# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 07:44:31 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 6-amino-3-[(1S,3R)-4'-chloro-3-hydroxy-1',2'-dihydrospiro[cyclopentane-1,3'-pyrrolo[2,3-b]pyridin]-5'-yl]-2-fluoro-N,N-dimethylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1c(N)ccc(c1F)c2cnc3NC[C@]4(CC[C@@H](O)C4)c3c2Cl
#
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
 2TR  2TR  "6-amino-3-[(1S,3R)-4'-chloro-3-hydroxy-1',2'-dihydrospiro[cyclopentane-1,3'-pyrrolo[2,3-b]pyridin]-5'-yl]-2-fluoro-N,N-dimethylbenzamide"  ligand  50  28  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2TR
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
 2TR  C4    C   C     0   0.503  -38.6180  -115.2120  219.0352
 2TR  C6    C   CR6   0  -0.346  -39.6823  -114.7658  219.9927
 2TR  C7    C   CR6   0   0.323  -40.4351  -113.6094  219.7292
 2TR  C8    C   CR16  0  -0.333  -41.3863  -113.2096  220.6793
 2TR  C10   C   CR6   0  -0.198  -40.7822  -115.0331  222.1618
 2TR  C13   C   CR6   0   0.040  -40.9133  -115.7620  223.4362
 2TR  C17   C   CR56  0   0.146  -40.6959  -115.9117  225.8297
 2TR  C20   C   CR5   0  -0.152  -40.5078  -115.6031  227.2920
 2TR  C21   C   CH2   0  -0.440  -41.6910  -114.7479  227.8267
 2TR  C22   C   CH2   0  -0.481  -41.0813  -113.9195  228.9479
 2TR  C24   C   CH2   0  -0.475  -39.2404  -114.8324  227.7265
 2TR  C26   C   CH2   0  -0.266  -40.5328  -117.0321  227.8853
 2TR  C1    C   CH3   0  -0.523  -37.7968  -116.9076  217.5099
 2TR  C11   C   CR6   0   0.585  -39.8663  -115.4180  221.1990
 2TR  C14   C   CR16  0  -0.112  -41.3779  -117.0673  223.4687
 2TR  C16   C   CR56  0   0.469  -41.1952  -117.2223  225.7037
 2TR  C18   C   CR6   0  -0.125  -40.5741  -115.1856  224.6772
 2TR  C23   C   CH1   0   0.077  -39.7272  -113.5315  228.3597
 2TR  C3    C   CH3   0  -0.521  -40.0173  -117.1739  218.4757
 2TR  C9    C   CR16  0  -0.256  -41.5483  -113.9069  221.8573
 2TR  F12   F   F     0  -0.299  -39.0991  -116.4947  221.4372
 2TR  N15   N   N     0  -0.449  -41.5284  -117.8056  224.5691
 2TR  N2    N   NT    0  -0.420  -38.8124  -116.3761  218.3948
 2TR  N27   N   NR15  0  -0.658  -41.3150  -117.8003  226.9312
 2TR  N28   N   NH2   0  -0.858  -40.3058  -112.9317  218.5455
 2TR  O25   O   OH1   0  -0.668  -38.7767  -113.0540  229.2808
 2TR  O5    O   O     0  -0.483  -37.6337  -114.5020  218.8589
 2TR  CL19  CL  CL    0  -0.107  -39.9960  -113.5581  224.7272
 2TR  H1    H   HCR6  0   0.264  -41.9955  -112.3356  220.4853
 2TR  H2    H   HCH2  0   0.238  -42.0604  -114.0886  227.0375
 2TR  H3    H   HCH2  0   0.251  -42.5313  -115.3667  228.1448
 2TR  H4    H   HCH2  0   0.239  -41.6951  -113.0610  229.2276
 2TR  H5    H   HCH2  0   0.225  -40.9308  -114.5294  229.8449
 2TR  H6    H   HCH2  0   0.245  -38.7129  -115.4086  228.4929
 2TR  H7    H   HCH2  0   0.248  -38.5332  -114.6736  226.9124
 2TR  H8    H   HCH2  0   0.249  -40.9782  -117.0501  228.8809
 2TR  H9    H   HCH2  0   0.242  -39.5133  -117.4274  227.9642
 2TR  H10   H   HCH3  0   0.260  -36.8758  -116.3415  217.5964
 2TR  H11   H   HCH3  0   0.245  -37.5951  -117.9484  217.7668
 2TR  H12   H   HCH3  0   0.243  -38.1354  -116.8730  216.4723
 2TR  H13   H   HCR6  0   0.257  -41.6570  -117.5453  222.5355
 2TR  H14   H   HCH1  0   0.195  -39.9039  -112.7904  227.5679
 2TR  H15   H   HCH3  0   0.265  -40.8218  -116.6346  218.9657
 2TR  H16   H   HCH3  0   0.252  -40.3506  -117.4253  217.4679
 2TR  H17   H   HCH3  0   0.244  -39.8368  -118.1063  219.0136
 2TR  H18   H   HCR6  0   0.262  -42.2881  -113.5682  222.5715
 2TR  H19   H   HNR5  0   0.385  -41.3282  -118.8064  226.9978
 2TR  H20   H   HNH2  0   0.388  -40.7189  -112.0132  218.5210
 2TR  H21   H   HNH2  0   0.386  -39.4028  -112.9551  218.0999
 2TR  H22   H   HOH1  0   0.446  -39.0713  -112.1948  229.5976

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
 2TR  C1   N2    single    1.448  0.020  1.448
 2TR  N2   C3    single    1.447  0.020  1.447
 2TR  N2   C4    single    1.343  0.020  1.343
 2TR  N28  C7    single    1.370  0.020  1.370
 2TR  O5   C4    double    1.226  0.020  1.226
 2TR  C4   C6    single    1.500  0.020  1.500
 2TR  C7   C6    aromatic  1.405  0.020  1.405
 2TR  C7   C8    aromatic  1.403  0.020  1.403
 2TR  C6   C11   aromatic  1.384  0.020  1.384
 2TR  C8   C9    aromatic  1.378  0.020  1.378
 2TR  C11  F12   single    1.343  0.020  1.343
 2TR  C11  C10   aromatic  1.383  0.020  1.383
 2TR  C9   C10   aromatic  1.396  0.020  1.396
 2TR  C10  C13   single    1.474  0.020  1.474
 2TR  C14  C13   aromatic  1.386  0.020  1.386
 2TR  C14  N15   aromatic  1.334  0.020  1.334
 2TR  C13  C18   aromatic  1.410  0.020  1.410
 2TR  N15  C16   aromatic  1.319  0.020  1.319
 2TR  C18  CL19  single    1.728  0.020  1.728
 2TR  C18  C17   aromatic  1.368  0.020  1.368
 2TR  C16  C17   aromatic  1.408  0.020  1.408
 2TR  C16  N27   single    1.362  0.020  1.362
 2TR  C17  C20   single    1.506  0.020  1.506
 2TR  N27  C26   single    1.453  0.020  1.453
 2TR  C20  C24   single    1.546  0.020  1.546
 2TR  C20  C21   single    1.555  0.020  1.555
 2TR  C20  C26   single    1.547  0.020  1.547
 2TR  C24  C23   single    1.526  0.020  1.526
 2TR  C21  C22   single    1.521  0.020  1.521
 2TR  C23  C22   single    1.526  0.020  1.526
 2TR  C23  O25   single    1.407  0.020  1.407
 2TR  C8   H1    single    0.930  0.020  1.080
 2TR  C21  H2    single    0.970  0.020  1.090
 2TR  C21  H3    single    0.970  0.020  1.090
 2TR  C22  H4    single    0.970  0.020  1.090
 2TR  C22  H5    single    0.970  0.020  1.090
 2TR  C24  H6    single    0.970  0.020  1.090
 2TR  C24  H7    single    0.970  0.020  1.090
 2TR  C26  H8    single    0.970  0.020  1.090
 2TR  C26  H9    single    0.970  0.020  1.090
 2TR  C1   H10   single    0.970  0.020  1.090
 2TR  C1   H11   single    0.970  0.020  1.090
 2TR  C1   H12   single    0.970  0.020  1.090
 2TR  C14  H13   single    0.930  0.020  1.080
 2TR  C23  H14   single    0.970  0.020  1.090
 2TR  C3   H15   single    0.970  0.020  1.090
 2TR  C3   H16   single    0.970  0.020  1.090
 2TR  C3   H17   single    0.970  0.020  1.090
 2TR  C9   H18   single    0.930  0.020  1.080
 2TR  N27  H19   single    0.890  0.020  1.040
 2TR  N28  H20   single    0.890  0.020  1.040
 2TR  N28  H21   single    0.890  0.020  1.040
 2TR  O25  H22   single    0.850  0.020  0.980

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
 2TR  O5    C4   N2   123.34  3.000
 2TR  O5    C4   C6   119.28  3.000
 2TR  N2    C4   C6   117.37  3.000
 2TR  C11   C6   C7   118.71  3.000
 2TR  C11   C6   C4   120.72  3.000
 2TR  C7    C6   C4   120.37  3.000
 2TR  N28   C7   C8   120.55  3.000
 2TR  C8    C7   C6   118.10  3.000
 2TR  N28   C7   C6   121.24  3.000
 2TR  H1    C8   C9   119.69  3.000
 2TR  H1    C8   C7   119.35  3.000
 2TR  C9    C8   C7   120.96  3.000
 2TR  C9    C10  C11  115.85  3.000
 2TR  C9    C10  C13  122.60  3.000
 2TR  C11   C10  C13  121.54  3.000
 2TR  C18   C13  C14  116.43  3.000
 2TR  C18   C13  C10  122.52  3.000
 2TR  C14   C13  C10  121.05  3.000
 2TR  C18   C17  C16  116.77  3.000
 2TR  C16   C17  C20  108.77  3.000
 2TR  C18   C17  C20  134.28  3.000
 2TR  C26   C20  C24  111.47  3.000
 2TR  C26   C20  C21  111.33  3.000
 2TR  C24   C20  C21  104.66  3.000
 2TR  C26   C20  C17  100.42  3.000
 2TR  C21   C20  C17  110.59  3.000
 2TR  C24   C20  C17  118.52  3.000
 2TR  H3    C21  H2   107.00  3.000
 2TR  H3    C21  C22  113.74  3.000
 2TR  H2    C21  C22  109.83  3.000
 2TR  H3    C21  C20  111.99  3.000
 2TR  H2    C21  C20  109.92  3.000
 2TR  C22   C21  C20  104.36  3.000
 2TR  H5    C22  H4   107.78  3.000
 2TR  H5    C22  C23  109.59  3.000
 2TR  H4    C22  C23  113.42  3.000
 2TR  H5    C22  C21  110.82  3.000
 2TR  H4    C22  C21  113.05  3.000
 2TR  C23   C22  C21  102.11  3.000
 2TR  H7    C24  H6   106.67  3.000
 2TR  H7    C24  C23  113.12  3.000
 2TR  H6    C24  C23  108.18  3.000
 2TR  H7    C24  C20  113.24  3.000
 2TR  H6    C24  C20  109.24  3.000
 2TR  C23   C24  C20  106.26  3.000
 2TR  H9    C26  H8   107.94  3.000
 2TR  H9    C26  N27  110.92  3.000
 2TR  H8    C26  N27  111.76  3.000
 2TR  H9    C26  C20  110.22  3.000
 2TR  H8    C26  C20  111.82  3.000
 2TR  N27   C26  C20  104.19  3.000
 2TR  H12   C1   H11  108.14  3.000
 2TR  H12   C1   H10  108.81  3.000
 2TR  H11   C1   H10  108.79  3.000
 2TR  H12   C1   N2   110.58  3.000
 2TR  H11   C1   N2   109.63  3.000
 2TR  H10   C1   N2   110.81  3.000
 2TR  F12   C11  C10  118.53  3.000
 2TR  C10   C11  C6   124.31  3.000
 2TR  F12   C11  C6   117.16  3.000
 2TR  H13   C14  N15  115.89  3.000
 2TR  H13   C14  C13  118.75  3.000
 2TR  N15   C14  C13  125.35  3.000
 2TR  N27   C16  N15  124.44  3.000
 2TR  N27   C16  C17  110.21  3.000
 2TR  N15   C16  C17  125.33  3.000
 2TR  CL19  C18  C17  120.37  3.000
 2TR  C17   C18  C13  120.22  3.000
 2TR  CL19  C18  C13  119.41  3.000
 2TR  H14   C23  O25  110.57  3.000
 2TR  H14   C23  C24  109.10  3.000
 2TR  O25   C23  C24  110.20  3.000
 2TR  H14   C23  C22  107.85  3.000
 2TR  O25   C23  C22  115.67  3.000
 2TR  C24   C23  C22  103.07  3.000
 2TR  H17   C3   H16  107.99  3.000
 2TR  H17   C3   H15  108.94  3.000
 2TR  H16   C3   H15  107.76  3.000
 2TR  H17   C3   N2   111.15  3.000
 2TR  H16   C3   N2   109.26  3.000
 2TR  H15   C3   N2   111.62  3.000
 2TR  H18   C9   C10  118.92  3.000
 2TR  H18   C9   C8   119.07  3.000
 2TR  C10   C9   C8   122.01  3.000
 2TR  C16   N15  C14  115.89  3.000
 2TR  C3    N2   C1   114.56  3.000
 2TR  C3    N2   C4   124.87  3.000
 2TR  C1    N2   C4   120.54  3.000
 2TR  H19   N27  C16  118.95  3.000
 2TR  H19   N27  C26  119.41  3.000
 2TR  C16   N27  C26  108.66  3.000
 2TR  H21   N28  H20  112.21  3.000
 2TR  H21   N28  C7   117.09  3.000
 2TR  H20   N28  C7   115.67  3.000
 2TR  H22   O25  C23  108.17  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
 2TR  CONST_01  C9    C8   C7   C6      0.00   0.0  0
 2TR  CONST_02  C9    C10  C11  C6      0.00   0.0  0
 2TR  CONST_03  C13   C10  C11  C6    180.00   0.0  0
 2TR  CONST_04  C10   C11  C6   C7      0.00   0.0  0
 2TR  CONST_05  C10   C9   C8   C7      0.00   0.0  0
 2TR  CONST_06  C11   C6   C7   C8      0.00   0.0  0
 2TR  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 2TR  CONST_08  C13   C10  C9   C8    180.00   0.0  0
 2TR  CONST_09  N15   C14  C13  C10   180.00   0.0  0
 2TR  CONST_10  C17   C18  C13  C10   180.00   0.0  0
 2TR  CONST_11  C16   N15  C14  C13     0.00   0.0  0
 2TR  CONST_12  C16   C17  C18  C13     0.00   0.0  0
 2TR  CONST_13  C14   C13  C18  C17     0.00   0.0  0
 2TR  CONST_14  C14   N15  C16  C17     0.00   0.0  0
 2TR  CONST_19  N15   C14  C13  C18     0.00   0.0  0
 2TR  CONST_20  N15   C16  C17  C18     0.00   0.0  0
 2TR  CONST_21  C20   C17  C18  C13   180.00   0.0  0
 2TR  CONST_22  N15   C16  C17  C20   180.00   0.0  0
 2TR  CONST_23  N27   C16  C17  C20     0.00   0.0  0
 2TR  CONST_24  C8    C7   C6   C4    180.00   0.0  0
 2TR  CONST_25  C10   C11  C6   C4    180.00   0.0  0
 2TR  CONST_26  F12   C11  C6   C7    180.00   0.0  0
 2TR  CONST_27  CL19  C18  C13  C10     0.00   0.0  0
 2TR  CONST_28  F12   C11  C10  C13     0.00   0.0  0
 2TR  CONST_29  CL19  C18  C17  C20     0.00   0.0  0
 2TR  CONST_30  N28   C7   C6   C11   180.00   0.0  0
 2TR  CONST_31  CL19  C18  C13  C14   180.00   0.0  0
 2TR  CONST_32  CL19  C18  C17  C16   180.00   0.0  0
 2TR  CONST_33  N28   C7   C8   C9    180.00   0.0  0
 2TR  CONST_34  F12   C11  C10  C9    180.00   0.0  0
 2TR  CONST_35  H1    C8   C7   C6    180.00   0.0  0
 2TR  CONST_36  H18   C9   C8   C7    180.00   0.0  0
 2TR  CONST_37  H1    C8   C9   C10   180.00   0.0  0
 2TR  CONST_38  H13   C14  C13  C10     0.00   0.0  0
 2TR  CONST_39  H18   C9   C10  C13     0.00   0.0  0
 2TR  CONST_40  H18   C9   C10  C11   180.00   0.0  0
 2TR  CONST_41  H13   C14  N15  C16   180.00   0.0  0
 2TR  CONST_42  H13   C14  C13  C18   180.00   0.0  0
 2TR  CONST_43  H20   N28  C7   C6    180.00   0.0  0
 2TR  CONST_47  C1    N2   C4   C6    180.00   0.0  0
 2TR  CONST_48  C3    N2   C4   C6      0.00   0.0  0
 2TR  CONST_49  O5    C4   N2   C1      0.00   0.0  0
 2TR  CONST_50  O5    C4   N2   C3    180.00   0.0  0
 2TR  Var_01    C26   N27  C16  C17   -16.58  30.0  1
 2TR  Var_02    C23   C22  C21  C20    40.54  30.0  1
 2TR  Var_03    C16   N27  C26  C20    27.16  30.0  1
 2TR  Var_04    N15   C16  N27  C26   164.73  30.0  1
 2TR  Var_05    H19   N27  C16  C17  -157.77  30.0  1
 2TR  Var_06    H4    C22  C21  C20   162.76  30.0  1
 2TR  Var_07    H5    C22  C21  C20   -76.11  30.0  1
 2TR  Var_08    H19   N27  C26  C20   168.14  30.0  1
 2TR  Var_09    H8    C26  N27  C16   148.08  30.0  1
 2TR  Var_10    H9    C26  N27  C16   -91.41  30.0  1
 2TR  Var_11    H2    C21  C22  C23   -77.25  30.0  1
 2TR  Var_12    H3    C21  C22  C23   162.87  30.0  1
 2TR  Var_13    H19   N27  C16  N15    23.54  30.0  1
 2TR  Var_14    N2    C4   C6   C7   -114.21  30.0  2
 2TR  Var_15    O5    C4   C6   C7     64.78  30.0  2
 2TR  Var_16    N2    C4   C6   C11    71.13  30.0  2
 2TR  Var_17    O5    C4   C6   C11  -109.88  30.0  2
 2TR  Var_18    H10   C1   N2   C4      9.52  30.0  3
 2TR  Var_19    H11   C1   N2   C4    129.62  30.0  3
 2TR  Var_20    H12   C1   N2   C4   -111.23  30.0  3
 2TR  Var_21    H15   C3   N2   C4     10.75  30.0  3
 2TR  Var_22    H16   C3   N2   C4    129.83  30.0  3
 2TR  Var_23    H17   C3   N2   C4   -111.09  30.0  3
 2TR  Var_24    H15   C3   N2   C1   -167.31  30.0  3
 2TR  Var_25    H16   C3   N2   C1    -48.23  30.0  3
 2TR  Var_26    H17   C3   N2   C1     70.84  30.0  3
 2TR  Var_27    H10   C1   N2   C3   -172.32  30.0  3
 2TR  Var_28    H11   C1   N2   C3    -52.22  30.0  3
 2TR  Var_29    H12   C1   N2   C3     66.93  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
 2TR  chir_01  C20  C24  C21  C26  positiv
 2TR  chir_02  C23  O25  C22  C24  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
 2TR  plan-1  C4    0.020
 2TR  plan-1  C6    0.020
 2TR  plan-1  C7    0.020
 2TR  plan-1  C8    0.020
 2TR  plan-1  C10   0.020
 2TR  plan-1  C13   0.020
 2TR  plan-1  C11   0.020
 2TR  plan-1  C9    0.020
 2TR  plan-1  F12   0.020
 2TR  plan-1  N28   0.020
 2TR  plan-1  H1    0.020
 2TR  plan-1  H18   0.020
 2TR  plan-2  C10   0.020
 2TR  plan-2  C13   0.020
 2TR  plan-2  C17   0.020
 2TR  plan-2  C20   0.020
 2TR  plan-2  C14   0.020
 2TR  plan-2  C16   0.020
 2TR  plan-2  C18   0.020
 2TR  plan-2  N15   0.020
 2TR  plan-2  N27   0.020
 2TR  plan-2  CL19  0.020
 2TR  plan-2  H13   0.020
 2TR  plan-3  C4    0.020
 2TR  plan-3  C6    0.020
 2TR  plan-3  C1    0.020
 2TR  plan-3  C3    0.020
 2TR  plan-3  N2    0.020
 2TR  plan-3  O5    0.020
 2TR  plan-4  C7    0.020
 2TR  plan-4  N28   0.020
 2TR  plan-4  H20   0.020
 2TR  plan-4  H21   0.020

