# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:48:27 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-[5-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(cc1)c2cnn3ccc(NCc4cccnc4)nc23
#
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
 H72  H72  4-[5-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-3-yl]benzamide  ligand  42  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H72
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
 H72  C4   C  CR16  0  -0.337   4.0025   0.6628   0.1698
 H72  C14  C  CR16  0  -0.319  -6.0398  -2.1291  -0.7949
 H72  C5   C  CR6   0   0.122   2.6047   0.6558   0.0682
 H72  C6   C  CR5   0  -0.221   1.8607   1.9001  -0.0262
 H72  C11  C  CH2   0  -0.327  -2.6557  -0.5474  -0.1895
 H72  C7   C  CR15  0  -0.074   2.3713   3.2160  -0.0604
 H72  C8   C  CR16  0   0.080  -0.9497   3.9825  -0.2603
 H72  C9   C  CR16  0  -0.451  -2.0111   3.1500  -0.2728
 H72  C10  C  CR6   0   0.559  -1.7692   1.7355  -0.1966
 H72  C12  C  CR6   0  -0.039  -3.9898  -1.2014   0.0196
 H72  C13  C  CR16  0  -0.170  -4.8038  -1.5551  -1.0486
 H72  N1   N  NH2   0  -0.818   4.3349  -4.1322  -0.0366
 H72  N2   N  N     0  -0.301   1.4413   4.1415  -0.1490
 H72  C3   C  CR16  0  -0.251   4.7216  -0.5124   0.2633
 H72  N3   N  N     0  -0.390   0.2915   3.4470  -0.1740
 H72  O1   O  O     0  -0.487   6.0517  -2.9409   0.8003
 H72  C2   C  CR6   0  -0.066   4.0805  -1.7502   0.2426
 H72  N4   N  NH1   0  -0.668  -2.8121   0.8933  -0.1911
 H72  C15  C  CR16  0  -0.066  -6.4164  -2.3276   0.5246
 H72  N5   N  N     0  -0.401  -5.6494  -1.9963   1.5578
 H72  C16  C  CR16  0  -0.078  -4.4698  -1.4472   1.3022
 H72  N6   N  N     0  -0.527  -0.5530   1.2346  -0.1216
 H72  C17  C  CR56  0   0.605   0.4771   2.0867  -0.1044
 H72  C18  C  CR16  0  -0.357   1.9651  -0.5902   0.0670
 H72  C19  C  CR16  0  -0.255   2.6903  -1.7660   0.1496
 H72  H1   H  HCR6  0   0.246   4.5448   1.5993   0.1818
 H72  H3   H  HCH2  0   0.265  -1.9651  -0.8325   0.6064
 H72  H4   H  HCH2  0   0.258  -2.2120  -0.8892  -1.1299
 H72  H5   H  HCR5  0   0.270   3.4072   3.5201  -0.0236
 H72  H6   H  HCR6  0   0.325  -1.0180   5.0591  -0.3131
 H72  H7   H  HCR6  0   0.298  -3.0140   3.5457  -0.3383
 H72  H8   H  HCR6  0   0.274  -4.4735  -1.3869  -2.0665
 H72  H9   H  HNH2  0   0.412   3.4577  -4.1610  -0.5254
 H72  H10  H  HNH2  0   0.404   4.8564  -4.9921   0.0125
 H72  H11  H  HCR6  0   0.258   5.7994  -0.4663   0.3449
 H72  H12  H  HNH1  0   0.410  -3.7311   1.2714  -0.3537
 H72  H13  H  HCR6  0   0.267  -7.3757  -2.7759   0.7575
 H72  H14  H  HCR6  0   0.263  -3.8599  -1.1889   2.1629
 H72  H15  H  HCR6  0   0.274   0.8871  -0.6416   0.0062
 H72  H16  H  HCR6  0   0.252   2.1393  -2.6983   0.1635
 H72  C1   C  C     0   0.486   4.9093  -2.9848   0.3595
 H72  H2   H  HCR6  0   0.274  -6.6991  -2.4196  -1.6013

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
 H72  C11  C12  single    1.500  0.020  1.500
 H72  C11  N4   single    1.449  0.020  1.449
 H72  C16  C12  aromatic  1.391  0.020  1.391
 H72  C16  N5   aromatic  1.326  0.020  1.326
 H72  O1   C1   double    1.225  0.020  1.225
 H72  C1   N1   single    1.343  0.020  1.343
 H72  C1   C2   single    1.492  0.020  1.492
 H72  C3   C2   aromatic  1.394  0.020  1.394
 H72  C3   C4   aromatic  1.381  0.020  1.381
 H72  C12  C13  aromatic  1.389  0.020  1.389
 H72  N4   C10  single    1.341  0.020  1.341
 H72  C2   C19  aromatic  1.393  0.020  1.393
 H72  N5   C15  aromatic  1.329  0.020  1.329
 H72  C4   C5   aromatic  1.402  0.020  1.402
 H72  N6   C10  aromatic  1.318  0.020  1.318
 H72  N6   C17  aromatic  1.337  0.020  1.337
 H72  C19  C18  aromatic  1.384  0.020  1.384
 H72  C10  C9   aromatic  1.437  0.020  1.437
 H72  C5   C18  aromatic  1.401  0.020  1.401
 H72  C5   C6   single    1.453  0.020  1.453
 H72  C17  C6   aromatic  1.398  0.020  1.398
 H72  C17  N3   aromatic  1.375  0.020  1.375
 H72  C6   C7   aromatic  1.412  0.020  1.412
 H72  C9   C8   aromatic  1.349  0.020  1.349
 H72  C13  C14  aromatic  1.386  0.020  1.386
 H72  C15  C14  aromatic  1.387  0.020  1.387
 H72  N3   C8   aromatic  1.355  0.020  1.355
 H72  N3   N2   aromatic  1.344  0.020  1.344
 H72  C7   N2   aromatic  1.315  0.020  1.315
 H72  C4   H1   single    0.930  0.020  1.080
 H72  C14  H2   single    0.930  0.020  1.080
 H72  C11  H3   single    0.970  0.020  1.090
 H72  C11  H4   single    0.970  0.020  1.090
 H72  C7   H5   single    0.930  0.020  1.080
 H72  C8   H6   single    0.930  0.020  1.080
 H72  C9   H7   single    0.930  0.020  1.080
 H72  C13  H8   single    0.930  0.020  1.080
 H72  N1   H9   single    0.860  0.020  1.020
 H72  N1   H10  single    0.860  0.020  1.020
 H72  C3   H11  single    0.930  0.020  1.080
 H72  N4   H12  single    0.860  0.020  1.020
 H72  C15  H13  single    0.930  0.020  1.080
 H72  C16  H14  single    0.930  0.020  1.080
 H72  C18  H15  single    0.930  0.020  1.080
 H72  C19  H16  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
 H72  H1   C4   C3   118.34  3.000
 H72  H1   C4   C5   120.32  3.000
 H72  C3   C4   C5   121.33  3.000
 H72  H2   C14  C15  120.38  3.000
 H72  H2   C14  C13  121.23  3.000
 H72  C15  C14  C13  118.39  3.000
 H72  C18  C5   C6   121.88  3.000
 H72  C6   C5   C4   120.74  3.000
 H72  C18  C5   C4   117.38  3.000
 H72  C17  C6   C7   103.42  3.000
 H72  C7   C6   C5   127.92  3.000
 H72  C17  C6   C5   128.66  3.000
 H72  H4   C11  H3   106.76  3.000
 H72  H4   C11  N4   110.69  3.000
 H72  H3   C11  N4   109.19  3.000
 H72  H4   C11  C12  110.13  3.000
 H72  H3   C11  C12  110.31  3.000
 H72  N4   C11  C12  109.73  3.000
 H72  H5   C7   N2   118.84  3.000
 H72  H5   C7   C6   127.47  3.000
 H72  N2   C7   C6   113.69  3.000
 H72  H6   C8   N3   117.07  3.000
 H72  H6   C8   C9   124.40  3.000
 H72  N3   C8   C9   118.53  3.000
 H72  H7   C9   C10  121.34  3.000
 H72  H7   C9   C8   120.33  3.000
 H72  C10  C9   C8   118.33  3.000
 H72  N6   C10  N4   118.62  3.000
 H72  N6   C10  C9   122.18  3.000
 H72  N4   C10  C9   119.19  3.000
 H72  C16  C12  C13  117.50  3.000
 H72  C13  C12  C11  121.66  3.000
 H72  C16  C12  C11  120.82  3.000
 H72  H8   C13  C12  120.29  3.000
 H72  H8   C13  C14  120.54  3.000
 H72  C12  C13  C14  119.17  3.000
 H72  H10  N1   H9   116.84  3.000
 H72  H10  N1   C1   119.59  3.000
 H72  H9   N1   C1   122.79  3.000
 H72  N3   N2   C7   104.04  3.000
 H72  H11  C3   C2   119.81  3.000
 H72  H11  C3   C4   119.18  3.000
 H72  C2   C3   C4   121.00  3.000
 H72  C17  N3   N2   113.27  3.000
 H72  N2   N3   C8   125.52  3.000
 H72  C17  N3   C8   121.21  3.000
 H72  C19  C2   C1   123.38  3.000
 H72  C19  C2   C3   118.03  3.000
 H72  C1   C2   C3   118.57  3.000
 H72  H12  N4   C10  118.26  3.000
 H72  H12  N4   C11  118.16  3.000
 H72  C10  N4   C11  122.73  3.000
 H72  H13  C15  N5   116.54  3.000
 H72  H13  C15  C14  120.26  3.000
 H72  N5   C15  C14  123.20  3.000
 H72  C16  N5   C15  117.83  3.000
 H72  H14  C16  N5   116.44  3.000
 H72  H14  C16  C12  119.66  3.000
 H72  N5   C16  C12  123.90  3.000
 H72  C17  N6   C10  118.01  3.000
 H72  N6   C17  N3   121.74  3.000
 H72  N3   C17  C6   105.57  3.000
 H72  N6   C17  C6   132.69  3.000
 H72  H15  C18  C19  119.05  3.000
 H72  H15  C18  C5   119.85  3.000
 H72  C19  C18  C5   121.10  3.000
 H72  H16  C19  C18  117.74  3.000
 H72  H16  C19  C2   121.10  3.000
 H72  C18  C19  C2   121.14  3.000
 H72  C2   C1   O1   121.11  3.000
 H72  C2   C1   N1   116.51  3.000
 H72  O1   C1   N1   122.38  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
 H72  CONST_01  C19  C2   C3   C4      0.00   0.0  0
 H72  CONST_02  C19  C18  C5   C4      0.00   0.0  0
 H72  CONST_03  C17  C6   C5   C4    180.00   0.0  0
 H72  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 H72  CONST_05  C16  C12  C13  C14     0.00   0.0  0
 H72  CONST_06  C16  N5   C15  C14     0.00   0.0  0
 H72  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 H72  CONST_08  C2   C19  C18  C5      0.00   0.0  0
 H72  CONST_09  N6   C17  C6   C5      0.00   0.0  0
 H72  CONST_10  N3   C17  C6   C5    180.00   0.0  0
 H72  CONST_11  N2   C7   C6   C5    180.00   0.0  0
 H72  CONST_12  C3   C4   C5   C6    180.00   0.0  0
 H72  CONST_13  C19  C18  C5   C6    180.00   0.0  0
 H72  CONST_14  C10  N6   C17  C6    180.00   0.0  0
 H72  CONST_15  C8   N3   C17  C6    180.00   0.0  0
 H72  CONST_16  N2   N3   C17  C6      0.00   0.0  0
 H72  CONST_17  N3   N2   C7   C6      0.00   0.0  0
 H72  CONST_18  C18  C5   C6   C7    180.00   0.0  0
 H72  CONST_19  N6   C17  C6   C7    180.00   0.0  0
 H72  CONST_20  N3   C17  C6   C7      0.00   0.0  0
 H72  CONST_21  C17  N3   N2   C7      0.00   0.0  0
 H72  CONST_22  C8   N3   N2   C7    180.00   0.0  0
 H72  CONST_23  N6   C10  C9   C8      0.00   0.0  0
 H72  CONST_24  N6   C17  N3   C8      0.00   0.0  0
 H72  CONST_25  C17  N6   C10  C9      0.00   0.0  0
 H72  CONST_26  C17  N3   C8   C9      0.00   0.0  0
 H72  CONST_27  N2   N3   C8   C9    180.00   0.0  0
 H72  CONST_28  N3   C17  N6   C10     0.00   0.0  0
 H72  CONST_29  N3   C8   C9   C10     0.00   0.0  0
 H72  CONST_30  C15  N5   C16  C12     0.00   0.0  0
 H72  CONST_31  C15  C14  C13  C12     0.00   0.0  0
 H72  CONST_32  N5   C16  C12  C13     0.00   0.0  0
 H72  CONST_33  N5   C15  C14  C13     0.00   0.0  0
 H72  CONST_34  N6   C17  N3   N2    180.00   0.0  0
 H72  CONST_35  C17  C6   C7   N2      0.00   0.0  0
 H72  CONST_36  C18  C19  C2   C3      0.00   0.0  0
 H72  CONST_37  C18  C5   C4   C3      0.00   0.0  0
 H72  CONST_38  C18  C5   C6   C17     0.00   0.0  0
 H72  CONST_39  C1   C2   C3   C4    180.00   0.0  0
 H72  CONST_40  C11  C12  C13  C14   180.00   0.0  0
 H72  CONST_41  N5   C16  C12  C11   180.00   0.0  0
 H72  CONST_42  N4   C10  C9   C8    180.00   0.0  0
 H72  CONST_43  C18  C19  C2   C1    180.00   0.0  0
 H72  CONST_44  C17  N6   C10  N4    180.00   0.0  0
 H72  CONST_45  H15  C18  C5   C4    180.00   0.0  0
 H72  CONST_46  H11  C3   C4   C5    180.00   0.0  0
 H72  CONST_47  H16  C19  C18  C5    180.00   0.0  0
 H72  CONST_48  H5   C7   C6   C5      0.00   0.0  0
 H72  CONST_49  H1   C4   C5   C6      0.00   0.0  0
 H72  CONST_50  H6   C8   C9   C10   180.00   0.0  0
 H72  CONST_51  H2   C14  C13  C12   180.00   0.0  0
 H72  CONST_52  H14  C16  C12  C13   180.00   0.0  0
 H72  CONST_53  H13  C15  C14  C13   180.00   0.0  0
 H72  CONST_54  H7   C9   C8   N3    180.00   0.0  0
 H72  CONST_55  H8   C13  C14  C15   180.00   0.0  0
 H72  CONST_56  N6   C10  N4   C11     0.00   0.0  0
 H72  CONST_57  C9   C10  N4   C11   180.00   0.0  0
 H72  CONST_58  H12  N4   C10  C9      0.00   0.0  0
 H72  CONST_59  H9   N1   C1   C2      0.00   0.0  0
 H72  CONST_60  H10  N1   C1   C2    180.00   0.0  0
 H72  Var_01    C12  C11  N4   C10   171.75  30.0  2
 H72  Var_02    N4   C11  C12  C13    90.85  30.0  3
 H72  Var_03    C3   C2   C1   N1   -161.72  30.0  2

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
 H72  plan-1  C4   0.020
 H72  plan-1  C5   0.020
 H72  plan-1  C6   0.020
 H72  plan-1  C3   0.020
 H72  plan-1  C2   0.020
 H72  plan-1  C18  0.020
 H72  plan-1  C19  0.020
 H72  plan-1  H1   0.020
 H72  plan-1  H11  0.020
 H72  plan-1  H15  0.020
 H72  plan-1  H16  0.020
 H72  plan-1  C1   0.020
 H72  plan-2  C14  0.020
 H72  plan-2  C11  0.020
 H72  plan-2  C12  0.020
 H72  plan-2  C13  0.020
 H72  plan-2  C15  0.020
 H72  plan-2  N5   0.020
 H72  plan-2  C16  0.020
 H72  plan-2  H8   0.020
 H72  plan-2  H13  0.020
 H72  plan-2  H14  0.020
 H72  plan-2  H2   0.020
 H72  plan-3  C5   0.020
 H72  plan-3  C6   0.020
 H72  plan-3  C7   0.020
 H72  plan-3  C8   0.020
 H72  plan-3  C9   0.020
 H72  plan-3  C10  0.020
 H72  plan-3  N2   0.020
 H72  plan-3  N3   0.020
 H72  plan-3  N4   0.020
 H72  plan-3  N6   0.020
 H72  plan-3  C17  0.020
 H72  plan-3  H5   0.020
 H72  plan-3  H6   0.020
 H72  plan-3  H7   0.020
 H72  plan-4  N1   0.020
 H72  plan-4  O1   0.020
 H72  plan-4  C2   0.020
 H72  plan-4  H9   0.020
 H72  plan-4  H10  0.020
 H72  plan-4  C1   0.020
 H72  plan-5  C11  0.020
 H72  plan-5  C10  0.020
 H72  plan-5  N4   0.020
 H72  plan-5  H12  0.020

