# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 19 02:21:10 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N-[5-({3-cyano-7-[(1-methyl-1H-imidazol-4-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl}amino)-2-methylphenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(Nc2cc(Nc3ccc(C)c(NC(C)=O)c3)nc4n2ncc4C#N)c1
#
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
 0Y4  0Y4  N-[5-({3-cyano-7-[(1-methyl-1H-imidazol-4-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl}amino)-2-methylphenyl]acetamide  ligand  49  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0Y4
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
 0Y4  C1   C  CH3   0  -0.753   6.3623   1.8086   0.6357
 0Y4  C2   C  CR6   0   0.042   5.0263   1.1531   0.4431
 0Y4  C3   C  CR16  0  -0.293   3.8660   1.9077   0.3601
 0Y4  C7   C  CR6   0   0.329   4.8984  -0.2399   0.3312
 0Y4  C9   C  C     0   0.502   6.3570  -2.1665  -0.2235
 0Y4  C11  C  CH3   0  -0.787   7.7537  -2.6750   0.0275
 0Y4  C13  C  CR6   0   0.586   0.0300  -0.3033  -0.2717
 0Y4  C14  C  CR16  0  -0.569  -0.9874  -1.2884  -0.3374
 0Y4  C15  C  CR6   0   0.684  -2.2955  -0.9118  -0.5055
 0Y4  N18  N  N     0  -0.523  -0.2280   0.9915  -0.3449
 0Y4  C19  C  CR5   0  -0.343  -2.1004   2.5796  -0.6885
 0Y4  C20  C  CR15  0   0.033  -3.4665   2.2955  -0.8964
 0Y4  C22  C  CSP   0  -0.007  -1.4482   3.8204  -0.6767
 0Y4  N23  N  NS    0  -0.271  -0.9066   4.8409  -0.6669
 0Y4  N29  N  N     0  -0.451  -5.7217  -1.8234  -0.7729
 0Y4  C30  C  CH3   0  -0.517  -7.0678  -0.6984   2.3676
 0Y4  C4   C  CR16  0  -0.313   2.6106   1.3495   0.1648
 0Y4  C5   C  CR6   0   0.369   2.4979  -0.0350   0.0597
 0Y4  C6   C  CR16  0  -0.420   3.6512  -0.8198   0.1490
 0Y4  N8   N  NH1   0  -0.736   6.0598  -1.0189   0.4438
 0Y4  O10  O  O     0  -0.471   5.5851  -2.7218  -0.9838
 0Y4  N12  N  NH1   0  -0.798   1.3027  -0.7357  -0.1095
 0Y4  N16  N  N     0  -0.456  -2.5292   0.4322  -0.6091
 0Y4  C17  C  CR56  0   0.690  -1.4953   1.3312  -0.5172
 0Y4  N21  N  N     0  -0.273  -3.7233   1.0140  -0.8560
 0Y4  N24  N  NH1   0  -0.750  -3.3215  -1.7848  -0.6188
 0Y4  C25  C  CR5   0   0.286  -4.5952  -1.5807  -0.0606
 0Y4  C26  C  CR15  0  -0.087  -4.8964  -1.1555   1.2028
 0Y4  N27  N  NR5   0  -0.396  -6.2583  -1.1212   1.2464
 0Y4  C28  C  CR15  0   0.089  -6.7046  -1.5381   0.0448
 0Y4  H1   H  HCH3  0   0.246   6.8421   1.5103   1.5719
 0Y4  H2   H  HCH3  0   0.251   7.0552   1.5687  -0.1733
 0Y4  H3   H  HCH3  0   0.261   6.2549   2.8916   0.6655
 0Y4  H4   H  HCR6  0   0.252   3.9413   2.9856   0.4406
 0Y4  H5   H  HCH3  0   0.268   7.7811  -3.7565  -0.0840
 0Y4  H6   H  HCH3  0   0.277   8.4298  -2.2462  -0.7148
 0Y4  H7   H  HCH3  0   0.257   8.1325  -2.4112   1.0139
 0Y4  H8   H  HCR6  0   0.304  -0.7534  -2.3373  -0.2211
 0Y4  H9   H  HCR5  0   0.293  -4.2590   3.0044  -1.0816
 0Y4  H10  H  HCH3  0   0.262  -6.9495   0.3684   2.5467
 0Y4  H11  H  HCH3  0   0.264  -8.1118  -0.9053   2.1498
 0Y4  H12  H  HCH3  0   0.263  -6.7833  -1.2435   3.2648
 0Y4  H13  H  HCR6  0   0.288   1.7455   1.9867   0.0979
 0Y4  H14  H  HCR6  0   0.279   3.5600  -1.8952   0.0924
 0Y4  H15  H  HNH1  0   0.415   6.8017  -0.6242   1.0002
 0Y4  H16  H  HNH1  0   0.423   1.4062  -1.7389  -0.0995
 0Y4  H17  H  HNH1  0   0.419  -3.0277  -2.7483  -0.6991
 0Y4  H18  H  HCR5  0   0.298  -4.2774  -0.8730   2.0385
 0Y4  H19  H  HCR5  0   0.283  -7.7579  -1.6198  -0.1779

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
 0Y4  N29  C28  aromatic  1.310  0.020  1.310
 0Y4  N29  C25  aromatic  1.355  0.020  1.355
 0Y4  C28  N27  aromatic  1.348  0.020  1.348
 0Y4  C25  N24  single    1.406  0.020  1.406
 0Y4  C25  C26  aromatic  1.367  0.020  1.367
 0Y4  N27  C30  single    1.446  0.020  1.446
 0Y4  N27  C26  aromatic  1.363  0.020  1.363
 0Y4  N24  C15  single    1.352  0.020  1.352
 0Y4  N21  C20  aromatic  1.308  0.020  1.308
 0Y4  N21  N16  aromatic  1.351  0.020  1.351
 0Y4  C20  C19  aromatic  1.411  0.020  1.411
 0Y4  N16  C15  aromatic  1.368  0.020  1.368
 0Y4  N16  C17  aromatic  1.373  0.020  1.373
 0Y4  C15  C14  aromatic  1.372  0.020  1.372
 0Y4  C19  C17  aromatic  1.398  0.020  1.398
 0Y4  C19  C22  single    1.402  0.020  1.402
 0Y4  C17  N18  aromatic  1.323  0.020  1.323
 0Y4  C14  C13  aromatic  1.418  0.020  1.418
 0Y4  C22  N23  triple    1.155  0.020  1.155
 0Y4  N18  C13  aromatic  1.322  0.020  1.322
 0Y4  C13  N12  single    1.354  0.020  1.354
 0Y4  N12  C5   single    1.396  0.020  1.396
 0Y4  C5   C6   aromatic  1.398  0.020  1.398
 0Y4  C5   C4   aromatic  1.393  0.020  1.393
 0Y4  C6   C7   aromatic  1.387  0.020  1.387
 0Y4  C11  C9   single    1.507  0.020  1.507
 0Y4  C4   C3   aromatic  1.388  0.020  1.388
 0Y4  C9   O10  double    1.217  0.020  1.217
 0Y4  C9   N8   single    1.360  0.020  1.360
 0Y4  C7   N8   single    1.403  0.020  1.403
 0Y4  C7   C2   aromatic  1.403  0.020  1.403
 0Y4  C3   C2   aromatic  1.387  0.020  1.387
 0Y4  C2   C1   single    1.501  0.020  1.501
 0Y4  C1   H1   single    0.970  0.020  1.090
 0Y4  C1   H2   single    0.970  0.020  1.090
 0Y4  C1   H3   single    0.970  0.020  1.090
 0Y4  C3   H4   single    0.930  0.020  1.080
 0Y4  C11  H5   single    0.970  0.020  1.090
 0Y4  C11  H6   single    0.970  0.020  1.090
 0Y4  C11  H7   single    0.970  0.020  1.090
 0Y4  C14  H8   single    0.930  0.020  1.080
 0Y4  C20  H9   single    0.930  0.020  1.080
 0Y4  C30  H10  single    0.970  0.020  1.090
 0Y4  C30  H11  single    0.970  0.020  1.090
 0Y4  C30  H12  single    0.970  0.020  1.090
 0Y4  C4   H13  single    0.930  0.020  1.080
 0Y4  C6   H14  single    0.930  0.020  1.080
 0Y4  N8   H15  single    0.860  0.020  1.020
 0Y4  N12  H16  single    0.860  0.020  1.020
 0Y4  N24  H17  single    0.890  0.020  1.040
 0Y4  C26  H18  single    0.930  0.020  1.080
 0Y4  C28  H19  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
 0Y4  H3   C1   H2   107.54  3.000
 0Y4  H3   C1   H1   106.93  3.000
 0Y4  H2   C1   H1   107.22  3.000
 0Y4  H3   C1   C2   110.51  3.000
 0Y4  H2   C1   C2   111.96  3.000
 0Y4  H1   C1   C2   112.42  3.000
 0Y4  C7   C2   C3   117.33  3.000
 0Y4  C3   C2   C1   120.99  3.000
 0Y4  C7   C2   C1   121.67  3.000
 0Y4  H4   C3   C4   118.26  3.000
 0Y4  H4   C3   C2   118.61  3.000
 0Y4  C4   C3   C2   123.13  3.000
 0Y4  N8   C7   C6   121.51  3.000
 0Y4  N8   C7   C2   117.99  3.000
 0Y4  C6   C7   C2   120.48  3.000
 0Y4  O10  C9   N8   123.54  3.000
 0Y4  N8   C9   C11  113.91  3.000
 0Y4  O10  C9   C11  122.52  3.000
 0Y4  H7   C11  H6   107.77  3.000
 0Y4  H7   C11  H5   108.97  3.000
 0Y4  H6   C11  H5   107.77  3.000
 0Y4  H7   C11  C9   113.04  3.000
 0Y4  H6   C11  C9   109.15  3.000
 0Y4  H5   C11  C9   109.98  3.000
 0Y4  N12  C13  N18  120.18  3.000
 0Y4  N12  C13  C14  117.27  3.000
 0Y4  N18  C13  C14  122.54  3.000
 0Y4  H8   C14  C15  119.09  3.000
 0Y4  H8   C14  C13  120.92  3.000
 0Y4  C15  C14  C13  119.95  3.000
 0Y4  N24  C15  N16  119.89  3.000
 0Y4  N16  C15  C14  116.23  3.000
 0Y4  N24  C15  C14  123.83  3.000
 0Y4  C17  N18  C13  116.45  3.000
 0Y4  C17  C19  C22  126.02  3.000
 0Y4  C22  C19  C20  129.06  3.000
 0Y4  C17  C19  C20  104.91  3.000
 0Y4  H9   C20  N21  120.32  3.000
 0Y4  H9   C20  C19  127.16  3.000
 0Y4  N21  C20  C19  112.52  3.000
 0Y4  N23  C22  C19  180.00  3.000
 0Y4  C28  N29  C25  104.87  3.000
 0Y4  H12  C30  H11  108.74  3.000
 0Y4  H12  C30  H10  109.10  3.000
 0Y4  H11  C30  H10  108.91  3.000
 0Y4  H12  C30  N27  110.28  3.000
 0Y4  H11  C30  N27  109.07  3.000
 0Y4  H10  C30  N27  110.70  3.000
 0Y4  H13  C4   C5   121.23  3.000
 0Y4  H13  C4   C3   119.84  3.000
 0Y4  C5   C4   C3   118.92  3.000
 0Y4  N12  C5   C6   115.62  3.000
 0Y4  C6   C5   C4   119.10  3.000
 0Y4  N12  C5   C4   125.27  3.000
 0Y4  H14  C6   C5   119.06  3.000
 0Y4  H14  C6   C7   119.91  3.000
 0Y4  C5   C6   C7   121.02  3.000
 0Y4  H15  N8   C9   116.13  3.000
 0Y4  H15  N8   C7   115.86  3.000
 0Y4  C9   N8   C7   127.58  3.000
 0Y4  H16  N12  C5   114.22  3.000
 0Y4  H16  N12  C13  114.54  3.000
 0Y4  C5   N12  C13  131.23  3.000
 0Y4  N21  N16  C17  113.32  3.000
 0Y4  C17  N16  C15  120.63  3.000
 0Y4  N21  N16  C15  126.00  3.000
 0Y4  N16  C17  C19  104.51  3.000
 0Y4  C19  C17  N18  131.28  3.000
 0Y4  N16  C17  N18  124.17  3.000
 0Y4  N16  N21  C20  104.72  3.000
 0Y4  H17  N24  C25  115.69  3.000
 0Y4  H17  N24  C15  113.69  3.000
 0Y4  C25  N24  C15  124.10  3.000
 0Y4  C26  C25  N24  127.74  3.000
 0Y4  C26  C25  N29  111.01  3.000
 0Y4  N24  C25  N29  121.24  3.000
 0Y4  H18  C26  N27  122.85  3.000
 0Y4  H18  C26  C25  132.21  3.000
 0Y4  N27  C26  C25  104.93  3.000
 0Y4  C28  N27  C26  107.13  3.000
 0Y4  C26  N27  C30  126.26  3.000
 0Y4  C28  N27  C30  126.60  3.000
 0Y4  H19  C28  N27  122.03  3.000
 0Y4  H19  C28  N29  125.92  3.000
 0Y4  N27  C28  N29  112.05  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
 0Y4  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 0Y4  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 0Y4  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 0Y4  CONST_04  C6   C7   C2   C3      0.00   0.0  0
 0Y4  CONST_05  C4   C5   C6   C7      0.00   0.0  0
 0Y4  CONST_06  C4   C3   C2   C7      0.00   0.0  0
 0Y4  CONST_07  N16  C15  C14  C13     0.00   0.0  0
 0Y4  CONST_08  N16  C17  N18  C13     0.00   0.0  0
 0Y4  CONST_09  C19  C17  N18  C13   180.00   0.0  0
 0Y4  CONST_10  N21  N16  C15  C14   180.00   0.0  0
 0Y4  CONST_11  C17  N16  C15  C14     0.00   0.0  0
 0Y4  CONST_12  C17  N18  C13  C14     0.00   0.0  0
 0Y4  CONST_13  C20  N21  N16  C15   180.00   0.0  0
 0Y4  CONST_14  C19  C17  N16  C15   180.00   0.0  0
 0Y4  CONST_15  N18  C17  N16  C15     0.00   0.0  0
 0Y4  CONST_16  N18  C13  C14  C15     0.00   0.0  0
 0Y4  CONST_17  N21  N16  C17  N18   180.00   0.0  0
 0Y4  CONST_18  C20  C19  C17  N18   180.00   0.0  0
 0Y4  CONST_19  N16  N21  C20  C19     0.00   0.0  0
 0Y4  CONST_20  N21  N16  C17  C19     0.00   0.0  0
 0Y4  CONST_21  C17  N16  N21  C20     0.00   0.0  0
 0Y4  CONST_22  N16  C17  C19  C20     0.00   0.0  0
 0Y4  CONST_23  C26  N27  C28  N29     0.00   0.0  0
 0Y4  CONST_24  N27  C26  C25  N29     0.00   0.0  0
 0Y4  CONST_25  N21  C20  C19  C17     0.00   0.0  0
 0Y4  CONST_26  N27  C28  N29  C25     0.00   0.0  0
 0Y4  CONST_27  C28  N27  C26  C25     0.00   0.0  0
 0Y4  CONST_28  C28  N29  C25  C26     0.00   0.0  0
 0Y4  CONST_29  C6   C7   C2   C1    180.00   0.0  0
 0Y4  CONST_30  C4   C3   C2   C1    180.00   0.0  0
 0Y4  CONST_31  N12  C5   C4   C3    180.00   0.0  0
 0Y4  CONST_32  N8   C7   C2   C3    180.00   0.0  0
 0Y4  CONST_33  N12  C5   C6   C7    180.00   0.0  0
 0Y4  CONST_34  N24  C15  C14  C13   180.00   0.0  0
 0Y4  CONST_35  N12  C13  C14  C15   180.00   0.0  0
 0Y4  CONST_36  C22  C19  C17  N18     0.00   0.0  0
 0Y4  CONST_37  N21  C20  C19  C22   180.00   0.0  0
 0Y4  CONST_38  N16  C17  C19  C22   180.00   0.0  0
 0Y4  CONST_39  C30  N27  C28  N29   180.00   0.0  0
 0Y4  CONST_40  C25  C26  N27  C30   180.00   0.0  0
 0Y4  CONST_41  N8   C7   C6   C5    180.00   0.0  0
 0Y4  CONST_42  C17  N18  C13  N12   180.00   0.0  0
 0Y4  CONST_43  N24  C15  N16  C17   180.00   0.0  0
 0Y4  CONST_44  N24  C15  N16  N21     0.00   0.0  0
 0Y4  CONST_45  C28  N29  C25  N24   180.00   0.0  0
 0Y4  CONST_46  N27  C26  C25  N24   180.00   0.0  0
 0Y4  CONST_47  H14  C6   C7   C2    180.00   0.0  0
 0Y4  CONST_48  H13  C4   C3   C2    180.00   0.0  0
 0Y4  CONST_49  H4   C3   C2   C7    180.00   0.0  0
 0Y4  CONST_50  H8   C14  C13  N18   180.00   0.0  0
 0Y4  CONST_51  H18  C26  C25  N29   180.00   0.0  0
 0Y4  CONST_52  H9   C20  N21  N16   180.00   0.0  0
 0Y4  CONST_53  H19  C28  N29  C25   180.00   0.0  0
 0Y4  CONST_57  C11  C9   N8   C7    180.00   0.0  0
 0Y4  CONST_58  O10  C9   N8   C7      0.00   0.0  0
 0Y4  Var_01    C6   C5   N12  C13  -177.67  30.0  2
 0Y4  Var_02    C25  N24  C15  C14   142.17  30.0  2
 0Y4  Var_03    C5   N12  C13  C14  -176.20  30.0  2
 0Y4  Var_04    N29  C25  N24  C15   134.93  30.0  1
 0Y4  Var_05    H1   C1   C2   C3    117.88  30.0  2
 0Y4  Var_06    H10  C30  N27  C26    67.58  30.0  2
 0Y4  Var_07    H5   C11  C9   N8    151.66  30.0  3

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
 0Y4  plan-1  N29  0.020
 0Y4  plan-1  C30  0.020
 0Y4  plan-1  N24  0.020
 0Y4  plan-1  C25  0.020
 0Y4  plan-1  C26  0.020
 0Y4  plan-1  N27  0.020
 0Y4  plan-1  C28  0.020
 0Y4  plan-1  H18  0.020
 0Y4  plan-1  H19  0.020
 0Y4  plan-2  C1   0.020
 0Y4  plan-2  C2   0.020
 0Y4  plan-2  C3   0.020
 0Y4  plan-2  C7   0.020
 0Y4  plan-2  C4   0.020
 0Y4  plan-2  C5   0.020
 0Y4  plan-2  C6   0.020
 0Y4  plan-2  N8   0.020
 0Y4  plan-2  N12  0.020
 0Y4  plan-2  H4   0.020
 0Y4  plan-2  H13  0.020
 0Y4  plan-2  H14  0.020
 0Y4  plan-3  C13  0.020
 0Y4  plan-3  C14  0.020
 0Y4  plan-3  C15  0.020
 0Y4  plan-3  N18  0.020
 0Y4  plan-3  C19  0.020
 0Y4  plan-3  C20  0.020
 0Y4  plan-3  C22  0.020
 0Y4  plan-3  N23  0.020
 0Y4  plan-3  N12  0.020
 0Y4  plan-3  N16  0.020
 0Y4  plan-3  C17  0.020
 0Y4  plan-3  N21  0.020
 0Y4  plan-3  N24  0.020
 0Y4  plan-3  H8   0.020
 0Y4  plan-3  H9   0.020
 0Y4  plan-4  C7   0.020
 0Y4  plan-4  C9   0.020
 0Y4  plan-4  C11  0.020
 0Y4  plan-4  N8   0.020
 0Y4  plan-4  O10  0.020
 0Y4  plan-4  H15  0.020

