# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:27:46 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: [1-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methylazanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CC1CCN(CC1)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
 HVE  HVE  '[1-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methylazanium'  ligand  35  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HVE
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
 HVE  C2   C  CH2   0  -0.307  -3.9958  -0.5214  -0.7913
 HVE  C3   C  CH1   0  -0.295  -2.9569  -0.6646   0.3135
 HVE  C5   C  CH2   0  -0.348  -0.9014  -0.7258  -1.1405
 HVE  C7   C  CH2   0  -0.330  -1.4861   1.3789  -0.1237
 HVE  C8   C  CH2   0  -0.454  -2.4282   0.6719   0.8500
 HVE  C11  C  CR16  0   0.038   2.4518   2.1565   0.6559
 HVE  C13  C  CR56  0   0.470   3.1218   0.0783   0.3736
 HVE  C15  C  CR15  0  -0.012   3.2377  -2.1187   0.0716
 HVE  C16  C  CR15  0  -0.446   1.9483  -1.7795  -0.2084
 HVE  N1   N  NT3   1  -0.782  -5.2377   0.1346  -0.3006
 HVE  C4   C  CH2   0  -0.442  -1.7887  -1.5222  -0.1913
 HVE  N6   N  NT    0  -0.471  -0.4135   0.4742  -0.4956
 HVE  C9   C  CR6   0   0.503   0.8615   0.6606  -0.0891
 HVE  N10  N  N     0  -0.492   1.2026   1.8974   0.2902
 HVE  N12  N  N     0  -0.455   3.4685   1.3226   0.7112
 HVE  N14  N  NR15  0  -0.655   3.9412  -0.9961   0.4158
 HVE  C17  C  CR56  0  -0.089   1.8482  -0.3584  -0.0354
 HVE  H22  H  HCH2  0   0.292  -3.6584   0.0665  -1.6422
 HVE  H23  H  HCH2  0   0.306  -4.2996  -1.4981  -1.1622
 HVE  H24  H  HCH1  0   0.277  -3.4400  -1.2016   1.1359
 HVE  H27  H  HCH2  0   0.276  -0.0786  -1.3190  -1.5235
 HVE  H28  H  HCH2  0   0.263  -1.4718  -0.4176  -2.0232
 HVE  H30  H  HCH2  0   0.242  -2.0149   1.6973  -1.0278
 HVE  H29  H  HCH2  0   0.281  -1.0752   2.2733   0.3344
 HVE  H31  H  HCH2  0   0.244  -3.2386   1.3511   1.1299
 HVE  H32  H  HCH2  0   0.259  -1.8811   0.4745   1.7754
 HVE  H34  H  HCR5  0   0.287   3.7117  -3.0862   0.0680
 HVE  H35  H  HCR5  0   0.255   1.1845  -2.4857  -0.4863
 HVE  H19  H  HNT3  0   0.470  -5.6419  -0.3665   0.4906
 HVE  H20  H  HNT3  0   0.469  -5.0830   1.0962  -0.0010
 HVE  H26  H  HCH2  0   0.256  -1.1959  -1.8511   0.6661
 HVE  H25  H  HCH2  0   0.253  -2.1573  -2.4227  -0.6884
 HVE  H21  H  HNR5  0   0.412   4.9124  -0.9718   0.6820
 HVE  H1   H  HNT3  0   0.481  -5.9525   0.1670  -1.0265
 HVE  H33  H  HCR6  0   0.243   2.6539   3.1840   0.9418

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
 HVE  C2   N1   single    1.488  0.020  1.488
 HVE  C2   C3   single    1.523  0.020  1.523
 HVE  C8   C3   single    1.534  0.020  1.534
 HVE  C8   C7   single    1.528  0.020  1.528
 HVE  C3   C4   single    1.535  0.020  1.535
 HVE  C4   C5   single    1.524  0.020  1.524
 HVE  C7   N6   single    1.452  0.020  1.452
 HVE  C11  N10  aromatic  1.327  0.020  1.327
 HVE  C11  N12  aromatic  1.316  0.020  1.316
 HVE  N10  C9   aromatic  1.338  0.020  1.338
 HVE  N12  C13  aromatic  1.335  0.020  1.335
 HVE  N6   C9   single    1.351  0.020  1.351
 HVE  N6   C5   single    1.447  0.020  1.447
 HVE  C9   C17  aromatic  1.419  0.020  1.419
 HVE  C13  C17  aromatic  1.407  0.020  1.407
 HVE  C13  N14  aromatic  1.352  0.020  1.352
 HVE  C17  C16  aromatic  1.435  0.020  1.435
 HVE  N14  C15  aromatic  1.369  0.020  1.369
 HVE  C16  C15  aromatic  1.362  0.020  1.362
 HVE  C2   H22  single    0.970  0.020  1.090
 HVE  C2   H23  single    0.970  0.020  1.090
 HVE  C3   H24  single    0.970  0.020  1.090
 HVE  C5   H27  single    0.970  0.020  1.090
 HVE  C5   H28  single    0.970  0.020  1.090
 HVE  C7   H30  single    0.970  0.020  1.090
 HVE  C7   H29  single    0.970  0.020  1.090
 HVE  C8   H31  single    0.970  0.020  1.090
 HVE  C8   H32  single    0.970  0.020  1.090
 HVE  C11  H33  single    0.930  0.020  1.080
 HVE  C15  H34  single    0.930  0.020  1.080
 HVE  C16  H35  single    0.930  0.020  1.080
 HVE  N1   H19  single    0.890  0.020  1.040
 HVE  N1   H20  single    0.890  0.020  1.040
 HVE  C4   H26  single    0.970  0.020  1.090
 HVE  C4   H25  single    0.970  0.020  1.090
 HVE  N14  H21  single    0.860  0.020  1.020
 HVE  N1   H1   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
 HVE  H23  C2   H22  107.76  3.000
 HVE  H23  C2   N1   105.97  3.000
 HVE  H22  C2   N1   106.18  3.000
 HVE  H23  C2   C3   110.69  3.000
 HVE  H22  C2   C3   113.99  3.000
 HVE  N1   C2   C3   111.81  3.000
 HVE  H24  C3   C4   108.00  3.000
 HVE  H24  C3   C8   108.46  3.000
 HVE  C4   C3   C8   109.85  3.000
 HVE  H24  C3   C2   106.86  3.000
 HVE  C4   C3   C2   109.46  3.000
 HVE  C8   C3   C2   114.00  3.000
 HVE  H28  C5   H27  105.34  3.000
 HVE  H28  C5   N6   107.54  3.000
 HVE  H27  C5   N6   110.81  3.000
 HVE  H28  C5   C4   110.23  3.000
 HVE  H27  C5   C4   112.09  3.000
 HVE  N6   C5   C4   110.61  3.000
 HVE  H29  C7   H30  106.96  3.000
 HVE  H29  C7   N6   109.99  3.000
 HVE  H30  C7   N6   109.06  3.000
 HVE  H29  C7   C8   110.22  3.000
 HVE  H30  C7   C8   111.28  3.000
 HVE  N6   C7   C8   109.29  3.000
 HVE  H32  C8   H31  105.45  3.000
 HVE  H32  C8   C7   108.33  3.000
 HVE  H31  C8   C7   109.42  3.000
 HVE  H32  C8   C3   108.14  3.000
 HVE  H31  C8   C3   112.03  3.000
 HVE  C7   C8   C3   113.12  3.000
 HVE  H33  C11  N12  116.42  3.000
 HVE  H33  C11  N10  115.63  3.000
 HVE  N12  C11  N10  127.95  3.000
 HVE  C17  C13  N14  108.12  3.000
 HVE  N14  C13  N12  125.13  3.000
 HVE  C17  C13  N12  126.71  3.000
 HVE  H34  C15  N14  120.74  3.000
 HVE  H34  C15  C16  129.74  3.000
 HVE  N14  C15  C16  109.50  3.000
 HVE  H35  C16  C17  129.13  3.000
 HVE  H35  C16  C15  124.13  3.000
 HVE  C17  C16  C15  106.73  3.000
 HVE  H1   N1   H20  106.61  3.000
 HVE  H1   N1   H19  106.87  3.000
 HVE  H20  N1   H19  107.20  3.000
 HVE  H1   N1   C2   111.38  3.000
 HVE  H20  N1   C2   112.73  3.000
 HVE  H19  N1   C2   111.72  3.000
 HVE  H25  C4   H26  106.97  3.000
 HVE  H25  C4   C5   110.10  3.000
 HVE  H26  C4   C5   109.27  3.000
 HVE  H25  C4   C3   110.70  3.000
 HVE  H26  C4   C3   108.84  3.000
 HVE  C5   C4   C3   110.86  3.000
 HVE  C9   N6   C7   122.29  3.000
 HVE  C9   N6   C5   124.51  3.000
 HVE  C7   N6   C5   112.45  3.000
 HVE  C17  C9   N10  118.40  3.000
 HVE  C17  C9   N6   124.63  3.000
 HVE  N10  C9   N6   116.96  3.000
 HVE  C9   N10  C11  119.91  3.000
 HVE  C13  N12  C11  112.29  3.000
 HVE  H21  N14  C15  125.57  3.000
 HVE  H21  N14  C13  124.99  3.000
 HVE  C15  N14  C13  109.42  3.000
 HVE  C9   C17  C16  139.01  3.000
 HVE  C16  C17  C13  106.21  3.000
 HVE  C9   C17  C13  114.67  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
 HVE  CONST_01  C17  C9   N10  C11    0.00   0.0  0
 HVE  CONST_02  C17  C13  N12  C11    0.00   0.0  0
 HVE  CONST_03  N14  C13  N12  C11  180.00   0.0  0
 HVE  CONST_04  N10  C11  N12  C13    0.00   0.0  0
 HVE  CONST_05  N10  C9   C17  C13    0.00   0.0  0
 HVE  CONST_06  C15  C16  C17  C13    0.00   0.0  0
 HVE  CONST_07  C16  C15  N14  C13    0.00   0.0  0
 HVE  CONST_08  N12  C13  N14  C15  180.00   0.0  0
 HVE  CONST_09  C17  C13  N14  C15    0.00   0.0  0
 HVE  CONST_10  C9   C17  C16  C15  180.00   0.0  0
 HVE  CONST_11  N10  C9   C17  C16  180.00   0.0  0
 HVE  CONST_12  N12  C13  C17  C16  180.00   0.0  0
 HVE  CONST_13  N14  C13  C17  C16    0.00   0.0  0
 HVE  CONST_14  N12  C11  N10  C9     0.00   0.0  0
 HVE  CONST_15  N12  C13  C17  C9     0.00   0.0  0
 HVE  CONST_16  N14  C13  C17  C9   180.00   0.0  0
 HVE  CONST_17  C17  C16  C15  N14    0.00   0.0  0
 HVE  CONST_18  N6   C9   N10  C11  180.00   0.0  0
 HVE  CONST_19  N6   C9   C17  C13  180.00   0.0  0
 HVE  CONST_20  N6   C9   C17  C16    0.00   0.0  0
 HVE  CONST_21  H33  C11  N12  C13  180.00   0.0  0
 HVE  CONST_22  H35  C16  C17  C13  180.00   0.0  0
 HVE  CONST_23  H34  C15  N14  C13  180.00   0.0  0
 HVE  CONST_24  H21  N14  C15  C16  180.00   0.0  0
 HVE  Var_01    N6   C7   C8   C3   -54.21  30.0  1
 HVE  Var_02    N6   C5   C4   C3    56.81  30.0  1
 HVE  Var_03    C8   C7   N6   C5    60.18  30.0  1
 HVE  Var_04    N10  C9   N6   C5   169.47  30.0  2
 HVE  Var_05    C4   C5   N6   C7   -62.56  30.0  1
 HVE  Var_06    H19  N1   C2   C3   -56.51  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
 HVE  chir_01  C3  C2  C8  C4  positiv

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
 HVE  plan-1  C11  0.020
 HVE  plan-1  C13  0.020
 HVE  plan-1  C15  0.020
 HVE  plan-1  C16  0.020
 HVE  plan-1  N6   0.020
 HVE  plan-1  C9   0.020
 HVE  plan-1  N10  0.020
 HVE  plan-1  N12  0.020
 HVE  plan-1  N14  0.020
 HVE  plan-1  C17  0.020
 HVE  plan-1  H34  0.020
 HVE  plan-1  H35  0.020
 HVE  plan-1  H21  0.020
 HVE  plan-1  H33  0.020

