# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:03:46 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)C(=O)NCc2ccc(Cl)cc2
#
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
 LJD  LJD  N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazole-4-carboxamide  ligand  29  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LJD
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
 LJD  N1   N   NR5   0  -0.265   4.7967   0.8467   0.2037
 LJD  N3   N   NH1   0  -0.645   0.7925  -0.9916  -0.9225
 LJD  C4   C   CR15  0  -0.067   3.2032   0.7675  -1.1750
 LJD  C5   C   C     0   0.511   1.7589  -1.0761   0.0123
 LJD  C6   C   CH2   0  -0.393  -0.4224  -1.7753  -0.8996
 LJD  C7   C   CR6   0   0.138  -1.5900  -1.0200  -0.3153
 LJD  C8   C   CR16  0  -0.301  -1.6429  -0.7356   1.0480
 LJD  C10  C   CR6   0  -0.052  -3.7177   0.4149   0.7499
 LJD  C1   C   CH3   0  -0.507   6.0457   1.3071   0.7631
 LJD  C11  C   CR16  0  -0.198  -3.6925   0.1440  -0.6072
 LJD  C12  C   CR16  0  -0.311  -2.6240  -0.5740  -1.1292
 LJD  C2   C   CR15  0   0.088   3.9706  -0.0751   0.7039
 LJD  C3   C   CR5   0  -0.285   2.9002  -0.1686  -0.1660
 LJD  C9   C   CR16  0  -0.198  -2.6998  -0.0201   1.5871
 LJD  N2   N   N     0  -0.273   4.3480   1.3709  -0.9374
 LJD  O1   O   O     0  -0.501   1.7147  -1.8608   0.9536
 LJD  CL1  CL  CL    0  -0.131  -5.0456   1.3078   1.4191
 LJD  H1   H   HNH1  0   0.404   0.8545  -0.2752  -1.6269
 LJD  H2   H   HCR5  0   0.264   2.6395   1.0218  -2.0611
 LJD  H3   H   HCH2  0   0.274  -0.6532  -2.0774  -1.9217
 LJD  H4   H   HCH2  0   0.270  -0.2352  -2.6864  -0.3331
 LJD  H5   H   HCR6  0   0.263  -0.8516  -1.0798   1.7024
 LJD  H6   H   HCH3  0   0.266   6.8460   1.1845   0.0371
 LJD  H7   H   HCH3  0   0.265   5.9710   2.3559   1.0429
 LJD  H8   H   HCH3  0   0.262   6.2756   0.7199   1.6468
 LJD  H9   H   HCR6  0   0.279  -4.4897   0.4849  -1.2537
 LJD  H10  H   HCR6  0   0.264  -2.6044  -0.7869  -2.1913
 LJD  H11  H   HCR5  0   0.301   4.1818  -0.5945   1.6244
 LJD  H12  H   HCR6  0   0.279  -2.7318   0.1925   2.6472

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
 LJD  N2   N1   aromatic  1.333  0.020  1.333
 LJD  N2   C4   aromatic  1.316  0.020  1.316
 LJD  C1   N1   single    1.444  0.020  1.444
 LJD  N1   C2   aromatic  1.335  0.020  1.335
 LJD  C4   C3   aromatic  1.409  0.020  1.409
 LJD  C2   C3   aromatic  1.383  0.020  1.383
 LJD  C3   C5   single    1.469  0.020  1.469
 LJD  C5   N3   single    1.347  0.020  1.347
 LJD  C5   O1   double    1.226  0.020  1.226
 LJD  N3   C6   single    1.446  0.020  1.446
 LJD  C6   C7   single    1.508  0.020  1.508
 LJD  C7   C12  aromatic  1.389  0.020  1.389
 LJD  C7   C8   aromatic  1.394  0.020  1.394
 LJD  C12  C11  aromatic  1.389  0.020  1.389
 LJD  C8   C9   aromatic  1.385  0.020  1.385
 LJD  C11  C10  aromatic  1.384  0.020  1.384
 LJD  C9   C10  aromatic  1.388  0.020  1.388
 LJD  C10  CL1  single    1.735  0.020  1.735
 LJD  N3   H1   single    0.860  0.020  1.020
 LJD  C4   H2   single    0.930  0.020  1.080
 LJD  C6   H3   single    0.970  0.020  1.090
 LJD  C6   H4   single    0.970  0.020  1.090
 LJD  C8   H5   single    0.930  0.020  1.080
 LJD  C1   H6   single    0.970  0.020  1.090
 LJD  C1   H7   single    0.970  0.020  1.090
 LJD  C1   H8   single    0.970  0.020  1.090
 LJD  C11  H9   single    0.930  0.020  1.080
 LJD  C12  H10  single    0.930  0.020  1.080
 LJD  C2   H11  single    0.930  0.020  1.080
 LJD  C9   H12  single    0.930  0.020  1.080

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
 LJD  N2   N1   C2   112.57  3.000
 LJD  C2   N1   C1   127.61  3.000
 LJD  N2   N1   C1   119.82  3.000
 LJD  H1   N3   C6   116.65  3.000
 LJD  H1   N3   C5   119.08  3.000
 LJD  C6   N3   C5   123.90  3.000
 LJD  H2   C4   N2   119.61  3.000
 LJD  H2   C4   C3   129.15  3.000
 LJD  N2   C4   C3   111.25  3.000
 LJD  O1   C5   C3   121.10  3.000
 LJD  O1   C5   N3   123.16  3.000
 LJD  C3   C5   N3   115.74  3.000
 LJD  H4   C6   H3   106.99  3.000
 LJD  H4   C6   C7   110.51  3.000
 LJD  H3   C6   C7   109.76  3.000
 LJD  H4   C6   N3   108.49  3.000
 LJD  H3   C6   N3   108.25  3.000
 LJD  C7   C6   N3   112.65  3.000
 LJD  C12  C7   C8   118.64  3.000
 LJD  C8   C7   C6   120.70  3.000
 LJD  C12  C7   C6   120.65  3.000
 LJD  H5   C8   C9   119.10  3.000
 LJD  H5   C8   C7   119.90  3.000
 LJD  C9   C8   C7   121.00  3.000
 LJD  CL1  C10  C9   119.35  3.000
 LJD  CL1  C10  C11  119.53  3.000
 LJD  C9   C10  C11  121.12  3.000
 LJD  H8   C1   H7   109.07  3.000
 LJD  H8   C1   H6   109.07  3.000
 LJD  H7   C1   H6   109.32  3.000
 LJD  H8   C1   N1   109.03  3.000
 LJD  H7   C1   N1   110.34  3.000
 LJD  H6   C1   N1   110.00  3.000
 LJD  H9   C11  C12  120.35  3.000
 LJD  H9   C11  C10  120.73  3.000
 LJD  C12  C11  C10  118.92  3.000
 LJD  H10  C12  C11  118.94  3.000
 LJD  H10  C12  C7   119.84  3.000
 LJD  C11  C12  C7   121.21  3.000
 LJD  H11  C2   C3   131.03  3.000
 LJD  H11  C2   N1   122.11  3.000
 LJD  C3   C2   N1   106.86  3.000
 LJD  C2   C3   C5   124.54  3.000
 LJD  C5   C3   C4   131.63  3.000
 LJD  C2   C3   C4   103.83  3.000
 LJD  H12  C9   C10  120.52  3.000
 LJD  H12  C9   C8   120.36  3.000
 LJD  C10  C9   C8   119.12  3.000
 LJD  C4   N2   N1   105.49  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
 LJD  CONST_01  C3   C4   N2   N1     0.00   0.0  0
 LJD  CONST_02  C4   C3   C2   N1     0.00   0.0  0
 LJD  CONST_03  C2   N1   N2   C4     0.00   0.0  0
 LJD  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 LJD  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 LJD  CONST_06  C11  C12  C7   C8     0.00   0.0  0
 LJD  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 LJD  CONST_08  C9   C8   C7   C12    0.00   0.0  0
 LJD  CONST_09  C9   C10  C11  C12    0.00   0.0  0
 LJD  CONST_10  N2   C4   C3   C2     0.00   0.0  0
 LJD  CONST_11  N2   N1   C2   C3     0.00   0.0  0
 LJD  CONST_12  C5   C3   C2   N1   180.00   0.0  0
 LJD  CONST_13  C1   N1   N2   C4   180.00   0.0  0
 LJD  CONST_14  N2   C4   C3   C5   180.00   0.0  0
 LJD  CONST_15  C11  C12  C7   C6   180.00   0.0  0
 LJD  CONST_16  C9   C8   C7   C6   180.00   0.0  0
 LJD  CONST_17  CL1  C10  C9   C8   180.00   0.0  0
 LJD  CONST_18  C3   C2   N1   C1   180.00   0.0  0
 LJD  CONST_19  CL1  C10  C11  C12  180.00   0.0  0
 LJD  CONST_20  H2   C4   N2   N1   180.00   0.0  0
 LJD  CONST_21  H11  C2   C3   C4   180.00   0.0  0
 LJD  CONST_22  H9   C11  C12  C7   180.00   0.0  0
 LJD  CONST_23  H12  C9   C8   C7   180.00   0.0  0
 LJD  CONST_24  H10  C12  C7   C8   180.00   0.0  0
 LJD  CONST_25  H5   C8   C9   C10  180.00   0.0  0
 LJD  CONST_26  C3   C5   N3   C6   180.00   0.0  0
 LJD  CONST_27  H1   N3   C5   C3     0.00   0.0  0
 LJD  CONST_28  O1   C5   N3   C6     0.00   0.0  0
 LJD  Var_01    C4   C3   C5   N3    -2.28  30.0  2
 LJD  Var_02    C12  C7   C6   N3   108.02  30.0  2
 LJD  Var_03    H6   C1   N1   C2   124.24  30.0  2
 LJD  Var_04    C7   C6   N3   C5    97.73  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
 LJD  plan-1  N1   0.020
 LJD  plan-1  C4   0.020
 LJD  plan-1  C5   0.020
 LJD  plan-1  C1   0.020
 LJD  plan-1  C2   0.020
 LJD  plan-1  C3   0.020
 LJD  plan-1  N2   0.020
 LJD  plan-1  H2   0.020
 LJD  plan-1  H11  0.020
 LJD  plan-2  C6   0.020
 LJD  plan-2  C7   0.020
 LJD  plan-2  C8   0.020
 LJD  plan-2  C10  0.020
 LJD  plan-2  C11  0.020
 LJD  plan-2  C12  0.020
 LJD  plan-2  C9   0.020
 LJD  plan-2  CL1  0.020
 LJD  plan-2  H5   0.020
 LJD  plan-2  H9   0.020
 LJD  plan-2  H10  0.020
 LJD  plan-2  H12  0.020
 LJD  plan-3  N3   0.020
 LJD  plan-3  C5   0.020
 LJD  plan-3  C6   0.020
 LJD  plan-3  C3   0.020
 LJD  plan-3  O1   0.020
 LJD  plan-3  H1   0.020

