# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:10:28 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 5-[(1R,3S)-3-aminocyclohexyl]-6-bromo-3-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2cnn3c(N)c(Br)c(nc23)[C@@H]4CCC[C@H](N)C4
#
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
 22K  22K  5-[(1R,3S)-3-aminocyclohexyl]-6-bromo-3-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-7-amine  ligand  44  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_22K
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
 22K  C01   C   CR5   0  -0.209   2.3829  -1.3406   0.1580
 22K  C02   C   CR56  0   0.550   1.0193  -1.0588   0.1780
 22K  N03   N   N     0  -0.432   0.3927  -2.2830   0.2340
 22K  N04   N   N     0  -0.315   1.2444  -3.3142   0.2556
 22K  C05   C   CR15  0  -0.088   2.4365  -2.7422   0.2095
 22K  N06   N   N     0  -0.474   0.3339   0.0851   0.1509
 22K  C07   C   CR6   0   0.337  -0.9792   0.0263   0.1639
 22K  C08   C   CR6   0  -0.335  -1.6654  -1.2110   0.2048
 22K  C09   C   CR6   0   0.693  -0.9610  -2.4112   0.2487
 22K  BR10  BR  BR    0  -0.023  -3.5464  -1.3175   0.1846
 22K  N11   N   NH2   0  -0.835  -1.4496  -3.6430   0.2956
 22K  C12   C   CR5   0  -0.136   3.4697  -0.3872   0.0873
 22K  C13   C   CR15  0  -0.139   3.4086   1.0201   0.1605
 22K  N14   N   N     0  -0.280   4.6072   1.5635   0.0488
 22K  N15   N   NR5   0  -0.265   5.4457   0.5459  -0.0981
 22K  C16   C   CR15  0  -0.006   4.8179  -0.6428  -0.0803
 22K  C17   C   CH3   0  -0.506   6.8630   0.7826  -0.2252
 22K  C18   C   CH1   0  -0.343  -1.7105   1.3393   0.0699
 22K  C19   C   CH2   0  -0.410  -0.9727   2.4833   0.7613
 22K  C20   C   CH1   0  -0.063  -1.7730   3.7771   0.6561
 22K  C21   C   CH2   0  -0.427  -2.0069   4.1312  -0.8080
 22K  C22   C   CH2   0  -0.443  -2.7117   3.0000  -1.5466
 22K  C23   C   CH2   0  -0.411  -1.9579   1.6825  -1.4071
 22K  N24   N   NH2   0  -0.806  -1.0497   4.8530   1.3196
 22K  H05   H   HCR5  0   0.270   3.3192  -3.3648   0.2170
 22K  HN11  H   HNH2  0   0.429  -0.8218  -4.4293   0.3431
 22K  HN1A  H   HNH2  0   0.426  -2.4376  -3.8235   0.3357
 22K  H13   H   HCR5  0   0.261   2.5320   1.6372   0.2852
 22K  H16   H   HCR5  0   0.284   5.3597  -1.5682  -0.1943
 22K  H17   H   HCH3  0   0.258   7.2773   1.1598   0.7084
 22K  H17A  H   HCH3  0   0.258   7.3558  -0.1522  -0.4764
 22K  H17B  H   HCH3  0   0.261   7.0516   1.5038  -1.0174
 22K  H18   H   HCH1  0   0.244  -2.6849   1.2421   0.5579
 22K  H19   H   HCH2  0   0.230  -0.8044   2.2341   1.8138
 22K  H19A  H   HCH2  0   0.229   0.0112   2.6326   0.3084
 22K  H20   H   HCH1  0   0.185  -2.7611   3.5944   1.1129
 22K  H21   H   HCH2  0   0.228  -2.5965   5.0504  -0.8795
 22K  H21A  H   HCH2  0   0.210  -1.0388   4.3379  -1.2776
 22K  H22   H   HCH2  0   0.216  -3.7259   2.8798  -1.1515
 22K  H22A  H   HCH2  0   0.235  -2.8215   3.2514  -2.6038
 22K  H23   H   HCH2  0   0.224  -0.9915   1.7509  -1.9173
 22K  H23A  H   HCH2  0   0.237  -2.5146   0.8804  -1.8979
 22K  HN24  H   HNH2  0   0.340  -1.6077   5.6985   1.2901
 22K  HN2A  H   HNH2  0   0.340  -0.9493   4.6328   2.3035

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
 22K  C05  C01   aromatic  1.404  0.020  1.404
 22K  C01  C02   aromatic  1.393  0.020  1.393
 22K  C01  C12   single    1.447  0.020  1.447
 22K  N03  C02   aromatic  1.376  0.020  1.376
 22K  C02  N06   aromatic  1.334  0.020  1.334
 22K  N04  N03   aromatic  1.338  0.020  1.338
 22K  C09  N03   aromatic  1.360  0.020  1.360
 22K  N04  C05   aromatic  1.323  0.020  1.323
 22K  C05  H05   single    0.930  0.020  1.080
 22K  N06  C07   aromatic  1.314  0.020  1.314
 22K  C08  C07   aromatic  1.415  0.020  1.415
 22K  C07  C18   single    1.506  0.020  1.506
 22K  C09  C08   aromatic  1.392  0.020  1.392
 22K  C08  BR10  single    1.884  0.020  1.884
 22K  N11  C09   single    1.326  0.020  1.326
 22K  N11  HN11  single    0.860  0.020  1.020
 22K  N11  HN1A  single    0.860  0.020  1.020
 22K  C12  C13   aromatic  1.411  0.020  1.411
 22K  C12  C16   aromatic  1.382  0.020  1.382
 22K  C13  N14   aromatic  1.321  0.020  1.321
 22K  C13  H13   single    0.930  0.020  1.080
 22K  N14  N15   aromatic  1.327  0.020  1.327
 22K  C16  N15   aromatic  1.344  0.020  1.344
 22K  N15  C17   single    1.443  0.020  1.443
 22K  C16  H16   single    0.930  0.020  1.080
 22K  C17  H17   single    0.970  0.020  1.090
 22K  C17  H17A  single    0.970  0.020  1.090
 22K  C17  H17B  single    0.970  0.020  1.090
 22K  C23  C18   single    1.536  0.020  1.536
 22K  C18  C19   single    1.527  0.020  1.527
 22K  C18  H18   single    0.970  0.020  1.090
 22K  C19  C20   single    1.525  0.020  1.525
 22K  C19  H19   single    0.970  0.020  1.090
 22K  C19  H19A  single    0.970  0.020  1.090
 22K  C21  C20   single    1.524  0.020  1.524
 22K  C20  N24   single    1.456  0.020  1.456
 22K  C20  H20   single    0.970  0.020  1.090
 22K  C22  C21   single    1.524  0.020  1.524
 22K  C21  H21   single    0.970  0.020  1.090
 22K  C21  H21A  single    0.970  0.020  1.090
 22K  C23  C22   single    1.524  0.020  1.524
 22K  C22  H22   single    0.970  0.020  1.090
 22K  C22  H22A  single    0.970  0.020  1.090
 22K  C23  H23   single    0.970  0.020  1.090
 22K  C23  H23A  single    0.970  0.020  1.090
 22K  N24  HN24  single    0.890  0.020  1.040
 22K  N24  HN2A  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
 22K  C12   C01  C05   129.12  3.000
 22K  C12   C01  C02   127.06  3.000
 22K  C05   C01  C02   103.82  3.000
 22K  N06   C02  N03   121.98  3.000
 22K  N06   C02  C01   132.56  3.000
 22K  N03   C02  C01   105.45  3.000
 22K  C09   N03  N04   124.12  3.000
 22K  C09   N03  C02   122.51  3.000
 22K  N04   N03  C02   113.36  3.000
 22K  C05   N04  N03   103.88  3.000
 22K  H05   C05  N04   119.14  3.000
 22K  H05   C05  C01   127.37  3.000
 22K  N04   C05  C01   113.49  3.000
 22K  C07   N06  C02   118.34  3.000
 22K  C18   C07  C08   121.91  3.000
 22K  C18   C07  N06   116.45  3.000
 22K  C08   C07  N06   121.58  3.000
 22K  BR10  C08  C09   117.17  3.000
 22K  BR10  C08  C07   122.21  3.000
 22K  C09   C08  C07   120.61  3.000
 22K  N11   C09  C08   127.99  3.000
 22K  N11   C09  N03   117.05  3.000
 22K  C08   C09  N03   114.96  3.000
 22K  HN1A  N11  HN11  118.07  3.000
 22K  HN1A  N11  C09   122.03  3.000
 22K  HN11  N11  C09   119.81  3.000
 22K  C16   C12  C13   103.48  3.000
 22K  C16   C12  C01   128.05  3.000
 22K  C13   C12  C01   128.47  3.000
 22K  H13   C13  N14   120.77  3.000
 22K  H13   C13  C12   127.71  3.000
 22K  N14   C13  C12   111.52  3.000
 22K  N15   N14  C13   105.51  3.000
 22K  C17   N15  C16   127.23  3.000
 22K  C17   N15  N14   120.32  3.000
 22K  C16   N15  N14   112.43  3.000
 22K  H16   C16  N15   121.52  3.000
 22K  H16   C16  C12   131.41  3.000
 22K  N15   C16  C12   107.07  3.000
 22K  H17B  C17  H17A  108.88  3.000
 22K  H17B  C17  H17   109.20  3.000
 22K  H17A  C17  H17   108.90  3.000
 22K  H17B  C17  N15   110.07  3.000
 22K  H17A  C17  N15   108.96  3.000
 22K  H17   C17  N15   110.80  3.000
 22K  H18   C18  C23   107.77  3.000
 22K  H18   C18  C19   107.16  3.000
 22K  C23   C18  C19   110.23  3.000
 22K  H18   C18  C07   109.10  3.000
 22K  C19   C18  C07   112.98  3.000
 22K  C23   C18  C07   109.45  3.000
 22K  H19A  C19  H19   106.92  3.000
 22K  H19A  C19  C20   109.14  3.000
 22K  H19   C19  C20   109.89  3.000
 22K  H19A  C19  C18   110.46  3.000
 22K  H19   C19  C18   109.82  3.000
 22K  C20   C19  C18   110.54  3.000
 22K  H20   C20  N24   112.23  3.000
 22K  H20   C20  C21   107.37  3.000
 22K  N24   C20  C21   110.01  3.000
 22K  H20   C20  C19   107.50  3.000
 22K  N24   C20  C19   109.55  3.000
 22K  C21   C20  C19   110.11  3.000
 22K  H21A  C21  H21   106.84  3.000
 22K  H21A  C21  C22   109.94  3.000
 22K  H21   C21  C22   110.04  3.000
 22K  H21A  C21  C20   108.66  3.000
 22K  H21   C21  C20   109.91  3.000
 22K  C22   C21  C20   111.35  3.000
 22K  H22A  C22  H22   106.35  3.000
 22K  H22A  C22  C23   109.71  3.000
 22K  H22   C22  C23   109.27  3.000
 22K  H22A  C22  C21   110.17  3.000
 22K  H22   C22  C21   109.58  3.000
 22K  C23   C22  C21   111.62  3.000
 22K  H23A  C23  H23   106.63  3.000
 22K  H23A  C23  C22   109.96  3.000
 22K  H23   C23  C22   109.86  3.000
 22K  H23A  C23  C18   110.48  3.000
 22K  H23   C23  C18   108.65  3.000
 22K  C22   C23  C18   111.14  3.000
 22K  HN2A  N24  HN24  105.32  3.000
 22K  HN2A  N24  C20   109.34  3.000
 22K  HN24  N24  C20   109.24  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
 22K  CONST_01  N03   N04  C05  C01     0.00   0.0  0
 22K  CONST_02  N04   N03  C02  C01     0.00   0.0  0
 22K  CONST_03  C09   N03  C02  C01   180.00   0.0  0
 22K  CONST_04  C07   N06  C02  C01   180.00   0.0  0
 22K  CONST_05  N14   C13  C12  C01   180.00   0.0  0
 22K  CONST_06  N15   C16  C12  C01   180.00   0.0  0
 22K  CONST_07  N04   C05  C01  C02     0.00   0.0  0
 22K  CONST_08  C13   C12  C01  C02     0.00   0.0  0
 22K  CONST_09  C16   C12  C01  C02   180.00   0.0  0
 22K  CONST_10  C05   N04  N03  C02     0.00   0.0  0
 22K  CONST_11  C08   C09  N03  C02     0.00   0.0  0
 22K  CONST_12  C08   C07  N06  C02     0.00   0.0  0
 22K  CONST_13  C05   C01  C02  N03     0.00   0.0  0
 22K  CONST_14  C12   C01  C02  N03   180.00   0.0  0
 22K  CONST_15  C07   N06  C02  N03     0.00   0.0  0
 22K  CONST_16  C07   C08  C09  N03     0.00   0.0  0
 22K  CONST_17  N06   C02  N03  N04   180.00   0.0  0
 22K  CONST_18  C08   C09  N03  N04   180.00   0.0  0
 22K  CONST_19  C12   C01  C05  N04   180.00   0.0  0
 22K  CONST_20  N06   C02  C01  C05   180.00   0.0  0
 22K  CONST_21  C13   C12  C01  C05   180.00   0.0  0
 22K  CONST_22  C16   C12  C01  C05     0.00   0.0  0
 22K  CONST_23  C09   N03  N04  C05   180.00   0.0  0
 22K  CONST_24  C12   C01  C02  N06     0.00   0.0  0
 22K  CONST_25  C09   N03  C02  N06     0.00   0.0  0
 22K  CONST_26  C09   C08  C07  N06     0.00   0.0  0
 22K  CONST_27  N15   N14  C13  C12     0.00   0.0  0
 22K  CONST_28  N14   N15  C16  C12     0.00   0.0  0
 22K  CONST_29  N15   C16  C12  C13     0.00   0.0  0
 22K  CONST_30  C16   N15  N14  C13     0.00   0.0  0
 22K  CONST_31  C16   C12  C13  N14     0.00   0.0  0
 22K  CONST_32  C18   C07  N06  C02   180.00   0.0  0
 22K  CONST_33  C18   C07  C08  C09   180.00   0.0  0
 22K  CONST_34  N11   C09  N03  C02   180.00   0.0  0
 22K  CONST_35  BR10  C08  C09  N03   180.00   0.0  0
 22K  CONST_36  N11   C09  N03  N04     0.00   0.0  0
 22K  CONST_37  BR10  C08  C07  N06   180.00   0.0  0
 22K  CONST_38  N11   C09  C08  C07   180.00   0.0  0
 22K  CONST_39  C18   C07  C08  BR10    0.00   0.0  0
 22K  CONST_40  C17   N15  C16  C12   180.00   0.0  0
 22K  CONST_41  C17   N15  N14  C13   180.00   0.0  0
 22K  CONST_42  H13   C13  C12  C01     0.00   0.0  0
 22K  CONST_43  H16   C16  C12  C01     0.00   0.0  0
 22K  CONST_44  H05   C05  C01  C02   180.00   0.0  0
 22K  CONST_45  HN11  N11  C09  N03     0.00   0.0  0
 22K  CONST_46  HN1A  N11  C09  N03   180.00   0.0  0
 22K  Var_01    C21   C22  C23  C18    54.17  30.0  1
 22K  Var_02    C23   C22  C21  C20   -54.83  30.0  1
 22K  Var_03    H17   C17  N15  N14    68.22  30.0  2

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
 22K  chir_01  C18  C07  C23  C19  positiv
 22K  chir_02  C20  N24  C21  C19  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
 22K  plan-1  C01   0.020
 22K  plan-1  C12   0.020
 22K  plan-1  C13   0.020
 22K  plan-1  N14   0.020
 22K  plan-1  N15   0.020
 22K  plan-1  C16   0.020
 22K  plan-1  C17   0.020
 22K  plan-1  H13   0.020
 22K  plan-1  H16   0.020
 22K  plan-2  C01   0.020
 22K  plan-2  C02   0.020
 22K  plan-2  N03   0.020
 22K  plan-2  N04   0.020
 22K  plan-2  C05   0.020
 22K  plan-2  N06   0.020
 22K  plan-2  C07   0.020
 22K  plan-2  C08   0.020
 22K  plan-2  C09   0.020
 22K  plan-2  BR10  0.020
 22K  plan-2  N11   0.020
 22K  plan-2  C12   0.020
 22K  plan-2  C18   0.020
 22K  plan-2  H05   0.020
 22K  plan-3  C09   0.020
 22K  plan-3  N11   0.020
 22K  plan-3  HN11  0.020
 22K  plan-3  HN1A  0.020

