# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:41:42 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC(CC1)(N2CCCC2)c3sc(nc3)c4ccc5[nH]ccc5c4
#
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
 2JR  2JR  5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole  ligand  50  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2JR
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
 2JR  CAH  C  CH2   0  -0.450  -3.4776   1.5127   0.7694
 2JR  CAI  C  CH2   0  -0.421  -4.9847   1.4622   0.5418
 2JR  CAJ  C  CH2   0  -0.430  -5.3245   1.6127  -0.9364
 2JR  CAT  C  CH2   0  -0.423  -4.5702   0.5973  -1.7874
 2JR  CAS  C  CH2   0  -0.454  -3.0718   0.6622  -1.5183
 2JR  CAR  C  CT    0   0.033  -2.7338   0.4287  -0.0345
 2JR  NAU  N  NT    0  -0.423  -3.2169  -0.8868   0.3747
 2JR  CAV  C  CH2   0  -0.288  -2.7677  -2.0502  -0.3676
 2JR  CAY  C  CH2   0  -0.456  -3.4119  -3.2142   0.3835
 2JR  CAX  C  CH2   0  -0.463  -3.5615  -2.7002   1.8286
 2JR  CAW  C  CH2   0  -0.279  -3.0863  -1.2449   1.7753
 2JR  CAQ  C  CR5   0  -0.153  -1.2422   0.5787   0.1915
 2JR  SAP  S  S2    0   0.197  -0.0629   0.0787  -0.9695
 2JR  CAG  C  CR15  0  -0.038  -0.5767   1.0222   1.2949
 2JR  NAF  N  N     0  -0.408   0.7828   0.9762   1.2529
 2JR  CAO  C  CR5   0   0.024   1.2131   0.4969   0.1251
 2JR  CAN  C  CR6   0   0.079   2.6242   0.3233  -0.2167
 2JR  CAM  C  CR16  0  -0.391   3.5949   0.8297   0.6380
 2JR  CAL  C  CR56  0   0.089   4.9422   0.6611   0.3208
 2JR  CAK  C  CR15  0  -0.420   6.1669   1.0417   0.9536
 2JR  CAA  C  CR15  0  -0.022   7.1750   0.5878   0.1545
 2JR  NAB  N  NR15  0  -0.678   6.6516  -0.0501  -0.9354
 2JR  CAC  C  CR56  0   0.348   5.2931  -0.0237  -0.8659
 2JR  CAD  C  CR16  0  -0.283   4.3285  -0.5372  -1.7314
 2JR  CAE  C  CR16  0  -0.343   3.0053  -0.3567  -1.3941
 2JR  H1   H  HCH2  0   0.235  -3.0919   2.4873   0.4552
 2JR  H2   H  HCH2  0   0.241  -3.2589   1.4319   1.8360
 2JR  H3   H  HCH2  0   0.221  -5.3843   0.5178   0.9205
 2JR  H4   H  HCH2  0   0.225  -5.4592   2.2595   1.1193
 2JR  H5   H  HCH2  0   0.226  -6.4017   1.5150  -1.0924
 2JR  H6   H  HCH2  0   0.208  -5.0530   2.6227  -1.2637
 2JR  H7   H  HCH2  0   0.222  -4.9396  -0.4101  -1.5782
 2JR  H8   H  HCH2  0   0.226  -4.7530   0.7854  -2.8479
 2JR  H9   H  HCH2  0   0.238  -2.5478  -0.0511  -2.1604
 2JR  H10  H  HCH2  0   0.240  -2.6943   1.6514  -1.7956
 2JR  H12  H  HCH2  0   0.234  -3.0852  -2.0059  -1.4100
 2JR  H13  H  HCH2  0   0.200  -1.6718  -2.1625  -0.3621
 2JR  H14  H  HCH2  0   0.233  -4.3865  -3.4492  -0.0450
 2JR  H15  H  HCH2  0   0.231  -2.8033  -4.1159   0.3178
 2JR  H16  H  HCH2  0   0.234  -4.5999  -2.7582   2.1554
 2JR  H17  H  HCH2  0   0.231  -2.9699  -3.2773   2.5388
 2JR  H18  H  HCH2  0   0.203  -2.0453  -1.1723   2.1275
 2JR  H19  H  HCH2  0   0.231  -3.6888  -0.5949   2.4110
 2JR  H20  H  HCR5  0   0.264  -1.0600   1.4043   2.1831
 2JR  H21  H  HCR6  0   0.250   3.3030   1.3517   1.5402
 2JR  H22  H  HCR5  0   0.251   6.2826   1.5811   1.8799
 2JR  H23  H  HCR5  0   0.285   8.2429   0.6694   0.2776
 2JR  H24  H  HNR5  0   0.413   7.1931  -0.4699  -1.6728
 2JR  H25  H  HCR6  0   0.267   4.6025  -1.0640  -2.6360
 2JR  H26  H  HCR6  0   0.249   2.2488  -0.7614  -2.0559

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
 2JR  CAD  CAE  aromatic  1.377  0.020  1.377
 2JR  CAD  CAC  aromatic  1.394  0.020  1.394
 2JR  CAE  CAN  aromatic  1.412  0.020  1.412
 2JR  NAB  CAC  aromatic  1.361  0.020  1.361
 2JR  NAB  CAA  aromatic  1.367  0.020  1.367
 2JR  CAC  CAL  aromatic  1.414  0.020  1.414
 2JR  NAF  CAG  aromatic  1.361  0.020  1.361
 2JR  NAF  CAO  aromatic  1.299  0.020  1.299
 2JR  CAY  CAX  single    1.541  0.020  1.541
 2JR  CAY  CAV  single    1.528  0.020  1.528
 2JR  CAN  CAO  single    1.462  0.020  1.462
 2JR  CAN  CAM  aromatic  1.389  0.020  1.389
 2JR  CAG  CAQ  aromatic  1.363  0.020  1.363
 2JR  CAA  CAK  aromatic  1.364  0.020  1.364
 2JR  CAO  SAP  aromatic  1.732  0.020  1.732
 2JR  CAL  CAM  aromatic  1.394  0.020  1.394
 2JR  CAL  CAK  aromatic  1.430  0.020  1.430
 2JR  CAX  CAW  single    1.532  0.020  1.532
 2JR  CAV  NAU  single    1.451  0.020  1.451
 2JR  CAW  NAU  single    1.451  0.020  1.451
 2JR  CAQ  SAP  aromatic  1.729  0.020  1.729
 2JR  CAQ  CAR  single    1.516  0.020  1.516
 2JR  NAU  CAR  single    1.460  0.020  1.460
 2JR  CAR  CAS  single    1.540  0.020  1.540
 2JR  CAR  CAH  single    1.541  0.020  1.541
 2JR  CAS  CAT  single    1.524  0.020  1.524
 2JR  CAH  CAI  single    1.525  0.020  1.525
 2JR  CAT  CAJ  single    1.525  0.020  1.525
 2JR  CAJ  CAI  single    1.524  0.020  1.524
 2JR  CAH  H1   single    0.970  0.020  1.090
 2JR  CAH  H2   single    0.970  0.020  1.090
 2JR  CAI  H3   single    0.970  0.020  1.090
 2JR  CAI  H4   single    0.970  0.020  1.090
 2JR  CAJ  H5   single    0.970  0.020  1.090
 2JR  CAJ  H6   single    0.970  0.020  1.090
 2JR  CAT  H7   single    0.970  0.020  1.090
 2JR  CAT  H8   single    0.970  0.020  1.090
 2JR  CAS  H9   single    0.970  0.020  1.090
 2JR  CAS  H10  single    0.970  0.020  1.090
 2JR  CAV  H12  single    0.970  0.020  1.090
 2JR  CAV  H13  single    0.970  0.020  1.090
 2JR  CAY  H14  single    0.970  0.020  1.090
 2JR  CAY  H15  single    0.970  0.020  1.090
 2JR  CAX  H16  single    0.970  0.020  1.090
 2JR  CAX  H17  single    0.970  0.020  1.090
 2JR  CAW  H18  single    0.970  0.020  1.090
 2JR  CAW  H19  single    0.970  0.020  1.090
 2JR  CAG  H20  single    0.930  0.020  1.080
 2JR  CAM  H21  single    0.930  0.020  1.080
 2JR  CAK  H22  single    0.930  0.020  1.080
 2JR  CAA  H23  single    0.930  0.020  1.080
 2JR  NAB  H24  single    0.860  0.020  1.020
 2JR  CAD  H25  single    0.930  0.020  1.080
 2JR  CAE  H26  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
 2JR  H2   CAH  H1   106.01  3.000
 2JR  H2   CAH  CAR  111.16  3.000
 2JR  H1   CAH  CAR  107.85  3.000
 2JR  H2   CAH  CAI  109.96  3.000
 2JR  H1   CAH  CAI  109.57  3.000
 2JR  CAR  CAH  CAI  112.08  3.000
 2JR  H4   CAI  H3   106.77  3.000
 2JR  H4   CAI  CAJ  110.10  3.000
 2JR  H3   CAI  CAJ  109.86  3.000
 2JR  H4   CAI  CAH  109.03  3.000
 2JR  H3   CAI  CAH  109.76  3.000
 2JR  CAJ  CAI  CAH  111.22  3.000
 2JR  H6   CAJ  H5   106.50  3.000
 2JR  H6   CAJ  CAT  108.94  3.000
 2JR  H5   CAJ  CAT  110.40  3.000
 2JR  H6   CAJ  CAI  108.99  3.000
 2JR  H5   CAJ  CAI  110.45  3.000
 2JR  CAT  CAJ  CAI  111.42  3.000
 2JR  H8   CAT  H7   106.74  3.000
 2JR  H8   CAT  CAS  109.18  3.000
 2JR  H7   CAT  CAS  109.74  3.000
 2JR  H8   CAT  CAJ  110.14  3.000
 2JR  H7   CAT  CAJ  109.87  3.000
 2JR  CAS  CAT  CAJ  111.07  3.000
 2JR  H10  CAS  H9   105.99  3.000
 2JR  H10  CAS  CAR  107.79  3.000
 2JR  H9   CAS  CAR  111.20  3.000
 2JR  H10  CAS  CAT  109.45  3.000
 2JR  H9   CAS  CAT  109.86  3.000
 2JR  CAR  CAS  CAT  112.31  3.000
 2JR  CAQ  CAR  NAU  111.90  3.000
 2JR  NAU  CAR  CAS  109.52  3.000
 2JR  CAQ  CAR  CAS  110.16  3.000
 2JR  CAS  CAR  CAH  106.86  3.000
 2JR  NAU  CAR  CAH  109.14  3.000
 2JR  CAQ  CAR  CAH  109.12  3.000
 2JR  CAW  NAU  CAV  105.54  3.000
 2JR  CAW  NAU  CAR  117.58  3.000
 2JR  CAV  NAU  CAR  118.46  3.000
 2JR  H13  CAV  H12  107.37  3.000
 2JR  H13  CAV  CAY  109.83  3.000
 2JR  H12  CAV  CAY  112.22  3.000
 2JR  H13  CAV  NAU  112.77  3.000
 2JR  H12  CAV  NAU  111.48  3.000
 2JR  CAY  CAV  NAU  103.23  3.000
 2JR  H15  CAY  H14  107.29  3.000
 2JR  H15  CAY  CAX  112.75  3.000
 2JR  H14  CAY  CAX  110.71  3.000
 2JR  H15  CAY  CAV  111.43  3.000
 2JR  H14  CAY  CAV  110.36  3.000
 2JR  CAX  CAY  CAV  104.35  3.000
 2JR  H17  CAX  H16  107.08  3.000
 2JR  H17  CAX  CAW  110.94  3.000
 2JR  H16  CAX  CAW  110.88  3.000
 2JR  H17  CAX  CAY  112.44  3.000
 2JR  H16  CAX  CAY  110.85  3.000
 2JR  CAW  CAX  CAY  104.72  3.000
 2JR  H19  CAW  H18  107.24  3.000
 2JR  H19  CAW  CAX  111.99  3.000
 2JR  H18  CAW  CAX  110.16  3.000
 2JR  H19  CAW  NAU  111.45  3.000
 2JR  H18  CAW  NAU  112.17  3.000
 2JR  CAX  CAW  NAU  103.89  3.000
 2JR  CAG  CAQ  SAP  107.74  3.000
 2JR  SAP  CAQ  CAR  122.85  3.000
 2JR  CAG  CAQ  CAR  129.30  3.000
 2JR  CAO  SAP  CAQ   90.48  3.000
 2JR  H20  CAG  NAF  118.94  3.000
 2JR  H20  CAG  CAQ  124.19  3.000
 2JR  NAF  CAG  CAQ  116.86  3.000
 2JR  CAO  NAF  CAG  111.73  3.000
 2JR  CAN  CAO  NAF  124.51  3.000
 2JR  CAN  CAO  SAP  122.30  3.000
 2JR  NAF  CAO  SAP  113.19  3.000
 2JR  CAE  CAN  CAM  120.00  3.000
 2JR  CAM  CAN  CAO  119.16  3.000
 2JR  CAE  CAN  CAO  120.83  3.000
 2JR  H21  CAM  CAL  120.56  3.000
 2JR  H21  CAM  CAN  120.02  3.000
 2JR  CAL  CAM  CAN  119.42  3.000
 2JR  CAC  CAL  CAK  106.72  3.000
 2JR  CAK  CAL  CAM  134.00  3.000
 2JR  CAC  CAL  CAM  119.28  3.000
 2JR  H22  CAK  CAA  126.19  3.000
 2JR  H22  CAK  CAL  127.24  3.000
 2JR  CAA  CAK  CAL  106.57  3.000
 2JR  H23  CAA  NAB  120.37  3.000
 2JR  H23  CAA  CAK  129.79  3.000
 2JR  NAB  CAA  CAK  109.83  3.000
 2JR  H24  NAB  CAC  125.64  3.000
 2JR  H24  NAB  CAA  124.93  3.000
 2JR  CAC  NAB  CAA  109.42  3.000
 2JR  CAD  CAC  NAB  130.70  3.000
 2JR  NAB  CAC  CAL  107.46  3.000
 2JR  CAD  CAC  CAL  121.84  3.000
 2JR  H25  CAD  CAE  120.78  3.000
 2JR  H25  CAD  CAC  121.54  3.000
 2JR  CAE  CAD  CAC  117.68  3.000
 2JR  H26  CAE  CAD  118.18  3.000
 2JR  H26  CAE  CAN  120.04  3.000
 2JR  CAD  CAE  CAN  121.77  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
 2JR  CONST_01  CAO  NAF  CAG  CAQ     0.00   0.0  0
 2JR  CONST_02  NAF  CAO  SAP  CAQ     0.00   0.0  0
 2JR  CONST_03  CAN  CAO  SAP  CAQ   180.00   0.0  0
 2JR  CONST_04  CAG  NAF  CAO  SAP     0.00   0.0  0
 2JR  CONST_05  CAE  CAN  CAO  SAP     0.00   0.0  0
 2JR  CONST_06  CAM  CAN  CAO  SAP   180.00   0.0  0
 2JR  CONST_07  NAF  CAG  CAQ  SAP     0.00   0.0  0
 2JR  CONST_08  CAN  CAO  NAF  CAG   180.00   0.0  0
 2JR  CONST_09  CAO  SAP  CAQ  CAG     0.00   0.0  0
 2JR  CONST_10  CAE  CAN  CAO  NAF   180.00   0.0  0
 2JR  CONST_11  CAM  CAN  CAO  NAF     0.00   0.0  0
 2JR  CONST_12  CAD  CAE  CAN  CAO   180.00   0.0  0
 2JR  CONST_13  CAL  CAM  CAN  CAO   180.00   0.0  0
 2JR  CONST_14  CAC  CAD  CAE  CAN     0.00   0.0  0
 2JR  CONST_15  CAC  CAL  CAM  CAN     0.00   0.0  0
 2JR  CONST_16  CAK  CAL  CAM  CAN   180.00   0.0  0
 2JR  CONST_17  CAD  CAE  CAN  CAM     0.00   0.0  0
 2JR  CONST_18  CAD  CAC  CAL  CAM     0.00   0.0  0
 2JR  CONST_19  NAB  CAC  CAL  CAM   180.00   0.0  0
 2JR  CONST_20  CAA  CAK  CAL  CAM   180.00   0.0  0
 2JR  CONST_21  CAE  CAD  CAC  CAL     0.00   0.0  0
 2JR  CONST_22  CAA  NAB  CAC  CAL     0.00   0.0  0
 2JR  CONST_23  CAE  CAN  CAM  CAL     0.00   0.0  0
 2JR  CONST_24  NAB  CAA  CAK  CAL     0.00   0.0  0
 2JR  CONST_25  CAC  NAB  CAA  CAK     0.00   0.0  0
 2JR  CONST_26  CAD  CAC  CAL  CAK   180.00   0.0  0
 2JR  CONST_27  NAB  CAC  CAL  CAK     0.00   0.0  0
 2JR  CONST_28  CAD  CAC  NAB  CAA   180.00   0.0  0
 2JR  CONST_29  CAC  CAL  CAK  CAA     0.00   0.0  0
 2JR  CONST_30  CAE  CAD  CAC  NAB   180.00   0.0  0
 2JR  CONST_31  NAF  CAG  CAQ  CAR   180.00   0.0  0
 2JR  CONST_32  CAO  SAP  CAQ  CAR   180.00   0.0  0
 2JR  CONST_33  H20  CAG  CAQ  CAR     0.00   0.0  0
 2JR  CONST_34  H26  CAE  CAN  CAO     0.00   0.0  0
 2JR  CONST_35  H21  CAM  CAN  CAO     0.00   0.0  0
 2JR  CONST_36  H25  CAD  CAE  CAN   180.00   0.0  0
 2JR  CONST_37  H22  CAK  CAL  CAM     0.00   0.0  0
 2JR  CONST_38  H24  NAB  CAC  CAL   180.00   0.0  0
 2JR  CONST_39  H23  CAA  CAK  CAL   180.00   0.0  0
 2JR  Var_01    CAG  CAQ  CAR  CAH    31.55  30.0  2
 2JR  Var_02    CAV  NAU  CAR  CAH   172.73  30.0  1
 2JR  Var_03    CAT  CAS  CAR  CAH   -58.49  30.0  1
 2JR  Var_04    CAT  CAJ  CAI  CAH    53.54  30.0  1
 2JR  Var_05    CAQ  CAR  CAH  CAI   177.48  30.0  1
 2JR  Var_06    CAS  CAT  CAJ  CAI   -53.42  30.0  1
 2JR  Var_07    CAR  CAS  CAT  CAJ    57.43  30.0  1
 2JR  Var_08    CAR  CAH  CAI  CAJ   -57.44  30.0  1
 2JR  Var_09    CAY  CAV  NAU  CAR   177.24  30.0  1
 2JR  Var_10    CAX  CAW  NAU  CAR  -175.11  30.0  1
 2JR  Var_11    CAX  CAY  CAV  NAU   -27.86  30.0  1
 2JR  Var_12    CAY  CAX  CAW  NAU    21.29  30.0  1
 2JR  Var_13    CAW  CAX  CAY  CAV     3.99  30.0  1

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
 2JR  plan-1  CAR  0.020
 2JR  plan-1  CAQ  0.020
 2JR  plan-1  SAP  0.020
 2JR  plan-1  CAG  0.020
 2JR  plan-1  NAF  0.020
 2JR  plan-1  CAO  0.020
 2JR  plan-1  CAN  0.020
 2JR  plan-1  H20  0.020
 2JR  plan-2  CAO  0.020
 2JR  plan-2  CAN  0.020
 2JR  plan-2  CAM  0.020
 2JR  plan-2  CAL  0.020
 2JR  plan-2  CAK  0.020
 2JR  plan-2  CAA  0.020
 2JR  plan-2  NAB  0.020
 2JR  plan-2  CAC  0.020
 2JR  plan-2  CAD  0.020
 2JR  plan-2  CAE  0.020
 2JR  plan-2  H21  0.020
 2JR  plan-2  H22  0.020
 2JR  plan-2  H23  0.020
 2JR  plan-2  H24  0.020
 2JR  plan-2  H25  0.020
 2JR  plan-2  H26  0.020

