# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:02:04 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: N-[(3R)-3-methyl-1,1-dioxo-1lambda~6~-thiolan-3-yl]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CC[S](=O)(=O)C1)NC(=O)C2CC2
#
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
 LK6  LK6  "N-[(3R)-3-methyl-1,1-dioxo-1lambda~6~-thiolan-3-yl]cyclopropanecarboxamide"
  ligand  29  14  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LK6
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
 LK6  N1   N  NH1   0  -0.673  34.5396  24.4447  103.4012
 LK6  C4   C  CH2   0  -0.603  37.1375  24.1980  104.7337
 LK6  C5   C  CH2   0  -0.627  34.7550  23.1788  105.4290
 LK6  C6   C  C     0   0.609  34.6235  25.4355  102.4877
 LK6  C7   C  CH1   0  -0.420  34.3908  24.9879  101.0862
 LK6  C8   C  CH2   0  -0.465  35.2522  25.5925  100.0067
 LK6  C1   C  CH3   0  -0.635  33.5488  25.3878  105.4614
 LK6  C2   C  CT    0   0.060  34.6928  24.5919  104.8455
 LK6  C3   C  CH2   0  -0.439  36.0727  25.1803  105.2014
 LK6  S1   S  S     0   1.225  36.3983  22.5603  104.9793
 LK6  O1   O  OS    0  -0.676  37.0155  21.8809  106.1162
 LK6  O2   O  OS    0  -0.677  36.3249  21.8410  103.7077
 LK6  O3   O  O     0  -0.491  34.8875  26.5965  102.7671
 LK6  C9   C  CH2   0  -0.464  33.8213  25.9758  100.1054
 LK6  H1   H  HNH1  0   0.405  34.2306  23.5470  103.0624
 LK6  H2   H  HCH2  0   0.313  38.0589  24.2460  105.3112
 LK6  H3   H  HCH2  0   0.305  37.3690  24.2999  103.6747
 LK6  H4   H  HCH2  0   0.323  34.6979  23.2170  106.5171
 LK6  H5   H  HCH2  0   0.326  33.9953  22.4917  105.0534
 LK6  H6   H  HCH1  0   0.279  34.1100  23.9499  100.9489
 LK6  H7   H  HCH2  0   0.262  35.5609  24.9344   99.2055
 LK6  H8   H  HCH2  0   0.256  35.9982  26.3146  100.3116
 LK6  H9   H  HCH3  0   0.237  33.6607  25.4433  106.5444
 LK6  H10  H  HCH3  0   0.250  33.5346  26.4033  105.0696
 LK6  H11  H  HCH3  0   0.242  32.5903  24.9188  105.2392
 LK6  H12  H  HCH2  0   0.292  36.2284  26.1623  104.7626
 LK6  H13  H  HCH2  0   0.268  36.1207  25.2943  106.2863
 LK6  H14  H  HCH2  0   0.256  33.5832  26.9638  100.4769
 LK6  H15  H  HCH2  0   0.261  33.1292  25.5879   99.3703

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
 LK6  C8  C9   single  1.485  0.020  1.485
 LK6  C8  C7   single  1.508  0.020  1.508
 LK6  C9  C7   single  1.504  0.020  1.504
 LK6  C7  C6   single  1.490  0.020  1.490
 LK6  C6  O3   double  1.223  0.020  1.223
 LK6  C6  N1   single  1.350  0.020  1.350
 LK6  N1  C2   single  1.460  0.020  1.460
 LK6  O2  S1   double  1.463  0.020  1.463
 LK6  C2  C1   single  1.524  0.020  1.524
 LK6  C2  C5   single  1.530  0.020  1.530
 LK6  C2  C3   single  1.542  0.020  1.542
 LK6  C4  S1   single  1.813  0.020  1.813
 LK6  C4  C3   single  1.522  0.020  1.522
 LK6  S1  C5   single  1.813  0.020  1.813
 LK6  S1  O1   double  1.461  0.020  1.461
 LK6  N1  H1   single  0.860  0.020  1.020
 LK6  C4  H2   single  0.970  0.020  1.090
 LK6  C4  H3   single  0.970  0.020  1.090
 LK6  C5  H4   single  0.970  0.020  1.090
 LK6  C5  H5   single  0.970  0.020  1.090
 LK6  C7  H6   single  0.970  0.020  1.090
 LK6  C8  H7   single  0.970  0.020  1.090
 LK6  C8  H8   single  0.970  0.020  1.090
 LK6  C1  H9   single  0.970  0.020  1.090
 LK6  C1  H10  single  0.970  0.020  1.090
 LK6  C1  H11  single  0.970  0.020  1.090
 LK6  C3  H12  single  0.970  0.020  1.090
 LK6  C3  H13  single  0.970  0.020  1.090
 LK6  C9  H14  single  0.970  0.020  1.090
 LK6  C9  H15  single  0.970  0.020  1.090

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
 LK6  H1   N1  C2   117.04  3.000
 LK6  H1   N1  C6   116.43  3.000
 LK6  C2   N1  C6   126.07  3.000
 LK6  H3   C4  H2   109.39  3.000
 LK6  H3   C4  S1   107.63  3.000
 LK6  H2   C4  S1   108.24  3.000
 LK6  H3   C4  C3   112.77  3.000
 LK6  H2   C4  C3   113.61  3.000
 LK6  S1   C4  C3   104.83  3.000
 LK6  H5   C5  H4   109.22  3.000
 LK6  H5   C5  S1   109.33  3.000
 LK6  H4   C5  S1   107.88  3.000
 LK6  H5   C5  C2   114.97  3.000
 LK6  H4   C5  C2   110.25  3.000
 LK6  S1   C5  C2   104.92  3.000
 LK6  O3   C6  C7   122.27  3.000
 LK6  O3   C6  N1   123.74  3.000
 LK6  C7   C6  N1   113.98  3.000
 LK6  H6   C7  C9   116.63  3.000
 LK6  H6   C7  C8   116.19  3.000
 LK6  C9   C7  C8    59.07  3.000
 LK6  H6   C7  C6   116.57  3.000
 LK6  C9   C7  C6   118.38  3.000
 LK6  C8   C7  C6   117.65  3.000
 LK6  H8   C8  H7   114.70  3.000
 LK6  H8   C8  C9   118.26  3.000
 LK6  H7   C8  C9   118.78  3.000
 LK6  H8   C8  C7   117.37  3.000
 LK6  H7   C8  C7   116.70  3.000
 LK6  C9   C8  C7    60.35  3.000
 LK6  H11  C1  H10  108.45  3.000
 LK6  H11  C1  H9   108.34  3.000
 LK6  H10  C1  H9   108.14  3.000
 LK6  H11  C1  C2   110.68  3.000
 LK6  H10  C1  C2   110.59  3.000
 LK6  H9   C1  C2   110.56  3.000
 LK6  C3   C2  C1   112.30  3.000
 LK6  C3   C2  C5   103.18  3.000
 LK6  C1   C2  C5   111.03  3.000
 LK6  C3   C2  N1   111.15  3.000
 LK6  C5   C2  N1   106.76  3.000
 LK6  C1   C2  N1   111.95  3.000
 LK6  H13  C3  H12  107.49  3.000
 LK6  H13  C3  C2   107.97  3.000
 LK6  H12  C3  C2   112.32  3.000
 LK6  H13  C3  C4   109.99  3.000
 LK6  H12  C3  C4   111.03  3.000
 LK6  C2   C3  C4   107.99  3.000
 LK6  O2   S1  O1   117.97  3.000
 LK6  O1   S1  C5   110.40  3.000
 LK6  O2   S1  C5   109.75  3.000
 LK6  O1   S1  C4   110.68  3.000
 LK6  C5   S1  C4    95.45  3.000
 LK6  O2   S1  C4   110.29  3.000
 LK6  H15  C9  H14  114.83  3.000
 LK6  H15  C9  C8   118.61  3.000
 LK6  H14  C9  C8   118.08  3.000
 LK6  H15  C9  C7   116.74  3.000
 LK6  H14  C9  C7   117.34  3.000
 LK6  C8   C9  C7    60.58  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
 LK6  CONST_01  C2   N1  C6  C7   180.00   0.0  0
 LK6  CONST_02  O3   C6  N1  C2     0.00   0.0  0
 LK6  CONST_03  H1   N1  C6  C7     0.00   0.0  0
 LK6  CONST_04  H1   N1  C6  O3   180.00   0.0  0
 LK6  Var_01    C2   C5  S1  C4    21.74  30.0  1
 LK6  Var_02    C3   C4  S1  C5     7.12  30.0  1
 LK6  Var_03    S1   C4  C3  C2   -34.55  30.0  1
 LK6  Var_04    C9   C8  C7  C6  -108.16  30.0  1
 LK6  Var_05    O2   S1  C5  C2   -92.12  30.0  1
 LK6  Var_06    O1   S1  C5  C2   136.19  30.0  1
 LK6  Var_07    O2   S1  C4  C3   120.52  30.0  1
 LK6  Var_08    O1   S1  C4  C3  -107.11  30.0  1
 LK6  Var_09    H4   C5  S1  C4   -95.80  30.0  1
 LK6  Var_10    H5   C5  S1  C4   145.54  30.0  1
 LK6  Var_11    H2   C4  S1  C5   128.69  30.0  1
 LK6  Var_12    H3   C4  S1  C5  -113.17  30.0  1
 LK6  Var_13    H14  C9  C8  C7   107.26  30.0  1
 LK6  Var_14    H15  C9  C8  C7  -106.30  30.0  1
 LK6  Var_15    H7   C8  C9  C7   106.10  30.0  1
 LK6  Var_16    H8   C8  C9  C7  -107.13  30.0  1
 LK6  Var_17    H6   C7  C9  C8  -105.97  30.0  1
 LK6  Var_18    H2   C4  C3  C2  -152.53  30.0  1
 LK6  Var_19    H3   C4  C3  C2    82.27  30.0  1
 LK6  Var_20    H12  C3  C4  S1  -158.10  30.0  1
 LK6  Var_21    H13  C3  C4  S1    83.05  30.0  1
 LK6  Var_22    C8   C7  C6  N1  -140.62  30.0  1
 LK6  Var_23    C9   C7  C6  N1   151.49  30.0  1
 LK6  Var_24    O3   C6  C7  C8    38.25  30.0  3
 LK6  Var_25    C9   C7  C6  O3   -29.63  30.0  1
 LK6  Var_26    H7   C8  C7  C6   142.35  30.0  1
 LK6  Var_27    H8   C8  C7  C6     0.42  30.0  1
 LK6  Var_28    H14  C9  C7  C6    -1.55  30.0  1
 LK6  Var_29    H15  C9  C7  C6  -143.71  30.0  1
 LK6  Var_30    H2   C4  S1  O1    14.47  30.0  1
 LK6  Var_31    H3   C4  S1  O1   132.60  30.0  1
 LK6  Var_32    H4   C5  S1  O1    18.65  30.0  1
 LK6  Var_33    H5   C5  S1  O1  -100.01  30.0  1
 LK6  Var_34    H2   C4  S1  O2  -117.91  30.0  1
 LK6  Var_35    H3   C4  S1  O2     0.23  30.0  1
 LK6  Var_36    H4   C5  S1  O2   150.35  30.0  1
 LK6  Var_37    H5   C5  S1  O2    31.68  30.0  1
 LK6  Var_38    H6   C7  C6  N1     4.36  30.0  1
 LK6  Var_39    H6   C7  C6  O3  -176.76  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
 LK6  chir_02  C2  C1  C5  C3  positiv
 LK6  chir_03  C7  C8  C9  C6  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
 LK6  plan-1  N1  0.020
 LK6  plan-1  C6  0.020
 LK6  plan-1  C7  0.020
 LK6  plan-1  C2  0.020
 LK6  plan-1  O3  0.020
 LK6  plan-1  H1  0.020

