# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:07:00 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(3-cyanophenyl)-N-(4-methylpyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccncc1NC(=O)Cc2cccc(c2)C#N
#
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
 UGP  UGP  2-(3-cyanophenyl)-N-(4-methylpyridin-3-yl)acetamide  ligand  32  19  .  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_UGP
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
 UGP  N1   N  NH1   0  -0.743   7.4761  -0.1941  21.0038
 UGP  C4   C  CR16  0  -0.084   7.3270   0.8379  18.8031
 UGP  C5   C  CR6   0   0.208   6.7302   0.4381  19.9948
 UGP  C6   C  C     0   0.551   8.6493   0.2677  21.5051
 UGP  C7   C  CH2   0  -0.696   9.1653  -0.5309  22.6905
 UGP  C8   C  CR6   0   0.157  10.6540  -0.4315  22.8290
 UGP  C10  C  CR16  0  -0.233  12.6235   0.7846  23.5374
 UGP  C13  C  CSP   0   0.055  13.6834  -2.3818  21.9448
 UGP  N2   N  NS    0  -0.252  14.3507  -3.2285  21.5376
 UGP  C12  C  CR6   0   0.024  12.8568  -1.3329  22.4487
 UGP  C11  C  CR16  0  -0.254  13.4422  -0.2190  23.0476
 UGP  C9   C  CR16  0  -0.275  11.2443   0.6789  23.4278
 UGP  C14  C  CR16  0  -0.292  11.4704  -1.4395  22.3381
 UGP  O    O  O     0  -0.453   9.2235   1.2469  21.0731
 UGP  C1   C  CR6   0   0.161   5.3612   0.6509  20.1749
 UGP  C    C  CH3   0  -0.740   4.6677   0.2423  21.4357
 UGP  N    N  N     0  -0.408   6.6662   1.4355  17.8224
 UGP  C3   C  CR16  0  -0.070   5.3653   1.6416  17.9887
 UGP  C2   C  CR16  0  -0.369   4.6789   1.2623  19.1298
 UGP  H1   H  HNH1  0   0.418   7.0510  -0.9848  21.4647
 UGP  H2   H  HCR6  0   0.271   8.3821   0.6574  18.6371
 UGP  H3   H  HCH2  0   0.313   8.6737  -0.1317  23.5832
 UGP  H4   H  HCH2  0   0.292   8.8541  -1.5740  22.6107
 UGP  H5   H  HCR6  0   0.275  13.0632   1.6531  24.0078
 UGP  H6   H  HCR6  0   0.282  14.5178  -0.1455  23.1311
 UGP  H7   H  HCR6  0   0.268  10.6192   1.4677  23.8268
 UGP  H8   H  HCR6  0   0.278  11.0349  -2.3138  21.8715
 UGP  H9   H  HCH3  0   0.259   4.6648  -0.8433  21.5568
 UGP  H10  H  HCH3  0   0.259   5.1638   0.6615  22.3124
 UGP  H11  H  HCH3  0   0.264   3.6319   0.5747  21.4382
 UGP  H12  H  HCR6  0   0.264   4.8402   2.1272  17.1741
 UGP  H13  H  HCR6  0   0.268   3.6169   1.4547  19.2098

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
 UGP  N    C3   aromatic  1.328  0.020  1.328
 UGP  N    C4   aromatic  1.325  0.020  1.325
 UGP  C3   C2   aromatic  1.385  0.020  1.385
 UGP  C4   C5   aromatic  1.392  0.020  1.392
 UGP  C2   C1   aromatic  1.390  0.020  1.390
 UGP  C5   C1   aromatic  1.397  0.020  1.397
 UGP  C5   N1   single    1.405  0.020  1.405
 UGP  C1   C    single    1.496  0.020  1.496
 UGP  N2   C13  triple    1.152  0.020  1.152
 UGP  N1   C6   single    1.357  0.020  1.357
 UGP  O    C6   double    1.215  0.020  1.215
 UGP  C13  C12  single    1.427  0.020  1.427
 UGP  C6   C7   single    1.520  0.020  1.520
 UGP  C14  C12  aromatic  1.395  0.020  1.395
 UGP  C14  C8   aromatic  1.387  0.020  1.387
 UGP  C12  C11  aromatic  1.394  0.020  1.394
 UGP  C7   C8   single    1.498  0.020  1.498
 UGP  C8   C9   aromatic  1.393  0.020  1.393
 UGP  C11  C10  aromatic  1.385  0.020  1.385
 UGP  C9   C10  aromatic  1.388  0.020  1.388
 UGP  N1   H1   single    0.860  0.020  1.020
 UGP  C4   H2   single    0.930  0.020  1.080
 UGP  C7   H3   single    0.970  0.020  1.090
 UGP  C7   H4   single    0.970  0.020  1.090
 UGP  C10  H5   single    0.930  0.020  1.080
 UGP  C11  H6   single    0.930  0.020  1.080
 UGP  C9   H7   single    0.930  0.020  1.080
 UGP  C14  H8   single    0.930  0.020  1.080
 UGP  C    H9   single    0.970  0.020  1.090
 UGP  C    H10  single    0.970  0.020  1.090
 UGP  C    H11  single    0.970  0.020  1.090
 UGP  C3   H12  single    0.930  0.020  1.080
 UGP  C2   H13  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
 UGP  H1   N1   C6   117.53  3.000
 UGP  H1   N1   C5   117.19  3.000
 UGP  C6   N1   C5   124.83  3.000
 UGP  H2   C4   N    116.59  3.000
 UGP  H2   C4   C5   120.07  3.000
 UGP  N    C4   C5   123.34  3.000
 UGP  C1   C5   C4   119.13  3.000
 UGP  C1   C5   N1   119.75  3.000
 UGP  C4   C5   N1   121.11  3.000
 UGP  O    C6   C7   122.73  3.000
 UGP  C7   C6   N1   113.76  3.000
 UGP  O    C6   N1   123.49  3.000
 UGP  H4   C7   H3   106.26  3.000
 UGP  H4   C7   C8   110.70  3.000
 UGP  H3   C7   C8   110.28  3.000
 UGP  H4   C7   C6   110.39  3.000
 UGP  H3   C7   C6   106.98  3.000
 UGP  C8   C7   C6   112.00  3.000
 UGP  C14  C8   C9   118.82  3.000
 UGP  C9   C8   C7   120.91  3.000
 UGP  C14  C8   C7   120.26  3.000
 UGP  H5   C10  C9   119.98  3.000
 UGP  H5   C10  C11  119.72  3.000
 UGP  C9   C10  C11  120.30  3.000
 UGP  C12  C13  N2   180.00  3.000
 UGP  C14  C12  C11  120.84  3.000
 UGP  C11  C12  C13  119.73  3.000
 UGP  C14  C12  C13  119.43  3.000
 UGP  H6   C11  C12  120.35  3.000
 UGP  H6   C11  C10  120.76  3.000
 UGP  C12  C11  C10  118.88  3.000
 UGP  H7   C9   C10  119.30  3.000
 UGP  H7   C9   C8   119.64  3.000
 UGP  C10  C9   C8   121.06  3.000
 UGP  H8   C14  C12  119.72  3.000
 UGP  H8   C14  C8   120.18  3.000
 UGP  C12  C14  C8   120.10  3.000
 UGP  C2   C1   C    121.77  3.000
 UGP  C    C1   C5   121.42  3.000
 UGP  C2   C1   C5   116.81  3.000
 UGP  H11  C    H10  108.28  3.000
 UGP  H11  C    H9   107.51  3.000
 UGP  H10  C    H9   107.10  3.000
 UGP  H11  C    C1   111.09  3.000
 UGP  H10  C    C1   111.20  3.000
 UGP  H9   C    C1   111.48  3.000
 UGP  C3   N    C4   117.78  3.000
 UGP  H12  C3   C2   120.13  3.000
 UGP  H12  C3   N    116.75  3.000
 UGP  C2   C3   N    123.12  3.000
 UGP  H13  C2   C3   119.91  3.000
 UGP  H13  C2   C1   120.29  3.000
 UGP  C3   C2   C1   119.80  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
 UGP  CONST_01  C2   C3   N    C4     0.00   0.0  0
 UGP  CONST_02  C2   C1   C5   C4     0.00   0.0  0
 UGP  CONST_03  C3   N    C4   C5     0.00   0.0  0
 UGP  CONST_04  C3   C2   C1   C5     0.00   0.0  0
 UGP  CONST_05  C11  C12  C14  C8     0.00   0.0  0
 UGP  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 UGP  CONST_07  C14  C12  C11  C10    0.00   0.0  0
 UGP  CONST_08  C14  C8   C9   C10    0.00   0.0  0
 UGP  CONST_09  C9   C8   C14  C12    0.00   0.0  0
 UGP  CONST_10  C9   C10  C11  C12    0.00   0.0  0
 UGP  CONST_11  N    C3   C2   C1     0.00   0.0  0
 UGP  CONST_12  N    C4   C5   C1     0.00   0.0  0
 UGP  CONST_13  N    C4   C5   N1   180.00   0.0  0
 UGP  CONST_14  C2   C1   C5   N1   180.00   0.0  0
 UGP  CONST_15  C    C1   C5   C4   180.00   0.0  0
 UGP  CONST_16  C12  C14  C8   C7   180.00   0.0  0
 UGP  CONST_17  C10  C9   C8   C7   180.00   0.0  0
 UGP  CONST_18  C13  C12  C14  C8   180.00   0.0  0
 UGP  CONST_19  C13  C12  C11  C10  180.00   0.0  0
 UGP  CONST_20  C3   C2   C1   C    180.00   0.0  0
 UGP  CONST_21  H12  C3   N    C4   180.00   0.0  0
 UGP  CONST_22  H13  C2   C1   C5   180.00   0.0  0
 UGP  CONST_23  H5   C10  C9   C8   180.00   0.0  0
 UGP  CONST_24  H8   C14  C12  C11  180.00   0.0  0
 UGP  CONST_25  H7   C9   C10  C11  180.00   0.0  0
 UGP  CONST_26  H6   C11  C10  C9   180.00   0.0  0
 UGP  CONST_27  H2   C4   C5   C1   180.00   0.0  0
 UGP  CONST_31  O    C6   N1   C5     0.00   0.0  0
 UGP  CONST_32  C7   C6   N1   C5   180.00   0.0  0
 UGP  Var_01    C14  C8   C7   C6   -98.40  30.0  2
 UGP  Var_02    H9   C    C1   C5   -65.81  30.0  2
 UGP  Var_03    C8   C7   C6   N1   154.33  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
 UGP  plan-1  C7   0.020
 UGP  plan-1  C8   0.020
 UGP  plan-1  C10  0.020
 UGP  plan-1  C13  0.020
 UGP  plan-1  N2   0.020
 UGP  plan-1  C12  0.020
 UGP  plan-1  C11  0.020
 UGP  plan-1  C9   0.020
 UGP  plan-1  C14  0.020
 UGP  plan-1  H5   0.020
 UGP  plan-1  H6   0.020
 UGP  plan-1  H7   0.020
 UGP  plan-1  H8   0.020
 UGP  plan-2  N1   0.020
 UGP  plan-2  C4   0.020
 UGP  plan-2  C5   0.020
 UGP  plan-2  C1   0.020
 UGP  plan-2  C    0.020
 UGP  plan-2  N    0.020
 UGP  plan-2  C3   0.020
 UGP  plan-2  C2   0.020
 UGP  plan-2  H2   0.020
 UGP  plan-2  H12  0.020
 UGP  plan-2  H13  0.020
 UGP  plan-3  N1   0.020
 UGP  plan-3  C5   0.020
 UGP  plan-3  C6   0.020
 UGP  plan-3  C7   0.020
 UGP  plan-3  O    0.020
 UGP  plan-3  H1   0.020

