# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:43:36 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (1S,3S)-N-{6-[5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl]pyridin-2-yl}cyclohexane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCC[C@@H](C1)Nc2cccc(n2)c3n[nH]c4cnc(cc34)c5cccnc5
#
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
 5E6  5E6  (1S,3S)-N-{6-[5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl]pyridin-2-yl}cyclohexane-1,3-diamine  ligand  52  29  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5E6
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
 5E6  C9   C  CH2   0  -0.438  -4.7352   0.3339  -0.6187
 5E6  C2   C  CR16  0  -0.350  -0.8575   4.0211   0.5526
 5E6  C10  C  CH2   0  -0.442  -4.2840  -0.6312  -1.7082
 5E6  C6   C  CR16  0  -0.402  -2.8744   2.7450   0.8489
 5E6  C1   C  CR16  0  -0.160  -2.2248   3.9604   0.7928
 5E6  C3   C  CR6   0   0.202  -0.1892   2.8147   0.3819
 5E6  N4   N  N     0  -0.510  -0.7970   1.6337   0.4361
 5E6  C5   C  CR6   0   0.502  -2.1106   1.5769   0.6618
 5E6  N7   N  NH1   0  -0.671  -2.6438   0.3328   0.7228
 5E6  C8   C  CH1   0  -0.110  -4.0625   0.0321   0.7262
 5E6  C11  C  CH2   0  -0.428  -4.5425  -2.0762  -1.2986
 5E6  C12  C  CH1   0  -0.070  -3.8404  -2.4113   0.0118
 5E6  C13  C  CH2   0  -0.446  -4.2749  -1.4335   1.1029
 5E6  N14  N  NH2   0  -0.802  -4.1748  -3.7664   0.4267
 5E6  C15  C  CR5   0   0.167   1.2501   2.7621   0.1218
 5E6  C16  C  CR56  0   0.054   2.0806   1.6109  -0.0367
 5E6  C17  C  CR16  0  -0.401   1.9324   0.2226  -0.0064
 5E6  C18  C  CR6   0   0.207   3.0622  -0.5442  -0.2218
 5E6  N19  N  N     0  -0.428   4.2861  -0.0088  -0.4331
 5E6  C20  C  CR16  0  -0.094   4.4515   1.2894  -0.4585
 5E6  C21  C  CR56  0   0.309   3.3570   2.1389  -0.2687
 5E6  N22  N  NR15  0  -0.529   3.2232   3.4840  -0.2397
 5E6  N24  N  N     0  -0.235   1.9738   3.8531  -0.0099
 5E6  C25  C  CR6   0  -0.016   3.0011  -2.0186  -0.2153
 5E6  C26  C  CR16  0  -0.177   4.1127  -2.7883   0.1219
 5E6  C27  C  CR16  0  -0.314   4.0048  -4.1680   0.1286
 5E6  C28  C  CR16  0  -0.071   2.7879  -4.7422  -0.2082
 5E6  N29  N  N     0  -0.398   1.7232  -4.0262  -0.5505
 5E6  C30  C  CR16  0  -0.106   1.8354  -2.7057  -0.5556
 5E6  H1   H  HCH2  0   0.239  -4.5396   1.3664  -0.9189
 5E6  H2   H  HCH2  0   0.224  -5.8184   0.2516  -0.4836
 5E6  H4   H  HCH2  0   0.236  -4.8043  -0.4033  -2.6409
 5E6  H5   H  HCH2  0   0.215  -3.2178  -0.4875  -1.9113
 5E6  H6   H  HCR6  0   0.274  -3.9372   2.7001   1.0385
 5E6  H7   H  HCR6  0   0.265  -2.7892   4.8727   0.9377
 5E6  H8   H  HNH1  0   0.374  -1.9987  -0.4115   0.5120
 5E6  H9   H  HCH1  0   0.252  -4.5335   0.6440   1.5020
 5E6  H10  H  HCH2  0   0.211  -5.6190  -2.2356  -1.1683
 5E6  H11  H  HCH2  0   0.230  -4.2114  -2.7618  -2.0843
 5E6  H12  H  HCH1  0   0.185  -2.7559  -2.2978  -0.1608
 5E6  H13  H  HCH2  0   0.242  -3.7560  -1.6550   2.0409
 5E6  H14  H  HCH2  0   0.235  -5.3423  -1.5863   1.2868
 5E6  H15  H  HNH2  0   0.342  -3.8473  -4.4197  -0.2752
 5E6  H16  H  HNH2  0   0.342  -3.6617  -3.9983   1.2693
 5E6  H18  H  HCR6  0   0.266   0.9702  -0.2203   0.2004
 5E6  H19  H  HCR6  0   0.283   5.4510   1.6732  -0.6297
 5E6  H23  H  HNR5  0   0.428   3.9347   4.1840  -0.3788
 5E6  H20  H  HCR6  0   0.267   5.0462  -2.3092   0.3845
 5E6  H21  H  HCR6  0   0.272   4.8477  -4.7913   0.3940
 5E6  H22  H  HCR6  0   0.267   2.6695  -5.8198  -0.2059
 5E6  H24  H  HCR6  0   0.251   0.9523  -2.1586  -0.8697
 5E6  H3   H  HCR6  0   0.256  -0.3346   4.9649   0.4984

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
 5E6  C20  N19  aromatic  1.309  0.020  1.309
 5E6  C20  C21  aromatic  1.398  0.020  1.398
 5E6  N22  C21  aromatic  1.352  0.020  1.352
 5E6  N22  N24  aromatic  1.323  0.020  1.323
 5E6  N19  C18  aromatic  1.353  0.020  1.353
 5E6  C21  C16  aromatic  1.401  0.020  1.401
 5E6  C30  N29  aromatic  1.325  0.020  1.325
 5E6  C30  C25  aromatic  1.395  0.020  1.395
 5E6  N24  C15  aromatic  1.316  0.020  1.316
 5E6  C18  C25  single    1.476  0.020  1.476
 5E6  C18  C17  aromatic  1.382  0.020  1.382
 5E6  N29  C28  aromatic  1.328  0.020  1.328
 5E6  C16  C15  aromatic  1.428  0.020  1.428
 5E6  C16  C17  aromatic  1.397  0.020  1.397
 5E6  C25  C26  aromatic  1.394  0.020  1.394
 5E6  C15  C3   single    1.464  0.020  1.464
 5E6  C28  C27  aromatic  1.387  0.020  1.387
 5E6  C26  C27  aromatic  1.384  0.020  1.384
 5E6  C3   C2   aromatic  1.390  0.020  1.390
 5E6  C3   N4   aromatic  1.329  0.020  1.329
 5E6  C2   C1   aromatic  1.390  0.020  1.390
 5E6  N4   C5   aromatic  1.334  0.020  1.334
 5E6  C1   C6   aromatic  1.379  0.020  1.379
 5E6  C5   C6   aromatic  1.408  0.020  1.408
 5E6  C5   N7   single    1.355  0.020  1.355
 5E6  C8   C9   single    1.534  0.020  1.534
 5E6  C8   N7   single    1.450  0.020  1.450
 5E6  C8   C13  single    1.528  0.020  1.528
 5E6  C9   C10  single    1.524  0.020  1.524
 5E6  C13  C12  single    1.528  0.020  1.528
 5E6  C10  C11  single    1.524  0.020  1.524
 5E6  C12  C11  single    1.524  0.020  1.524
 5E6  C12  N14  single    1.456  0.020  1.456
 5E6  C9   H1   single    0.970  0.020  1.090
 5E6  C9   H2   single    0.970  0.020  1.090
 5E6  C2   H3   single    0.930  0.020  1.080
 5E6  C10  H4   single    0.970  0.020  1.090
 5E6  C10  H5   single    0.970  0.020  1.090
 5E6  C6   H6   single    0.930  0.020  1.080
 5E6  C1   H7   single    0.930  0.020  1.080
 5E6  N7   H8   single    0.860  0.020  1.020
 5E6  C8   H9   single    0.970  0.020  1.090
 5E6  C11  H10  single    0.970  0.020  1.090
 5E6  C11  H11  single    0.970  0.020  1.090
 5E6  C12  H12  single    0.970  0.020  1.090
 5E6  C13  H13  single    0.970  0.020  1.090
 5E6  C13  H14  single    0.970  0.020  1.090
 5E6  N14  H15  single    0.890  0.020  1.040
 5E6  N14  H16  single    0.890  0.020  1.040
 5E6  C17  H18  single    0.930  0.020  1.080
 5E6  C20  H19  single    0.930  0.020  1.080
 5E6  N22  H23  single    0.860  0.020  1.020
 5E6  C26  H20  single    0.930  0.020  1.080
 5E6  C27  H21  single    0.930  0.020  1.080
 5E6  C28  H22  single    0.930  0.020  1.080
 5E6  C30  H24  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
 5E6  H2   C9   H1   106.38  3.000
 5E6  H2   C9   C8   108.12  3.000
 5E6  H1   C9   C8   110.38  3.000
 5E6  H2   C9   C10  109.49  3.000
 5E6  H1   C9   C10  110.42  3.000
 5E6  C8   C9   C10  111.87  3.000
 5E6  H3   C2   C3   121.30  3.000
 5E6  H3   C2   C1   121.54  3.000
 5E6  C3   C2   C1   117.16  3.000
 5E6  H5   C10  H4   106.15  3.000
 5E6  H5   C10  C11  109.84  3.000
 5E6  H4   C10  C11  110.28  3.000
 5E6  H5   C10  C9   109.75  3.000
 5E6  H4   C10  C9   109.72  3.000
 5E6  C11  C10  C9   110.99  3.000
 5E6  H6   C6   C5   121.49  3.000
 5E6  H6   C6   C1   120.47  3.000
 5E6  C5   C6   C1   118.04  3.000
 5E6  H7   C1   C6   119.45  3.000
 5E6  H7   C1   C2   119.96  3.000
 5E6  C6   C1   C2   120.60  3.000
 5E6  C15  C3   N4   115.15  3.000
 5E6  N4   C3   C2   123.12  3.000
 5E6  C15  C3   C2   121.73  3.000
 5E6  C5   N4   C3   119.67  3.000
 5E6  N7   C5   N4   115.74  3.000
 5E6  N7   C5   C6   122.84  3.000
 5E6  N4   C5   C6   121.42  3.000
 5E6  H8   N7   C8   118.28  3.000
 5E6  H8   N7   C5   114.65  3.000
 5E6  C8   N7   C5   125.13  3.000
 5E6  H9   C8   C13  107.55  3.000
 5E6  H9   C8   N7   107.86  3.000
 5E6  C13  C8   N7   109.60  3.000
 5E6  H9   C8   C9   108.83  3.000
 5E6  C13  C8   C9   110.12  3.000
 5E6  N7   C8   C9   112.72  3.000
 5E6  H11  C11  H10  106.95  3.000
 5E6  H11  C11  C12  109.89  3.000
 5E6  H10  C11  C12  108.56  3.000
 5E6  H11  C11  C10  110.48  3.000
 5E6  H10  C11  C10  109.66  3.000
 5E6  C12  C11  C10  111.19  3.000
 5E6  H12  C12  N14  111.46  3.000
 5E6  H12  C12  C13  108.97  3.000
 5E6  N14  C12  C13  109.07  3.000
 5E6  H12  C12  C11  107.19  3.000
 5E6  N14  C12  C11  110.11  3.000
 5E6  C13  C12  C11  110.01  3.000
 5E6  H14  C13  H13  106.87  3.000
 5E6  H14  C13  C12  107.94  3.000
 5E6  H13  C13  C12  110.34  3.000
 5E6  H14  C13  C8   108.13  3.000
 5E6  H13  C13  C8   109.85  3.000
 5E6  C12  C13  C8   113.46  3.000
 5E6  H16  N14  H15  105.35  3.000
 5E6  H16  N14  C12  109.48  3.000
 5E6  H15  N14  C12  109.17  3.000
 5E6  N24  C15  C16  109.71  3.000
 5E6  C16  C15  C3   128.35  3.000
 5E6  N24  C15  C3   121.93  3.000
 5E6  C21  C16  C17  118.36  3.000
 5E6  C17  C16  C15  137.49  3.000
 5E6  C21  C16  C15  104.15  3.000
 5E6  H18  C17  C18  122.07  3.000
 5E6  H18  C17  C16  120.44  3.000
 5E6  C18  C17  C16  117.47  3.000
 5E6  C25  C18  N19  115.70  3.000
 5E6  C25  C18  C17  121.31  3.000
 5E6  N19  C18  C17  122.98  3.000
 5E6  C20  N19  C18  120.67  3.000
 5E6  H19  C20  C21  121.86  3.000
 5E6  H19  C20  N19  118.08  3.000
 5E6  C21  C20  N19  120.06  3.000
 5E6  N22  C21  C20  133.21  3.000
 5E6  N22  C21  C16  106.34  3.000
 5E6  C20  C21  C16  120.45  3.000
 5E6  H23  N22  N24  119.80  3.000
 5E6  H23  N22  C21  128.19  3.000
 5E6  N24  N22  C21  112.01  3.000
 5E6  N22  N24  C15  107.79  3.000
 5E6  C30  C25  C26  116.96  3.000
 5E6  C26  C25  C18  121.33  3.000
 5E6  C30  C25  C18  121.71  3.000
 5E6  H20  C26  C27  120.51  3.000
 5E6  H20  C26  C25  120.17  3.000
 5E6  C27  C26  C25  119.32  3.000
 5E6  H21  C27  C28  120.32  3.000
 5E6  H21  C27  C26  121.00  3.000
 5E6  C28  C27  C26  118.68  3.000
 5E6  H22  C28  N29  116.67  3.000
 5E6  H22  C28  C27  120.45  3.000
 5E6  N29  C28  C27  122.88  3.000
 5E6  C30  N29  C28  118.06  3.000
 5E6  H24  C30  N29  115.76  3.000
 5E6  H24  C30  C25  120.14  3.000
 5E6  N29  C30  C25  124.09  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
 5E6  CONST_01  N24  C15  C3   C2     0.00   0.0  0
 5E6  CONST_02  C16  C15  C3   C2   180.00   0.0  0
 5E6  CONST_03  C5   N4   C3   C2     0.00   0.0  0
 5E6  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 5E6  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 5E6  CONST_06  C3   N4   C5   C6     0.00   0.0  0
 5E6  CONST_07  C15  C3   C2   C1   180.00   0.0  0
 5E6  CONST_08  N4   C3   C2   C1     0.00   0.0  0
 5E6  CONST_09  N4   C5   C6   C1     0.00   0.0  0
 5E6  CONST_10  N22  N24  C15  C3   180.00   0.0  0
 5E6  CONST_11  C21  C16  C15  C3   180.00   0.0  0
 5E6  CONST_12  C17  C16  C15  C3     0.00   0.0  0
 5E6  CONST_13  N24  C15  C3   N4   180.00   0.0  0
 5E6  CONST_14  C16  C15  C3   N4     0.00   0.0  0
 5E6  CONST_15  C15  C3   N4   C5   180.00   0.0  0
 5E6  CONST_16  C21  N22  N24  C15    0.00   0.0  0
 5E6  CONST_17  C20  C21  C16  C15  180.00   0.0  0
 5E6  CONST_18  N22  C21  C16  C15    0.00   0.0  0
 5E6  CONST_19  C18  C17  C16  C15  180.00   0.0  0
 5E6  CONST_20  N19  C20  C21  C16    0.00   0.0  0
 5E6  CONST_21  N24  N22  C21  C16    0.00   0.0  0
 5E6  CONST_22  N22  N24  C15  C16    0.00   0.0  0
 5E6  CONST_23  N19  C18  C17  C16    0.00   0.0  0
 5E6  CONST_24  C25  C18  C17  C16  180.00   0.0  0
 5E6  CONST_25  C20  N19  C18  C17    0.00   0.0  0
 5E6  CONST_28  C20  C21  C16  C17    0.00   0.0  0
 5E6  CONST_29  N22  C21  C16  C17  180.00   0.0  0
 5E6  CONST_30  N24  C15  C16  C17  180.00   0.0  0
 5E6  CONST_31  C21  C20  N19  C18    0.00   0.0  0
 5E6  CONST_32  N29  C30  C25  C18  180.00   0.0  0
 5E6  CONST_33  C27  C26  C25  C18  180.00   0.0  0
 5E6  CONST_34  C21  C16  C17  C18    0.00   0.0  0
 5E6  CONST_35  N22  C21  C20  N19  180.00   0.0  0
 5E6  CONST_38  C25  C18  N19  C20  180.00   0.0  0
 5E6  CONST_39  N24  N22  C21  C20  180.00   0.0  0
 5E6  CONST_40  N24  C15  C16  C21    0.00   0.0  0
 5E6  CONST_41  C28  N29  C30  C25    0.00   0.0  0
 5E6  CONST_42  C28  C27  C26  C25    0.00   0.0  0
 5E6  CONST_43  N29  C30  C25  C26    0.00   0.0  0
 5E6  CONST_44  N29  C28  C27  C26    0.00   0.0  0
 5E6  CONST_45  C30  N29  C28  C27    0.00   0.0  0
 5E6  CONST_46  C30  C25  C26  C27    0.00   0.0  0
 5E6  CONST_47  N7   C5   C6   C1   180.00   0.0  0
 5E6  CONST_48  N7   C5   N4   C3   180.00   0.0  0
 5E6  CONST_49  C8   N7   C5   C6     0.00   0.0  0
 5E6  CONST_50  C8   N7   C5   N4   180.00   0.0  0
 5E6  CONST_51  H6   C6   C1   C2   180.00   0.0  0
 5E6  CONST_52  H3   C2   C1   C6   180.00   0.0  0
 5E6  CONST_53  H7   C1   C2   C3   180.00   0.0  0
 5E6  CONST_54  H23  N22  N24  C15  180.00   0.0  0
 5E6  CONST_55  H18  C17  C16  C15    0.00   0.0  0
 5E6  CONST_56  H19  C20  C21  C16  180.00   0.0  0
 5E6  CONST_57  H24  C30  C25  C18    0.00   0.0  0
 5E6  CONST_58  H20  C26  C25  C18    0.00   0.0  0
 5E6  CONST_59  H21  C27  C26  C25  180.00   0.0  0
 5E6  CONST_60  H22  C28  C27  C26  180.00   0.0  0
 5E6  CONST_61  H8   N7   C5   C6   180.00   0.0  0
 5E6  Var_01    C12  C11  C10  C9   -57.44  30.0  1
 5E6  Var_02    C11  C10  C9   C8    56.26  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
 5E6  chir_01  C8   C9   N7   C13  positiv
 5E6  chir_02  C12  N14  C11  C13  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
 5E6  plan-1  C2   0.020
 5E6  plan-1  C6   0.020
 5E6  plan-1  C1   0.020
 5E6  plan-1  C3   0.020
 5E6  plan-1  N4   0.020
 5E6  plan-1  C5   0.020
 5E6  plan-1  N7   0.020
 5E6  plan-1  C15  0.020
 5E6  plan-1  H6   0.020
 5E6  plan-1  H7   0.020
 5E6  plan-1  H3   0.020
 5E6  plan-2  C18  0.020
 5E6  plan-2  C25  0.020
 5E6  plan-2  C26  0.020
 5E6  plan-2  C27  0.020
 5E6  plan-2  C28  0.020
 5E6  plan-2  N29  0.020
 5E6  plan-2  C30  0.020
 5E6  plan-2  H20  0.020
 5E6  plan-2  H21  0.020
 5E6  plan-2  H22  0.020
 5E6  plan-2  H24  0.020
 5E6  plan-3  C3   0.020
 5E6  plan-3  C15  0.020
 5E6  plan-3  C16  0.020
 5E6  plan-3  C17  0.020
 5E6  plan-3  C18  0.020
 5E6  plan-3  N19  0.020
 5E6  plan-3  C20  0.020
 5E6  plan-3  C21  0.020
 5E6  plan-3  N22  0.020
 5E6  plan-3  N24  0.020
 5E6  plan-3  C25  0.020
 5E6  plan-3  H18  0.020
 5E6  plan-3  H19  0.020
 5E6  plan-3  H23  0.020
 5E6  plan-4  C5   0.020
 5E6  plan-4  N7   0.020
 5E6  plan-4  C8   0.020
 5E6  plan-4  H8   0.020

