# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:57:23 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-(2,5-dimethylthiophen-3-yl)-1H-pyrazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(C)c(c1)c2[nH]nc(c2)C(N)=O
#
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
 TJM  TJM  5-(2,5-dimethylthiophen-3-yl)-1H-pyrazole-3-carboxamide  ligand  26  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TJM
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
 TJM  C1    C  CH3   0  -0.715  -4.0483   2.2344   0.3771
 TJM  C2    C  CR5   0  -0.167  -3.0446   1.1493   0.1879
 TJM  C3    C  CR15  0  -0.248  -1.6933   1.2168   0.2995
 TJM  C4    C  CR5   0   0.168  -1.0328  -0.0291   0.0588
 TJM  C5    C  CR5   0  -0.245  -1.9043  -1.0406  -0.2472
 TJM  C6    C  CH3   0  -0.752  -1.6257  -2.4670  -0.5885
 TJM  S7    S  S2    0   0.223  -3.5246  -0.4575  -0.2232
 TJM  C8    C  CR5   0   0.386   0.4159  -0.1532   0.1214
 TJM  C9    C  CR15  0  -0.518   1.4077   0.7315  -0.2488
 TJM  C10   C  CR5   0   0.123   2.6056   0.0649   0.0494
 TJM  N11   N  N     0  -0.271   2.3751  -1.1319   0.5663
 TJM  N12   N  NR15  0  -0.489   1.0626  -1.2422   0.5978
 TJM  C13   C  C     0   0.466   3.9789   0.5755  -0.1674
 TJM  O14   O  O     0  -0.483   4.1588   1.6730  -0.6782
 TJM  N15   N  NH2   0  -0.809   4.9646  -0.2397   0.2270
 TJM  H11C  H  HCH3  0   0.255  -4.6238   2.4145  -0.5319
 TJM  H12C  H  HCH3  0   0.255  -4.7573   1.9986   1.1715
 TJM  H13C  H  HCH3  0   0.257  -3.5441   3.1618   0.6437
 TJM  H3    H  HCR5  0   0.262  -1.1698   2.1259   0.5641
 TJM  H61C  H  HCH3  0   0.263  -1.6080  -3.1025   0.2991
 TJM  H62C  H  HCH3  0   0.266  -2.3835  -2.8720  -1.2581
 TJM  H63C  H  HCH3  0   0.257  -0.6644  -2.5669  -1.0924
 TJM  H9    H  HCR5  0   0.273   1.2787   1.7074  -0.6860
 TJM  H12   H  HNR5  0   0.428   0.6459  -2.0652   1.0056
 TJM  H151  H  HNH2  0   0.410   4.7700  -1.1251   0.6631
 TJM  H152  H  HNH2  0   0.406   5.9267   0.0386   0.1274

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
 TJM  C1   C2    single    1.490  0.020  1.490
 TJM  C2   C3    aromatic  1.358  0.020  1.358
 TJM  C2   S7    aromatic  1.727  0.020  1.727
 TJM  C3   C4    aromatic  1.431  0.020  1.431
 TJM  C4   C5    aromatic  1.370  0.020  1.370
 TJM  C4   C8    single    1.455  0.020  1.455
 TJM  C5   C6    single    1.493  0.020  1.493
 TJM  C5   S7    aromatic  1.722  0.020  1.722
 TJM  C8   C9    aromatic  1.380  0.020  1.380
 TJM  C8   N12   aromatic  1.353  0.020  1.353
 TJM  C9   C10   aromatic  1.403  0.020  1.403
 TJM  C10  N11   aromatic  1.324  0.020  1.324
 TJM  C10  C13   single    1.481  0.020  1.481
 TJM  N11  N12   aromatic  1.318  0.020  1.318
 TJM  C13  O14   double    1.224  0.020  1.224
 TJM  C13  N15   single    1.339  0.020  1.339
 TJM  C1   H11C  single    0.970  0.020  1.090
 TJM  C1   H12C  single    0.970  0.020  1.090
 TJM  C1   H13C  single    0.970  0.020  1.090
 TJM  C3   H3    single    0.930  0.020  1.080
 TJM  C6   H61C  single    0.970  0.020  1.090
 TJM  C6   H62C  single    0.970  0.020  1.090
 TJM  C6   H63C  single    0.970  0.020  1.090
 TJM  C9   H9    single    0.930  0.020  1.080
 TJM  N12  H12   single    0.860  0.020  1.020
 TJM  N15  H151  single    0.860  0.020  1.020
 TJM  N15  H152  single    0.860  0.020  1.020

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
 TJM  H13C  C1   H12C  107.87  3.000
 TJM  H13C  C1   H11C  107.92  3.000
 TJM  H12C  C1   H11C  107.44  3.000
 TJM  H13C  C1   C2    109.84  3.000
 TJM  H12C  C1   C2    111.89  3.000
 TJM  H11C  C1   C2    111.71  3.000
 TJM  S7    C2   C3    110.04  3.000
 TJM  S7    C2   C1    121.37  3.000
 TJM  C3    C2   C1    128.59  3.000
 TJM  H3    C3   C4    123.34  3.000
 TJM  H3    C3   C2    122.93  3.000
 TJM  C4    C3   C2    113.73  3.000
 TJM  C8    C4   C5    125.45  3.000
 TJM  C8    C4   C3    121.77  3.000
 TJM  C5    C4   C3    112.77  3.000
 TJM  S7    C5   C6    120.15  3.000
 TJM  S7    C5   C4    110.21  3.000
 TJM  C6    C5   C4    129.64  3.000
 TJM  H63C  C6   H62C  107.18  3.000
 TJM  H63C  C6   H61C  107.94  3.000
 TJM  H62C  C6   H61C  107.14  3.000
 TJM  H63C  C6   C5    110.97  3.000
 TJM  H62C  C6   C5    111.47  3.000
 TJM  H61C  C6   C5    111.92  3.000
 TJM  C5    S7   C2     93.26  3.000
 TJM  N12   C8   C9    105.48  3.000
 TJM  N12   C8   C4    124.02  3.000
 TJM  C9    C8   C4    130.50  3.000
 TJM  H9    C9   C10   128.25  3.000
 TJM  H9    C9   C8    127.14  3.000
 TJM  C10   C9   C8    104.60  3.000
 TJM  C13   C10  N11   122.03  3.000
 TJM  C13   C10  C9    126.63  3.000
 TJM  N11   C10  C9    111.34  3.000
 TJM  N12   N11  C10   104.98  3.000
 TJM  H12   N12  N11   119.30  3.000
 TJM  H12   N12  C8    126.99  3.000
 TJM  N11   N12  C8    113.60  3.000
 TJM  N15   C13  O14   124.11  3.000
 TJM  N15   C13  C10   115.44  3.000
 TJM  O14   C13  C10   120.44  3.000
 TJM  H152  N15  H151  118.12  3.000
 TJM  H152  N15  C13   120.42  3.000
 TJM  H151  N15  C13   121.42  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
 TJM  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 TJM  CONST_02  C8    C4   C3   C2   180.00   0.0  0
 TJM  CONST_03  C4    C5   S7   C2     0.00   0.0  0
 TJM  CONST_04  C5    S7   C2   C3     0.00   0.0  0
 TJM  CONST_05  S7    C5   C4   C3     0.00   0.0  0
 TJM  CONST_08  S7    C2   C3   C4     0.00   0.0  0
 TJM  CONST_09  C10   C9   C8   C4   180.00   0.0  0
 TJM  CONST_10  N11   N12  C8   C4   180.00   0.0  0
 TJM  CONST_13  C8    C4   C5   S7   180.00   0.0  0
 TJM  CONST_14  N11   C10  C9   C8     0.00   0.0  0
 TJM  CONST_15  C10   N11  N12  C8     0.00   0.0  0
 TJM  CONST_16  N11   N12  C8   C9     0.00   0.0  0
 TJM  CONST_17  N12   N11  C10  C9     0.00   0.0  0
 TJM  CONST_18  N12   C8   C9   C10    0.00   0.0  0
 TJM  CONST_19  C4    C3   C2   C1   180.00   0.0  0
 TJM  CONST_20  C5    S7   C2   C1   180.00   0.0  0
 TJM  CONST_21  C6    C5   S7   C2   180.00   0.0  0
 TJM  CONST_22  C6    C5   C4   C3   180.00   0.0  0
 TJM  CONST_23  C8    C4   C5   C6     0.00   0.0  0
 TJM  CONST_24  C13   C10  C9   C8   180.00   0.0  0
 TJM  CONST_25  C13   C10  N11  N12  180.00   0.0  0
 TJM  CONST_26  H9    C9   C8   C4     0.00   0.0  0
 TJM  CONST_27  H12   N12  C8   C4     0.00   0.0  0
 TJM  CONST_28  H3    C3   C4   C5   180.00   0.0  0
 TJM  CONST_29  H151  N15  C13  C10    0.00   0.0  0
 TJM  CONST_30  H152  N15  C13  C10  180.00   0.0  0
 TJM  Var_01    O14   C13  C10  C9    -1.53  30.0  2
 TJM  Var_02    H11C  C1   C2   C3   119.24  30.0  2
 TJM  Var_03    H61C  C6   C5   C4    89.98  30.0  2

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
 TJM  plan-1  C1    0.020
 TJM  plan-1  C2    0.020
 TJM  plan-1  C3    0.020
 TJM  plan-1  C4    0.020
 TJM  plan-1  C5    0.020
 TJM  plan-1  C6    0.020
 TJM  plan-1  S7    0.020
 TJM  plan-1  C8    0.020
 TJM  plan-1  H3    0.020
 TJM  plan-2  C4    0.020
 TJM  plan-2  C8    0.020
 TJM  plan-2  C9    0.020
 TJM  plan-2  C10   0.020
 TJM  plan-2  N11   0.020
 TJM  plan-2  N12   0.020
 TJM  plan-2  C13   0.020
 TJM  plan-2  H9    0.020
 TJM  plan-2  H12   0.020
 TJM  plan-3  C10   0.020
 TJM  plan-3  C13   0.020
 TJM  plan-3  O14   0.020
 TJM  plan-3  N15   0.020
 TJM  plan-3  H151  0.020
 TJM  plan-3  H152  0.020

