# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:23:11 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-[4-[[4-(dimethylamino)cyclohexyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]cyclohexane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@@H]1CC[C@H](CC1)Nc2ncnc3[nH]cc([C@@H]4CC[C@H](CC4)C(N)=O)c23
#
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
 CJT  CJT  4-[4-[[4-(dimethylamino)cyclohexyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]cyclohexane-1-carboxamide  ligand  60  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CJT
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
 CJT  C1   C  CH1   0  -0.007  -4.3460   1.4857  -0.1977
 CJT  C2   C  CH2   0  -0.467  -4.1165   0.2394  -1.0568
 CJT  C3   C  CH2   0  -0.431  -2.6721  -0.2451  -0.9944
 CJT  C7   C  CR6   0   0.469  -0.4126  -2.2058   0.2719
 CJT  C8   C  CR16  0   0.033  -0.8894  -4.4214  -0.0952
 CJT  C9   C  CR56  0   0.476   1.2470  -3.8820   0.0167
 CJT  C10  C  CR56  0  -0.126   0.9634  -2.5252   0.2191
 CJT  C11  C  CR5   0   0.064   2.2171  -1.8319   0.3266
 CJT  C12  C  CR15  0  -0.083   3.1766  -2.7953   0.1898
 CJT  C13  C  CH1   0  -0.386   2.4404  -0.3583   0.4805
 CJT  C14  C  CH2   0  -0.436   2.1117   0.3917  -0.8183
 CJT  C15  C  CH2   0  -0.420   2.2931   1.8968  -0.6654
 CJT  C16  C  CH1   0  -0.381   3.7155   2.2308  -0.2307
 CJT  C19  C  C     0   0.536   3.9214   3.7210  -0.0307
 CJT  O    O  O     0  -0.493   3.0191   4.4706   0.3174
 CJT  N5   N  NH2   0  -0.803   5.1776   4.1483  -0.2372
 CJT  C17  C  CH2   0  -0.425   4.0641   1.4866   1.0662
 CJT  C18  C  CH2   0  -0.423   3.8662  -0.0167   0.9118
 CJT  N4   N  NR15  0  -0.669   2.5900  -4.0237   0.0053
 CJT  N3   N  N     0  -0.456   0.3498  -4.8608  -0.1426
 CJT  N2   N  N     0  -0.491  -1.3147  -3.1742   0.0964
 CJT  N1   N  NH1   0  -0.686  -0.8530  -0.9586   0.5150
 CJT  C4   C  CH1   0  -0.049  -2.2381  -0.5382   0.4373
 CJT  C5   C  CH2   0  -0.450  -2.4466   0.6974   1.2995
 CJT  C6   C  CH2   0  -0.463  -3.8885   1.1878   1.2332
 CJT  N    N  NT    0  -0.419  -5.7459   1.9106  -0.2287
 CJT  C    C  CH3   0  -0.529  -6.2243   2.1532  -1.5772
 CJT  H1   H  HCH1  0   0.177  -3.7004   2.2931  -0.5991
 CJT  H2   H  HCH2  0   0.218  -4.7910  -0.5541  -0.7153
 CJT  H3   H  HCH2  0   0.243  -4.3623   0.4305  -2.1017
 CJT  H4   H  HCH2  0   0.242  -2.5568  -1.1384  -1.6113
 CJT  H5   H  HCH2  0   0.213  -2.0092   0.5198  -1.4153
 CJT  H6   H  HCR6  0   0.242  -1.6700  -5.1637  -0.2292
 CJT  H7   H  HCR5  0   0.285   4.2505  -2.7076   0.2059
 CJT  H8   H  HCH1  0   0.227   1.7776   0.0172   1.2736
 CJT  H9   H  HCH2  0   0.229   2.7646   0.0119  -1.6115
 CJT  H10  H  HCH2  0   0.226   1.0909   0.1774  -1.1477
 CJT  H11  H  HCH2  0   0.242   2.0547   2.3945  -1.6083
 CJT  H12  H  HCH2  0   0.220   1.5847   2.2761   0.0769
 CJT  H13  H  HCH1  0   0.252   4.4055   1.8843  -1.0101
 CJT  H14  H  HCH3  0   0.189  -5.3711   3.9556   0.2786
 CJT  H15  H  HCH3  0   0.233  -7.0316   3.3875   0.4863
 CJT  H16  H  HCH3  0   0.237  -5.8030   2.9029   1.6347
 CJT  H17  H  HNH2  0   0.405   5.9172   3.5129  -0.4816
 CJT  H18  H  HNH2  0   0.397   5.4342   5.1017  -0.0393
 CJT  H19  H  HCH2  0   0.244   5.0984   1.6901   1.3534
 CJT  H20  H  HCH2  0   0.228   3.4321   1.8617   1.8783
 CJT  H21  H  HCH2  0   0.242   4.1049  -0.5174   1.8533
 CJT  H22  H  HCH2  0   0.222   4.5725  -0.3932   0.1643
 CJT  H23  H  HNR5  0   0.409   3.0830  -4.8920  -0.1236
 CJT  H24  H  HNH1  0   0.393  -0.1637  -0.2294   0.5872
 CJT  H25  H  HCH1  0   0.240  -2.8535  -1.3502   0.8318
 CJT  H26  H  HCH2  0   0.248  -2.1804   0.4815   2.3368
 CJT  H27  H  HCH2  0   0.216  -1.7740   1.4961   0.9615
 CJT  H28  H  HCH2  0   0.245  -3.9699   2.0712   1.8670
 CJT  H29  H  HCH2  0   0.220  -4.5541   0.4300   1.6609
 CJT  H31  H  HCH3  0   0.237  -6.2440   1.2390  -2.1674
 CJT  H32  H  HCH3  0   0.233  -7.2479   2.5260  -1.5358
 CJT  H33  H  HCH3  0   0.189  -5.6213   2.8959  -2.1240
 CJT  C20  C  CH3   0  -0.529  -5.9861   3.0917   0.5787

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
 CJT  N3   C8   aromatic  1.316  0.020  1.316
 CJT  N3   C9   aromatic  1.337  0.020  1.337
 CJT  C8   N2   aromatic  1.332  0.020  1.332
 CJT  N4   C9   aromatic  1.351  0.020  1.351
 CJT  N4   C12  aromatic  1.374  0.020  1.374
 CJT  C9   C10  aromatic  1.401  0.020  1.401
 CJT  N2   C7   aromatic  1.335  0.020  1.335
 CJT  C12  C11  aromatic  1.367  0.020  1.367
 CJT  C10  C7   aromatic  1.414  0.020  1.414
 CJT  C10  C11  aromatic  1.437  0.020  1.437
 CJT  C7   N1   single    1.345  0.020  1.345
 CJT  C11  C13  single    1.498  0.020  1.498
 CJT  N1   C4   single    1.450  0.020  1.450
 CJT  C4   C5   single    1.521  0.020  1.521
 CJT  C4   C3   single    1.524  0.020  1.524
 CJT  C13  C14  single    1.535  0.020  1.535
 CJT  C13  C18  single    1.528  0.020  1.528
 CJT  C14  C15  single    1.524  0.020  1.524
 CJT  C5   C6   single    1.524  0.020  1.524
 CJT  C18  C17  single    1.524  0.020  1.524
 CJT  C6   C1   single    1.532  0.020  1.532
 CJT  C3   C2   single    1.525  0.020  1.525
 CJT  C20  N    single    1.451  0.020  1.451
 CJT  C2   C1   single    1.531  0.020  1.531
 CJT  C15  C16  single    1.524  0.020  1.524
 CJT  C1   N    single    1.463  0.020  1.463
 CJT  C17  C16  single    1.535  0.020  1.535
 CJT  C16  C19  single    1.518  0.020  1.518
 CJT  N    C    single    1.451  0.020  1.451
 CJT  C19  N5   single    1.343  0.020  1.343
 CJT  C19  O    double    1.224  0.020  1.224
 CJT  C1   H1   single    0.970  0.020  1.090
 CJT  C2   H2   single    0.970  0.020  1.090
 CJT  C2   H3   single    0.970  0.020  1.090
 CJT  C3   H4   single    0.970  0.020  1.090
 CJT  C3   H5   single    0.970  0.020  1.090
 CJT  C8   H6   single    0.930  0.020  1.080
 CJT  C12  H7   single    0.930  0.020  1.080
 CJT  C13  H8   single    0.970  0.020  1.090
 CJT  C14  H9   single    0.970  0.020  1.090
 CJT  C14  H10  single    0.970  0.020  1.090
 CJT  C15  H11  single    0.970  0.020  1.090
 CJT  C15  H12  single    0.970  0.020  1.090
 CJT  C16  H13  single    0.970  0.020  1.090
 CJT  C20  H14  single    0.970  0.020  1.090
 CJT  C20  H15  single    0.970  0.020  1.090
 CJT  C20  H16  single    0.970  0.020  1.090
 CJT  N5   H17  single    0.860  0.020  1.020
 CJT  N5   H18  single    0.860  0.020  1.020
 CJT  C17  H19  single    0.970  0.020  1.090
 CJT  C17  H20  single    0.970  0.020  1.090
 CJT  C18  H21  single    0.970  0.020  1.090
 CJT  C18  H22  single    0.970  0.020  1.090
 CJT  N4   H23  single    0.860  0.020  1.020
 CJT  N1   H24  single    0.860  0.020  1.020
 CJT  C4   H25  single    0.970  0.020  1.090
 CJT  C5   H26  single    0.970  0.020  1.090
 CJT  C5   H27  single    0.970  0.020  1.090
 CJT  C6   H28  single    0.970  0.020  1.090
 CJT  C6   H29  single    0.970  0.020  1.090
 CJT  C    H31  single    0.970  0.020  1.090
 CJT  C    H32  single    0.970  0.020  1.090
 CJT  C    H33  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
 CJT  H1   C1   N    109.75  3.000
 CJT  H1   C1   C6   107.81  3.000
 CJT  N    C1   C6   111.23  3.000
 CJT  H1   C1   C2   107.59  3.000
 CJT  N    C1   C2   111.59  3.000
 CJT  C6   C1   C2   108.73  3.000
 CJT  H3   C2   H2   106.66  3.000
 CJT  H3   C2   C3   107.97  3.000
 CJT  H2   C2   C3   109.89  3.000
 CJT  H3   C2   C1   111.18  3.000
 CJT  H2   C2   C1   108.80  3.000
 CJT  C3   C2   C1   112.19  3.000
 CJT  H5   C3   H4   106.86  3.000
 CJT  H5   C3   C4   108.82  3.000
 CJT  H4   C3   C4   110.08  3.000
 CJT  H5   C3   C2   109.60  3.000
 CJT  H4   C3   C2   109.69  3.000
 CJT  C4   C3   C2   111.67  3.000
 CJT  N1   C7   N2   118.37  3.000
 CJT  N1   C7   C10  122.35  3.000
 CJT  N2   C7   C10  119.27  3.000
 CJT  H6   C8   N2   115.38  3.000
 CJT  H6   C8   N3   116.39  3.000
 CJT  N2   C8   N3   128.23  3.000
 CJT  N3   C9   N4   126.11  3.000
 CJT  N4   C9   C10  107.71  3.000
 CJT  N3   C9   C10  126.18  3.000
 CJT  C11  C10  C9   107.55  3.000
 CJT  C11  C10  C7   137.53  3.000
 CJT  C9   C10  C7   114.92  3.000
 CJT  C13  C11  C12  126.80  3.000
 CJT  C13  C11  C10  127.76  3.000
 CJT  C12  C11  C10  105.37  3.000
 CJT  H7   C12  N4   120.02  3.000
 CJT  H7   C12  C11  129.85  3.000
 CJT  N4   C12  C11  110.13  3.000
 CJT  H8   C13  C18  106.40  3.000
 CJT  H8   C13  C14  108.31  3.000
 CJT  C18  C13  C14  109.23  3.000
 CJT  H8   C13  C11  108.67  3.000
 CJT  C18  C13  C11  112.82  3.000
 CJT  C14  C13  C11  111.20  3.000
 CJT  H10  C14  H9   105.68  3.000
 CJT  H10  C14  C15  109.56  3.000
 CJT  H9   C14  C15  110.13  3.000
 CJT  H10  C14  C13  111.03  3.000
 CJT  H9   C14  C13  108.40  3.000
 CJT  C15  C14  C13  111.85  3.000
 CJT  H12  C15  H11  106.64  3.000
 CJT  H12  C15  C16  109.56  3.000
 CJT  H11  C15  C16  110.48  3.000
 CJT  H12  C15  C14  109.48  3.000
 CJT  H11  C15  C14  109.72  3.000
 CJT  C16  C15  C14  110.86  3.000
 CJT  H13  C16  C17  107.71  3.000
 CJT  H13  C16  C19  108.57  3.000
 CJT  C17  C16  C19  109.50  3.000
 CJT  H13  C16  C15  108.37  3.000
 CJT  C19  C16  C15  112.29  3.000
 CJT  C17  C16  C15  110.28  3.000
 CJT  N5   C19  O    122.60  3.000
 CJT  O    C19  C16  122.62  3.000
 CJT  N5   C19  C16  114.77  3.000
 CJT  H18  N5   H17  117.31  3.000
 CJT  H18  N5   C19  120.62  3.000
 CJT  H17  N5   C19  121.64  3.000
 CJT  H20  C17  H19  106.71  3.000
 CJT  H20  C17  C18  109.75  3.000
 CJT  H19  C17  C18  109.47  3.000
 CJT  H20  C17  C16  109.22  3.000
 CJT  H19  C17  C16  110.29  3.000
 CJT  C18  C17  C16  111.29  3.000
 CJT  H22  C18  H21  106.83  3.000
 CJT  H22  C18  C17  108.93  3.000
 CJT  H21  C18  C17  109.65  3.000
 CJT  H22  C18  C13  109.40  3.000
 CJT  H21  C18  C13  110.15  3.000
 CJT  C17  C18  C13  111.73  3.000
 CJT  H23  N4   C12  125.40  3.000
 CJT  H23  N4   C9   125.35  3.000
 CJT  C12  N4   C9   109.25  3.000
 CJT  C9   N3   C8   112.53  3.000
 CJT  C8   N2   C7   118.85  3.000
 CJT  H24  N1   C4   116.63  3.000
 CJT  H24  N1   C7   117.44  3.000
 CJT  C4   N1   C7   124.90  3.000
 CJT  H25  C4   C5   108.77  3.000
 CJT  H25  C4   N1   107.66  3.000
 CJT  C5   C4   N1   109.64  3.000
 CJT  H25  C4   C3   108.77  3.000
 CJT  C5   C4   C3   109.70  3.000
 CJT  N1   C4   C3   112.22  3.000
 CJT  H27  C5   H26  106.68  3.000
 CJT  H27  C5   C6   109.40  3.000
 CJT  H26  C5   C6   109.60  3.000
 CJT  H27  C5   C4   109.42  3.000
 CJT  H26  C5   C4   110.13  3.000
 CJT  C6   C5   C4   111.49  3.000
 CJT  H29  C6   H28  106.75  3.000
 CJT  H29  C6   C5   109.58  3.000
 CJT  H28  C6   C5   107.82  3.000
 CJT  H29  C6   C1   108.53  3.000
 CJT  H28  C6   C1   111.30  3.000
 CJT  C5   C6   C1   112.69  3.000
 CJT  C    N    C20  109.06  3.000
 CJT  C    N    C1   112.56  3.000
 CJT  C20  N    C1   112.52  3.000
 CJT  H33  C    H32  107.59  3.000
 CJT  H33  C    H31  107.87  3.000
 CJT  H32  C    H31  106.91  3.000
 CJT  H33  C    N    113.16  3.000
 CJT  H32  C    N    109.36  3.000
 CJT  H31  C    N    111.68  3.000
 CJT  H16  C20  H15  106.89  3.000
 CJT  H16  C20  H14  107.84  3.000
 CJT  H15  C20  H14  107.42  3.000
 CJT  H16  C20  N    111.78  3.000
 CJT  H15  C20  N    109.41  3.000
 CJT  H14  C20  N    113.22  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
 CJT  CONST_01  N3   C8   N2   C7     0.00   0.0  0
 CJT  CONST_02  N3   C9   C10  C7     0.00   0.0  0
 CJT  CONST_03  N4   C9   C10  C7   180.00   0.0  0
 CJT  CONST_04  C12  C11  C10  C7   180.00   0.0  0
 CJT  CONST_05  N4   C9   N3   C8   180.00   0.0  0
 CJT  CONST_06  C10  C9   N3   C8     0.00   0.0  0
 CJT  CONST_07  C10  C7   N2   C8     0.00   0.0  0
 CJT  CONST_08  N2   C8   N3   C9     0.00   0.0  0
 CJT  CONST_09  C11  C12  N4   C9     0.00   0.0  0
 CJT  CONST_10  N2   C7   C10  C9     0.00   0.0  0
 CJT  CONST_11  C12  C11  C10  C9     0.00   0.0  0
 CJT  CONST_12  C12  N4   C9   C10    0.00   0.0  0
 CJT  CONST_13  N4   C12  C11  C10    0.00   0.0  0
 CJT  CONST_14  N3   C9   C10  C11  180.00   0.0  0
 CJT  CONST_15  N4   C9   C10  C11    0.00   0.0  0
 CJT  CONST_16  N2   C7   C10  C11  180.00   0.0  0
 CJT  CONST_17  N3   C9   N4   C12  180.00   0.0  0
 CJT  CONST_18  C13  C11  C10  C7     0.00   0.0  0
 CJT  CONST_19  C13  C11  C10  C9   180.00   0.0  0
 CJT  CONST_20  N4   C12  C11  C13  180.00   0.0  0
 CJT  CONST_21  N1   C7   N2   C8   180.00   0.0  0
 CJT  CONST_22  N1   C7   C10  C9   180.00   0.0  0
 CJT  CONST_23  N1   C7   C10  C11    0.00   0.0  0
 CJT  CONST_24  C4   N1   C7   C10  180.00   0.0  0
 CJT  CONST_25  C4   N1   C7   N2     0.00   0.0  0
 CJT  CONST_26  H6   C8   N2   C7   180.00   0.0  0
 CJT  CONST_27  H7   C12  N4   C9   180.00   0.0  0
 CJT  CONST_28  H23  N4   C9   C10  180.00   0.0  0
 CJT  CONST_29  H24  N1   C7   C10    0.00   0.0  0
 CJT  CONST_30  H17  N5   C19  C16    0.00   0.0  0
 CJT  CONST_31  H18  N5   C19  C16  180.00   0.0  0
 CJT  Var_01    C4   C5   C6   C1   -56.65  30.0  1
 CJT  Var_02    C4   C3   C2   C1    57.11  30.0  1
 CJT  Var_03    C16  C15  C14  C13   57.46  30.0  1
 CJT  Var_04    C16  C17  C18  C13  -56.61  30.0  1
 CJT  Var_05    H14  C20  N    C1    57.87  30.0  3
 CJT  Var_06    H31  C    N    C1    65.43  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
 CJT  chir_01  C1   C6   C2   N    negativ
 CJT  chir_02  C13  C11  C14  C18  positiv
 CJT  chir_03  C16  C15  C17  C19  positiv
 CJT  chir_04  C4   N1   C5   C3   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
 CJT  plan-1  C16  0.020
 CJT  plan-1  C19  0.020
 CJT  plan-1  O    0.020
 CJT  plan-1  N5   0.020
 CJT  plan-1  H17  0.020
 CJT  plan-1  H18  0.020
 CJT  plan-2  C7   0.020
 CJT  plan-2  N1   0.020
 CJT  plan-2  C4   0.020
 CJT  plan-2  H24  0.020
 CJT  plan-3  C7   0.020
 CJT  plan-3  C8   0.020
 CJT  plan-3  C9   0.020
 CJT  plan-3  C10  0.020
 CJT  plan-3  C11  0.020
 CJT  plan-3  C12  0.020
 CJT  plan-3  C13  0.020
 CJT  plan-3  N4   0.020
 CJT  plan-3  N3   0.020
 CJT  plan-3  N2   0.020
 CJT  plan-3  N1   0.020
 CJT  plan-3  H6   0.020
 CJT  plan-3  H7   0.020
 CJT  plan-3  H23  0.020

