# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:23:40 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-(cyclohexylamino)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(NC2CCCCC2)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
 GJG  GJG  6-(cyclohexylamino)pyridine-3-carboxamide  ligand  33  16  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GJG
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
 GJG  N3   N  N     0  -0.467  -1.1046  -1.5195   0.3548
 GJG  C4   C  CR6   0   0.512  -0.2008  -0.6049  -0.0230
 GJG  C5   C  CR16  0  -0.073  -2.3817  -1.1852   0.3762
 GJG  C8   C  CR16  0  -0.153  -1.9225   1.0263  -0.3335
 GJG  C10  C  CR16  0  -0.391  -0.5890   0.7075  -0.3699
 GJG  C13  C  CH2   0  -0.444   3.4209  -1.0671  -0.6826
 GJG  C15  C  CH2   0  -0.439   3.8412   1.4964   0.7013
 GJG  O7   O  O     0  -0.492  -4.6530   1.6224   0.0213
 GJG  N9   N  NH2   0  -0.824  -5.2021  -0.5543   0.1716
 GJG  C1   C  CR6   0  -0.167  -2.8755   0.0685   0.0326
 GJG  N6   N  NH1   0  -0.657   1.0782  -1.0234  -0.0637
 GJG  C11  C  CH1   0  -0.063   2.2400  -0.1869  -0.2818
 GJG  C14  C  CH2   0  -0.437   4.6794  -0.2377  -0.9152
 GJG  C16  C  CH2   0  -0.430   5.0222   0.6198   0.2983
 GJG  C12  C  CH2   0  -0.431   2.5888   0.6607   0.9443
 GJG  H1   H  HCR6  0   0.250  -3.0476  -1.9747   0.7116
 GJG  H2   H  HCR6  0   0.268  -2.2369   2.0276  -0.5969
 GJG  H3   H  HCR6  0   0.272   0.1405   1.4523  -0.6541
 GJG  H4   H  HCH2  0   0.221   3.6056  -1.7965   0.1148
 GJG  H5   H  HCH2  0   0.243   3.1675  -1.6341  -1.5814
 GJG  H6   H  HCH2  0   0.233   4.0812   2.0723   1.5977
 GJG  H7   H  HCH2  0   0.214   3.6442   2.2257  -0.0921
 GJG  H8   H  HNH2  0   0.403  -6.1857  -0.3398   0.1748
 GJG  H9   H  HNH2  0   0.408  -4.9524  -1.5223   0.0764
 GJG  H10  H  HNH1  0   0.381   1.2374  -1.9527   0.2959
 GJG  H11  H  HCH1  0   0.232   2.0277   0.4841  -1.1223
 GJG  H12  H  HCH2  0   0.234   5.5128  -0.8991  -1.1617
 GJG  H13  H  HCH2  0   0.215   4.5288   0.4102  -1.7851
 GJG  H14  H  HCH2  0   0.230   5.8971   1.2389   0.0859
 GJG  H15  H  HCH2  0   0.212   5.2971  -0.0275   1.1381
 GJG  H16  H  HCH2  0   0.217   2.7486  -0.0103   1.7950
 GJG  H17  H  HCH2  0   0.237   1.7470   1.3070   1.2066
 GJG  C2   C  C     0   0.486  -4.3092   0.4464   0.0718

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
 GJG  C10  C8   aromatic  1.372  0.020  1.372
 GJG  C10  C4   aromatic  1.412  0.020  1.412
 GJG  C8   C1   aromatic  1.400  0.020  1.400
 GJG  O7   C2   double    1.226  0.020  1.226
 GJG  N6   C4   single    1.346  0.020  1.346
 GJG  N6   C11  single    1.448  0.020  1.448
 GJG  C4   N3   aromatic  1.340  0.020  1.340
 GJG  C1   C2   single    1.483  0.020  1.483
 GJG  C1   C5   aromatic  1.391  0.020  1.391
 GJG  C2   N9   single    1.345  0.020  1.345
 GJG  C13  C11  single    1.526  0.020  1.526
 GJG  C13  C14  single    1.525  0.020  1.525
 GJG  C11  C12  single    1.531  0.020  1.531
 GJG  N3   C5   aromatic  1.320  0.020  1.320
 GJG  C12  C15  single    1.525  0.020  1.525
 GJG  C14  C16  single    1.525  0.020  1.525
 GJG  C16  C15  single    1.525  0.020  1.525
 GJG  C5   H1   single    0.930  0.020  1.080
 GJG  C8   H2   single    0.930  0.020  1.080
 GJG  C10  H3   single    0.930  0.020  1.080
 GJG  C13  H4   single    0.970  0.020  1.090
 GJG  C13  H5   single    0.970  0.020  1.090
 GJG  C15  H6   single    0.970  0.020  1.090
 GJG  C15  H7   single    0.970  0.020  1.090
 GJG  N9   H8   single    0.860  0.020  1.020
 GJG  N9   H9   single    0.860  0.020  1.020
 GJG  N6   H10  single    0.860  0.020  1.020
 GJG  C11  H11  single    0.970  0.020  1.090
 GJG  C14  H12  single    0.970  0.020  1.090
 GJG  C14  H13  single    0.970  0.020  1.090
 GJG  C16  H14  single    0.970  0.020  1.090
 GJG  C16  H15  single    0.970  0.020  1.090
 GJG  C12  H16  single    0.970  0.020  1.090
 GJG  C12  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
 GJG  C5   N3   C4   118.95  3.000
 GJG  N6   C4   C10  122.87  3.000
 GJG  N6   C4   N3   115.91  3.000
 GJG  C10  C4   N3   121.21  3.000
 GJG  H1   C5   C1   120.94  3.000
 GJG  H1   C5   N3   114.46  3.000
 GJG  C1   C5   N3   124.60  3.000
 GJG  H2   C8   C1   119.94  3.000
 GJG  H2   C8   C10  119.42  3.000
 GJG  C1   C8   C10  120.65  3.000
 GJG  H3   C10  C8   120.21  3.000
 GJG  H3   C10  C4   121.31  3.000
 GJG  C8   C10  C4   118.48  3.000
 GJG  H5   C13  H4   106.99  3.000
 GJG  H5   C13  C14  110.38  3.000
 GJG  H4   C13  C14  109.50  3.000
 GJG  H5   C13  C11  109.62  3.000
 GJG  H4   C13  C11  108.84  3.000
 GJG  C14  C13  C11  111.40  3.000
 GJG  H7   C15  H6   106.44  3.000
 GJG  H7   C15  C12  109.42  3.000
 GJG  H6   C15  C12  109.79  3.000
 GJG  H7   C15  C16  109.30  3.000
 GJG  H6   C15  C16  110.48  3.000
 GJG  C12  C15  C16  111.29  3.000
 GJG  H9   N9   H8   116.66  3.000
 GJG  H9   N9   C2   123.03  3.000
 GJG  H8   N9   C2   119.36  3.000
 GJG  C2   C1   C8   119.38  3.000
 GJG  C2   C1   C5   124.50  3.000
 GJG  C8   C1   C5   116.09  3.000
 GJG  H10  N6   C11  117.32  3.000
 GJG  H10  N6   C4   115.18  3.000
 GJG  C11  N6   C4   125.95  3.000
 GJG  H11  C11  C12  108.62  3.000
 GJG  H11  C11  N6   108.28  3.000
 GJG  C12  C11  N6   112.46  3.000
 GJG  H11  C11  C13  107.55  3.000
 GJG  C12  C11  C13  110.69  3.000
 GJG  N6   C11  C13  109.10  3.000
 GJG  H13  C14  H12  106.50  3.000
 GJG  H13  C14  C16  109.29  3.000
 GJG  H12  C14  C16  110.40  3.000
 GJG  H13  C14  C13  109.24  3.000
 GJG  H12  C14  C13  109.56  3.000
 GJG  C16  C14  C13  111.71  3.000
 GJG  H15  C16  H14  106.44  3.000
 GJG  H15  C16  C14  109.53  3.000
 GJG  H14  C16  C14  110.12  3.000
 GJG  H15  C16  C15  109.36  3.000
 GJG  H14  C16  C15  110.23  3.000
 GJG  C14  C16  C15  111.06  3.000
 GJG  H17  C12  H16  106.75  3.000
 GJG  H17  C12  C11  110.13  3.000
 GJG  H16  C12  C11  108.43  3.000
 GJG  H17  C12  C15  110.28  3.000
 GJG  H16  C12  C15  109.85  3.000
 GJG  C11  C12  C15  111.28  3.000
 GJG  C1   C2   N9   117.01  3.000
 GJG  N9   C2   O7   122.04  3.000
 GJG  C1   C2   O7   120.95  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
 GJG  CONST_01  C8   C10  C4   N3     0.00   0.0  0
 GJG  CONST_02  C8   C1   C5   N3     0.00   0.0  0
 GJG  CONST_03  C1   C8   C10  C4     0.00   0.0  0
 GJG  CONST_04  C1   C5   N3   C4     0.00   0.0  0
 GJG  CONST_05  C10  C8   C1   C5     0.00   0.0  0
 GJG  CONST_06  C10  C4   N3   C5     0.00   0.0  0
 GJG  CONST_07  C2   C1   C5   N3   180.00   0.0  0
 GJG  CONST_08  N6   C4   N3   C5   180.00   0.0  0
 GJG  CONST_09  N6   C4   C10  C8   180.00   0.0  0
 GJG  CONST_10  C2   C1   C8   C10  180.00   0.0  0
 GJG  CONST_11  C11  N6   C4   N3   180.00   0.0  0
 GJG  CONST_12  C11  N6   C4   C10    0.00   0.0  0
 GJG  CONST_13  H3   C10  C4   N3   180.00   0.0  0
 GJG  CONST_14  H2   C8   C10  C4   180.00   0.0  0
 GJG  CONST_15  H1   C5   N3   C4   180.00   0.0  0
 GJG  CONST_16  H10  N6   C4   N3     0.00   0.0  0
 GJG  CONST_17  H8   N9   C2   C1   180.00   0.0  0
 GJG  CONST_18  H9   N9   C2   C1     0.00   0.0  0
 GJG  Var_01    C15  C16  C14  C13  -54.81  30.0  1
 GJG  Var_02    C16  C14  C13  C11   55.16  30.0  1
 GJG  Var_03    C16  C15  C12  C11  -56.02  30.0  1
 GJG  Var_04    C12  C15  C16  C14   55.18  30.0  1
 GJG  Var_05    O7   C2   C1   C5   165.12  30.0  2

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
 GJG  chir_01  C11  N6  C13  C12  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
 GJG  plan-1  N3   0.020
 GJG  plan-1  C4   0.020
 GJG  plan-1  C5   0.020
 GJG  plan-1  C8   0.020
 GJG  plan-1  C10  0.020
 GJG  plan-1  C1   0.020
 GJG  plan-1  N6   0.020
 GJG  plan-1  H1   0.020
 GJG  plan-1  H2   0.020
 GJG  plan-1  H3   0.020
 GJG  plan-1  C2   0.020
 GJG  plan-2  O7   0.020
 GJG  plan-2  N9   0.020
 GJG  plan-2  C1   0.020
 GJG  plan-2  H8   0.020
 GJG  plan-2  H9   0.020
 GJG  plan-2  C2   0.020
 GJG  plan-3  C4   0.020
 GJG  plan-3  N6   0.020
 GJG  plan-3  C11  0.020
 GJG  plan-3  H10  0.020

