# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:09:47 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc(cc1)C(=O)NCc2cnn(C)c2
#
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
 B0Y  B0Y  5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide  ligand  32  17  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B0Y
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
 B0Y  N1   N  NH1   0  -0.662  -0.5842  -1.0255  -0.1075
 B0Y  N3   N  NR5   0  -0.261  -4.3852   1.1355  -0.2779
 B0Y  C4   C  CR15  0  -0.220   4.1247  -0.9406   0.0481
 B0Y  C5   C  CR15  0  -0.170   3.0165  -1.8089  -0.0934
 B0Y  C6   C  CR5   0  -0.323   1.8166  -1.1626  -0.0063
 B0Y  C7   C  C     0   0.558   0.4976  -1.8201  -0.1103
 B0Y  C8   C  CH2   0  -0.333  -1.9334  -1.5579  -0.2162
 B0Y  C10  C  CR15  0  -0.063  -3.3925   0.0475   1.2286
 B0Y  C1   C  CH3   0  -0.658   4.5541   2.5649  -0.7072
 B0Y  C3   C  CR5   0  -0.128   3.7701   0.3630   0.2486
 B0Y  S1   S  S2    0   0.218   2.0565   0.5277   0.2604
 B0Y  O1   O  O     0  -0.495   0.4176  -3.0404  -0.1881
 B0Y  C9   C  CR5   0  -0.206  -2.9357  -0.4790   0.0077
 B0Y  N2   N  N     0  -0.288  -4.2668   1.0182   1.0410
 B0Y  C11  C  CR15  0   0.037  -3.6086   0.2626  -0.9398
 B0Y  H1   H  HNH1  0   0.403  -0.4886  -0.0229  -0.1349
 B0Y  H2   H  HCR5  0   0.266   5.1552  -1.2654   0.0068
 B0Y  H3   H  HCR5  0   0.270   3.1015  -2.8739  -0.2548
 B0Y  H4   H  HCH2  0   0.254  -2.0828  -2.0118  -1.1991
 B0Y  H5   H  HCH2  0   0.257  -2.0639  -2.3509   0.5225
 B0Y  H6   H  HCR5  0   0.259  -3.1133  -0.2533   2.2280
 B0Y  H7   H  HCH3  0   0.233   4.8004   2.1085  -1.6658
 B0Y  H8   H  HCH3  0   0.227   3.5490   2.9815  -0.7810
 B0Y  H9   H  HCH3  0   0.240   5.2430   3.3922  -0.5386
 B0Y  H10  H  HCH2  0   0.258   5.6847   1.1838   0.5037
 B0Y  H11  H  HCH2  0   0.258   4.4356   2.0389   1.3796
 B0Y  H12  H  HCR5  0   0.293  -3.5865   0.2210  -2.0174
 B0Y  H13  H  HCH3  0   0.261  -5.0175   3.1114  -0.5054
 B0Y  H14  H  HCH3  0   0.258  -5.2168   2.0732  -1.9236
 B0Y  H15  H  HCH3  0   0.260  -6.3120   1.8993  -0.5448
 B0Y  C12  C  CH3   0  -0.506  -5.2865   2.1120  -0.8406
 B0Y  C2   C  CH2   0  -0.499   4.6592   1.5494   0.4286

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
 B0Y  C2   C1   single    1.527  0.020  1.527
 B0Y  C2   C3   single    1.493  0.020  1.493
 B0Y  C3   S1   aromatic  1.722  0.020  1.722
 B0Y  C3   C4   aromatic  1.366  0.020  1.366
 B0Y  S1   C6   aromatic  1.728  0.020  1.728
 B0Y  C4   C5   aromatic  1.415  0.020  1.415
 B0Y  C5   C6   aromatic  1.366  0.020  1.366
 B0Y  C6   C7   single    1.477  0.020  1.477
 B0Y  C7   O1   double    1.225  0.020  1.225
 B0Y  C7   N1   single    1.342  0.020  1.342
 B0Y  N1   C8   single    1.455  0.020  1.455
 B0Y  C8   C9   single    1.490  0.020  1.490
 B0Y  C9   C11  aromatic  1.379  0.020  1.379
 B0Y  C9   C10  aromatic  1.406  0.020  1.406
 B0Y  C11  N3   aromatic  1.343  0.020  1.343
 B0Y  C10  N2   aromatic  1.320  0.020  1.320
 B0Y  N3   N2   aromatic  1.329  0.020  1.329
 B0Y  N3   C12  single    1.443  0.020  1.443
 B0Y  N1   H1   single    0.860  0.020  1.020
 B0Y  C4   H2   single    0.930  0.020  1.080
 B0Y  C5   H3   single    0.930  0.020  1.080
 B0Y  C8   H4   single    0.970  0.020  1.090
 B0Y  C8   H5   single    0.970  0.020  1.090
 B0Y  C10  H6   single    0.930  0.020  1.080
 B0Y  C1   H7   single    0.970  0.020  1.090
 B0Y  C1   H8   single    0.970  0.020  1.090
 B0Y  C1   H9   single    0.970  0.020  1.090
 B0Y  C2   H10  single    0.970  0.020  1.090
 B0Y  C2   H11  single    0.970  0.020  1.090
 B0Y  C11  H12  single    0.930  0.020  1.080
 B0Y  C12  H13  single    0.970  0.020  1.090
 B0Y  C12  H14  single    0.970  0.020  1.090
 B0Y  C12  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
 B0Y  H1   N1   C8   116.76  3.000
 B0Y  H1   N1   C7   120.84  3.000
 B0Y  C8   N1   C7   122.05  3.000
 B0Y  C12  N3   C11  127.50  3.000
 B0Y  C12  N3   N2   120.14  3.000
 B0Y  C11  N3   N2   112.35  3.000
 B0Y  H2   C4   C3   122.67  3.000
 B0Y  H2   C4   C5   123.94  3.000
 B0Y  C3   C4   C5   113.39  3.000
 B0Y  H3   C5   C6   123.03  3.000
 B0Y  H3   C5   C4   123.93  3.000
 B0Y  C6   C5   C4   113.04  3.000
 B0Y  S1   C6   C7   124.76  3.000
 B0Y  C7   C6   C5   124.70  3.000
 B0Y  S1   C6   C5   110.54  3.000
 B0Y  O1   C7   C6   120.39  3.000
 B0Y  O1   C7   N1   122.49  3.000
 B0Y  C6   C7   N1   117.12  3.000
 B0Y  H5   C8   H4   106.89  3.000
 B0Y  H5   C8   C9   110.13  3.000
 B0Y  H4   C8   C9   110.12  3.000
 B0Y  H5   C8   N1   109.04  3.000
 B0Y  H4   C8   N1   110.24  3.000
 B0Y  C9   C8   N1   110.35  3.000
 B0Y  H6   C10  N2   120.50  3.000
 B0Y  H6   C10  C9   127.96  3.000
 B0Y  N2   C10  C9   111.54  3.000
 B0Y  H9   C1   H8   107.65  3.000
 B0Y  H9   C1   H7   108.13  3.000
 B0Y  H8   C1   H7   107.98  3.000
 B0Y  H9   C1   C2   110.26  3.000
 B0Y  H8   C1   C2   111.58  3.000
 B0Y  H7   C1   C2   111.11  3.000
 B0Y  S1   C3   C2   121.05  3.000
 B0Y  S1   C3   C4   110.53  3.000
 B0Y  C2   C3   C4   128.42  3.000
 B0Y  C3   S1   C6    92.50  3.000
 B0Y  C11  C9   C10  103.70  3.000
 B0Y  C10  C9   C8   128.34  3.000
 B0Y  C11  C9   C8   127.94  3.000
 B0Y  C10  N2   N3   105.36  3.000
 B0Y  H12  C11  C9   130.99  3.000
 B0Y  H12  C11  N3   121.96  3.000
 B0Y  C9   C11  N3   107.05  3.000
 B0Y  H15  C12  H14  108.94  3.000
 B0Y  H15  C12  H13  109.20  3.000
 B0Y  H14  C12  H13  108.92  3.000
 B0Y  H15  C12  N3   110.51  3.000
 B0Y  H14  C12  N3   108.94  3.000
 B0Y  H13  C12  N3   110.30  3.000
 B0Y  H11  C2   H10  106.41  3.000
 B0Y  H11  C2   C3   109.81  3.000
 B0Y  H10  C2   C3   107.55  3.000
 B0Y  H11  C2   C1   109.60  3.000
 B0Y  H10  C2   C1   109.79  3.000
 B0Y  C3   C2   C1   113.43  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
 B0Y  CONST_01  C10  C9   C11  N3     0.00   0.0  0
 B0Y  CONST_02  C9   C10  N2   N3     0.00   0.0  0
 B0Y  CONST_03  C6   S1   C3   C4     0.00   0.0  0
 B0Y  CONST_04  S1   C6   C5   C4     0.00   0.0  0
 B0Y  CONST_05  S1   C3   C4   C5     0.00   0.0  0
 B0Y  CONST_06  C3   S1   C6   C5     0.00   0.0  0
 B0Y  CONST_07  C3   C4   C5   C6     0.00   0.0  0
 B0Y  CONST_08  C11  N3   N2   C10    0.00   0.0  0
 B0Y  CONST_09  N2   N3   C11  C9     0.00   0.0  0
 B0Y  CONST_10  C11  C9   C10  N2     0.00   0.0  0
 B0Y  CONST_11  C8   C9   C11  N3   180.00   0.0  0
 B0Y  CONST_12  C7   C6   C5   C4   180.00   0.0  0
 B0Y  CONST_13  C2   C3   C4   C5   180.00   0.0  0
 B0Y  CONST_14  C2   C3   S1   C6   180.00   0.0  0
 B0Y  CONST_15  C3   S1   C6   C7   180.00   0.0  0
 B0Y  CONST_16  N2   C10  C9   C8   180.00   0.0  0
 B0Y  CONST_17  C12  N3   N2   C10  180.00   0.0  0
 B0Y  CONST_18  C12  N3   C11  C9   180.00   0.0  0
 B0Y  CONST_19  H6   C10  N2   N3   180.00   0.0  0
 B0Y  CONST_20  H2   C4   C5   C6   180.00   0.0  0
 B0Y  CONST_21  H12  C11  C9   C10  180.00   0.0  0
 B0Y  CONST_22  H3   C5   C4   C3   180.00   0.0  0
 B0Y  CONST_23  C8   N1   C7   C6   180.00   0.0  0
 B0Y  CONST_24  H1   N1   C7   C6     0.00   0.0  0
 B0Y  CONST_25  O1   C7   N1   C8     0.00   0.0  0
 B0Y  Var_01    S1   C6   C7   N1     5.80  30.0  2
 B0Y  Var_02    C11  C9   C8   N1    97.26  30.0  2
 B0Y  Var_03    C1   C2   C3   C4   114.34  30.0  2
 B0Y  Var_04    H13  C12  N3   N2    58.74  30.0  2
 B0Y  Var_05    C9   C8   N1   C7   171.96  30.0  3
 B0Y  Var_06    H7   C1   C2   C3   -58.49  30.0  3

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
 B0Y  plan-1  C4   0.020
 B0Y  plan-1  C5   0.020
 B0Y  plan-1  C6   0.020
 B0Y  plan-1  C7   0.020
 B0Y  plan-1  C3   0.020
 B0Y  plan-1  S1   0.020
 B0Y  plan-1  H2   0.020
 B0Y  plan-1  H3   0.020
 B0Y  plan-1  C2   0.020
 B0Y  plan-2  N3   0.020
 B0Y  plan-2  C8   0.020
 B0Y  plan-2  C10  0.020
 B0Y  plan-2  C9   0.020
 B0Y  plan-2  N2   0.020
 B0Y  plan-2  C11  0.020
 B0Y  plan-2  H6   0.020
 B0Y  plan-2  H12  0.020
 B0Y  plan-2  C12  0.020
 B0Y  plan-3  N1   0.020
 B0Y  plan-3  C6   0.020
 B0Y  plan-3  C7   0.020
 B0Y  plan-3  C8   0.020
 B0Y  plan-3  O1   0.020
 B0Y  plan-3  H1   0.020

