# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:47:55 2021
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-(3-cyanophenyl)-N-(pyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1cccc(c1)C#N)Nc2cccnc2
#
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
 UH1  UH1  2-(3-cyanophenyl)-N-(pyridin-3-yl)acetamide  ligand  29  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UH1
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
 UH1  N1   N  NH1   0  -0.748   7.4670  -0.0148  21.0566
 UH1  C4   C  CR16  0  -0.232  12.5920   0.6517  23.7581
 UH1  C5   C  CR16  0  -0.254  13.4448  -0.3118  23.2470
 UH1  C6   C  CR6   0   0.023  12.9039  -1.3790  22.5320
 UH1  C7   C  CSP   0   0.055  13.7675  -2.3835  21.9994
 UH1  C8   C  CR16  0  -0.294  11.5278  -1.4801  22.3296
 UH1  C10  C  CR16  0  -0.247   5.4041   0.1070  19.8688
 UH1  C13  C  CR16  0  -0.118   7.1986   1.4825  19.0999
 UH1  N    N  NS    0  -0.252  14.4643  -3.1921  21.5654
 UH1  C3   C  CR16  0  -0.275  11.2227   0.5512  23.5562
 UH1  C2   C  CR6   0   0.166  10.6771  -0.5126  22.8427
 UH1  C1   C  CH2   0  -0.707   9.2007  -0.6017  22.6104
 UH1  C    C  C     0   0.560   8.7703   0.1845  21.3815
 UH1  O    O  O     0  -0.447   9.5220   0.9170  20.7715
 UH1  C9   C  CR6   0   0.300   6.7242   0.5347  20.0124
 UH1  N2   N  N     0  -0.391   6.4458   1.9736  18.1228
 UH1  C12  C  CR16  0  -0.086   5.1942   1.5593  17.9948
 UH1  C11  C  CR16  0  -0.308   4.6294   0.6240  18.8497
 UH1  H1   H  HNH1  0   0.424   6.9580  -0.6616  21.6414
 UH1  H2   H  HCR6  0   0.275  12.9968   1.4850  24.3158
 UH1  H3   H  HCR6  0   0.282  14.5128  -0.2425  23.4014
 UH1  H4   H  HCR6  0   0.278  11.1269  -2.3190  21.7749
 UH1  H5   H  HCR6  0   0.287   4.9903  -0.6249  20.5528
 UH1  H6   H  HCR6  0   0.281   8.2095   1.8552  19.1584
 UH1  H7   H  HCR6  0   0.268  10.5688   1.3101  23.9678
 UH1  H8   H  HCH2  0   0.314   8.6526  -0.2108  23.4729
 UH1  H9   H  HCH2  0   0.305   8.8893  -1.6433  22.4997
 UH1  H10  H  HCR6  0   0.264   4.6159   1.9869  17.1839
 UH1  H11  H  HCR6  0   0.276   3.6043   0.3065  18.7194

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
 UH1  N2   C12  aromatic  1.325  0.020  1.325
 UH1  N2   C13  aromatic  1.328  0.020  1.328
 UH1  C12  C11  aromatic  1.387  0.020  1.387
 UH1  C13  C9   aromatic  1.399  0.020  1.399
 UH1  C11  C10  aromatic  1.381  0.020  1.381
 UH1  C9   C10  aromatic  1.395  0.020  1.395
 UH1  C9   N1   single    1.394  0.020  1.394
 UH1  N    C7   triple    1.152  0.020  1.152
 UH1  N1   C    single    1.358  0.020  1.358
 UH1  O    C    double    1.214  0.020  1.214
 UH1  C7   C6   single    1.428  0.020  1.428
 UH1  C    C1   single    1.521  0.020  1.521
 UH1  C8   C6   aromatic  1.395  0.020  1.395
 UH1  C8   C2   aromatic  1.387  0.020  1.387
 UH1  C6   C5   aromatic  1.394  0.020  1.394
 UH1  C1   C2   single    1.497  0.020  1.497
 UH1  C2   C3   aromatic  1.392  0.020  1.392
 UH1  C5   C4   aromatic  1.385  0.020  1.385
 UH1  C3   C4   aromatic  1.388  0.020  1.388
 UH1  N1   H1   single    0.860  0.020  1.020
 UH1  C4   H2   single    0.930  0.020  1.080
 UH1  C5   H3   single    0.930  0.020  1.080
 UH1  C8   H4   single    0.930  0.020  1.080
 UH1  C10  H5   single    0.930  0.020  1.080
 UH1  C13  H6   single    0.930  0.020  1.080
 UH1  C3   H7   single    0.930  0.020  1.080
 UH1  C1   H8   single    0.970  0.020  1.090
 UH1  C1   H9   single    0.970  0.020  1.090
 UH1  C12  H10  single    0.930  0.020  1.080
 UH1  C11  H11  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
 UH1  H1   N1   C9   114.69  3.000
 UH1  H1   N1   C    116.06  3.000
 UH1  C9   N1   C    129.25  3.000
 UH1  H2   C4   C3   120.01  3.000
 UH1  H2   C4   C5   119.74  3.000
 UH1  C3   C4   C5   120.24  3.000
 UH1  H3   C5   C6   120.37  3.000
 UH1  H3   C5   C4   120.73  3.000
 UH1  C6   C5   C4   118.89  3.000
 UH1  C8   C6   C7   119.45  3.000
 UH1  C8   C6   C5   120.86  3.000
 UH1  C7   C6   C5   119.69  3.000
 UH1  N    C7   C6   180.00  3.000
 UH1  H4   C8   C2   120.20  3.000
 UH1  H4   C8   C6   119.73  3.000
 UH1  C2   C8   C6   120.07  3.000
 UH1  H5   C10  C11  120.30  3.000
 UH1  H5   C10  C9   120.22  3.000
 UH1  C11  C10  C9   119.48  3.000
 UH1  H6   C13  N2   116.32  3.000
 UH1  H6   C13  C9   121.09  3.000
 UH1  N2   C13  C9   122.59  3.000
 UH1  H7   C3   C2   119.57  3.000
 UH1  H7   C3   C4   119.32  3.000
 UH1  C2   C3   C4   121.10  3.000
 UH1  C1   C2   C3   120.76  3.000
 UH1  C3   C2   C8   118.84  3.000
 UH1  C1   C2   C8   120.39  3.000
 UH1  H9   C1   H8   106.12  3.000
 UH1  H9   C1   C    109.28  3.000
 UH1  H8   C1   C    108.09  3.000
 UH1  H9   C1   C2   110.70  3.000
 UH1  H8   C1   C2   110.51  3.000
 UH1  C    C1   C2   111.94  3.000
 UH1  O    C    C1   122.86  3.000
 UH1  C1   C    N1   112.90  3.000
 UH1  O    C    N1   124.24  3.000
 UH1  C13  C9   C10  117.49  3.000
 UH1  C10  C9   N1   117.41  3.000
 UH1  C13  C9   N1   125.10  3.000
 UH1  C12  N2   C13  119.42  3.000
 UH1  H10  C12  C11  120.65  3.000
 UH1  H10  C12  N2   116.94  3.000
 UH1  C11  C12  N2   122.41  3.000
 UH1  H11  C11  C12  120.65  3.000
 UH1  H11  C11  C10  120.73  3.000
 UH1  C12  C11  C10  118.62  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
 UH1  CONST_01  C8   C6   C5   C4     0.00   0.0  0
 UH1  CONST_02  C8   C2   C3   C4     0.00   0.0  0
 UH1  CONST_03  C2   C8   C6   C5     0.00   0.0  0
 UH1  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 UH1  CONST_05  C3   C2   C8   C6     0.00   0.0  0
 UH1  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 UH1  CONST_07  N2   C12  C11  C10    0.00   0.0  0
 UH1  CONST_08  N2   C13  C9   C10    0.00   0.0  0
 UH1  CONST_09  C11  C12  N2   C13    0.00   0.0  0
 UH1  CONST_10  C11  C10  C9   C13    0.00   0.0  0
 UH1  CONST_11  C12  N2   C13  C9     0.00   0.0  0
 UH1  CONST_12  C12  C11  C10  C9     0.00   0.0  0
 UH1  CONST_13  N2   C13  C9   N1   180.00   0.0  0
 UH1  CONST_14  C11  C10  C9   N1   180.00   0.0  0
 UH1  CONST_15  C7   C6   C5   C4   180.00   0.0  0
 UH1  CONST_16  C1   C2   C3   C4   180.00   0.0  0
 UH1  CONST_17  C1   C2   C8   C6   180.00   0.0  0
 UH1  CONST_18  C2   C8   C6   C7   180.00   0.0  0
 UH1  CONST_19  H4   C8   C6   C5   180.00   0.0  0
 UH1  CONST_20  H7   C3   C4   C5   180.00   0.0  0
 UH1  CONST_21  H2   C4   C5   C6   180.00   0.0  0
 UH1  CONST_22  H3   C5   C6   C8   180.00   0.0  0
 UH1  CONST_23  H10  C12  C11  C10  180.00   0.0  0
 UH1  CONST_24  H6   C13  C9   C10  180.00   0.0  0
 UH1  CONST_25  H5   C10  C9   C13  180.00   0.0  0
 UH1  CONST_26  H11  C11  C10  C9   180.00   0.0  0
 UH1  CONST_27  C    N1   C9   C10  180.00   0.0  0
 UH1  CONST_28  C    N1   C9   C13    0.00   0.0  0
 UH1  CONST_29  H1   N1   C9   C10    0.00   0.0  0
 UH1  CONST_30  C9   N1   C    C1   180.00   0.0  0
 UH1  CONST_31  C9   N1   C    O      0.00   0.0  0
 UH1  Var_01    C    C1   C2   C8   -93.31  30.0  3
 UH1  Var_02    C2   C1   C    N1   172.38  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
 UH1  plan-1  C4   0.020
 UH1  plan-1  C5   0.020
 UH1  plan-1  C6   0.020
 UH1  plan-1  C7   0.020
 UH1  plan-1  C8   0.020
 UH1  plan-1  N    0.020
 UH1  plan-1  C3   0.020
 UH1  plan-1  C2   0.020
 UH1  plan-1  C1   0.020
 UH1  plan-1  H2   0.020
 UH1  plan-1  H3   0.020
 UH1  plan-1  H4   0.020
 UH1  plan-1  H7   0.020
 UH1  plan-2  N1   0.020
 UH1  plan-2  C10  0.020
 UH1  plan-2  C13  0.020
 UH1  plan-2  C9   0.020
 UH1  plan-2  N2   0.020
 UH1  plan-2  C12  0.020
 UH1  plan-2  C11  0.020
 UH1  plan-2  H5   0.020
 UH1  plan-2  H6   0.020
 UH1  plan-2  H10  0.020
 UH1  plan-2  H11  0.020
 UH1  plan-3  N1   0.020
 UH1  plan-3  C1   0.020
 UH1  plan-3  C    0.020
 UH1  plan-3  O    0.020
 UH1  plan-3  C9   0.020
 UH1  plan-3  H1   0.020

