# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 13:24:23 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-(benzylamino)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(NCc2ccccc2)nc1
#
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
 4FD  4FD  6-(benzylamino)pyridine-3-carboxamide  ligand  30  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4FD
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
 4FD  N1   N  NH2   0  -0.821   5.4505  -1.1040  -0.0580
 4FD  C4   C  CR6   0  -0.164   3.2997  -0.0339   0.1370
 4FD  C5   C  CR16  0  -0.150   2.5702   1.1594   0.1324
 4FD  C6   C  CR16  0  -0.399   1.2019   1.1391   0.0248
 4FD  C7   C  CR6   0   0.516   0.5542  -0.1117  -0.0511
 4FD  C10  C  CR6   0   0.075  -3.1142   0.4127  -0.1336
 4FD  C13  C  CR16  0  -0.263  -5.7269  -0.5253   0.1621
 4FD  C15  C  CR16  0  -0.282  -3.6342   0.1581   1.1335
 4FD  C17  C  CR16  0  -0.073   2.5601  -1.2094   0.0559
 4FD  C12  C  CR16  0  -0.242  -5.2153  -0.2765  -1.1040
 4FD  C14  C  CR16  0  -0.242  -4.9330  -0.3061   1.2820
 4FD  C11  C  CR16  0  -0.294  -3.9141   0.1891  -1.2491
 4FD  C2   C  C     0   0.484   4.7768   0.0138   0.2667
 4FD  C9   C  CH2   0  -0.339  -1.6951   0.8862  -0.2868
 4FD  N16  N  N     0  -0.463   1.2437  -1.2592  -0.0327
 4FD  N8   N  NH1   0  -0.646  -0.7861  -0.2281  -0.1295
 4FD  O3   O  O     0  -0.491   5.3429   1.0266   0.6628
 4FD  H1   H  HNH2  0   0.409   5.0220  -1.8729  -0.5421
 4FD  H2   H  HNH2  0   0.403   6.4564  -1.1046  -0.0127
 4FD  H3   H  HCR6  0   0.269   3.0863   2.1082   0.2007
 4FD  H4   H  HCR6  0   0.278   0.6407   2.0627  -0.0014
 4FD  H5   H  HCR6  0   0.258  -6.7408  -0.8864   0.2774
 4FD  H6   H  HCR6  0   0.254  -3.0208   0.3291   2.0104
 4FD  H7   H  HCR6  0   0.256   3.0508  -2.1777   0.0827
 4FD  H8   H  HCR6  0   0.258  -5.8282  -0.4441  -1.9803
 4FD  H9   H  HCR6  0   0.258  -5.3273  -0.4945   2.2721
 4FD  H10  H  HCR6  0   0.255  -3.5186   0.3829  -2.2391
 4FD  H11  H  HCH2  0   0.251  -1.5637   1.3712  -1.2606
 4FD  H12  H  HCH2  0   0.257  -1.4800   1.6388   0.4759
 4FD  H13  H  HNH1  0   0.390  -1.1387  -1.1546  -0.3120

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
 4FD  C13  C12  aromatic  1.388  0.020  1.388
 4FD  C13  C14  aromatic  1.390  0.020  1.390
 4FD  C12  C11  aromatic  1.390  0.020  1.390
 4FD  C14  C15  aromatic  1.387  0.020  1.387
 4FD  C11  C10  aromatic  1.391  0.020  1.391
 4FD  C15  C10  aromatic  1.393  0.020  1.393
 4FD  C10  C9   single    1.504  0.020  1.504
 4FD  C9   N8   single    1.447  0.020  1.447
 4FD  N8   C7   single    1.348  0.020  1.348
 4FD  C6   C7   aromatic  1.411  0.020  1.411
 4FD  C6   C5   aromatic  1.373  0.020  1.373
 4FD  C7   N16  aromatic  1.339  0.020  1.339
 4FD  C5   C4   aromatic  1.399  0.020  1.399
 4FD  N16  C17  aromatic  1.320  0.020  1.320
 4FD  C4   C17  aromatic  1.391  0.020  1.391
 4FD  C4   C2   single    1.484  0.020  1.484
 4FD  C2   O3   double    1.226  0.020  1.226
 4FD  C2   N1   single    1.345  0.020  1.345
 4FD  N1   H1   single    0.860  0.020  1.020
 4FD  N1   H2   single    0.860  0.020  1.020
 4FD  C5   H3   single    0.930  0.020  1.080
 4FD  C6   H4   single    0.930  0.020  1.080
 4FD  C13  H5   single    0.930  0.020  1.080
 4FD  C15  H6   single    0.930  0.020  1.080
 4FD  C17  H7   single    0.930  0.020  1.080
 4FD  C12  H8   single    0.930  0.020  1.080
 4FD  C14  H9   single    0.930  0.020  1.080
 4FD  C11  H10  single    0.930  0.020  1.080
 4FD  C9   H11  single    0.970  0.020  1.090
 4FD  C9   H12  single    0.970  0.020  1.090
 4FD  N8   H13  single    0.860  0.020  1.020

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
 4FD  H2   N1   H1   116.58  3.000
 4FD  H2   N1   C2   119.34  3.000
 4FD  H1   N1   C2   122.60  3.000
 4FD  C2   C4   C17  124.17  3.000
 4FD  C2   C4   C5   119.48  3.000
 4FD  C17  C4   C5   116.32  3.000
 4FD  H3   C5   C6   119.56  3.000
 4FD  H3   C5   C4   119.94  3.000
 4FD  C6   C5   C4   120.50  3.000
 4FD  H4   C6   C7   121.19  3.000
 4FD  H4   C6   C5   120.44  3.000
 4FD  C7   C6   C5   118.36  3.000
 4FD  N8   C7   N16  116.04  3.000
 4FD  N16  C7   C6   121.52  3.000
 4FD  N8   C7   C6   122.44  3.000
 4FD  C9   C10  C11  120.77  3.000
 4FD  C9   C10  C15  120.16  3.000
 4FD  C11  C10  C15  119.04  3.000
 4FD  H5   C13  C14  120.11  3.000
 4FD  H5   C13  C12  120.14  3.000
 4FD  C14  C13  C12  119.74  3.000
 4FD  H6   C15  C14  119.74  3.000
 4FD  H6   C15  C10  119.72  3.000
 4FD  C14  C15  C10  120.53  3.000
 4FD  H7   C17  N16  114.74  3.000
 4FD  H7   C17  C4   120.78  3.000
 4FD  N16  C17  C4   124.46  3.000
 4FD  H8   C12  C11  119.84  3.000
 4FD  H8   C12  C13  120.14  3.000
 4FD  C11  C12  C13  120.03  3.000
 4FD  H9   C14  C15  119.82  3.000
 4FD  H9   C14  C13  120.10  3.000
 4FD  C15  C14  C13  120.08  3.000
 4FD  H10  C11  C12  119.81  3.000
 4FD  H10  C11  C10  119.62  3.000
 4FD  C12  C11  C10  120.58  3.000
 4FD  O3   C2   C4   120.97  3.000
 4FD  O3   C2   N1   122.23  3.000
 4FD  C4   C2   N1   116.80  3.000
 4FD  H12  C9   H11  106.96  3.000
 4FD  H12  C9   N8   109.32  3.000
 4FD  H11  C9   N8   111.24  3.000
 4FD  H12  C9   C10  109.35  3.000
 4FD  H11  C9   C10  110.06  3.000
 4FD  N8   C9   C10  109.83  3.000
 4FD  C17  N16  C7   118.82  3.000
 4FD  H13  N8   C9   117.93  3.000
 4FD  H13  N8   C7   115.97  3.000
 4FD  C9   N8   C7   124.38  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
 4FD  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 4FD  CONST_02  C7   N16  C17  C4      0.00   0.0  0
 4FD  CONST_03  N16  C7   C6   C5      0.00   0.0  0
 4FD  CONST_04  N16  C17  C4   C5      0.00   0.0  0
 4FD  CONST_05  C17  N16  C7   C6      0.00   0.0  0
 4FD  CONST_06  C17  C4   C5   C6      0.00   0.0  0
 4FD  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 4FD  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 4FD  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 4FD  CONST_10  C12  C11  C10  C15     0.00   0.0  0
 4FD  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 4FD  CONST_12  C11  C10  C15  C14     0.00   0.0  0
 4FD  CONST_13  N8   C7   C6   C5    180.00   0.0  0
 4FD  CONST_14  C2   C4   C5   C6    180.00   0.0  0
 4FD  CONST_15  N8   C7   N16  C17   180.00   0.0  0
 4FD  CONST_16  C9   C10  C11  C12   180.00   0.0  0
 4FD  CONST_17  C9   C10  C15  C14   180.00   0.0  0
 4FD  CONST_18  N16  C17  C4   C2    180.00   0.0  0
 4FD  CONST_19  H4   C6   C5   C4    180.00   0.0  0
 4FD  CONST_20  H7   C17  C4   C5    180.00   0.0  0
 4FD  CONST_21  H3   C5   C6   C7    180.00   0.0  0
 4FD  CONST_22  H8   C12  C11  C10   180.00   0.0  0
 4FD  CONST_23  H9   C14  C15  C10   180.00   0.0  0
 4FD  CONST_24  H10  C11  C12  C13   180.00   0.0  0
 4FD  CONST_25  H6   C15  C14  C13   180.00   0.0  0
 4FD  CONST_26  H5   C13  C14  C15   180.00   0.0  0
 4FD  CONST_27  C9   N8   C7   C6      0.00   0.0  0
 4FD  CONST_28  N16  C7   N8   C9    180.00   0.0  0
 4FD  CONST_29  H13  N8   C7   C6    180.00   0.0  0
 4FD  CONST_30  H1   N1   C2   C4      0.00   0.0  0
 4FD  CONST_31  H2   N1   C2   C4    180.00   0.0  0
 4FD  Var_01    C5   C4   C2   N1   -164.21  30.0  2
 4FD  Var_02    C10  C9   N8   C7   -171.69  30.0  1
 4FD  Var_03    N8   C9   C10  C15    77.53  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
 4FD  plan-1  C4   0.020
 4FD  plan-1  C5   0.020
 4FD  plan-1  C6   0.020
 4FD  plan-1  C7   0.020
 4FD  plan-1  C17  0.020
 4FD  plan-1  C2   0.020
 4FD  plan-1  N16  0.020
 4FD  plan-1  N8   0.020
 4FD  plan-1  H3   0.020
 4FD  plan-1  H4   0.020
 4FD  plan-1  H7   0.020
 4FD  plan-2  C10  0.020
 4FD  plan-2  C13  0.020
 4FD  plan-2  C15  0.020
 4FD  plan-2  C12  0.020
 4FD  plan-2  C14  0.020
 4FD  plan-2  C11  0.020
 4FD  plan-2  C9   0.020
 4FD  plan-2  H5   0.020
 4FD  plan-2  H6   0.020
 4FD  plan-2  H8   0.020
 4FD  plan-2  H9   0.020
 4FD  plan-2  H10  0.020
 4FD  plan-3  N1   0.020
 4FD  plan-3  C4   0.020
 4FD  plan-3  C2   0.020
 4FD  plan-3  O3   0.020
 4FD  plan-3  H1   0.020
 4FD  plan-3  H2   0.020
 4FD  plan-4  C7   0.020
 4FD  plan-4  C9   0.020
 4FD  plan-4  N8   0.020
 4FD  plan-4  H13  0.020

