# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 08:04:51 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (3S,4S)-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
 I73  I73  (3S,4S)-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  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I73
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
 I73  O1   O  OH1   0  -0.673  -5.8175   0.5779  -1.7828
 I73  C42  C  CH1   0   0.076  -5.6342   1.1116  -0.4882
 I73  C43  C  CH2   0  -0.346  -6.6024   2.2715  -0.2325
 I73  N44  N  NH1   0  -0.577  -6.4207   2.9250   1.0494
 I73  C45  C  CH2   0  -0.315  -5.0456   3.3636   1.2276
 I73  C46  C  CH2   0  -0.429  -4.0170   2.2569   1.0180
 I73  C41  C  CH1   0  -0.327  -4.1900   1.5847  -0.3464
 I73  C40  C  CH2   0  -0.224  -3.2096   0.4316  -0.5436
 I73  N18  N  NH1   0  -0.695  -1.8470   0.9080  -0.4877
 I73  C5   C  CR6   0   0.543  -0.7767   0.0967  -0.3607
 I73  C4   C  CR16  0  -0.572   0.5233   0.6764  -0.4495
 I73  C3   C  CR6   0   0.697   1.6246  -0.1267  -0.2819
 I73  N2   N  N     0  -0.451   1.3768  -1.4521  -0.0559
 I73  N1   N  N     0  -0.342   2.3280  -2.3840   0.1188
 I73  C9   C  CR15  0  -0.058   1.6412  -3.5013   0.2926
 I73  C8   C  CR5   0  -0.178   0.2508  -3.3203   0.2371
 I73  C26  C  CH1   0  -0.331  -0.8374  -4.3404   0.3675
 I73  C28  C  CH3   0  -0.640  -0.8541  -5.2923  -0.8301
 I73  C27  C  CH3   0  -0.644  -0.7221  -5.1263   1.6737
 I73  C7   C  CR56  0   0.545   0.0989  -1.9586   0.0035
 I73  N6   N  N     0  -0.532  -0.9886  -1.1896  -0.1499
 I73  N10  N  NH1   0  -0.675   2.9093   0.2495  -0.2956
 I73  C11  C  CH2   0  -0.337   3.3247   1.5944  -0.6306
 I73  C12  C  CR6   0   0.074   4.7802   1.7808  -0.3005
 I73  C17  C  CR16  0  -0.299   5.7286   1.9152  -1.3076
 I73  C16  C  CR16  0  -0.241   7.0736   2.0747  -0.9941
 I73  C15  C  CR16  0  -0.263   7.4802   2.0956   0.3321
 I73  C14  C  CR16  0  -0.241   6.5376   1.9591   1.3451
 I73  C13  C  CR16  0  -0.280   5.1966   1.8021   1.0293
 I73  H1   H  HOH1  0   0.451  -6.6975   0.1909  -1.8251
 I73  H2   H  HCH1  0   0.191  -5.8145   0.3400   0.2787
 I73  H3   H  HCH2  0   0.218  -6.4676   3.0152  -1.0262
 I73  H4   H  HCH2  0   0.236  -7.6332   1.9125  -0.3046
 I73  H5   H  HNH1  0   0.341  -6.6577   2.2742   1.7895
 I73  H7   H  HCH2  0   0.217  -4.8530   4.1736   0.5154
 I73  H8   H  HCH2  0   0.237  -4.9409   3.7932   2.2258
 I73  H9   H  HCH2  0   0.235  -3.0102   2.6691   1.1162
 I73  H10  H  HCH2  0   0.217  -4.1248   1.5056   1.8089
 I73  H11  H  HCH1  0   0.228  -4.0113   2.3381  -1.1283
 I73  H12  H  HCH2  0   0.226  -3.3579  -0.3093   0.2451
 I73  H13  H  HCH2  0   0.235  -3.4055  -0.0727  -1.4943
 I73  H14  H  HNH1  0   0.392  -1.6735   1.8536  -0.7867
 I73  H15  H  HCR6  0   0.285   0.6367   1.7323  -0.6446
 I73  H16  H  HCR5  0   0.258   2.1755  -4.4263   0.4597
 I73  H17  H  HCH1  0   0.232  -1.7884  -3.7982   0.3802
 I73  H18  H  HCH3  0   0.214   0.0719  -5.8697  -0.8784
 I73  H19  H  HCH3  0   0.223  -1.6828  -5.9990  -0.7564
 I73  H20  H  HCH3  0   0.226  -0.9565  -4.7480  -1.7695
 I73  H21  H  HCH3  0   0.228  -0.7412  -4.4655   2.5411
 I73  H22  H  HCH3  0   0.224  -1.5437  -5.8383   1.7748
 I73  H23  H  HCH3  0   0.214   0.2102  -5.6946   1.7079
 I73  H24  H  HNH1  0   0.408   3.5993  -0.4863  -0.3227
 I73  H25  H  HCH2  0   0.258   3.1437   1.8122  -1.6882
 I73  H26  H  HCH2  0   0.262   2.7253   2.3022  -0.0525
 I73  H27  H  HCR6  0   0.255   5.4172   1.8960  -2.3452
 I73  H28  H  HCR6  0   0.258   7.8018   2.1800  -1.7876
 I73  H29  H  HCR6  0   0.258   8.5272   2.2192   0.5772
 I73  H30  H  HCR6  0   0.258   6.8477   1.9798   2.3820
 I73  H31  H  HCR6  0   0.256   4.4652   1.7029   1.8226

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
 I73  C14  C15  aromatic  1.391  0.020  1.391
 I73  C14  C13  aromatic  1.387  0.020  1.387
 I73  C15  C16  aromatic  1.387  0.020  1.387
 I73  C13  C12  aromatic  1.394  0.020  1.394
 I73  C16  C17  aromatic  1.390  0.020  1.390
 I73  C12  C17  aromatic  1.390  0.020  1.390
 I73  C12  C11  single    1.504  0.020  1.504
 I73  N10  C11  single    1.447  0.020  1.447
 I73  N10  C3   single    1.339  0.020  1.339
 I73  N1   C9   aromatic  1.323  0.020  1.323
 I73  N1   N2   aromatic  1.343  0.020  1.343
 I73  C9   C8   aromatic  1.403  0.020  1.403
 I73  C3   N2   aromatic  1.367  0.020  1.367
 I73  C3   C4   aromatic  1.373  0.020  1.373
 I73  N2   C7   aromatic  1.376  0.020  1.376
 I73  C8   C7   aromatic  1.390  0.020  1.390
 I73  C8   C26  single    1.497  0.020  1.497
 I73  C27  C26  single    1.529  0.020  1.529
 I73  C4   C5   aromatic  1.426  0.020  1.426
 I73  C7   N6   aromatic  1.341  0.020  1.341
 I73  C5   N6   aromatic  1.321  0.020  1.321
 I73  C5   N18  single    1.349  0.020  1.349
 I73  C26  C28  single    1.530  0.020  1.530
 I73  N18  C40  single    1.445  0.020  1.445
 I73  C40  C41  single    1.526  0.020  1.526
 I73  C41  C46  single    1.531  0.020  1.531
 I73  C41  C42  single    1.526  0.020  1.526
 I73  C46  C45  single    1.525  0.020  1.525
 I73  C45  N44  single    1.454  0.020  1.454
 I73  C42  C43  single    1.532  0.020  1.532
 I73  C42  O1   single    1.412  0.020  1.412
 I73  C43  N44  single    1.450  0.020  1.450
 I73  O1   H1   single    0.850  0.020  0.980
 I73  C42  H2   single    0.970  0.020  1.090
 I73  C43  H3   single    0.970  0.020  1.090
 I73  C43  H4   single    0.970  0.020  1.090
 I73  N44  H5   single    0.890  0.020  1.040
 I73  C45  H7   single    0.970  0.020  1.090
 I73  C45  H8   single    0.970  0.020  1.090
 I73  C46  H9   single    0.970  0.020  1.090
 I73  C46  H10  single    0.970  0.020  1.090
 I73  C41  H11  single    0.970  0.020  1.090
 I73  C40  H12  single    0.970  0.020  1.090
 I73  C40  H13  single    0.970  0.020  1.090
 I73  N18  H14  single    0.860  0.020  1.020
 I73  C4   H15  single    0.930  0.020  1.080
 I73  C9   H16  single    0.930  0.020  1.080
 I73  C26  H17  single    0.970  0.020  1.090
 I73  C28  H18  single    0.970  0.020  1.090
 I73  C28  H19  single    0.970  0.020  1.090
 I73  C28  H20  single    0.970  0.020  1.090
 I73  C27  H21  single    0.970  0.020  1.090
 I73  C27  H22  single    0.970  0.020  1.090
 I73  C27  H23  single    0.970  0.020  1.090
 I73  N10  H24  single    0.860  0.020  1.020
 I73  C11  H25  single    0.970  0.020  1.090
 I73  C11  H26  single    0.970  0.020  1.090
 I73  C17  H27  single    0.930  0.020  1.080
 I73  C16  H28  single    0.930  0.020  1.080
 I73  C15  H29  single    0.930  0.020  1.080
 I73  C14  H30  single    0.930  0.020  1.080
 I73  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
 I73  H1   O1   C42  108.12  3.000
 I73  H2   C42  C41  107.88  3.000
 I73  H2   C42  C43  108.08  3.000
 I73  C41  C42  C43  110.35  3.000
 I73  H2   C42  O1   110.60  3.000
 I73  C43  C42  O1   110.92  3.000
 I73  C41  C42  O1   108.97  3.000
 I73  H4   C43  H3   106.91  3.000
 I73  H4   C43  N44  108.91  3.000
 I73  H3   C43  N44  108.60  3.000
 I73  H4   C43  C42  109.63  3.000
 I73  H3   C43  C42  108.37  3.000
 I73  N44  C43  C42  114.16  3.000
 I73  H5   N44  C45  108.98  3.000
 I73  H5   N44  C43  109.08  3.000
 I73  C45  N44  C43  111.27  3.000
 I73  H8   C45  H7   106.65  3.000
 I73  H8   C45  C46  110.27  3.000
 I73  H7   C45  C46  109.18  3.000
 I73  H8   C45  N44  108.75  3.000
 I73  H7   C45  N44  108.03  3.000
 I73  C46  C45  N44  113.70  3.000
 I73  H10  C46  H9   106.52  3.000
 I73  H10  C46  C41  109.33  3.000
 I73  H9   C46  C41  110.48  3.000
 I73  H10  C46  C45  109.38  3.000
 I73  H9   C46  C45  109.60  3.000
 I73  C41  C46  C45  111.40  3.000
 I73  H11  C41  C40  108.73  3.000
 I73  H11  C41  C46  108.32  3.000
 I73  C40  C41  C46  111.99  3.000
 I73  H11  C41  C42  107.44  3.000
 I73  C46  C41  C42  109.02  3.000
 I73  C40  C41  C42  111.20  3.000
 I73  H13  C40  H12  106.89  3.000
 I73  H13  C40  N18  110.77  3.000
 I73  H12  C40  N18  108.89  3.000
 I73  H13  C40  C41  110.22  3.000
 I73  H12  C40  C41  109.39  3.000
 I73  N18  C40  C41  110.59  3.000
 I73  H14  N18  C5   117.14  3.000
 I73  H14  N18  C40  117.44  3.000
 I73  C5   N18  C40  123.62  3.000
 I73  N6   C5   C4   123.51  3.000
 I73  N6   C5   N18  118.26  3.000
 I73  C4   C5   N18  118.22  3.000
 I73  H15  C4   C3   120.64  3.000
 I73  H15  C4   C5   120.29  3.000
 I73  C3   C4   C5   119.06  3.000
 I73  N10  C3   N2   116.61  3.000
 I73  N2   C3   C4   116.22  3.000
 I73  N10  C3   C4   127.16  3.000
 I73  C7   N2   N1   113.38  3.000
 I73  C7   N2   C3   122.16  3.000
 I73  N1   N2   C3   124.46  3.000
 I73  C9   N1   N2   103.62  3.000
 I73  H16  C9   C8   127.31  3.000
 I73  H16  C9   N1   119.10  3.000
 I73  C8   C9   N1   113.59  3.000
 I73  C7   C8   C26  127.06  3.000
 I73  C26  C8   C9   128.97  3.000
 I73  C7   C8   C9   103.97  3.000
 I73  H17  C26  C27  108.08  3.000
 I73  H17  C26  C28  107.92  3.000
 I73  C27  C26  C28  110.48  3.000
 I73  H17  C26  C8   107.15  3.000
 I73  C28  C26  C8   111.32  3.000
 I73  C27  C26  C8   111.71  3.000
 I73  H20  C28  H19  108.06  3.000
 I73  H20  C28  H18  107.78  3.000
 I73  H19  C28  H18  107.72  3.000
 I73  H20  C28  C26  111.39  3.000
 I73  H19  C28  C26  110.99  3.000
 I73  H18  C28  C26  110.74  3.000
 I73  H23  C27  H22  107.46  3.000
 I73  H23  C27  H21  107.77  3.000
 I73  H22  C27  H21  107.96  3.000
 I73  H23  C27  C26  111.01  3.000
 I73  H22  C27  C26  110.95  3.000
 I73  H21  C27  C26  111.52  3.000
 I73  N6   C7   C8   132.05  3.000
 I73  N6   C7   N2   122.50  3.000
 I73  C8   C7   N2   105.45  3.000
 I73  C7   N6   C5   116.54  3.000
 I73  H24  N10  C11  118.38  3.000
 I73  H24  N10  C3   116.85  3.000
 I73  C11  N10  C3   122.62  3.000
 I73  H26  C11  H25  106.95  3.000
 I73  H26  C11  C12  109.54  3.000
 I73  H25  C11  C12  110.33  3.000
 I73  H26  C11  N10  108.78  3.000
 I73  H25  C11  N10  111.17  3.000
 I73  C12  C11  N10  110.01  3.000
 I73  C13  C12  C17  119.08  3.000
 I73  C17  C12  C11  120.88  3.000
 I73  C13  C12  C11  120.03  3.000
 I73  H27  C17  C16  119.74  3.000
 I73  H27  C17  C12  119.74  3.000
 I73  C16  C17  C12  120.52  3.000
 I73  H28  C16  C15  120.15  3.000
 I73  H28  C16  C17  119.79  3.000
 I73  C15  C16  C17  120.06  3.000
 I73  H29  C15  C14  120.13  3.000
 I73  H29  C15  C16  120.12  3.000
 I73  C14  C15  C16  119.76  3.000
 I73  H30  C14  C13  119.82  3.000
 I73  H30  C14  C15  120.12  3.000
 I73  C13  C14  C15  120.05  3.000
 I73  H31  C13  C14  119.76  3.000
 I73  H31  C13  C12  119.71  3.000
 I73  C14  C13  C12  120.53  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
 I73  CONST_01  N2   C3   C4   C5     0.00   0.0  0
 I73  CONST_02  N2   C7   N6   C5     0.00   0.0  0
 I73  CONST_03  C8   C7   N6   C5   180.00   0.0  0
 I73  CONST_04  N1   N2   C3   C4   180.00   0.0  0
 I73  CONST_05  C7   N2   C3   C4     0.00   0.0  0
 I73  CONST_06  C7   N6   C5   C4     0.00   0.0  0
 I73  CONST_07  C9   N1   N2   C3   180.00   0.0  0
 I73  CONST_08  C8   C7   N2   C3   180.00   0.0  0
 I73  CONST_09  N6   C7   N2   C3     0.00   0.0  0
 I73  CONST_10  N6   C5   C4   C3     0.00   0.0  0
 I73  CONST_11  C8   C9   N1   N2     0.00   0.0  0
 I73  CONST_12  C9   C8   C7   N2     0.00   0.0  0
 I73  CONST_13  C7   C8   C9   N1     0.00   0.0  0
 I73  CONST_14  C8   C7   N2   N1     0.00   0.0  0
 I73  CONST_15  N6   C7   N2   N1   180.00   0.0  0
 I73  CONST_16  C7   N2   N1   C9     0.00   0.0  0
 I73  CONST_17  N6   C7   C8   C9   180.00   0.0  0
 I73  CONST_18  C15  C14  C13  C12    0.00   0.0  0
 I73  CONST_19  C15  C16  C17  C12    0.00   0.0  0
 I73  CONST_20  C14  C15  C16  C17    0.00   0.0  0
 I73  CONST_21  C14  C13  C12  C17    0.00   0.0  0
 I73  CONST_22  C13  C14  C15  C16    0.00   0.0  0
 I73  CONST_23  C13  C12  C17  C16    0.00   0.0  0
 I73  CONST_24  C3   C4   C5   N18  180.00   0.0  0
 I73  CONST_25  C7   N6   C5   N18  180.00   0.0  0
 I73  CONST_26  N10  C3   C4   C5   180.00   0.0  0
 I73  CONST_27  C26  C8   C7   N2   180.00   0.0  0
 I73  CONST_28  C26  C8   C9   N1   180.00   0.0  0
 I73  CONST_29  N10  C3   N2   N1     0.00   0.0  0
 I73  CONST_30  N6   C7   C8   C26    0.00   0.0  0
 I73  CONST_31  N10  C3   N2   C7   180.00   0.0  0
 I73  CONST_32  C14  C13  C12  C11  180.00   0.0  0
 I73  CONST_33  C16  C17  C12  C11  180.00   0.0  0
 I73  CONST_34  H16  C9   N1   N2   180.00   0.0  0
 I73  CONST_35  H15  C4   C3   N2   180.00   0.0  0
 I73  CONST_36  H30  C14  C13  C12  180.00   0.0  0
 I73  CONST_37  H28  C16  C17  C12  180.00   0.0  0
 I73  CONST_38  H29  C15  C16  C17  180.00   0.0  0
 I73  CONST_39  H31  C13  C12  C17  180.00   0.0  0
 I73  CONST_40  H27  C17  C16  C15  180.00   0.0  0
 I73  CONST_41  C4   C5   N18  C40  180.00   0.0  0
 I73  CONST_42  N6   C5   N18  C40    0.00   0.0  0
 I73  CONST_43  C11  N10  C3   C4     0.00   0.0  0
 I73  CONST_44  C11  N10  C3   N2   180.00   0.0  0
 I73  CONST_45  H24  N10  C3   C4   180.00   0.0  0
 I73  CONST_46  H14  N18  C5   C4     0.00   0.0  0
 I73  Var_01    C45  N44  C43  C42   54.22  30.0  1
 I73  Var_02    C46  C45  N44  C43  -53.33  30.0  1
 I73  Var_03    C41  C46  C45  N44   54.49  30.0  1
 I73  Var_04    C5   N18  C40  C41  166.20  30.0  1
 I73  Var_05    C12  C11  N10  C3   168.96  30.0  3
 I73  Var_06    C27  C26  C8   C9    55.67  30.0  2
 I73  Var_07    C13  C12  C11  N10  -68.96  30.0  2
 I73  Var_08    H21  C27  C26  C8    57.34  30.0  3
 I73  Var_09    H18  C28  C26  C8    63.50  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
 I73  chir_01  C42  C41  C43  O1   negativ
 I73  chir_02  C41  C42  C46  C40  negativ

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
 I73  plan-1  C11  0.020
 I73  plan-1  C12  0.020
 I73  plan-1  C17  0.020
 I73  plan-1  C16  0.020
 I73  plan-1  C15  0.020
 I73  plan-1  C14  0.020
 I73  plan-1  C13  0.020
 I73  plan-1  H27  0.020
 I73  plan-1  H28  0.020
 I73  plan-1  H29  0.020
 I73  plan-1  H30  0.020
 I73  plan-1  H31  0.020
 I73  plan-2  N18  0.020
 I73  plan-2  C5   0.020
 I73  plan-2  C4   0.020
 I73  plan-2  C3   0.020
 I73  plan-2  N2   0.020
 I73  plan-2  N1   0.020
 I73  plan-2  C9   0.020
 I73  plan-2  C8   0.020
 I73  plan-2  C26  0.020
 I73  plan-2  C7   0.020
 I73  plan-2  N6   0.020
 I73  plan-2  N10  0.020
 I73  plan-2  H15  0.020
 I73  plan-2  H16  0.020
 I73  plan-3  C40  0.020
 I73  plan-3  N18  0.020
 I73  plan-3  C5   0.020
 I73  plan-3  H14  0.020
 I73  plan-4  C3   0.020
 I73  plan-4  N10  0.020
 I73  plan-4  C11  0.020
 I73  plan-4  H24  0.020

