# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:38:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-[3-(methylsulfanyl)-1-phenyl-1H-indazol-6-yl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nn(c2ccccc2)c3cc(NC(=O)C4CCNCC4)ccc13
#
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
 TR3  TR3  N-[3-(methylsulfanyl)-1-phenyl-1H-indazol-6-yl]piperidine-4-carboxamide  ligand  48  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TR3
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
 TR3  C1    C  CR16  0  -0.364   0.1653  -2.4703   0.6622
 TR3  C2    C  CR16  0  -0.310  -1.1919  -2.6625   0.6425
 TR3  C3    C  CR56  0  -0.109  -2.0181  -1.5543   0.4366
 TR3  C4    C  CR56  0   0.504  -1.4473  -0.2860   0.2700
 TR3  C5    C  CR16  0  -0.406  -0.0653  -0.0750   0.2647
 TR3  C6    C  CR6   0   0.390   0.7367  -1.1867   0.4641
 TR3  N10   N  N     0  -0.266  -3.6764  -0.0687   0.1055
 TR3  N11   N  NR5   0  -0.528  -2.4874   0.5781   0.0878
 TR3  C12   C  CR5   0   0.067  -3.4202  -1.3293   0.3146
 TR3  C13   C  CR16  0  -0.259  -2.4029   4.6967  -0.6476
 TR3  C14   C  CR16  0  -0.250  -3.3182   3.8842  -1.3058
 TR3  C15   C  CR16  0  -0.290  -3.3455   2.5188  -1.0693
 TR3  C16   C  CR6   0   0.342  -2.4571   1.9617  -0.1534
 TR3  C17   C  CR16  0  -0.316  -1.5553   2.7728   0.5284
 TR3  C18   C  CR16  0  -0.252  -1.5242   4.1354   0.2679
 TR3  S24   S  S2    0   0.043  -4.6424  -2.5641   0.4301
 TR3  C25   C  CH3   0  -0.767  -6.1410  -1.6022   0.1363
 TR3  C26   C  C     0   0.577   2.9656  -0.0937   0.2465
 TR3  N27   N  NH1   0  -0.752   2.1298  -1.1404   0.4893
 TR3  O28   O  O     0  -0.462   2.5781   1.0337  -0.0025
 TR3  C30   C  CH2   0  -0.320   6.7851   0.2891   0.6871
 TR3  C31   C  CH2   0  -0.424   5.3083   0.6634   0.7954
 TR3  C32   C  CH1   0  -0.408   4.4343  -0.4678   0.2605
 TR3  C33   C  CH2   0  -0.427   4.8749  -0.8539  -1.1595
 TR3  C34   C  CH2   0  -0.315   6.3705  -1.1626  -1.1866
 TR3  N35   N  NH1   0  -0.574   7.2035  -0.1010  -0.6491
 TR3  H1    H  HCR6  0   0.275   0.8209  -3.3176   0.8213
 TR3  H2    H  HCR6  0   0.263  -1.6026  -3.6542   0.7814
 TR3  H5    H  HCR6  0   0.298   0.3579   0.9011   0.1032
 TR3  H13   H  HCR6  0   0.261  -2.3791   5.7603  -0.8442
 TR3  H14   H  HCR6  0   0.264  -4.0100   4.3137  -2.0186
 TR3  H15   H  HCR6  0   0.271  -4.0507   1.8860  -1.5905
 TR3  H17   H  HCR6  0   0.281  -0.8961   2.3533   1.2766
 TR3  H18   H  HCR6  0   0.265  -0.8178   4.7598   0.7984
 TR3  H25   H  HCH3  0   0.276  -6.2796  -0.8463   0.9054
 TR3  H25A  H  HCH3  0   0.277  -6.1165  -1.1314  -0.8434
 TR3  H25B  H  HCH3  0   0.285  -6.9666  -2.3090   0.1749
 TR3  HN27  H  HNH1  0   0.418   2.5787  -2.0207   0.6914
 TR3  H30   H  HCH2  0   0.239   7.4047   1.1245   1.0190
 TR3  H30A  H  HCH2  0   0.216   6.9987  -0.5433   1.3673
 TR3  H31   H  HCH2  0   0.238   5.0569   0.8779   1.8375
 TR3  H31A  H  HCH2  0   0.226   5.1187   1.5771   0.2260
 TR3  H32   H  HCH1  0   0.256   4.5730  -1.3444   0.9047
 TR3  H33   H  HCH2  0   0.241   4.3086  -1.7190  -1.5142
 TR3  H33A  H  HCH2  0   0.230   4.6631  -0.0270  -1.8454
 TR3  H34   H  HCH2  0   0.218   6.5634  -2.0739  -0.6096
 TR3  H34A  H  HCH2  0   0.240   6.6848  -1.3720  -2.2109
 TR3  HN35  H  HNH1  0   0.340   7.1437   0.7051  -1.2611

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
 TR3  C1   C2    aromatic  1.371  0.020  1.371
 TR3  C1   C6    aromatic  1.419  0.020  1.419
 TR3  C2   C3    aromatic  1.397  0.020  1.397
 TR3  C3   C4    aromatic  1.401  0.020  1.401
 TR3  C3   C12   aromatic  1.425  0.020  1.425
 TR3  C4   C5    aromatic  1.398  0.020  1.398
 TR3  C4   N11   aromatic  1.364  0.020  1.364
 TR3  C5   C6    aromatic  1.385  0.020  1.385
 TR3  C6   N27   single    1.394  0.020  1.394
 TR3  N10  N11   aromatic  1.354  0.020  1.354
 TR3  N10  C12   aromatic  1.303  0.020  1.303
 TR3  N11  C16   single    1.405  0.020  1.405
 TR3  C12  S24   single    1.741  0.020  1.741
 TR3  C13  C14   aromatic  1.390  0.020  1.390
 TR3  C13  C18   aromatic  1.388  0.020  1.388
 TR3  C14  C15   aromatic  1.386  0.020  1.386
 TR3  C15  C16   aromatic  1.392  0.020  1.392
 TR3  C16  C17   aromatic  1.391  0.020  1.391
 TR3  C17  C18   aromatic  1.388  0.020  1.388
 TR3  S24  C25   single    1.805  0.020  1.805
 TR3  C26  N27   single    1.361  0.020  1.361
 TR3  C26  O28   double    1.218  0.020  1.218
 TR3  C26  C32   single    1.516  0.020  1.516
 TR3  C30  C31   single    1.527  0.020  1.527
 TR3  C30  N35   single    1.453  0.020  1.453
 TR3  C31  C32   single    1.526  0.020  1.526
 TR3  C32  C33   single    1.536  0.020  1.536
 TR3  C33  C34   single    1.527  0.020  1.527
 TR3  C34  N35   single    1.453  0.020  1.453
 TR3  C1   H1    single    0.930  0.020  1.080
 TR3  C2   H2    single    0.930  0.020  1.080
 TR3  C5   H5    single    0.930  0.020  1.080
 TR3  C13  H13   single    0.930  0.020  1.080
 TR3  C14  H14   single    0.930  0.020  1.080
 TR3  C15  H15   single    0.930  0.020  1.080
 TR3  C17  H17   single    0.930  0.020  1.080
 TR3  C18  H18   single    0.930  0.020  1.080
 TR3  C25  H25   single    0.970  0.020  1.090
 TR3  C25  H25A  single    0.970  0.020  1.090
 TR3  C25  H25B  single    0.970  0.020  1.090
 TR3  N27  HN27  single    0.860  0.020  1.020
 TR3  C30  H30   single    0.970  0.020  1.090
 TR3  C30  H30A  single    0.970  0.020  1.090
 TR3  C31  H31   single    0.970  0.020  1.090
 TR3  C31  H31A  single    0.970  0.020  1.090
 TR3  C32  H32   single    0.970  0.020  1.090
 TR3  C33  H33   single    0.970  0.020  1.090
 TR3  C33  H33A  single    0.970  0.020  1.090
 TR3  C34  H34   single    0.970  0.020  1.090
 TR3  C34  H34A  single    0.970  0.020  1.090
 TR3  N35  HN35  single    0.890  0.020  1.040

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
 TR3  H1    C1   C6    118.98  3.000
 TR3  H1    C1   C2    119.45  3.000
 TR3  C6    C1   C2    121.57  3.000
 TR3  H2    C2   C3    121.41  3.000
 TR3  H2    C2   C1    120.15  3.000
 TR3  C3    C2   C1    118.44  3.000
 TR3  C12   C3   C4    104.34  3.000
 TR3  C12   C3   C2    136.00  3.000
 TR3  C4    C3   C2    119.65  3.000
 TR3  N11   C4   C5    131.10  3.000
 TR3  N11   C4   C3    106.19  3.000
 TR3  C5    C4   C3    122.68  3.000
 TR3  H5    C5   C6    121.46  3.000
 TR3  H5    C5   C4    121.75  3.000
 TR3  C6    C5   C4    116.79  3.000
 TR3  N27   C6   C5    123.68  3.000
 TR3  N27   C6   C1    115.46  3.000
 TR3  C5    C6   C1    120.86  3.000
 TR3  C12   N10  N11   106.95  3.000
 TR3  C16   N11  N10   119.46  3.000
 TR3  C16   N11  C4    129.07  3.000
 TR3  N10   N11  C4    111.42  3.000
 TR3  S24   C12  N10   123.96  3.000
 TR3  S24   C12  C3    124.95  3.000
 TR3  N10   C12  C3    111.09  3.000
 TR3  H13   C13  C18   120.24  3.000
 TR3  H13   C13  C14   120.21  3.000
 TR3  C18   C13  C14   119.54  3.000
 TR3  H14   C14  C15   119.39  3.000
 TR3  H14   C14  C13   120.06  3.000
 TR3  C15   C14  C13   120.54  3.000
 TR3  H15   C15  C16   119.94  3.000
 TR3  H15   C15  C14   120.47  3.000
 TR3  C16   C15  C14   119.59  3.000
 TR3  C17   C16  C15   120.18  3.000
 TR3  C17   C16  N11   120.26  3.000
 TR3  C15   C16  N11   119.56  3.000
 TR3  H17   C17  C18   119.80  3.000
 TR3  H17   C17  C16   120.52  3.000
 TR3  C18   C17  C16   119.67  3.000
 TR3  H18   C18  C17   119.30  3.000
 TR3  H18   C18  C13   120.23  3.000
 TR3  C17   C18  C13   120.46  3.000
 TR3  C25   S24  C12   101.19  3.000
 TR3  H25B  C25  H25A  109.30  3.000
 TR3  H25B  C25  H25   109.27  3.000
 TR3  H25A  C25  H25   109.83  3.000
 TR3  H25B  C25  S24   106.15  3.000
 TR3  H25A  C25  S24   111.02  3.000
 TR3  H25   C25  S24   111.18  3.000
 TR3  C32   C26  O28   122.60  3.000
 TR3  C32   C26  N27   113.80  3.000
 TR3  O28   C26  N27   123.57  3.000
 TR3  HN27  N27  C26   115.70  3.000
 TR3  HN27  N27  C6    114.79  3.000
 TR3  C26   N27  C6    129.48  3.000
 TR3  H30A  C30  H30   106.38  3.000
 TR3  H30A  C30  N35   108.10  3.000
 TR3  H30   C30  N35   108.75  3.000
 TR3  H30A  C30  C31   109.30  3.000
 TR3  H30   C30  C31   109.85  3.000
 TR3  N35   C30  C31   114.16  3.000
 TR3  H31A  C31  H31   107.01  3.000
 TR3  H31A  C31  C32   109.73  3.000
 TR3  H31   C31  C32   110.35  3.000
 TR3  H31A  C31  C30   109.61  3.000
 TR3  H31   C31  C30   109.76  3.000
 TR3  C32   C31  C30   110.32  3.000
 TR3  H32   C32  C33   107.81  3.000
 TR3  H32   C32  C31   108.31  3.000
 TR3  C33   C32  C31   110.24  3.000
 TR3  H32   C32  C26   108.99  3.000
 TR3  C33   C32  C26   109.36  3.000
 TR3  C31   C32  C26   112.04  3.000
 TR3  H33A  C33  H33   107.10  3.000
 TR3  H33A  C33  C34   109.33  3.000
 TR3  H33   C33  C34   109.97  3.000
 TR3  H33A  C33  C32   109.50  3.000
 TR3  H33   C33  C32   110.50  3.000
 TR3  C34   C33  C32   110.37  3.000
 TR3  H34A  C34  H34   106.50  3.000
 TR3  H34A  C34  N35   108.80  3.000
 TR3  H34   C34  N35   108.18  3.000
 TR3  H34A  C34  C33   109.72  3.000
 TR3  H34   C34  C33   109.34  3.000
 TR3  N35   C34  C33   114.03  3.000
 TR3  HN35  N35  C34   108.90  3.000
 TR3  HN35  N35  C30   108.94  3.000
 TR3  C34   N35  C30   111.79  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
 TR3  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 TR3  CONST_02  C12   C3   C2   C1   180.00   0.0  0
 TR3  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 TR3  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 TR3  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 TR3  CONST_06  N11   C4   C3   C2   180.00   0.0  0
 TR3  CONST_07  N10   C12  C3   C2   180.00   0.0  0
 TR3  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 TR3  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 TR3  CONST_10  N10   N11  C4   C3     0.00   0.0  0
 TR3  CONST_11  C16   N11  C4   C3   180.00   0.0  0
 TR3  CONST_12  N11   N10  C12  C3     0.00   0.0  0
 TR3  CONST_13  N10   C12  C3   C4     0.00   0.0  0
 TR3  CONST_14  C12   N10  N11  C4     0.00   0.0  0
 TR3  CONST_17  C12   C3   C4   C5   180.00   0.0  0
 TR3  CONST_18  N10   N11  C4   C5   180.00   0.0  0
 TR3  CONST_19  C16   N11  C4   C5     0.00   0.0  0
 TR3  CONST_20  N11   C4   C5   C6   180.00   0.0  0
 TR3  CONST_23  C12   C3   C4   N11    0.00   0.0  0
 TR3  CONST_24  C14   C15  C16  N11  180.00   0.0  0
 TR3  CONST_25  C18   C17  C16  N11  180.00   0.0  0
 TR3  CONST_26  C16   N11  N10  C12  180.00   0.0  0
 TR3  CONST_27  C16   C15  C14  C13    0.00   0.0  0
 TR3  CONST_28  C16   C17  C18  C13    0.00   0.0  0
 TR3  CONST_29  C17   C18  C13  C14    0.00   0.0  0
 TR3  CONST_30  C17   C16  C15  C14    0.00   0.0  0
 TR3  CONST_31  C18   C13  C14  C15    0.00   0.0  0
 TR3  CONST_32  C18   C17  C16  C15    0.00   0.0  0
 TR3  CONST_33  N27   C6   C1   C2   180.00   0.0  0
 TR3  CONST_34  S24   C12  C3   C2     0.00   0.0  0
 TR3  CONST_35  S24   C12  C3   C4   180.00   0.0  0
 TR3  CONST_36  N27   C6   C5   C4   180.00   0.0  0
 TR3  CONST_37  S24   C12  N10  N11  180.00   0.0  0
 TR3  CONST_38  H5    C5   C6   C1   180.00   0.0  0
 TR3  CONST_39  H1    C1   C2   C3   180.00   0.0  0
 TR3  CONST_40  H2    C2   C3   C4   180.00   0.0  0
 TR3  CONST_41  H15   C15  C16  N11    0.00   0.0  0
 TR3  CONST_42  H17   C17  C16  N11    0.00   0.0  0
 TR3  CONST_43  H18   C18  C13  C14  180.00   0.0  0
 TR3  CONST_44  H13   C13  C14  C15  180.00   0.0  0
 TR3  CONST_45  H14   C14  C15  C16  180.00   0.0  0
 TR3  CONST_46  C32   C26  N27  C6   180.00   0.0  0
 TR3  CONST_47  C26   N27  C6   C1   180.00   0.0  0
 TR3  CONST_48  C26   N27  C6   C5     0.00   0.0  0
 TR3  CONST_49  HN27  N27  C6   C1     0.00   0.0  0
 TR3  CONST_50  O28   C26  N27  C6     0.00   0.0  0
 TR3  Var_01    C33   C34  N35  C30   53.57  30.0  1
 TR3  Var_02    C34   N35  C30  C31  -53.74  30.0  1
 TR3  Var_03    N35   C30  C31  C32   54.38  30.0  1
 TR3  Var_04    N35   C34  C33  C32  -54.02  30.0  1
 TR3  Var_05    H25   C25  S24  C12  -62.19  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
 TR3  chir_01  C32  C26  C31  C33  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
 TR3  plan-1  N11   0.020
 TR3  plan-1  C13   0.020
 TR3  plan-1  C14   0.020
 TR3  plan-1  C15   0.020
 TR3  plan-1  C16   0.020
 TR3  plan-1  C17   0.020
 TR3  plan-1  C18   0.020
 TR3  plan-1  H13   0.020
 TR3  plan-1  H14   0.020
 TR3  plan-1  H15   0.020
 TR3  plan-1  H17   0.020
 TR3  plan-1  H18   0.020
 TR3  plan-2  C1    0.020
 TR3  plan-2  C2    0.020
 TR3  plan-2  C3    0.020
 TR3  plan-2  C4    0.020
 TR3  plan-2  C5    0.020
 TR3  plan-2  C6    0.020
 TR3  plan-2  N10   0.020
 TR3  plan-2  N11   0.020
 TR3  plan-2  C12   0.020
 TR3  plan-2  C16   0.020
 TR3  plan-2  S24   0.020
 TR3  plan-2  N27   0.020
 TR3  plan-2  H1    0.020
 TR3  plan-2  H2    0.020
 TR3  plan-2  H5    0.020
 TR3  plan-3  C6    0.020
 TR3  plan-3  C26   0.020
 TR3  plan-3  N27   0.020
 TR3  plan-3  O28   0.020
 TR3  plan-3  C32   0.020
 TR3  plan-3  HN27  0.020

