# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:55:49 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-amino-2-[(2,2-dimethylpropyl)amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)CNc1ncc(C(N)=O)c(N)n1
#
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
 4H8  4H8  4-amino-2-[(2,2-dimethylpropyl)amino]pyrimidine-5-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_4H8
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
 4H8  C4   C  CH3   0  -0.640   4.2472   0.7578   1.2680
 4H8  C5   C  CH2   0  -0.201   2.5601  -0.6769   0.0624
 4H8  C7   C  CR6   0   0.607   0.2358   0.1475  -0.0216
 4H8  C10  C  CR6   0  -0.279  -2.4225  -0.2589  -0.1220
 4H8  N12  N  NH2   0  -0.820  -4.2979  -1.7545   0.0641
 4H8  C9   C  CR16  0  -0.026  -1.4890  -1.2816  -0.1964
 4H8  C14  C  CR6   0   0.504  -1.8619   1.0532  -0.0393
 4H8  C11  C  C     0   0.517  -3.8760  -0.4966  -0.1665
 4H8  C1   C  CH3   0  -0.635   4.1928   0.7322  -1.2406
 4H8  C3   C  CH3   0  -0.638   4.9517  -1.2779   0.0212
 4H8  C2   C  CT    0  -0.163   3.9799  -0.0983   0.0270
 4H8  N8   N  N     0  -0.490  -0.1795  -1.1225  -0.1527
 4H8  N16  N  N     0  -0.519  -0.5453   1.2261   0.0233
 4H8  N15  N  NH2   0  -0.824  -2.6165   2.1522   0.0048
 4H8  N6   N  NH1   0  -0.658   1.5550   0.3610   0.0589
 4H8  O13  O  O     0  -0.510  -4.6782   0.4044  -0.4180
 4H8  H1   H  HCH3  0   0.222   3.5914   1.6291   1.3299
 4H8  H2   H  HCH3  0   0.229   4.1151   0.1778   2.1837
 4H8  H3   H  HCH3  0   0.233   5.2720   1.1331   1.2594
 4H8  H4   H  HCH2  0   0.235   2.4161  -1.3293  -0.8035
 4H8  H5   H  HCH2  0   0.230   2.4530  -1.3099   0.9511
 4H8  H6   H  HNH2  0   0.408  -3.7104  -2.4566   0.4775
 4H8  H7   H  HNH2  0   0.403  -5.2884  -1.9350   0.0789
 4H8  H8   H  HCR6  0   0.257  -1.8190  -2.3087  -0.3190
 4H8  H9   H  HCH3  0   0.229   5.2141   1.1156  -1.2788
 4H8  H10  H  HCH3  0   0.226   4.0325   0.1304  -2.1377
 4H8  H11  H  HCH3  0   0.224   3.5224   1.5920  -1.2939
 4H8  H12  H  HCH3  0   0.227   4.8283  -1.9011   0.9094
 4H8  H13  H  HCH3  0   0.227   4.8034  -1.9124  -0.8550
 4H8  H14  H  HCH3  0   0.231   5.9839  -0.9240   0.0041
 4H8  H15  H  HNH2  0   0.412  -3.6083   2.0816  -0.1518
 4H8  H16  H  HNH2  0   0.393  -2.1703   3.0533   0.0077
 4H8  H17  H  HNH1  0   0.389   1.8378   1.3162   0.2044

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
 4H8  C1   C2   single    1.530  0.020  1.530
 4H8  C3   C2   single    1.528  0.020  1.528
 4H8  C4   C2   single    1.531  0.020  1.531
 4H8  C2   C5   single    1.534  0.020  1.534
 4H8  C5   N6   single    1.445  0.020  1.445
 4H8  N6   C7   single    1.339  0.020  1.339
 4H8  N16  C7   aromatic  1.332  0.020  1.332
 4H8  N16  C14  aromatic  1.329  0.020  1.329
 4H8  C7   N8   aromatic  1.343  0.020  1.343
 4H8  N15  C14  single    1.334  0.020  1.334
 4H8  C14  C10  aromatic  1.429  0.020  1.429
 4H8  N8   C9   aromatic  1.320  0.020  1.320
 4H8  C10  C9   aromatic  1.387  0.020  1.387
 4H8  C10  C11  single    1.473  0.020  1.473
 4H8  O13  C11  double    1.232  0.020  1.232
 4H8  C11  N12  single    1.347  0.020  1.347
 4H8  C4   H1   single    0.970  0.020  1.090
 4H8  C4   H2   single    0.970  0.020  1.090
 4H8  C4   H3   single    0.970  0.020  1.090
 4H8  C5   H4   single    0.970  0.020  1.090
 4H8  C5   H5   single    0.970  0.020  1.090
 4H8  N12  H6   single    0.860  0.020  1.020
 4H8  N12  H7   single    0.860  0.020  1.020
 4H8  C9   H8   single    0.930  0.020  1.080
 4H8  C1   H9   single    0.970  0.020  1.090
 4H8  C1   H10  single    0.970  0.020  1.090
 4H8  C1   H11  single    0.970  0.020  1.090
 4H8  C3   H12  single    0.970  0.020  1.090
 4H8  C3   H13  single    0.970  0.020  1.090
 4H8  C3   H14  single    0.970  0.020  1.090
 4H8  N15  H15  single    0.860  0.020  1.020
 4H8  N15  H16  single    0.860  0.020  1.020
 4H8  N6   H17  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
 4H8  H3   C4   H2   107.62  3.000
 4H8  H3   C4   H1   106.85  3.000
 4H8  H2   C4   H1   107.67  3.000
 4H8  H3   C4   C2   110.48  3.000
 4H8  H2   C4   C2   111.20  3.000
 4H8  H1   C4   C2   112.78  3.000
 4H8  H5   C5   H4   106.53  3.000
 4H8  H5   C5   N6   110.42  3.000
 4H8  H4   C5   N6   109.57  3.000
 4H8  H5   C5   C2   109.09  3.000
 4H8  H4   C5   C2   109.19  3.000
 4H8  N6   C5   C2   111.90  3.000
 4H8  N6   C7   N16  116.52  3.000
 4H8  N16  C7   N8   125.99  3.000
 4H8  N6   C7   N8   117.49  3.000
 4H8  C11  C10  C14  122.47  3.000
 4H8  C11  C10  C9   122.92  3.000
 4H8  C14  C10  C9   114.59  3.000
 4H8  H7   N12  H6   116.36  3.000
 4H8  H7   N12  C11  118.57  3.000
 4H8  H6   N12  C11  122.69  3.000
 4H8  H8   C9   N8   114.79  3.000
 4H8  H8   C9   C10  119.94  3.000
 4H8  N8   C9   C10  125.25  3.000
 4H8  N15  C14  N16  116.85  3.000
 4H8  N15  C14  C10  122.44  3.000
 4H8  N16  C14  C10  120.70  3.000
 4H8  O13  C11  N12  120.93  3.000
 4H8  N12  C11  C10  117.04  3.000
 4H8  O13  C11  C10  122.03  3.000
 4H8  H11  C1   H10  107.68  3.000
 4H8  H11  C1   H9   107.23  3.000
 4H8  H10  C1   H9   107.59  3.000
 4H8  H11  C1   C2   112.49  3.000
 4H8  H10  C1   C2   111.16  3.000
 4H8  H9   C1   C2   110.48  3.000
 4H8  H14  C3   H13  107.71  3.000
 4H8  H14  C3   H12  107.74  3.000
 4H8  H13  C3   H12  107.80  3.000
 4H8  H14  C3   C2   110.56  3.000
 4H8  H13  C3   C2   111.42  3.000
 4H8  H12  C3   C2   111.45  3.000
 4H8  C3   C2   C1   109.10  3.000
 4H8  C3   C2   C5   107.31  3.000
 4H8  C1   C2   C5   110.65  3.000
 4H8  C5   C2   C4   110.72  3.000
 4H8  C3   C2   C4   108.88  3.000
 4H8  C1   C2   C4   110.10  3.000
 4H8  C9   N8   C7   115.10  3.000
 4H8  C14  N16  C7   118.28  3.000
 4H8  H16  N15  H15  120.03  3.000
 4H8  H16  N15  C14  119.17  3.000
 4H8  H15  N15  C14  119.64  3.000
 4H8  H17  N6   C7   115.90  3.000
 4H8  H17  N6   C5   119.07  3.000
 4H8  C7   N6   C5   124.82  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
 4H8  CONST_01  C10  C14  N16  C7      0.00   0.0  0
 4H8  CONST_02  C10  C9   N8   C7      0.00   0.0  0
 4H8  CONST_03  N16  C7   N8   C9      0.00   0.0  0
 4H8  CONST_04  N16  C14  C10  C9      0.00   0.0  0
 4H8  CONST_05  N8   C7   N16  C14     0.00   0.0  0
 4H8  CONST_06  N8   C9   C10  C14     0.00   0.0  0
 4H8  CONST_07  N15  C14  N16  C7    180.00   0.0  0
 4H8  CONST_08  N6   C7   N8   C9    180.00   0.0  0
 4H8  CONST_09  N15  C14  C10  C9    180.00   0.0  0
 4H8  CONST_10  N6   C7   N16  C14   180.00   0.0  0
 4H8  CONST_11  N16  C14  C10  C11   180.00   0.0  0
 4H8  CONST_12  N8   C9   C10  C11   180.00   0.0  0
 4H8  CONST_13  H8   C9   N8   C7    180.00   0.0  0
 4H8  CONST_14  N16  C7   N6   C5    180.00   0.0  0
 4H8  CONST_15  N8   C7   N6   C5      0.00   0.0  0
 4H8  CONST_16  H15  N15  C14  C10     0.00   0.0  0
 4H8  CONST_17  H16  N15  C14  C10   180.00   0.0  0
 4H8  CONST_18  H17  N6   C7   N8    180.00   0.0  0
 4H8  CONST_20  H7   N12  C11  C10   180.00   0.0  0
 4H8  Var_01    C14  C10  C11  N12  -165.18  30.0  2
 4H8  Var_02    C2   C5   N6   C7    174.42  30.0  1
 4H8  Var_03    N6   C5   C2   C4     61.79  30.0  3
 4H8  Var_04    H9   C1   C2   C4     59.12  30.0  3
 4H8  Var_05    H12  C3   C2   C4     60.12  30.0  3
 4H8  Var_06    H1   C4   C2   C5    -62.88  30.0  3

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
 4H8  plan-1  C7   0.020
 4H8  plan-1  C10  0.020
 4H8  plan-1  C9   0.020
 4H8  plan-1  C14  0.020
 4H8  plan-1  C11  0.020
 4H8  plan-1  N8   0.020
 4H8  plan-1  N16  0.020
 4H8  plan-1  N15  0.020
 4H8  plan-1  N6   0.020
 4H8  plan-1  H8   0.020
 4H8  plan-2  C10  0.020
 4H8  plan-2  N12  0.020
 4H8  plan-2  C11  0.020
 4H8  plan-2  O13  0.020
 4H8  plan-2  H6   0.020
 4H8  plan-2  H7   0.020
 4H8  plan-3  C14  0.020
 4H8  plan-3  N15  0.020
 4H8  plan-3  H15  0.020
 4H8  plan-3  H16  0.020
 4H8  plan-4  C5   0.020
 4H8  plan-4  C7   0.020
 4H8  plan-4  N6   0.020
 4H8  plan-4  H17  0.020

