# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:45:48 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-(5-cyanopyridin-3-yl)-N-(pyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1cncc(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
 UGM  UGM  2-(5-cyanopyridin-3-yl)-N-(pyridin-3-yl)acetamide  ligand  28  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_UGM
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
 UGM  N1   N  NS    0  -0.241  14.6929  -2.6525  21.4573
 UGM  N3   N  N     0  -0.391   6.4930   1.4163  17.7506
 UGM  C4   C  CR16  0  -0.030  13.2593  -0.0912  23.3390
 UGM  C5   C  CR6   0  -0.080  12.8855  -1.1345  22.4919
 UGM  C6   C  CSP   0   0.054  13.8822  -1.9757  21.9172
 UGM  C7   C  CR16  0  -0.152  11.5366  -1.3396  22.2216
 UGM  C8   C  CR6   0   0.299   6.6779   0.5529  19.9720
 UGM  C10  C  CR16  0  -0.308   4.5249   0.9957  19.0155
 UGM  N    N  N     0  -0.391  12.3736   0.7098  23.9011
 UGM  C3   C  CR16  0  -0.064  11.0874   0.5076  23.6402
 UGM  C2   C  CR6   0   0.060  10.6059  -0.4986  22.8096
 UGM  C1   C  CH2   0  -0.703   9.1416  -0.6496  22.5535
 UGM  C    C  C     0   0.565   8.7419  -0.0910  21.1960
 UGM  O    O  O     0  -0.447   9.5495   0.1211  20.3144
 UGM  N2   N  NH1   0  -0.748   7.4064   0.1124  21.0774
 UGM  C12  C  CR16  0  -0.116   7.2347   0.9990  18.7695
 UGM  C11  C  CR16  0  -0.085   5.1732   1.4172  17.8637
 UGM  C9   C  CR16  0  -0.246   5.2875   0.5581  20.0800
 UGM  H1   H  HCR6  0   0.292  14.3050   0.0857  23.5615
 UGM  H2   H  HCR6  0   0.293  11.2268  -2.1522  21.5772
 UGM  H3   H  HCR6  0   0.276   3.4457   1.0087  19.0774
 UGM  H4   H  HCR6  0   0.279  10.3892   1.1825  24.1243
 UGM  H5   H  HCH2  0   0.303   8.5642  -0.1672  23.3451
 UGM  H6   H  HCH2  0   0.321   8.8592  -1.7070  22.5717
 UGM  H7   H  HNH1  0   0.425   6.8478  -0.1185  21.8863
 UGM  H8   H  HCR6  0   0.281   8.3036   1.0222  18.6238
 UGM  H9   H  HCR6  0   0.264   4.6079   1.7668  17.0076
 UGM  H10  H  HCR6  0   0.289   4.8105   0.2187  20.9920

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
 UGM  N3   C11  aromatic  1.325  0.020  1.325
 UGM  N3   C12  aromatic  1.328  0.020  1.328
 UGM  C11  C10  aromatic  1.387  0.020  1.387
 UGM  C12  C8   aromatic  1.398  0.020  1.398
 UGM  C10  C9   aromatic  1.381  0.020  1.381
 UGM  C8   C9   aromatic  1.395  0.020  1.395
 UGM  C8   N2   single    1.395  0.020  1.395
 UGM  N1   C6   triple    1.152  0.020  1.152
 UGM  O    C    double    1.214  0.020  1.214
 UGM  C6   C5   single    1.425  0.020  1.425
 UGM  N2   C    single    1.356  0.020  1.356
 UGM  C    C1   single    1.521  0.020  1.521
 UGM  C7   C5   aromatic  1.391  0.020  1.391
 UGM  C7   C2   aromatic  1.385  0.020  1.385
 UGM  C5   C4   aromatic  1.395  0.020  1.395
 UGM  C1   C2   single    1.494  0.020  1.494
 UGM  C2   C3   aromatic  1.391  0.020  1.391
 UGM  C4   N    aromatic  1.320  0.020  1.320
 UGM  C3   N    aromatic  1.328  0.020  1.328
 UGM  C4   H1   single    0.930  0.020  1.080
 UGM  C7   H2   single    0.930  0.020  1.080
 UGM  C10  H3   single    0.930  0.020  1.080
 UGM  C3   H4   single    0.930  0.020  1.080
 UGM  C1   H5   single    0.970  0.020  1.090
 UGM  C1   H6   single    0.970  0.020  1.090
 UGM  N2   H7   single    0.860  0.020  1.020
 UGM  C12  H8   single    0.930  0.020  1.080
 UGM  C11  H9   single    0.930  0.020  1.080
 UGM  C9   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
 UGM  C11  N3   C12  119.43  3.000
 UGM  H1   C4   N    117.45  3.000
 UGM  H1   C4   C5   120.36  3.000
 UGM  N    C4   C5   122.19  3.000
 UGM  C7   C5   C6   120.85  3.000
 UGM  C7   C5   C4   119.22  3.000
 UGM  C6   C5   C4   119.93  3.000
 UGM  C5   C6   N1   180.00  3.000
 UGM  H2   C7   C2   121.08  3.000
 UGM  H2   C7   C5   120.26  3.000
 UGM  C2   C7   C5   118.65  3.000
 UGM  C9   C8   C12  117.54  3.000
 UGM  C9   C8   N2   117.41  3.000
 UGM  C12  C8   N2   125.04  3.000
 UGM  H3   C10  C9   120.74  3.000
 UGM  H3   C10  C11  120.69  3.000
 UGM  C9   C10  C11  118.58  3.000
 UGM  C3   N    C4   118.28  3.000
 UGM  H4   C3   C2   119.59  3.000
 UGM  H4   C3   N    116.16  3.000
 UGM  C2   C3   N    124.26  3.000
 UGM  C1   C2   C3   120.98  3.000
 UGM  C3   C2   C7   117.39  3.000
 UGM  C1   C2   C7   121.62  3.000
 UGM  H6   C1   H5   106.16  3.000
 UGM  H6   C1   C    107.56  3.000
 UGM  H5   C1   C    110.23  3.000
 UGM  H6   C1   C2   110.33  3.000
 UGM  H5   C1   C2   110.44  3.000
 UGM  C    C1   C2   111.92  3.000
 UGM  N2   C    O    124.42  3.000
 UGM  N2   C    C1   113.07  3.000
 UGM  O    C    C1   122.50  3.000
 UGM  H7   N2   C    116.13  3.000
 UGM  H7   N2   C8   114.71  3.000
 UGM  C    N2   C8   129.11  3.000
 UGM  H8   C12  C8   121.16  3.000
 UGM  H8   C12  N3   116.30  3.000
 UGM  C8   C12  N3   122.54  3.000
 UGM  H9   C11  C10  120.67  3.000
 UGM  H9   C11  N3   116.90  3.000
 UGM  C10  C11  N3   122.43  3.000
 UGM  H10  C9   C10  120.33  3.000
 UGM  H10  C9   C8   120.19  3.000
 UGM  C10  C9   C8   119.48  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
 UGM  CONST_01  C9   C10  C11  N3     0.00   0.0  0
 UGM  CONST_02  C9   C8   C12  N3     0.00   0.0  0
 UGM  CONST_03  C2   C7   C5   C4     0.00   0.0  0
 UGM  CONST_04  C2   C3   N    C4     0.00   0.0  0
 UGM  CONST_05  C3   C2   C7   C5     0.00   0.0  0
 UGM  CONST_06  C3   N    C4   C5     0.00   0.0  0
 UGM  CONST_07  N    C4   C5   C7     0.00   0.0  0
 UGM  CONST_08  N    C3   C2   C7     0.00   0.0  0
 UGM  CONST_09  C11  N3   C12  C8     0.00   0.0  0
 UGM  CONST_10  C11  C10  C9   C8     0.00   0.0  0
 UGM  CONST_11  C12  N3   C11  C10    0.00   0.0  0
 UGM  CONST_12  C12  C8   C9   C10    0.00   0.0  0
 UGM  CONST_13  N2   C8   C12  N3   180.00   0.0  0
 UGM  CONST_14  C1   C2   C7   C5   180.00   0.0  0
 UGM  CONST_15  C2   C7   C5   C6   180.00   0.0  0
 UGM  CONST_16  N    C4   C5   C6   180.00   0.0  0
 UGM  CONST_17  N2   C8   C9   C10  180.00   0.0  0
 UGM  CONST_18  C1   C2   C3   N    180.00   0.0  0
 UGM  CONST_19  H3   C10  C11  N3   180.00   0.0  0
 UGM  CONST_20  H2   C7   C5   C4   180.00   0.0  0
 UGM  CONST_21  H4   C3   N    C4   180.00   0.0  0
 UGM  CONST_22  H1   C4   C5   C7   180.00   0.0  0
 UGM  CONST_23  H9   C11  N3   C12  180.00   0.0  0
 UGM  CONST_24  H10  C9   C8   C12  180.00   0.0  0
 UGM  CONST_25  H8   C12  N3   C11  180.00   0.0  0
 UGM  CONST_26  C12  C8   N2   C      0.00   0.0  0
 UGM  CONST_27  C9   C8   N2   C    180.00   0.0  0
 UGM  CONST_28  H7   N2   C8   C12  180.00   0.0  0
 UGM  CONST_29  O    C    N2   C8     0.00   0.0  0
 UGM  CONST_30  C1   C    N2   C8   180.00   0.0  0
 UGM  Var_01    C    C1   C2   C7   -77.19  30.0  3
 UGM  Var_02    O    C    C1   C2    17.66  30.0  1

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
 UGM  plan-1  N3   0.020
 UGM  plan-1  C8   0.020
 UGM  plan-1  C10  0.020
 UGM  plan-1  N2   0.020
 UGM  plan-1  C12  0.020
 UGM  plan-1  C11  0.020
 UGM  plan-1  C9   0.020
 UGM  plan-1  H3   0.020
 UGM  plan-1  H8   0.020
 UGM  plan-1  H9   0.020
 UGM  plan-1  H10  0.020
 UGM  plan-2  N1   0.020
 UGM  plan-2  C4   0.020
 UGM  plan-2  C5   0.020
 UGM  plan-2  C6   0.020
 UGM  plan-2  C7   0.020
 UGM  plan-2  N    0.020
 UGM  plan-2  C3   0.020
 UGM  plan-2  C2   0.020
 UGM  plan-2  C1   0.020
 UGM  plan-2  H1   0.020
 UGM  plan-2  H2   0.020
 UGM  plan-2  H4   0.020
 UGM  plan-3  C8   0.020
 UGM  plan-3  C1   0.020
 UGM  plan-3  C    0.020
 UGM  plan-3  O    0.020
 UGM  plan-3  N2   0.020
 UGM  plan-3  H7   0.020

