# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:06:07 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)CCC(=O)c1sccc1)c2cccnc2
#
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
 479  479  4-oxo-N-[(1S)-1-(pyridin-3-yl)ethyl]-4-(thiophen-2-yl)butanamide  ligand  36  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_479
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
 479  C4   C  CH2   0  -0.585  -1.7727  -0.0426   0.1078
 479  C5   C  C     0   0.389  -2.8522   0.9928   0.2919
 479  C6   C  CR5   0  -0.291  -4.2411   0.5709   0.0558
 479  N1   N  N     0  -0.402   5.8404   1.3776  -0.7855
 479  C7   C  CR15  0  -0.181  -5.3562   1.3594   0.1854
 479  C8   C  CR15  0  -0.177  -6.5536   0.6704  -0.1062
 479  C9   C  CR15  0  -0.443  -6.3316  -0.6320  -0.4544
 479  C10  C  CR6   0   0.046   4.2734  -0.3122  -0.1124
 479  C11  C  CR16  0  -0.200   5.0180  -0.5411   1.0375
 479  C12  C  CR16  0  -0.314   6.1728   0.1929   1.2588
 479  C13  C  CR16  0  -0.071   6.5412   1.1419   0.3180
 479  C14  C  CR16  0  -0.092   4.7408   0.6635  -0.9886
 479  O1   O  O     0  -0.401  -2.6122   2.1350   0.6257
 479  S    S  S2    0   0.248  -4.6750  -1.0274  -0.4289
 479  C3   C  CH2   0  -0.581  -0.3732   0.4911   0.3558
 479  C2   C  C     0   0.575   0.6700  -0.6031   0.2475
 479  O    O  O     0  -0.501   0.4483  -1.7539   0.5979
 479  N    N  NH1   0  -0.638   1.8614  -0.1977  -0.2243
 479  C1   C  CH1   0  -0.175   3.0041  -1.0819  -0.3901
 479  C    C  CH3   0  -0.648   3.0083  -1.7494  -1.7630
 479  H1   H  HCH2  0   0.286  -1.9843  -0.8800   0.7791
 479  H2   H  HCH2  0   0.285  -1.8527  -0.4477  -0.9066
 479  H3   H  HCR5  0   0.277  -5.3119   2.3980   0.4808
 479  H4   H  HCR5  0   0.277  -7.5369   1.1147  -0.0594
 479  H5   H  HCR5  0   0.309  -7.0634  -1.3783  -0.7244
 479  H6   H  HCR6  0   0.272   4.6973  -1.2887   1.7530
 479  H7   H  HCR6  0   0.273   6.7766   0.0356   2.1420
 479  H8   H  HCR6  0   0.266   7.4382   1.7344   0.4594
 479  H9   H  HCR6  0   0.262   4.1994   0.8818  -1.9049
 479  H10  H  HCH2  0   0.264  -0.1448   1.3071  -0.3314
 479  H11  H  HCH2  0   0.284  -0.3034   0.9088   1.3643
 479  H12  H  HNH1  0   0.404   1.9477   0.7525  -0.5490
 479  H13  H  HCH1  0   0.270   2.9172  -1.8614   0.3686
 479  H14  H  HCH3  0   0.239   3.8594  -2.4243  -1.8561
 479  H15  H  HCH3  0   0.245   2.0975  -2.3323  -1.8988
 479  H16  H  HCH3  0   0.229   3.0644  -1.0180  -2.5698

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
 479  C13  C12  aromatic  1.386  0.020  1.386
 479  C13  N1   aromatic  1.328  0.020  1.328
 479  C12  C11  aromatic  1.386  0.020  1.386
 479  N1   C14  aromatic  1.327  0.020  1.327
 479  C11  C10  aromatic  1.389  0.020  1.389
 479  C8   C9   aromatic  1.366  0.020  1.366
 479  C8   C7   aromatic  1.412  0.020  1.412
 479  O    C2   double    1.223  0.020  1.223
 479  C9   S    aromatic  1.703  0.020  1.703
 479  C14  C10  aromatic  1.392  0.020  1.392
 479  C10  C1   single    1.510  0.020  1.510
 479  C7   C6   aromatic  1.372  0.020  1.372
 479  S    C6   aromatic  1.726  0.020  1.726
 479  C6   C5   single    1.471  0.020  1.471
 479  C2   N    single    1.344  0.020  1.344
 479  C2   C3   single    1.516  0.020  1.516
 479  C4   C5   single    1.507  0.020  1.507
 479  C4   C3   single    1.518  0.020  1.518
 479  C1   N    single    1.454  0.020  1.454
 479  C1   C    single    1.527  0.020  1.527
 479  C5   O1   double    1.214  0.020  1.214
 479  C4   H1   single    0.970  0.020  1.090
 479  C4   H2   single    0.970  0.020  1.090
 479  C7   H3   single    0.930  0.020  1.080
 479  C8   H4   single    0.930  0.020  1.080
 479  C9   H5   single    0.930  0.020  1.080
 479  C11  H6   single    0.930  0.020  1.080
 479  C12  H7   single    0.930  0.020  1.080
 479  C13  H8   single    0.930  0.020  1.080
 479  C14  H9   single    0.930  0.020  1.080
 479  C3   H10  single    0.970  0.020  1.090
 479  C3   H11  single    0.970  0.020  1.090
 479  N    H12  single    0.860  0.020  1.020
 479  C1   H13  single    0.970  0.020  1.090
 479  C    H14  single    0.970  0.020  1.090
 479  C    H15  single    0.970  0.020  1.090
 479  C    H16  single    0.970  0.020  1.090

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
 479  H2   C4   H1   105.73  3.000
 479  H2   C4   C3   110.40  3.000
 479  H1   C4   C3   110.31  3.000
 479  H2   C4   C5   108.35  3.000
 479  H1   C4   C5   108.20  3.000
 479  C3   C4   C5   113.51  3.000
 479  O1   C5   C6   120.05  3.000
 479  O1   C5   C4   122.57  3.000
 479  C6   C5   C4   117.38  3.000
 479  S    C6   C7   110.76  3.000
 479  S    C6   C5   123.25  3.000
 479  C7   C6   C5   125.99  3.000
 479  C14  N1   C13  117.97  3.000
 479  H3   C7   C8   124.07  3.000
 479  H3   C7   C6   123.02  3.000
 479  C8   C7   C6   112.91  3.000
 479  H4   C8   C9   123.44  3.000
 479  H4   C8   C7   124.22  3.000
 479  C9   C8   C7   112.34  3.000
 479  H5   C9   S    120.17  3.000
 479  H5   C9   C8   127.78  3.000
 479  S    C9   C8   112.05  3.000
 479  C1   C10  C14  121.58  3.000
 479  C1   C10  C11  121.25  3.000
 479  C14  C10  C11  117.17  3.000
 479  H6   C11  C12  120.43  3.000
 479  H6   C11  C10  120.12  3.000
 479  C12  C11  C10  119.44  3.000
 479  H7   C12  C13  120.37  3.000
 479  H7   C12  C11  121.24  3.000
 479  C13  C12  C11  118.39  3.000
 479  H8   C13  C12  120.36  3.000
 479  H8   C13  N1   116.60  3.000
 479  C12  C13  N1   123.03  3.000
 479  H9   C14  C10  120.28  3.000
 479  H9   C14  N1   115.73  3.000
 479  C10  C14  N1   123.99  3.000
 479  C9   S    C6    91.94  3.000
 479  H11  C3   H10  106.37  3.000
 479  H11  C3   C2   107.31  3.000
 479  H10  C3   C2   110.54  3.000
 479  H11  C3   C4   110.10  3.000
 479  H10  C3   C4   110.67  3.000
 479  C2   C3   C4   111.66  3.000
 479  N    C2   O    123.02  3.000
 479  N    C2   C3   114.67  3.000
 479  O    C2   C3   122.28  3.000
 479  H12  N    C1   117.98  3.000
 479  H12  N    C2   118.25  3.000
 479  C1   N    C2   123.58  3.000
 479  H13  C1   C    108.25  3.000
 479  H13  C1   N    107.00  3.000
 479  C    C1   N    111.75  3.000
 479  H13  C1   C10  107.65  3.000
 479  C    C1   C10  112.70  3.000
 479  N    C1   C10  109.24  3.000
 479  H16  C    H15  108.04  3.000
 479  H16  C    H14  108.18  3.000
 479  H15  C    H14  108.10  3.000
 479  H16  C    C1   111.86  3.000
 479  H15  C    C1   110.09  3.000
 479  H14  C    C1   110.46  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
 479  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 479  CONST_02  C8   C9   S    C6     0.00   0.0  0
 479  CONST_03  C11  C12  C13  N1     0.00   0.0  0
 479  CONST_04  C11  C10  C14  N1     0.00   0.0  0
 479  CONST_05  S    C9   C8   C7     0.00   0.0  0
 479  CONST_06  C9   S    C6   C7     0.00   0.0  0
 479  CONST_07  S    C6   C7   C8     0.00   0.0  0
 479  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 479  CONST_09  C13  N1   C14  C10    0.00   0.0  0
 479  CONST_10  C14  N1   C13  C12    0.00   0.0  0
 479  CONST_11  C14  C10  C11  C12    0.00   0.0  0
 479  CONST_12  C8   C7   C6   C5   180.00   0.0  0
 479  CONST_13  C9   S    C6   C5   180.00   0.0  0
 479  CONST_14  C1   C10  C14  N1   180.00   0.0  0
 479  CONST_15  C1   C10  C11  C12  180.00   0.0  0
 479  CONST_16  H4   C8   C7   C6   180.00   0.0  0
 479  CONST_17  H5   C9   S    C6   180.00   0.0  0
 479  CONST_18  H7   C12  C13  N1   180.00   0.0  0
 479  CONST_19  H3   C7   C8   C9   180.00   0.0  0
 479  CONST_20  H8   C13  C12  C11  180.00   0.0  0
 479  CONST_21  H9   C14  C10  C11  180.00   0.0  0
 479  CONST_22  H6   C11  C12  C13  180.00   0.0  0
 479  CONST_23  C1   N    C2   C3   180.00   0.0  0
 479  CONST_24  C1   N    C2   O      0.00   0.0  0
 479  CONST_25  H12  N    C2   C3     0.00   0.0  0
 479  Var_01    C7   C6   C5   C4   179.24  30.0  2
 479  Var_02    C3   C4   C5   C6   179.24  30.0  1
 479  Var_03    O    C2   C3   C4   -34.44  30.0  2
 479  Var_04    C2   C3   C4   C5   176.31  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 479  chir_01  C1  C10  N  C  negativ

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
 479  plan-1  C5   0.020
 479  plan-1  C6   0.020
 479  plan-1  C7   0.020
 479  plan-1  C8   0.020
 479  plan-1  C9   0.020
 479  plan-1  S    0.020
 479  plan-1  H3   0.020
 479  plan-1  H4   0.020
 479  plan-1  H5   0.020
 479  plan-2  N1   0.020
 479  plan-2  C10  0.020
 479  plan-2  C11  0.020
 479  plan-2  C12  0.020
 479  plan-2  C13  0.020
 479  plan-2  C14  0.020
 479  plan-2  C1   0.020
 479  plan-2  H6   0.020
 479  plan-2  H7   0.020
 479  plan-2  H8   0.020
 479  plan-2  H9   0.020
 479  plan-3  C3   0.020
 479  plan-3  C2   0.020
 479  plan-3  O    0.020
 479  plan-3  N    0.020
 479  plan-3  C1   0.020
 479  plan-3  H12  0.020
 479  plan-4  C4   0.020
 479  plan-4  C5   0.020
 479  plan-4  C6   0.020
 479  plan-4  O1   0.020

