# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 15:56:51 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-[(3~{S})-5,5-dimethyloxolan-3-yl]-6-methoxy-3-(2-methoxypyridin-4-yl)pyrazolo[1,5-a]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccn1)c2cnn3cc(OC)c(nc23)[C@H]4COC(C)(C)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
 HJF  HJF  5-[(3~{S})-5,5-dimethyloxolan-3-yl]-6-methoxy-3-(2-methoxypyridin-4-yl)pyrazolo[1,5-a]pyrimidine  ligand  48  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJF
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
 HJF  C1   C  CR6   0   0.283  12.6553  -0.9370   3.7007
 HJF  C2   C  CR6   0   0.195  13.9281  -1.0631   4.3586
 HJF  C4   C  CR56  0   0.578  12.9016  -1.8776   6.2281
 HJF  C6   C  CR16  0  -0.053  11.5250  -1.2870   4.3749
 HJF  N3   N  N     0  -0.446  14.0134  -1.5233   5.5730
 HJF  C7   C  CR5   0  -0.206  12.6673  -2.4205   7.4977
 HJF  C8   C  CR15  0  -0.063  11.2718  -2.5639   7.5337
 HJF  C11  C  CH3   0  -0.444  11.4558  -0.3225   1.7585
 HJF  C12  C  CR15  0  -0.371  15.1740  -0.6844   3.6037
 HJF  C13  C  CH2   0  -0.158  15.1819   0.8072   3.1585
 HJF  C15  C  CR5   0   0.219  16.9156   0.6281   4.6525
 HJF  C26  C  CH3   0  -0.446  17.6263  -1.5419   8.5929
 HJF  C21  C  CR6   0   0.514  15.8109  -2.7631   9.5139
 HJF  C20  C  CR16  0  -0.570  14.9483  -2.3549   8.4960
 HJF  N22  N  N     0  -0.441  15.4405  -3.5379  10.5197
 HJF  C23  C  CR16  0  -0.063  14.1756  -3.9396  10.5485
 HJF  C24  C  CR16  0  -0.429  13.2344  -3.6048   9.5970
 HJF  C19  C  CR6   0   0.228  13.6226  -2.7882   8.5287
 HJF  N9   N  N     0  -0.294  10.6738  -2.1626   6.4241
 HJF  N5   N  N     0  -0.362  11.6707  -1.7555   5.6405
 HJF  O10  O  O2    0  -0.455  12.6847  -0.4784   2.4452
 HJF  C16  C  CH2   0  -0.457  16.4837  -0.8187   4.3883
 HJF  C18  C  CH3   0  -0.672  18.4235   0.7845   4.7237
 HJF  C17  C  CH3   0  -0.673  16.2631   1.2011   5.9096
 HJF  O14  O  O     0  -0.496  16.4504   1.3153   3.4948
 HJF  H1   H  HCR6  0   0.331  10.5159  -1.2378   3.9930
 HJF  H2   H  HCR5  0   0.276  10.6691  -2.9423   8.3458
 HJF  H3   H  HCH3  0   0.269  11.7013   0.0516   0.7687
 HJF  H4   H  HCH3  0   0.238  10.9286  -1.2749   1.6594
 HJF  H5   H  HCH3  0   0.238  10.8042   0.3973   2.2606
 HJF  H6   H  HCR5  0   0.289  15.2053  -1.3193   2.7138
 HJF  H7   H  HCH2  0   0.238  15.0422   0.9188   2.0836
 HJF  H8   H  HCH2  0   0.208  14.3837   1.3715   3.6573
 HJF  H9   H  HCH3  0   0.265  18.6743  -1.3928   8.8401
 HJF  H10  H  HCH3  0   0.233  17.5599  -1.9655   7.5873
 HJF  H11  H  HCH3  0   0.231  17.1221  -0.5725   8.6027
 HJF  H12  H  HCR6  0   0.290  15.2853  -1.7196   7.6899
 HJF  H13  H  HCR6  0   0.262  13.8962  -4.5752  11.3819
 HJF  H14  H  HCR6  0   0.256  12.2280  -3.9894   9.6848
 HJF  H15  H  HCH2  0   0.265  16.3826  -1.3986   5.3041
 HJF  H16  H  HCH2  0   0.247  17.2299  -1.3153   3.7651
 HJF  H17  H  HCH3  0   0.229  18.8185   0.2118   5.5635
 HJF  H18  H  HCH3  0   0.231  18.9011   0.4188   3.8135
 HJF  H19  H  HCH3  0   0.231  18.7103   1.8274   4.8695
 HJF  H20  H  HCH3  0   0.233  16.6312   0.6867   6.7973
 HJF  H21  H  HCH3  0   0.232  16.5010   2.2610   6.0152
 HJF  H22  H  HCH3  0   0.233  15.1768   1.0992   5.9064
 HJF  O25  O  O2    0  -0.445  17.1025  -2.4129   9.5756

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
 HJF  C11  O10  single    1.416  0.020  1.416
 HJF  O10  C1   single    1.337  0.020  1.337
 HJF  C13  C12  single    1.557  0.020  1.557
 HJF  C13  O14  single    1.407  0.020  1.407
 HJF  C12  C2   single    1.505  0.020  1.505
 HJF  C12  C16  single    1.533  0.020  1.533
 HJF  C1   C2   aromatic  1.438  0.020  1.438
 HJF  C1   C6   aromatic  1.362  0.020  1.362
 HJF  O14  C15  single    1.424  0.020  1.424
 HJF  C18  C15  single    1.518  0.020  1.518
 HJF  C2   N3   aromatic  1.301  0.020  1.301
 HJF  C6   N5   aromatic  1.357  0.020  1.357
 HJF  C16  C15  single    1.533  0.020  1.533
 HJF  C15  C17  single    1.528  0.020  1.528
 HJF  N3   C4   aromatic  1.338  0.020  1.338
 HJF  N5   C4   aromatic  1.369  0.020  1.369
 HJF  N5   N9   aromatic  1.332  0.020  1.332
 HJF  C4   C7   aromatic  1.401  0.020  1.401
 HJF  N9   C8   aromatic  1.323  0.020  1.323
 HJF  C7   C8   aromatic  1.403  0.020  1.403
 HJF  C7   C19  single    1.453  0.020  1.453
 HJF  C19  C20  aromatic  1.395  0.020  1.395
 HJF  C19  C24  aromatic  1.400  0.020  1.400
 HJF  C20  C21  aromatic  1.395  0.020  1.395
 HJF  C26  O25  single    1.414  0.020  1.414
 HJF  C24  C23  aromatic  1.380  0.020  1.380
 HJF  C21  O25  single    1.340  0.020  1.340
 HJF  C21  N22  aromatic  1.323  0.020  1.323
 HJF  C23  N22  aromatic  1.327  0.020  1.327
 HJF  C6   H1   single    0.930  0.020  1.080
 HJF  C8   H2   single    0.930  0.020  1.080
 HJF  C11  H3   single    0.970  0.020  1.090
 HJF  C11  H4   single    0.970  0.020  1.090
 HJF  C11  H5   single    0.970  0.020  1.090
 HJF  C12  H6   single    0.970  0.020  1.090
 HJF  C13  H7   single    0.970  0.020  1.090
 HJF  C13  H8   single    0.970  0.020  1.090
 HJF  C26  H9   single    0.970  0.020  1.090
 HJF  C26  H10  single    0.970  0.020  1.090
 HJF  C26  H11  single    0.970  0.020  1.090
 HJF  C20  H12  single    0.930  0.020  1.080
 HJF  C23  H13  single    0.930  0.020  1.080
 HJF  C24  H14  single    0.930  0.020  1.080
 HJF  C16  H15  single    0.970  0.020  1.090
 HJF  C16  H16  single    0.970  0.020  1.090
 HJF  C18  H17  single    0.970  0.020  1.090
 HJF  C18  H18  single    0.970  0.020  1.090
 HJF  C18  H19  single    0.970  0.020  1.090
 HJF  C17  H20  single    0.970  0.020  1.090
 HJF  C17  H21  single    0.970  0.020  1.090
 HJF  C17  H22  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
 HJF  O10  C1   C6   124.84  3.000
 HJF  C6   C1   C2   119.04  3.000
 HJF  O10  C1   C2   116.11  3.000
 HJF  C12  C2   N3   120.18  3.000
 HJF  N3   C2   C1   121.05  3.000
 HJF  C12  C2   C1   118.75  3.000
 HJF  N5   C4   C7   105.85  3.000
 HJF  C7   C4   N3   133.27  3.000
 HJF  N5   C4   N3   120.87  3.000
 HJF  H1   C6   N5   116.47  3.000
 HJF  H1   C6   C1   126.06  3.000
 HJF  N5   C6   C1   117.47  3.000
 HJF  C4   N3   C2   119.74  3.000
 HJF  C19  C7   C8   127.57  3.000
 HJF  C19  C7   C4   129.15  3.000
 HJF  C8   C7   C4   103.25  3.000
 HJF  H2   C8   N9   119.00  3.000
 HJF  H2   C8   C7   127.60  3.000
 HJF  N9   C8   C7   113.39  3.000
 HJF  H5   C11  H4   109.14  3.000
 HJF  H5   C11  H3   109.06  3.000
 HJF  H4   C11  H3   109.06  3.000
 HJF  H5   C11  O10  111.53  3.000
 HJF  H4   C11  O10  111.50  3.000
 HJF  H3   C11  O10  106.47  3.000
 HJF  H6   C12  C16  109.96  3.000
 HJF  H6   C12  C13  108.87  3.000
 HJF  C16  C12  C13  103.06  3.000
 HJF  H6   C12  C2   106.61  3.000
 HJF  C16  C12  C2   115.38  3.000
 HJF  C13  C12  C2   112.87  3.000
 HJF  H8   C13  H7   107.60  3.000
 HJF  H8   C13  O14  111.18  3.000
 HJF  H7   C13  O14  108.32  3.000
 HJF  H8   C13  C12  111.04  3.000
 HJF  H7   C13  C12  112.31  3.000
 HJF  O14  C13  C12  106.39  3.000
 HJF  O14  C15  C17  110.38  3.000
 HJF  C17  C15  C18  110.31  3.000
 HJF  O14  C15  C18  108.23  3.000
 HJF  C17  C15  C16  112.05  3.000
 HJF  C18  C15  C16  112.66  3.000
 HJF  O14  C15  C16  102.90  3.000
 HJF  H11  C26  H10  108.90  3.000
 HJF  H11  C26  H9   108.73  3.000
 HJF  H10  C26  H9   108.71  3.000
 HJF  H11  C26  O25  111.68  3.000
 HJF  H10  C26  O25  112.22  3.000
 HJF  H9   C26  O25  106.48  3.000
 HJF  N22  C21  C20  123.58  3.000
 HJF  N22  C21  O25  112.84  3.000
 HJF  C20  C21  O25  123.58  3.000
 HJF  H12  C20  C19  119.77  3.000
 HJF  H12  C20  C21  121.58  3.000
 HJF  C19  C20  C21  118.65  3.000
 HJF  C23  N22  C21  117.43  3.000
 HJF  H13  C23  C24  119.76  3.000
 HJF  H13  C23  N22  116.07  3.000
 HJF  C24  C23  N22  124.17  3.000
 HJF  H14  C24  C19  121.85  3.000
 HJF  H14  C24  C23  119.53  3.000
 HJF  C19  C24  C23  118.61  3.000
 HJF  C24  C19  C20  117.56  3.000
 HJF  C24  C19  C7   120.46  3.000
 HJF  C20  C19  C7   121.98  3.000
 HJF  N5   N9   C8   104.36  3.000
 HJF  N9   N5   C6   125.01  3.000
 HJF  N9   N5   C4   113.15  3.000
 HJF  C6   N5   C4   121.82  3.000
 HJF  C11  O10  C1   118.29  3.000
 HJF  H16  C16  H15  107.53  3.000
 HJF  H16  C16  C15  109.59  3.000
 HJF  H15  C16  C15  112.58  3.000
 HJF  H16  C16  C12  109.37  3.000
 HJF  H15  C16  C12  113.45  3.000
 HJF  C15  C16  C12  104.26  3.000
 HJF  H19  C18  H18  108.47  3.000
 HJF  H19  C18  H17  107.69  3.000
 HJF  H18  C18  H17  107.93  3.000
 HJF  H19  C18  C15  111.46  3.000
 HJF  H18  C18  C15  111.18  3.000
 HJF  H17  C18  C15  109.99  3.000
 HJF  H22  C17  H21  107.94  3.000
 HJF  H22  C17  H20  107.13  3.000
 HJF  H21  C17  H20  107.81  3.000
 HJF  H22  C17  C15  112.81  3.000
 HJF  H21  C17  C15  110.53  3.000
 HJF  H20  C17  C15  110.42  3.000
 HJF  C15  O14  C13  108.32  3.000
 HJF  C21  O25  C26  119.09  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
 HJF  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 HJF  CONST_02  C4   N5   C6   C1      0.00   0.0  0
 HJF  CONST_03  N9   N5   C6   C1    180.00   0.0  0
 HJF  CONST_04  N5   C6   C1   C2      0.00   0.0  0
 HJF  CONST_05  N5   C4   N3   C2      0.00   0.0  0
 HJF  CONST_06  C7   C4   N3   C2    180.00   0.0  0
 HJF  CONST_07  C8   N9   N5   C4      0.00   0.0  0
 HJF  CONST_08  N9   C8   C7   C4      0.00   0.0  0
 HJF  CONST_11  N3   C2   C1   C6      0.00   0.0  0
 HJF  CONST_12  N3   C4   N5   C6      0.00   0.0  0
 HJF  CONST_13  C7   C4   N5   C6    180.00   0.0  0
 HJF  CONST_14  C8   N9   N5   C6    180.00   0.0  0
 HJF  CONST_15  N9   N5   C4   N3    180.00   0.0  0
 HJF  CONST_16  C8   C7   C4   N3    180.00   0.0  0
 HJF  CONST_17  C19  C7   C4   N3      0.00   0.0  0
 HJF  CONST_18  N9   N5   C4   C7      0.00   0.0  0
 HJF  CONST_19  N5   N9   C8   C7      0.00   0.0  0
 HJF  CONST_20  C21  C20  C19  C7    180.00   0.0  0
 HJF  CONST_21  C23  C24  C19  C7    180.00   0.0  0
 HJF  CONST_22  N5   C4   C7   C8      0.00   0.0  0
 HJF  CONST_23  C20  C19  C7   C8    180.00   0.0  0
 HJF  CONST_24  C24  C19  C7   C8      0.00   0.0  0
 HJF  CONST_25  C24  C19  C20  C21     0.00   0.0  0
 HJF  CONST_26  C24  C23  N22  C21     0.00   0.0  0
 HJF  CONST_27  C23  C24  C19  C20     0.00   0.0  0
 HJF  CONST_28  C23  N22  C21  C20     0.00   0.0  0
 HJF  CONST_29  C19  C20  C21  N22     0.00   0.0  0
 HJF  CONST_30  C19  C24  C23  N22     0.00   0.0  0
 HJF  CONST_31  N5   C4   C7   C19   180.00   0.0  0
 HJF  CONST_32  N9   C8   C7   C19   180.00   0.0  0
 HJF  CONST_33  C12  C2   N3   C4    180.00   0.0  0
 HJF  CONST_34  C12  C2   C1   C6    180.00   0.0  0
 HJF  CONST_35  O10  C1   C2   N3    180.00   0.0  0
 HJF  CONST_36  O10  C1   C2   C12     0.00   0.0  0
 HJF  CONST_37  C19  C20  C21  O25   180.00   0.0  0
 HJF  CONST_38  C23  N22  C21  O25   180.00   0.0  0
 HJF  CONST_39  O10  C1   C6   N5    180.00   0.0  0
 HJF  CONST_40  H1   C6   C1   C2    180.00   0.0  0
 HJF  CONST_41  H2   C8   C7   C4    180.00   0.0  0
 HJF  CONST_42  H12  C20  C19  C7      0.00   0.0  0
 HJF  CONST_43  H14  C24  C19  C7      0.00   0.0  0
 HJF  CONST_44  H13  C23  N22  C21   180.00   0.0  0
 HJF  Var_01    O14  C15  C16  C12   -32.99  30.0  1
 HJF  Var_02    C16  C15  O14  C13    40.26  30.0  1
 HJF  Var_03    H7   C13  O14  C15  -151.80  30.0  1
 HJF  Var_04    C20  C21  O25  C26     2.50  30.0  2
 HJF  Var_05    H17  C18  C15  C16   -63.08  30.0  3
 HJF  Var_06    H20  C17  C15  C16    66.89  30.0  3
 HJF  Var_07    H3   C11  O10  C1   -179.77  30.0  3
 HJF  Var_08    H9   C26  O25  C21   179.67  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
 HJF  chir_01  C12  C13  C2  C16  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
 HJF  plan-1  C7   0.020
 HJF  plan-1  C21  0.020
 HJF  plan-1  C20  0.020
 HJF  plan-1  N22  0.020
 HJF  plan-1  C23  0.020
 HJF  plan-1  C24  0.020
 HJF  plan-1  C19  0.020
 HJF  plan-1  H12  0.020
 HJF  plan-1  H13  0.020
 HJF  plan-1  H14  0.020
 HJF  plan-1  O25  0.020
 HJF  plan-2  C1   0.020
 HJF  plan-2  C2   0.020
 HJF  plan-2  C4   0.020
 HJF  plan-2  C6   0.020
 HJF  plan-2  N3   0.020
 HJF  plan-2  C7   0.020
 HJF  plan-2  C8   0.020
 HJF  plan-2  C12  0.020
 HJF  plan-2  C19  0.020
 HJF  plan-2  N9   0.020
 HJF  plan-2  N5   0.020
 HJF  plan-2  O10  0.020
 HJF  plan-2  H1   0.020
 HJF  plan-2  H2   0.020

