# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:41:23 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2S,3S)-3-{[7-(benzylamino)-3-(propan-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1cnn2c(NCc3ccccc3)cc(N[C@@H](CO)[C@H](O)CO)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
 NS9  NS9  (2S,3S)-3-{[7-(benzylamino)-3-(propan-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol  ligand  55  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NS9
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
 NS9  N1    N  N     0  -0.342   1.5150  -2.4623  -0.3639
 NS9  N2    N  N     0  -0.451   0.7413  -1.3778  -0.1963
 NS9  C3    C  CR6   0   0.699   1.2134  -0.1061  -0.0327
 NS9  C4    C  CR16  0  -0.577   0.2679   0.8783   0.1342
 NS9  C5    C  CR6   0   0.552  -1.1101   0.5203   0.1292
 NS9  N6    N  N     0  -0.529  -1.5395  -0.7182  -0.0186
 NS9  C7    C  CR56  0   0.547  -0.6043  -1.6643  -0.1820
 NS9  C8    C  CR5   0  -0.177  -0.6925  -3.0403  -0.3542
 NS9  C9    C  CR15  0  -0.058   0.6444  -3.4544  -0.4577
 NS9  N10   N  NH1   0  -0.674   2.5386   0.0553  -0.0524
 NS9  C11   C  CH2   0  -0.336   3.1710   1.3412   0.1591
 NS9  C12   C  CR6   0   0.063   4.6652   1.1877   0.1214
 NS9  C13   C  CR16  0  -0.289   5.3914   1.0528   1.3003
 NS9  C14   C  CR16  0  -0.241   6.7689   0.8803   1.2641
 NS9  C15   C  CR16  0  -0.262   7.4314   0.8379   0.0447
 NS9  C16   C  CR16  0  -0.241   6.7128   0.9687  -1.1372
 NS9  C17   C  CR16  0  -0.281   5.3365   1.1428  -1.0977
 NS9  N18   N  NH1   0  -0.690  -2.0246   1.5115   0.2637
 NS9  C19   C  CH1   0  -0.172  -3.4354   1.2741   0.4744
 NS9  C20   C  CH1   0   0.013  -4.2404   2.4165  -0.1714
 NS9  C21   C  CH2   0  -0.157  -4.0381   2.4291  -1.6790
 NS9  O22   O  OH1   0  -0.671  -4.7180   3.5370  -2.2212
 NS9  C23   C  CH2   0  -0.142  -3.7537   1.0748   1.9494
 NS9  O24   O  OH1   0  -0.675  -3.4466   2.2617   2.6446
 NS9  O25   O  OH1   0  -0.659  -5.6037   2.3411   0.1708
 NS9  C26   C  CH1   0  -0.332  -1.9413  -3.8649  -0.3941
 NS9  C27   C  CH3   0  -0.642  -2.0923  -4.6017  -1.7253
 NS9  C28   C  CH3   0  -0.642  -1.9951  -4.8509   0.7742
 NS9  H4    H  HCR6  0   0.288   0.5678   1.9074   0.2682
 NS9  H9    H  HCR5  0   0.258   1.0090  -4.4622  -0.5997
 NS9  HN10  H  HNH1  0   0.411   3.1118  -0.7710  -0.1279
 NS9  H11   H  HCH2  0   0.260   2.8461   2.0427  -0.6150
 NS9  H11A  H  HCH2  0   0.260   2.8598   1.7595   1.1215
 NS9  H13   H  HCR6  0   0.255   4.8769   1.0889   2.2534
 NS9  H14   H  HCR6  0   0.259   7.3244   0.7795   2.1874
 NS9  H15   H  HCR6  0   0.259   8.5054   0.7078   0.0146
 NS9  H16   H  HCR6  0   0.259   7.2256   0.9392  -2.0899
 NS9  H17   H  HCR6  0   0.256   4.7798   1.2526  -2.0210
 NS9  HN18  H  HNH1  0   0.390  -1.6725   2.4075   0.5616
 NS9  H19   H  HCH1  0   0.259  -3.6903   0.3388  -0.0312
 NS9  H20   H  HCH1  0   0.230  -3.8898   3.3721   0.2336
 NS9  H21   H  HCH2  0   0.209  -2.9654   2.4688  -1.8960
 NS9  H21A  H  HCH2  0   0.189  -4.4113   1.4798  -2.0948
 NS9  HO22  H  HOH1  0   0.455  -4.5353   3.5636  -3.1643
 NS9  H23   H  HCH2  0   0.199  -4.8059   0.7916   2.0641
 NS9  H23A  H  HCH2  0   0.209  -3.1557   0.2284   2.3094
 NS9  HO24  H  HOH1  0   0.457  -3.5790   2.1054   3.5834
 NS9  HO25  H  HOH1  0   0.443  -5.9783   1.5450  -0.2227
 NS9  H26   H  HCH1  0   0.233  -2.7852  -3.1750  -0.2933
 NS9  H27   H  HCH3  0   0.214  -1.2833  -5.3216  -1.8696
 NS9  H27A  H  HCH3  0   0.224  -3.0332  -5.1546  -1.7598
 NS9  H27B  H  HCH3  0   0.227  -2.0776  -3.9103  -2.5684
 NS9  H28   H  HCH3  0   0.223  -2.9223  -5.4271   0.7585
 NS9  H28A  H  HCH3  0   0.215  -1.1644  -5.5578   0.7243
 NS9  H28B  H  HCH3  0   0.227  -1.9371  -4.3344   1.7329

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
 NS9  N1   C9    aromatic  1.323  0.020  1.323
 NS9  N1   N2    aromatic  1.343  0.020  1.343
 NS9  N2   C3    aromatic  1.366  0.020  1.366
 NS9  N2   C7    aromatic  1.376  0.020  1.376
 NS9  N10  C3    single    1.335  0.020  1.335
 NS9  C3   C4    aromatic  1.375  0.020  1.375
 NS9  C4   C5    aromatic  1.424  0.020  1.424
 NS9  C4   H4    single    0.930  0.020  1.080
 NS9  N6   C5    aromatic  1.319  0.020  1.319
 NS9  C5   N18   single    1.355  0.020  1.355
 NS9  C7   N6    aromatic  1.340  0.020  1.340
 NS9  C8   C7    aromatic  1.390  0.020  1.390
 NS9  C9   C8    aromatic  1.403  0.020  1.403
 NS9  C8   C26   single    1.497  0.020  1.497
 NS9  C9   H9    single    0.930  0.020  1.080
 NS9  N10  C11   single    1.448  0.020  1.448
 NS9  N10  HN10  single    0.860  0.020  1.020
 NS9  C12  C11   single    1.503  0.020  1.503
 NS9  C11  H11   single    0.970  0.020  1.090
 NS9  C11  H11A  single    0.970  0.020  1.090
 NS9  C13  C12   aromatic  1.391  0.020  1.391
 NS9  C12  C17   aromatic  1.393  0.020  1.393
 NS9  C14  C13   aromatic  1.389  0.020  1.389
 NS9  C13  H13   single    0.930  0.020  1.080
 NS9  C14  C15   aromatic  1.388  0.020  1.388
 NS9  C14  H14   single    0.930  0.020  1.080
 NS9  C15  C16   aromatic  1.389  0.020  1.389
 NS9  C15  H15   single    0.930  0.020  1.080
 NS9  C16  C17   aromatic  1.388  0.020  1.388
 NS9  C16  H16   single    0.930  0.020  1.080
 NS9  C17  H17   single    0.930  0.020  1.080
 NS9  N18  C19   single    1.446  0.020  1.446
 NS9  N18  HN18  single    0.890  0.020  1.040
 NS9  C23  C19   single    1.522  0.020  1.522
 NS9  C19  C20   single    1.540  0.020  1.540
 NS9  C19  H19   single    0.970  0.020  1.090
 NS9  C20  O25   single    1.408  0.020  1.408
 NS9  C20  C21   single    1.521  0.020  1.521
 NS9  C20  H20   single    0.970  0.020  1.090
 NS9  O22  C21   single    1.408  0.020  1.408
 NS9  C21  H21   single    0.970  0.020  1.090
 NS9  C21  H21A  single    0.970  0.020  1.090
 NS9  O22  HO22  single    0.850  0.020  0.980
 NS9  C23  O24   single    1.409  0.020  1.409
 NS9  C23  H23   single    0.970  0.020  1.090
 NS9  C23  H23A  single    0.970  0.020  1.090
 NS9  O24  HO24  single    0.850  0.020  0.980
 NS9  O25  HO25  single    0.850  0.020  0.980
 NS9  C28  C26   single    1.530  0.020  1.530
 NS9  C26  C27   single    1.529  0.020  1.529
 NS9  C26  H26   single    0.970  0.020  1.090
 NS9  C27  H27   single    0.970  0.020  1.090
 NS9  C27  H27A  single    0.970  0.020  1.090
 NS9  C27  H27B  single    0.970  0.020  1.090
 NS9  C28  H28   single    0.970  0.020  1.090
 NS9  C28  H28A  single    0.970  0.020  1.090
 NS9  C28  H28B  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
 NS9  C9    N1   N2    103.61  3.000
 NS9  C7    N2   C3    122.04  3.000
 NS9  C7    N2   N1    113.37  3.000
 NS9  C3    N2   N1    124.58  3.000
 NS9  N10   C3   C4    126.71  3.000
 NS9  C4    C3   N2    116.31  3.000
 NS9  N10   C3   N2    116.98  3.000
 NS9  H4    C4   C5    120.58  3.000
 NS9  H4    C4   C3    120.40  3.000
 NS9  C5    C4   C3    119.02  3.000
 NS9  N18   C5   N6    118.56  3.000
 NS9  N18   C5   C4    117.96  3.000
 NS9  N6    C5   C4    123.47  3.000
 NS9  C7    N6   C5    116.70  3.000
 NS9  C8    C7   N6    132.05  3.000
 NS9  C8    C7   N2    105.49  3.000
 NS9  N6    C7   N2    122.46  3.000
 NS9  C26   C8   C9    129.07  3.000
 NS9  C26   C8   C7    126.99  3.000
 NS9  C9    C8   C7    103.93  3.000
 NS9  H9    C9   C8    127.30  3.000
 NS9  H9    C9   N1    119.10  3.000
 NS9  C8    C9   N1    113.60  3.000
 NS9  HN10  N10  C11   119.35  3.000
 NS9  HN10  N10  C3    117.79  3.000
 NS9  C11   N10  C3    122.58  3.000
 NS9  H11A  C11  H11   107.01  3.000
 NS9  H11A  C11  C12   110.11  3.000
 NS9  H11   C11  C12   110.07  3.000
 NS9  H11A  C11  N10   110.10  3.000
 NS9  H11   C11  N10   109.65  3.000
 NS9  C12   C11  N10   109.86  3.000
 NS9  C17   C12  C13   119.15  3.000
 NS9  C17   C12  C11   120.31  3.000
 NS9  C13   C12  C11   120.52  3.000
 NS9  H13   C13  C14   119.87  3.000
 NS9  H13   C13  C12   119.62  3.000
 NS9  C14   C13  C12   120.51  3.000
 NS9  H14   C14  C15   120.10  3.000
 NS9  H14   C14  C13   119.89  3.000
 NS9  C15   C14  C13   120.00  3.000
 NS9  H15   C15  C16   120.06  3.000
 NS9  H15   C15  C14   120.11  3.000
 NS9  C16   C15  C14   119.83  3.000
 NS9  H16   C16  C17   119.89  3.000
 NS9  H16   C16  C15   120.08  3.000
 NS9  C17   C16  C15   120.04  3.000
 NS9  H17   C17  C16   119.86  3.000
 NS9  H17   C17  C12   119.67  3.000
 NS9  C16   C17  C12   120.47  3.000
 NS9  HN18  N18  C19   116.35  3.000
 NS9  HN18  N18  C5    116.35  3.000
 NS9  C19   N18  C5    123.55  3.000
 NS9  H19   C19  C23   106.70  3.000
 NS9  H19   C19  C20   108.60  3.000
 NS9  C23   C19  C20   113.22  3.000
 NS9  H19   C19  N18   107.49  3.000
 NS9  C20   C19  N18   109.10  3.000
 NS9  C23   C19  N18   111.51  3.000
 NS9  H20   C20  O25   105.48  3.000
 NS9  H20   C20  C21   108.45  3.000
 NS9  O25   C20  C21   111.73  3.000
 NS9  H20   C20  C19   108.96  3.000
 NS9  C21   C20  C19   110.63  3.000
 NS9  O25   C20  C19   111.39  3.000
 NS9  H21A  C21  H21   106.76  3.000
 NS9  H21A  C21  O22   111.65  3.000
 NS9  H21   C21  O22   111.59  3.000
 NS9  H21A  C21  C20   108.78  3.000
 NS9  H21   C21  C20   109.09  3.000
 NS9  O22   C21  C20   108.89  3.000
 NS9  HO22  O22  C21   107.92  3.000
 NS9  H23A  C23  H23   106.84  3.000
 NS9  H23A  C23  O24   111.66  3.000
 NS9  H23   C23  O24   112.04  3.000
 NS9  H23A  C23  C19   107.76  3.000
 NS9  H23   C23  C19   109.64  3.000
 NS9  O24   C23  C19   108.80  3.000
 NS9  HO24  O24  C23   108.35  3.000
 NS9  HO25  O25  C20   108.75  3.000
 NS9  H26   C26  C28   107.99  3.000
 NS9  H26   C26  C27   107.92  3.000
 NS9  C28   C26  C27   110.54  3.000
 NS9  H26   C26  C8    107.07  3.000
 NS9  C27   C26  C8    111.77  3.000
 NS9  C28   C26  C8    111.35  3.000
 NS9  H27B  C27  H27A  107.96  3.000
 NS9  H27B  C27  H27   107.80  3.000
 NS9  H27A  C27  H27   107.47  3.000
 NS9  H27B  C27  C26   111.49  3.000
 NS9  H27A  C27  C26   110.89  3.000
 NS9  H27   C27  C26   111.06  3.000
 NS9  H28B  C28  H28A  107.84  3.000
 NS9  H28B  C28  H28   107.93  3.000
 NS9  H28A  C28  H28   107.68  3.000
 NS9  H28B  C28  C26   111.36  3.000
 NS9  H28A  C28  C26   110.84  3.000
 NS9  H28   C28  C26   111.04  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
 NS9  CONST_01  C7    C8   C9   N1      0.00   0.0  0
 NS9  CONST_02  C4    C3   N2   N1    180.00   0.0  0
 NS9  CONST_03  N6    C7   N2   N1    180.00   0.0  0
 NS9  CONST_04  C8    C7   N2   N1      0.00   0.0  0
 NS9  CONST_05  C8    C9   N1   N2      0.00   0.0  0
 NS9  CONST_06  C5    C4   C3   N2      0.00   0.0  0
 NS9  CONST_07  C5    N6   C7   N2      0.00   0.0  0
 NS9  CONST_08  C9    C8   C7   N2      0.00   0.0  0
 NS9  CONST_09  C9    N1   N2   C3    180.00   0.0  0
 NS9  CONST_10  N6    C7   N2   C3      0.00   0.0  0
 NS9  CONST_11  C8    C7   N2   C3    180.00   0.0  0
 NS9  CONST_12  N6    C5   C4   C3      0.00   0.0  0
 NS9  CONST_13  C7    N2   C3   C4      0.00   0.0  0
 NS9  CONST_14  C7    N6   C5   C4      0.00   0.0  0
 NS9  CONST_15  C8    C7   N6   C5    180.00   0.0  0
 NS9  CONST_16  C9    C8   C7   N6    180.00   0.0  0
 NS9  CONST_17  C9    N1   N2   C7      0.00   0.0  0
 NS9  CONST_18  C15   C14  C13  C12     0.00   0.0  0
 NS9  CONST_19  C15   C16  C17  C12     0.00   0.0  0
 NS9  CONST_20  C16   C17  C12  C13     0.00   0.0  0
 NS9  CONST_21  C16   C15  C14  C13     0.00   0.0  0
 NS9  CONST_22  C17   C12  C13  C14     0.00   0.0  0
 NS9  CONST_23  C17   C16  C15  C14     0.00   0.0  0
 NS9  CONST_24  C26   C8   C9   N1    180.00   0.0  0
 NS9  CONST_25  N10   C3   N2   N1      0.00   0.0  0
 NS9  CONST_26  C26   C8   C7   N2    180.00   0.0  0
 NS9  CONST_27  N18   C5   C4   C3    180.00   0.0  0
 NS9  CONST_28  N10   C3   C4   C5    180.00   0.0  0
 NS9  CONST_29  C26   C8   C7   N6      0.00   0.0  0
 NS9  CONST_30  N10   C3   N2   C7    180.00   0.0  0
 NS9  CONST_31  N18   C5   N6   C7    180.00   0.0  0
 NS9  CONST_32  C14   C13  C12  C11   180.00   0.0  0
 NS9  CONST_33  C16   C17  C12  C11   180.00   0.0  0
 NS9  CONST_34  H9    C9   N1   N2    180.00   0.0  0
 NS9  CONST_35  H4    C4   C3   N2    180.00   0.0  0
 NS9  CONST_36  H14   C14  C13  C12   180.00   0.0  0
 NS9  CONST_37  H16   C16  C17  C12   180.00   0.0  0
 NS9  CONST_38  H17   C17  C12  C13   180.00   0.0  0
 NS9  CONST_39  H15   C15  C14  C13   180.00   0.0  0
 NS9  CONST_40  H13   C13  C14  C15   180.00   0.0  0
 NS9  CONST_41  C11   N10  C3   N2    180.00   0.0  0
 NS9  CONST_42  C11   N10  C3   C4      0.00   0.0  0
 NS9  CONST_43  C19   N18  C5   C4    180.00   0.0  0
 NS9  CONST_44  C19   N18  C5   N6      0.00   0.0  0
 NS9  CONST_45  HN10  N10  C3   N2      0.00   0.0  0
 NS9  CONST_46  HN18  N18  C5   C4      0.00   0.0  0
 NS9  Var_01    C12   C11  N10  C3    178.17  30.0  3
 NS9  Var_02    C28   C26  C8   C7   -116.06  30.0  2
 NS9  Var_03    C13   C12  C11  N10   -96.60  30.0  2
 NS9  Var_04    H28   C28  C26  C8    178.18  30.0  3
 NS9  Var_05    H27   C27  C26  C8     63.66  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
 NS9  chir_01  C19  N18  C23  C20  negativ
 NS9  chir_02  C20  O25  C19  C21  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
 NS9  plan-1  C11   0.020
 NS9  plan-1  C12   0.020
 NS9  plan-1  C13   0.020
 NS9  plan-1  C14   0.020
 NS9  plan-1  C15   0.020
 NS9  plan-1  C16   0.020
 NS9  plan-1  C17   0.020
 NS9  plan-1  H13   0.020
 NS9  plan-1  H14   0.020
 NS9  plan-1  H15   0.020
 NS9  plan-1  H16   0.020
 NS9  plan-1  H17   0.020
 NS9  plan-2  N1    0.020
 NS9  plan-2  N2    0.020
 NS9  plan-2  C3    0.020
 NS9  plan-2  C4    0.020
 NS9  plan-2  C5    0.020
 NS9  plan-2  N6    0.020
 NS9  plan-2  C7    0.020
 NS9  plan-2  C8    0.020
 NS9  plan-2  C9    0.020
 NS9  plan-2  N10   0.020
 NS9  plan-2  N18   0.020
 NS9  plan-2  C26   0.020
 NS9  plan-2  H4    0.020
 NS9  plan-2  H9    0.020
 NS9  plan-3  C3    0.020
 NS9  plan-3  N10   0.020
 NS9  plan-3  C11   0.020
 NS9  plan-3  HN10  0.020
 NS9  plan-4  C5    0.020
 NS9  plan-4  N18   0.020
 NS9  plan-4  C19   0.020
 NS9  plan-4  HN18  0.020

