# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:13:45 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-amino-2-(cyclopentylamino)pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cnc(NC2CCCC2)nc1N
#
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
 4GT  4GT  4-amino-2-(cyclopentylamino)pyrimidine-5-carboxamide  ligand  31  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_4GT
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
 4GT  C5   C  CR16  0  -0.027   1.2413  -1.1785   0.0824
 4GT  C4   C  CR6   0  -0.280   2.2995  -0.2857  -0.0056
 4GT  C15  C  CR6   0   0.505   1.9093   1.0874  -0.0796
 4GT  C7   C  CR6   0   0.608  -0.2841   0.4723   0.1192
 4GT  C2   C  C     0   0.521   3.7091  -0.7103  -0.0541
 4GT  C11  C  CH2   0  -0.445  -5.1304  -0.1438   0.4215
 4GT  C12  C  CH2   0  -0.459  -4.5933  -1.0736  -0.6898
 4GT  C10  C  CH2   0  -0.460  -3.9186   0.6654   0.9223
 4GT  C13  C  CH2   0  -0.439  -3.2298  -0.4973  -1.0594
 4GT  C9   C  CR15  0  -0.051  -2.7004  -0.0121   0.2903
 4GT  N6   N  N     0  -0.488  -0.0337  -0.8475   0.1397
 4GT  N14  N  N     0  -0.520   0.6273   1.4354  -0.0024
 4GT  N16  N  NH2   0  -0.824   2.7915   2.0776  -0.2097
 4GT  N1   N  NH2   0  -0.823   3.9798  -1.9888   0.2701
 4GT  N8   N  NH1   0  -0.660  -1.5601   0.8685   0.2350
 4GT  O3   O  O     0  -0.512   4.6122   0.0599  -0.3876
 4GT  H1   H  HCR6  0   0.255   1.4307  -2.2475   0.0875
 4GT  H3   H  HCH2  0   0.232  -5.5883  -0.7195   1.2259
 4GT  H4   H  HCH2  0   0.226  -4.4694  -2.0877  -0.3028
 4GT  H5   H  HCH2  0   0.235  -5.2691  -1.1407  -1.5425
 4GT  H6   H  HCH2  0   0.229  -3.9820   1.6989   0.5689
 4GT  H7   H  HCH2  0   0.244  -3.8495   0.7043   2.0097
 4GT  H8   H  HCH2  0   0.237  -2.5656  -1.2182  -1.5376
 4GT  H9   H  HCH2  0   0.218  -3.3385   0.3572  -1.7349
 4GT  H10  H  HCR5  0   0.244  -2.4224  -0.8852   0.8855
 4GT  H11  H  HNH2  0   0.413   3.7670   1.8668  -0.3394
 4GT  H12  H  HNH2  0   0.393   2.4624   3.0253  -0.2731
 4GT  H13  H  HNH2  0   0.409   3.3147  -2.5938   0.7177
 4GT  H14  H  HNH2  0   0.403   4.9404  -2.2897   0.2869
 4GT  H15  H  HNH1  0   0.386  -1.7258   1.8582   0.1370
 4GT  H2   H  HCH2  0   0.232  -5.9028   0.5220   0.0362

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
 4GT  C11  C12  single    1.545  0.020  1.545
 4GT  C11  C10  single    1.541  0.020  1.541
 4GT  C12  C13  single    1.526  0.020  1.526
 4GT  C10  C9   single    1.531  0.020  1.531
 4GT  C13  C9   single    1.529  0.020  1.529
 4GT  C9   N8   single    1.442  0.020  1.442
 4GT  N8   C7   single    1.341  0.020  1.341
 4GT  N14  C7   aromatic  1.332  0.020  1.332
 4GT  N14  C15  aromatic  1.331  0.020  1.331
 4GT  C7   N6   aromatic  1.344  0.020  1.344
 4GT  N16  C15  single    1.333  0.020  1.333
 4GT  C15  C4   aromatic  1.429  0.020  1.429
 4GT  N6   C5   aromatic  1.319  0.020  1.319
 4GT  C4   C5   aromatic  1.387  0.020  1.387
 4GT  C4   C2   single    1.473  0.020  1.473
 4GT  O3   C2   double    1.233  0.020  1.233
 4GT  C2   N1   single    1.346  0.020  1.346
 4GT  C5   H1   single    0.930  0.020  1.080
 4GT  C11  H2   single    0.970  0.020  1.090
 4GT  C11  H3   single    0.970  0.020  1.090
 4GT  C12  H4   single    0.970  0.020  1.090
 4GT  C12  H5   single    0.970  0.020  1.090
 4GT  C10  H6   single    0.970  0.020  1.090
 4GT  C10  H7   single    0.970  0.020  1.090
 4GT  C13  H8   single    0.970  0.020  1.090
 4GT  C13  H9   single    0.970  0.020  1.090
 4GT  C9   H10  single    0.970  0.020  1.090
 4GT  N16  H11  single    0.860  0.020  1.020
 4GT  N16  H12  single    0.860  0.020  1.020
 4GT  N1   H13  single    0.860  0.020  1.020
 4GT  N1   H14  single    0.860  0.020  1.020
 4GT  N8   H15  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
 4GT  H1   C5   N6   114.56  3.000
 4GT  H1   C5   C4   120.06  3.000
 4GT  N6   C5   C4   125.37  3.000
 4GT  C2   C4   C15  122.44  3.000
 4GT  C2   C4   C5   123.13  3.000
 4GT  C15  C4   C5   114.41  3.000
 4GT  N16  C15  N14  116.69  3.000
 4GT  N16  C15  C4   122.56  3.000
 4GT  N14  C15  C4   120.75  3.000
 4GT  N8   C7   N14  116.45  3.000
 4GT  N14  C7   N6   125.76  3.000
 4GT  N8   C7   N6   117.79  3.000
 4GT  O3   C2   N1   120.74  3.000
 4GT  N1   C2   C4   117.27  3.000
 4GT  O3   C2   C4   121.99  3.000
 4GT  H3   C11  H2   106.61  3.000
 4GT  H3   C11  C10  111.58  3.000
 4GT  H2   C11  C10  110.57  3.000
 4GT  H3   C11  C12  111.04  3.000
 4GT  H2   C11  C12  111.08  3.000
 4GT  C10  C11  C12  106.04  3.000
 4GT  H5   C12  H4   106.88  3.000
 4GT  H5   C12  C13  112.82  3.000
 4GT  H4   C12  C13  109.58  3.000
 4GT  H5   C12  C11  112.58  3.000
 4GT  H4   C12  C11  110.07  3.000
 4GT  C13  C12  C11  104.93  3.000
 4GT  H7   C10  H6   106.99  3.000
 4GT  H7   C10  C9   112.16  3.000
 4GT  H6   C10  C9   109.33  3.000
 4GT  H7   C10  C11  113.12  3.000
 4GT  H6   C10  C11  110.21  3.000
 4GT  C9   C10  C11  105.02  3.000
 4GT  H9   C13  H8   107.81  3.000
 4GT  H9   C13  C9   109.35  3.000
 4GT  H8   C13  C9   112.70  3.000
 4GT  H9   C13  C12  110.83  3.000
 4GT  H8   C13  C12  113.63  3.000
 4GT  C9   C13  C12  102.44  3.000
 4GT  H10  C9   N8   107.92  3.000
 4GT  H10  C9   C13  108.39  3.000
 4GT  N8   C9   C13  115.71  3.000
 4GT  H10  C9   C10  109.35  3.000
 4GT  N8   C9   C10  112.02  3.000
 4GT  C13  C9   C10  103.26  3.000
 4GT  C7   N6   C5   115.22  3.000
 4GT  C7   N14  C15  118.40  3.000
 4GT  H12  N16  H11  120.44  3.000
 4GT  H12  N16  C15  119.34  3.000
 4GT  H11  N16  C15  119.91  3.000
 4GT  H14  N1   H13  116.38  3.000
 4GT  H14  N1   C2   118.66  3.000
 4GT  H13  N1   C2   123.11  3.000
 4GT  H15  N8   C9   118.24  3.000
 4GT  H15  N8   C7   115.98  3.000
 4GT  C9   N8   C7   125.12  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
 4GT  CONST_01  N14  C7   N6   C5     0.00   0.0  0
 4GT  CONST_02  N14  C15  C4   C5     0.00   0.0  0
 4GT  CONST_03  C7   N14  C15  C4     0.00   0.0  0
 4GT  CONST_04  C7   N6   C5   C4     0.00   0.0  0
 4GT  CONST_05  N6   C7   N14  C15    0.00   0.0  0
 4GT  CONST_06  N6   C5   C4   C15    0.00   0.0  0
 4GT  CONST_07  N8   C7   N6   C5   180.00   0.0  0
 4GT  CONST_08  N16  C15  C4   C5   180.00   0.0  0
 4GT  CONST_09  N8   C7   N14  C15  180.00   0.0  0
 4GT  CONST_10  N16  C15  N14  C7   180.00   0.0  0
 4GT  CONST_11  N14  C15  C4   C2   180.00   0.0  0
 4GT  CONST_12  N6   C5   C4   C2   180.00   0.0  0
 4GT  CONST_13  N14  C7   N8   C9   180.00   0.0  0
 4GT  CONST_14  N6   C7   N8   C9     0.00   0.0  0
 4GT  CONST_15  H1   C5   C4   C15  180.00   0.0  0
 4GT  CONST_16  H11  N16  C15  C4     0.00   0.0  0
 4GT  CONST_17  H12  N16  C15  C4   180.00   0.0  0
 4GT  CONST_18  H15  N8   C7   N6   180.00   0.0  0
 4GT  CONST_19  H13  N1   C2   C4     0.00   0.0  0
 4GT  CONST_20  H14  N1   C2   C4   180.00   0.0  0
 4GT  Var_01    C9   C13  C12  C11   36.25  30.0  1
 4GT  Var_02    C9   C10  C11  C12  -10.84  30.0  1
 4GT  Var_03    C13  C12  C11  C10  -15.77  30.0  1
 4GT  Var_04    O3   C2   C4   C5   165.74  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
 4GT  chir_01  C9  C10  C13  N8  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
 4GT  plan-1  C5   0.020
 4GT  plan-1  C4   0.020
 4GT  plan-1  C15  0.020
 4GT  plan-1  C7   0.020
 4GT  plan-1  C2   0.020
 4GT  plan-1  N6   0.020
 4GT  plan-1  N14  0.020
 4GT  plan-1  N16  0.020
 4GT  plan-1  N8   0.020
 4GT  plan-1  H1   0.020
 4GT  plan-2  C15  0.020
 4GT  plan-2  N16  0.020
 4GT  plan-2  H11  0.020
 4GT  plan-2  H12  0.020
 4GT  plan-3  C7   0.020
 4GT  plan-3  C9   0.020
 4GT  plan-3  N8   0.020
 4GT  plan-3  H15  0.020
 4GT  plan-4  C4   0.020
 4GT  plan-4  C2   0.020
 4GT  plan-4  N1   0.020
 4GT  plan-4  O3   0.020
 4GT  plan-4  H13  0.020
 4GT  plan-4  H14  0.020

