# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 20:17:53 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: ~{N}4,~{N}4-dimethyl-~{N}1-(5-propan-2-ylpyrrolo[3,2-d]pyrimidin-4-yl)cyclohexane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1ccc2ncnc(N[C@@H]3CC[C@H](CC3)N(C)C)c12
#
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
 CJN  CJN  ~{N}4,~{N}4-dimethyl-~{N}1-(5-propan-2-ylpyrrolo[3,2-d]pyrimidin-4-yl)cyclohexane-1,4-diamine  ligand  49  22  .  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_CJN
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
 CJN  C1   C  CH3   0  -0.650   2.2220  -2.5310  -1.1556
 CJN  C2   C  CH1   0  -0.146   2.8229  -2.1170   0.1830
 CJN  C3   C  CH3   0  -0.686   3.8800  -3.1105   0.6390
 CJN  C7   C  CR56  0   0.169   3.5242   1.4793  -0.1057
 CJN  C9   C  CR16  0   0.008   1.8642   2.9563   0.0376
 CJN  C11  C  CR6   0   0.530   1.2643   0.7477   0.3030
 CJN  C13  C  CH1   0  -0.051  -1.1283   0.1789   0.5535
 CJN  C15  C  CH2   0  -0.452  -1.8884  -0.8999   1.3165
 CJN  C16  C  CH2   0  -0.440  -3.3884  -0.6258   1.3188
 CJN  C19  C  CH2   0  -0.459  -3.1829   0.6036  -0.8517
 CJN  C20  C  CH2   0  -0.429  -1.6817   0.3374  -0.8620
 CJN  C22  C  CH3   0  -0.521  -5.9614  -0.7026  -1.4076
 CJN  C24  C  CR56  0   0.208   2.6285   0.4203   0.1215
 CJN  N4   N  NR5   0  -0.510   3.3513  -0.7533   0.1143
 CJN  C5   C  CR15  0  -0.008   4.6528  -0.4382  -0.1308
 CJN  C6   C  CR15  0  -0.426   4.8124   0.9141  -0.2648
 CJN  N8   N  N     0  -0.456   3.1478   2.7744  -0.1458
 CJN  N10  N  N     0  -0.488   0.9245   2.0334   0.2485
 CJN  C17  C  CH1   0  -0.052  -3.9340  -0.5032  -0.1028
 CJN  N21  N  NT    0  -0.414  -5.3888  -0.3979  -0.1152
 CJN  C23  C  CH3   0  -0.531  -5.9151   0.8470   0.4024
 CJN  H1   H  HCH3  0   0.243   2.9941  -2.5594  -1.9256
 CJN  H2   H  HCH3  0   0.246   1.7837  -3.5259  -1.0779
 CJN  H3   H  HCH3  0   0.231   1.4405  -1.8488  -1.4941
 CJN  H4   H  HCH1  0   0.256   2.0546  -2.1194   0.9584
 CJN  H5   H  HCH3  0   0.238   4.6634  -3.2517  -0.1058
 CJN  H6   H  HCH3  0   0.253   4.3389  -2.8098   1.5805
 CJN  H7   H  HCH3  0   0.261   3.4017  -4.0768   0.7924
 CJN  H8   H  HCR6  0   0.237   1.5074   3.9817   0.0135
 CJN  H14  H  HCH1  0   0.240  -1.2431   1.1271   1.0842
 CJN  H9   H  HCH2  0   0.218  -1.6991  -1.8761   0.8534
 CJN  H10  H  HCH2  0   0.246  -1.5166  -0.9595   2.3420
 CJN  H11  H  HCH2  0   0.235  -3.9122  -1.4291   1.8418
 CJN  H12  H  HCH2  0   0.218  -3.5784   0.2934   1.8822
 CJN  H13  H  HCH2  0   0.218  -3.3796   1.5715  -0.3781
 CJN  H15  H  HCH2  0   0.236  -3.5419   0.6846  -1.8810
 CJN  H16  H  HCH2  0   0.241  -1.1558   1.1470  -1.3728
 CJN  H17  H  HCH2  0   0.212  -1.4746  -0.5792  -1.4259
 CJN  H19  H  HCH3  0   0.228  -5.6007  -1.6703  -1.7606
 CJN  H20  H  HCH3  0   0.229  -7.0482  -0.7663  -1.3235
 CJN  H21  H  HCH3  0   0.191  -5.7401   0.0426  -2.1870
 CJN  H22  H  HCR5  0   0.292   5.4043  -1.2073  -0.1926
 CJN  H23  H  HCR5  0   0.252   5.7380   1.4344  -0.4505
 CJN  H24  H  HNH1  0   0.393   0.5031  -1.1268   0.4636
 CJN  H18  H  HCH1  0   0.216  -3.7012  -1.4507  -0.6060
 CJN  H26  H  HCH3  0   0.195  -5.7007   1.7208  -0.2304
 CJN  H27  H  HCH3  0   0.231  -7.0004   0.7715   0.4927
 CJN  H28  H  HCH3  0   0.233  -5.5241   1.0532   1.3986
 CJN  N12  N  NH1   0  -0.686   0.2871  -0.1496   0.5492

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
 CJN  C23  N21  single    1.447  0.020  1.447
 CJN  N21  C17  single    1.459  0.020  1.459
 CJN  N21  C22  single    1.446  0.020  1.446
 CJN  C17  C16  single    1.528  0.020  1.528
 CJN  C17  C19  single    1.533  0.020  1.533
 CJN  C16  C15  single    1.525  0.020  1.525
 CJN  C15  C13  single    1.524  0.020  1.524
 CJN  C1   C2   single    1.525  0.020  1.525
 CJN  C3   C2   single    1.521  0.020  1.521
 CJN  C19  C20  single    1.525  0.020  1.525
 CJN  C2   N4   single    1.464  0.020  1.464
 CJN  C20  C13  single    1.528  0.020  1.528
 CJN  C13  N12  single    1.453  0.020  1.453
 CJN  N12  C11  single    1.349  0.020  1.349
 CJN  N4   C24  aromatic  1.378  0.020  1.378
 CJN  N4   C5   aromatic  1.361  0.020  1.361
 CJN  C11  C24  aromatic  1.415  0.020  1.415
 CJN  C11  N10  aromatic  1.331  0.020  1.331
 CJN  C24  C7   aromatic  1.405  0.020  1.405
 CJN  C5   C6   aromatic  1.368  0.020  1.368
 CJN  N10  C9   aromatic  1.334  0.020  1.334
 CJN  C7   C6   aromatic  1.416  0.020  1.416
 CJN  C7   N8   aromatic  1.349  0.020  1.349
 CJN  C9   N8   aromatic  1.309  0.020  1.309
 CJN  C1   H1   single    0.970  0.020  1.090
 CJN  C1   H2   single    0.970  0.020  1.090
 CJN  C1   H3   single    0.970  0.020  1.090
 CJN  C2   H4   single    0.970  0.020  1.090
 CJN  C3   H5   single    0.970  0.020  1.090
 CJN  C3   H6   single    0.970  0.020  1.090
 CJN  C3   H7   single    0.970  0.020  1.090
 CJN  C9   H8   single    0.930  0.020  1.080
 CJN  C13  H14  single    0.970  0.020  1.090
 CJN  C15  H9   single    0.970  0.020  1.090
 CJN  C15  H10  single    0.970  0.020  1.090
 CJN  C16  H11  single    0.970  0.020  1.090
 CJN  C16  H12  single    0.970  0.020  1.090
 CJN  C19  H13  single    0.970  0.020  1.090
 CJN  C19  H15  single    0.970  0.020  1.090
 CJN  C20  H16  single    0.970  0.020  1.090
 CJN  C20  H17  single    0.970  0.020  1.090
 CJN  C22  H19  single    0.970  0.020  1.090
 CJN  C22  H20  single    0.970  0.020  1.090
 CJN  C22  H21  single    0.970  0.020  1.090
 CJN  C5   H22  single    0.930  0.020  1.080
 CJN  C6   H23  single    0.930  0.020  1.080
 CJN  N12  H24  single    0.860  0.020  1.020
 CJN  C17  H18  single    0.970  0.020  1.090
 CJN  C23  H26  single    0.970  0.020  1.090
 CJN  C23  H27  single    0.970  0.020  1.090
 CJN  C23  H28  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
 CJN  H3   C1   H2   107.74  3.000
 CJN  H3   C1   H1   107.72  3.000
 CJN  H2   C1   H1   108.13  3.000
 CJN  H3   C1   C2   112.64  3.000
 CJN  H2   C1   C2   110.10  3.000
 CJN  H1   C1   C2   110.36  3.000
 CJN  H4   C2   N4   106.82  3.000
 CJN  H4   C2   C3   105.95  3.000
 CJN  N4   C2   C3   111.82  3.000
 CJN  H4   C2   C1   110.23  3.000
 CJN  N4   C2   C1   110.73  3.000
 CJN  C3   C2   C1   111.09  3.000
 CJN  H7   C3   H6   107.94  3.000
 CJN  H7   C3   H5   107.27  3.000
 CJN  H6   C3   H5   108.87  3.000
 CJN  H7   C3   C2   108.46  3.000
 CJN  H6   C3   C2   111.81  3.000
 CJN  H5   C3   C2   112.30  3.000
 CJN  N8   C7   C6   129.32  3.000
 CJN  N8   C7   C24  123.39  3.000
 CJN  C6   C7   C24  107.29  3.000
 CJN  H8   C9   N10  115.17  3.000
 CJN  H8   C9   N8   116.75  3.000
 CJN  N10  C9   N8   128.07  3.000
 CJN  N12  C11  N10  117.71  3.000
 CJN  N10  C11  C24  117.68  3.000
 CJN  N12  C11  C24  124.61  3.000
 CJN  H14  C13  N12  107.45  3.000
 CJN  H14  C13  C20  108.77  3.000
 CJN  N12  C13  C20  111.93  3.000
 CJN  H14  C13  C15  108.58  3.000
 CJN  N12  C13  C15  109.10  3.000
 CJN  C20  C13  C15  110.89  3.000
 CJN  H10  C15  H9   106.80  3.000
 CJN  H10  C15  C16  110.07  3.000
 CJN  H9   C15  C16  109.29  3.000
 CJN  H10  C15  C13  109.80  3.000
 CJN  H9   C15  C13  109.42  3.000
 CJN  C16  C15  C13  111.35  3.000
 CJN  H12  C16  H11  106.73  3.000
 CJN  H12  C16  C17  110.47  3.000
 CJN  H11  C16  C17  109.48  3.000
 CJN  H12  C16  C15  108.81  3.000
 CJN  H11  C16  C15  109.88  3.000
 CJN  C17  C16  C15  111.36  3.000
 CJN  H15  C19  H13  106.43  3.000
 CJN  H15  C19  C17  110.65  3.000
 CJN  H13  C19  C17  109.81  3.000
 CJN  H15  C19  C20  109.26  3.000
 CJN  H13  C19  C20  109.51  3.000
 CJN  C17  C19  C20  111.08  3.000
 CJN  H17  C20  H16  106.76  3.000
 CJN  H17  C20  C19  109.61  3.000
 CJN  H16  C20  C19  110.36  3.000
 CJN  H17  C20  C13  108.75  3.000
 CJN  H16  C20  C13  109.62  3.000
 CJN  C19  C20  C13  111.62  3.000
 CJN  H21  C22  H20  107.11  3.000
 CJN  H21  C22  H19  107.75  3.000
 CJN  H20  C22  H19  107.58  3.000
 CJN  H21  C22  N21  114.24  3.000
 CJN  H20  C22  N21  109.73  3.000
 CJN  H19  C22  N21  110.19  3.000
 CJN  N4   C24  C11  134.70  3.000
 CJN  C11  C24  C7   117.45  3.000
 CJN  N4   C24  C7   107.85  3.000
 CJN  C5   N4   C24  107.77  3.000
 CJN  C5   N4   C2   124.69  3.000
 CJN  C24  N4   C2   127.12  3.000
 CJN  H22  C5   C6   128.23  3.000
 CJN  H22  C5   N4   120.80  3.000
 CJN  C6   C5   N4   110.97  3.000
 CJN  H23  C6   C5   126.44  3.000
 CJN  H23  C6   C7   127.45  3.000
 CJN  C5   C6   C7   106.11  3.000
 CJN  C9   N8   C7   113.74  3.000
 CJN  C11  N10  C9   119.67  3.000
 CJN  H18  C17  N21  105.65  3.000
 CJN  H18  C17  C19  107.18  3.000
 CJN  N21  C17  C19  115.62  3.000
 CJN  H18  C17  C16  106.36  3.000
 CJN  C19  C17  C16  109.73  3.000
 CJN  N21  C17  C16  111.71  3.000
 CJN  C23  N21  C17  114.94  3.000
 CJN  C17  N21  C22  112.79  3.000
 CJN  C23  N21  C22  110.91  3.000
 CJN  H28  C23  H27  107.11  3.000
 CJN  H28  C23  H26  107.80  3.000
 CJN  H27  C23  H26  107.24  3.000
 CJN  H28  C23  N21  111.05  3.000
 CJN  H27  C23  N21  109.37  3.000
 CJN  H26  C23  N21  113.99  3.000
 CJN  H24  N12  C13  115.45  3.000
 CJN  H24  N12  C11  118.40  3.000
 CJN  C13  N12  C11  123.76  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
 CJN  CONST_01  C5   N4   C24  C7     0.00   0.0  0
 CJN  CONST_02  N10  C11  C24  C7     0.00   0.0  0
 CJN  CONST_03  N4   C5   C6   C7     0.00   0.0  0
 CJN  CONST_04  N10  C9   N8   C7     0.00   0.0  0
 CJN  CONST_05  C24  C11  N10  C9     0.00   0.0  0
 CJN  CONST_06  C24  C7   N8   C9     0.00   0.0  0
 CJN  CONST_07  C6   C7   N8   C9   180.00   0.0  0
 CJN  CONST_08  C5   N4   C24  C11  180.00   0.0  0
 CJN  CONST_09  C6   C7   C24  C11  180.00   0.0  0
 CJN  CONST_10  N8   C7   C24  C11    0.00   0.0  0
 CJN  CONST_11  N8   C9   N10  C11    0.00   0.0  0
 CJN  CONST_12  C6   C5   N4   C24    0.00   0.0  0
 CJN  CONST_13  C5   C6   C7   C24    0.00   0.0  0
 CJN  CONST_14  N10  C11  C24  N4   180.00   0.0  0
 CJN  CONST_15  C6   C7   C24  N4     0.00   0.0  0
 CJN  CONST_16  N8   C7   C24  N4   180.00   0.0  0
 CJN  CONST_17  N8   C7   C6   C5   180.00   0.0  0
 CJN  CONST_18  C11  C24  N4   C2     0.00   0.0  0
 CJN  CONST_19  C7   C24  N4   C2   180.00   0.0  0
 CJN  CONST_20  C6   C5   N4   C2   180.00   0.0  0
 CJN  CONST_21  N12  C11  C24  C7   180.00   0.0  0
 CJN  CONST_22  N12  C11  N10  C9   180.00   0.0  0
 CJN  CONST_23  N12  C11  C24  N4     0.00   0.0  0
 CJN  CONST_24  C24  C11  N12  C13  180.00   0.0  0
 CJN  CONST_25  N10  C11  N12  C13    0.00   0.0  0
 CJN  CONST_26  H22  C5   C6   C7   180.00   0.0  0
 CJN  CONST_27  H8   C9   N8   C7   180.00   0.0  0
 CJN  CONST_28  H23  C6   C7   C24  180.00   0.0  0
 CJN  CONST_29  H24  N12  C11  C24    0.00   0.0  0
 CJN  Var_01    C17  C16  C15  C13   56.63  30.0  1
 CJN  Var_02    C17  C19  C20  C13  -56.20  30.0  1
 CJN  Var_03    C24  N4   C2   C1    75.68  30.0  2
 CJN  Var_04    H1   C1   C2   N4    63.78  30.0  3
 CJN  Var_05    H5   C3   C2   N4   -68.72  30.0  3
 CJN  Var_06    H26  C23  N21  C17   68.49  30.0  3
 CJN  Var_07    H19  C22  N21  C17   52.69  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
 CJN  chir_01  C13  C15  C20  N12  positiv
 CJN  chir_02  C17  N21  C16  C19  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
 CJN  plan-1  C2   0.020
 CJN  plan-1  C7   0.020
 CJN  plan-1  C9   0.020
 CJN  plan-1  C11  0.020
 CJN  plan-1  C24  0.020
 CJN  plan-1  N4   0.020
 CJN  plan-1  C5   0.020
 CJN  plan-1  C6   0.020
 CJN  plan-1  N8   0.020
 CJN  plan-1  N10  0.020
 CJN  plan-1  H8   0.020
 CJN  plan-1  H22  0.020
 CJN  plan-1  H23  0.020
 CJN  plan-1  N12  0.020
 CJN  plan-2  C11  0.020
 CJN  plan-2  C13  0.020
 CJN  plan-2  H24  0.020
 CJN  plan-2  N12  0.020

