# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:55:02 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(methylsulfanyl)pyrimidin-4-yl}cyclopropane-1-sulfonimidoamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(cc(n1)C2(CC2)[S@](N)(=N)=O)N3CCOC[C@H]3C
#
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
 VK1  VK1  "1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(methylsulfanyl)pyrimidin-4-yl}cyclopropane-1-sulfonimidoamide"
  ligand  43  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VK1
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
 VK1  C10  C  CH1   0  -0.142  -16.7966  20.3333  -5.9512
 VK1  C15  C  CH2   0  -0.329  -15.9421  18.0164  -5.9379
 VK1  C17  C  CR6   0   0.221  -20.5302  18.9515  -6.5080
 VK1  C03  C  CT    0  -0.292  -20.3792  15.3872  -6.9628
 VK1  C04  C  CH2   0  -0.453  -21.0526  14.5844  -5.8917
 VK1  C05  C  CH2   0  -0.454  -19.6841  14.2112  -6.3534
 VK1  C06  C  CR6   0   0.324  -19.9517  16.7883  -6.6844
 VK1  C07  C  CR16  0  -0.456  -18.6380  17.1003  -6.4346
 VK1  C08  C  CR6   0   0.605  -18.3351  18.4578  -6.1834
 VK1  C11  C  CH3   0  -0.661  -16.4914  20.7627  -7.3823
 VK1  C12  C  CH2   0  -0.185  -15.6661  20.6513  -4.9836
 VK1  C14  C  CH2   0  -0.185  -14.8580  18.4993  -4.9911
 VK1  C19  C  CH3   0  -0.766  -20.9857  21.6857  -6.3509
 VK1  N01  N  NC2   0  -0.868  -22.5051  15.9566  -8.6576
 VK1  N09  N  NT    0  -0.502  -17.0966  18.8992  -5.8851
 VK1  N16  N  N     0  -0.470  -19.3138  19.3702  -6.2425
 VK1  N20  N  N     0  -0.471  -20.9235  17.7057  -6.7199
 VK1  N21  N  N     0  -0.857  -21.1609  13.7344  -8.8428
 VK1  O13  O  O2    0  -0.472  -14.5316  19.8495  -5.2073
 VK1  O22  O  OS    0  -0.670  -20.1683  16.0821  -9.4812
 VK1  S02  S  S     0   1.216  -21.0082  15.2323  -8.6322
 VK1  H1   H  HCH1  0   0.277  -17.6734  20.8749  -5.6003
 VK1  H2   H  HCH2  0   0.270  -16.2197  17.0118  -5.6245
 VK1  H3   H  HCH2  0   0.248  -15.5539  17.9463  -6.9600
 VK1  H4   H  HCH2  0   0.278  -21.1630  15.0663  -4.9286
 VK1  H5   H  HCH2  0   0.280  -21.8814  13.9506  -6.1804
 VK1  H6   H  HCH2  0   0.285  -19.5808  13.3235  -6.9605
 VK1  H7   H  HCH2  0   0.276  -18.8467  14.4218  -5.7012
 VK1  H8   H  HCR6  0   0.283  -17.8862  16.3284  -6.4584
 VK1  H9   H  HCH3  0   0.236  -16.2954  21.8350  -7.4193
 VK1  H10  H  HCH3  0   0.232  -15.6190  20.2494  -7.7868
 VK1  H11  H  HCH3  0   0.239  -17.3399  20.5585  -8.0358
 VK1  H12  H  HCH2  0   0.243  -15.3676  21.6932  -5.1096
 VK1  H13  H  HCH2  0   0.220  -16.0248  20.5267  -3.9518
 VK1  H14  H  HCH2  0   0.210  -15.1893  18.3465  -3.9544
 VK1  H15  H  HCH2  0   0.249  -13.9568  17.9054  -5.1473
 VK1  H16  H  HCH3  0   0.280  -21.7512  22.4569  -6.4125
 VK1  H17  H  HCH3  0   0.274  -20.5166  21.7257  -5.3713
 VK1  H18  H  HCH3  0   0.274  -20.2417  21.8608  -7.1239
 VK1  H19  H  HNC2  0   0.400  -23.1763  15.4402  -8.0994
 VK1  H20  H  HNC2  0   0.402  -22.4578  16.9203  -8.3367
 VK1  H21  H  H     0   0.369  -21.6302  13.5127  -9.7148
 VK1  S18  S  S2    0   0.043  -21.8369  20.1182  -6.6090

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
 VK1  O22  S02  double    1.466  0.020  1.466
 VK1  N21  S02  double    1.520  0.020  1.520
 VK1  N01  S02  single    1.663  0.020  1.663
 VK1  S02  C03  single    1.791  0.020  1.791
 VK1  C11  C10  single    1.525  0.020  1.525
 VK1  S18  C17  single    1.755  0.020  1.755
 VK1  S18  C19  single    1.802  0.020  1.802
 VK1  N20  C17  aromatic  1.323  0.020  1.323
 VK1  N20  C06  aromatic  1.337  0.020  1.337
 VK1  C03  C05  single    1.496  0.020  1.496
 VK1  C03  C06  single    1.491  0.020  1.491
 VK1  C03  C04  single    1.498  0.020  1.498
 VK1  C05  C04  single    1.492  0.020  1.492
 VK1  C17  N16  aromatic  1.314  0.020  1.314
 VK1  C06  C07  aromatic  1.373  0.020  1.373
 VK1  N16  C08  aromatic  1.339  0.020  1.339
 VK1  C07  C08  aromatic  1.413  0.020  1.413
 VK1  C08  N09  single    1.348  0.020  1.348
 VK1  C10  N09  single    1.467  0.020  1.467
 VK1  C10  C12  single    1.522  0.020  1.522
 VK1  C15  N09  single    1.454  0.020  1.454
 VK1  C15  C14  single    1.518  0.020  1.518
 VK1  C12  O13  single    1.407  0.020  1.407
 VK1  O13  C14  single    1.406  0.020  1.406
 VK1  C10  H1   single    0.970  0.020  1.090
 VK1  C15  H2   single    0.970  0.020  1.090
 VK1  C15  H3   single    0.970  0.020  1.090
 VK1  C04  H4   single    0.970  0.020  1.090
 VK1  C04  H5   single    0.970  0.020  1.090
 VK1  C05  H6   single    0.970  0.020  1.090
 VK1  C05  H7   single    0.970  0.020  1.090
 VK1  C07  H8   single    0.930  0.020  1.080
 VK1  C11  H9   single    0.970  0.020  1.090
 VK1  C11  H10  single    0.970  0.020  1.090
 VK1  C11  H11  single    0.970  0.020  1.090
 VK1  C12  H12  single    0.970  0.020  1.090
 VK1  C12  H13  single    0.970  0.020  1.090
 VK1  C14  H14  single    0.970  0.020  1.090
 VK1  C14  H15  single    0.970  0.020  1.090
 VK1  C19  H16  single    0.970  0.020  1.090
 VK1  C19  H17  single    0.970  0.020  1.090
 VK1  C19  H18  single    0.970  0.020  1.090
 VK1  N01  H19  single    0.890  0.020  1.040
 VK1  N01  H20  single    0.890  0.020  1.040
 VK1  N21  H21  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
 VK1  H1   C10  N09  107.89  3.000
 VK1  H1   C10  C12  106.82  3.000
 VK1  N09  C10  C12  109.13  3.000
 VK1  H1   C10  C11  108.87  3.000
 VK1  C12  C10  C11  112.91  3.000
 VK1  N09  C10  C11  111.01  3.000
 VK1  H3   C15  H2   107.46  3.000
 VK1  H3   C15  N09  110.73  3.000
 VK1  H2   C15  N09  110.33  3.000
 VK1  H3   C15  C14  110.43  3.000
 VK1  H2   C15  C14  107.23  3.000
 VK1  N09  C15  C14  110.55  3.000
 VK1  S18  C17  N20  113.29  3.000
 VK1  N20  C17  N16  127.42  3.000
 VK1  S18  C17  N16  119.29  3.000
 VK1  S02  C03  C06  110.86  3.000
 VK1  C06  C03  C05  121.97  3.000
 VK1  S02  C03  C05  118.36  3.000
 VK1  C06  C03  C04  119.92  3.000
 VK1  C05  C03  C04   59.76  3.000
 VK1  S02  C03  C04  117.53  3.000
 VK1  H5   C04  H4   114.83  3.000
 VK1  H5   C04  C05  118.25  3.000
 VK1  H4   C04  C05  118.70  3.000
 VK1  H5   C04  C03  117.85  3.000
 VK1  H4   C04  C03  116.31  3.000
 VK1  C05  C04  C03   60.03  3.000
 VK1  H7   C05  H6   115.12  3.000
 VK1  H7   C05  C04  118.34  3.000
 VK1  H6   C05  C04  117.86  3.000
 VK1  H7   C05  C03  116.88  3.000
 VK1  H6   C05  C03  117.49  3.000
 VK1  C04  C05  C03   60.21  3.000
 VK1  N20  C06  C07  122.98  3.000
 VK1  C07  C06  C03  121.45  3.000
 VK1  N20  C06  C03  115.56  3.000
 VK1  H8   C07  C08  122.84  3.000
 VK1  H8   C07  C06  120.04  3.000
 VK1  C08  C07  C06  117.10  3.000
 VK1  N16  C08  N09  117.26  3.000
 VK1  N09  C08  C07  123.41  3.000
 VK1  N16  C08  C07  119.33  3.000
 VK1  H11  C11  H10  108.20  3.000
 VK1  H11  C11  H9   107.68  3.000
 VK1  H10  C11  H9   107.85  3.000
 VK1  H11  C11  C10  110.73  3.000
 VK1  H10  C11  C10  112.07  3.000
 VK1  H9   C11  C10  110.16  3.000
 VK1  H13  C12  H12  107.81  3.000
 VK1  H13  C12  O13  110.35  3.000
 VK1  H12  C12  O13  107.77  3.000
 VK1  H13  C12  C10  109.31  3.000
 VK1  H12  C12  C10  109.23  3.000
 VK1  O13  C12  C10  112.26  3.000
 VK1  H15  C14  H14  107.97  3.000
 VK1  H15  C14  O13  108.01  3.000
 VK1  H14  C14  O13  110.40  3.000
 VK1  H15  C14  C15  109.12  3.000
 VK1  H14  C14  C15  109.19  3.000
 VK1  O13  C14  C15  112.05  3.000
 VK1  H18  C19  H17  109.85  3.000
 VK1  H18  C19  H16  109.08  3.000
 VK1  H17  C19  H16  109.18  3.000
 VK1  H18  C19  S18  111.19  3.000
 VK1  H17  C19  S18  111.41  3.000
 VK1  H16  C19  S18  106.02  3.000
 VK1  H20  N01  H19  109.86  3.000
 VK1  H20  N01  S02  111.47  3.000
 VK1  H19  N01  S02  111.43  3.000
 VK1  C08  N09  C15  121.50  3.000
 VK1  C15  N09  C10  115.44  3.000
 VK1  C08  N09  C10  119.87  3.000
 VK1  C08  N16  C17  117.93  3.000
 VK1  C06  N20  C17  115.19  3.000
 VK1  H21  N21  S02  112.38  3.000
 VK1  C14  O13  C12  109.61  3.000
 VK1  O22  S02  N21  123.27  3.000
 VK1  N21  S02  N01  109.67  3.000
 VK1  O22  S02  N01  104.74  3.000
 VK1  N01  S02  C03  107.02  3.000
 VK1  N21  S02  C03  104.46  3.000
 VK1  O22  S02  C03  106.77  3.000
 VK1  C19  S18  C17  102.61  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
 VK1  CONST_01  C07  C06  N20  C17     0.00   0.0  0
 VK1  CONST_02  C07  C08  N16  C17     0.00   0.0  0
 VK1  CONST_03  N16  C17  N20  C06     0.00   0.0  0
 VK1  CONST_04  N16  C08  C07  C06     0.00   0.0  0
 VK1  CONST_05  N20  C17  N16  C08     0.00   0.0  0
 VK1  CONST_06  N20  C06  C07  C08     0.00   0.0  0
 VK1  CONST_07  C03  C06  N20  C17   180.00   0.0  0
 VK1  CONST_08  N09  C08  N16  C17   180.00   0.0  0
 VK1  CONST_09  C08  C07  C06  C03   180.00   0.0  0
 VK1  CONST_10  N09  C08  C07  C06   180.00   0.0  0
 VK1  CONST_11  S18  C17  N20  C06   180.00   0.0  0
 VK1  CONST_12  S18  C17  N16  C08   180.00   0.0  0
 VK1  CONST_13  H8   C07  C06  C03     0.00   0.0  0
 VK1  CONST_14  H8   C07  C08  N09     0.00   0.0  0
 VK1  CONST_15  H8   C07  C08  N16   180.00   0.0  0
 VK1  CONST_16  H8   C07  C06  N20   180.00   0.0  0
 VK1  Var_01    N16  C08  N09  C10   -14.36  30.0  1
 VK1  Var_02    C07  C08  N09  C10   165.48  30.0  1
 VK1  Var_03    C14  C15  N09  C10    46.71  30.0  1
 VK1  Var_04    C14  O13  C12  C10   -62.50  30.0  1
 VK1  Var_05    N16  C08  N09  C15  -173.25  30.0  1
 VK1  Var_06    C07  C08  N09  C15     6.59  30.0  1
 VK1  Var_07    C12  O13  C14  C15    61.15  30.0  1
 VK1  Var_08    N20  C06  C03  C04   -78.54  30.0  2
 VK1  Var_09    C07  C06  C03  C04   102.61  30.0  2
 VK1  Var_10    C06  C03  C05  C04   108.47  30.0  1
 VK1  Var_11    N20  C06  C03  C05  -149.53  30.0  2
 VK1  Var_12    C07  C06  C03  C05    31.61  30.0  2
 VK1  Var_13    C14  C15  N09  C08  -153.52  30.0  1
 VK1  Var_14    O13  C14  C15  N09   -52.78  30.0  1
 VK1  Var_15    S02  C03  C05  C04  -107.06  30.0  1
 VK1  Var_16    S02  C03  C06  C07  -115.21  30.0  3
 VK1  Var_17    S02  C03  C06  N20    63.64  30.0  3
 VK1  Var_18    H2   C15  N09  C10   165.14  30.0  1
 VK1  Var_19    H3   C15  N09  C10   -76.02  30.0  1
 VK1  Var_20    H4   C04  C05  C03  -105.52  30.0  1
 VK1  Var_21    H5   C04  C05  C03   107.59  30.0  1
 VK1  Var_22    H6   C05  C04  C03  -107.40  30.0  1
 VK1  Var_23    H7   C05  C04  C03   106.45  30.0  1
 VK1  Var_24    H6   C05  C03  C06  -143.53  30.0  1
 VK1  Var_25    H7   C05  C03  C06    -0.37  30.0  1
 VK1  Var_26    H4   C04  C03  C06    -2.35  30.0  1
 VK1  Var_27    H5   C04  C03  C06   139.92  30.0  1
 VK1  Var_28    H2   C15  N09  C08   -35.09  30.0  1
 VK1  Var_29    H3   C15  N09  C08    83.75  30.0  1
 VK1  Var_30    H14  C14  O13  C12   -60.79  30.0  1
 VK1  Var_31    H15  C14  O13  C12  -178.63  30.0  1
 VK1  Var_32    H12  C12  O13  C14   177.18  30.0  1
 VK1  Var_33    H13  C12  O13  C14    59.70  30.0  1
 VK1  Var_34    H14  C14  C15  N09    69.85  30.0  1
 VK1  Var_35    H15  C14  C15  N09  -172.35  30.0  1
 VK1  Var_36    H2   C15  C14  O13  -173.09  30.0  1
 VK1  Var_37    H3   C15  C14  O13    70.12  30.0  1
 VK1  Var_38    O22  S02  C03  C04  -178.68  30.0  2
 VK1  Var_39    N21  S02  C03  C04   -46.66  30.0  2
 VK1  Var_40    N01  S02  C03  C04    69.60  30.0  2
 VK1  Var_41    O22  S02  C03  C05  -110.02  30.0  2
 VK1  Var_42    N21  S02  C03  C05    22.00  30.0  2
 VK1  Var_43    N01  S02  C03  C05   138.26  30.0  2
 VK1  Var_44    O22  S02  C03  C06    38.14  30.0  2
 VK1  Var_45    N21  S02  C03  C06   170.16  30.0  2
 VK1  Var_46    N01  S02  C03  C06   -73.58  30.0  2
 VK1  Var_47    N20  C17  S18  C19  -177.70  30.0  2
 VK1  Var_48    N16  C17  S18  C19     2.32  30.0  2
 VK1  Var_49    H6   C05  C03  S02     0.95  30.0  1
 VK1  Var_50    H7   C05  C03  S02   144.10  30.0  1
 VK1  Var_51    H4   C04  C03  S02  -142.09  30.0  1
 VK1  Var_52    H5   C04  C03  S02     0.18  30.0  1
 VK1  Var_53    H16  C19  S18  C17   179.47  30.0  3
 VK1  Var_54    H17  C19  S18  C17   -61.86  30.0  3
 VK1  Var_55    H18  C19  S18  C17    61.04  30.0  3
 VK1  Var_56    H19  N01  S02  C03   -67.30  30.0  3
 VK1  Var_57    H20  N01  S02  C03    55.83  30.0  3
 VK1  Var_58    H19  N01  S02  N21    45.46  30.0  3
 VK1  Var_59    H20  N01  S02  N21   168.59  30.0  3
 VK1  Var_60    H19  N01  S02  O22   179.59  30.0  3
 VK1  Var_61    H20  N01  S02  O22   -57.28  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
 VK1  chir_01  C10  C11  N09  C12  negativ
 VK1  chir_02  S02  N21  N01  C03  both
 VK1  chir_03  C03  C05  C06  C04  both

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
 VK1  plan-1  C17  0.020
 VK1  plan-1  C03  0.020
 VK1  plan-1  C06  0.020
 VK1  plan-1  C07  0.020
 VK1  plan-1  C08  0.020
 VK1  plan-1  N09  0.020
 VK1  plan-1  N16  0.020
 VK1  plan-1  N20  0.020
 VK1  plan-1  H8   0.020
 VK1  plan-1  S18  0.020

