# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:40:32 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(NC(=O)c2ccccc2NCc3ccncc3)cc1
#
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
 8ST  8ST  N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide  ligand  40  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8ST
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
 8ST  CL16  CL  CL    0  -0.134  -6.7122   1.2622   0.3257
 8ST  C13   C   CR6   0  -0.059  -5.1600   0.4920   0.2670
 8ST  C12   C   CR16  0  -0.199  -4.9170  -0.6248   1.0514
 8ST  C11   C   CR16  0  -0.358  -3.6762  -1.2318   0.9991
 8ST  C14   C   CR16  0  -0.200  -4.1715   0.9929  -0.5614
 8ST  C15   C   CR16  0  -0.316  -2.9255   0.3840  -0.6139
 8ST  C10   C   CR6   0   0.392  -2.6634  -0.7402   0.1712
 8ST  N9    N   NH1   0  -0.752  -1.4540  -1.4368   0.1865
 8ST  C7    C   C     0   0.551  -0.2740  -1.1226  -0.4097
 8ST  O8    O   O     0  -0.479  -0.0995  -0.0795  -1.0268
 8ST  C2    C   CR6   0  -0.143   0.7971  -2.1399  -0.2439
 8ST  C3    C   CR6   0   0.382   2.1576  -1.7445  -0.1572
 8ST  C4    C   CR16  0  -0.353   3.1208  -2.7527   0.0127
 8ST  C5    C   CR16  0  -0.238   2.7620  -4.0867   0.0705
 8ST  C6    C   CR16  0  -0.281   1.4346  -4.4758  -0.0479
 8ST  C1    C   CR16  0  -0.292   0.4713  -3.4959  -0.2027
 8ST  N17   N   NH1   0  -0.709   2.5136  -0.4264  -0.1902
 8ST  C18   C   CH2   0  -0.322   3.8891   0.0006  -0.2009
 8ST  C19   C   CR6   0   0.168   3.9855   1.4946  -0.0662
 8ST  C24   C   CR16  0  -0.374   4.9156   2.2166  -0.8039
 8ST  C23   C   CR16  0  -0.059   5.0005   3.5889  -0.6273
 8ST  N22   N   N     0  -0.408   4.2324   4.2694   0.2146
 8ST  C21   C   CR16  0  -0.057   3.3422   3.5779   0.9180
 8ST  C20   C   CR16  0  -0.365   3.1799   2.2050   0.8169
 8ST  H12   H   HCR6  0   0.284  -5.6830  -1.0251   1.7006
 8ST  H11   H   HCR6  0   0.282  -3.4959  -2.1058   1.6128
 8ST  H14   H   HCR6  0   0.282  -4.3582   1.8631  -1.1758
 8ST  H15   H   HCR6  0   0.291  -2.1780   0.7985  -1.2685
 8ST  HN9   H   HNH1  0   0.425  -1.4496  -2.2536   0.7783
 8ST  H4    H   HCR6  0   0.277   4.1690  -2.4982   0.0817
 8ST  H5    H   HCR6  0   0.263   3.5378  -4.8320   0.1901
 8ST  H6    H   HCR6  0   0.256   1.1570  -5.5203  -0.0269
 8ST  H1    H   HCR6  0   0.265  -0.5615  -3.8005  -0.3223
 8ST  HN17  H   HNH1  0   0.399   1.8624   0.1781  -0.6666
 8ST  H18   H   HCH2  0   0.266   4.4163  -0.4479   0.6471
 8ST  H18A  H   HCH2  0   0.249   4.4226  -0.3222  -1.1041
 8ST  H24   H   HCR6  0   0.268   5.5693   1.7250  -1.5134
 8ST  H23   H   HCR6  0   0.265   5.7230   4.1625  -1.1974
 8ST  H21   H   HCR6  0   0.264   2.7219   4.1449   1.6032
 8ST  H20   H   HCR6  0   0.269   2.4354   1.7058   1.4230

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
 8ST  CL16  C13   single    1.734  0.020  1.734
 8ST  C13   C14   aromatic  1.384  0.020  1.384
 8ST  C13   C12   aromatic  1.386  0.020  1.386
 8ST  C12   C11   aromatic  1.382  0.020  1.382
 8ST  C12   H12   single    0.930  0.020  1.080
 8ST  C11   C10   aromatic  1.397  0.020  1.397
 8ST  C11   H11   single    0.930  0.020  1.080
 8ST  C14   C15   aromatic  1.388  0.020  1.388
 8ST  C14   H14   single    0.930  0.020  1.080
 8ST  C15   C10   aromatic  1.396  0.020  1.396
 8ST  C15   H15   single    0.930  0.020  1.080
 8ST  C10   N9    single    1.396  0.020  1.396
 8ST  C7    N9    single    1.359  0.020  1.359
 8ST  N9    HN9   single    0.860  0.020  1.020
 8ST  O8    C7    double    1.224  0.020  1.224
 8ST  C7    C2    single    1.486  0.020  1.486
 8ST  C2    C3    aromatic  1.420  0.020  1.420
 8ST  C2    C1    aromatic  1.395  0.020  1.395
 8ST  N17   C3    single    1.366  0.020  1.366
 8ST  C3    C4    aromatic  1.405  0.020  1.405
 8ST  C4    C5    aromatic  1.383  0.020  1.383
 8ST  C4    H4    single    0.930  0.020  1.080
 8ST  C6    C5    aromatic  1.388  0.020  1.388
 8ST  C5    H5    single    0.930  0.020  1.080
 8ST  C1    C6    aromatic  1.383  0.020  1.383
 8ST  C6    H6    single    0.930  0.020  1.080
 8ST  C1    H1    single    0.930  0.020  1.080
 8ST  C18   N17   single    1.440  0.020  1.440
 8ST  N17   HN17  single    0.890  0.020  1.040
 8ST  C18   C19   single    1.503  0.020  1.503
 8ST  C18   H18   single    0.970  0.020  1.090
 8ST  C18   H18A  single    0.970  0.020  1.090
 8ST  C19   C20   aromatic  1.391  0.020  1.391
 8ST  C19   C24   aromatic  1.389  0.020  1.389
 8ST  C24   C23   aromatic  1.386  0.020  1.386
 8ST  C24   H24   single    0.930  0.020  1.080
 8ST  C23   N22   aromatic  1.327  0.020  1.327
 8ST  C23   H23   single    0.930  0.020  1.080
 8ST  C21   N22   aromatic  1.329  0.020  1.329
 8ST  C20   C21   aromatic  1.386  0.020  1.386
 8ST  C21   H21   single    0.930  0.020  1.080
 8ST  C20   H20   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
 8ST  C14   C13  C12   120.35  3.000
 8ST  C12   C13  CL16  119.72  3.000
 8ST  C14   C13  CL16  119.94  3.000
 8ST  H12   C12  C11   119.75  3.000
 8ST  H12   C12  C13   120.92  3.000
 8ST  C11   C12  C13   119.32  3.000
 8ST  H11   C11  C10   119.93  3.000
 8ST  H11   C11  C12   118.84  3.000
 8ST  C10   C11  C12   121.23  3.000
 8ST  H14   C14  C15   119.11  3.000
 8ST  H14   C14  C13   120.54  3.000
 8ST  C15   C14  C13   120.35  3.000
 8ST  H15   C15  C10   121.44  3.000
 8ST  H15   C15  C14   118.52  3.000
 8ST  C10   C15  C14   120.04  3.000
 8ST  N9    C10  C15   124.80  3.000
 8ST  N9    C10  C11   116.48  3.000
 8ST  C15   C10  C11   118.71  3.000
 8ST  HN9   N9   C7    116.16  3.000
 8ST  HN9   N9   C10   114.48  3.000
 8ST  C7    N9   C10   129.21  3.000
 8ST  C2    C7   O8    122.45  3.000
 8ST  C2    C7   N9    114.74  3.000
 8ST  O8    C7   N9    122.81  3.000
 8ST  C1    C2   C3    119.52  3.000
 8ST  C1    C2   C7    120.01  3.000
 8ST  C3    C2   C7    120.45  3.000
 8ST  N17   C3   C4    121.13  3.000
 8ST  C4    C3   C2    117.69  3.000
 8ST  N17   C3   C2    121.15  3.000
 8ST  H4    C4   C5    118.43  3.000
 8ST  H4    C4   C3    120.24  3.000
 8ST  C5    C4   C3    121.31  3.000
 8ST  H5    C5   C6    120.11  3.000
 8ST  H5    C5   C4    118.89  3.000
 8ST  C6    C5   C4    120.99  3.000
 8ST  H6    C6   C1    120.53  3.000
 8ST  H6    C6   C5    120.98  3.000
 8ST  C1    C6   C5    118.49  3.000
 8ST  H1    C1   C6    118.51  3.000
 8ST  H1    C1   C2    119.51  3.000
 8ST  C6    C1   C2    121.96  3.000
 8ST  HN17  N17  C18   115.83  3.000
 8ST  HN17  N17  C3    114.94  3.000
 8ST  C18   N17  C3    122.36  3.000
 8ST  H18A  C18  H18   106.43  3.000
 8ST  H18A  C18  C19   109.57  3.000
 8ST  H18   C18  C19   107.87  3.000
 8ST  H18A  C18  N17   112.53  3.000
 8ST  H18   C18  N17   109.44  3.000
 8ST  C19   C18  N17   110.81  3.000
 8ST  C20   C19  C24   117.36  3.000
 8ST  C24   C19  C18   120.79  3.000
 8ST  C20   C19  C18   121.84  3.000
 8ST  H24   C24  C23   119.73  3.000
 8ST  H24   C24  C19   121.07  3.000
 8ST  C23   C24  C19   119.20  3.000
 8ST  H23   C23  N22   116.60  3.000
 8ST  H23   C23  C24   119.83  3.000
 8ST  N22   C23  C24   123.57  3.000
 8ST  C21   N22  C23   117.17  3.000
 8ST  H21   C21  C20   119.80  3.000
 8ST  H21   C21  N22   116.47  3.000
 8ST  C20   C21  N22   123.73  3.000
 8ST  H20   C20  C21   119.78  3.000
 8ST  H20   C20  C19   121.24  3.000
 8ST  C21   C20  C19   118.98  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
 8ST  CONST_01  C10  C15  C14  C13      0.00   0.0  0
 8ST  CONST_02  C10  C11  C12  C13      0.00   0.0  0
 8ST  CONST_03  C15  C14  C13  C12      0.00   0.0  0
 8ST  CONST_04  C15  C10  C11  C12      0.00   0.0  0
 8ST  CONST_05  C14  C13  C12  C11      0.00   0.0  0
 8ST  CONST_06  C14  C15  C10  C11      0.00   0.0  0
 8ST  CONST_07  C5   C4   C3   C2       0.00   0.0  0
 8ST  CONST_08  C5   C6   C1   C2       0.00   0.0  0
 8ST  CONST_09  C6   C1   C2   C3       0.00   0.0  0
 8ST  CONST_10  C6   C5   C4   C3       0.00   0.0  0
 8ST  CONST_11  C1   C2   C3   C4       0.00   0.0  0
 8ST  CONST_12  C1   C6   C5   C4       0.00   0.0  0
 8ST  CONST_13  N22  C21  C20  C19      0.00   0.0  0
 8ST  CONST_14  N22  C23  C24  C19      0.00   0.0  0
 8ST  CONST_15  C21  C20  C19  C24      0.00   0.0  0
 8ST  CONST_16  C21  N22  C23  C24      0.00   0.0  0
 8ST  CONST_17  C20  C19  C24  C23      0.00   0.0  0
 8ST  CONST_18  C20  C21  N22  C23      0.00   0.0  0
 8ST  CONST_19  C15  C14  C13  CL16   180.00   0.0  0
 8ST  CONST_20  C11  C12  C13  CL16   180.00   0.0  0
 8ST  CONST_21  N9   C10  C11  C12    180.00   0.0  0
 8ST  CONST_22  N9   C10  C15  C14    180.00   0.0  0
 8ST  CONST_23  C4   C3   C2   C7     180.00   0.0  0
 8ST  CONST_24  C6   C1   C2   C7     180.00   0.0  0
 8ST  CONST_25  N17  C3   C4   C5     180.00   0.0  0
 8ST  CONST_26  N17  C3   C2   C1     180.00   0.0  0
 8ST  CONST_27  C21  C20  C19  C18    180.00   0.0  0
 8ST  CONST_28  C23  C24  C19  C18    180.00   0.0  0
 8ST  CONST_29  H15  C15  C14  C13    180.00   0.0  0
 8ST  CONST_30  H11  C11  C12  C13    180.00   0.0  0
 8ST  CONST_31  H14  C14  C13  C12    180.00   0.0  0
 8ST  CONST_32  H12  C12  C13  C14    180.00   0.0  0
 8ST  CONST_33  H4   C4   C3   C2     180.00   0.0  0
 8ST  CONST_34  H6   C6   C1   C2     180.00   0.0  0
 8ST  CONST_35  H1   C1   C2   C3     180.00   0.0  0
 8ST  CONST_36  H5   C5   C4   C3     180.00   0.0  0
 8ST  CONST_37  H21  C21  C20  C19    180.00   0.0  0
 8ST  CONST_38  H23  C23  C24  C19    180.00   0.0  0
 8ST  CONST_39  H20  C20  C19  C24    180.00   0.0  0
 8ST  CONST_40  H24  C24  C23  N22    180.00   0.0  0
 8ST  CONST_41  C2   C7   N9   C10    180.00   0.0  0
 8ST  CONST_42  C7   N9   C10  C11    180.00   0.0  0
 8ST  CONST_43  C7   N9   C10  C15      0.00   0.0  0
 8ST  CONST_44  C18  N17  C3   C2     180.00   0.0  0
 8ST  CONST_45  C18  N17  C3   C4       0.00   0.0  0
 8ST  CONST_46  HN9  N9   C10  C11      0.00   0.0  0
 8ST  CONST_48  O8   C7   N9   C10      0.00   0.0  0
 8ST  Var_01    C3   C2   C7   N9    -147.16  30.0  2
 8ST  Var_02    C19  C18  N17  C3    -172.96  30.0  1
 8ST  Var_03    C20  C19  C18  N17     41.59  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
 8ST  plan-1  CL16  0.020
 8ST  plan-1  C13   0.020
 8ST  plan-1  C12   0.020
 8ST  plan-1  C11   0.020
 8ST  plan-1  C14   0.020
 8ST  plan-1  C15   0.020
 8ST  plan-1  C10   0.020
 8ST  plan-1  N9    0.020
 8ST  plan-1  H12   0.020
 8ST  plan-1  H11   0.020
 8ST  plan-1  H14   0.020
 8ST  plan-1  H15   0.020
 8ST  plan-2  C7    0.020
 8ST  plan-2  C2    0.020
 8ST  plan-2  C3    0.020
 8ST  plan-2  C4    0.020
 8ST  plan-2  C5    0.020
 8ST  plan-2  C6    0.020
 8ST  plan-2  C1    0.020
 8ST  plan-2  N17   0.020
 8ST  plan-2  H4    0.020
 8ST  plan-2  H5    0.020
 8ST  plan-2  H6    0.020
 8ST  plan-2  H1    0.020
 8ST  plan-3  C18   0.020
 8ST  plan-3  C19   0.020
 8ST  plan-3  C24   0.020
 8ST  plan-3  C23   0.020
 8ST  plan-3  N22   0.020
 8ST  plan-3  C21   0.020
 8ST  plan-3  C20   0.020
 8ST  plan-3  H24   0.020
 8ST  plan-3  H23   0.020
 8ST  plan-3  H21   0.020
 8ST  plan-3  H20   0.020
 8ST  plan-4  C10   0.020
 8ST  plan-4  N9    0.020
 8ST  plan-4  C7    0.020
 8ST  plan-4  O8    0.020
 8ST  plan-4  C2    0.020
 8ST  plan-4  HN9   0.020
 8ST  plan-5  C3    0.020
 8ST  plan-5  N17   0.020
 8ST  plan-5  C18   0.020
 8ST  plan-5  HN17  0.020

