# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:48:33 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (3S,4S)-pyrrolidine-3,4-diyl bis(naphthalen-1-ylacetate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1cccc2ccccc12)O[C@H]3CNC[C@@H]3OC(=O)Cc4cccc5ccccc45
#
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
 S47  S47  '(3S,4S)-pyrrolidine-3,4-diyl bis(naphthalen-1-ylacetate)'  ligand  58  33  .  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_S47
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
 S47  C1    C  CH1   0  -0.012   0.7412   3.0419   0.2285
 S47  N1    N  NH1   0  -0.617   0.0023   5.1802  -0.4432
 S47  O1    O  O2    0  -0.464   1.3446   2.1321  -0.6951
 S47  C2    C  C     0   0.595   2.5768   1.7079  -0.4385
 S47  O2    O  O     0  -0.427   3.2270   2.0708   0.5068
 S47  O3    O  O2    0  -0.465  -1.4044   2.1396   0.8099
 S47  C4    C  CH1   0   0.004  -0.7581   3.0678  -0.0555
 S47  O4    O  O     0  -0.425  -3.2342   2.0731  -0.4755
 S47  C5    C  C     0   0.598  -2.6216   1.7079   0.4925
 S47  C6    C  CH2   0  -0.718   3.0637   0.7409  -1.4920
 S47  C7    C  CH2   0  -0.298   1.1894   4.5024   0.0636
 S47  C13   C  CR6   0   0.132   3.9644  -0.3157  -0.9213
 S47  C14   C  CR16  0  -0.335   5.3062  -0.3001  -1.1961
 S47  C15   C  CR16  0  -0.244   6.1753  -1.2826  -0.6796
 S47  C16   C  CR16  0  -0.329   5.6874  -2.2790   0.1164
 S47  C17   C  CR66  0   0.113   4.3084  -2.3349   0.4282
 S47  C18   C  CR66  0   0.119   3.4316  -1.3468  -0.0948
 S47  C19   C  CR16  0  -0.337   2.0570  -1.4302   0.2362
 S47  C20   C  CR16  0  -0.335  -5.3623  -0.3351   1.1440
 S47  C21   C  CR16  0  -0.258   2.4546  -3.4084   1.5559
 S47  C22   C  CR16  0  -0.309   3.7876  -3.3583   1.2542
 S47  C23   C  CR16  0  -0.243   1.5812  -2.4316   1.0396
 S47  C24   C  CR16  0  -0.244  -6.2096  -1.3161   0.5902
 S47  C25   C  CR16  0  -0.329  -5.6943  -2.2919  -0.2138
 S47  C26   C  CR66  0   0.113  -4.3082  -2.3279  -0.4959
 S47  C27   C  CR66  0   0.119  -3.4531  -1.3420   0.0657
 S47  C28   C  CR16  0  -0.309  -3.7596  -3.3302  -1.3296
 S47  C29   C  CR16  0  -0.258  -2.4200  -3.3618  -1.6030
 S47  C30   C  CR16  0  -0.243  -1.5677  -2.3877  -1.0477
 S47  C31   C  CR16  0  -0.337  -2.0704  -1.4072  -0.2349
 S47  C32   C  CH2   0  -0.310  -1.1305   4.5244   0.1805
 S47  C33   C  CR6   0   0.131  -4.0146  -0.3315   0.8988
 S47  C34   C  CH2   0  -0.719  -3.1384   0.7212   1.5131
 S47  H1    H  HCH1  0   0.278   0.9273   2.6950   1.2469
 S47  HN1   H  HNH1  0   0.363   0.0214   6.1729  -0.2558
 S47  H4    H  HCH1  0   0.272  -0.9449   2.8055  -1.0997
 S47  H6    H  HCH2  0   0.289   2.2188   0.3087  -2.0308
 S47  H6A   H  HCH2  0   0.321   3.6158   1.3352  -2.2267
 S47  H7    H  HCH2  0   0.228   1.5168   4.8814   1.0384
 S47  H7A   H  HCH2  0   0.247   2.0282   4.6053  -0.6270
 S47  H14   H  HCR6  0   0.257   5.7123   0.4835  -1.8242
 S47  H15   H  HCR6  0   0.260   7.2295  -1.2399  -0.9192
 S47  H16   H  HCR6  0   0.257   6.3480  -3.0375   0.5189
 S47  H19   H  HCR6  0   0.228   1.3611  -0.6950  -0.1487
 S47  H21   H  HCR6  0   0.261   2.0667  -4.1954   2.1890
 S47  H22   H  HCR6  0   0.258   4.4656  -4.1054   1.6490
 S47  H23   H  HCR6  0   0.258   0.5271  -2.4762   1.2813
 S47  H24   H  HCR6  0   0.260  -7.2692  -1.2883   0.8077
 S47  H25   H  HCR6  0   0.257  -6.3378  -3.0490  -0.6455
 S47  H28   H  HCR6  0   0.258  -4.4213  -4.0759  -1.7534
 S47  H29   H  HCR6  0   0.261  -2.0102  -4.1321  -2.2428
 S47  H30   H  HCR6  0   0.258  -0.5083  -2.4182  -1.2672
 S47  H31   H  HCR6  0   0.229  -1.3895  -0.6753   0.1820
 S47  H32   H  HCH2  0   0.217  -1.2262   4.7139   1.2606
 S47  H32A  H  HCH2  0   0.253  -2.0688   4.8018  -0.2995
 S47  H34   H  HCH2  0   0.293  -2.3092   0.2838   2.0720
 S47  H34A  H  HCH2  0   0.321  -3.7172   1.3008   2.2389
 S47  H20   H  HCR6  0   0.257  -5.7905   0.4322   1.7774

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
 S47  O1   C1    single    1.430  0.020  1.430
 S47  C7   C1    single    1.537  0.020  1.537
 S47  C1   C4    single    1.526  0.020  1.526
 S47  C1   H1    single    0.970  0.020  1.090
 S47  C7   N1    single    1.458  0.020  1.458
 S47  N1   C32   single    1.450  0.020  1.450
 S47  N1   HN1   single    0.890  0.020  1.040
 S47  C2   O1    single    1.328  0.020  1.328
 S47  C6   C2    single    1.511  0.020  1.511
 S47  C2   O2    double    1.203  0.020  1.203
 S47  C4   O3    single    1.424  0.020  1.424
 S47  O3   C5    single    1.330  0.020  1.330
 S47  C32  C4    single    1.522  0.020  1.522
 S47  C4   H4    single    0.970  0.020  1.090
 S47  C5   O4    double    1.202  0.020  1.202
 S47  C5   C34   single    1.511  0.020  1.511
 S47  C6   C13   single    1.501  0.020  1.501
 S47  C6   H6    single    0.970  0.020  1.090
 S47  C6   H6A   single    0.970  0.020  1.090
 S47  C7   H7    single    0.970  0.020  1.090
 S47  C7   H7A   single    0.970  0.020  1.090
 S47  C13  C14   aromatic  1.370  0.020  1.370
 S47  C13  C18   aromatic  1.425  0.020  1.425
 S47  C14  C15   aromatic  1.410  0.020  1.410
 S47  C14  H14   single    0.930  0.020  1.080
 S47  C15  C16   aromatic  1.365  0.020  1.365
 S47  C15  H15   single    0.930  0.020  1.080
 S47  C17  C16   aromatic  1.415  0.020  1.415
 S47  C16  H16   single    0.930  0.020  1.080
 S47  C18  C17   aromatic  1.421  0.020  1.421
 S47  C17  C22   aromatic  1.414  0.020  1.414
 S47  C19  C18   aromatic  1.416  0.020  1.416
 S47  C19  C23   aromatic  1.369  0.020  1.369
 S47  C19  H19   single    0.930  0.020  1.080
 S47  C33  C20   aromatic  1.370  0.020  1.370
 S47  C24  C20   aromatic  1.410  0.020  1.410
 S47  C20  H20   single    0.930  0.020  1.080
 S47  C23  C21   aromatic  1.408  0.020  1.408
 S47  C21  C22   aromatic  1.368  0.020  1.368
 S47  C21  H21   single    0.930  0.020  1.080
 S47  C22  H22   single    0.930  0.020  1.080
 S47  C23  H23   single    0.930  0.020  1.080
 S47  C25  C24   aromatic  1.365  0.020  1.365
 S47  C24  H24   single    0.930  0.020  1.080
 S47  C26  C25   aromatic  1.415  0.020  1.415
 S47  C25  H25   single    0.930  0.020  1.080
 S47  C28  C26   aromatic  1.414  0.020  1.414
 S47  C26  C27   aromatic  1.421  0.020  1.421
 S47  C31  C27   aromatic  1.416  0.020  1.416
 S47  C27  C33   aromatic  1.425  0.020  1.425
 S47  C29  C28   aromatic  1.368  0.020  1.368
 S47  C28  H28   single    0.930  0.020  1.080
 S47  C29  C30   aromatic  1.408  0.020  1.408
 S47  C29  H29   single    0.930  0.020  1.080
 S47  C30  C31   aromatic  1.369  0.020  1.369
 S47  C30  H30   single    0.930  0.020  1.080
 S47  C31  H31   single    0.930  0.020  1.080
 S47  C32  H32   single    0.970  0.020  1.090
 S47  C32  H32A  single    0.970  0.020  1.090
 S47  C33  C34   single    1.501  0.020  1.501
 S47  C34  H34   single    0.970  0.020  1.090
 S47  C34  H34A  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
 S47  H1    C1   C7   110.63  3.000
 S47  H1    C1   C4   110.27  3.000
 S47  C7    C1   C4   104.50  3.000
 S47  H1    C1   O1   109.17  3.000
 S47  C4    C1   O1   107.76  3.000
 S47  C7    C1   O1   114.35  3.000
 S47  HN1   N1   C32  112.29  3.000
 S47  HN1   N1   C7   112.15  3.000
 S47  C32   N1   C7   106.04  3.000
 S47  C2    O1   C1   118.03  3.000
 S47  C6    C2   O2   124.52  3.000
 S47  O2    C2   O1   123.83  3.000
 S47  C6    C2   O1   111.64  3.000
 S47  C5    O3   C4   118.81  3.000
 S47  H4    C4   C32  109.64  3.000
 S47  H4    C4   O3   110.28  3.000
 S47  C32   C4   O3   114.74  3.000
 S47  H4    C4   C1   109.98  3.000
 S47  C32   C4   C1   103.17  3.000
 S47  O3    C4   C1   108.76  3.000
 S47  C34   C5   O4   124.61  3.000
 S47  C34   C5   O3   111.34  3.000
 S47  O4    C5   O3   124.05  3.000
 S47  H6A   C6   H6   105.91  3.000
 S47  H6A   C6   C13  109.56  3.000
 S47  H6    C6   C13  111.93  3.000
 S47  H6A   C6   C2   106.45  3.000
 S47  H6    C6   C2   110.38  3.000
 S47  C13   C6   C2   112.26  3.000
 S47  H7A   C7   H7   107.49  3.000
 S47  H7A   C7   N1   111.22  3.000
 S47  H7    C7   N1   113.06  3.000
 S47  H7A   C7   C1   112.44  3.000
 S47  H7    C7   C1   108.69  3.000
 S47  N1    C7   C1   103.99  3.000
 S47  C18   C13  C14  119.40  3.000
 S47  C18   C13  C6   120.36  3.000
 S47  C14   C13  C6   120.24  3.000
 S47  H14   C14  C15  119.05  3.000
 S47  H14   C14  C13  119.46  3.000
 S47  C15   C14  C13  121.50  3.000
 S47  H15   C15  C16  120.40  3.000
 S47  H15   C15  C14  119.47  3.000
 S47  C16   C15  C14  120.13  3.000
 S47  H16   C16  C17  118.99  3.000
 S47  H16   C16  C15  120.64  3.000
 S47  C17   C16  C15  120.37  3.000
 S47  C22   C17  C18  119.40  3.000
 S47  C22   C17  C16  121.07  3.000
 S47  C18   C17  C16  119.53  3.000
 S47  C19   C18  C17  118.16  3.000
 S47  C19   C18  C13  122.76  3.000
 S47  C17   C18  C13  119.08  3.000
 S47  H19   C19  C23  118.80  3.000
 S47  H19   C19  C18  120.04  3.000
 S47  C23   C19  C18  121.16  3.000
 S47  H20   C20  C33  119.46  3.000
 S47  H20   C20  C24  119.02  3.000
 S47  C33   C20  C24  121.52  3.000
 S47  H21   C21  C23  119.78  3.000
 S47  H21   C21  C22  120.35  3.000
 S47  C23   C21  C22  119.88  3.000
 S47  H22   C22  C21  120.28  3.000
 S47  H22   C22  C17  118.77  3.000
 S47  C21   C22  C17  120.94  3.000
 S47  H23   C23  C21  119.57  3.000
 S47  H23   C23  C19  119.98  3.000
 S47  C21   C23  C19  120.45  3.000
 S47  H24   C24  C25  120.42  3.000
 S47  H24   C24  C20  119.46  3.000
 S47  C25   C24  C20  120.12  3.000
 S47  H25   C25  C26  118.99  3.000
 S47  H25   C25  C24  120.66  3.000
 S47  C26   C25  C24  120.35  3.000
 S47  C28   C26  C27  119.42  3.000
 S47  C27   C26  C25  119.55  3.000
 S47  C28   C26  C25  121.03  3.000
 S47  C33   C27  C31  122.78  3.000
 S47  C33   C27  C26  119.08  3.000
 S47  C31   C27  C26  118.14  3.000
 S47  H28   C28  C29  120.28  3.000
 S47  H28   C28  C26  118.78  3.000
 S47  C29   C28  C26  120.94  3.000
 S47  H29   C29  C30  119.76  3.000
 S47  H29   C29  C28  120.37  3.000
 S47  C30   C29  C28  119.87  3.000
 S47  H30   C30  C31  120.00  3.000
 S47  H30   C30  C29  119.53  3.000
 S47  C31   C30  C29  120.48  3.000
 S47  H31   C31  C30  118.79  3.000
 S47  H31   C31  C27  120.06  3.000
 S47  C30   C31  C27  121.15  3.000
 S47  H32A  C32  H32  108.27  3.000
 S47  H32A  C32  C4   112.71  3.000
 S47  H32   C32  C4   109.76  3.000
 S47  H32A  C32  N1   111.60  3.000
 S47  H32   C32  N1   114.34  3.000
 S47  C4    C32  N1   100.08  3.000
 S47  C34   C33  C27  120.43  3.000
 S47  C34   C33  C20  120.19  3.000
 S47  C27   C33  C20  119.38  3.000
 S47  H34A  C34  H34  105.93  3.000
 S47  H34A  C34  C33  109.52  3.000
 S47  H34   C34  C33  111.84  3.000
 S47  H34A  C34  C5   106.44  3.000
 S47  H34   C34  C5   110.35  3.000
 S47  C33   C34  C5   112.41  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
 S47  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 S47  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 S47  CONST_03  C22  C17  C18  C13   180.00   0.0  0
 S47  CONST_04  C23  C19  C18  C13   180.00   0.0  0
 S47  CONST_05  C17  C18  C13  C14     0.00   0.0  0
 S47  CONST_06  C19  C18  C13  C14   180.00   0.0  0
 S47  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 S47  CONST_08  C18  C13  C14  C15     0.00   0.0  0
 S47  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 S47  CONST_10  C22  C17  C16  C15   180.00   0.0  0
 S47  CONST_11  C19  C18  C17  C16   180.00   0.0  0
 S47  CONST_12  C21  C22  C17  C16   180.00   0.0  0
 S47  CONST_13  C23  C19  C18  C17     0.00   0.0  0
 S47  CONST_14  C23  C21  C22  C17     0.00   0.0  0
 S47  CONST_15  C21  C22  C17  C18     0.00   0.0  0
 S47  CONST_16  C21  C23  C19  C18     0.00   0.0  0
 S47  CONST_17  C22  C17  C18  C19     0.00   0.0  0
 S47  CONST_18  C22  C21  C23  C19     0.00   0.0  0
 S47  CONST_19  C26  C27  C33  C20     0.00   0.0  0
 S47  CONST_20  C31  C27  C33  C20   180.00   0.0  0
 S47  CONST_21  C26  C25  C24  C20     0.00   0.0  0
 S47  CONST_22  C27  C33  C20  C24     0.00   0.0  0
 S47  CONST_23  C28  C26  C25  C24   180.00   0.0  0
 S47  CONST_24  C27  C26  C25  C24     0.00   0.0  0
 S47  CONST_25  C33  C20  C24  C25     0.00   0.0  0
 S47  CONST_26  C29  C28  C26  C25   180.00   0.0  0
 S47  CONST_27  C31  C27  C26  C25   180.00   0.0  0
 S47  CONST_28  C33  C27  C26  C25     0.00   0.0  0
 S47  CONST_29  C30  C29  C28  C26     0.00   0.0  0
 S47  CONST_30  C30  C31  C27  C26     0.00   0.0  0
 S47  CONST_31  C29  C28  C26  C27     0.00   0.0  0
 S47  CONST_32  C29  C30  C31  C27     0.00   0.0  0
 S47  CONST_33  C31  C27  C26  C28     0.00   0.0  0
 S47  CONST_34  C33  C27  C26  C28   180.00   0.0  0
 S47  CONST_35  C31  C30  C29  C28     0.00   0.0  0
 S47  CONST_36  C33  C27  C31  C30   180.00   0.0  0
 S47  CONST_37  C15  C14  C13  C6    180.00   0.0  0
 S47  CONST_38  C17  C18  C13  C6    180.00   0.0  0
 S47  CONST_39  C19  C18  C13  C6      0.00   0.0  0
 S47  CONST_40  C34  C33  C20  C24   180.00   0.0  0
 S47  CONST_41  C34  C33  C27  C26   180.00   0.0  0
 S47  CONST_42  C34  C33  C27  C31     0.00   0.0  0
 S47  CONST_43  H15  C15  C14  C13   180.00   0.0  0
 S47  CONST_44  H19  C19  C18  C13     0.00   0.0  0
 S47  CONST_45  H16  C16  C15  C14   180.00   0.0  0
 S47  CONST_46  H14  C14  C15  C16   180.00   0.0  0
 S47  CONST_47  H22  C22  C17  C16     0.00   0.0  0
 S47  CONST_48  H21  C21  C22  C17   180.00   0.0  0
 S47  CONST_49  H23  C23  C19  C18   180.00   0.0  0
 S47  CONST_50  H25  C25  C24  C20   180.00   0.0  0
 S47  CONST_51  H20  C20  C24  C25   180.00   0.0  0
 S47  CONST_52  H28  C28  C26  C25     0.00   0.0  0
 S47  CONST_53  H24  C24  C25  C26   180.00   0.0  0
 S47  CONST_54  H29  C29  C28  C26   180.00   0.0  0
 S47  CONST_55  H31  C31  C27  C26   180.00   0.0  0
 S47  CONST_56  H30  C30  C31  C27   180.00   0.0  0
 S47  Var_01    C32  N1   C7   C1     34.26  30.0  1
 S47  Var_02    C7   N1   C32  C4    -47.55  30.0  1
 S47  Var_03    C14  C13  C6   C2   -108.79  30.0  2
 S47  Var_04    C20  C33  C34  C5   -109.56  30.0  3
 S47  Var_05    C6   C2   O1   C1    179.16  30.0  2
 S47  Var_06    C13  C6   C2   O1   -146.25  30.0  1
 S47  Var_07    C33  C34  C5   O3   -146.83  30.0  3
 S47  Var_08    O4   C5   O3   C4     -1.57  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
 S47  chir_01  C1  O1  C7  C4   negativ
 S47  chir_02  C4  O3  C1  C32  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
 S47  plan-1  C6   0.020
 S47  plan-1  C13  0.020
 S47  plan-1  C14  0.020
 S47  plan-1  C15  0.020
 S47  plan-1  C16  0.020
 S47  plan-1  C17  0.020
 S47  plan-1  C18  0.020
 S47  plan-1  C19  0.020
 S47  plan-1  C21  0.020
 S47  plan-1  C22  0.020
 S47  plan-1  C23  0.020
 S47  plan-1  H14  0.020
 S47  plan-1  H15  0.020
 S47  plan-1  H16  0.020
 S47  plan-1  H19  0.020
 S47  plan-1  H21  0.020
 S47  plan-1  H22  0.020
 S47  plan-1  H23  0.020
 S47  plan-2  O1   0.020
 S47  plan-2  C2   0.020
 S47  plan-2  O2   0.020
 S47  plan-2  C6   0.020
 S47  plan-3  C20  0.020
 S47  plan-3  C24  0.020
 S47  plan-3  C25  0.020
 S47  plan-3  C26  0.020
 S47  plan-3  C27  0.020
 S47  plan-3  C28  0.020
 S47  plan-3  C29  0.020
 S47  plan-3  C30  0.020
 S47  plan-3  C31  0.020
 S47  plan-3  C33  0.020
 S47  plan-3  C34  0.020
 S47  plan-3  H24  0.020
 S47  plan-3  H25  0.020
 S47  plan-3  H28  0.020
 S47  plan-3  H29  0.020
 S47  plan-3  H30  0.020
 S47  plan-3  H31  0.020
 S47  plan-3  H20  0.020
 S47  plan-4  O3   0.020
 S47  plan-4  O4   0.020
 S47  plan-4  C5   0.020
 S47  plan-4  C34  0.020

