# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:06:06 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1,3-thiazolidin-3-yl[(2S,4S)-4-{4-[2-(trifluoromethyl)quinolin-4-yl]piperazin-1-yl}pyrrolidin-2-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc(N2CCN(CC2)[C@@H]3CN[C@@H](C3)C(=O)N4CCSC4)c5ccccc5n1
#
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
 W61  W61  1,3-thiazolidin-3-yl[(2S,4S)-4-{4-[2-(trifluoromethyl)quinolin-4-yl]piperazin-1-yl}pyrrolidin-2-yl]methanone  ligand  58  32  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W61
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
 W61  C1    C  CR6   0   0.445   3.2522   0.2421  -0.1468
 W61  C2    C  CR16  0  -0.416   3.7456  -0.9539  -0.6260
 W61  C3    C  CR6   0  -0.036   5.1306  -1.0967  -0.7972
 W61  N4    N  N     0  -0.463   6.0207  -0.1864  -0.5356
 W61  C5    C  CR66  0   0.177   5.5681   1.0191  -0.1146
 W61  C6    C  CR66  0   0.048   4.1917   1.3037   0.0609
 W61  C7    C  CR16  0  -0.315   3.8081   2.6290   0.3625
 W61  C8    C  CR16  0  -0.248   4.7508   3.6024   0.5609
 W61  C9    C  CR16  0  -0.254   6.1218   3.2979   0.4619
 W61  C10   C  CR16  0  -0.296   6.5215   2.0352   0.1195
 W61  C11   C  CT    0   1.038   5.6531  -2.4088  -1.3283
 W61  N20   N  NT    0  -0.510   1.9103   0.4530   0.0918
 W61  C21   C  CH2   0  -0.329   0.9551  -0.4536  -0.5174
 W61  C22   C  CH2   0  -0.285  -0.4296   0.1672  -0.4952
 W61  N23   N  NT    0  -0.436  -0.8444   0.4895   0.8589
 W61  C24   C  CH2   0  -0.293   0.1237   1.3922   1.4589
 W61  C26   C  CH1   0  -0.073  -2.1864   1.0446   0.8969
 W61  C27   C  CH2   0  -0.295  -2.6897   1.2978   2.3386
 W61  N28   N  NH1   0  -0.596  -4.0987   0.8976   2.3960
 W61  C29   C  CH1   0  -0.233  -4.5166   0.6188   1.0329
 W61  C30   C  CH2   0  -0.475  -3.2542   0.1215   0.3141
 W61  C32   C  CH2   0  -0.340   1.5045   0.7724   1.4595
 W61  C33   C  C     0   0.569  -5.6235  -0.4198   1.0005
 W61  N46   N  NT    0  -0.474  -6.4736  -0.3878  -0.0410
 W61  C47   C  CH2   0  -0.405  -6.4163   0.5888  -1.1195
 W61  S48   S  S2    0  -0.003  -7.4164  -0.1130  -2.4544
 W61  C49   C  CH2   0  -0.598  -8.4911  -0.8893  -1.2184
 W61  C50   C  CH2   0  -0.245  -7.5395  -1.3812  -0.1434
 W61  F52   F  F     0  -0.317   5.3542  -2.5466  -2.6285
 W61  F53   F  F     0  -0.295   6.9710  -2.5199  -1.2076
 W61  F54   F  F     0  -0.311   5.1003  -3.4512  -0.6938
 W61  O57   O  O     0  -0.494  -5.7063  -1.2732   1.8749
 W61  H2    H  HCR6  0   0.293   3.0883  -1.7892  -0.8215
 W61  H7    H  HCR6  0   0.276   2.7591   2.8886   0.4039
 W61  H8    H  HCR6  0   0.267   4.4403   4.6147   0.7821
 W61  H9    H  HCR6  0   0.267   6.8580   4.0720   0.6330
 W61  H10   H  HCR6  0   0.266   7.5693   1.7906   0.0027
 W61  H21   H  HCH2  0   0.264   1.2371  -0.6350  -1.5552
 W61  H21A  H  HCH2  0   0.227   0.9287  -1.4235  -0.0010
 W61  H22   H  HCH2  0   0.202  -0.4360   1.0590  -1.1442
 W61  H22A  H  HCH2  0   0.255  -1.1205  -0.5556  -0.9305
 W61  H24   H  HCH2  0   0.204   0.1639   2.3614   0.9317
 W61  H24A  H  HCH2  0   0.255  -0.1531   1.5998   2.4933
 W61  H26   H  HCH1  0   0.213  -2.2190   1.9959   0.3362
 W61  H27   H  HCH2  0   0.232  -2.1098   0.7117   3.0546
 W61  H27A  H  HCH2  0   0.226  -2.5714   2.3498   2.6078
 W61  HN28  H  HNH1  0   0.349  -4.1785   0.0428   2.9319
 W61  H29   H  HCH1  0   0.268  -4.8519   1.5502   0.5647
 W61  H30   H  HCH2  0   0.255  -3.3287   0.1731  -0.7726
 W61  H30A  H  HCH2  0   0.243  -3.0500  -0.9156   0.5985
 W61  H32   H  HCH2  0   0.243   1.4957  -0.1431   2.0667
 W61  H32A  H  HCH2  0   0.271   2.2094   1.4575   1.9244
 W61  H47   H  HCH2  0   0.289  -6.8197   1.5539  -0.8056
 W61  H47A  H  HCH2  0   0.293  -5.4052   0.7350  -1.4949
 W61  H49   H  HCH2  0   0.284  -9.2012  -0.1617  -0.8250
 W61  H49A  H  HCH2  0   0.301  -9.0431  -1.7069  -1.6773
 W61  H50   H  HCH2  0   0.256  -7.1242  -2.3544  -0.4140
 W61  H50A  H  HCH2  0   0.266  -8.0569  -1.4849   0.8103

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
 W61  C1   C2    aromatic  1.380  0.020  1.380
 W61  C1   C6    aromatic  1.433  0.020  1.433
 W61  C1   N20   single    1.379  0.020  1.379
 W61  C2   C3    aromatic  1.403  0.020  1.403
 W61  C3   N4    aromatic  1.300  0.020  1.300
 W61  C3   C11   single    1.509  0.020  1.509
 W61  N4   C5    aromatic  1.355  0.020  1.355
 W61  C5   C6    aromatic  1.416  0.020  1.416
 W61  C5   C10   aromatic  1.413  0.020  1.413
 W61  C6   C7    aromatic  1.412  0.020  1.412
 W61  C7   C8    aromatic  1.370  0.020  1.370
 W61  C8   C9    aromatic  1.408  0.020  1.408
 W61  C9   C10   aromatic  1.368  0.020  1.368
 W61  C11  F52   single    1.341  0.020  1.341
 W61  C11  F53   single    1.328  0.020  1.328
 W61  C11  F54   single    1.340  0.020  1.340
 W61  N20  C21   single    1.451  0.020  1.451
 W61  N20  C32   single    1.462  0.020  1.462
 W61  C21  C22   single    1.518  0.020  1.518
 W61  C22  N23   single    1.452  0.020  1.452
 W61  N23  C24   single    1.453  0.020  1.453
 W61  N23  C26   single    1.453  0.020  1.453
 W61  C24  C32   single    1.514  0.020  1.514
 W61  C26  C27   single    1.548  0.020  1.548
 W61  C26  C30   single    1.527  0.020  1.527
 W61  C27  N28   single    1.466  0.020  1.466
 W61  N28  C29   single    1.453  0.020  1.453
 W61  C29  C30   single    1.535  0.020  1.535
 W61  C29  C33   single    1.518  0.020  1.518
 W61  C33  N46   single    1.345  0.020  1.345
 W61  C33  O57   double    1.225  0.020  1.225
 W61  N46  C47   single    1.456  0.020  1.456
 W61  N46  C50   single    1.461  0.020  1.461
 W61  C47  S48   single    1.809  0.020  1.809
 W61  S48  C49   single    1.813  0.020  1.813
 W61  C49  C50   single    1.518  0.020  1.518
 W61  C2   H2    single    0.930  0.020  1.080
 W61  C7   H7    single    0.930  0.020  1.080
 W61  C8   H8    single    0.930  0.020  1.080
 W61  C9   H9    single    0.930  0.020  1.080
 W61  C10  H10   single    0.930  0.020  1.080
 W61  C21  H21   single    0.970  0.020  1.090
 W61  C21  H21A  single    0.970  0.020  1.090
 W61  C22  H22   single    0.970  0.020  1.090
 W61  C22  H22A  single    0.970  0.020  1.090
 W61  C24  H24   single    0.970  0.020  1.090
 W61  C24  H24A  single    0.970  0.020  1.090
 W61  C26  H26   single    0.970  0.020  1.090
 W61  C27  H27   single    0.970  0.020  1.090
 W61  C27  H27A  single    0.970  0.020  1.090
 W61  N28  HN28  single    0.890  0.020  1.040
 W61  C29  H29   single    0.970  0.020  1.090
 W61  C30  H30   single    0.970  0.020  1.090
 W61  C30  H30A  single    0.970  0.020  1.090
 W61  C32  H32   single    0.970  0.020  1.090
 W61  C32  H32A  single    0.970  0.020  1.090
 W61  C47  H47   single    0.970  0.020  1.090
 W61  C47  H47A  single    0.970  0.020  1.090
 W61  C49  H49   single    0.970  0.020  1.090
 W61  C49  H49A  single    0.970  0.020  1.090
 W61  C50  H50   single    0.970  0.020  1.090
 W61  C50  H50A  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
 W61  N20   C1   C6   119.98  3.000
 W61  N20   C1   C2   122.72  3.000
 W61  C6    C1   C2   117.27  3.000
 W61  H2    C2   C3   119.98  3.000
 W61  H2    C2   C1   121.02  3.000
 W61  C3    C2   C1   118.92  3.000
 W61  C11   C3   N4   116.28  3.000
 W61  C11   C3   C2   118.25  3.000
 W61  N4    C3   C2   125.47  3.000
 W61  C5    N4   C3   117.19  3.000
 W61  C10   C5   C6   119.39  3.000
 W61  C10   C5   N4   117.78  3.000
 W61  C6    C5   N4   122.81  3.000
 W61  C7    C6   C5   118.61  3.000
 W61  C7    C6   C1   123.24  3.000
 W61  C5    C6   C1   118.06  3.000
 W61  H7    C7   C8   119.44  3.000
 W61  H7    C7   C6   119.79  3.000
 W61  C8    C7   C6   120.73  3.000
 W61  H8    C8   C9   119.76  3.000
 W61  H8    C8   C7   119.81  3.000
 W61  C9    C8   C7   120.42  3.000
 W61  H9    C9   C10  120.08  3.000
 W61  H9    C9   C8   119.78  3.000
 W61  C10   C9   C8   120.12  3.000
 W61  H10   C10  C9   121.23  3.000
 W61  H10   C10  C5   118.22  3.000
 W61  C9    C10  C5   120.54  3.000
 W61  F54   C11  F53  107.54  3.000
 W61  F54   C11  F52  106.69  3.000
 W61  F53   C11  F52  107.50  3.000
 W61  F54   C11  C3   111.53  3.000
 W61  F53   C11  C3   112.61  3.000
 W61  F52   C11  C3   110.69  3.000
 W61  C32   N20  C21  110.28  3.000
 W61  C32   N20  C1   117.73  3.000
 W61  C21   N20  C1   118.18  3.000
 W61  H21A  C21  H21  107.85  3.000
 W61  H21A  C21  C22  109.40  3.000
 W61  H21   C21  C22  108.53  3.000
 W61  H21A  C21  N20  111.71  3.000
 W61  H21   C21  N20  109.47  3.000
 W61  C22   C21  N20  109.81  3.000
 W61  H22A  C22  H22  107.30  3.000
 W61  H22A  C22  N23  109.77  3.000
 W61  H22   C22  N23  111.56  3.000
 W61  H22A  C22  C21  107.52  3.000
 W61  H22   C22  C21  109.11  3.000
 W61  N23   C22  C21  111.41  3.000
 W61  C26   N23  C24  111.55  3.000
 W61  C26   N23  C22  111.90  3.000
 W61  C24   N23  C22  109.42  3.000
 W61  H24A  C24  H24  107.15  3.000
 W61  H24A  C24  C32  108.00  3.000
 W61  H24   C24  C32  109.05  3.000
 W61  H24A  C24  N23  109.93  3.000
 W61  H24   C24  N23  111.86  3.000
 W61  C32   C24  N23  110.71  3.000
 W61  H26   C26  C30  107.82  3.000
 W61  H26   C26  C27  108.80  3.000
 W61  C30   C26  C27  103.12  3.000
 W61  H26   C26  N23  110.06  3.000
 W61  C30   C26  N23  113.89  3.000
 W61  C27   C26  N23  112.79  3.000
 W61  H27A  C27  H27  107.33  3.000
 W61  H27A  C27  N28  110.94  3.000
 W61  H27   C27  N28  109.77  3.000
 W61  H27A  C27  C26  110.60  3.000
 W61  H27   C27  C26  110.50  3.000
 W61  N28   C27  C26  107.72  3.000
 W61  HN28  N28  C29  108.18  3.000
 W61  HN28  N28  C27  109.10  3.000
 W61  C29   N28  C27  106.99  3.000
 W61  H29   C29  C33  110.46  3.000
 W61  H29   C29  C30  109.09  3.000
 W61  C33   C29  C30  111.59  3.000
 W61  H29   C29  N28  109.03  3.000
 W61  C33   C29  N28  111.16  3.000
 W61  C30   C29  N28  105.36  3.000
 W61  H30A  C30  H30  108.45  3.000
 W61  H30A  C30  C29  109.79  3.000
 W61  H30   C30  C29  113.27  3.000
 W61  H30A  C30  C26  110.06  3.000
 W61  H30   C30  C26  113.55  3.000
 W61  C29   C30  C26  101.57  3.000
 W61  H32A  C32  H32  107.10  3.000
 W61  H32A  C32  C24  109.48  3.000
 W61  H32   C32  C24  109.52  3.000
 W61  H32A  C32  N20  110.96  3.000
 W61  H32   C32  N20  109.71  3.000
 W61  C24   C32  N20  110.02  3.000
 W61  O57   C33  N46  121.80  3.000
 W61  O57   C33  C29  120.72  3.000
 W61  N46   C33  C29  117.46  3.000
 W61  C50   N46  C47  115.65  3.000
 W61  C50   N46  C33  119.96  3.000
 W61  C47   N46  C33  124.39  3.000
 W61  H47A  C47  H47  108.88  3.000
 W61  H47A  C47  S48  108.12  3.000
 W61  H47   C47  S48  110.53  3.000
 W61  H47A  C47  N46  112.46  3.000
 W61  H47   C47  N46  111.42  3.000
 W61  S48   C47  N46  105.34  3.000
 W61  C49   S48  C47   89.47  3.000
 W61  H49A  C49  H49  108.86  3.000
 W61  H49A  C49  C50  111.92  3.000
 W61  H49   C49  C50  111.67  3.000
 W61  H49A  C49  S48  109.58  3.000
 W61  H49   C49  S48  110.27  3.000
 W61  C50   C49  S48  104.48  3.000
 W61  H50A  C50  H50  108.21  3.000
 W61  H50A  C50  C49  110.67  3.000
 W61  H50   C50  C49  110.60  3.000
 W61  H50A  C50  N46  110.47  3.000
 W61  H50   C50  N46  110.24  3.000
 W61  C49   C50  N46  106.67  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
 W61  CONST_01  N4   C3   C2   C1      0.00   0.0  0
 W61  CONST_02  N4   C5   C6   C1      0.00   0.0  0
 W61  CONST_03  C10  C5   C6   C1    180.00   0.0  0
 W61  CONST_04  C8   C7   C6   C1    180.00   0.0  0
 W61  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 W61  CONST_06  C7   C6   C1   C2    180.00   0.0  0
 W61  CONST_07  C5   N4   C3   C2      0.00   0.0  0
 W61  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 W61  CONST_09  C6   C5   N4   C3      0.00   0.0  0
 W61  CONST_10  C10  C5   N4   C3    180.00   0.0  0
 W61  CONST_11  C7   C6   C5   N4    180.00   0.0  0
 W61  CONST_12  C9   C10  C5   N4    180.00   0.0  0
 W61  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 W61  CONST_14  C8   C9   C10  C5      0.00   0.0  0
 W61  CONST_15  C9   C10  C5   C6      0.00   0.0  0
 W61  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 W61  CONST_17  C10  C5   C6   C7      0.00   0.0  0
 W61  CONST_18  C10  C9   C8   C7      0.00   0.0  0
 W61  CONST_19  N20  C1   C2   C3    180.00   0.0  0
 W61  CONST_20  N20  C1   C6   C5    180.00   0.0  0
 W61  CONST_21  N20  C1   C6   C7      0.00   0.0  0
 W61  CONST_22  C11  C3   C2   C1    180.00   0.0  0
 W61  CONST_23  C11  C3   N4   C5    180.00   0.0  0
 W61  CONST_24  C47  N46  C33  C29     0.00   0.0  0
 W61  CONST_25  C50  N46  C33  C29   180.00   0.0  0
 W61  CONST_26  H7   C7   C6   C1      0.00   0.0  0
 W61  CONST_27  H2   C2   C3   N4    180.00   0.0  0
 W61  CONST_28  H10  C10  C5   N4      0.00   0.0  0
 W61  CONST_29  H9   C9   C10  C5    180.00   0.0  0
 W61  CONST_30  H8   C8   C7   C6    180.00   0.0  0
 W61  CONST_31  O57  C33  N46  C47   180.00   0.0  0
 W61  CONST_32  O57  C33  N46  C50     0.00   0.0  0
 W61  Var_01    C22  C21  N20  C1   -162.93  30.0  1
 W61  Var_02    C24  C32  N20  C1    161.99  30.0  1
 W61  Var_03    C21  N20  C1   C2    -17.46  30.0  2
 W61  Var_04    N23  C22  C21  N20   -57.87  30.0  1
 W61  Var_05    N23  C24  C32  N20    58.59  30.0  1
 W61  Var_06    C24  N23  C22  C21    57.71  30.0  1
 W61  Var_07    C32  C24  N23  C22   -57.91  30.0  1
 W61  Var_08    C29  N28  C27  C26    -8.62  30.0  1
 W61  Var_09    S48  C49  C50  N46    36.26  30.0  1
 W61  Var_10    C49  C50  N46  C47   -12.96  30.0  1
 W61  Var_11    C50  C49  S48  C47   -40.06  30.0  1
 W61  Var_12    C50  N46  C47  S48   -16.55  30.0  1
 W61  Var_13    H47  C47  S48  C49   -87.96  30.0  1
 W61  Var_14    F52  C11  C3   C2     71.72  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
 W61  chir_01  C26  N23  C27  C30  positiv
 W61  chir_02  C29  N28  C33  C30  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
 W61  plan-1  C29  0.020
 W61  plan-1  C33  0.020
 W61  plan-1  N46  0.020
 W61  plan-1  C47  0.020
 W61  plan-1  C50  0.020
 W61  plan-1  O57  0.020
 W61  plan-2  C1   0.020
 W61  plan-2  C2   0.020
 W61  plan-2  C3   0.020
 W61  plan-2  N4   0.020
 W61  plan-2  C5   0.020
 W61  plan-2  C6   0.020
 W61  plan-2  C7   0.020
 W61  plan-2  C8   0.020
 W61  plan-2  C9   0.020
 W61  plan-2  C10  0.020
 W61  plan-2  C11  0.020
 W61  plan-2  N20  0.020
 W61  plan-2  H2   0.020
 W61  plan-2  H7   0.020
 W61  plan-2  H8   0.020
 W61  plan-2  H9   0.020
 W61  plan-2  H10  0.020

