# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:29:51 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 1-methyl-N-[(thiophen-2-yl)methyl]-1H-pyrazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nccc1C(=O)NCc2sccc2
#
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
 JO1  JO1  1-methyl-N-[(thiophen-2-yl)methyl]-1H-pyrazole-5-carboxamide  ligand  26  15  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JO1
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
 JO1  C10   C  CH2   0  -0.342  -1.1186  -0.7809  -1.7056
 JO1  C13   C  CR15  0  -0.176  -4.2573   0.1351   0.1903
 JO1  C01   C  CH3   0  -0.521   3.0259  -0.7031   1.7696
 JO1  C03   C  CR5   0   0.392   2.3014   0.1706  -0.4993
 JO1  C04   C  CR15  0  -0.532   2.8384   1.1005  -1.3694
 JO1  C05   C  CR15  0  -0.072   4.0150   1.5200  -0.7466
 JO1  C07   C  C     0   0.499   1.0664  -0.6340  -0.6248
 JO1  C11   C  CR5   0  -0.198  -2.2145  -0.5020  -0.7238
 JO1  C12   C  CR15  0  -0.187  -3.4501   0.0114  -0.9801
 JO1  C14   C  CR15  0  -0.472  -3.6224  -0.2936   1.3150
 JO1  N02   N  NR5   0  -0.391   3.1477   0.0803   0.5542
 JO1  N06   N  N     0  -0.219   4.1887   0.8911   0.4096
 JO1  N09   N  NH1   0  -0.615   0.1221  -0.1036  -1.4001
 JO1  O08   O  O     0  -0.461   0.9381  -1.7176  -0.0496
 JO1  S15   S  S2    0   0.227  -2.0392  -0.8627   0.9571
 JO1  H102  H  HCH2  0   0.225  -0.9295  -1.8530  -1.7613
 JO1  H101  H  HCH2  0   0.258  -1.4447  -0.4594  -2.6931
 JO1  H131  H  HCR5  0   0.261  -5.2653   0.5275   0.1874
 JO1  H012  H  HCH3  0   0.227   3.2366  -1.7544   1.5854
 JO1  H011  H  HCH3  0   0.284   3.7510  -0.3222   2.4821
 JO1  H013  H  HCH3  0   0.294   2.0289  -0.6005   2.1873
 JO1  H041  H  HCR5  0   0.273   2.4249   1.4382  -2.3057
 JO1  H051  H  HCR5  0   0.262   4.7272   2.2575  -1.0858
 JO1  H121  H  HCR5  0   0.275  -3.7664   0.3151  -1.9697
 JO1  H141  H  HCR5  0   0.298  -3.9885  -0.3123   2.3312
 JO1  H091  H  HNH1  0   0.410   0.2333   0.8372  -1.7539

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
 JO1  C10  C11   single    1.498  0.020  1.498
 JO1  C10  N09   single    1.446  0.020  1.446
 JO1  O08  C07   double    1.233  0.020  1.233
 JO1  C11  S15   aromatic  1.728  0.020  1.728
 JO1  C11  C12   aromatic  1.362  0.020  1.362
 JO1  S15  C14   aromatic  1.720  0.020  1.720
 JO1  N09  C07   single    1.332  0.020  1.332
 JO1  C07  C03   single    1.479  0.020  1.479
 JO1  C12  C13   aromatic  1.427  0.020  1.427
 JO1  C14  C13   aromatic  1.361  0.020  1.361
 JO1  C03  C04   aromatic  1.382  0.020  1.382
 JO1  C03  N02   aromatic  1.354  0.020  1.354
 JO1  C04  C05   aromatic  1.396  0.020  1.396
 JO1  C01  N02   single    1.451  0.020  1.451
 JO1  N02  N06   aromatic  1.327  0.020  1.327
 JO1  C05  N06   aromatic  1.328  0.020  1.328
 JO1  C10  H102  single    0.970  0.020  1.090
 JO1  C10  H101  single    0.970  0.020  1.090
 JO1  C13  H131  single    0.930  0.020  1.080
 JO1  C01  H012  single    0.970  0.020  1.090
 JO1  C01  H011  single    0.970  0.020  1.090
 JO1  C01  H013  single    0.970  0.020  1.090
 JO1  C04  H041  single    0.930  0.020  1.080
 JO1  C05  H051  single    0.930  0.020  1.080
 JO1  C12  H121  single    0.930  0.020  1.080
 JO1  C14  H141  single    0.930  0.020  1.080
 JO1  N09  H091  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
 JO1  H101  C10  H102  107.22  3.000
 JO1  H101  C10  N09   108.08  3.000
 JO1  H102  C10  N09   108.82  3.000
 JO1  H101  C10  C11   108.69  3.000
 JO1  H102  C10  C11   110.10  3.000
 JO1  N09   C10  C11   113.71  3.000
 JO1  H131  C13  C14   123.45  3.000
 JO1  H131  C13  C12   123.81  3.000
 JO1  C14   C13  C12   112.74  3.000
 JO1  H013  C01  H011  109.13  3.000
 JO1  H013  C01  H012  109.53  3.000
 JO1  H011  C01  H012  108.71  3.000
 JO1  H013  C01  N02   110.39  3.000
 JO1  H011  C01  N02   107.71  3.000
 JO1  H012  C01  N02   111.32  3.000
 JO1  N02   C03  C07   123.46  3.000
 JO1  N02   C03  C04   106.96  3.000
 JO1  C07   C03  C04   129.56  3.000
 JO1  H041  C04  C05   128.09  3.000
 JO1  H041  C04  C03   127.49  3.000
 JO1  C05   C04  C03   104.41  3.000
 JO1  H051  C05  N06   120.72  3.000
 JO1  H051  C05  C04   128.39  3.000
 JO1  N06   C05  C04   110.88  3.000
 JO1  O08   C07  N09   123.20  3.000
 JO1  N09   C07  C03   115.13  3.000
 JO1  O08   C07  C03   121.67  3.000
 JO1  S15   C11  C12   110.71  3.000
 JO1  C12   C11  C10   127.63  3.000
 JO1  S15   C11  C10   121.63  3.000
 JO1  H121  C12  C11   122.88  3.000
 JO1  H121  C12  C13   124.06  3.000
 JO1  C11   C12  C13   113.04  3.000
 JO1  H141  C14  S15   120.13  3.000
 JO1  H141  C14  C13   128.67  3.000
 JO1  S15   C14  C13   111.20  3.000
 JO1  N06   N02  C03   111.38  3.000
 JO1  N06   N02  C01   119.13  3.000
 JO1  C03   N02  C01   129.42  3.000
 JO1  N02   N06  C05   106.36  3.000
 JO1  H091  N09  C07   119.75  3.000
 JO1  H091  N09  C10   117.14  3.000
 JO1  C07   N09  C10   123.00  3.000
 JO1  C14   S15  C11    92.29  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
 JO1  CONST_01  S15   C11  C12  C13    0.00   0.0  0
 JO1  CONST_02  C11   S15  C14  C13    0.00   0.0  0
 JO1  CONST_03  N06   C05  C04  C03    0.00   0.0  0
 JO1  CONST_04  C05   N06  N02  C03    0.00   0.0  0
 JO1  CONST_05  N06   N02  C03  C04    0.00   0.0  0
 JO1  CONST_06  N02   N06  C05  C04    0.00   0.0  0
 JO1  CONST_07  N02   C03  C04  C05    0.00   0.0  0
 JO1  CONST_08  C14   C13  C12  C11    0.00   0.0  0
 JO1  CONST_09  C14   S15  C11  C12    0.00   0.0  0
 JO1  CONST_10  S15   C14  C13  C12    0.00   0.0  0
 JO1  CONST_11  C14   S15  C11  C10  180.00   0.0  0
 JO1  CONST_12  C13   C12  C11  C10  180.00   0.0  0
 JO1  CONST_13  C04   C03  N02  C01  180.00   0.0  0
 JO1  CONST_14  C05   N06  N02  C01  180.00   0.0  0
 JO1  CONST_15  C07   C03  C04  C05  180.00   0.0  0
 JO1  CONST_16  N06   N02  C03  C07  180.00   0.0  0
 JO1  CONST_17  H051  C05  C04  C03  180.00   0.0  0
 JO1  CONST_18  H141  C14  S15  C11  180.00   0.0  0
 JO1  CONST_19  H131  C13  C12  C11  180.00   0.0  0
 JO1  CONST_20  H121  C12  C13  C14  180.00   0.0  0
 JO1  CONST_21  H041  C04  C03  N02  180.00   0.0  0
 JO1  CONST_22  C03   C07  N09  C10  180.00   0.0  0
 JO1  CONST_23  H091  N09  C07  C03    0.00   0.0  0
 JO1  CONST_24  O08   C07  N09  C10    0.00   0.0  0
 JO1  Var_01    O08   C07  C03  C04  154.19  30.0  2
 JO1  Var_02    N09   C10  C11  C12  123.08  30.0  2
 JO1  Var_03    H012  C01  N02  C03   75.76  30.0  2
 JO1  Var_04    C11   C10  N09  C07   89.44  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
 JO1  plan-1  C01   0.020
 JO1  plan-1  C03   0.020
 JO1  plan-1  C04   0.020
 JO1  plan-1  C05   0.020
 JO1  plan-1  C07   0.020
 JO1  plan-1  N02   0.020
 JO1  plan-1  N06   0.020
 JO1  plan-1  H041  0.020
 JO1  plan-1  H051  0.020
 JO1  plan-2  C10   0.020
 JO1  plan-2  C13   0.020
 JO1  plan-2  C11   0.020
 JO1  plan-2  C12   0.020
 JO1  plan-2  C14   0.020
 JO1  plan-2  S15   0.020
 JO1  plan-2  H131  0.020
 JO1  plan-2  H121  0.020
 JO1  plan-2  H141  0.020
 JO1  plan-3  C10   0.020
 JO1  plan-3  C03   0.020
 JO1  plan-3  C07   0.020
 JO1  plan-3  N09   0.020
 JO1  plan-3  O08   0.020
 JO1  plan-3  H091  0.020

