# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 03:34:22 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCN(C1)c2ncnc3[nH]ccc23
#
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
 5JT  5JT  (3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-amine  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_5JT
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
 5JT  C2   C  CR16  0   0.036  -1.7629  -2.1601   0.4473
 5JT  C4   C  CR6   0   0.497  -0.2698  -0.5810  -0.3298
 5JT  C5   C  CR56  0  -0.091  -1.2585   0.4112  -0.0948
 5JT  C6   C  CR56  0   0.469  -2.4803  -0.0798   0.4007
 5JT  C8   C  CR15  0  -0.014  -2.6525   2.1312   0.2804
 5JT  N10  N  NT    0  -0.480   0.9519  -0.3391  -0.8513
 5JT  C11  C  CH2   0  -0.329   1.3577   0.9195  -1.4460
 5JT  C12  C  CH2   0  -0.446   2.3742   1.6316  -0.5642
 5JT  C13  C  CH2   0  -0.451   3.5684   0.7101  -0.3266
 5JT  C14  C  CH1   0  -0.114   3.1289  -0.6577   0.2148
 5JT  N1   N  N     0  -0.490  -0.5611  -1.8511  -0.0220
 5JT  N3   N  N     0  -0.456  -2.7780  -1.3529   0.6725
 5JT  N7   N  NR15  0  -0.656  -3.3053   0.9720   0.6036
 5JT  C9   C  CR15  0  -0.446  -1.3933   1.8389  -0.1493
 5JT  C15  C  CH2   0  -0.313   2.0620  -1.2655  -0.6978
 5JT  N16  N  NH2   0  -0.792   2.6369  -0.6346   1.5868
 5JT  H1   H  HCR6  0   0.242  -1.9246  -3.2114   0.6648
 5JT  H2   H  HCR5  0   0.286  -3.1385   3.0863   0.3898
 5JT  H3   H  HCH2  0   0.251   1.8232   0.6891  -2.4113
 5JT  H4   H  HCH2  0   0.265   0.4943   1.5357  -1.6721
 5JT  H5   H  HCH2  0   0.244   2.6936   2.5574  -1.0467
 5JT  H6   H  HCH2  0   0.224   1.9058   1.9162   0.3832
 5JT  H7   H  HCH2  0   0.219   4.0992   0.5682  -1.2742
 5JT  H8   H  HCH2  0   0.238   4.2806   1.1686   0.3643
 5JT  H9   H  HCH1  0   0.241   3.9887  -1.3339   0.1922
 5JT  H10  H  HNR5  0   0.412  -4.2437   0.9095   0.9643
 5JT  H11  H  HCR5  0   0.255  -0.6680   2.5778  -0.4438
 5JT  H12  H  HCH2  0   0.270   1.7026  -2.2053  -0.2898
 5JT  H13  H  HCH2  0   0.238   2.4928  -1.4680  -1.6834
 5JT  H14  H  HNH2  0   0.347   3.3522  -0.2456   2.1898
 5JT  H15  H  HNH2  0   0.342   1.8475  -0.0040   1.6673

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
 5JT  C2   N3   aromatic  1.316  0.020  1.316
 5JT  C2   N1   aromatic  1.327  0.020  1.327
 5JT  N3   C6   aromatic  1.335  0.020  1.335
 5JT  N1   C4   aromatic  1.339  0.020  1.339
 5JT  C4   N10  single    1.350  0.020  1.350
 5JT  C4   C5   aromatic  1.420  0.020  1.420
 5JT  C6   C5   aromatic  1.407  0.020  1.407
 5JT  C6   N7   aromatic  1.352  0.020  1.352
 5JT  C11  N10  single    1.450  0.020  1.450
 5JT  C11  C12  single    1.522  0.020  1.522
 5JT  N10  C15  single    1.454  0.020  1.454
 5JT  C5   C9   aromatic  1.435  0.020  1.435
 5JT  N7   C8   aromatic  1.369  0.020  1.369
 5JT  C15  C14  single    1.530  0.020  1.530
 5JT  C9   C8   aromatic  1.362  0.020  1.362
 5JT  C12  C13  single    1.527  0.020  1.527
 5JT  C14  C13  single    1.535  0.020  1.535
 5JT  C14  N16  single    1.458  0.020  1.458
 5JT  C2   H1   single    0.930  0.020  1.080
 5JT  C8   H2   single    0.930  0.020  1.080
 5JT  C11  H3   single    0.970  0.020  1.090
 5JT  C11  H4   single    0.970  0.020  1.090
 5JT  C12  H5   single    0.970  0.020  1.090
 5JT  C12  H6   single    0.970  0.020  1.090
 5JT  C13  H7   single    0.970  0.020  1.090
 5JT  C13  H8   single    0.970  0.020  1.090
 5JT  C14  H9   single    0.970  0.020  1.090
 5JT  N7   H10  single    0.860  0.020  1.020
 5JT  C9   H11  single    0.930  0.020  1.080
 5JT  C15  H12  single    0.970  0.020  1.090
 5JT  C15  H13  single    0.970  0.020  1.090
 5JT  N16  H14  single    0.890  0.020  1.040
 5JT  N16  H15  single    0.890  0.020  1.040

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
 5JT  H1   C2   N3   116.40  3.000
 5JT  H1   C2   N1   115.55  3.000
 5JT  N3   C2   N1   128.05  3.000
 5JT  N1   C4   N10  117.10  3.000
 5JT  N10  C4   C5   124.66  3.000
 5JT  N1   C4   C5   118.24  3.000
 5JT  C9   C5   C6   106.20  3.000
 5JT  C9   C5   C4   138.95  3.000
 5JT  C6   C5   C4   114.77  3.000
 5JT  N7   C6   N3   125.10  3.000
 5JT  N7   C6   C5   108.14  3.000
 5JT  N3   C6   C5   126.73  3.000
 5JT  H2   C8   C9   129.74  3.000
 5JT  H2   C8   N7   120.77  3.000
 5JT  C9   C8   N7   109.49  3.000
 5JT  C15  N10  C11  112.50  3.000
 5JT  C15  N10  C4   122.41  3.000
 5JT  C11  N10  C4   124.55  3.000
 5JT  H4   C11  H3   105.90  3.000
 5JT  H4   C11  C12  112.74  3.000
 5JT  H3   C11  C12  108.96  3.000
 5JT  H4   C11  N10  110.84  3.000
 5JT  H3   C11  N10  107.31  3.000
 5JT  C12  C11  N10  110.81  3.000
 5JT  H6   C12  H5   106.70  3.000
 5JT  H6   C12  C13  110.91  3.000
 5JT  H5   C12  C13  110.59  3.000
 5JT  H6   C12  C11  109.71  3.000
 5JT  H5   C12  C11  109.63  3.000
 5JT  C13  C12  C11  109.27  3.000
 5JT  H8   C13  H7   106.58  3.000
 5JT  H8   C13  C14  109.72  3.000
 5JT  H7   C13  C14  109.17  3.000
 5JT  H8   C13  C12  110.78  3.000
 5JT  H7   C13  C12  108.82  3.000
 5JT  C14  C13  C12  111.63  3.000
 5JT  H9   C14  N16  107.13  3.000
 5JT  H9   C14  C15  106.87  3.000
 5JT  N16  C14  C15  109.41  3.000
 5JT  H9   C14  C13  108.56  3.000
 5JT  N16  C14  C13  114.48  3.000
 5JT  C15  C14  C13  110.07  3.000
 5JT  C4   N1   C2   119.95  3.000
 5JT  C6   N3   C2   112.20  3.000
 5JT  H10  N7   C8   125.55  3.000
 5JT  H10  N7   C6   125.02  3.000
 5JT  C8   N7   C6   109.40  3.000
 5JT  H11  C9   C8   124.18  3.000
 5JT  H11  C9   C5   129.05  3.000
 5JT  C8   C9   C5   106.76  3.000
 5JT  H13  C15  H12  107.97  3.000
 5JT  H13  C15  C14  109.64  3.000
 5JT  H12  C15  C14  110.52  3.000
 5JT  H13  C15  N10  108.86  3.000
 5JT  H12  C15  N10  109.79  3.000
 5JT  C14  C15  N10  110.02  3.000
 5JT  H15  N16  H14  105.29  3.000
 5JT  H15  N16  C14  110.33  3.000
 5JT  H14  N16  C14  109.15  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
 5JT  CONST_01  C5   C6   N3   C2      0.00   0.0  0
 5JT  CONST_02  N7   C6   N3   C2    180.00   0.0  0
 5JT  CONST_03  C5   C4   N1   C2      0.00   0.0  0
 5JT  CONST_04  N3   C2   N1   C4      0.00   0.0  0
 5JT  CONST_05  N3   C6   C5   C4      0.00   0.0  0
 5JT  CONST_06  N7   C6   C5   C4    180.00   0.0  0
 5JT  CONST_07  C8   C9   C5   C4    180.00   0.0  0
 5JT  CONST_08  C8   N7   C6   C5      0.00   0.0  0
 5JT  CONST_09  N7   C8   C9   C5      0.00   0.0  0
 5JT  CONST_10  N1   C2   N3   C6      0.00   0.0  0
 5JT  CONST_11  N1   C4   C5   C6      0.00   0.0  0
 5JT  CONST_12  C8   C9   C5   C6      0.00   0.0  0
 5JT  CONST_13  C9   C8   N7   C6      0.00   0.0  0
 5JT  CONST_14  N3   C6   N7   C8    180.00   0.0  0
 5JT  CONST_15  C9   C5   C4   N1    180.00   0.0  0
 5JT  CONST_16  C9   C5   C6   N3    180.00   0.0  0
 5JT  CONST_17  C9   C5   C6   N7      0.00   0.0  0
 5JT  CONST_18  N10  C4   N1   C2    180.00   0.0  0
 5JT  CONST_19  N10  C4   C5   C6    180.00   0.0  0
 5JT  CONST_20  C9   C5   C4   N10     0.00   0.0  0
 5JT  CONST_21  H1   C2   N1   C4    180.00   0.0  0
 5JT  CONST_22  H11  C9   C5   C4      0.00   0.0  0
 5JT  CONST_23  H10  N7   C6   C5    180.00   0.0  0
 5JT  CONST_24  H2   C8   C9   C5    180.00   0.0  0
 5JT  Var_01    C12  C11  N10  C4    109.95  30.0  1
 5JT  Var_02    C14  C15  N10  C4   -111.31  30.0  1
 5JT  Var_03    C11  N10  C4   C5    -10.47  30.0  2
 5JT  Var_04    C13  C12  C11  N10    56.58  30.0  1
 5JT  Var_05    C14  C13  C12  C11   -53.24  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
 5JT  chir_01  C14  C15  C13  N16  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
 5JT  plan-1  C2   0.020
 5JT  plan-1  C4   0.020
 5JT  plan-1  C5   0.020
 5JT  plan-1  C6   0.020
 5JT  plan-1  C8   0.020
 5JT  plan-1  N10  0.020
 5JT  plan-1  N1   0.020
 5JT  plan-1  N3   0.020
 5JT  plan-1  N7   0.020
 5JT  plan-1  C9   0.020
 5JT  plan-1  H1   0.020
 5JT  plan-1  H2   0.020
 5JT  plan-1  H10  0.020
 5JT  plan-1  H11  0.020

