# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:16:56 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: N-[2-({4-[3-(propan-2-ylamino)pyridin-2-yl]piperazin-1-yl}carbonyl)-1H-indol-5-yl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Nc1cccnc1N2CCN(CC2)C(=O)c3[nH]c4ccc(N[S](C)(=O)=O)cc4c3
#
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
 SPP  SPP  N-[2-({4-[3-(propan-2-ylamino)pyridin-2-yl]piperazin-1-yl}carbonyl)-1H-indol-5-yl]methanesulfonamide  ligand  60  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SPP
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
 SPP  C2    C  CR6   0   0.369   4.7962  -0.1293  -1.2060
 SPP  C3    C  CR6   0   0.270   6.0937  -0.2631  -0.6453
 SPP  C4    C  CR16  0  -0.247   7.1531  -0.3522  -1.5446
 SPP  C5    C  CR16  0  -0.328   6.8972  -0.3477  -2.9108
 SPP  C6    C  CR16  0  -0.116   5.5911  -0.2651  -3.3481
 SPP  C8    C  CH2   0  -0.319   3.5782   1.3168   0.2854
 SPP  C9    C  CH2   0  -0.323   2.5929   1.2570   1.4374
 SPP  C11   C  CH2   0  -0.342   1.4514  -0.5817   0.3606
 SPP  C12   C  CH2   0  -0.272   2.4358  -0.4980  -0.7966
 SPP  C     C  C     0   0.511   0.2477   1.5364   0.8628
 SPP  C14   C  CR5   0   0.203  -1.0655   0.9056   0.5828
 SPP  C15   C  CR15  0  -0.402  -2.0392   1.3760  -0.2538
 SPP  C16   C  CR16  0  -0.376  -4.4126   0.4339  -0.7288
 SPP  C17   C  CR6   0   0.255  -5.2696  -0.5876  -0.3708
 SPP  C18   C  CR16  0  -0.272  -4.8867  -1.5638   0.5694
 SPP  C19   C  CR16  0  -0.309  -3.6482  -1.5293   1.1701
 SPP  C20   C  CR56  0   0.356  -2.7798  -0.5017   0.8020
 SPP  C21   C  CR56  0   0.071  -3.1431   0.4829  -0.1426
 SPP  CA    C  CH1   0  -0.114   7.4300  -0.7661   1.3801
 SPP  CB    C  CH3   0  -0.658   7.3651  -0.3689   2.8477
 SPP  CC    C  CH3   0  -0.656   7.6180  -2.2738   1.2234
 SPP  CE    C  CH3   0  -0.796  -7.6986   1.6278  -0.0120
 SPP  N     N  NH1   0  -0.672   6.2320  -0.2761   0.7189
 SPP  N1    N  N     0  -0.416   4.5687  -0.1469  -2.5012
 SPP  N7    N  NT    0  -0.512   3.7138  -0.0084  -0.3162
 SPP  N10   N  NT    0  -0.462   1.3154   0.7187   1.0027
 SPP  N13   N  NR15  0  -0.723  -1.5116  -0.2283   1.2130
 SPP  ND    N  NC1   0  -0.816  -6.5578  -0.6949  -0.9679
 SPP  O     O  O     0  -0.474   0.3028   2.7502   1.0000
 SPP  OS1   O  OS    0  -0.659  -7.8079  -0.6901   1.2107
 SPP  OS2   O  OS    0  -0.669  -9.0345  -0.4269  -0.9661
 SPP  S     S  S     0   1.318  -7.8802  -0.1371  -0.1313
 SPP  H4    H  HCR6  0   0.272   8.1722  -0.4482  -1.1939
 SPP  H5    H  HCR6  0   0.260   7.7099  -0.4249  -3.6202
 SPP  H6    H  HCR6  0   0.247   5.3508  -0.2882  -4.4047
 SPP  H81   H  HCH2  0   0.236   3.2365   2.0515  -0.4579
 SPP  H82   H  HCH2  0   0.266   4.5446   1.6542   0.6615
 SPP  H91   H  HCH2  0   0.254   2.9852   0.5999   2.2195
 SPP  H92   H  HCH2  0   0.271   2.4541   2.2448   1.8680
 SPP  H111  H  HCH2  0   0.281   0.4953  -0.9328  -0.0180
 SPP  H112  H  HCH2  0   0.253   1.8071  -1.3050   1.0987
 SPP  H121  H  HCH2  0   0.256   2.5642  -1.4949  -1.2196
 SPP  H122  H  HCH2  0   0.216   2.0145   0.1420  -1.5836
 SPP  H15   H  HCR5  0   0.261  -1.9645   2.2467  -0.8855
 SPP  H16   H  HCR6  0   0.264  -4.7163   1.1838  -1.4498
 SPP  H18   H  HCR6  0   0.264  -5.5774  -2.3599   0.8088
 SPP  H19   H  HCR6  0   0.269  -3.3599  -2.2840   1.8899
 SPP  HA    H  HCH1  0   0.238   8.2876  -0.2548   0.9349
 SPP  HB1   H  HCH3  0   0.234   8.2645  -0.6922   3.3713
 SPP  HB2   H  HCH3  0   0.237   7.2747   0.7116   2.9604
 SPP  HB3   H  HCH3  0   0.222   6.5089  -0.8356   3.3412
 SPP  HC1   H  HCH3  0   0.229   8.5432  -2.5979   1.7015
 SPP  HC2   H  HCH3  0   0.221   6.7912  -2.8133   1.6903
 SPP  HC3   H  HCH3  0   0.234   7.6644  -2.5732   0.1757
 SPP  HE1   H  HCH3  0   0.293  -7.6920   2.0537  -1.0125
 SPP  HE2   H  HCH3  0   0.308  -8.5482   2.0124   0.5500
 SPP  HE3   H  HCH3  0   0.291  -6.7742   1.8674   0.5087
 SPP  HN    H  HNH1  0   0.366   5.3711  -0.5309   1.1864
 SPP  HN3   H  HNR5  0   0.419  -1.0212  -0.7198   1.9431
 SPP  HND   H  HNC1  0   0.419  -6.5986  -0.4353  -1.9483

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
 SPP  C2   C3    aromatic  1.420  0.020  1.420
 SPP  C2   N1    aromatic  1.315  0.020  1.315
 SPP  C2   N7    single    1.406  0.020  1.406
 SPP  C3   C4    aromatic  1.392  0.020  1.392
 SPP  C3   N     single    1.371  0.020  1.371
 SPP  C4   C5    aromatic  1.390  0.020  1.390
 SPP  C4   H4    single    0.930  0.020  1.080
 SPP  C5   C6    aromatic  1.380  0.020  1.380
 SPP  C5   H5    single    0.930  0.020  1.080
 SPP  C6   N1    aromatic  1.333  0.020  1.333
 SPP  C6   H6    single    0.930  0.020  1.080
 SPP  C8   C9    single    1.517  0.020  1.517
 SPP  C8   N7    single    1.462  0.020  1.462
 SPP  C8   H81   single    0.970  0.020  1.090
 SPP  C8   H82   single    0.970  0.020  1.090
 SPP  C9   N10   single    1.453  0.020  1.453
 SPP  C9   H91   single    0.970  0.020  1.090
 SPP  C9   H92   single    0.970  0.020  1.090
 SPP  C11  C12   single    1.522  0.020  1.522
 SPP  C11  N10   single    1.457  0.020  1.457
 SPP  C11  H111  single    0.970  0.020  1.090
 SPP  C11  H112  single    0.970  0.020  1.090
 SPP  C12  N7    single    1.450  0.020  1.450
 SPP  C12  H121  single    0.970  0.020  1.090
 SPP  C12  H122  single    0.970  0.020  1.090
 SPP  C    C14   single    1.483  0.020  1.483
 SPP  C    N10   single    1.352  0.020  1.352
 SPP  C    O     double    1.223  0.020  1.223
 SPP  C14  C15   aromatic  1.367  0.020  1.367
 SPP  C14  N13   aromatic  1.372  0.020  1.372
 SPP  C15  C21   aromatic  1.424  0.020  1.424
 SPP  C15  H15   single    0.930  0.020  1.080
 SPP  C16  C17   aromatic  1.381  0.020  1.381
 SPP  C16  C21   aromatic  1.399  0.020  1.399
 SPP  C16  H16   single    0.930  0.020  1.080
 SPP  C17  C18   aromatic  1.408  0.020  1.408
 SPP  C17  ND    single    1.424  0.020  1.424
 SPP  C18  C19   aromatic  1.377  0.020  1.377
 SPP  C18  H18   single    0.930  0.020  1.080
 SPP  C19  C20   aromatic  1.395  0.020  1.395
 SPP  C19  H19   single    0.930  0.020  1.080
 SPP  C20  C21   aromatic  1.412  0.020  1.412
 SPP  C20  N13   aromatic  1.361  0.020  1.361
 SPP  CA   CB    single    1.522  0.020  1.522
 SPP  CA   CC    single    1.527  0.020  1.527
 SPP  CA   N     single    1.453  0.020  1.453
 SPP  CA   HA    single    0.970  0.020  1.090
 SPP  CB   HB1   single    0.970  0.020  1.090
 SPP  CB   HB2   single    0.970  0.020  1.090
 SPP  CB   HB3   single    0.970  0.020  1.090
 SPP  CC   HC1   single    0.970  0.020  1.090
 SPP  CC   HC2   single    0.970  0.020  1.090
 SPP  CC   HC3   single    0.970  0.020  1.090
 SPP  CE   S     single    1.778  0.020  1.778
 SPP  CE   HE1   single    0.970  0.020  1.090
 SPP  CE   HE2   single    0.970  0.020  1.090
 SPP  CE   HE3   single    0.970  0.020  1.090
 SPP  N    HN    single    0.890  0.020  1.040
 SPP  N13  HN3   single    0.860  0.020  1.020
 SPP  ND   S     single    1.661  0.020  1.661
 SPP  ND   HND   single    0.890  0.020  1.040
 SPP  OS1  S     double    1.453  0.020  1.453
 SPP  OS2  S     double    1.454  0.020  1.454

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
 SPP  N7    C2   N1    119.42  3.000
 SPP  N7    C2   C3    117.49  3.000
 SPP  N1    C2   C3    123.08  3.000
 SPP  N     C3   C4    124.41  3.000
 SPP  N     C3   C2    119.08  3.000
 SPP  C4    C3   C2    116.50  3.000
 SPP  H4    C4   C5    119.49  3.000
 SPP  H4    C4   C3    120.86  3.000
 SPP  C5    C4   C3    119.64  3.000
 SPP  H5    C5   C6    120.51  3.000
 SPP  H5    C5   C4    120.41  3.000
 SPP  C6    C5   C4    119.08  3.000
 SPP  H6    C6   N1    116.82  3.000
 SPP  H6    C6   C5    121.17  3.000
 SPP  N1    C6   C5    122.01  3.000
 SPP  H82   C8   H81   107.57  3.000
 SPP  H82   C8   N7    109.89  3.000
 SPP  H81   C8   N7    110.88  3.000
 SPP  H82   C8   C9    109.02  3.000
 SPP  H81   C8   C9    109.74  3.000
 SPP  N7    C8   C9    109.70  3.000
 SPP  H92   C9   H91   107.97  3.000
 SPP  H92   C9   N10   110.07  3.000
 SPP  H91   C9   N10   107.85  3.000
 SPP  H92   C9   C8    110.37  3.000
 SPP  H91   C9   C8    109.49  3.000
 SPP  N10   C9   C8    111.01  3.000
 SPP  H112  C11  H111  107.93  3.000
 SPP  H112  C11  N10   108.87  3.000
 SPP  H111  C11  N10   111.09  3.000
 SPP  H112  C11  C12   109.85  3.000
 SPP  H111  C11  C12   108.79  3.000
 SPP  N10   C11  C12   110.28  3.000
 SPP  H122  C12  H121  107.45  3.000
 SPP  H122  C12  N7    112.25  3.000
 SPP  H121  C12  N7    109.47  3.000
 SPP  H122  C12  C11   109.20  3.000
 SPP  H121  C12  C11   108.71  3.000
 SPP  N7    C12  C11   109.68  3.000
 SPP  O     C    N10   123.58  3.000
 SPP  O     C    C14   118.89  3.000
 SPP  N10   C    C14   117.48  3.000
 SPP  N13   C14  C15   109.50  3.000
 SPP  N13   C14  C     123.55  3.000
 SPP  C15   C14  C     126.85  3.000
 SPP  H15   C15  C21   127.28  3.000
 SPP  H15   C15  C14   125.94  3.000
 SPP  C21   C15  C14   106.77  3.000
 SPP  H16   C16  C21   120.58  3.000
 SPP  H16   C16  C17   120.70  3.000
 SPP  C21   C16  C17   118.71  3.000
 SPP  ND    C17  C18   118.27  3.000
 SPP  ND    C17  C16   120.57  3.000
 SPP  C18   C17  C16   121.15  3.000
 SPP  H18   C18  C19   119.78  3.000
 SPP  H18   C18  C17   118.99  3.000
 SPP  C19   C18  C17   121.22  3.000
 SPP  H19   C19  C20   121.57  3.000
 SPP  H19   C19  C18   120.82  3.000
 SPP  C20   C19  C18   117.60  3.000
 SPP  N13   C20  C21   107.56  3.000
 SPP  N13   C20  C19   130.43  3.000
 SPP  C21   C20  C19   122.01  3.000
 SPP  C20   C21  C16   119.30  3.000
 SPP  C20   C21  C15   106.86  3.000
 SPP  C16   C21  C15   133.83  3.000
 SPP  HA    CA   N     107.67  3.000
 SPP  HA    CA   CC    108.86  3.000
 SPP  N     CA   CC    112.80  3.000
 SPP  HA    CA   CB    107.71  3.000
 SPP  N     CA   CB    108.40  3.000
 SPP  CC    CA   CB    111.22  3.000
 SPP  HB3   CB   HB2   108.16  3.000
 SPP  HB3   CB   HB1   107.63  3.000
 SPP  HB2   CB   HB1   108.23  3.000
 SPP  HB3   CB   CA    110.94  3.000
 SPP  HB2   CB   CA    111.22  3.000
 SPP  HB1   CB   CA    110.53  3.000
 SPP  HC3   CC   HC2   107.89  3.000
 SPP  HC3   CC   HC1   107.66  3.000
 SPP  HC2   CC   HC1   107.94  3.000
 SPP  HC3   CC   CA    112.01  3.000
 SPP  HC2   CC   CA    110.52  3.000
 SPP  HC1   CC   CA    110.66  3.000
 SPP  HE3   CE   HE2   109.77  3.000
 SPP  HE3   CE   HE1   110.42  3.000
 SPP  HE2   CE   HE1   109.96  3.000
 SPP  HE3   CE   S     109.73  3.000
 SPP  HE2   CE   S     107.79  3.000
 SPP  HE1   CE   S     109.12  3.000
 SPP  HN    N    CA    113.95  3.000
 SPP  HN    N    C3    112.09  3.000
 SPP  CA    N    C3    122.61  3.000
 SPP  C6    N1   C2    119.62  3.000
 SPP  C12   N7   C8    111.14  3.000
 SPP  C12   N7   C2    116.08  3.000
 SPP  C8    N7   C2    114.19  3.000
 SPP  C     N10  C11   124.61  3.000
 SPP  C     N10  C9    120.08  3.000
 SPP  C11   N10  C9    112.37  3.000
 SPP  HN3   N13  C20   125.06  3.000
 SPP  HN3   N13  C14   125.30  3.000
 SPP  C20   N13  C14   109.29  3.000
 SPP  HND   ND   S     111.62  3.000
 SPP  HND   ND   C17   114.97  3.000
 SPP  S     ND   C17   118.93  3.000
 SPP  OS2   S    OS1   119.60  3.000
 SPP  OS2   S    ND    106.02  3.000
 SPP  OS1   S    ND    107.31  3.000
 SPP  OS2   S    CE    108.51  3.000
 SPP  OS1   S    CE    108.10  3.000
 SPP  ND    S    CE    106.60  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
 SPP  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 SPP  CONST_02  C5   C6   N1   C2      0.00   0.0  0
 SPP  CONST_03  C6   N1   C2   C3      0.00   0.0  0
 SPP  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 SPP  CONST_05  N1   C2   C3   C4      0.00   0.0  0
 SPP  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 SPP  CONST_07  C16  C21  C15  C14   180.00   0.0  0
 SPP  CONST_08  C20  C21  C15  C14     0.00   0.0  0
 SPP  CONST_09  C19  C20  N13  C14   180.00   0.0  0
 SPP  CONST_10  C21  C20  N13  C14     0.00   0.0  0
 SPP  CONST_11  C20  N13  C14  C15     0.00   0.0  0
 SPP  CONST_12  C17  C16  C21  C15   180.00   0.0  0
 SPP  CONST_13  C19  C20  C21  C15   180.00   0.0  0
 SPP  CONST_14  N13  C20  C21  C15     0.00   0.0  0
 SPP  CONST_15  C19  C18  C17  C16     0.00   0.0  0
 SPP  CONST_16  C19  C20  C21  C16     0.00   0.0  0
 SPP  CONST_17  N13  C20  C21  C16   180.00   0.0  0
 SPP  CONST_18  C20  C21  C16  C17     0.00   0.0  0
 SPP  CONST_19  C20  C19  C18  C17     0.00   0.0  0
 SPP  CONST_20  C21  C16  C17  C18     0.00   0.0  0
 SPP  CONST_21  C21  C20  C19  C18     0.00   0.0  0
 SPP  CONST_22  N13  C20  C19  C18   180.00   0.0  0
 SPP  CONST_23  N13  C14  C15  C21     0.00   0.0  0
 SPP  CONST_24  N7   C2   C3   C4    180.00   0.0  0
 SPP  CONST_25  N7   C2   N1   C6    180.00   0.0  0
 SPP  CONST_26  N    C3   C4   C5    180.00   0.0  0
 SPP  CONST_27  C21  C15  C14  C     180.00   0.0  0
 SPP  CONST_28  C20  N13  C14  C     180.00   0.0  0
 SPP  CONST_29  ND   C17  C18  C19   180.00   0.0  0
 SPP  CONST_30  ND   C17  C16  C21   180.00   0.0  0
 SPP  CONST_31  N1   C2   C3   N     180.00   0.0  0
 SPP  CONST_32  N7   C2   C3   N       0.00   0.0  0
 SPP  CONST_33  C14  C    N10  C9    180.00   0.0  0
 SPP  CONST_35  H4   C4   C3   C2    180.00   0.0  0
 SPP  CONST_36  H6   C6   N1   C2    180.00   0.0  0
 SPP  CONST_37  H5   C5   C4   C3    180.00   0.0  0
 SPP  CONST_38  HN3  N13  C14  C15   180.00   0.0  0
 SPP  CONST_39  H16  C16  C21  C15     0.00   0.0  0
 SPP  CONST_40  H18  C18  C17  C16   180.00   0.0  0
 SPP  CONST_41  H15  C15  C21  C16     0.00   0.0  0
 SPP  CONST_42  H19  C19  C18  C17   180.00   0.0  0
 SPP  CONST_43  O    C    N10  C9      0.00   0.0  0
 SPP  Var_01    C9   C8   N7   C2   -167.60  30.0  1
 SPP  Var_02    C11  C12  N7   C2    167.70  30.0  1
 SPP  Var_03    C8   N7   C2   C3     77.04  30.0  2
 SPP  Var_04    C11  N10  C9   C8     54.88  30.0  1
 SPP  Var_05    C12  C11  N10  C9    -55.32  30.0  1
 SPP  Var_06    N10  C9   C8   N7    -55.46  30.0  1
 SPP  Var_07    N10  C11  C12  N7     56.95  30.0  1
 SPP  Var_08    N10  C    C14  C15  -141.69  30.0  2
 SPP  Var_09    CB   CA   N    C3    168.25  30.0  2
 SPP  Var_10    CE   S    ND   C17    66.57  30.0  3
 SPP  Var_11    HC1  CC   CA   CB    -59.96  30.0  3
 SPP  Var_12    HB1  CB   CA   CC     57.26  30.0  3
 SPP  Var_13    HE1  CE   S    ND     61.63  30.0  3

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
 SPP  plan-1  C2   0.020
 SPP  plan-1  C3   0.020
 SPP  plan-1  C4   0.020
 SPP  plan-1  C5   0.020
 SPP  plan-1  C6   0.020
 SPP  plan-1  N    0.020
 SPP  plan-1  N1   0.020
 SPP  plan-1  N7   0.020
 SPP  plan-1  H4   0.020
 SPP  plan-1  H5   0.020
 SPP  plan-1  H6   0.020
 SPP  plan-2  C    0.020
 SPP  plan-2  C14  0.020
 SPP  plan-2  C15  0.020
 SPP  plan-2  C16  0.020
 SPP  plan-2  C17  0.020
 SPP  plan-2  C18  0.020
 SPP  plan-2  C19  0.020
 SPP  plan-2  C20  0.020
 SPP  plan-2  C21  0.020
 SPP  plan-2  N13  0.020
 SPP  plan-2  ND   0.020
 SPP  plan-2  H15  0.020
 SPP  plan-2  H16  0.020
 SPP  plan-2  H18  0.020
 SPP  plan-2  H19  0.020
 SPP  plan-2  HN3  0.020
 SPP  plan-3  C3   0.020
 SPP  plan-3  CA   0.020
 SPP  plan-3  N    0.020
 SPP  plan-3  HN   0.020
 SPP  plan-4  C17  0.020
 SPP  plan-4  ND   0.020
 SPP  plan-4  S    0.020
 SPP  plan-4  HND  0.020
 SPP  plan-5  C9   0.020
 SPP  plan-5  C11  0.020
 SPP  plan-5  C    0.020
 SPP  plan-5  C14  0.020
 SPP  plan-5  N10  0.020
 SPP  plan-5  O    0.020

