# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:26:37 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-{4-[(3S)-4'-oxo-1',4',5',6'-tetrahydrospiro[piperidine-3,7'-pyrrolo[3,2-c]pyridin]-2'-yl]pyridin-2-yl}-3-(trifluoromethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(c1)C(=O)Nc2cc(ccn2)c3[nH]c4c(c3)C(=O)NC[C@@]45CCCNC5
#
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
 I85  I85  N-{4-[(3S)-4'-oxo-1',4',5',6'-tetrahydrospiro[piperidine-3,7'-pyrrolo[3,2-c]pyridin]-2'-yl]pyridin-2-yl}-3-(trifluoromethyl)benzamide  ligand  56  34  .  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_I85
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
 I85  N1    N  NH1   0  -0.750   2.3113  -0.3992   0.0823
 I85  N2    N  NH1   0  -0.582  -8.0492  -1.4581   1.0147
 I85  C3    C  CH2   0  -0.314  -8.5021  -1.7593  -0.3341
 I85  C4    C  CR16  0  -0.530  -0.0640  -0.3087   0.0749
 I85  N5    N  N     0  -0.431   1.0908  -2.4036   0.1291
 I85  N6    N  NR15  0  -0.738  -3.7733  -0.7391   0.1542
 I85  C7    C  CR6   0  -0.250  -6.2118   0.0101   0.1199
 I85  N8    N  NR16  0  -0.652  -6.2037   2.4925  -0.0294
 I85  C9    C  CR6   0   0.472  -4.8728   2.6571  -0.2162
 I85  C10   C  CH2   0  -0.409  -6.6999  -0.3083  -1.3093
 I85  C11   C  CH2   0  -0.460  -8.1841  -0.6607  -1.3435
 I85  C12   C  CH2   0  -0.290  -6.6396  -1.1361   1.0590
 I85  O13   O  O     0  -0.492  -4.3687   3.7243  -0.5479
 I85  C14   C  CR56  0   0.477  -4.7322   0.2023   0.1108
 I85  C15   C  CR56  0  -0.159  -4.1087   1.4254  -0.0367
 I85  C16   C  CR15  0  -0.412  -2.7166   1.1982  -0.0786
 I85  C17   C  CR5   0   0.366  -2.5268  -0.1598   0.0500
 I85  C18   C  CR6   0   0.196  -1.3032  -0.9391   0.0809
 I85  C19   C  CR16  0  -0.409  -1.3049  -2.3388   0.1181
 I85  C20   C  CR16  0  -0.054  -0.0957  -3.0017   0.1430
 I85  C21   C  CR6   0   0.565   1.0961  -1.0824   0.0967
 I85  C22   C  C     0  -0.258  -6.7755   1.3401   0.6417
 I85  C23   C  C     0   0.534   3.5781  -0.8889   0.1965
 I85  C24   C  CR6   0  -0.034   4.6440   0.1645   0.2193
 I85  C25   C  CR16  0  -0.285   4.4484   1.4353   0.7561
 I85  C26   C  CR16  0  -0.224   5.4890   2.3492   0.7794
 I85  C27   C  CR16  0  -0.281   6.7306   2.0129   0.2609
 I85  C28   C  CR6   0  -0.173   6.9291   0.7452  -0.2699
 I85  C29   C  CR16  0  -0.291   5.8944  -0.1802  -0.2785
 I85  O30   O  O     0  -0.431   3.8686  -2.0643   0.2625
 I85  C31   C  CT    0   1.056   8.2531   0.3331  -0.8356
 I85  F32   F  F     0  -0.300   9.1563   1.3151  -0.8029
 I85  F33   F  F     0  -0.313   8.7745  -0.7037  -0.1642
 I85  F34   F  F     0  -0.312   8.1430  -0.0588  -2.1126
 I85  HN1   H  HNH1  0   0.429   2.2233   0.5959  -0.0529
 I85  H3    H  HCH2  0   0.218  -8.0173  -2.6896  -0.6499
 I85  H3A   H  HCH2  0   0.240  -9.5748  -1.9589  -0.3062
 I85  H4    H  HCR6  0   0.272   0.0102   0.7713   0.0623
 I85  HN6   H  HNR5  0   0.423  -3.9429  -1.7260   0.2670
 I85  HN8   H  HNR6  0   0.397  -6.7782   3.3187  -0.0958
 I85  H10   H  HCH2  0   0.247  -6.4889   0.5338  -1.9726
 I85  H10A  H  HCH2  0   0.235  -6.1210  -1.1565  -1.6894
 I85  H11   H  HCH2  0   0.239  -8.4588  -0.9851  -2.3500
 I85  H11A  H  HCH2  0   0.224  -8.7926   0.2230  -1.1277
 I85  H12   H  HCH2  0   0.254  -6.3564  -0.8989   2.0879
 I85  H12A  H  HCH2  0   0.229  -6.0922  -2.0441   0.7809
 I85  H16   H  HCR5  0   0.261  -1.9474   1.9457  -0.1901
 I85  H19   H  HCR6  0   0.256  -2.2146  -2.9226   0.1217
 I85  H20   H  HCR6  0   0.267  -0.0809  -4.0853   0.1713
 I85  H22   H  H     0   0.262  -7.8539   1.3850   0.5017
 I85  H22A  H  H     0   0.246  -6.5907   1.3964   1.7221
 I85  H25   H  HCR6  0   0.275   3.4974   1.7214   1.1876
 I85  H26   H  HCR6  0   0.280   5.3346   3.3296   1.2081
 I85  H27   H  HCR6  0   0.281   7.5278   2.7422   0.2830
 I85  H29   H  HCR6  0   0.282   6.0461  -1.1746  -0.6793
 I85  HN2   H  HNH1  0   0.349  -8.5984  -0.7013   1.4041

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
 I85  N1   C21   single    1.394  0.020  1.394
 I85  N1   C23   single    1.363  0.020  1.363
 I85  N2   C3    single    1.454  0.020  1.454
 I85  N2   C12   single    1.447  0.020  1.447
 I85  C3   C11   single    1.525  0.020  1.525
 I85  C4   C18   aromatic  1.390  0.020  1.390
 I85  C4   C21   aromatic  1.395  0.020  1.395
 I85  N5   C20   aromatic  1.329  0.020  1.329
 I85  N5   C21   aromatic  1.322  0.020  1.322
 I85  N6   C14   aromatic  1.344  0.020  1.344
 I85  N6   C17   aromatic  1.379  0.020  1.379
 I85  C7   C10   single    1.543  0.020  1.543
 I85  C7   C12   single    1.542  0.020  1.542
 I85  C7   C14   single    1.492  0.020  1.492
 I85  C7   C22   single    1.536  0.020  1.536
 I85  N8   C9    single    1.354  0.020  1.354
 I85  N8   C22   single    1.451  0.020  1.451
 I85  C9   O13   double    1.226  0.020  1.226
 I85  C9   C15   single    1.461  0.020  1.461
 I85  C10  C11   single    1.526  0.020  1.526
 I85  C14  C15   aromatic  1.381  0.020  1.381
 I85  C15  C16   aromatic  1.411  0.020  1.411
 I85  C16  C17   aromatic  1.377  0.020  1.377
 I85  C17  C18   single    1.451  0.020  1.451
 I85  C18  C19   aromatic  1.400  0.020  1.400
 I85  C19  C20   aromatic  1.379  0.020  1.379
 I85  C23  C24   single    1.499  0.020  1.499
 I85  C23  O30   double    1.213  0.020  1.213
 I85  C24  C25   aromatic  1.393  0.020  1.393
 I85  C24  C29   aromatic  1.389  0.020  1.389
 I85  C25  C26   aromatic  1.385  0.020  1.385
 I85  C26  C27   aromatic  1.387  0.020  1.387
 I85  C27  C28   aromatic  1.389  0.020  1.389
 I85  C28  C29   aromatic  1.388  0.020  1.388
 I85  C28  C31   single    1.498  0.020  1.498
 I85  C31  F32   single    1.335  0.020  1.335
 I85  C31  F33   single    1.341  0.020  1.341
 I85  C31  F34   single    1.340  0.020  1.340
 I85  N1   HN1   single    0.860  0.020  1.020
 I85  N2   HN2   single    0.890  0.020  1.040
 I85  C3   H3    single    0.970  0.020  1.090
 I85  C3   H3A   single    0.970  0.020  1.090
 I85  C4   H4    single    0.930  0.020  1.080
 I85  N6   HN6   single    0.860  0.020  1.020
 I85  N8   HN8   single    0.890  0.020  1.040
 I85  C10  H10   single    0.970  0.020  1.090
 I85  C10  H10A  single    0.970  0.020  1.090
 I85  C11  H11   single    0.970  0.020  1.090
 I85  C11  H11A  single    0.970  0.020  1.090
 I85  C12  H12   single    0.970  0.020  1.090
 I85  C12  H12A  single    0.970  0.020  1.090
 I85  C16  H16   single    0.930  0.020  1.080
 I85  C19  H19   single    0.930  0.020  1.080
 I85  C20  H20   single    0.930  0.020  1.080
 I85  C22  H22   single    0.970  0.020  1.090
 I85  C22  H22A  single    0.970  0.020  1.090
 I85  C25  H25   single    0.930  0.020  1.080
 I85  C26  H26   single    0.930  0.020  1.080
 I85  C27  H27   single    0.930  0.020  1.080
 I85  C29  H29   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
 I85  HN1   N1   C23  116.55  3.000
 I85  HN1   N1   C21  114.14  3.000
 I85  C23   N1   C21  129.29  3.000
 I85  HN2   N2   C12  110.50  3.000
 I85  HN2   N2   C3   110.03  3.000
 I85  C12   N2   C3   112.20  3.000
 I85  H3A   C3   H3   106.67  3.000
 I85  H3A   C3   C11  110.70  3.000
 I85  H3    C3   C11  109.19  3.000
 I85  H3A   C3   N2   108.67  3.000
 I85  H3    C3   N2   107.78  3.000
 I85  C11   C3   N2   113.56  3.000
 I85  H4    C4   C21  119.78  3.000
 I85  H4    C4   C18  120.89  3.000
 I85  C21   C4   C18  119.33  3.000
 I85  C21   N5   C20  116.99  3.000
 I85  HN6   N6   C17  124.90  3.000
 I85  HN6   N6   C14  124.70  3.000
 I85  C17   N6   C14  110.38  3.000
 I85  C22   C7   C14  104.74  3.000
 I85  C22   C7   C12  109.57  3.000
 I85  C14   C7   C12  111.99  3.000
 I85  C22   C7   C10  112.16  3.000
 I85  C14   C7   C10  109.54  3.000
 I85  C12   C7   C10  108.83  3.000
 I85  HN8   N8   C22  117.17  3.000
 I85  HN8   N8   C9   116.83  3.000
 I85  C22   N8   C9   123.21  3.000
 I85  C15   C9   O13  123.52  3.000
 I85  C15   C9   N8   113.25  3.000
 I85  O13   C9   N8   123.18  3.000
 I85  H10A  C10  H10  106.51  3.000
 I85  H10A  C10  C11  109.12  3.000
 I85  H10   C10  C11  110.63  3.000
 I85  H10A  C10  C7   108.30  3.000
 I85  H10   C10  C7   110.00  3.000
 I85  C11   C10  C7   112.09  3.000
 I85  H11A  C11  H11  106.35  3.000
 I85  H11A  C11  C10  110.48  3.000
 I85  H11   C11  C10  109.50  3.000
 I85  H11A  C11  C3   109.58  3.000
 I85  H11   C11  C3   110.08  3.000
 I85  C10   C11  C3   110.75  3.000
 I85  H12A  C12  H12  106.82  3.000
 I85  H12A  C12  C7   108.82  3.000
 I85  H12   C12  C7   109.87  3.000
 I85  H12A  C12  N2   107.13  3.000
 I85  H12   C12  N2   109.24  3.000
 I85  C7    C12  N2   114.64  3.000
 I85  C15   C14  C7   124.23  3.000
 I85  C15   C14  N6   107.56  3.000
 I85  C7    C14  N6   128.09  3.000
 I85  C16   C15  C14  107.82  3.000
 I85  C16   C15  C9   130.41  3.000
 I85  C14   C15  C9   121.60  3.000
 I85  H16   C16  C17  126.50  3.000
 I85  H16   C16  C15  126.52  3.000
 I85  C17   C16  C15  106.97  3.000
 I85  C18   C17  C16  130.37  3.000
 I85  C18   C17  N6   122.36  3.000
 I85  C16   C17  N6   107.26  3.000
 I85  C19   C18  C17  122.44  3.000
 I85  C19   C18  C4   117.03  3.000
 I85  C17   C18  C4   120.53  3.000
 I85  H19   C19  C20  118.57  3.000
 I85  H19   C19  C18  122.75  3.000
 I85  C20   C19  C18  118.68  3.000
 I85  H20   C20  C19  119.53  3.000
 I85  H20   C20  N5   115.98  3.000
 I85  C19   C20  N5   124.49  3.000
 I85  N5    C21  C4   123.48  3.000
 I85  N5    C21  N1   119.58  3.000
 I85  C4    C21  N1   116.94  3.000
 I85  H22A  C22  H22  106.94  3.000
 I85  H22A  C22  N8   110.38  3.000
 I85  H22   C22  N8   107.35  3.000
 I85  H22A  C22  C7   108.49  3.000
 I85  H22   C22  C7   110.84  3.000
 I85  N8    C22  C7   112.71  3.000
 I85  O30   C23  C24  120.67  3.000
 I85  O30   C23  N1   125.13  3.000
 I85  C24   C23  N1   114.19  3.000
 I85  C29   C24  C25  119.39  3.000
 I85  C29   C24  C23  117.40  3.000
 I85  C25   C24  C23  123.17  3.000
 I85  H25   C25  C26  118.60  3.000
 I85  H25   C25  C24  121.19  3.000
 I85  C26   C25  C24  120.18  3.000
 I85  H26   C26  C27  119.74  3.000
 I85  H26   C26  C25  119.84  3.000
 I85  C27   C26  C25  120.42  3.000
 I85  H27   C27  C28  121.23  3.000
 I85  H27   C27  C26  119.28  3.000
 I85  C28   C27  C26  119.49  3.000
 I85  C31   C28  C29  118.24  3.000
 I85  C31   C28  C27  121.46  3.000
 I85  C29   C28  C27  120.29  3.000
 I85  H29   C29  C28  120.67  3.000
 I85  H29   C29  C24  119.12  3.000
 I85  C28   C29  C24  120.21  3.000
 I85  F34   C31  F33  106.44  3.000
 I85  F34   C31  F32  107.10  3.000
 I85  F33   C31  F32  107.07  3.000
 I85  F34   C31  C28  111.57  3.000
 I85  F33   C31  C28  111.56  3.000
 I85  F32   C31  C28  112.74  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
 I85  CONST_01  N6   C17  C18  C4   180.00   0.0  0
 I85  CONST_02  C16  C17  C18  C4     0.00   0.0  0
 I85  CONST_03  C20  C19  C18  C4     0.00   0.0  0
 I85  CONST_04  C20  N5   C21  C4     0.00   0.0  0
 I85  CONST_05  C18  C19  C20  N5     0.00   0.0  0
 I85  CONST_06  C18  C4   C21  N5     0.00   0.0  0
 I85  CONST_07  C16  C15  C14  N6     0.00   0.0  0
 I85  CONST_08  C15  C16  C17  N6     0.00   0.0  0
 I85  CONST_09  C19  C18  C17  N6     0.00   0.0  0
 I85  CONST_10  C16  C17  N6   C14    0.00   0.0  0
 I85  CONST_11  C18  C17  N6   C14  180.00   0.0  0
 I85  CONST_12  C17  C16  C15  C14    0.00   0.0  0
 I85  CONST_13  C17  N6   C14  C15    0.00   0.0  0
 I85  CONST_14  C18  C17  C16  C15  180.00   0.0  0
 I85  CONST_15  C19  C18  C17  C16  180.00   0.0  0
 I85  CONST_16  C21  C4   C18  C17  180.00   0.0  0
 I85  CONST_17  C20  C19  C18  C17  180.00   0.0  0
 I85  CONST_18  C21  C4   C18  C19    0.00   0.0  0
 I85  CONST_19  C21  N5   C20  C19    0.00   0.0  0
 I85  CONST_20  C27  C26  C25  C24    0.00   0.0  0
 I85  CONST_21  C27  C28  C29  C24    0.00   0.0  0
 I85  CONST_22  C28  C29  C24  C25    0.00   0.0  0
 I85  CONST_23  C28  C27  C26  C25    0.00   0.0  0
 I85  CONST_24  C29  C24  C25  C26    0.00   0.0  0
 I85  CONST_25  C29  C28  C27  C26    0.00   0.0  0
 I85  CONST_27  C18  C4   C21  N1   180.00   0.0  0
 I85  CONST_28  C20  N5   C21  N1   180.00   0.0  0
 I85  CONST_29  C26  C25  C24  C23  180.00   0.0  0
 I85  CONST_30  C28  C29  C24  C23  180.00   0.0  0
 I85  CONST_31  C31  C28  C29  C24  180.00   0.0  0
 I85  CONST_32  C31  C28  C27  C26  180.00   0.0  0
 I85  CONST_33  C22  N8   C9   O13  180.00   0.0  0
 I85  CONST_34  H19  C19  C18  C4   180.00   0.0  0
 I85  CONST_35  H4   C4   C21  N5   180.00   0.0  0
 I85  CONST_36  H16  C16  C17  N6   180.00   0.0  0
 I85  CONST_37  HN6  N6   C14  C7     0.00   0.0  0
 I85  CONST_38  H20  C20  C19  C18  180.00   0.0  0
 I85  CONST_39  H26  C26  C25  C24  180.00   0.0  0
 I85  CONST_40  H29  C29  C24  C25  180.00   0.0  0
 I85  CONST_41  H27  C27  C26  C25  180.00   0.0  0
 I85  CONST_42  H25  C25  C26  C27  180.00   0.0  0
 I85  CONST_43  HN8  N8   C9   C15  180.00   0.0  0
 I85  CONST_44  C24  C23  N1   C21  180.00   0.0  0
 I85  CONST_45  C23  N1   C21  C4   180.00   0.0  0
 I85  CONST_46  C23  N1   C21  N5     0.00   0.0  0
 I85  CONST_47  HN1  N1   C21  C4     0.00   0.0  0
 I85  CONST_48  O30  C23  N1   C21    0.00   0.0  0
 I85  Var_01    C10  C11  C3   N2    53.23  30.0  1
 I85  Var_02    C7   C12  N2   C3    55.05  30.0  1
 I85  Var_03    C7   C10  C11  C3   -52.17  30.0  1
 I85  Var_04    C9   N8   C22  C7   -48.27  30.0  1
 I85  Var_05    C14  C15  C9   N8     8.93  30.0  1
 I85  Var_06    C12  N2   C3   C11  -54.39  30.0  1
 I85  Var_07    C25  C24  C23  N1    31.64  30.0  2
 I85  Var_08    F32  C31  C28  C27   -2.04  30.0  2

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
 I85  chir_01  C7  C12  C14  C22  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
 I85  plan-1  N1   0.020
 I85  plan-1  C4   0.020
 I85  plan-1  N5   0.020
 I85  plan-1  C17  0.020
 I85  plan-1  C18  0.020
 I85  plan-1  C19  0.020
 I85  plan-1  C20  0.020
 I85  plan-1  C21  0.020
 I85  plan-1  H4   0.020
 I85  plan-1  H19  0.020
 I85  plan-1  H20  0.020
 I85  plan-2  N6   0.020
 I85  plan-2  C7   0.020
 I85  plan-2  C9   0.020
 I85  plan-2  C14  0.020
 I85  plan-2  C15  0.020
 I85  plan-2  C16  0.020
 I85  plan-2  C17  0.020
 I85  plan-2  C18  0.020
 I85  plan-2  HN6  0.020
 I85  plan-2  H16  0.020
 I85  plan-3  C23  0.020
 I85  plan-3  C24  0.020
 I85  plan-3  C25  0.020
 I85  plan-3  C26  0.020
 I85  plan-3  C27  0.020
 I85  plan-3  C28  0.020
 I85  plan-3  C29  0.020
 I85  plan-3  C31  0.020
 I85  plan-3  H25  0.020
 I85  plan-3  H26  0.020
 I85  plan-3  H27  0.020
 I85  plan-3  H29  0.020
 I85  plan-4  N1   0.020
 I85  plan-4  C21  0.020
 I85  plan-4  C23  0.020
 I85  plan-4  C24  0.020
 I85  plan-4  O30  0.020
 I85  plan-4  HN1  0.020
 I85  plan-5  N8   0.020
 I85  plan-5  C9   0.020
 I85  plan-5  O13  0.020
 I85  plan-5  C15  0.020
 I85  plan-5  C22  0.020
 I85  plan-5  HN8  0.020

