# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:41:51 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-({6-[(3R)-3-aminopiperidin-1-yl]-3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl}methyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C=C(N2CCC[C@@H](N)C2)N(Cc3ccccc3C#N)C1=O
#
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
 T22  T22  2-({6-[(3R)-3-aminopiperidin-1-yl]-3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl}methyl)benzonitrile  ligand  46  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T22
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
 T22  O26   O  O     0  -0.483  -2.2005  -1.5145   2.0482
 T22  C25   C  CR6   0   0.766  -1.4699  -1.5551   1.0782
 T22  N2    N  NR6   0  -0.583  -1.5699  -2.5561   0.1479
 T22  C1    C  CH3   0  -0.530  -2.6046  -3.5515   0.3881
 T22  N15   N  NR6   0  -0.590  -0.5186  -0.5727   0.8475
 T22  C16   C  CH2   0  -0.421  -0.7075   0.7109   1.5319
 T22  C17   C  CR6   0   0.177  -0.7805   1.8805   0.5852
 T22  C22   C  CR6   0  -0.003  -1.6630   1.9020  -0.5019
 T22  C23   C  CSP   0   0.019  -2.5436   0.8067  -0.7525
 T22  N24   N  NS    0  -0.248  -3.2827  -0.0533  -0.9608
 T22  C21   C  CR16  0  -0.235  -1.7288   3.0038  -1.3564
 T22  C20   C  CR16  0  -0.261  -0.9272   4.1059  -1.1214
 T22  C19   C  CR16  0  -0.220  -0.0670   4.1064  -0.0317
 T22  C18   C  CR16  0  -0.306   0.0026   3.0043   0.8078
 T22  C6    C  CR6   0   0.672   0.4028  -0.6879  -0.1815
 T22  C5    C  CR16  0  -0.570   0.2272  -1.6439  -1.1290
 T22  C3    C  CR6   0   0.586  -0.8304  -2.6006  -1.0374
 T22  O4    O  O     0  -0.487  -1.0553  -3.4583  -1.8776
 T22  N7    N  NT    0  -0.484   1.4016   0.2381  -0.1899
 T22  C14   C  CH2   0  -0.328   2.2982   0.3390   0.9560
 T22  C11   C  CH1   0  -0.081   3.5919  -0.4505   0.7414
 T22  N13   N  NH2   0  -0.792   4.4165  -0.2871   1.9272
 T22  C10   C  CH2   0  -0.449   4.2617  -0.0443  -0.5704
 T22  C9    C  CH2   0  -0.447   3.2952  -0.1538  -1.7444
 T22  C8    C  CH2   0  -0.338   2.0201   0.6231  -1.4485
 T22  H1    H  HCH3  0   0.251  -3.5953  -3.1032   0.3272
 T22  H1A   H  HCH3  0   0.264  -2.5221  -4.3262  -0.3639
 T22  H1B   H  HCH3  0   0.255  -2.4790  -3.9987   1.3708
 T22  H16   H  HCH2  0   0.319  -1.6377   0.6357   2.0922
 T22  H16A  H  HCH2  0   0.291   0.0720   0.8855   2.2713
 T22  H21   H  HCR6  0   0.284  -2.4142   2.9928  -2.1929
 T22  H20   H  HCR6  0   0.274  -0.9789   4.9609  -1.7812
 T22  H19   H  HCR6  0   0.274   0.5592   4.9668   0.1639
 T22  H18   H  HCR6  0   0.271   0.6874   3.0138   1.6467
 T22  H5    H  HCR6  0   0.279   0.9443  -1.7699  -1.9246
 T22  H14   H  HCH2  0   0.239   2.5317   1.3962   1.1263
 T22  H14A  H  HCH2  0   0.267   1.8159  -0.0393   1.8551
 T22  H11   H  HCH1  0   0.228   3.3212  -1.5107   0.6772
 T22  HN13  H  HNH2  0   0.350   5.2040  -0.9219   1.8824
 T22  HN1A  H  HNH2  0   0.339   4.8175   0.6444   1.9358
 T22  H10   H  HCH2  0   0.215   4.6150   0.9905  -0.4827
 T22  H10A  H  HCH2  0   0.240   5.1449  -0.6649  -0.7421
 T22  H9    H  HCH2  0   0.244   3.7497   0.2367  -2.6571
 T22  H9A   H  HCH2  0   0.230   3.0596  -1.2048  -1.9357
 T22  H8    H  HCH2  0   0.266   1.2875   0.5215  -2.2484
 T22  H8A   H  HCH2  0   0.255   2.2546   1.6900  -1.3696

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
 T22  O26  C25   double    1.215  0.020  1.215
 T22  N2   C25   single    1.370  0.020  1.370
 T22  C25  N15   single    1.387  0.020  1.387
 T22  C1   N2    single    1.456  0.020  1.456
 T22  N2   C3    single    1.398  0.020  1.398
 T22  C1   H1    single    0.970  0.020  1.090
 T22  C1   H1A   single    0.970  0.020  1.090
 T22  C1   H1B   single    0.970  0.020  1.090
 T22  N15  C16   single    1.467  0.020  1.467
 T22  N15  C6    single    1.386  0.020  1.386
 T22  C16  C17   single    1.506  0.020  1.506
 T22  C16  H16   single    0.970  0.020  1.090
 T22  C16  H16A  single    0.970  0.020  1.090
 T22  C18  C17   aromatic  1.388  0.020  1.388
 T22  C17  C22   aromatic  1.400  0.020  1.400
 T22  C22  C21   aromatic  1.396  0.020  1.396
 T22  C22  C23   single    1.428  0.020  1.428
 T22  C23  N24   triple    1.153  0.020  1.153
 T22  C20  C21   aromatic  1.383  0.020  1.383
 T22  C21  H21   single    0.930  0.020  1.080
 T22  C19  C20   aromatic  1.388  0.020  1.388
 T22  C20  H20   single    0.930  0.020  1.080
 T22  C18  C19   aromatic  1.387  0.020  1.387
 T22  C19  H19   single    0.930  0.020  1.080
 T22  C18  H18   single    0.930  0.020  1.080
 T22  C5   C6    double    1.357  0.020  1.357
 T22  C6   N7    single    1.362  0.020  1.362
 T22  C3   C5    single    1.429  0.020  1.429
 T22  C5   H5    single    0.930  0.020  1.080
 T22  O4   C3    double    1.222  0.020  1.222
 T22  C8   N7    single    1.454  0.020  1.454
 T22  N7   C14   single    1.458  0.020  1.458
 T22  C14  C11   single    1.531  0.020  1.531
 T22  C14  H14   single    0.970  0.020  1.090
 T22  C14  H14A  single    0.970  0.020  1.090
 T22  C10  C11   single    1.528  0.020  1.528
 T22  C11  N13   single    1.454  0.020  1.454
 T22  C11  H11   single    0.970  0.020  1.090
 T22  N13  HN13  single    0.890  0.020  1.040
 T22  N13  HN1A  single    0.890  0.020  1.040
 T22  C9   C10   single    1.525  0.020  1.525
 T22  C10  H10   single    0.970  0.020  1.090
 T22  C10  H10A  single    0.970  0.020  1.090
 T22  C8   C9    single    1.522  0.020  1.522
 T22  C9   H9    single    0.970  0.020  1.090
 T22  C9   H9A   single    0.970  0.020  1.090
 T22  C8   H8    single    0.970  0.020  1.090
 T22  C8   H8A   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
 T22  N15   C25  N2    117.04  3.000
 T22  N15   C25  O26   121.44  3.000
 T22  N2    C25  O26   121.51  3.000
 T22  C3    N2   C1    119.62  3.000
 T22  C3    N2   C25   124.09  3.000
 T22  C1    N2   C25   116.06  3.000
 T22  H1B   C1   H1A   108.95  3.000
 T22  H1B   C1   H1    108.96  3.000
 T22  H1A   C1   H1    108.96  3.000
 T22  H1B   C1   N2    110.39  3.000
 T22  H1A   C1   N2    108.69  3.000
 T22  H1    C1   N2    110.85  3.000
 T22  C6    N15  C16   120.31  3.000
 T22  C6    N15  C25   121.37  3.000
 T22  C16   N15  C25   117.00  3.000
 T22  H16A  C16  H16   105.86  3.000
 T22  H16A  C16  C17   109.70  3.000
 T22  H16   C16  C17   109.62  3.000
 T22  H16A  C16  N15   111.41  3.000
 T22  H16   C16  N15   106.84  3.000
 T22  C17   C16  N15   113.11  3.000
 T22  C18   C17  C22   117.89  3.000
 T22  C22   C17  C16   122.02  3.000
 T22  C18   C17  C16   120.04  3.000
 T22  C21   C22  C23   117.98  3.000
 T22  C23   C22  C17   120.88  3.000
 T22  C21   C22  C17   121.13  3.000
 T22  N24   C23  C22   180.00  3.000
 T22  H21   C21  C20   120.45  3.000
 T22  H21   C21  C22   119.69  3.000
 T22  C20   C21  C22   119.85  3.000
 T22  H20   C20  C19   120.55  3.000
 T22  H20   C20  C21   119.93  3.000
 T22  C19   C20  C21   119.53  3.000
 T22  H19   C19  C18   119.56  3.000
 T22  H19   C19  C20   120.05  3.000
 T22  C18   C19  C20   120.38  3.000
 T22  H18   C18  C19   119.57  3.000
 T22  H18   C18  C17   119.22  3.000
 T22  C19   C18  C17   121.20  3.000
 T22  N7    C6   C5    124.71  3.000
 T22  N7    C6   N15   115.82  3.000
 T22  C5    C6   N15   119.39  3.000
 T22  H5    C5   C3    117.46  3.000
 T22  H5    C5   C6    120.75  3.000
 T22  C3    C5   C6    121.50  3.000
 T22  O4    C3   C5    124.21  3.000
 T22  O4    C3   N2    120.55  3.000
 T22  C5    C3   N2    115.12  3.000
 T22  C8    N7   C14   113.59  3.000
 T22  C14   N7   C6    119.54  3.000
 T22  C8    N7   C6    119.82  3.000
 T22  H14A  C14  H14   107.54  3.000
 T22  H14A  C14  C11   108.12  3.000
 T22  H14   C14  C11   109.83  3.000
 T22  H14A  C14  N7    110.65  3.000
 T22  H14   C14  N7    108.65  3.000
 T22  C11   C14  N7    111.95  3.000
 T22  H11   C11  C10   108.37  3.000
 T22  H11   C11  N13   107.26  3.000
 T22  C10   C11  N13   114.95  3.000
 T22  H11   C11  C14   107.36  3.000
 T22  N13   C11  C14   107.89  3.000
 T22  C10   C11  C14   110.72  3.000
 T22  HN1A  N13  HN13  105.59  3.000
 T22  HN1A  N13  C11   109.54  3.000
 T22  HN13  N13  C11   109.55  3.000
 T22  H10A  C10  H10   106.74  3.000
 T22  H10A  C10  C9    110.52  3.000
 T22  H10   C10  C9    109.48  3.000
 T22  H10A  C10  C11   109.76  3.000
 T22  H10   C10  C11   108.86  3.000
 T22  C9    C10  C11   111.35  3.000
 T22  H9A   C9   H9    106.68  3.000
 T22  H9A   C9   C8    110.12  3.000
 T22  H9    C9   C8    109.19  3.000
 T22  H9A   C9   C10   109.89  3.000
 T22  H9    C9   C10   110.73  3.000
 T22  C8    C9   C10   110.16  3.000
 T22  H8A   C8   H8    106.72  3.000
 T22  H8A   C8   C9    109.38  3.000
 T22  H8    C8   C9    111.90  3.000
 T22  H8A   C8   N7    106.66  3.000
 T22  H8    C8   N7    108.95  3.000
 T22  C9    C8   N7    112.92  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
 T22  CONST_01  C20  C19  C18  C17     0.00   0.0  0
 T22  CONST_02  C20  C21  C22  C17     0.00   0.0  0
 T22  CONST_03  C19  C18  C17  C22     0.00   0.0  0
 T22  CONST_04  C19  C20  C21  C22     0.00   0.0  0
 T22  CONST_05  C18  C17  C22  C21     0.00   0.0  0
 T22  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 T22  CONST_07  C5   C6   N15  C25     0.00   0.0  0
 T22  CONST_08  N7   C6   N15  C25   180.00   0.0  0
 T22  CONST_09  C6   N15  C25  N2      0.00   0.0  0
 T22  CONST_10  C3   N2   C25  N15     0.00   0.0  0
 T22  CONST_15  C19  C18  C17  C16   180.00   0.0  0
 T22  CONST_16  C21  C22  C17  C16   180.00   0.0  0
 T22  CONST_17  C18  C17  C22  C23   180.00   0.0  0
 T22  CONST_18  C20  C21  C22  C23   180.00   0.0  0
 T22  CONST_19  C3   N2   C25  O26   180.00   0.0  0
 T22  CONST_20  C6   N15  C25  O26   180.00   0.0  0
 T22  CONST_22  N15  C25  N2   C1    180.00   0.0  0
 T22  CONST_25  H19  C19  C18  C17   180.00   0.0  0
 T22  CONST_26  H21  C21  C22  C17   180.00   0.0  0
 T22  CONST_27  H18  C18  C17  C22   180.00   0.0  0
 T22  CONST_28  H20  C20  C21  C22   180.00   0.0  0
 T22  CONST_29  C1   N2   C25  O26     0.00   0.0  0
 T22  Var_01    C9   C8   N7   C6    -95.37  30.0  1
 T22  Var_02    C11  C14  N7   C6     96.10  30.0  1
 T22  Var_03    C10  C9   C8   N7    -53.69  30.0  1
 T22  Var_04    C8   C9   C10  C11    53.18  30.0  1
 T22  Var_05    C17  C16  N15  C25  -122.73  30.0  3
 T22  Var_06    C18  C17  C16  N15  -130.24  30.0  2
 T22  Var_07    H1   C1   N2   C25    65.15  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
 T22  chir_01  C11  C14  C10  N13  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
 T22  plan-1  O26  0.020
 T22  plan-1  C25  0.020
 T22  plan-1  N2   0.020
 T22  plan-1  C1   0.020
 T22  plan-1  N15  0.020
 T22  plan-1  C16  0.020
 T22  plan-1  C6   0.020
 T22  plan-1  C5   0.020
 T22  plan-1  C3   0.020
 T22  plan-1  O4   0.020
 T22  plan-1  N7   0.020
 T22  plan-1  C14  0.020
 T22  plan-1  C8   0.020
 T22  plan-1  H5   0.020
 T22  plan-2  C16  0.020
 T22  plan-2  C17  0.020
 T22  plan-2  C22  0.020
 T22  plan-2  C23  0.020
 T22  plan-2  N24  0.020
 T22  plan-2  C21  0.020
 T22  plan-2  C20  0.020
 T22  plan-2  C19  0.020
 T22  plan-2  C18  0.020
 T22  plan-2  H21  0.020
 T22  plan-2  H20  0.020
 T22  plan-2  H19  0.020
 T22  plan-2  H18  0.020

