# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:00:32 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-[(cyclopentylmethyl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(NCC2CCCC2)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
 4GN  4GN  6-[(cyclopentylmethyl)amino]pyridine-3-carboxamide  ligand  33  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4GN
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
 4GN  C2   C  CR16  0  -0.151   2.3060   1.1480  -0.0904
 4GN  C3   C  CR16  0  -0.401   0.9426   1.0371   0.0165
 4GN  C11  C  CR16  0  -0.074   2.4757  -1.1792   0.3226
 4GN  C1   C  CR6   0  -0.166   3.1233   0.0205   0.0450
 4GN  C4   C  CR6   0   0.514   0.3906  -0.2351   0.2786
 4GN  C    C  C     0   0.484   4.5950   0.1690  -0.0616
 4GN  C5   C  CH2   0  -0.248  -1.9253   0.6193   0.3567
 4GN  N2   N  N     0  -0.464   1.1675  -1.3147   0.4391
 4GN  N    N  NH2   0  -0.822   5.3078  -0.9580  -0.2355
 4GN  N1   N  NH1   0  -0.654  -0.9363  -0.4330   0.3764
 4GN  O    O  O     0  -0.492   5.1259   1.2717   0.0149
 4GN  C8   C  CH2   0  -0.445  -5.6690   0.5278  -0.1672
 4GN  C9   C  CH2   0  -0.451  -5.2586  -0.8777  -0.6392
 4GN  C7   C  CH2   0  -0.436  -4.4018   1.1460   0.4640
 4GN  C10  C  CH2   0  -0.420  -3.7404  -0.8070  -0.7771
 4GN  C6   C  CH1   0  -0.290  -3.3291   0.0476   0.4220
 4GN  H1   H  HCR6  0   0.268   2.7476   2.1157  -0.2887
 4GN  H2   H  HCR6  0   0.277   0.3118   1.9077  -0.0931
 4GN  H3   H  HCR6  0   0.254   3.0424  -2.0915   0.4844
 4GN  H4   H  HCH2  0   0.238  -1.7694   1.3140   1.1916
 4GN  H5   H  HCH2  0   0.228  -1.8259   1.2071  -0.5627
 4GN  H6   H  HNH2  0   0.409   4.8846  -1.8424  -0.4543
 4GN  H7   H  HNH2  0   0.402   6.3079  -0.8987  -0.3327
 4GN  H8   H  HNH1  0   0.385  -1.2227  -1.3499   0.6811
 4GN  H10  H  HCH2  0   0.229  -6.4980   0.4852   0.5398
 4GN  H11  H  HCH2  0   0.221  -5.5173  -1.6202   0.1203
 4GN  H12  H  HCH2  0   0.231  -5.7572  -1.1771  -1.5620
 4GN  H13  H  HCH2  0   0.224  -4.0674   2.0063  -0.1229
 4GN  H14  H  HCH2  0   0.237  -4.5702   1.5068   1.4795
 4GN  H15  H  HCH2  0   0.233  -3.2711  -1.7923  -0.7957
 4GN  H16  H  HCH2  0   0.214  -3.4629  -0.2945  -1.7046
 4GN  H17  H  HCH1  0   0.237  -3.4140  -0.5658   1.3282
 4GN  H9   H  HCH2  0   0.227  -6.0084   1.1324  -1.0097

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
 4GN  C9   C8   single    1.538  0.020  1.538
 4GN  C9   C10  single    1.526  0.020  1.526
 4GN  C8   C7   single    1.545  0.020  1.545
 4GN  C10  C6   single    1.529  0.020  1.529
 4GN  C7   C6   single    1.536  0.020  1.536
 4GN  C6   C5   single    1.517  0.020  1.517
 4GN  C5   N1   single    1.444  0.020  1.444
 4GN  N1   C4   single    1.345  0.020  1.345
 4GN  C3   C4   aromatic  1.411  0.020  1.411
 4GN  C3   C2   aromatic  1.372  0.020  1.372
 4GN  C4   N2   aromatic  1.340  0.020  1.340
 4GN  C2   C1   aromatic  1.399  0.020  1.399
 4GN  N2   C11  aromatic  1.320  0.020  1.320
 4GN  C1   C11  aromatic  1.391  0.020  1.391
 4GN  C1   C    single    1.483  0.020  1.483
 4GN  O    C    double    1.226  0.020  1.226
 4GN  C    N    single    1.345  0.020  1.345
 4GN  C2   H1   single    0.930  0.020  1.080
 4GN  C3   H2   single    0.930  0.020  1.080
 4GN  C11  H3   single    0.930  0.020  1.080
 4GN  C5   H4   single    0.970  0.020  1.090
 4GN  C5   H5   single    0.970  0.020  1.090
 4GN  N    H6   single    0.860  0.020  1.020
 4GN  N    H7   single    0.860  0.020  1.020
 4GN  N1   H8   single    0.860  0.020  1.020
 4GN  C8   H9   single    0.970  0.020  1.090
 4GN  C8   H10  single    0.970  0.020  1.090
 4GN  C9   H11  single    0.970  0.020  1.090
 4GN  C9   H12  single    0.970  0.020  1.090
 4GN  C7   H13  single    0.970  0.020  1.090
 4GN  C7   H14  single    0.970  0.020  1.090
 4GN  C10  H15  single    0.970  0.020  1.090
 4GN  C10  H16  single    0.970  0.020  1.090
 4GN  C6   H17  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
 4GN  H1   C2   C1   120.00  3.000
 4GN  H1   C2   C3   119.48  3.000
 4GN  C1   C2   C3   120.52  3.000
 4GN  H2   C3   C4   121.11  3.000
 4GN  H2   C3   C2   120.46  3.000
 4GN  C4   C3   C2   118.43  3.000
 4GN  H3   C11  N2   114.68  3.000
 4GN  H3   C11  C1   120.75  3.000
 4GN  N2   C11  C1   124.56  3.000
 4GN  C    C1   C11  124.24  3.000
 4GN  C    C1   C2   119.47  3.000
 4GN  C11  C1   C2   116.25  3.000
 4GN  N1   C4   N2   116.41  3.000
 4GN  N2   C4   C3   121.45  3.000
 4GN  N1   C4   C3   122.14  3.000
 4GN  O    C    N    122.15  3.000
 4GN  N    C    C1   116.83  3.000
 4GN  O    C    C1   121.01  3.000
 4GN  H5   C5   H4   106.61  3.000
 4GN  H5   C5   C6   108.80  3.000
 4GN  H4   C5   C6   109.71  3.000
 4GN  H5   C5   N1   109.89  3.000
 4GN  H4   C5   N1   110.71  3.000
 4GN  C6   C5   N1   111.00  3.000
 4GN  C4   N2   C11  118.77  3.000
 4GN  H7   N    H6   116.70  3.000
 4GN  H7   N    C    119.33  3.000
 4GN  H6   N    C    122.86  3.000
 4GN  H8   N1   C5   118.19  3.000
 4GN  H8   N1   C4   115.87  3.000
 4GN  C5   N1   C4   124.56  3.000
 4GN  H10  C8   H9   106.61  3.000
 4GN  H10  C8   C7   111.98  3.000
 4GN  H9   C8   C7   110.42  3.000
 4GN  H10  C8   C9   111.48  3.000
 4GN  H9   C8   C9   110.63  3.000
 4GN  C7   C8   C9   105.79  3.000
 4GN  H12  C9   H11  107.05  3.000
 4GN  H12  C9   C10  113.02  3.000
 4GN  H11  C9   C10  109.25  3.000
 4GN  H12  C9   C8   112.85  3.000
 4GN  H11  C9   C8   110.14  3.000
 4GN  C10  C9   C8   104.53  3.000
 4GN  H14  C7   H13  106.66  3.000
 4GN  H14  C7   C6   111.71  3.000
 4GN  H13  C7   C6   109.53  3.000
 4GN  H14  C7   C8   112.71  3.000
 4GN  H13  C7   C8   110.26  3.000
 4GN  C6   C7   C8   105.99  3.000
 4GN  H16  C10  H15  107.40  3.000
 4GN  H16  C10  C6   109.53  3.000
 4GN  H15  C10  C6   113.72  3.000
 4GN  H16  C10  C9   110.50  3.000
 4GN  H15  C10  C9   112.80  3.000
 4GN  C6   C10  C9   102.86  3.000
 4GN  H17  C6   C10  108.33  3.000
 4GN  H17  C6   C7   108.85  3.000
 4GN  C10  C6   C7   103.49  3.000
 4GN  H17  C6   C5   108.52  3.000
 4GN  C7   C6   C5   112.20  3.000
 4GN  C10  C6   C5   115.20  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
 4GN  CONST_01  N2   C4   C3   C2     0.00   0.0  0
 4GN  CONST_02  N2   C11  C1   C2     0.00   0.0  0
 4GN  CONST_03  C11  N2   C4   C3     0.00   0.0  0
 4GN  CONST_04  C11  C1   C2   C3     0.00   0.0  0
 4GN  CONST_05  C4   C3   C2   C1     0.00   0.0  0
 4GN  CONST_06  C4   N2   C11  C1     0.00   0.0  0
 4GN  CONST_07  N1   C4   C3   C2   180.00   0.0  0
 4GN  CONST_08  C    C1   C2   C3   180.00   0.0  0
 4GN  CONST_09  N1   C4   N2   C11  180.00   0.0  0
 4GN  CONST_10  N2   C11  C1   C    180.00   0.0  0
 4GN  CONST_11  H3   C11  C1   C2   180.00   0.0  0
 4GN  CONST_12  H1   C2   C1   C11  180.00   0.0  0
 4GN  CONST_13  H2   C3   C2   C1   180.00   0.0  0
 4GN  CONST_14  C5   N1   C4   C3     0.00   0.0  0
 4GN  CONST_15  N2   C4   N1   C5   180.00   0.0  0
 4GN  CONST_16  H8   N1   C4   C3   180.00   0.0  0
 4GN  CONST_17  H6   N    C    C1     0.00   0.0  0
 4GN  CONST_18  H7   N    C    C1   180.00   0.0  0
 4GN  Var_01    C6   C10  C9   C8    38.81  30.0  1
 4GN  Var_02    C6   C7   C8   C9    -3.69  30.0  1
 4GN  Var_03    C10  C9   C8   C7   -21.63  30.0  1
 4GN  Var_04    O    C    C1   C2    15.44  30.0  2
 4GN  Var_05    C6   C5   N1   C4   177.33  30.0  1

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
 4GN  chir_01  C6  C10  C7  C5  positiv

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
 4GN  plan-1  C2   0.020
 4GN  plan-1  C3   0.020
 4GN  plan-1  C11  0.020
 4GN  plan-1  C1   0.020
 4GN  plan-1  C4   0.020
 4GN  plan-1  C    0.020
 4GN  plan-1  N2   0.020
 4GN  plan-1  N1   0.020
 4GN  plan-1  H1   0.020
 4GN  plan-1  H2   0.020
 4GN  plan-1  H3   0.020
 4GN  plan-2  C4   0.020
 4GN  plan-2  C5   0.020
 4GN  plan-2  N1   0.020
 4GN  plan-2  H8   0.020
 4GN  plan-3  C1   0.020
 4GN  plan-3  C    0.020
 4GN  plan-3  N    0.020
 4GN  plan-3  O    0.020
 4GN  plan-3  H6   0.020
 4GN  plan-3  H7   0.020

