# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:30:39 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-[(1H-pyrazol-1-yl)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1ccc(Cn2cccn2)cc1
#
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
 JOY  JOY  4-[(1H-pyrazol-1-yl)methyl]benzonitrile  ligand  23  14  .  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_JOY
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
 JOY  C10   C  CR15  0  -0.517   3.7913   0.3001   1.2439
 JOY  N12   N  N     0  -0.281   2.5142   1.0183  -0.4667
 JOY  C13   C  CR16  0  -0.288  -0.8173   0.1406  -1.4908
 JOY  N01   N  NS    0  -0.250  -5.0002   0.6260   0.8291
 JOY  C03   C  CR6   0  -0.006  -2.6025   0.0076   0.1057
 JOY  C04   C  CR16  0  -0.224  -1.8143  -0.7971   0.9299
 JOY  C05   C  CR16  0  -0.274  -0.5326  -1.1261   0.5310
 JOY  C06   C  CR6   0   0.151  -0.0231  -0.6613  -0.6794
 JOY  C07   C  CH2   0  -0.403   1.3849  -1.0080  -1.0873
 JOY  N08   N  NR5   0  -0.256   2.3544  -0.2893  -0.2908
 JOY  C09   C  CR15  0   0.049   3.0930  -0.7670   0.7291
 JOY  C11   C  CR15  0  -0.047   3.3866   1.3882   0.4531
 JOY  C14   C  CR16  0  -0.225  -2.1052   0.4768  -1.1081
 JOY  H101  H  HCR5  0   0.263   4.4923   0.2937   2.0611
 JOY  H131  H  HCR6  0   0.274  -0.4314   0.5065  -2.4333
 JOY  H041  H  HCR6  0   0.284  -2.2057  -1.1631   1.8691
 JOY  H051  H  HCR6  0   0.270   0.0750  -1.7556   1.1695
 JOY  H072  H  HCH2  0   0.293   1.5720  -2.0734  -0.9549
 JOY  H071  H  HCH2  0   0.291   1.5519  -0.7711  -2.1375
 JOY  H091  H  HCR5  0   0.294   3.0763  -1.8092   1.0037
 JOY  H111  H  HCR5  0   0.260   3.7040   2.4179   0.5185
 JOY  H141  H  HCR6  0   0.285  -2.7183   1.1000  -1.7443
 JOY  C02   C  CSP   0   0.058  -3.9295   0.3480   0.5066

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
 JOY  C11  N12   aromatic  1.321  0.020  1.321
 JOY  C11  C10   aromatic  1.405  0.020  1.405
 JOY  N01  C02   triple    1.152  0.020  1.152
 JOY  N12  N08   aromatic  1.329  0.020  1.329
 JOY  C02  C03   single    1.427  0.020  1.427
 JOY  C14  C03   aromatic  1.393  0.020  1.393
 JOY  C14  C13   aromatic  1.385  0.020  1.385
 JOY  C03  C04   aromatic  1.396  0.020  1.396
 JOY  C13  C06   aromatic  1.390  0.020  1.390
 JOY  C10  C09   aromatic  1.375  0.020  1.375
 JOY  C04  C05   aromatic  1.382  0.020  1.382
 JOY  N08  C07   single    1.446  0.020  1.446
 JOY  N08  C09   aromatic  1.347  0.020  1.347
 JOY  C06  C05   aromatic  1.393  0.020  1.393
 JOY  C06  C07   single    1.506  0.020  1.506
 JOY  C10  H101  single    0.930  0.020  1.080
 JOY  C13  H131  single    0.930  0.020  1.080
 JOY  C04  H041  single    0.930  0.020  1.080
 JOY  C05  H051  single    0.930  0.020  1.080
 JOY  C07  H072  single    0.970  0.020  1.090
 JOY  C07  H071  single    0.970  0.020  1.090
 JOY  C09  H091  single    0.930  0.020  1.080
 JOY  C11  H111  single    0.930  0.020  1.080
 JOY  C14  H141  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
 JOY  H101  C10  C11   128.28  3.000
 JOY  H101  C10  C09   127.60  3.000
 JOY  C11   C10  C09   104.12  3.000
 JOY  C11   N12  N08   105.24  3.000
 JOY  H131  C13  C14   119.35  3.000
 JOY  H131  C13  C06   119.98  3.000
 JOY  C14   C13  C06   120.67  3.000
 JOY  C14   C03  C04   120.47  3.000
 JOY  C04   C03  C02   119.78  3.000
 JOY  C14   C03  C02   119.75  3.000
 JOY  H041  C04  C05   120.38  3.000
 JOY  H041  C04  C03   120.25  3.000
 JOY  C05   C04  C03   119.38  3.000
 JOY  H051  C05  C06   120.06  3.000
 JOY  H051  C05  C04   119.24  3.000
 JOY  C06   C05  C04   120.69  3.000
 JOY  C07   C06  C05   120.02  3.000
 JOY  C07   C06  C13   120.58  3.000
 JOY  C05   C06  C13   119.39  3.000
 JOY  H071  C07  H072  107.66  3.000
 JOY  H071  C07  N08   108.67  3.000
 JOY  H072  C07  N08   107.69  3.000
 JOY  H071  C07  C06   110.75  3.000
 JOY  H072  C07  C06   110.64  3.000
 JOY  N08   C07  C06   111.29  3.000
 JOY  C09   N08  C07   127.49  3.000
 JOY  C09   N08  N12   112.53  3.000
 JOY  C07   N08  N12   119.78  3.000
 JOY  H091  C09  N08   121.82  3.000
 JOY  H091  C09  C10   131.51  3.000
 JOY  N08   C09  C10   106.66  3.000
 JOY  H111  C11  N12   120.24  3.000
 JOY  H111  C11  C10   128.32  3.000
 JOY  N12   C11  C10   111.44  3.000
 JOY  H141  C14  C03   120.29  3.000
 JOY  H141  C14  C13   120.31  3.000
 JOY  C03   C14  C13   119.40  3.000
 JOY  C03   C02  N01   180.00  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
 JOY  CONST_01  N08   N12  C11  C10    0.00   0.0  0
 JOY  CONST_02  N12   N08  C09  C10    0.00   0.0  0
 JOY  CONST_03  C09   C10  C11  N12    0.00   0.0  0
 JOY  CONST_04  C04   C03  C14  C13    0.00   0.0  0
 JOY  CONST_05  C04   C05  C06  C13    0.00   0.0  0
 JOY  CONST_06  C06   C13  C14  C03    0.00   0.0  0
 JOY  CONST_07  C06   C05  C04  C03    0.00   0.0  0
 JOY  CONST_08  C14   C03  C04  C05    0.00   0.0  0
 JOY  CONST_09  C14   C13  C06  C05    0.00   0.0  0
 JOY  CONST_10  C11   C10  C09  N08    0.00   0.0  0
 JOY  CONST_11  C11   N12  N08  C09    0.00   0.0  0
 JOY  CONST_12  C07   N08  C09  C10  180.00   0.0  0
 JOY  CONST_13  C02   C03  C14  C13  180.00   0.0  0
 JOY  CONST_14  C05   C04  C03  C02  180.00   0.0  0
 JOY  CONST_15  C07   C06  C05  C04  180.00   0.0  0
 JOY  CONST_16  C11   N12  N08  C07  180.00   0.0  0
 JOY  CONST_17  C14   C13  C06  C07  180.00   0.0  0
 JOY  CONST_18  H101  C10  C11  N12  180.00   0.0  0
 JOY  CONST_19  H091  C09  N08  N12  180.00   0.0  0
 JOY  CONST_20  H051  C05  C06  C13  180.00   0.0  0
 JOY  CONST_21  H131  C13  C14  C03  180.00   0.0  0
 JOY  CONST_22  H141  C14  C03  C04  180.00   0.0  0
 JOY  CONST_23  H041  C04  C05  C06  180.00   0.0  0
 JOY  CONST_24  H111  C11  N12  N08  180.00   0.0  0
 JOY  Var_01    C06   C07  N08  N12  -71.35  30.0  2
 JOY  Var_02    N08   C07  C06  C13  106.90  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
 JOY  plan-1  C10   0.020
 JOY  plan-1  N12   0.020
 JOY  plan-1  C07   0.020
 JOY  plan-1  N08   0.020
 JOY  plan-1  C09   0.020
 JOY  plan-1  C11   0.020
 JOY  plan-1  H101  0.020
 JOY  plan-1  H091  0.020
 JOY  plan-1  H111  0.020
 JOY  plan-2  C13   0.020
 JOY  plan-2  N01   0.020
 JOY  plan-2  C03   0.020
 JOY  plan-2  C04   0.020
 JOY  plan-2  C05   0.020
 JOY  plan-2  C06   0.020
 JOY  plan-2  C07   0.020
 JOY  plan-2  C14   0.020
 JOY  plan-2  H131  0.020
 JOY  plan-2  H041  0.020
 JOY  plan-2  H051  0.020
 JOY  plan-2  H141  0.020
 JOY  plan-2  C02   0.020

