40.2835  4.0225
 VKS  H16  H   HCR6  0   0.265  22.5121  43.3942  3.6290
 VKS  H17  H   HNH2  0   0.396  22.5951  38.1719  5.8131
 VKS  H18  H   HNH2  0   0.402  21.2999  38.7926  6.7473
 VKS  H19  H   HCH2  0   0.257  24.8613  42.4003  1.2096
 VKS  H20  H   HCH2  0   0.272  23.9007  43.3608  2.2911
 VKS  H21  H   HNH2  0   0.355  29.3575  44.0949  4.2535
 VKS  H22  H   HNH2  0   0.344  28.7924  44.1497  2.7405
 VKS  H24  H   HNH2  0   0.394  14.5663  38.6301  6.3053
 VKS  H25  H   HNH2  0   0.394  15.2373  39.1657  7.7709

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
 VKS  C15  O1   single    1.419  0.020  1.419
 VKS  C15  C13  single    1.537  0.020  1.537
 VKS  O1   C16  single    1.425  0.020  1.425
 VKS  C10  N5   single    1.451  0.020  1.451
 VKS  C10  C14  single    1.525  0.020  1.525
 VKS  C11  N5   single    1.452  0.020  1.452
 VKS  C11  C12  single    1.525  0.020  1.525
 VKS  N5   C8   single    1.352  0.020  1.352
 VKS  C14  C13  single    1.529  0.020  1.529
 VKS  C13  C12  single    1.540  0.020  1.540
 VKS  C13  C17  single    1.543  0.020  1.543
 VKS  C16  C18  single    1.512  0.020  1.512
 VKS  C16  C17  single    1.536  0.020  1.536
 VKS  C8   C7   aromatic  1.423  0.020  1.423
 VKS  C8   N3   aromatic  1.330  0.020  1.330
 VKS  C7   N2   aromatic  1.310  0.020  1.310
 VKS  C17  N6   single    1.451  0.020  1.451
 VKS  C1   C5   aromatic  1.380  0.020  1.380
 VKS  C1   N1   aromatic  1.327  0.020  1.327
 VKS  N3   C9   aromatic  1.328  0.020  1.328
 VKS  C5   C4   aromatic  1.395  0.020  1.395
 VKS  N2   C6   aromatic  1.323  0.020  1.323
 VKS  N1   C2   aromatic  1.331  0.020  1.331
 VKS  C9   C6   aromatic  1.412  0.020  1.412
 VKS  C9   N4   single    1.346  0.020  1.346
 VKS  C6   S1   single    1.758  0.020  1.758
 VKS  C4   C3   aromatic  1.384  0.020  1.384
 VKS  C4   S1   single    1.764  0.020  1.764
 VKS  C2   C3   aromatic  1.408  0.020  1.408
 VKS  C2   N7   single    1.354  0.020  1.354
 VKS  C3   CL1  single    1.732  0.020  1.732
 VKS  C1   H1   single    0.930  0.020  1.080
 VKS  C11  H2   single    0.970  0.020  1.090
 VKS  C11  H3   single    0.970  0.020  1.090
 VKS  C12  H4   single    0.970  0.020  1.090
 VKS  C12  H5   single    0.970  0.020  1.090
 VKS  C14  H6   single    0.970  0.020  1.090
 VKS  C14  H7   single    0.970  0.020  1.090
 VKS  C15  H8   single    0.970  0.020  1.090
 VKS  C15  H9   single    0.970  0.020  1.090
 VKS  C16  H10  single    0.970  0.020  1.090
 VKS  C17  H11  single    0.970  0.020  1.090
 VKS  C18  H12  single    0.970  0.020  1.090
 VKS  C18  H13  single    0.970  0.020  1.090
 VKS  C18  H14  single    0.970  0.020  1.090
 VKS  C5   H15  single    0.930  0.020  1.080
 VKS  C7   H16  single    0.930  0.020  1.080
 VKS  N4   H17  single    0.890  0.020  1.040
 VKS  N4   H18  single    0.890  0.020  1.040
 VKS  C10  H19  single    0.970  0.020  1.090
 VKS  C10  H20  single    0.970  0.020  1.090
 VKS  N6   H21  single    0.890  0.020  1.040
 VKS  N6   H22  single    0.890  0.020  1.040
 VKS  N7   H24  single    0.890  0.020  1.040
 VKS  N7   H25  single    0.890  0.020  1.040

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
 VKS  H1   C1   C5   119.37  3.000
 VKS  H1   C1   N1   115.96  3.000
 VKS  C5   C1   N1   124.67  3.000
 VKS  N7   C2   N1   117.51  3.000
 VKS  N7   C2   C3   121.80  3.000
 VKS  N1   C2   C3   120.67  3.000
 VKS  CL1  C3   C4   120.08  3.000
 VKS  CL1  C3   C2   119.61  3.000
 VKS  C4   C3   C2   120.31  3.000
 VKS  C16  O1   C15  110.30  3.000
 VKS  H3   C11  H2   107.22  3.000
 VKS  H3   C11  N5   107.90  3.000
 VKS  H2   C11  N5   109.86  3.000
 VKS  H3   C11  C12  110.66  3.000
 VKS  H2   C11  C12  110.62  3.000
 VKS  N5   C11  C12  110.50  3.000
 VKS  H5   C12  H4   106.57  3.000
 VKS  H5   C12  C13  111.27  3.000
 VKS  H4   C12  C13  109.01  3.000
 VKS  H5   C12  C11  108.55  3.000
 VKS  H4   C12  C11  108.55  3.000
 VKS  C13  C12  C11  112.68  3.000
 VKS  C17  C13  C15  100.53  3.000
 VKS  C17  C13  C14  113.58  3.000
 VKS  C15  C13  C14  112.90  3.000
 VKS  C17  C13  C12  109.80  3.000
 VKS  C14  C13  C12  108.91  3.000
 VKS  C15  C13  C12  110.92  3.000
 VKS  H7   C14  H6   106.70  3.000
 VKS  H7   C14  C10  108.81  3.000
 VKS  H6   C14  C10  108.96  3.000
 VKS  H7   C14  C13  109.42  3.000
 VKS  H6   C14  C13  110.86  3.000
 VKS  C10  C14  C13  111.93  3.000
 VKS  H9   C15  H8   106.78  3.000
 VKS  H9   C15  C13  112.93  3.000
 VKS  H8   C15  C13  110.90  3.000
 VKS  H9   C15  O1   109.38  3.000
 VKS  H8   C15  O1   109.71  3.000
 VKS  C13  C15  O1   107.13  3.000
 VKS  H10  C16  C18  107.91  3.000
 VKS  H10  C16  C17  108.48  3.000
 VKS  C18  C16  C17  116.00  3.000
 VKS  H10  C16  O1   109.28  3.000
 VKS  C17  C16  O1   104.94  3.000
 VKS  C18  C16  O1   110.08  3.000
 VKS  H11  C17  N6   107.40  3.000
 VKS  H11  C17  C16  110.10  3.000
 VKS  N6   C17  C16  115.93  3.000
 VKS  H11  C17  C13  110.56  3.000
 VKS  N6   C17  C13  111.90  3.000
 VKS  C16  C17  C13  100.88  3.000
 VKS  H14  C18  H13  108.01  3.000
 VKS  H14  C18  H12  108.13  3.000
 VKS  H13  C18  H12  107.40  3.000
 VKS  H14  C18  C16  112.26  3.000
 VKS  H13  C18  C16  110.97  3.000
 VKS  H12  C18  C16  109.91  3.000
 VKS  C2   N1   C1   118.66  3.000
 VKS  S1   C4   C5   123.68  3.000
 VKS  S1   C4   C3   118.28  3.000
 VKS  C5   C4   C3   118.04  3.000
 VKS  H15  C5   C4   121.87  3.000
 VKS  H15  C5   C1   120.48  3.000
 VKS  C4   C5   C1   117.65  3.000
 VKS  C6   S1   C4   102.95  3.000
 VKS  C9   C6   N2   119.99  3.000
 VKS  C9   C6   S1   121.49  3.000
 VKS  N2   C6   S1   118.43  3.000
 VKS  C7   N2   C6   120.28  3.000
 VKS  H16  C7   C8   122.91  3.000
 VKS  H16  C7   N2   116.71  3.000
 VKS  C8   C7   N2   120.37  3.000
 VKS  N5   C8   N3   117.73  3.000
 VKS  N3   C8   C7   119.46  3.000
 VKS  N5   C8   C7   122.80  3.000
 VKS  C9   N3   C8   119.77  3.000
 VKS  N4   C9   N3   117.42  3.000
 VKS  N4   C9   C6   122.43  3.000
 VKS  N3   C9   C6   120.11  3.000
 VKS  H18  N4   H17  116.75  3.000
 VKS  H18  N4   C9   119.85  3.000
 VKS  H17  N4   C9   117.95  3.000
 VKS  H20  C10  H19  105.56  3.000
 VKS  H20  C10  N5   111.30  3.000
 VKS  H19  C10  N5   107.80  3.000
 VKS  H20  C10  C14  110.58  3.000
 VKS  H19  C10  C14  110.59  3.000
 VKS  N5   C10  C14  110.86  3.000
 VKS  C10  N5   C8   123.10  3.000
 VKS  C8   N5   C11  121.16  3.000
 VKS  C10  N5   C11  111.83  3.000
 VKS  H22  N6   H21  105.79  3.000
 VKS  H22  N6   C17  111.21  3.000
 VKS  H21  N6   C17  109.73  3.000
 VKS  H25  N7   H24  115.19  3.000
 VKS  H25  N7   C2   119.79  3.000
 VKS  H24  N7   C2   116.42  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
 VKS  CONST_01  C3   C4   C5   C1     0.00   0.0  0
 VKS  CONST_02  C3   C2   N1   C1     0.00   0.0  0
 VKS  CONST_03  C5   C1   N1   C2     0.00   0.0  0
 VKS  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 VKS  CONST_05  C4   C5   C1   N1     0.00   0.0  0
 VKS  CONST_06  C4   C3   C2   N1     0.00   0.0  0
 VKS  CONST_07  C8   C7   N2   C6     0.00   0.0  0
 VKS  CONST_08  C8   N3   C9   C6     0.00   0.0  0
 VKS  CONST_09  N3   C8   C7   N2     0.00   0.0  0
 VKS  CONST_10  N3   C9   C6   N2     0.00   0.0  0
 VKS  CONST_11  C9   N3   C8   C7     0.00   0.0  0
 VKS  CONST_12  C9   C6   N2   C7     0.00   0.0  0
 VKS  CONST_13  N5   C8   C7   N2   180.00   0.0  0
 VKS  CONST_14  N5   C8   N3   C9   180.00   0.0  0
 VKS  CONST_15  S1   C4   C5   C1   180.00   0.0  0
 VKS  CONST_16  N7   C2   N1   C1   180.00   0.0  0
 VKS  CONST_17  S1   C4   C3   C2   180.00   0.0  0
 VKS  CONST_18  CL1  C3   C2   N1   180.00   0.0  0
 VKS  CONST_19  N7   C2   C3   C4   180.00   0.0  0
 VKS  CONST_20  CL1  C3   C4   C5   180.00   0.0  0
 VKS  CONST_21  C7   N2   C6   S1   180.00   0.0  0
 VKS  CONST_22  N3   C9   C6   S1   180.00   0.0  0
 VKS  CONST_23  N4   C9   C6   N2   180.00   0.0  0
 VKS  CONST_24  N4   C9   N3   C8   180.00   0.0  0
 VKS  CONST_25  H1   C1   N1   C2   180.00   0.0  0
 VKS  CONST_26  H15  C5   C4   C3   180.00   0.0  0
 VKS  CONST_27  H16  C7   N2   C6   180.00   0.0  0
 VKS  CONST_28  H24  N7   C2   C3   180.00   0.0  0
 VKS  CONST_30  H17  N4   C9   C6   180.00   0.0  0
 VKS  Var_01    C14  C13  C15  O1   149.58  30.0  3
 VKS  Var_02    C14  C10  N5   C11  -60.49  30.0  1
 VKS  Var_03    C7   C8   N5   C11  168.44  30.0  2
 VKS  Var_04    C15  C13  C12  C11  -74.09  30.0  1
 VKS  Var_05    C10  N5   C11  C12   59.48  30.0  1
 VKS  Var_06    C10  C14  C13  C12  -51.09  30.0  1
 VKS  Var_07    N5   C10  C14  C13   56.64  30.0  1
 VKS  Var_08    N5   C11  C12  C13  -55.13  30.0  1
 VKS  Var_09    N2   C6   S1   C4    99.74  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
 VKS  chir_01  C16  O1  C18  C17  negativ
 VKS  chir_02  C17  N6  C13  C16  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
 VKS  plan-1  C1   0.020
 VKS  plan-1  C2   0.020
 VKS  plan-1  C3   0.020
 VKS  plan-1  N1   0.020
 VKS  plan-1  C4   0.020
 VKS  plan-1  C5   0.020
 VKS  plan-1  S1   0.020
 VKS  plan-1  CL1  0.020
 VKS  plan-1  N7   0.020
 VKS  plan-1  H1   0.020
 VKS  plan-1  H15  0.020
 VKS  plan-2  S1   0.020
 VKS  plan-2  C6   0.020
 VKS  plan-2  N2   0.020
 VKS  plan-2  C7   0.020
 VKS  plan-2  C8   0.020
 VKS  plan-2  N3   0.020
 VKS  plan-2  C9   0.020
 VKS  plan-2  N4   0.020
 VKS  plan-2  N5   0.020
 VKS  plan-2  H16  0.020
 VKS  plan-3  C9   0.020
 VKS  plan-3  N4   0.020
 VKS  plan-3  H17  0.020
 VKS  plan-3  H18  0.020
 VKS  plan-4  C2   0.020
 VKS  plan-4  N7   0.020
 VKS  plan-4  H24  0.020
 VKS  plan-4  H25  0.020

