# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 15:30:39 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-(cyclopentylamino)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(NC2CCCC2)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
 4GO  4GO  6-(cyclopentylamino)pyridine-3-carboxamide  ligand  30  15  .  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_4GO
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
 4GO  C2   C  CR16  0  -0.152   1.6107   1.0673  -0.2366
 4GO  C3   C  CR16  0  -0.394   0.2702   0.7812  -0.2819
 4GO  C10  C  CR16  0  -0.072   2.0302  -1.2078   0.2632
 4GO  C1   C  CR6   0  -0.168   2.5476   0.0623   0.0315
 4GO  C4   C  CR6   0   0.513  -0.1418  -0.5494  -0.0545
 4GO  C    C  C     0   0.490   3.9890   0.4115   0.0796
 4GO  N2   N  N     0  -0.466   0.7463  -1.5132   0.2245
 4GO  N    N  NH2   0  -0.827   4.8658  -0.6023   0.1820
 4GO  N1   N  NH1   0  -0.658  -1.4299  -0.9367  -0.1190
 4GO  O    O  O     0  -0.493   4.3543   1.5814   0.0327
 4GO  C7   C  CH2   0  -0.447  -4.9787   0.1295  -0.4137
 4GO  C8   C  CH2   0  -0.457  -4.4298   1.1526   0.6108
 4GO  C6   C  CH2   0  -0.450  -3.8107  -0.8153  -0.7388
 4GO  C9   C  CH2   0  -0.440  -3.0514   0.6259   1.0089
 4GO  C5   C  CR15  0  -0.077  -2.5659  -0.0633  -0.2684
 4GO  H1   H  HCR6  0   0.268   1.9438   2.0816  -0.4121
 4GO  H2   H  HCR6  0   0.273  -0.4452   1.5650  -0.4843
 4GO  H3   H  HCR6  0   0.248   2.6800  -2.0421   0.5097
 4GO  H4   H  HNH2  0   0.409   4.6017  -1.5690   0.1239
 4GO  H5   H  HNH2  0   0.403   5.8524  -0.4030   0.1900
 4GO  H6   H  HNH1  0   0.381  -1.6087  -1.8902   0.1589
 4GO  H8   H  HCH2  0   0.233  -5.3341   0.6359  -1.3113
 4GO  H9   H  HCH2  0   0.230  -4.3331   2.1354   0.1452
 4GO  H10  H  HCH2  0   0.236  -5.0884   1.2754   1.4705
 4GO  H11  H  HCH2  0   0.229  -3.9012  -1.7430  -0.1655
 4GO  H12  H  HCH2  0   0.246  -3.7593  -1.0902  -1.7926
 4GO  H13  H  HCH2  0   0.240  -2.3781   1.4075   1.3646
 4GO  H14  H  HCH2  0   0.223  -3.1369  -0.1245   1.8008
 4GO  H15  H  HCR5  0   0.243  -2.3254   0.7018  -1.0137
 4GO  H7   H  HCH2  0   0.234  -5.8273  -0.4245  -0.0127

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
 4GO  C7   C8   single    1.548  0.020  1.548
 4GO  C7   C6   single    1.537  0.020  1.537
 4GO  C8   C9   single    1.528  0.020  1.528
 4GO  C6   C5   single    1.528  0.020  1.528
 4GO  C9   C5   single    1.530  0.020  1.530
 4GO  C5   N1   single    1.441  0.020  1.441
 4GO  N1   C4   single    1.347  0.020  1.347
 4GO  C3   C4   aromatic  1.411  0.020  1.411
 4GO  C3   C2   aromatic  1.371  0.020  1.371
 4GO  C4   N2   aromatic  1.340  0.020  1.340
 4GO  C2   C1   aromatic  1.400  0.020  1.400
 4GO  N2   C10  aromatic  1.320  0.020  1.320
 4GO  C1   C10  aromatic  1.391  0.020  1.391
 4GO  C1   C    single    1.484  0.020  1.484
 4GO  C    O    double    1.227  0.020  1.227
 4GO  C    N    single    1.344  0.020  1.344
 4GO  C2   H1   single    0.930  0.020  1.080
 4GO  C3   H2   single    0.930  0.020  1.080
 4GO  C10  H3   single    0.930  0.020  1.080
 4GO  N    H4   single    0.860  0.020  1.020
 4GO  N    H5   single    0.860  0.020  1.020
 4GO  N1   H6   single    0.860  0.020  1.020
 4GO  C7   H7   single    0.970  0.020  1.090
 4GO  C7   H8   single    0.970  0.020  1.090
 4GO  C8   H9   single    0.970  0.020  1.090
 4GO  C8   H10  single    0.970  0.020  1.090
 4GO  C6   H11  single    0.970  0.020  1.090
 4GO  C6   H12  single    0.970  0.020  1.090
 4GO  C9   H13  single    0.970  0.020  1.090
 4GO  C9   H14  single    0.970  0.020  1.090
 4GO  C5   H15  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
 4GO  H1   C2   C1   119.87  3.000
 4GO  H1   C2   C3   119.42  3.000
 4GO  C1   C2   C3   120.71  3.000
 4GO  H2   C3   C4   121.39  3.000
 4GO  H2   C3   C2   120.14  3.000
 4GO  C4   C3   C2   118.47  3.000
 4GO  H3   C10  N2   114.26  3.000
 4GO  H3   C10  C1   121.12  3.000
 4GO  N2   C10  C1   124.62  3.000
 4GO  C    C1   C10  124.81  3.000
 4GO  C    C1   C2   119.17  3.000
 4GO  C10  C1   C2   116.01  3.000
 4GO  N1   C4   N2   115.92  3.000
 4GO  N2   C4   C3   121.21  3.000
 4GO  N1   C4   C3   122.86  3.000
 4GO  O    C    N    121.87  3.000
 4GO  N    C    C1   117.29  3.000
 4GO  O    C    C1   120.83  3.000
 4GO  C4   N2   C10  118.96  3.000
 4GO  H5   N    H4   116.68  3.000
 4GO  H5   N    C    119.38  3.000
 4GO  H4   N    C    123.39  3.000
 4GO  H6   N1   C5   117.50  3.000
 4GO  H6   N1   C4   115.34  3.000
 4GO  C5   N1   C4   125.79  3.000
 4GO  H8   C7   H7   106.57  3.000
 4GO  H8   C7   C6   111.04  3.000
 4GO  H7   C7   C6   110.92  3.000
 4GO  H8   C7   C8   110.70  3.000
 4GO  H7   C7   C8   111.62  3.000
 4GO  C6   C7   C8   106.06  3.000
 4GO  H10  C8   H9   106.76  3.000
 4GO  H10  C8   C9   112.24  3.000
 4GO  H9   C8   C9   109.97  3.000
 4GO  H10  C8   C7   112.46  3.000
 4GO  H9   C8   C7   110.12  3.000
 4GO  C9   C8   C7   105.33  3.000
 4GO  H12  C6   H11  107.25  3.000
 4GO  H12  C6   C5   112.53  3.000
 4GO  H11  C6   C5   108.86  3.000
 4GO  H12  C6   C7   113.28  3.000
 4GO  H11  C6   C7   110.33  3.000
 4GO  C5   C6   C7   104.56  3.000
 4GO  H14  C9   H13  107.67  3.000
 4GO  H14  C9   C5   108.66  3.000
 4GO  H13  C9   C5   113.51  3.000
 4GO  H14  C9   C8   110.75  3.000
 4GO  H13  C9   C8   113.24  3.000
 4GO  C5   C9   C8   102.94  3.000
 4GO  H15  C5   C9   108.86  3.000
 4GO  H15  C5   C6   108.25  3.000
 4GO  C9   C5   C6   102.71  3.000
 4GO  H15  C5   N1   108.72  3.000
 4GO  C9   C5   N1   115.88  3.000
 4GO  C6   C5   N1   112.07  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
 4GO  CONST_01  N2   C4   C3   C2     0.00   0.0  0
 4GO  CONST_02  N2   C10  C1   C2     0.00   0.0  0
 4GO  CONST_03  C10  N2   C4   C3     0.00   0.0  0
 4GO  CONST_04  C10  C1   C2   C3     0.00   0.0  0
 4GO  CONST_05  C4   C3   C2   C1     0.00   0.0  0
 4GO  CONST_06  C4   N2   C10  C1     0.00   0.0  0
 4GO  CONST_07  N1   C4   C3   C2   180.00   0.0  0
 4GO  CONST_08  C    C1   C2   C3   180.00   0.0  0
 4GO  CONST_09  N1   C4   N2   C10  180.00   0.0  0
 4GO  CONST_10  N2   C10  C1   C    180.00   0.0  0
 4GO  CONST_11  C5   N1   C4   C3     0.00   0.0  0
 4GO  CONST_12  C5   N1   C4   N2   180.00   0.0  0
 4GO  CONST_13  H3   C10  C1   C2   180.00   0.0  0
 4GO  CONST_14  H1   C2   C1   C10  180.00   0.0  0
 4GO  CONST_15  H2   C3   C2   C1   180.00   0.0  0
 4GO  CONST_16  H6   N1   C4   C3   180.00   0.0  0
 4GO  CONST_17  H4   N    C    C1     0.00   0.0  0
 4GO  CONST_18  H5   N    C    C1   180.00   0.0  0
 4GO  Var_01    C5   C9   C8   C7    32.07  30.0  1
 4GO  Var_02    C5   C6   C7   C8   -17.52  30.0  1
 4GO  Var_03    C9   C8   C7   C6    -9.06  30.0  1
 4GO  Var_04    O    C    C1   C2     7.96  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
 4GO  chir_01  C5  C6  C9  N1  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
 4GO  plan-1  C2   0.020
 4GO  plan-1  C3   0.020
 4GO  plan-1  C10  0.020
 4GO  plan-1  C1   0.020
 4GO  plan-1  C4   0.020
 4GO  plan-1  C    0.020
 4GO  plan-1  N2   0.020
 4GO  plan-1  N1   0.020
 4GO  plan-1  H1   0.020
 4GO  plan-1  H2   0.020
 4GO  plan-1  H3   0.020
 4GO  plan-2  C4   0.020
 4GO  plan-2  N1   0.020
 4GO  plan-2  C5   0.020
 4GO  plan-2  H6   0.020
 4GO  plan-3  C1   0.020
 4GO  plan-3  C    0.020
 4GO  plan-3  N    0.020
 4GO  plan-3  O    0.020
 4GO  plan-3  H4   0.020
 4GO  plan-3  H5   0.020

