# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:57:08 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (phenylmethyl) 1~{H}-pyrazole-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(OCc1ccccc1)c2c[nH]nc2
#
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
 JF5  JF5  '(phenylmethyl) 1~{H}-pyrazole-4-carboxylate'  ligand  25  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JF5
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
 JF5  C10  C  CR6   0   0.080   2.2019  -0.5097   0.0199
 JF5  C13  C  CR16  0  -0.261   4.4381   1.1587   0.0179
 JF5  C15  C  CR16  0  -0.291   2.7790  -0.1051  -1.1801
 JF5  O01  O  O     0  -0.460  -1.5388  -2.2862   0.0340
 JF5  C02  C  C     0   0.545  -1.3569  -1.0906   0.0236
 JF5  C03  C  CR5   0  -0.274  -2.4225  -0.0980   0.0158
 JF5  C04  C  CR15  0   0.071  -3.7778  -0.3704   0.0249
 JF5  N05  N  NR15  0  -0.417  -4.3898   0.8119   0.0121
 JF5  N06  N  N     0  -0.258  -3.5491   1.8473  -0.0044
 JF5  C07  C  CR15  0  -0.054  -2.3491   1.3113  -0.0024
 JF5  O08  O  O2    0  -0.458  -0.1569  -0.5226   0.0170
 JF5  C09  C  CH2   0  -0.250   0.9890  -1.3885   0.0217
 JF5  C11  C  CR16  0  -0.290   2.7536  -0.0679   1.2191
 JF5  C12  C  CR16  0  -0.242   3.8668   0.7610   1.2201
 JF5  C14  C  CR16  0  -0.242   3.8926   0.7238  -1.1831
 JF5  H1   H  HCR6  0   0.259   5.3089   1.8013   0.0172
 JF5  H2   H  HCR6  0   0.256   2.3592  -0.4446  -2.1196
 JF5  H3   H  HCR5  0   0.305  -4.3211  -1.3008   0.0393
 JF5  H4   H  HNR5  0   0.432  -5.3847   0.9757   0.0159
 JF5  H5   H  HCR5  0   0.270  -1.4699   1.9366  -0.0141
 JF5  H6   H  HCH2  0   0.253   0.9708  -2.0327  -0.8596
 JF5  H7   H  HCH2  0   0.253   0.9687  -2.0248   0.9087
 JF5  H8   H  HCR6  0   0.256   2.3142  -0.3785   2.1597
 JF5  H9   H  HCR6  0   0.259   4.2909   1.0920   2.1590
 JF5  H10  H  HCR6  0   0.259   4.3362   1.0261  -2.1228

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
 JF5  O01  C02  double    1.209  0.020  1.209
 JF5  N05  C04  aromatic  1.331  0.020  1.331
 JF5  N05  N06  aromatic  1.334  0.020  1.334
 JF5  C04  C03  aromatic  1.382  0.020  1.382
 JF5  C03  C07  aromatic  1.411  0.020  1.411
 JF5  C03  C02  single    1.456  0.020  1.456
 JF5  N06  C07  aromatic  1.314  0.020  1.314
 JF5  C02  O08  single    1.328  0.020  1.328
 JF5  O08  C09  single    1.436  0.020  1.436
 JF5  C09  C10  single    1.498  0.020  1.498
 JF5  C10  C11  aromatic  1.392  0.020  1.392
 JF5  C10  C15  aromatic  1.392  0.020  1.392
 JF5  C11  C12  aromatic  1.388  0.020  1.388
 JF5  C15  C14  aromatic  1.388  0.020  1.388
 JF5  C12  C13  aromatic  1.389  0.020  1.389
 JF5  C14  C13  aromatic  1.389  0.020  1.389
 JF5  C13  H1   single    0.930  0.020  1.080
 JF5  C15  H2   single    0.930  0.020  1.080
 JF5  C04  H3   single    0.930  0.020  1.080
 JF5  N05  H4   single    0.860  0.020  1.020
 JF5  C07  H5   single    0.930  0.020  1.080
 JF5  C09  H6   single    0.970  0.020  1.090
 JF5  C09  H7   single    0.970  0.020  1.090
 JF5  C11  H8   single    0.930  0.020  1.080
 JF5  C12  H9   single    0.930  0.020  1.080
 JF5  C14  H10  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
 JF5  C11  C10  C09  120.41  3.000
 JF5  C11  C10  C15  119.09  3.000
 JF5  C09  C10  C15  120.49  3.000
 JF5  H1   C13  C14  120.09  3.000
 JF5  H1   C13  C12  120.09  3.000
 JF5  C14  C13  C12  119.82  3.000
 JF5  H2   C15  C14  119.73  3.000
 JF5  H2   C15  C10  119.73  3.000
 JF5  C14  C15  C10  120.54  3.000
 JF5  O08  C02  C03  111.70  3.000
 JF5  O08  C02  O01  123.98  3.000
 JF5  C03  C02  O01  124.32  3.000
 JF5  C07  C03  C04  104.36  3.000
 JF5  C07  C03  C02  129.98  3.000
 JF5  C04  C03  C02  125.66  3.000
 JF5  H3   C04  N05  122.35  3.000
 JF5  H3   C04  C03  131.65  3.000
 JF5  N05  C04  C03  105.99  3.000
 JF5  H4   N05  N06  119.72  3.000
 JF5  H4   N05  C04  126.71  3.000
 JF5  N06  N05  C04  113.56  3.000
 JF5  C07  N06  N05  105.00  3.000
 JF5  H5   C07  N06  120.51  3.000
 JF5  H5   C07  C03  128.41  3.000
 JF5  N06  C07  C03  111.08  3.000
 JF5  C09  O08  C02  117.59  3.000
 JF5  H7   C09  H6   108.16  3.000
 JF5  H7   C09  O08  109.82  3.000
 JF5  H6   C09  O08  109.86  3.000
 JF5  H7   C09  C10  110.97  3.000
 JF5  H6   C09  C10  111.02  3.000
 JF5  O08  C09  C10  107.00  3.000
 JF5  H8   C11  C12  119.73  3.000
 JF5  H8   C11  C10  119.74  3.000
 JF5  C12  C11  C10  120.53  3.000
 JF5  H9   C12  C11  119.84  3.000
 JF5  H9   C12  C13  120.15  3.000
 JF5  C11  C12  C13  120.01  3.000
 JF5  H10  C14  C15  119.83  3.000
 JF5  H10  C14  C13  120.16  3.000
 JF5  C15  C14  C13  120.01  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
 JF5  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 JF5  CONST_02  C13  C14  C15  C10    0.00   0.0  0
 JF5  CONST_03  C12  C11  C10  C15    0.00   0.0  0
 JF5  CONST_04  C12  C13  C14  C15    0.00   0.0  0
 JF5  CONST_05  N06  N05  C04  C03    0.00   0.0  0
 JF5  CONST_06  N05  N06  C07  C03    0.00   0.0  0
 JF5  CONST_07  C07  N06  N05  C04    0.00   0.0  0
 JF5  CONST_08  N06  C07  C03  C04    0.00   0.0  0
 JF5  CONST_09  C07  C03  C04  N05    0.00   0.0  0
 JF5  CONST_10  C14  C15  C10  C11    0.00   0.0  0
 JF5  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 JF5  CONST_12  N05  C04  C03  C02  180.00   0.0  0
 JF5  CONST_13  N06  C07  C03  C02  180.00   0.0  0
 JF5  CONST_14  C12  C11  C10  C09  180.00   0.0  0
 JF5  CONST_15  C14  C15  C10  C09  180.00   0.0  0
 JF5  CONST_16  H9   C12  C11  C10  180.00   0.0  0
 JF5  CONST_17  H10  C14  C15  C10  180.00   0.0  0
 JF5  CONST_18  H8   C11  C12  C13  180.00   0.0  0
 JF5  CONST_19  H2   C15  C14  C13  180.00   0.0  0
 JF5  CONST_20  H1   C13  C14  C15  180.00   0.0  0
 JF5  CONST_21  H4   N05  C04  C03  180.00   0.0  0
 JF5  CONST_22  H5   C07  C03  C04  180.00   0.0  0
 JF5  CONST_23  H3   C04  N05  N06  180.00   0.0  0
 JF5  Var_01    O08  C09  C10  C15  -90.31  30.0  2
 JF5  Var_02    C04  C03  C02  O01    0.30  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
 JF5  plan-1  C02  0.020
 JF5  plan-1  C03  0.020
 JF5  plan-1  C04  0.020
 JF5  plan-1  N05  0.020
 JF5  plan-1  N06  0.020
 JF5  plan-1  C07  0.020
 JF5  plan-1  H3   0.020
 JF5  plan-1  H4   0.020
 JF5  plan-1  H5   0.020
 JF5  plan-2  C10  0.020
 JF5  plan-2  C13  0.020
 JF5  plan-2  C15  0.020
 JF5  plan-2  C09  0.020
 JF5  plan-2  C11  0.020
 JF5  plan-2  C12  0.020
 JF5  plan-2  C14  0.020
 JF5  plan-2  H1   0.020
 JF5  plan-2  H2   0.020
 JF5  plan-2  H8   0.020
 JF5  plan-2  H9   0.020
 JF5  plan-2  H10  0.020
 JF5  plan-3  O01  0.020
 JF5  plan-3  C02  0.020
 JF5  plan-3  C03  0.020
 JF5  plan-3  O08  0.020

