# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:22:54 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: ~{N}-[(1-pyrimidin-2-ylpiperidin-4-yl)methyl]pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1CCN(CC1)c2ncccn2)N3CCCC3
#
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
 5T4  5T4  ~{N}-[(1-pyrimidin-2-ylpiperidin-4-yl)methyl]pyrrolidine-1-carboxamide  ligand  44  21  .  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_5T4
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
 5T4  C1   C  CR16  0  -0.402   6.1459   1.0122  -0.8880
 5T4  C2   C  CR16  0  -0.011   5.9054  -0.0467  -0.0270
 5T4  C3   C  CR6   0   0.632   3.6884   0.4381   0.0423
 5T4  C4   C  CH2   0  -0.326   2.1736  -1.0416   1.2828
 5T4  C5   C  CH2   0  -0.436   1.4398  -2.0501   0.4044
 5T4  C6   C  CH1   0  -0.302   0.1755  -1.4600  -0.2284
 5T4  C8   C  CH2   0  -0.324   1.2636   0.8186   0.0242
 5T4  C9   C  CH2   0  -0.235  -0.9490  -1.3502   0.8031
 5T4  C10  C  C     0   0.733  -3.1446  -0.2388   0.8671
 5T4  C13  C  CH2   0  -0.483  -6.4494   0.7149  -0.3102
 5T4  C14  C  CH2   0  -0.248  -5.3804   0.7568   0.7760
 5T4  O    O  O     0  -0.562  -3.0256   0.0708   2.0523
 5T4  N4   N  NR5   0  -0.511  -4.2539   0.0755   0.1555
 5T4  C12  C  CH2   0  -0.475  -5.6370   0.7613  -1.6008
 5T4  C11  C  CH2   0  -0.289  -4.4220  -0.1030  -1.2795
 5T4  N3   N  NH1   0  -0.692  -2.1719  -0.9005   0.1831
 5T4  C7   C  CH2   0  -0.428   0.5004  -0.1220  -0.9005
 5T4  N2   N  NT    0  -0.480   2.4575   0.1710   0.5376
 5T4  N1   N  N     0  -0.472   3.8142   1.4815  -0.7911
 5T4  C    C  CR16  0  -0.011   5.0273   1.7516  -1.2375
 5T4  N    N  N     0  -0.472   4.7051  -0.3427   0.4375
 5T4  H1   H  HCR6  0   0.268   7.1319   1.2409  -1.2624
 5T4  H2   H  HCR6  0   0.266   6.7173  -0.6878   0.3011
 5T4  H3   H  HCH2  0   0.240   1.5640  -0.7709   2.1506
 5T4  H4   H  HCH2  0   0.271   3.0986  -1.4643   1.6622
 5T4  H5   H  HCH2  0   0.238   2.1159  -2.3818  -0.3887
 5T4  H6   H  HCH2  0   0.237   1.1924  -2.9348   0.9974
 5T4  H7   H  HCH1  0   0.244  -0.1633  -2.1558  -1.0048
 5T4  H8   H  HCH2  0   0.270   1.5385   1.7307  -0.4964
 5T4  H9   H  HCH2  0   0.238   0.6425   1.1113   0.8770
 5T4  H10  H  HCH2  0   0.230  -1.0821  -2.3278   1.2820
 5T4  H11  H  HCH2  0   0.234  -0.6891  -0.6508   1.5980
 5T4  H13  H  HCH2  0   0.249  -7.1586   1.5368  -0.2212
 5T4  H14  H  HCH2  0   0.224  -5.1243   1.7889   1.0360
 5T4  H15  H  HCH2  0   0.239  -5.6948   0.2547   1.6914
 5T4  H16  H  HCH2  0   0.250  -6.1821   0.3974  -2.4709
 5T4  H17  H  HCH2  0   0.239  -5.3197   1.7851  -1.8096
 5T4  H18  H  HCH2  0   0.245  -3.5363   0.2211  -1.8316
 5T4  H19  H  HCH2  0   0.236  -4.6068  -1.1533  -1.5324
 5T4  H20  H  HNH1  0   0.399  -2.3988  -1.3220  -0.7032
 5T4  H21  H  HCH2  0   0.234   1.1093  -0.3079  -1.7900
 5T4  H22  H  HCH2  0   0.238  -0.4134   0.3680  -1.2433
 5T4  H23  H  HCR6  0   0.266   5.1120   2.5991  -1.9100
 5T4  H12  H  HCH2  0   0.237  -7.0135  -0.2186  -0.2525

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
 5T4  N1   C    aromatic  1.321  0.020  1.321
 5T4  N1   C3   aromatic  1.341  0.020  1.341
 5T4  C    C1   aromatic  1.386  0.020  1.386
 5T4  C8   N2   single    1.452  0.020  1.452
 5T4  C8   C7   single    1.524  0.020  1.524
 5T4  N2   C3   single    1.353  0.020  1.353
 5T4  N2   C4   single    1.451  0.020  1.451
 5T4  C3   N    aromatic  1.341  0.020  1.341
 5T4  C1   C2   aromatic  1.386  0.020  1.386
 5T4  C4   C5   single    1.526  0.020  1.526
 5T4  N    C2   aromatic  1.321  0.020  1.321
 5T4  C7   C6   single    1.532  0.020  1.532
 5T4  C6   C5   single    1.532  0.020  1.532
 5T4  C6   C9   single    1.530  0.020  1.530
 5T4  C11  C12  single    1.525  0.020  1.525
 5T4  C11  N4   single    1.456  0.020  1.456
 5T4  C12  C13  single    1.526  0.020  1.526
 5T4  N3   C9   single    1.443  0.020  1.443
 5T4  N3   C10  single    1.361  0.020  1.361
 5T4  N4   C10  single    1.355  0.020  1.355
 5T4  N4   C14  single    1.455  0.020  1.455
 5T4  C10  O    double    1.231  0.020  1.231
 5T4  C13  C14  single    1.525  0.020  1.525
 5T4  C1   H1   single    0.930  0.020  1.080
 5T4  C2   H2   single    0.930  0.020  1.080
 5T4  C4   H3   single    0.970  0.020  1.090
 5T4  C4   H4   single    0.970  0.020  1.090
 5T4  C5   H5   single    0.970  0.020  1.090
 5T4  C5   H6   single    0.970  0.020  1.090
 5T4  C6   H7   single    0.970  0.020  1.090
 5T4  C8   H8   single    0.970  0.020  1.090
 5T4  C8   H9   single    0.970  0.020  1.090
 5T4  C9   H10  single    0.970  0.020  1.090
 5T4  C9   H11  single    0.970  0.020  1.090
 5T4  C13  H12  single    0.970  0.020  1.090
 5T4  C13  H13  single    0.970  0.020  1.090
 5T4  C14  H14  single    0.970  0.020  1.090
 5T4  C14  H15  single    0.970  0.020  1.090
 5T4  C12  H16  single    0.970  0.020  1.090
 5T4  C12  H17  single    0.970  0.020  1.090
 5T4  C11  H18  single    0.970  0.020  1.090
 5T4  C11  H19  single    0.970  0.020  1.090
 5T4  N3   H20  single    0.860  0.020  1.020
 5T4  C7   H21  single    0.970  0.020  1.090
 5T4  C7   H22  single    0.970  0.020  1.090
 5T4  C    H23  single    0.930  0.020  1.080

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
 5T4  H1   C1   C    122.47  3.000
 5T4  H1   C1   C2   122.41  3.000
 5T4  C    C1   C2   115.11  3.000
 5T4  H2   C2   N    116.18  3.000
 5T4  H2   C2   C1   120.63  3.000
 5T4  N    C2   C1   123.19  3.000
 5T4  N    C3   N1   124.39  3.000
 5T4  N    C3   N2   117.82  3.000
 5T4  N1   C3   N2   117.79  3.000
 5T4  H4   C4   H3   107.09  3.000
 5T4  H4   C4   N2   109.76  3.000
 5T4  H3   C4   N2   108.03  3.000
 5T4  H4   C4   C5   110.71  3.000
 5T4  H3   C4   C5   110.62  3.000
 5T4  N2   C4   C5   110.53  3.000
 5T4  H6   C5   H5   106.72  3.000
 5T4  H6   C5   C6   110.42  3.000
 5T4  H5   C5   C6   109.12  3.000
 5T4  H6   C5   C4   109.35  3.000
 5T4  H5   C5   C4   108.71  3.000
 5T4  C6   C5   C4   112.35  3.000
 5T4  H7   C6   C7   108.01  3.000
 5T4  H7   C6   C9   107.21  3.000
 5T4  C7   C6   C9   112.89  3.000
 5T4  H7   C6   C5   107.64  3.000
 5T4  C9   C6   C5   110.84  3.000
 5T4  C7   C6   C5   110.03  3.000
 5T4  H9   C8   H8   107.02  3.000
 5T4  H9   C8   N2   108.07  3.000
 5T4  H8   C8   N2   109.64  3.000
 5T4  H9   C8   C7   110.70  3.000
 5T4  H8   C8   C7   110.76  3.000
 5T4  N2   C8   C7   110.55  3.000
 5T4  H11  C9   H10  106.40  3.000
 5T4  H11  C9   N3   108.39  3.000
 5T4  H10  C9   N3   111.26  3.000
 5T4  H11  C9   C6   111.25  3.000
 5T4  H10  C9   C6   108.64  3.000
 5T4  N3   C9   C6   110.83  3.000
 5T4  N3   C10  N4   115.72  3.000
 5T4  N4   C10  O    121.78  3.000
 5T4  N3   C10  O    122.50  3.000
 5T4  H13  C13  H12  107.72  3.000
 5T4  H13  C13  C12  113.13  3.000
 5T4  H12  C13  C12  110.22  3.000
 5T4  H13  C13  C14  112.19  3.000
 5T4  H12  C13  C14  110.37  3.000
 5T4  C12  C13  C14  103.21  3.000
 5T4  H15  C14  H14  107.59  3.000
 5T4  H15  C14  N4   111.44  3.000
 5T4  H14  C14  N4   111.19  3.000
 5T4  H15  C14  C13  112.54  3.000
 5T4  H14  C14  C13  111.05  3.000
 5T4  N4   C14  C13  103.07  3.000
 5T4  C11  N4   C14  112.85  3.000
 5T4  C14  N4   C10  121.22  3.000
 5T4  C11  N4   C10  125.72  3.000
 5T4  H17  C12  H16  107.81  3.000
 5T4  H17  C12  C11  109.88  3.000
 5T4  H16  C12  C11  112.19  3.000
 5T4  H17  C12  C13  110.18  3.000
 5T4  H16  C12  C13  113.52  3.000
 5T4  C11  C12  C13  103.22  3.000
 5T4  H19  C11  H18  107.72  3.000
 5T4  H19  C11  C12  111.10  3.000
 5T4  H18  C11  C12  111.79  3.000
 5T4  H19  C11  N4   111.37  3.000
 5T4  H18  C11  N4   111.59  3.000
 5T4  C12  C11  N4   103.31  3.000
 5T4  H20  N3   C10  118.99  3.000
 5T4  H20  N3   C9   116.02  3.000
 5T4  C10  N3   C9   122.77  3.000
 5T4  H22  C7   H21  106.67  3.000
 5T4  H22  C7   C8   109.43  3.000
 5T4  H21  C7   C8   108.64  3.000
 5T4  H22  C7   C6   110.61  3.000
 5T4  H21  C7   C6   109.05  3.000
 5T4  C8   C7   C6   112.27  3.000
 5T4  C8   N2   C4   113.16  3.000
 5T4  C4   N2   C3   122.05  3.000
 5T4  C8   N2   C3   122.03  3.000
 5T4  C    N1   C3   117.09  3.000
 5T4  H23  C    N1   116.16  3.000
 5T4  H23  C    C1   120.67  3.000
 5T4  N1   C    C1   123.17  3.000
 5T4  C3   N    C2   117.05  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
 5T4  CONST_01  C3   N1   C    C1      0.00   0.0  0
 5T4  CONST_02  C3   N    C2   C1      0.00   0.0  0
 5T4  CONST_03  N1   C    C1   C2      0.00   0.0  0
 5T4  CONST_04  N1   C3   N    C2      0.00   0.0  0
 5T4  CONST_05  N    C3   N1   C       0.00   0.0  0
 5T4  CONST_06  N    C2   C1   C       0.00   0.0  0
 5T4  CONST_07  N2   C3   N    C2    180.00   0.0  0
 5T4  CONST_08  C    N1   C3   N2    180.00   0.0  0
 5T4  CONST_09  H23  C    C1   C2    180.00   0.0  0
 5T4  CONST_10  H2   C2   N    C3    180.00   0.0  0
 5T4  CONST_11  H1   C1   C    N1    180.00   0.0  0
 5T4  CONST_12  O    C10  N4   C14     0.00   0.0  0
 5T4  CONST_13  C11  N4   C10  O     180.00   0.0  0
 5T4  CONST_14  N3   C10  N4   C14   180.00   0.0  0
 5T4  CONST_15  N3   C10  N4   C11     0.00   0.0  0
 5T4  CONST_16  N4   C10  N3   C9    180.00   0.0  0
 5T4  CONST_18  O    C10  N3   C9      0.00   0.0  0
 5T4  Var_01    C7   C8   N2   C3    102.30  30.0  1
 5T4  Var_02    C5   C4   N2   C3   -102.45  30.0  1
 5T4  Var_03    N1   C3   N2   C4    170.68  30.0  2
 5T4  Var_04    N2   C8   C7   C6     54.49  30.0  1
 5T4  Var_05    N2   C4   C5   C6    -54.27  30.0  1
 5T4  Var_06    N4   C11  C12  C13   -29.90  30.0  1
 5T4  Var_07    C11  N4   C14  C13    13.07  30.0  1
 5T4  Var_08    C12  C11  N4   C14    10.64  30.0  1
 5T4  Var_09    C11  C12  C13  C14    38.14  30.0  1
 5T4  Var_10    C12  C13  C14  N4    -31.31  30.0  1
 5T4  Var_11    C10  N3   C9   C6   -154.07  30.0  1

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
 5T4  chir_01  C6  C7  C5  C9  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
 5T4  plan-1  C9   0.020
 5T4  plan-1  C10  0.020
 5T4  plan-1  C14  0.020
 5T4  plan-1  O    0.020
 5T4  plan-1  N4   0.020
 5T4  plan-1  C11  0.020
 5T4  plan-1  N3   0.020
 5T4  plan-1  H20  0.020
 5T4  plan-2  C1   0.020
 5T4  plan-2  C2   0.020
 5T4  plan-2  C3   0.020
 5T4  plan-2  N2   0.020
 5T4  plan-2  N1   0.020
 5T4  plan-2  C    0.020
 5T4  plan-2  N    0.020
 5T4  plan-2  H1   0.020
 5T4  plan-2  H2   0.020
 5T4  plan-2  H23  0.020

