# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 15:21:10 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-[(1-methyl-1H-pyrazol-4-yl)methyl]-5-{[(1S,2S)-2-(pyridin-2-yl)cyclopropyl]methoxy}pyrazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(CNc2cc(OC[C@H]3C[C@@H]3c4ccccn4)nc5ccnn25)cn1
#
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
 5AY  5AY  N-[(1-methyl-1H-pyrazol-4-yl)methyl]-5-{[(1S,2S)-2-(pyridin-2-yl)cyclopropyl]methoxy}pyrazolo[1,5-a]pyrimidin-7-amine  ligand  49  28  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5AY
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
 5AY  C2   C  CR16  0  -0.567   0.9203  -0.0128  -0.0042
 5AY  C3   C  CR6   0   0.710   2.1086  -0.6859   0.1900
 5AY  N4   N  N     0  -0.447   2.0017  -2.0068   0.5258
 5AY  C7   C  CR5   0  -0.181   5.0435   1.4590  -0.3938
 5AY  C9   C  CH2   0  -0.162  -2.6565  -0.6786   0.0839
 5AY  C10  C  CH1   0  -0.277  -3.7117   0.3295  -0.2457
 5AY  C11  C  CH2   0  -0.466  -4.0597   0.6052  -1.6665
 5AY  C12  C  CH1   0  -0.369  -5.0198  -0.1691  -0.8022
 5AY  C13  C  CR6   0   0.343  -6.3087   0.4144  -0.3638
 5AY  C15  C  CR16  0  -0.150  -7.6931   2.2451   0.3231
 5AY  N19  N  N     0  -0.331   3.0488  -2.8120   0.7593
 5AY  C20  C  CR15  0  -0.009   2.4944  -3.9762   1.0503
 5AY  C21  C  CR15  0  -0.574   1.0957  -3.9440   1.0098
 5AY  N23  N  N     0  -0.286   7.1108   1.4892  -1.2881
 5AY  C    C  CR56  0   0.578   0.7865  -2.6380   0.6627
 5AY  N    N  N     0  -0.534  -0.3759  -1.9937   0.4697
 5AY  C1   C  CR6   0   0.536  -0.2865  -0.7302   0.1476
 5AY  N5   N  NH1   0  -0.667   3.3358  -0.1838   0.0775
 5AY  C6   C  CH2   0  -0.361   3.5863   1.2156  -0.2167
 5AY  C8   C  CR15  0   0.036   5.9153   2.0466   0.4972
 5AY  C14  C  CR16  0  -0.374  -6.4568   1.7731  -0.0781
 5AY  C16  C  CR16  0  -0.332  -8.7528   1.3543   0.4316
 5AY  C17  C  CR16  0  -0.081  -8.5112   0.0256   0.1281
 5AY  N18  N  N     0  -0.444  -7.3272  -0.4372  -0.2592
 5AY  N22  N  NR5   0  -0.262   7.1273   2.0433  -0.0796
 5AY  C24  C  CR15  0  -0.061   5.8575   1.1303  -1.4923
 5AY  C25  C  CH3   0  -0.505   8.3600   2.5609   0.4643
 5AY  H1   H  HCR6  0   0.293   0.9087   1.0343  -0.2652
 5AY  H2   H  HCH2  0   0.242  -2.7718  -1.0460   1.1067
 5AY  H3   H  HCH2  0   0.231  -2.7166  -1.5391  -0.5885
 5AY  H4   H  HCH1  0   0.276  -3.7815   1.1629   0.4467
 5AY  H5   H  HCH2  0   0.264  -4.3273   1.6168  -1.9448
 5AY  H6   H  HCH2  0   0.266  -3.5397   0.0526  -2.4395
 5AY  H7   H  HCH1  0   0.266  -5.0849  -1.2341  -0.9958
 5AY  H8   H  HCR6  0   0.273  -7.8294   3.2949   0.5475
 5AY  H9   H  HCR5  0   0.270   3.1254  -4.8199   1.2866
 5AY  H10  H  HCR5  0   0.265   0.4041  -4.7456   1.2052
 5AY  H11  H  HNH1  0   0.413   4.1136  -0.7784   0.3217
 5AY  H12  H  HCH2  0   0.262   3.1954   1.8454   0.5880
 5AY  H13  H  HCH2  0   0.263   3.0453   1.4906  -1.1263
 5AY  H14  H  HCR5  0   0.294   5.7496   2.4615   1.4789
 5AY  H15  H  HCR6  0   0.264  -5.6214   2.4555  -0.1676
 5AY  H16  H  HCR6  0   0.268  -9.7362   1.6791   0.7414
 5AY  H17  H  HCR6  0   0.259  -9.3098  -0.7047   0.1994
 5AY  H18  H  HCR5  0   0.261   5.5673   0.6504  -2.4157
 5AY  H19  H  HCH3  0   0.260   9.0926   1.7634   0.5720
 5AY  H20  H  HCH3  0   0.261   8.7646   3.3335  -0.1862
 5AY  H21  H  HCH3  0   0.259   8.1609   2.9916   1.4410
 5AY  O    O  O2    0  -0.472  -1.3945  -0.0260  -0.0639

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
 5AY  C20  N19  aromatic  1.322  0.020  1.322
 5AY  C20  C21  aromatic  1.400  0.020  1.400
 5AY  N19  N4   aromatic  1.341  0.020  1.341
 5AY  C21  C    aromatic  1.386  0.020  1.386
 5AY  N4   C    aromatic  1.376  0.020  1.376
 5AY  N4   C3   aromatic  1.367  0.020  1.367
 5AY  C    N    aromatic  1.343  0.020  1.343
 5AY  N5   C3   single    1.331  0.020  1.331
 5AY  N5   C6   single    1.452  0.020  1.452
 5AY  C3   C2   aromatic  1.379  0.020  1.379
 5AY  N    C1   aromatic  1.307  0.020  1.307
 5AY  C8   C7   aromatic  1.378  0.020  1.378
 5AY  C8   N22  aromatic  1.342  0.020  1.342
 5AY  C6   C7   single    1.488  0.020  1.488
 5AY  C25  N22  single    1.443  0.020  1.443
 5AY  C2   C1   aromatic  1.412  0.020  1.412
 5AY  C1   O    single    1.330  0.020  1.330
 5AY  C7   C24  aromatic  1.406  0.020  1.406
 5AY  N22  N23  aromatic  1.330  0.020  1.330
 5AY  C9   O    single    1.428  0.020  1.428
 5AY  C9   C10  single    1.496  0.020  1.496
 5AY  C24  N23  aromatic  1.320  0.020  1.320
 5AY  C10  C12  single    1.506  0.020  1.506
 5AY  C10  C11  single    1.489  0.020  1.489
 5AY  C12  C11  single    1.506  0.020  1.506
 5AY  C12  C13  single    1.481  0.020  1.481
 5AY  N18  C13  aromatic  1.332  0.020  1.332
 5AY  N18  C17  aromatic  1.329  0.020  1.329
 5AY  C13  C14  aromatic  1.396  0.020  1.396
 5AY  C17  C16  aromatic  1.384  0.020  1.384
 5AY  C14  C15  aromatic  1.383  0.020  1.383
 5AY  C16  C15  aromatic  1.389  0.020  1.389
 5AY  C2   H1   single    0.930  0.020  1.080
 5AY  C9   H2   single    0.970  0.020  1.090
 5AY  C9   H3   single    0.970  0.020  1.090
 5AY  C10  H4   single    0.970  0.020  1.090
 5AY  C11  H5   single    0.970  0.020  1.090
 5AY  C11  H6   single    0.970  0.020  1.090
 5AY  C12  H7   single    0.970  0.020  1.090
 5AY  C15  H8   single    0.930  0.020  1.080
 5AY  C20  H9   single    0.930  0.020  1.080
 5AY  C21  H10  single    0.930  0.020  1.080
 5AY  N5   H11  single    0.860  0.020  1.020
 5AY  C6   H12  single    0.970  0.020  1.090
 5AY  C6   H13  single    0.970  0.020  1.090
 5AY  C8   H14  single    0.930  0.020  1.080
 5AY  C14  H15  single    0.930  0.020  1.080
 5AY  C16  H16  single    0.930  0.020  1.080
 5AY  C17  H17  single    0.930  0.020  1.080
 5AY  C24  H18  single    0.930  0.020  1.080
 5AY  C25  H19  single    0.970  0.020  1.090
 5AY  C25  H20  single    0.970  0.020  1.090
 5AY  C25  H21  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
 5AY  H1   C2   C1   120.64  3.000
 5AY  H1   C2   C3   121.12  3.000
 5AY  C1   C2   C3   118.24  3.000
 5AY  N5   C3   N4   117.22  3.000
 5AY  N5   C3   C2   126.76  3.000
 5AY  N4   C3   C2   116.02  3.000
 5AY  C    N4   N19  113.37  3.000
 5AY  C    N4   C3   122.45  3.000
 5AY  N19  N4   C3   124.18  3.000
 5AY  C24  C7   C8   103.80  3.000
 5AY  C24  C7   C6   128.44  3.000
 5AY  C8   C7   C6   127.75  3.000
 5AY  H3   C9   H2   107.76  3.000
 5AY  H3   C9   O    110.15  3.000
 5AY  H2   C9   O    110.10  3.000
 5AY  H3   C9   C10  110.85  3.000
 5AY  H2   C9   C10  111.00  3.000
 5AY  O    C9   C10  107.01  3.000
 5AY  H4   C10  C12  115.71  3.000
 5AY  H4   C10  C11  116.84  3.000
 5AY  C12  C10  C11   60.38  3.000
 5AY  H4   C10  C9   114.97  3.000
 5AY  C11  C10  C9   119.99  3.000
 5AY  C12  C10  C9   118.08  3.000
 5AY  H6   C11  H5   114.33  3.000
 5AY  H6   C11  C12  116.95  3.000
 5AY  H5   C11  C12  118.05  3.000
 5AY  H6   C11  C10  118.32  3.000
 5AY  H5   C11  C10  118.43  3.000
 5AY  C12  C11  C10   60.40  3.000
 5AY  H7   C12  C13  112.80  3.000
 5AY  H7   C12  C11  116.15  3.000
 5AY  C13  C12  C11  121.47  3.000
 5AY  H7   C12  C10  116.31  3.000
 5AY  C13  C12  C10  121.05  3.000
 5AY  C11  C12  C10   59.22  3.000
 5AY  N18  C13  C14  121.68  3.000
 5AY  C14  C13  C12  122.42  3.000
 5AY  N18  C13  C12  115.90  3.000
 5AY  H8   C15  C16  120.67  3.000
 5AY  H8   C15  C14  120.25  3.000
 5AY  C16  C15  C14  119.08  3.000
 5AY  C20  N19  N4   103.86  3.000
 5AY  H9   C20  C21  127.46  3.000
 5AY  H9   C20  N19  119.42  3.000
 5AY  C21  C20  N19  113.11  3.000
 5AY  H10  C21  C    127.13  3.000
 5AY  H10  C21  C20  128.29  3.000
 5AY  C    C21  C20  104.58  3.000
 5AY  C24  N23  N22  105.41  3.000
 5AY  N    C    C21  132.92  3.000
 5AY  N    C    N4   122.01  3.000
 5AY  C21  C    N4   105.07  3.000
 5AY  C1   N    C    116.10  3.000
 5AY  O    C1   N    119.62  3.000
 5AY  O    C1   C2   115.21  3.000
 5AY  N    C1   C2   125.18  3.000
 5AY  H11  N5   C6   118.95  3.000
 5AY  H11  N5   C3   117.91  3.000
 5AY  C6   N5   C3   122.68  3.000
 5AY  H13  C6   H12  106.87  3.000
 5AY  H13  C6   N5   109.01  3.000
 5AY  H12  C6   N5   110.13  3.000
 5AY  H13  C6   C7   110.14  3.000
 5AY  H12  C6   C7   110.08  3.000
 5AY  N5   C6   C7   110.54  3.000
 5AY  H14  C8   N22  122.06  3.000
 5AY  H14  C8   C7   130.94  3.000
 5AY  N22  C8   C7   107.00  3.000
 5AY  H15  C14  C15  119.92  3.000
 5AY  H15  C14  C13  120.98  3.000
 5AY  C15  C14  C13  119.09  3.000
 5AY  H16  C16  C17  120.66  3.000
 5AY  H16  C16  C15  121.60  3.000
 5AY  C17  C16  C15  117.74  3.000
 5AY  H17  C17  N18  116.15  3.000
 5AY  H17  C17  C16  120.23  3.000
 5AY  N18  C17  C16  123.62  3.000
 5AY  C17  N18  C13  118.79  3.000
 5AY  C25  N22  C8   127.48  3.000
 5AY  C25  N22  N23  120.17  3.000
 5AY  C8   N22  N23  112.36  3.000
 5AY  H18  C24  N23  120.54  3.000
 5AY  H18  C24  C7   128.03  3.000
 5AY  N23  C24  C7   111.43  3.000
 5AY  H21  C25  H20  108.92  3.000
 5AY  H21  C25  H19  108.97  3.000
 5AY  H20  C25  H19  109.22  3.000
 5AY  H21  C25  N22  108.94  3.000
 5AY  H20  C25  N22  110.30  3.000
 5AY  H19  C25  N22  110.46  3.000
 5AY  C1   O    C9   118.54  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
 5AY  CONST_01  N19  N4   C3   C2    180.00   0.0  0
 5AY  CONST_02  C    N4   C3   C2      0.00   0.0  0
 5AY  CONST_03  C    N    C1   C2      0.00   0.0  0
 5AY  CONST_04  C20  N19  N4   C3    180.00   0.0  0
 5AY  CONST_05  C21  C    N4   C3    180.00   0.0  0
 5AY  CONST_06  N    C    N4   C3      0.00   0.0  0
 5AY  CONST_07  N    C1   C2   C3      0.00   0.0  0
 5AY  CONST_08  C21  C20  N19  N4      0.00   0.0  0
 5AY  CONST_09  C20  C21  C    N4      0.00   0.0  0
 5AY  CONST_10  C1   N    C    N4      0.00   0.0  0
 5AY  CONST_11  C1   C2   C3   N4      0.00   0.0  0
 5AY  CONST_12  N23  N22  C8   C7      0.00   0.0  0
 5AY  CONST_13  N22  N23  C24  C7      0.00   0.0  0
 5AY  CONST_14  C16  C17  N18  C13     0.00   0.0  0
 5AY  CONST_15  C16  C15  C14  C13     0.00   0.0  0
 5AY  CONST_16  N18  C13  C14  C15     0.00   0.0  0
 5AY  CONST_17  N18  C17  C16  C15     0.00   0.0  0
 5AY  CONST_18  C    C21  C20  N19     0.00   0.0  0
 5AY  CONST_19  C21  C    N4   N19     0.00   0.0  0
 5AY  CONST_20  N    C    N4   N19   180.00   0.0  0
 5AY  CONST_21  C    N4   N19  C20     0.00   0.0  0
 5AY  CONST_22  N    C    C21  C20   180.00   0.0  0
 5AY  CONST_23  C1   N    C    C21   180.00   0.0  0
 5AY  CONST_24  C8   C7   C24  N23     0.00   0.0  0
 5AY  CONST_25  C24  N23  N22  C8      0.00   0.0  0
 5AY  CONST_26  C17  N18  C13  C14     0.00   0.0  0
 5AY  CONST_27  C17  C16  C15  C14     0.00   0.0  0
 5AY  CONST_28  C24  C7   C8   N22     0.00   0.0  0
 5AY  CONST_29  C17  N18  C13  C12   180.00   0.0  0
 5AY  CONST_30  C15  C14  C13  C12   180.00   0.0  0
 5AY  CONST_31  O    C1   C2   C3    180.00   0.0  0
 5AY  CONST_32  C25  N22  C8   C7    180.00   0.0  0
 5AY  CONST_33  N5   C3   N4   N19     0.00   0.0  0
 5AY  CONST_34  C6   C7   C24  N23   180.00   0.0  0
 5AY  CONST_35  N5   C3   N4   C     180.00   0.0  0
 5AY  CONST_36  O    C1   N    C     180.00   0.0  0
 5AY  CONST_37  N5   C3   C2   C1    180.00   0.0  0
 5AY  CONST_38  N22  C8   C7   C6    180.00   0.0  0
 5AY  CONST_39  C25  N22  N23  C24   180.00   0.0  0
 5AY  CONST_40  H9   C20  N19  N4    180.00   0.0  0
 5AY  CONST_41  H10  C21  C    N4    180.00   0.0  0
 5AY  CONST_42  H1   C2   C3   N4    180.00   0.0  0
 5AY  CONST_43  H15  C14  C13  C12     0.00   0.0  0
 5AY  CONST_44  H17  C17  N18  C13   180.00   0.0  0
 5AY  CONST_45  H8   C15  C14  C13   180.00   0.0  0
 5AY  CONST_46  H14  C8   N22  N23   180.00   0.0  0
 5AY  CONST_47  H18  C24  C7   C8    180.00   0.0  0
 5AY  CONST_48  H16  C16  C15  C14   180.00   0.0  0
 5AY  CONST_49  C6   N5   C3   C2      0.00   0.0  0
 5AY  CONST_50  C6   N5   C3   N4    180.00   0.0  0
 5AY  CONST_51  H11  N5   C3   C2    180.00   0.0  0
 5AY  Var_01    N18  C13  C12  C10  -143.74  30.0  2
 5AY  Var_02    C13  C12  C11  C10   109.84  30.0  1
 5AY  Var_03    C7   C6   N5   C3   -175.27  30.0  3
 5AY  Var_04    N    C1   O    C9      0.66  30.0  1
 5AY  Var_05    O    C9   C10  C11    81.46  30.0  1
 5AY  Var_06    C8   C7   C6   N5   -103.62  30.0  2
 5AY  Var_07    H19  C25  N22  N23   -61.80  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
 5AY  chir_01  C10  C9   C12  C11  both
 5AY  chir_02  C12  C10  C11  C13  both

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
 5AY  plan-1  C7   0.020
 5AY  plan-1  N23  0.020
 5AY  plan-1  C6   0.020
 5AY  plan-1  C8   0.020
 5AY  plan-1  N22  0.020
 5AY  plan-1  C24  0.020
 5AY  plan-1  C25  0.020
 5AY  plan-1  H14  0.020
 5AY  plan-1  H18  0.020
 5AY  plan-2  C12  0.020
 5AY  plan-2  C13  0.020
 5AY  plan-2  C15  0.020
 5AY  plan-2  C14  0.020
 5AY  plan-2  C16  0.020
 5AY  plan-2  C17  0.020
 5AY  plan-2  N18  0.020
 5AY  plan-2  H8   0.020
 5AY  plan-2  H15  0.020
 5AY  plan-2  H16  0.020
 5AY  plan-2  H17  0.020
 5AY  plan-3  C2   0.020
 5AY  plan-3  C3   0.020
 5AY  plan-3  N4   0.020
 5AY  plan-3  N19  0.020
 5AY  plan-3  C20  0.020
 5AY  plan-3  C21  0.020
 5AY  plan-3  C    0.020
 5AY  plan-3  N    0.020
 5AY  plan-3  C1   0.020
 5AY  plan-3  N5   0.020
 5AY  plan-3  H1   0.020
 5AY  plan-3  H9   0.020
 5AY  plan-3  H10  0.020
 5AY  plan-3  O    0.020
 5AY  plan-4  C3   0.020
 5AY  plan-4  N5   0.020
 5AY  plan-4  C6   0.020
 5AY  plan-4  H11  0.020

