# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 05:00:00 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (3R,4R)-4-({[7-(benzylamino)-3-(propan-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}methyl)piperidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1cnn2c(NCc3ccccc3)cc(NC[C@H]4CCNC[C@@H]4O)nc12
#
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
 I74  I74  (3R,4R)-4-({[7-(benzylamino)-3-(propan-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}methyl)piperidin-3-ol  ligand  59  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I74
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
 I74  O1   O  OH1   0  -0.673   5.7073   0.4268  -1.7864
 I74  C42  C  CH1   0   0.087   5.6374   1.0304  -0.5121
 I74  C43  C  CH2   0  -0.322   6.6598   2.1575  -0.3872
 I74  N44  N  NH1   0  -0.599   6.5550   2.7818   0.9155
 I74  C45  C  CH2   0  -0.293   5.2550   3.4014   1.0934
 I74  C46  C  CH2   0  -0.417   4.1709   2.3387   1.0227
 I74  C41  C  CH1   0  -0.334   4.2245   1.5699  -0.3010
 I74  C40  C  CH2   0  -0.218   3.1988   0.4436  -0.3526
 I74  N18  N  NH1   0  -0.695   1.8559   0.9605  -0.2169
 I74  C5   C  CR6   0   0.540   0.7715   0.1613  -0.1299
 I74  C4   C  CR16  0  -0.572  -0.5206   0.7634  -0.1408
 I74  C3   C  CR6   0   0.697  -1.6298  -0.0414  -0.0360
 I74  N2   N  N     0  -0.451  -1.3959  -1.3837   0.0772
 I74  N1   N  N     0  -0.343  -2.3566  -2.3150   0.1932
 I74  C9   C  CR15  0  -0.058  -1.6814  -3.4498   0.2758
 I74  C8   C  CR5   0  -0.177  -0.2897  -3.2809   0.2171
 I74  C26  C  CH1   0  -0.332   0.7878  -4.3190   0.2677
 I74  C28  C  CH3   0  -0.643   0.7122  -5.1484   1.5501
 I74  C27  C  CH3   0  -0.641   0.7454  -5.2297  -0.9608
 I74  C7   C  CR56  0   0.544  -0.1241  -1.9070   0.0849
 I74  N6   N  N     0  -0.533   0.9701  -1.1404  -0.0246
 I74  N10  N  NH1   0  -0.675  -2.9069   0.3487  -0.0343
 I74  C11  C  CH2   0  -0.334  -3.3017   1.7391  -0.1163
 I74  C12  C  CR6   0   0.061  -4.8011   1.8412  -0.1022
 I74  C17  C  CR16  0  -0.283  -5.4902   1.8943   1.1061
 I74  C16  C  CR16  0  -0.241  -6.8771   1.9506   1.1238
 I74  C15  C  CR16  0  -0.262  -7.5876   1.9514  -0.0698
 I74  C14  C  CR16  0  -0.241  -6.9071   1.8971  -1.2793
 I74  C13  C  CR16  0  -0.286  -5.5200   1.8396  -1.2937
 I74  H1   H  HOH1  0   0.451   6.5533  -0.0258  -1.8588
 I74  H2   H  HCH1  0   0.193   5.8428   0.2947   0.2810
 I74  H3   H  HCH2  0   0.233   7.6673   1.7491  -0.5056
 I74  H4   H  HCH2  0   0.189   6.4941   2.8644  -1.2180
 I74  H5   H  HNH1  0   0.355   7.2846   3.4744   1.0190
 I74  H7   H  HCH2  0   0.234   5.2275   3.8986   2.0649
 I74  H8   H  HCH2  0   0.189   5.0501   4.1718   0.3311
 I74  H9   H  HCH2  0   0.218   4.2962   1.6379   1.8547
 I74  H10  H  HCH2  0   0.236   3.1943   2.8092   1.1498
 I74  H11  H  HCH1  0   0.227   4.0192   2.2787  -1.1167
 I74  H12  H  HCH2  0   0.234   3.3002  -0.1203  -1.2844
 I74  H13  H  HCH2  0   0.222   3.3943  -0.2600   0.4612
 I74  H14  H  HNH1  0   0.393   1.6990   1.9261  -0.4541
 I74  H15  H  HCR6  0   0.286  -0.6250   1.8351  -0.2282
 I74  H16  H  HCR5  0   0.257  -2.2251  -4.3785   0.3797
 I74  H17  H  HCH1  0   0.232   1.7459  -3.7896   0.2623
 I74  H18  H  HCH3  0   0.214  -0.2237  -5.7099   1.5972
 I74  H19  H  HCH3  0   0.224   1.5307  -5.8693   1.5983
 I74  H20  H  HCH3  0   0.227   0.7665  -4.5174   2.4379
 I74  H21  H  HCH3  0   0.227   0.8200  -4.6555  -1.8849
 I74  H22  H  HCH3  0   0.223   1.5661  -5.9492  -0.9427
 I74  H23  H  HCH3  0   0.214  -0.1897  -5.7936  -0.9934
 I74  H24  H  HNH1  0   0.411  -3.6136  -0.3639   0.0618
 I74  H25  H  HCH2  0   0.259  -2.8790   2.2983   0.7245
 I74  H26  H  HCH2  0   0.259  -2.9038   2.1864  -1.0323
 I74  H27  H  HCR6  0   0.256  -4.9373   1.8978   2.0382
 I74  H28  H  HCR6  0   0.259  -7.4032   1.9967   2.0686
 I74  H29  H  HCR6  0   0.259  -8.6688   1.9970  -0.0572
 I74  H30  H  HCR6  0   0.259  -7.4568   1.9009  -2.2116
 I74  H31  H  HCR6  0   0.255  -4.9906   1.7983  -2.2384

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
 I74  C14  C15  aromatic  1.389  0.020  1.389
 I74  C14  C13  aromatic  1.388  0.020  1.388
 I74  C15  C16  aromatic  1.389  0.020  1.389
 I74  C13  C12  aromatic  1.392  0.020  1.392
 I74  C16  C17  aromatic  1.388  0.020  1.388
 I74  C12  C17  aromatic  1.392  0.020  1.392
 I74  C12  C11  single    1.503  0.020  1.503
 I74  N10  C11  single    1.448  0.020  1.448
 I74  N10  C3   single    1.335  0.020  1.335
 I74  N1   C9   aromatic  1.323  0.020  1.323
 I74  N1   N2   aromatic  1.343  0.020  1.343
 I74  C9   C8   aromatic  1.403  0.020  1.403
 I74  C3   N2   aromatic  1.367  0.020  1.367
 I74  C3   C4   aromatic  1.374  0.020  1.374
 I74  N2   C7   aromatic  1.375  0.020  1.375
 I74  C4   C5   aromatic  1.426  0.020  1.426
 I74  C8   C7   aromatic  1.390  0.020  1.390
 I74  C8   C26  single    1.497  0.020  1.497
 I74  C7   N6   aromatic  1.341  0.020  1.341
 I74  C28  C26  single    1.529  0.020  1.529
 I74  C26  C27  single    1.530  0.020  1.530
 I74  C5   N6   aromatic  1.321  0.020  1.321
 I74  C5   N18  single    1.350  0.020  1.350
 I74  N18  C40  single    1.445  0.020  1.445
 I74  C40  C41  single    1.524  0.020  1.524
 I74  C41  C46  single    1.532  0.020  1.532
 I74  C41  C42  single    1.527  0.020  1.527
 I74  C46  C45  single    1.520  0.020  1.520
 I74  O1   C42  single    1.412  0.020  1.412
 I74  C42  C43  single    1.527  0.020  1.527
 I74  C45  N44  single    1.451  0.020  1.451
 I74  C43  N44  single    1.448  0.020  1.448
 I74  O1   H1   single    0.850  0.020  0.980
 I74  C42  H2   single    0.970  0.020  1.090
 I74  C43  H3   single    0.970  0.020  1.090
 I74  C43  H4   single    0.970  0.020  1.090
 I74  N44  H5   single    0.890  0.020  1.040
 I74  C45  H7   single    0.970  0.020  1.090
 I74  C45  H8   single    0.970  0.020  1.090
 I74  C46  H9   single    0.970  0.020  1.090
 I74  C46  H10  single    0.970  0.020  1.090
 I74  C41  H11  single    0.970  0.020  1.090
 I74  C40  H12  single    0.970  0.020  1.090
 I74  C40  H13  single    0.970  0.020  1.090
 I74  N18  H14  single    0.860  0.020  1.020
 I74  C4   H15  single    0.930  0.020  1.080
 I74  C9   H16  single    0.930  0.020  1.080
 I74  C26  H17  single    0.970  0.020  1.090
 I74  C28  H18  single    0.970  0.020  1.090
 I74  C28  H19  single    0.970  0.020  1.090
 I74  C28  H20  single    0.970  0.020  1.090
 I74  C27  H21  single    0.970  0.020  1.090
 I74  C27  H22  single    0.970  0.020  1.090
 I74  C27  H23  single    0.970  0.020  1.090
 I74  N10  H24  single    0.860  0.020  1.020
 I74  C11  H25  single    0.970  0.020  1.090
 I74  C11  H26  single    0.970  0.020  1.090
 I74  C17  H27  single    0.930  0.020  1.080
 I74  C16  H28  single    0.930  0.020  1.080
 I74  C15  H29  single    0.930  0.020  1.080
 I74  C14  H30  single    0.930  0.020  1.080
 I74  C13  H31  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
 I74  H1   O1   C42  108.21  3.000
 I74  H2   C42  C41  108.00  3.000
 I74  H2   C42  C43  108.02  3.000
 I74  C41  C42  C43  110.33  3.000
 I74  H2   C42  O1   110.81  3.000
 I74  C43  C42  O1   110.88  3.000
 I74  C41  C42  O1   108.76  3.000
 I74  H4   C43  H3   107.22  3.000
 I74  H4   C43  N44  112.97  3.000
 I74  H3   C43  N44  108.97  3.000
 I74  H4   C43  C42  108.11  3.000
 I74  H3   C43  C42  109.41  3.000
 I74  N44  C43  C42  110.08  3.000
 I74  H5   N44  C45  109.95  3.000
 I74  H5   N44  C43  109.57  3.000
 I74  C45  N44  C43  111.04  3.000
 I74  H8   C45  H7   107.00  3.000
 I74  H8   C45  C46  108.89  3.000
 I74  H7   C45  C46  109.99  3.000
 I74  H8   C45  N44  112.34  3.000
 I74  H7   C45  N44  109.03  3.000
 I74  C46  C45  N44  109.56  3.000
 I74  H10  C46  H9   106.85  3.000
 I74  H10  C46  C41  110.38  3.000
 I74  H9   C46  C41  109.35  3.000
 I74  H10  C46  C45  109.35  3.000
 I74  H9   C46  C45  109.30  3.000
 I74  C41  C46  C45  111.48  3.000
 I74  H11  C41  C40  108.99  3.000
 I74  H11  C41  C46  108.11  3.000
 I74  C40  C41  C46  112.12  3.000
 I74  H11  C41  C42  107.33  3.000
 I74  C46  C41  C42  109.22  3.000
 I74  C40  C41  C42  110.91  3.000
 I74  H13  C40  H12  106.60  3.000
 I74  H13  C40  N18  109.05  3.000
 I74  H12  C40  N18  110.52  3.000
 I74  H13  C40  C41  109.27  3.000
 I74  H12  C40  C41  110.33  3.000
 I74  N18  C40  C41  110.97  3.000
 I74  H14  N18  C5   117.25  3.000
 I74  H14  N18  C40  117.76  3.000
 I74  C5   N18  C40  122.73  3.000
 I74  N6   C5   C4   123.58  3.000
 I74  N6   C5   N18  117.89  3.000
 I74  C4   C5   N18  118.53  3.000
 I74  H15  C4   C3   120.60  3.000
 I74  H15  C4   C5   120.48  3.000
 I74  C3   C4   C5   118.92  3.000
 I74  N10  C3   N2   116.76  3.000
 I74  N2   C3   C4   116.30  3.000
 I74  N10  C3   C4   126.93  3.000
 I74  C7   N2   N1   113.40  3.000
 I74  C7   N2   C3   122.16  3.000
 I74  N1   N2   C3   124.44  3.000
 I74  C9   N1   N2   103.60  3.000
 I74  H16  C9   C8   127.32  3.000
 I74  H16  C9   N1   119.09  3.000
 I74  C8   C9   N1   113.59  3.000
 I74  C7   C8   C26  127.07  3.000
 I74  C26  C8   C9   128.97  3.000
 I74  C7   C8   C9   103.95  3.000
 I74  H17  C26  C27  107.95  3.000
 I74  H17  C26  C28  108.04  3.000
 I74  C27  C26  C28  110.44  3.000
 I74  H17  C26  C8   107.12  3.000
 I74  C27  C26  C8   111.45  3.000
 I74  C28  C26  C8   111.65  3.000
 I74  H20  C28  H19  107.99  3.000
 I74  H20  C28  H18  107.75  3.000
 I74  H19  C28  H18  107.52  3.000
 I74  H20  C28  C26  111.50  3.000
 I74  H19  C28  C26  110.99  3.000
 I74  H18  C28  C26  110.93  3.000
 I74  H23  C27  H22  107.69  3.000
 I74  H23  C27  H21  107.76  3.000
 I74  H22  C27  H21  108.04  3.000
 I74  H23  C27  C26  110.79  3.000
 I74  H22  C27  C26  110.99  3.000
 I74  H21  C27  C26  111.42  3.000
 I74  N6   C7   C8   132.09  3.000
 I74  N6   C7   N2   122.46  3.000
 I74  C8   C7   N2   105.45  3.000
 I74  C7   N6   C5   116.57  3.000
 I74  H24  N10  C11  119.54  3.000
 I74  H24  N10  C3   117.65  3.000
 I74  C11  N10  C3   122.78  3.000
 I74  H26  C11  H25  107.08  3.000
 I74  H26  C11  C12  110.05  3.000
 I74  H25  C11  C12  110.08  3.000
 I74  H26  C11  N10  109.93  3.000
 I74  H25  C11  N10  109.98  3.000
 I74  C12  C11  N10  109.69  3.000
 I74  C13  C12  C17  119.18  3.000
 I74  C17  C12  C11  120.31  3.000
 I74  C13  C12  C11  120.48  3.000
 I74  H27  C17  C16  119.91  3.000
 I74  H27  C17  C12  119.62  3.000
 I74  C16  C17  C12  120.48  3.000
 I74  H28  C16  C15  120.09  3.000
 I74  H28  C16  C17  119.90  3.000
 I74  C15  C16  C17  120.01  3.000
 I74  H29  C15  C14  120.08  3.000
 I74  H29  C15  C16  120.07  3.000
 I74  C14  C15  C16  119.85  3.000
 I74  H30  C14  C13  119.91  3.000
 I74  H30  C14  C15  120.08  3.000
 I74  C13  C14  C15  120.01  3.000
 I74  H31  C13  C14  119.91  3.000
 I74  H31  C13  C12  119.61  3.000
 I74  C14  C13  C12  120.48  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
 I74  CONST_01  N2   C3   C4   C5      0.00   0.0  0
 I74  CONST_02  N2   C7   N6   C5      0.00   0.0  0
 I74  CONST_03  C8   C7   N6   C5    180.00   0.0  0
 I74  CONST_04  N1   N2   C3   C4    180.00   0.0  0
 I74  CONST_05  C7   N2   C3   C4      0.00   0.0  0
 I74  CONST_06  C7   N6   C5   C4      0.00   0.0  0
 I74  CONST_07  C9   N1   N2   C3    180.00   0.0  0
 I74  CONST_08  C8   C7   N2   C3    180.00   0.0  0
 I74  CONST_09  N6   C7   N2   C3      0.00   0.0  0
 I74  CONST_10  N6   C5   C4   C3      0.00   0.0  0
 I74  CONST_11  C8   C9   N1   N2      0.00   0.0  0
 I74  CONST_12  C9   C8   C7   N2      0.00   0.0  0
 I74  CONST_13  C7   C8   C9   N1      0.00   0.0  0
 I74  CONST_14  C8   C7   N2   N1      0.00   0.0  0
 I74  CONST_15  N6   C7   N2   N1    180.00   0.0  0
 I74  CONST_16  C7   N2   N1   C9      0.00   0.0  0
 I74  CONST_17  N6   C7   C8   C9    180.00   0.0  0
 I74  CONST_18  C15  C14  C13  C12     0.00   0.0  0
 I74  CONST_19  C15  C16  C17  C12     0.00   0.0  0
 I74  CONST_20  C14  C15  C16  C17     0.00   0.0  0
 I74  CONST_21  C14  C13  C12  C17     0.00   0.0  0
 I74  CONST_22  C13  C14  C15  C16     0.00   0.0  0
 I74  CONST_23  C13  C12  C17  C16     0.00   0.0  0
 I74  CONST_24  C3   C4   C5   N18   180.00   0.0  0
 I74  CONST_25  C7   N6   C5   N18   180.00   0.0  0
 I74  CONST_26  N10  C3   C4   C5    180.00   0.0  0
 I74  CONST_27  C26  C8   C7   N2    180.00   0.0  0
 I74  CONST_28  C26  C8   C9   N1    180.00   0.0  0
 I74  CONST_29  N10  C3   N2   N1      0.00   0.0  0
 I74  CONST_30  N6   C7   C8   C26     0.00   0.0  0
 I74  CONST_31  N10  C3   N2   C7    180.00   0.0  0
 I74  CONST_32  C14  C13  C12  C11   180.00   0.0  0
 I74  CONST_33  C16  C17  C12  C11   180.00   0.0  0
 I74  CONST_34  H16  C9   N1   N2    180.00   0.0  0
 I74  CONST_35  H15  C4   C3   N2    180.00   0.0  0
 I74  CONST_36  H30  C14  C13  C12   180.00   0.0  0
 I74  CONST_37  H28  C16  C17  C12   180.00   0.0  0
 I74  CONST_38  H29  C15  C16  C17   180.00   0.0  0
 I74  CONST_39  H31  C13  C12  C17   180.00   0.0  0
 I74  CONST_40  H27  C17  C16  C15   180.00   0.0  0
 I74  CONST_41  C4   C5   N18  C40   180.00   0.0  0
 I74  CONST_42  N6   C5   N18  C40     0.00   0.0  0
 I74  CONST_43  C11  N10  C3   C4      0.00   0.0  0
 I74  CONST_44  C11  N10  C3   N2    180.00   0.0  0
 I74  CONST_45  H24  N10  C3   C4    180.00   0.0  0
 I74  CONST_46  H14  N18  C5   C4      0.00   0.0  0
 I74  Var_01    C45  N44  C43  C42   -63.00  30.0  1
 I74  Var_02    C46  C45  N44  C43    62.08  30.0  1
 I74  Var_03    C41  C46  C45  N44   -57.26  30.0  1
 I74  Var_04    C5   N18  C40  C41  -174.90  30.0  2
 I74  Var_05    C12  C11  N10  C3    179.55  30.0  3
 I74  Var_06    C28  C26  C8   C9    -58.14  30.0  2
 I74  Var_07    C13  C12  C11  N10   -91.24  30.0  2
 I74  Var_08    H18  C28  C26  C8     63.26  30.0  3
 I74  Var_09    H21  C27  C26  C8     56.51  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
 I74  chir_01  C42  C41  O1   C43  negativ
 I74  chir_02  C41  C42  C46  C40  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
 I74  plan-1  C11  0.020
 I74  plan-1  C12  0.020
 I74  plan-1  C17  0.020
 I74  plan-1  C16  0.020
 I74  plan-1  C15  0.020
 I74  plan-1  C14  0.020
 I74  plan-1  C13  0.020
 I74  plan-1  H27  0.020
 I74  plan-1  H28  0.020
 I74  plan-1  H29  0.020
 I74  plan-1  H30  0.020
 I74  plan-1  H31  0.020
 I74  plan-2  N18  0.020
 I74  plan-2  C5   0.020
 I74  plan-2  C4   0.020
 I74  plan-2  C3   0.020
 I74  plan-2  N2   0.020
 I74  plan-2  N1   0.020
 I74  plan-2  C9   0.020
 I74  plan-2  C8   0.020
 I74  plan-2  C26  0.020
 I74  plan-2  C7   0.020
 I74  plan-2  N6   0.020
 I74  plan-2  N10  0.020
 I74  plan-2  H15  0.020
 I74  plan-2  H16  0.020
 I74  plan-3  C40  0.020
 I74  plan-3  N18  0.020
 I74  plan-3  C5   0.020
 I74  plan-3  H14  0.020
 I74  plan-4  C3   0.020
 I74  plan-4  N10  0.020
 I74  plan-4  C11  0.020
 I74  plan-4  H24  0.020

