# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:35:42 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-({4-[(1S,4S)-5-(cyanoacetyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyrimidin-2-yl}amino)-N-ethylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)c1ccc(Nc2nccc(n2)N3C[C@@H]4C[C@H]3CN4C(=O)CC#N)cc1
#
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
 G5D  G5D  4-({4-[(1S,4S)-5-(cyanoacetyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyrimidin-2-yl}amino)-N-ethylbenzamide  ligand  53  30  .  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_G5D
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
 G5D  N3   N  NT    0  -0.482    3.0151  -0.8518   1.1612
 G5D  C4   C  CR16  0  -0.001    0.3860  -3.0324   0.0048
 G5D  N2   N  N     0  -0.497   -0.6656  -2.2080   0.0299
 G5D  C7   C  CH2   0  -0.262    3.7827   1.2535   0.2611
 G5D  C6   C  CH1   0  -0.186    5.2577  -0.3860   1.1784
 G5D  C9   C  CR6   0   0.370   -2.7609  -0.1347   0.2384
 G5D  C13  C  CR16  0  -0.262   -4.7844  -1.2351  -0.4708
 G5D  C20  C  CH2   0  -0.261   -9.0258   1.1765  -0.9894
 G5D  C21  C  CH3   0  -0.696   -9.4706   2.6181  -0.8323
 G5D  C8   C  CH1   0  -0.185    3.2813   0.5394   1.5195
 G5D  C16  C  CH2   0  -0.433    4.5779   0.3820   2.3083
 G5D  C19  C  CSP   0   0.144    6.3955   1.6885  -3.1323
 G5D  C1   C  CR6   0   0.602   -0.4016  -0.9746   0.4340
 G5D  N1   N  N     0  -0.534    0.7843  -0.4927   0.7988
 G5D  C2   C  CR6   0   0.568    1.8224  -1.3253   0.7719
 G5D  C3   C  CR16  0  -0.452    1.6569  -2.6679   0.3610
 G5D  C5   C  CH2   0  -0.253    4.2868  -1.5515   0.9802
 G5D  N4   N  NT    0  -0.450    5.0528   0.5426   0.0619
 G5D  C10  C  CR16  0  -0.346   -3.5211   1.0180   0.4826
 G5D  C11  C  CR16  0  -0.281   -4.8790   1.0401   0.2414
 G5D  C12  C  CR6   0  -0.058   -5.5392  -0.0874  -0.2484
 G5D  C14  C  CR16  0  -0.303   -3.4190  -1.2708  -0.2470
 G5D  C15  C  C     0   0.530   -7.0056  -0.1293  -0.5070
 G5D  O1   O  O     0  -0.499   -7.6206  -1.1903  -0.5186
 G5D  N6   N  NH1   0  -0.649   -7.6070   1.0531  -0.7209
 G5D  C17  C  C     0   0.574    5.8522   0.6033  -1.0052
 G5D  O2   O  O     0  -0.479    6.8571  -0.0728  -1.1503
 G5D  N7   N  NS    0  -0.260    7.1480   1.7627  -3.9978
 G5D  H2   H  HCR6  0   0.267    0.1855  -4.0471  -0.3208
 G5D  H6   H  HCH2  0   0.274    3.1003   1.1305  -0.5811
 G5D  H7   H  HCH2  0   0.272    3.9369   2.3211   0.4376
 G5D  H5   H  HCH1  0   0.288    6.2982  -0.6675   1.3050
 G5D  H12  H  HCR6  0   0.256   -5.2690  -2.1291  -0.8408
 G5D  H19  H  HCH2  0   0.238   -9.5718   0.5387  -0.2940
 G5D  H20  H  HCH2  0   0.232   -9.2581   0.8190  -1.9972
 G5D  H23  H  HCH3  0   0.244  -10.5370   2.7046  -1.0359
 G5D  H21  H  HCH3  0   0.234   -9.2900   2.9791   0.1806
 G5D  H22  H  HCH3  0   0.232   -8.9480   3.2767  -1.5280
 G5D  H8   H  HCH1  0   0.288    2.4389   1.0174   2.0080
 G5D  H9   H  HNH1  0   0.407   -1.0866   0.8521   0.8275
 G5D  H18  H  HCH2  0   0.344    5.2893   2.6100  -1.6330
 G5D  H17  H  HCH2  0   0.348    4.4540   1.3320  -2.4934
 G5D  H15  H  HCH2  0   0.276    4.4619  -0.2035   3.2195
 G5D  H16  H  HCH2  0   0.276    5.0613   1.3306   2.5393
 G5D  H1   H  HCR6  0   0.278    2.4710  -3.3759   0.3355
 G5D  H4   H  HCH2  0   0.264    4.4364  -2.3366   1.7268
 G5D  H3   H  HCH2  0   0.266    4.3729  -1.9953  -0.0134
 G5D  H10  H  HCR6  0   0.272   -3.0394   1.9050   0.8760
 G5D  H11  H  HCR6  0   0.256   -5.4204   1.9495   0.4709
 G5D  H13  H  HCR6  0   0.288   -2.8656  -2.1736  -0.4452
 G5D  H14  H  HNH1  0   0.401   -7.0372   1.8675  -0.8840
 G5D  N5   N  NH1   0  -0.769   -1.4078  -0.0482   0.5044
 G5D  C18  C  CH2   0  -0.693    5.4188   1.6132  -2.0625

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
 G5D  N7   C19  triple    1.149  0.020  1.149
 G5D  C19  C18  single    1.451  0.020  1.451
 G5D  C18  C17  single    1.525  0.020  1.525
 G5D  C17  O2   double    1.220  0.020  1.220
 G5D  C17  N4   single    1.335  0.020  1.335
 G5D  C5   C6   single    1.530  0.020  1.530
 G5D  C5   N3   single    1.463  0.020  1.463
 G5D  C3   C4   aromatic  1.369  0.020  1.369
 G5D  C3   C2   aromatic  1.414  0.020  1.414
 G5D  C4   N2   aromatic  1.336  0.020  1.336
 G5D  C6   N4   single    1.467  0.020  1.467
 G5D  C6   C16  single    1.526  0.020  1.526
 G5D  N4   C7   single    1.469  0.020  1.469
 G5D  N3   C2   single    1.341  0.020  1.341
 G5D  N3   C8   single    1.461  0.020  1.461
 G5D  C2   N1   aromatic  1.331  0.020  1.331
 G5D  N2   C1   aromatic  1.324  0.020  1.324
 G5D  C7   C8   single    1.531  0.020  1.531
 G5D  C16  C8   single    1.526  0.020  1.526
 G5D  N1   C1   aromatic  1.331  0.020  1.331
 G5D  C1   N5   single    1.369  0.020  1.369
 G5D  N5   C9   single    1.382  0.020  1.382
 G5D  C9   C14  aromatic  1.400  0.020  1.400
 G5D  C9   C10  aromatic  1.402  0.020  1.402
 G5D  C14  C13  aromatic  1.384  0.020  1.384
 G5D  C10  C11  aromatic  1.379  0.020  1.379
 G5D  C13  C12  aromatic  1.392  0.020  1.392
 G5D  C11  C12  aromatic  1.395  0.020  1.395
 G5D  C12  C15  single    1.490  0.020  1.490
 G5D  N6   C15  single    1.344  0.020  1.344
 G5D  N6   C20  single    1.449  0.020  1.449
 G5D  C15  O1   double    1.226  0.020  1.226
 G5D  C20  C21  single    1.517  0.020  1.517
 G5D  C4   H2   single    0.930  0.020  1.080
 G5D  C7   H6   single    0.970  0.020  1.090
 G5D  C7   H7   single    0.970  0.020  1.090
 G5D  C6   H5   single    0.970  0.020  1.090
 G5D  C13  H12  single    0.930  0.020  1.080
 G5D  C20  H19  single    0.970  0.020  1.090
 G5D  C20  H20  single    0.970  0.020  1.090
 G5D  C21  H23  single    0.970  0.020  1.090
 G5D  C21  H21  single    0.970  0.020  1.090
 G5D  C21  H22  single    0.970  0.020  1.090
 G5D  C8   H8   single    0.970  0.020  1.090
 G5D  N5   H9   single    0.860  0.020  1.020
 G5D  C18  H18  single    0.970  0.020  1.090
 G5D  C18  H17  single    0.970  0.020  1.090
 G5D  C16  H15  single    0.970  0.020  1.090
 G5D  C16  H16  single    0.970  0.020  1.090
 G5D  C3   H1   single    0.930  0.020  1.080
 G5D  C5   H4   single    0.970  0.020  1.090
 G5D  C5   H3   single    0.970  0.020  1.090
 G5D  C10  H10  single    0.930  0.020  1.080
 G5D  C11  H11  single    0.930  0.020  1.080
 G5D  C14  H13  single    0.930  0.020  1.080
 G5D  N6   H14  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
 G5D  C5   N3   C2   124.64  3.000
 G5D  C2   N3   C8   124.71  3.000
 G5D  C5   N3   C8   109.11  3.000
 G5D  H2   C4   C3   119.92  3.000
 G5D  H2   C4   N2   115.95  3.000
 G5D  C3   C4   N2   124.14  3.000
 G5D  C1   N2   C4   115.05  3.000
 G5D  H7   C7   H6   108.85  3.000
 G5D  H7   C7   N4   111.88  3.000
 G5D  H6   C7   N4   112.43  3.000
 G5D  H7   C7   C8   111.65  3.000
 G5D  H6   C7   C8   112.15  3.000
 G5D  N4   C7   C8    99.72  3.000
 G5D  H5   C6   N4   112.77  3.000
 G5D  H5   C6   C5   115.21  3.000
 G5D  N4   C6   C5   107.16  3.000
 G5D  H5   C6   C16  118.12  3.000
 G5D  N4   C6   C16  100.53  3.000
 G5D  C5   C6   C16  101.34  3.000
 G5D  C14  C9   C10  118.21  3.000
 G5D  C10  C9   N5   116.49  3.000
 G5D  C14  C9   N5   125.31  3.000
 G5D  H12  C13  C14  118.41  3.000
 G5D  H12  C13  C12  119.55  3.000
 G5D  C14  C13  C12  122.04  3.000
 G5D  H20  C20  H19  106.86  3.000
 G5D  H20  C20  N6   110.53  3.000
 G5D  H19  C20  N6   108.80  3.000
 G5D  H20  C20  C21  110.10  3.000
 G5D  H19  C20  C21  110.06  3.000
 G5D  N6   C20  C21  110.42  3.000
 G5D  H22  C21  H21  108.25  3.000
 G5D  H22  C21  H23  107.56  3.000
 G5D  H21  C21  H23  108.04  3.000
 G5D  H22  C21  C20  111.54  3.000
 G5D  H21  C21  C20  111.24  3.000
 G5D  H23  C21  C20  110.08  3.000
 G5D  H8   C8   C16  118.20  3.000
 G5D  H8   C8   C7   114.76  3.000
 G5D  C16  C8   C7   101.23  3.000
 G5D  H8   C8   N3   112.86  3.000
 G5D  C16  C8   N3   100.57  3.000
 G5D  C7   C8   N3   107.59  3.000
 G5D  H16  C16  H15  109.75  3.000
 G5D  H16  C16  C8   113.38  3.000
 G5D  H15  C16  C8   113.42  3.000
 G5D  H16  C16  C6   113.43  3.000
 G5D  H15  C16  C6   113.34  3.000
 G5D  C8   C16  C6    92.74  3.000
 G5D  N7   C19  C18  180.00  3.000
 G5D  N1   C1   N5   113.31  3.000
 G5D  N5   C1   N2   119.95  3.000
 G5D  N1   C1   N2   126.75  3.000
 G5D  C2   N1   C1   117.57  3.000
 G5D  C3   C2   N1   120.57  3.000
 G5D  N1   C2   N3   117.83  3.000
 G5D  C3   C2   N3   121.59  3.000
 G5D  H1   C3   C2   122.79  3.000
 G5D  H1   C3   C4   121.29  3.000
 G5D  C2   C3   C4   115.92  3.000
 G5D  H3   C5   H4   108.58  3.000
 G5D  H3   C5   C6   112.19  3.000
 G5D  H4   C5   C6   111.82  3.000
 G5D  H3   C5   N3   112.07  3.000
 G5D  H4   C5   N3   112.19  3.000
 G5D  C6   C5   N3    99.87  3.000
 G5D  C17  N4   C6   123.62  3.000
 G5D  C6   N4   C7   108.90  3.000
 G5D  C17  N4   C7   127.18  3.000
 G5D  H10  C10  C11  119.22  3.000
 G5D  H10  C10  C9   119.68  3.000
 G5D  C11  C10  C9   121.10  3.000
 G5D  H11  C11  C12  121.08  3.000
 G5D  H11  C11  C10  117.95  3.000
 G5D  C12  C11  C10  120.94  3.000
 G5D  C15  C12  C11  123.33  3.000
 G5D  C15  C12  C13  118.88  3.000
 G5D  C11  C12  C13  117.77  3.000
 G5D  H13  C14  C13  119.91  3.000
 G5D  H13  C14  C9   120.16  3.000
 G5D  C13  C14  C9   119.93  3.000
 G5D  N6   C15  O1   122.37  3.000
 G5D  O1   C15  C12  121.31  3.000
 G5D  N6   C15  C12  116.32  3.000
 G5D  H14  N6   C15  118.96  3.000
 G5D  H14  N6   C20  117.06  3.000
 G5D  C15  N6   C20  122.86  3.000
 G5D  O2   C17  N4   124.29  3.000
 G5D  N4   C17  C18  114.47  3.000
 G5D  O2   C17  C18  121.24  3.000
 G5D  H9   N5   C1   112.72  3.000
 G5D  H9   N5   C9   115.42  3.000
 G5D  C1   N5   C9   131.86  3.000
 G5D  H17  C18  H18  106.55  3.000
 G5D  H17  C18  C17  110.71  3.000
 G5D  H18  C18  C17  111.41  3.000
 G5D  H17  C18  C19  108.47  3.000
 G5D  H18  C18  C19  108.80  3.000
 G5D  C17  C18  C19  110.75  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
 G5D  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 G5D  CONST_02  N1   C1   N2   C4      0.00   0.0  0
 G5D  CONST_03  C2   C3   C4   N2      0.00   0.0  0
 G5D  CONST_04  C2   N1   C1   N2      0.00   0.0  0
 G5D  CONST_05  C12  C13  C14  C9      0.00   0.0  0
 G5D  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 G5D  CONST_07  C10  C9   C14  C13     0.00   0.0  0
 G5D  CONST_08  C10  C11  C12  C13     0.00   0.0  0
 G5D  CONST_09  C3   C4   N2   C1      0.00   0.0  0
 G5D  CONST_10  C3   C2   N1   C1      0.00   0.0  0
 G5D  CONST_11  C14  C9   C10  C11     0.00   0.0  0
 G5D  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 G5D  CONST_13  C4   C3   C2   N3    180.00   0.0  0
 G5D  CONST_14  C1   N1   C2   N3    180.00   0.0  0
 G5D  CONST_15  N5   C1   N2   C4    180.00   0.0  0
 G5D  CONST_16  N5   C9   C14  C13   180.00   0.0  0
 G5D  CONST_17  C2   N1   C1   N5    180.00   0.0  0
 G5D  CONST_18  C11  C10  C9   N5    180.00   0.0  0
 G5D  CONST_19  C15  C12  C11  C10   180.00   0.0  0
 G5D  CONST_20  C15  C12  C13  C14   180.00   0.0  0
 G5D  CONST_21  H1   C3   C2   N3      0.00   0.0  0
 G5D  CONST_22  H12  C13  C14  C9    180.00   0.0  0
 G5D  CONST_23  H11  C11  C10  C9    180.00   0.0  0
 G5D  CONST_24  H2   C4   N2   C1    180.00   0.0  0
 G5D  CONST_25  H13  C14  C9   C10   180.00   0.0  0
 G5D  CONST_26  H10  C10  C11  C12   180.00   0.0  0
 G5D  CONST_27  C18  C17  N4   C7      0.00   0.0  0
 G5D  CONST_28  O2   C17  N4   C7    180.00   0.0  0
 G5D  CONST_29  C18  C17  N4   C6    180.00   0.0  0
 G5D  CONST_30  O2   C17  N4   C6      0.00   0.0  0
 G5D  CONST_31  C12  C15  N6   C20   180.00   0.0  0
 G5D  CONST_32  H14  N6   C15  C12     0.00   0.0  0
 G5D  CONST_33  O1   C15  N6   C20     0.00   0.0  0
 G5D  Var_01    C2   N3   C5   C6    162.65  30.0  1
 G5D  Var_02    C8   C7   N4   C6     -4.32  30.0  1
 G5D  Var_03    C3   C2   N3   C8    176.04  30.0  2
 G5D  Var_04    C9   N5   C1   N2      1.08  30.0  2
 G5D  Var_05    C14  C9   N5   C1     -2.86  30.0  2
 G5D  Var_06    N6   C15  C12  C13  -158.25  30.0  2
 G5D  Var_07    N4   C17  C18  C19   175.52  30.0  3
 G5D  Var_08    C15  N6   C20  C21   165.40  30.0  2
 G5D  Var_09    H23  C21  C20  N6    179.96  30.0  3

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
 G5D  chir_01  C6  C5  N4   C16  negativ
 G5D  chir_02  C8  N3  C16  C7   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
 G5D  plan-1  C9   0.020
 G5D  plan-1  C13  0.020
 G5D  plan-1  C10  0.020
 G5D  plan-1  C11  0.020
 G5D  plan-1  C12  0.020
 G5D  plan-1  C14  0.020
 G5D  plan-1  C15  0.020
 G5D  plan-1  H12  0.020
 G5D  plan-1  H10  0.020
 G5D  plan-1  H11  0.020
 G5D  plan-1  H13  0.020
 G5D  plan-1  N5   0.020
 G5D  plan-2  N3   0.020
 G5D  plan-2  C4   0.020
 G5D  plan-2  N2   0.020
 G5D  plan-2  C1   0.020
 G5D  plan-2  N1   0.020
 G5D  plan-2  C2   0.020
 G5D  plan-2  C3   0.020
 G5D  plan-2  H2   0.020
 G5D  plan-2  H1   0.020
 G5D  plan-2  N5   0.020
 G5D  plan-3  C20  0.020
 G5D  plan-3  C12  0.020
 G5D  plan-3  C15  0.020
 G5D  plan-3  O1   0.020
 G5D  plan-3  N6   0.020
 G5D  plan-3  H14  0.020
 G5D  plan-4  C7   0.020
 G5D  plan-4  C6   0.020
 G5D  plan-4  N4   0.020
 G5D  plan-4  C17  0.020
 G5D  plan-4  O2   0.020
 G5D  plan-4  C18  0.020

