# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:41:39 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-(4-chlorophenyl)-3-methyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]thieno[2,3-c]pyrazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nn(c2ccc(Cl)cc2)c3sc(cc13)C(=O)NC[C@H]4CCCO4
#
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
 5M6  5M6  1-(4-chlorophenyl)-3-methyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]thieno[2,3-c]pyrazole-5-carboxamide  ligand  43  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5M6
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
 5M6  N3   N   NR5   0  -0.492  -2.2643   1.2571   0.0063
 5M6  C6   C   CR5   0  -0.316   1.4819   1.7717  -0.2487
 5M6  C7   C   CR15  0  -0.246   0.7961   2.9339  -0.0762
 5M6  C8   C   CR5   0   0.241  -1.8486   3.3587   0.2230
 5M6  C10  C   CR6   0   0.377  -3.0624   0.1060  -0.0308
 5M6  C15  C   CR16  0  -0.302  -4.2931   0.0955   0.6188
 5M6  C17  C   CR6   0  -0.051  -4.6291  -2.1724  -0.0778
 5M6  C20  C   CR16  0  -0.202  -3.4064  -2.1700  -0.7280
 5M6  C22  C   CH3   0  -0.739  -2.1057   4.8081   0.4239
 5M6  C24  C   CH2   0  -0.503   6.6558  -1.6029  -0.6001
 5M6  C1   C   CR55  0   0.171  -0.9269   1.3739  -0.1141
 5M6  C2   C   CR55  0  -0.025  -0.6018   2.7107   0.0144
 5M6  N4   N   N     0  -0.276  -2.8178   2.4751   0.2151
 5M6  S5   S   S2    0   0.257   0.4340   0.3602  -0.3395
 5M6  C9   C   C     0   0.558   2.9512   1.6642  -0.3734
 5M6  N11  N   NH1   0  -0.669   3.4759   0.4445  -0.1565
 5M6  O12  O   O     0  -0.482   3.6178   2.6461  -0.6677
 5M6  O13  O   O2    0  -0.508   4.5470  -2.1433   0.3515
 5M6  C14  C   CR16  0  -0.326  -2.6259  -1.0251  -0.7108
 5M6  C16  C   CH2   0  -0.276   4.8956   0.1782  -0.2284
 5M6  C18  C   CH1   0   0.027   5.1568  -1.2718  -0.5962
 5M6  C19  C   CR16  0  -0.201  -5.0789  -1.0433   0.5904
 5M6  CL1  CL  CL    0  -0.121  -5.6098  -3.5981  -0.1050
 5M6  C23  C   CH2   0  -0.169   5.5534  -2.8197   1.0879
 5M6  C25  C   CH2   0  -0.482   6.7203  -2.9445   0.1251
 5M6  H1   H   HCR5  0   0.279   1.2806   3.8969  -0.0023
 5M6  H2   H   HCR6  0   0.288  -4.6388   0.9708   1.1495
 5M6  H3   H   HCR6  0   0.291  -3.0615  -3.0448  -1.2613
 5M6  H4   H   HCH3  0   0.256  -1.5349   5.1872   1.2721
 5M6  H5   H   HCH3  0   0.258  -1.8014   5.3817  -0.4524
 5M6  H6   H   HCH3  0   0.258  -3.1616   4.9953   0.6079
 5M6  H8   H   HCH2  0   0.241   7.2172  -0.8458  -0.0458
 5M6  H9   H   HNH1  0   0.397   2.9236  -0.2515   0.3220
 5M6  H10  H   HCR6  0   0.282  -1.6960  -1.0296  -1.2646
 5M6  H11  H   HCH2  0   0.256   5.3387   0.8220  -0.9881
 5M6  H12  H   HCH2  0   0.241   5.3846   0.4158   0.7234
 5M6  H13  H   HCH1  0   0.235   4.7043  -1.4766  -1.5727
 5M6  H14  H   HCR6  0   0.289  -6.0331  -1.0482   1.0990
 5M6  H15  H   HCH2  0   0.205   5.8463  -2.2470   1.9772
 5M6  H16  H   HCH2  0   0.233   5.1537  -3.7783   1.4220
 5M6  H17  H   HCH2  0   0.238   6.5582  -3.7711  -0.5698
 5M6  H18  H   HCH2  0   0.247   7.6702  -3.1096   0.6325
 5M6  H7   H   HCH2  0   0.258   7.0618  -1.6394  -1.6099

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
 5M6  C23  C25  single    1.518  0.020  1.518
 5M6  C23  O13  single    1.419  0.020  1.419
 5M6  C25  C24  single    1.526  0.020  1.526
 5M6  C24  C18  single    1.535  0.020  1.535
 5M6  O13  C18  single    1.425  0.020  1.425
 5M6  C18  C16  single    1.519  0.020  1.519
 5M6  C16  N11  single    1.446  0.020  1.446
 5M6  N11  C9   single    1.345  0.020  1.345
 5M6  C22  C8   single    1.486  0.020  1.486
 5M6  C7   C6   aromatic  1.360  0.020  1.360
 5M6  C7   C2   aromatic  1.419  0.020  1.419
 5M6  C9   O12  double    1.223  0.020  1.223
 5M6  C9   C6   single    1.478  0.020  1.478
 5M6  C6   S5   aromatic  1.760  0.020  1.760
 5M6  C2   C8   aromatic  1.421  0.020  1.421
 5M6  C2   C1   aromatic  1.382  0.020  1.382
 5M6  C8   N4   aromatic  1.312  0.020  1.312
 5M6  N4   N3   aromatic  1.354  0.020  1.354
 5M6  C1   S5   aromatic  1.712  0.020  1.712
 5M6  C1   N3   aromatic  1.348  0.020  1.348
 5M6  N3   C10  single    1.401  0.020  1.401
 5M6  C10  C15  aromatic  1.392  0.020  1.392
 5M6  C10  C14  aromatic  1.390  0.020  1.390
 5M6  C15  C19  aromatic  1.384  0.020  1.384
 5M6  C14  C20  aromatic  1.386  0.020  1.386
 5M6  C19  C17  aromatic  1.387  0.020  1.387
 5M6  C20  C17  aromatic  1.385  0.020  1.385
 5M6  C17  CL1  single    1.731  0.020  1.731
 5M6  C7   H1   single    0.930  0.020  1.080
 5M6  C15  H2   single    0.930  0.020  1.080
 5M6  C20  H3   single    0.930  0.020  1.080
 5M6  C22  H4   single    0.970  0.020  1.090
 5M6  C22  H5   single    0.970  0.020  1.090
 5M6  C22  H6   single    0.970  0.020  1.090
 5M6  C24  H7   single    0.970  0.020  1.090
 5M6  C24  H8   single    0.970  0.020  1.090
 5M6  N11  H9   single    0.860  0.020  1.020
 5M6  C14  H10  single    0.930  0.020  1.080
 5M6  C16  H11  single    0.970  0.020  1.090
 5M6  C16  H12  single    0.970  0.020  1.090
 5M6  C18  H13  single    0.970  0.020  1.090
 5M6  C19  H14  single    0.930  0.020  1.080
 5M6  C23  H15  single    0.970  0.020  1.090
 5M6  C23  H16  single    0.970  0.020  1.090
 5M6  C25  H17  single    0.970  0.020  1.090
 5M6  C25  H18  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
 5M6  N4   N3   C1   109.97  3.000
 5M6  C1   N3   C10  129.34  3.000
 5M6  N4   N3   C10  120.68  3.000
 5M6  C9   C6   S5   121.94  3.000
 5M6  S5   C6   C7   113.05  3.000
 5M6  C9   C6   C7   125.01  3.000
 5M6  H1   C7   C2   125.29  3.000
 5M6  H1   C7   C6   122.96  3.000
 5M6  C2   C7   C6   111.74  3.000
 5M6  N4   C8   C2   109.90  3.000
 5M6  N4   C8   C22  122.02  3.000
 5M6  C2   C8   C22  128.08  3.000
 5M6  C14  C10  C15  120.00  3.000
 5M6  C14  C10  N3   120.17  3.000
 5M6  C15  C10  N3   119.83  3.000
 5M6  H2   C15  C19  119.67  3.000
 5M6  H2   C15  C10  120.41  3.000
 5M6  C19  C15  C10  119.92  3.000
 5M6  CL1  C17  C19  119.63  3.000
 5M6  CL1  C17  C20  119.63  3.000
 5M6  C19  C17  C20  120.74  3.000
 5M6  H3   C20  C14  119.67  3.000
 5M6  H3   C20  C17  120.79  3.000
 5M6  C14  C20  C17  119.54  3.000
 5M6  H6   C22  H5   108.44  3.000
 5M6  H6   C22  H4   108.46  3.000
 5M6  H5   C22  H4   107.23  3.000
 5M6  H6   C22  C8   111.01  3.000
 5M6  H5   C22  C8   110.86  3.000
 5M6  H4   C22  C8   110.71  3.000
 5M6  H8   C24  H7   107.57  3.000
 5M6  H8   C24  C25  110.24  3.000
 5M6  H7   C24  C25  113.28  3.000
 5M6  H8   C24  C18  110.53  3.000
 5M6  H7   C24  C18  111.95  3.000
 5M6  C25  C24  C18  103.27  3.000
 5M6  S5   C1   C2   113.46  3.000
 5M6  S5   C1   N3   138.53  3.000
 5M6  C2   C1   N3   108.00  3.000
 5M6  C1   C2   C8   104.39  3.000
 5M6  C1   C2   C7   112.22  3.000
 5M6  C8   C2   C7   143.37  3.000
 5M6  C8   N4   N3   107.75  3.000
 5M6  C1   S5   C6    89.52  3.000
 5M6  O12  C9   N11  123.65  3.000
 5M6  O12  C9   C6   120.25  3.000
 5M6  N11  C9   C6   116.10  3.000
 5M6  H9   N11  C16  115.70  3.000
 5M6  H9   N11  C9   119.23  3.000
 5M6  C16  N11  C9   122.81  3.000
 5M6  C23  O13  C18  109.47  3.000
 5M6  H10  C14  C20  118.31  3.000
 5M6  H10  C14  C10  121.57  3.000
 5M6  C20  C14  C10  120.09  3.000
 5M6  H12  C16  H11  107.21  3.000
 5M6  H12  C16  C18  109.91  3.000
 5M6  H11  C16  C18  108.98  3.000
 5M6  H12  C16  N11  110.78  3.000
 5M6  H11  C16  N11  108.96  3.000
 5M6  C18  C16  N11  110.90  3.000
 5M6  H13  C18  C16  108.86  3.000
 5M6  H13  C18  O13  107.56  3.000
 5M6  C16  C18  O13  110.45  3.000
 5M6  H13  C18  C24  111.15  3.000
 5M6  C16  C18  C24  111.99  3.000
 5M6  O13  C18  C24  106.72  3.000
 5M6  H14  C19  C17  120.60  3.000
 5M6  H14  C19  C15  119.68  3.000
 5M6  C17  C19  C15  119.71  3.000
 5M6  H16  C23  H15  107.94  3.000
 5M6  H16  C23  C25  113.81  3.000
 5M6  H15  C23  C25  110.59  3.000
 5M6  H16  C23  O13  108.54  3.000
 5M6  H15  C23  O13  111.16  3.000
 5M6  C25  C23  O13  104.79  3.000
 5M6  H18  C25  H17  108.13  3.000
 5M6  H18  C25  C23  112.78  3.000
 5M6  H17  C25  C23  110.60  3.000
 5M6  H18  C25  C24  113.03  3.000
 5M6  H17  C25  C24  110.90  3.000
 5M6  C23  C25  C24  101.34  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
 5M6  CONST_01  C2   C8   N4   N3      0.00   0.0  0
 5M6  CONST_02  C7   C2   C1   N3    180.00   0.0  0
 5M6  CONST_03  C8   C2   C1   N3      0.00   0.0  0
 5M6  CONST_04  C6   S5   C1   N3    180.00   0.0  0
 5M6  CONST_05  C19  C15  C10  N3    180.00   0.0  0
 5M6  CONST_06  C20  C14  C10  N3    180.00   0.0  0
 5M6  CONST_07  C8   C2   C7   C6    180.00   0.0  0
 5M6  CONST_08  C1   C2   C7   C6      0.00   0.0  0
 5M6  CONST_09  C2   C1   S5   C6      0.00   0.0  0
 5M6  CONST_10  C1   S5   C6   C7      0.00   0.0  0
 5M6  CONST_11  N4   C8   C2   C7    180.00   0.0  0
 5M6  CONST_12  S5   C1   C2   C7      0.00   0.0  0
 5M6  CONST_13  S5   C1   C2   C8    180.00   0.0  0
 5M6  CONST_14  C1   N3   N4   C8      0.00   0.0  0
 5M6  CONST_15  C10  N3   N4   C8    180.00   0.0  0
 5M6  CONST_16  C2   C1   N3   C10   180.00   0.0  0
 5M6  CONST_17  S5   C1   N3   C10     0.00   0.0  0
 5M6  CONST_18  C17  C19  C15  C10     0.00   0.0  0
 5M6  CONST_19  C17  C20  C14  C10     0.00   0.0  0
 5M6  CONST_22  C20  C14  C10  C15     0.00   0.0  0
 5M6  CONST_23  C20  C17  C19  C15     0.00   0.0  0
 5M6  CONST_24  N4   C8   C2   C1      0.00   0.0  0
 5M6  CONST_26  S5   C6   C7   C2      0.00   0.0  0
 5M6  CONST_27  N4   N3   C1   C2      0.00   0.0  0
 5M6  CONST_28  S5   C1   N3   N4    180.00   0.0  0
 5M6  CONST_30  C19  C15  C10  C14     0.00   0.0  0
 5M6  CONST_31  C19  C17  C20  C14     0.00   0.0  0
 5M6  CONST_32  C22  C8   N4   N3    180.00   0.0  0
 5M6  CONST_33  C22  C8   C2   C7      0.00   0.0  0
 5M6  CONST_34  CL1  C17  C19  C15   180.00   0.0  0
 5M6  CONST_35  C1   C2   C8   C22   180.00   0.0  0
 5M6  CONST_36  C9   C6   S5   C1    180.00   0.0  0
 5M6  CONST_37  C9   C6   C7   C2    180.00   0.0  0
 5M6  CONST_38  CL1  C17  C20  C14   180.00   0.0  0
 5M6  CONST_39  H2   C15  C10  N3      0.00   0.0  0
 5M6  CONST_40  H10  C14  C10  N3      0.00   0.0  0
 5M6  CONST_41  H1   C7   C2   C8      0.00   0.0  0
 5M6  CONST_42  H14  C19  C15  C10   180.00   0.0  0
 5M6  CONST_43  H3   C20  C14  C10   180.00   0.0  0
 5M6  CONST_44  C16  N11  C9   C6    180.00   0.0  0
 5M6  CONST_46  C16  N11  C9   O12     0.00   0.0  0
 5M6  Var_01    O13  C23  C25  C24    38.12  30.0  1
 5M6  Var_02    C23  C25  C24  C18   -31.33  30.0  1
 5M6  Var_03    C25  C23  O13  C18   -30.46  30.0  1
 5M6  Var_04    N11  C9   C6   C7    161.68  30.0  2
 5M6  Var_05    H4   C22  C8   C2    -56.64  30.0  2
 5M6  Var_06    C18  C16  N11  C9   -153.13  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
 5M6  chir_01  C18  C24  O13  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
 5M6  plan-1  N3   0.020
 5M6  plan-1  C10  0.020
 5M6  plan-1  C15  0.020
 5M6  plan-1  C17  0.020
 5M6  plan-1  C20  0.020
 5M6  plan-1  C14  0.020
 5M6  plan-1  C19  0.020
 5M6  plan-1  CL1  0.020
 5M6  plan-1  H2   0.020
 5M6  plan-1  H3   0.020
 5M6  plan-1  H10  0.020
 5M6  plan-1  H14  0.020
 5M6  plan-2  N3   0.020
 5M6  plan-2  C6   0.020
 5M6  plan-2  C7   0.020
 5M6  plan-2  C8   0.020
 5M6  plan-2  C10  0.020
 5M6  plan-2  C22  0.020
 5M6  plan-2  C1   0.020
 5M6  plan-2  C2   0.020
 5M6  plan-2  N4   0.020
 5M6  plan-2  S5   0.020
 5M6  plan-2  C9   0.020
 5M6  plan-2  H1   0.020
 5M6  plan-3  C6   0.020
 5M6  plan-3  C9   0.020
 5M6  plan-3  N11  0.020
 5M6  plan-3  O12  0.020
 5M6  plan-3  C16  0.020
 5M6  plan-3  H9   0.020

