# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 13:53:23 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccccc1[C@H]2CCCN2C(=O)CNC(=O)NCc3ccc(N)cc3
#
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
 6B4  6B4  1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea  ligand  54  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6B4
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
 6B4  CAA  C  CH3   0  -0.793  -5.9251   3.0786   1.7462
 6B4  SAT  S  S2    0   0.021  -5.2106   1.4381   1.5416
 6B4  CAY  C  CR6   0  -0.171  -4.5820   1.4553  -0.1115
 6B4  CAG  C  CR16  0  -0.252  -4.8038   2.5221  -0.9815
 6B4  CAE  C  CR16  0  -0.256  -4.3138   2.4891  -2.2784
 6B4  CAF  C  CR16  0  -0.256  -3.6016   1.3862  -2.7230
 6B4  CAH  C  CR16  0  -0.302  -3.3799   0.3259  -1.8570
 6B4  CAZ  C  CR6   0   0.169  -3.8507   0.3415  -0.5500
 6B4  CBA  C  CH1   0  -0.120  -3.6397  -0.8504   0.3528
 6B4  CAP  C  CH2   0  -0.462  -4.7720  -1.8852   0.2230
 6B4  CAM  C  CH2   0  -0.468  -4.0791  -3.2229   0.4455
 6B4  CAQ  C  CH2   0  -0.286  -2.7375  -3.0237  -0.2441
 6B4  N1   N  NT    0  -0.491  -2.4416  -1.6215   0.0330
 6B4  C    C  C     0   0.527  -1.2232  -1.0843   0.1908
 6B4  O    O  O     0  -0.488  -1.0603   0.0714   0.5590
 6B4  CA   C  CH2   0  -0.362  -0.0445  -1.9909  -0.1219
 6B4  N    N  NH1   0  -0.698   1.1656  -1.2265  -0.0698
 6B4  CAU  C  C     0   0.753   2.3767  -1.8083  -0.2586
 6B4  OAC  O  O     0  -0.558   2.4963  -2.9923  -0.5663
 6B4  N2   N  NH1   0  -0.680   3.4435  -0.9907  -0.0921
 6B4  CAO  C  CH2   0  -0.303   4.8024  -1.4536  -0.3016
 6B4  CAX  C  CR6   0   0.016   5.7697  -0.3332  -0.0472
 6B4  CAK  C  CR16  0  -0.279   6.1076   0.5692  -1.0528
 6B4  CAI  C  CR16  0  -0.315   6.9709   1.6256  -0.8177
 6B4  CAW  C  CR6   0   0.297   7.5305   1.8223   0.4512
 6B4  N3   N  NH2   0  -0.860   8.3439   2.9039   0.7068
 6B4  CAJ  C  CR16  0  -0.314   7.1966   0.9144   1.4636
 6B4  CAL  C  CR16  0  -0.282   6.3303  -0.1362   1.2116
 6B4  H1   H  HCH3  0   0.276  -5.1807   3.8604   1.6089
 6B4  H2   H  HCH3  0   0.274  -6.7669   3.2432   1.0766
 6B4  H3   H  HCH3  0   0.296  -6.2869   3.1147   2.7720
 6B4  H4   H  HCR6  0   0.264  -5.3604   3.3908  -0.6594
 6B4  H5   H  HCR6  0   0.257  -4.4948   3.3280  -2.9377
 6B4  H6   H  HCR6  0   0.254  -3.2186   1.3501  -3.7342
 6B4  H7   H  HCR6  0   0.247  -2.8212  -0.5334  -2.2077
 6B4  H8   H  HCH1  0   0.265  -3.5624  -0.5112   1.3916
 6B4  H9   H  HCH2  0   0.261  -5.5755  -1.6891   0.9307
 6B4  H10  H  HCH2  0   0.246  -5.1956  -1.8463  -0.7828
 6B4  H11  H  HCH2  0   0.245  -3.9268  -3.4062   1.5109
 6B4  H12  H  HCH2  0   0.257  -4.6349  -4.0638   0.0329
 6B4  H13  H  HCH2  0   0.265  -1.9656  -3.6829   0.1498
 6B4  H14  H  HCH2  0   0.249  -2.8172  -3.1982  -1.3211
 6B4  H15  H  HCH2  0   0.268  -0.0355  -2.8175   0.5991
 6B4  H16  H  HCH2  0   0.268  -0.1870  -2.4454  -1.1070
 6B4  H17  H  HNH1  0   0.391   1.0917  -0.2829   0.2779
 6B4  H18  H  HCH2  0   0.239   5.0220  -2.2900   0.3672
 6B4  H19  H  HCH2  0   0.237   4.9243  -1.8254  -1.3230
 6B4  H20  H  HCR6  0   0.247   5.6944   0.4432  -2.0473
 6B4  H21  H  HCR6  0   0.254   7.2189   2.3070  -1.6236
 6B4  H22  H  HCR6  0   0.254   7.6210   1.0348   2.4538
 6B4  H23  H  HCR6  0   0.247   6.0932  -0.8233   2.0161
 6B4  H24  H  HNH1  0   0.392   3.3057  -0.0165   0.1206
 6B4  H25  H  HNH2  0   0.379   8.8058   3.3069  -0.0923
 6B4  H26  H  HNH2  0   0.379   8.9647   2.8143   1.4948

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
 6B4  CAA  SAT  single    1.801  0.020  1.801
 6B4  SAT  CAY  single    1.769  0.020  1.769
 6B4  CAG  CAY  aromatic  1.394  0.020  1.394
 6B4  CAG  CAE  aromatic  1.387  0.020  1.387
 6B4  CAY  CAZ  aromatic  1.403  0.020  1.403
 6B4  CAE  CAF  aromatic  1.386  0.020  1.386
 6B4  CAZ  CBA  single    1.510  0.020  1.510
 6B4  CAZ  CAH  aromatic  1.389  0.020  1.389
 6B4  CBA  CAP  single    1.539  0.020  1.539
 6B4  CBA  N1   single    1.460  0.020  1.460
 6B4  CAF  CAH  aromatic  1.387  0.020  1.387
 6B4  OAC  CAU  double    1.229  0.020  1.229
 6B4  CAP  CAM  single    1.523  0.020  1.523
 6B4  CA   N    single    1.432  0.020  1.432
 6B4  CA   C    single    1.520  0.020  1.520
 6B4  CAU  N    single    1.357  0.020  1.357
 6B4  CAU  N2   single    1.354  0.020  1.354
 6B4  CAO  CAX  single    1.502  0.020  1.502
 6B4  N1   C    single    1.341  0.020  1.341
 6B4  N1   CAQ  single    1.460  0.020  1.460
 6B4  CAM  CAQ  single    1.522  0.020  1.522
 6B4  C    O    double    1.224  0.020  1.224
 6B4  CAX  CAL  aromatic  1.392  0.020  1.392
 6B4  CAX  CAK  aromatic  1.393  0.020  1.393
 6B4  CAL  CAJ  aromatic  1.385  0.020  1.385
 6B4  CAK  CAI  aromatic  1.384  0.020  1.384
 6B4  CAJ  CAW  aromatic  1.400  0.020  1.400
 6B4  CAI  CAW  aromatic  1.401  0.020  1.401
 6B4  CAW  N3   single    1.377  0.020  1.377
 6B4  N2   CAO  single    1.451  0.020  1.451
 6B4  CAA  H1   single    0.970  0.020  1.090
 6B4  CAA  H2   single    0.970  0.020  1.090
 6B4  CAA  H3   single    0.970  0.020  1.090
 6B4  CAG  H4   single    0.930  0.020  1.080
 6B4  CAE  H5   single    0.930  0.020  1.080
 6B4  CAF  H6   single    0.930  0.020  1.080
 6B4  CAH  H7   single    0.930  0.020  1.080
 6B4  CBA  H8   single    0.970  0.020  1.090
 6B4  CAP  H9   single    0.970  0.020  1.090
 6B4  CAP  H10  single    0.970  0.020  1.090
 6B4  CAM  H11  single    0.970  0.020  1.090
 6B4  CAM  H12  single    0.970  0.020  1.090
 6B4  CAQ  H13  single    0.970  0.020  1.090
 6B4  CAQ  H14  single    0.970  0.020  1.090
 6B4  CA   H15  single    0.970  0.020  1.090
 6B4  CA   H16  single    0.970  0.020  1.090
 6B4  N    H17  single    0.860  0.020  1.020
 6B4  CAO  H18  single    0.970  0.020  1.090
 6B4  CAO  H19  single    0.970  0.020  1.090
 6B4  CAK  H20  single    0.930  0.020  1.080
 6B4  CAI  H21  single    0.930  0.020  1.080
 6B4  CAJ  H22  single    0.930  0.020  1.080
 6B4  CAL  H23  single    0.930  0.020  1.080
 6B4  N2   H24  single    0.860  0.020  1.020
 6B4  N3   H25  single    0.890  0.020  1.040
 6B4  N3   H26  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
 6B4  H3   CAA  H2   108.53  3.000
 6B4  H3   CAA  H1   108.82  3.000
 6B4  H2   CAA  H1   110.06  3.000
 6B4  H3   CAA  SAT  105.61  3.000
 6B4  H2   CAA  SAT  112.01  3.000
 6B4  H1   CAA  SAT  111.63  3.000
 6B4  CAY  SAT  CAA  103.79  3.000
 6B4  CAZ  CAY  CAG  119.69  3.000
 6B4  CAZ  CAY  SAT  118.02  3.000
 6B4  CAG  CAY  SAT  122.28  3.000
 6B4  H4   CAG  CAE  118.67  3.000
 6B4  H4   CAG  CAY  120.72  3.000
 6B4  CAE  CAG  CAY  120.61  3.000
 6B4  H5   CAE  CAF  120.49  3.000
 6B4  H5   CAE  CAG  119.48  3.000
 6B4  CAF  CAE  CAG  120.03  3.000
 6B4  H6   CAF  CAH  120.10  3.000
 6B4  H6   CAF  CAE  120.55  3.000
 6B4  CAH  CAF  CAE  119.35  3.000
 6B4  H7   CAH  CAZ  119.23  3.000
 6B4  H7   CAH  CAF  119.13  3.000
 6B4  CAZ  CAH  CAF  121.64  3.000
 6B4  CBA  CAZ  CAH  120.41  3.000
 6B4  CAH  CAZ  CAY  118.67  3.000
 6B4  CBA  CAZ  CAY  120.84  3.000
 6B4  H8   CBA  N1   108.26  3.000
 6B4  H8   CBA  CAP  109.87  3.000
 6B4  N1   CBA  CAP  103.30  3.000
 6B4  H8   CBA  CAZ  109.42  3.000
 6B4  N1   CBA  CAZ  113.61  3.000
 6B4  CAP  CBA  CAZ  112.17  3.000
 6B4  H10  CAP  H9   107.82  3.000
 6B4  H10  CAP  CAM  110.02  3.000
 6B4  H9   CAP  CAM  113.52  3.000
 6B4  H10  CAP  CBA  109.82  3.000
 6B4  H9   CAP  CBA  111.54  3.000
 6B4  CAM  CAP  CBA  104.10  3.000
 6B4  H12  CAM  H11  108.14  3.000
 6B4  H12  CAM  CAQ  112.29  3.000
 6B4  H11  CAM  CAQ  109.95  3.000
 6B4  H12  CAM  CAP  113.00  3.000
 6B4  H11  CAM  CAP  110.70  3.000
 6B4  CAQ  CAM  CAP  102.70  3.000
 6B4  H14  CAQ  H13  108.13  3.000
 6B4  H14  CAQ  N1   110.79  3.000
 6B4  H13  CAQ  N1   111.67  3.000
 6B4  H14  CAQ  CAM  111.16  3.000
 6B4  H13  CAQ  CAM  112.45  3.000
 6B4  N1   CAQ  CAM  102.62  3.000
 6B4  C    N1   CAQ  126.26  3.000
 6B4  CAQ  N1   CBA  112.49  3.000
 6B4  C    N1   CBA  120.54  3.000
 6B4  CA   C    O    121.47  3.000
 6B4  O    C    N1   122.33  3.000
 6B4  CA   C    N1   116.21  3.000
 6B4  H16  CA   H15  106.25  3.000
 6B4  H16  CA   N    111.37  3.000
 6B4  H15  CA   N    111.80  3.000
 6B4  H16  CA   C    109.39  3.000
 6B4  H15  CA   C    108.71  3.000
 6B4  N    CA   C    109.24  3.000
 6B4  H17  N    CAU  120.97  3.000
 6B4  H17  N    CA   116.75  3.000
 6B4  CAU  N    CA   121.35  3.000
 6B4  N2   CAU  OAC  122.39  3.000
 6B4  N2   CAU  N    115.29  3.000
 6B4  OAC  CAU  N    122.32  3.000
 6B4  H24  N2   CAO  117.88  3.000
 6B4  H24  N2   CAU  120.16  3.000
 6B4  CAO  N2   CAU  121.83  3.000
 6B4  H19  CAO  H18  106.79  3.000
 6B4  H19  CAO  CAX  109.87  3.000
 6B4  H18  CAO  CAX  109.74  3.000
 6B4  H19  CAO  N2   110.35  3.000
 6B4  H18  CAO  N2   110.11  3.000
 6B4  CAX  CAO  N2   109.92  3.000
 6B4  CAL  CAX  CAK  117.61  3.000
 6B4  CAK  CAX  CAO  121.15  3.000
 6B4  CAL  CAX  CAO  121.21  3.000
 6B4  H20  CAK  CAI  118.81  3.000
 6B4  H20  CAK  CAX  119.64  3.000
 6B4  CAI  CAK  CAX  121.54  3.000
 6B4  H21  CAI  CAW  119.59  3.000
 6B4  H21  CAI  CAK  119.74  3.000
 6B4  CAW  CAI  CAK  120.67  3.000
 6B4  CAJ  CAW  N3   121.06  3.000
 6B4  N3   CAW  CAI  120.95  3.000
 6B4  CAJ  CAW  CAI  117.95  3.000
 6B4  H26  N3   H25  111.94  3.000
 6B4  H26  N3   CAW  116.06  3.000
 6B4  H25  N3   CAW  115.97  3.000
 6B4  H22  CAJ  CAL  119.69  3.000
 6B4  H22  CAJ  CAW  119.68  3.000
 6B4  CAL  CAJ  CAW  120.63  3.000
 6B4  H23  CAL  CAJ  118.86  3.000
 6B4  H23  CAL  CAX  119.55  3.000
 6B4  CAJ  CAL  CAX  121.59  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
 6B4  CONST_01  CAF  CAE  CAG  CAY    0.00   0.0  0
 6B4  CONST_02  CAF  CAH  CAZ  CAY    0.00   0.0  0
 6B4  CONST_03  CAH  CAZ  CAY  CAG    0.00   0.0  0
 6B4  CONST_04  CAH  CAF  CAE  CAG    0.00   0.0  0
 6B4  CONST_05  CAZ  CAY  CAG  CAE    0.00   0.0  0
 6B4  CONST_06  CAZ  CAH  CAF  CAE    0.00   0.0  0
 6B4  CONST_07  CAW  CAJ  CAL  CAX    0.00   0.0  0
 6B4  CONST_08  CAW  CAI  CAK  CAX    0.00   0.0  0
 6B4  CONST_09  CAJ  CAL  CAX  CAK    0.00   0.0  0
 6B4  CONST_10  CAJ  CAW  CAI  CAK    0.00   0.0  0
 6B4  CONST_11  CAL  CAX  CAK  CAI    0.00   0.0  0
 6B4  CONST_12  CAL  CAJ  CAW  CAI    0.00   0.0  0
 6B4  CONST_13  CBA  CAZ  CAY  CAG  180.00   0.0  0
 6B4  CONST_14  CBA  CAZ  CAH  CAF  180.00   0.0  0
 6B4  CONST_15  CAE  CAG  CAY  SAT  180.00   0.0  0
 6B4  CONST_16  CBA  CAZ  CAY  SAT    0.00   0.0  0
 6B4  CONST_17  CAH  CAZ  CAY  SAT  180.00   0.0  0
 6B4  CONST_18  CAJ  CAL  CAX  CAO  180.00   0.0  0
 6B4  CONST_19  CAI  CAK  CAX  CAO  180.00   0.0  0
 6B4  CONST_20  N3   CAW  CAI  CAK  180.00   0.0  0
 6B4  CONST_21  CAL  CAJ  CAW  N3   180.00   0.0  0
 6B4  CONST_22  H5   CAE  CAG  CAY  180.00   0.0  0
 6B4  CONST_23  H7   CAH  CAZ  CAY  180.00   0.0  0
 6B4  CONST_24  H6   CAF  CAE  CAG  180.00   0.0  0
 6B4  CONST_25  H4   CAG  CAE  CAF  180.00   0.0  0
 6B4  CONST_26  H22  CAJ  CAL  CAX  180.00   0.0  0
 6B4  CONST_27  H21  CAI  CAK  CAX  180.00   0.0  0
 6B4  CONST_28  H23  CAL  CAX  CAK  180.00   0.0  0
 6B4  CONST_29  H20  CAK  CAI  CAW  180.00   0.0  0
 6B4  CONST_30  CA   C    N1   CBA  180.00   0.0  0
 6B4  CONST_31  O    C    N1   CBA    0.00   0.0  0
 6B4  CONST_32  CA   C    N1   CAQ    0.00   0.0  0
 6B4  CONST_33  O    C    N1   CAQ  180.00   0.0  0
 6B4  CONST_36  OAC  CAU  N    CA     0.00   0.0  0
 6B4  CONST_37  CAO  N2   CAU  OAC    0.00   0.0  0
 6B4  CONST_38  N2   CAU  N    CA   180.00   0.0  0
 6B4  CONST_39  CAO  N2   CAU  N    180.00   0.0  0
 6B4  CONST_40  H17  N    CAU  OAC  180.00   0.0  0
 6B4  CONST_41  H24  N2   CAU  OAC  180.00   0.0  0
 6B4  Var_01    CAQ  CAM  CAP  CBA  -37.37  30.0  1
 6B4  Var_02    CAM  CAQ  N1   CBA  -21.80  30.0  1
 6B4  Var_03    N1   CAQ  CAM  CAP   35.81  30.0  1
 6B4  Var_04    CAG  CAY  SAT  CAA   -6.10  30.0  2
 6B4  Var_05    CAL  CAX  CAO  N2    91.77  30.0  2
 6B4  Var_06    N    CA   C    N1   172.73  30.0  2
 6B4  Var_07    CAX  CAO  N2   CAU  179.89  30.0  3
 6B4  Var_08    H1   CAA  SAT  CAY  -59.67  30.0  3
 6B4  Var_09    CAU  N    CA   C    177.33  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
 6B4  chir_01  CBA  CAZ  CAP  N1  negativ

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
 6B4  plan-1  SAT  0.020
 6B4  plan-1  CAY  0.020
 6B4  plan-1  CAG  0.020
 6B4  plan-1  CAE  0.020
 6B4  plan-1  CAF  0.020
 6B4  plan-1  CAH  0.020
 6B4  plan-1  CAZ  0.020
 6B4  plan-1  CBA  0.020
 6B4  plan-1  H4   0.020
 6B4  plan-1  H5   0.020
 6B4  plan-1  H6   0.020
 6B4  plan-1  H7   0.020
 6B4  plan-2  CAO  0.020
 6B4  plan-2  CAX  0.020
 6B4  plan-2  CAK  0.020
 6B4  plan-2  CAI  0.020
 6B4  plan-2  CAW  0.020
 6B4  plan-2  N3   0.020
 6B4  plan-2  CAJ  0.020
 6B4  plan-2  CAL  0.020
 6B4  plan-2  H20  0.020
 6B4  plan-2  H21  0.020
 6B4  plan-2  H22  0.020
 6B4  plan-2  H23  0.020
 6B4  plan-3  CA   0.020
 6B4  plan-3  N    0.020
 6B4  plan-3  CAU  0.020
 6B4  plan-3  OAC  0.020
 6B4  plan-3  N2   0.020
 6B4  plan-3  CAO  0.020
 6B4  plan-3  H17  0.020
 6B4  plan-3  H24  0.020
 6B4  plan-4  CAW  0.020
 6B4  plan-4  N3   0.020
 6B4  plan-4  H25  0.020
 6B4  plan-4  H26  0.020
 6B4  plan-5  CBA  0.020
 6B4  plan-5  CAQ  0.020
 6B4  plan-5  N1   0.020
 6B4  plan-5  C    0.020
 6B4  plan-5  O    0.020
 6B4  plan-5  CA   0.020

