# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:07:11 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-[(3~{R})-3-(4-azanyl-3-iodanyl-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC[C@H](C1)n2nc(I)c3c(N)ncnc23
#
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
 J0B  J0B  1-[(3~{R})-3-(4-azanyl-3-iodanyl-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]propan-1-one  ligand  38  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J0B
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
 J0B  C12  C  CH3   0  -0.650   7.2022   0.3572   1.3974
 J0B  C1   C  CR56  0   0.604  -0.1937   1.5110  -0.2259
 J0B  C5   C  CH1   0  -0.095   1.8711   0.1834  -0.7535
 J0B  C3   C  CR6   0   0.474  -2.4041   2.2680   0.2495
 J0B  C10  C  C     0   0.567   4.8068  -0.2397   0.8410
 J0B  N2   N  NR5   0  -0.392   0.4535   0.3659  -0.5163
 J0B  C6   C  CH2   0  -0.443   2.1409  -0.3654  -2.1512
 J0B  C11  C  CH2   0  -0.596   6.2665  -0.3728   0.4497
 J0B  N    N  N     0  -0.479  -1.8709   3.4876   0.3582
 J0B  C    C  CR16  0   0.068  -0.5619   3.6429   0.1737
 J0B  O    O  O     0  -0.499   4.4754   0.4045   1.8265
 J0B  C2   C  CR56  0  -0.174  -1.5443   1.1866  -0.0627
 J0B  C4   C  CR5   0  -0.068  -1.5772  -0.2100  -0.2839
 J0B  C7   C  CH2   0  -0.440   3.6289  -0.6402  -2.3444
 J0B  C8   C  CH2   0  -0.328   4.1799  -1.5026  -1.2156
 J0B  C9   C  CH2   0  -0.309   2.4789  -0.7237   0.3207
 J0B  I    I  I     0   0.105  -3.2073  -1.4942  -0.2326
 J0B  N1   N  N     0  -0.462   0.3411   2.7286  -0.1154
 J0B  N3   N  N     0  -0.225  -0.3903  -0.6779  -0.5500
 J0B  N5   N  NT    0  -0.459   3.8956  -0.8836   0.0691
 J0B  H1   H  HCH3  0   0.227   7.0102   1.4293   1.4076
 J0B  H2   H  HCH3  0   0.227   7.1128  -0.0099   2.4189
 J0B  H3   H  HCH3  0   0.231   8.2343   0.2087   1.0812
 J0B  H4   H  HCH1  0   0.276   2.3103   1.1786  -0.6561
 J0B  H5   H  HNH2  0   0.411  -4.2621   2.9513   0.6706
 J0B  H6   H  HNH2  0   0.411  -4.1847   1.2535   0.3990
 J0B  H7   H  HCH2  0   0.239   1.5770  -1.2927  -2.2866
 J0B  H8   H  HCH2  0   0.257   1.7807   0.3415  -2.9009
 J0B  H9   H  HCH2  0   0.264   6.4058   0.0051  -0.5672
 J0B  H10  H  HCH2  0   0.268   6.5311  -1.4331   0.4066
 J0B  H11  H  HCR6  0   0.259  -0.1976   4.6595   0.2771
 J0B  H12  H  HCH2  0   0.251   3.7922  -1.1407  -3.3004
 J0B  H13  H  HCH2  0   0.233   4.1856   0.3008  -2.3771
 J0B  H14  H  HCH2  0   0.250   3.7099  -2.4905  -1.2324
 J0B  H15  H  HCH2  0   0.279   5.2467  -1.6641  -1.3397
 J0B  H16  H  HCH2  0   0.276   2.3187  -0.3084   1.3124
 J0B  H17  H  HCH2  0   0.256   1.9995  -1.7067   0.2884
 J0B  N4   N  NH2   0  -0.812  -3.7137   2.1399   0.4385

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
 J0B  I    C4   single    2.076  0.020  2.076
 J0B  N3   C4   aromatic  1.303  0.020  1.303
 J0B  N3   N2   aromatic  1.343  0.020  1.343
 J0B  C8   N5   single    1.454  0.020  1.454
 J0B  C8   C7   single    1.524  0.020  1.524
 J0B  C9   N5   single    1.448  0.020  1.448
 J0B  C9   C5   single    1.532  0.020  1.532
 J0B  C4   C2   aromatic  1.414  0.020  1.414
 J0B  C12  C11  single    1.519  0.020  1.519
 J0B  N5   C10  single    1.357  0.020  1.357
 J0B  C11  C10  single    1.517  0.020  1.517
 J0B  C10  O    double    1.223  0.020  1.223
 J0B  C6   C7   single    1.525  0.020  1.525
 J0B  C6   C5   single    1.526  0.020  1.526
 J0B  N2   C5   single    1.449  0.020  1.449
 J0B  N2   C1   aromatic  1.347  0.020  1.347
 J0B  C2   C1   aromatic  1.399  0.020  1.399
 J0B  C2   C3   aromatic  1.416  0.020  1.416
 J0B  N4   C3   single    1.329  0.020  1.329
 J0B  C1   N1   aromatic  1.334  0.020  1.334
 J0B  C3   N    aromatic  1.335  0.020  1.335
 J0B  N1   C    aromatic  1.317  0.020  1.317
 J0B  N    C    aromatic  1.331  0.020  1.331
 J0B  C12  H1   single    0.970  0.020  1.090
 J0B  C12  H2   single    0.970  0.020  1.090
 J0B  C12  H3   single    0.970  0.020  1.090
 J0B  C5   H4   single    0.970  0.020  1.090
 J0B  N4   H5   single    0.860  0.020  1.020
 J0B  N4   H6   single    0.860  0.020  1.020
 J0B  C6   H7   single    0.970  0.020  1.090
 J0B  C6   H8   single    0.970  0.020  1.090
 J0B  C11  H9   single    0.970  0.020  1.090
 J0B  C11  H10  single    0.970  0.020  1.090
 J0B  C    H11  single    0.930  0.020  1.080
 J0B  C7   H12  single    0.970  0.020  1.090
 J0B  C7   H13  single    0.970  0.020  1.090
 J0B  C8   H14  single    0.970  0.020  1.090
 J0B  C8   H15  single    0.970  0.020  1.090
 J0B  C9   H16  single    0.970  0.020  1.090
 J0B  C9   H17  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
 J0B  H3   C12  H2   107.69  3.000
 J0B  H3   C12  H1   107.69  3.000
 J0B  H2   C12  H1   107.97  3.000
 J0B  H3   C12  C11  109.69  3.000
 J0B  H2   C12  C11  111.88  3.000
 J0B  H1   C12  C11  111.74  3.000
 J0B  N1   C1   C2   126.08  3.000
 J0B  N1   C1   N2   126.94  3.000
 J0B  C2   C1   N2   106.97  3.000
 J0B  H4   C5   C9   108.51  3.000
 J0B  H4   C5   C6   109.78  3.000
 J0B  C9   C5   C6   111.05  3.000
 J0B  H4   C5   N2   105.31  3.000
 J0B  C6   C5   N2   111.62  3.000
 J0B  C9   C5   N2   110.37  3.000
 J0B  C2   C3   N    118.22  3.000
 J0B  N    C3   N4   118.01  3.000
 J0B  C2   C3   N4   123.76  3.000
 J0B  N5   C10  O    121.76  3.000
 J0B  O    C10  C11  120.98  3.000
 J0B  N5   C10  C11  117.25  3.000
 J0B  N3   N2   C5   120.85  3.000
 J0B  C5   N2   C1   127.77  3.000
 J0B  N3   N2   C1   111.37  3.000
 J0B  H8   C6   H7   107.09  3.000
 J0B  H8   C6   C7   110.58  3.000
 J0B  H7   C6   C7   109.54  3.000
 J0B  H8   C6   C5   109.75  3.000
 J0B  H7   C6   C5   109.10  3.000
 J0B  C7   C6   C5   110.69  3.000
 J0B  H10  C11  H9   105.52  3.000
 J0B  H10  C11  C10  109.15  3.000
 J0B  H9   C11  C10  109.39  3.000
 J0B  H10  C11  C12  109.97  3.000
 J0B  H9   C11  C12  109.62  3.000
 J0B  C10  C11  C12  112.93  3.000
 J0B  C    N    C3   119.20  3.000
 J0B  H11  C    N1   116.18  3.000
 J0B  H11  C    N    115.24  3.000
 J0B  N1   C    N    128.58  3.000
 J0B  C4   C2   C3   140.74  3.000
 J0B  C3   C2   C1   115.77  3.000
 J0B  C4   C2   C1   103.49  3.000
 J0B  N3   C4   I    119.88  3.000
 J0B  N3   C4   C2   111.42  3.000
 J0B  I    C4   C2   128.70  3.000
 J0B  H13  C7   H12  106.98  3.000
 J0B  H13  C7   C8   108.96  3.000
 J0B  H12  C7   C8   109.59  3.000
 J0B  H13  C7   C6   110.20  3.000
 J0B  H12  C7   C6   109.85  3.000
 J0B  C8   C7   C6   111.16  3.000
 J0B  H15  C8   H14  106.61  3.000
 J0B  H15  C8   N5   110.87  3.000
 J0B  H14  C8   N5   108.29  3.000
 J0B  H15  C8   C7   110.78  3.000
 J0B  H14  C8   C7   110.14  3.000
 J0B  N5   C8   C7   110.05  3.000
 J0B  H17  C9   H16  107.80  3.000
 J0B  H17  C9   N5   108.93  3.000
 J0B  H16  C9   N5   110.18  3.000
 J0B  H17  C9   C5   109.73  3.000
 J0B  H16  C9   C5   110.80  3.000
 J0B  N5   C9   C5   109.38  3.000
 J0B  C    N1   C1   112.14  3.000
 J0B  C4   N3   N2   106.74  3.000
 J0B  C9   N5   C8   113.07  3.000
 J0B  C9   N5   C10  120.39  3.000
 J0B  C8   N5   C10  124.98  3.000
 J0B  H6   N4   H5   117.71  3.000
 J0B  H6   N4   C3   122.77  3.000
 J0B  H5   N4   C3   119.46  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
 J0B  CONST_01  C4   N3   N2   C1      0.00   0.0  0
 J0B  CONST_02  N3   C4   C2   C1      0.00   0.0  0
 J0B  CONST_03  N    C3   C2   C1      0.00   0.0  0
 J0B  CONST_04  N    C    N1   C1      0.00   0.0  0
 J0B  CONST_05  N3   C4   C2   C3    180.00   0.0  0
 J0B  CONST_06  N2   C1   C2   C3    180.00   0.0  0
 J0B  CONST_07  N1   C1   C2   C3      0.00   0.0  0
 J0B  CONST_08  N1   C    N    C3      0.00   0.0  0
 J0B  CONST_09  C2   C4   N3   N2      0.00   0.0  0
 J0B  CONST_10  C4   C2   C1   N2      0.00   0.0  0
 J0B  CONST_11  C    N1   C1   N2    180.00   0.0  0
 J0B  CONST_12  C4   C2   C3   N     180.00   0.0  0
 J0B  CONST_13  C2   C1   N1   C       0.00   0.0  0
 J0B  CONST_14  C2   C3   N    C       0.00   0.0  0
 J0B  CONST_15  N3   N2   C1   C2      0.00   0.0  0
 J0B  CONST_16  N1   C1   C2   C4    180.00   0.0  0
 J0B  CONST_17  N3   N2   C1   N1    180.00   0.0  0
 J0B  CONST_18  C4   N3   N2   C5    180.00   0.0  0
 J0B  CONST_19  C2   C1   N2   C5    180.00   0.0  0
 J0B  CONST_20  N1   C1   N2   C5      0.00   0.0  0
 J0B  CONST_21  I    C4   C2   C1    180.00   0.0  0
 J0B  CONST_22  N4   C3   C2   C1    180.00   0.0  0
 J0B  CONST_23  C4   C2   C3   N4      0.00   0.0  0
 J0B  CONST_24  C    N    C3   N4    180.00   0.0  0
 J0B  CONST_25  I    C4   C2   C3      0.00   0.0  0
 J0B  CONST_26  I    C4   N3   N2    180.00   0.0  0
 J0B  CONST_27  H11  C    N1   C1    180.00   0.0  0
 J0B  CONST_28  C8   N5   C10  C11     0.00   0.0  0
 J0B  CONST_29  C9   N5   C10  C11   180.00   0.0  0
 J0B  CONST_30  C8   N5   C10  O     180.00   0.0  0
 J0B  CONST_31  C9   N5   C10  O       0.00   0.0  0
 J0B  CONST_32  H5   N4   C3   N       0.00   0.0  0
 J0B  CONST_33  H6   N4   C3   N     180.00   0.0  0
 J0B  Var_01    C8   N5   C9   C5    -61.06  30.0  1
 J0B  Var_02    C8   C7   C6   C5     51.87  30.0  1
 J0B  Var_03    N5   C8   C7   C6    -54.95  30.0  1
 J0B  Var_04    C9   N5   C8   C7     60.77  30.0  1
 J0B  Var_05    N5   C10  C11  C12  -178.60  30.0  3
 J0B  Var_06    H1   C12  C11  C10   -61.92  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
 J0B  chir_01  C5  C9  C6  N2  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
 J0B  plan-1  C1   0.020
 J0B  plan-1  C5   0.020
 J0B  plan-1  C3   0.020
 J0B  plan-1  N2   0.020
 J0B  plan-1  N    0.020
 J0B  plan-1  C    0.020
 J0B  plan-1  C2   0.020
 J0B  plan-1  C4   0.020
 J0B  plan-1  I    0.020
 J0B  plan-1  N1   0.020
 J0B  plan-1  N3   0.020
 J0B  plan-1  H11  0.020
 J0B  plan-1  N4   0.020
 J0B  plan-2  C3   0.020
 J0B  plan-2  H5   0.020
 J0B  plan-2  H6   0.020
 J0B  plan-2  N4   0.020
 J0B  plan-3  C10  0.020
 J0B  plan-3  C11  0.020
 J0B  plan-3  O    0.020
 J0B  plan-3  C8   0.020
 J0B  plan-3  C9   0.020
 J0B  plan-3  N5   0.020

