# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 08:52:31 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 1-(4-aminobenzyl)-3-{2-[(2R)-2-(naphthalen-1-yl)pyrrolidin-1-yl]-2-oxoethyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(CNC(=O)NCC(=O)N2CCC[C@@H]2c3cccc4ccccc34)cc1
#
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
 671  671  1-(4-aminobenzyl)-3-{2-[(2R)-2-(naphthalen-1-yl)pyrrolidin-1-yl]-2-oxoethyl}urea  ligand  56  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_671
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
 671  CAJ  C  CR16  0  -0.277  -5.8289  -0.7525  -0.9263
 671  CAH  C  CR16  0  -0.312  -6.6739  -1.8453  -0.8587
 671  CAX  C  CR6   0   0.289  -7.5971  -1.9736   0.1886
 671  NAA  N  NH2   0  -0.859  -8.4064  -3.0861   0.2881
 671  CAI  C  CR16  0  -0.314  -7.6332  -0.9644   1.1558
 671  CAK  C  CR16  0  -0.298  -6.7769   0.1235   1.0750
 671  CAY  C  CR6   0   0.036  -5.8627   0.2558   0.0364
 671  CAR  C  CH2   0  -0.313  -4.9356   1.4357  -0.0452
 671  NAU  N  NH1   0  -0.678  -3.5649   1.0194   0.1754
 671  CAV  C  C     0   0.750  -2.5222   1.8506  -0.0929
 671  OAB  O  O     0  -0.554  -2.6620   2.9208  -0.6795
 671  N    N  NH1   0  -0.697  -1.3098   1.4001   0.3109
 671  CA   C  CH2   0  -0.363  -0.1167   2.1609   0.0902
 671  C    C  C     0   0.524   1.0944   1.3160   0.4488
 671  O    O  O     0  -0.489   0.9744   0.2187   0.9775
 671  NBD  N  NT    0  -0.492   2.2902   1.8407   0.1449
 671  CAS  C  CH2   0  -0.287   2.5383   3.1953  -0.3362
 671  CAO  C  CH2   0  -0.467   3.9095   3.5079   0.2431
 671  CAQ  C  CH2   0  -0.465   4.6232   2.1638   0.1741
 671  CBC  C  CH1   0  -0.119   3.5214   1.1287   0.4739
 671  CAZ  C  CR6   0   0.134   3.7176  -0.1415  -0.3204
 671  CBB  C  CR66  0   0.087   4.6040  -1.1496   0.1600
 671  CAN  C  CR16  0  -0.341   5.2929  -1.0480   1.3955
 671  CAE  C  CR16  0  -0.248   6.1365  -2.0383   1.8214
 671  CAD  C  CR16  0  -0.262   6.3442  -3.1901   1.0370
 671  CAL  C  CR16  0  -0.309   5.6993  -3.3203  -0.1613
 671  CBA  C  CR66  0   0.107   4.8225  -2.3131  -0.6297
 671  CAM  C  CR16  0  -0.332   4.1660  -2.4460  -1.8744
 671  CAF  C  CR16  0  -0.244   3.3304  -1.4611  -2.3180
 671  CAG  C  CR16  0  -0.333   3.1105  -0.3096  -1.5376
 671  H1   H  HCR6  0   0.247  -5.1300  -0.6818  -1.7521
 671  H2   H  HCR6  0   0.255  -6.6241  -2.6096  -1.6256
 671  H3   H  HNH2  0   0.378  -8.5848  -3.5720  -0.5762
 671  H4   H  HNH2  0   0.378  -9.2520  -2.9608   0.8213
 671  H5   H  HCR6  0   0.253  -8.3361  -1.0335   1.9777
 671  H6   H  HCR6  0   0.247  -6.8299   0.8873   1.8424
 671  H7   H  HCH2  0   0.246  -5.0016   1.8973  -1.0316
 671  H8   H  HCH2  0   0.236  -5.2456   2.1967   0.6797
 671  H9   H  HNH1  0   0.388  -3.4241   0.2619   0.8249
 671  H10  H  HNH1  0   0.392  -1.2099   0.5185   0.7900
 671  H11  H  HCH2  0   0.270  -0.0390   2.4823  -0.9523
 671  H12  H  HCH2  0   0.268  -0.0991   3.0747   0.6974
 671  H13  H  HCH2  0   0.249   2.5509   3.2249  -1.4298
 671  H14  H  HCH2  0   0.266   1.7750   3.8900   0.0108
 671  H15  H  HCH2  0   0.257   4.4240   4.2899  -0.3135
 671  H16  H  HCH2  0   0.245   3.8085   3.8391   1.2786
 671  H17  H  HCH2  0   0.246   5.0216   1.9996  -0.8291
 671  H18  H  HCH2  0   0.261   5.4517   2.0816   0.8760
 671  H19  H  HCH1  0   0.265   3.5048   0.8969   1.5421
 671  H20  H  HCR6  0   0.251   5.1635  -0.1789   2.0266
 671  H21  H  HCR6  0   0.259   6.6488  -1.9356   2.7690
 671  H22  H  HCR6  0   0.258   7.0134  -3.9658   1.3853
 671  H23  H  HCR6  0   0.255   5.8523  -4.2006  -0.7745
 671  H24  H  HCR6  0   0.253   4.3372  -3.3346  -2.4698
 671  H25  H  HCR6  0   0.256   2.8298  -1.5582  -3.2725
 671  H26  H  HCR6  0   0.246   2.4431   0.4530  -1.9195

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
 671  CAD  CAE  aromatic  1.409  0.020  1.409
 671  CAD  CAL  aromatic  1.367  0.020  1.367
 671  CAE  CAN  aromatic  1.369  0.020  1.369
 671  CAL  CBA  aromatic  1.415  0.020  1.415
 671  CAN  CBB  aromatic  1.418  0.020  1.418
 671  CBA  CBB  aromatic  1.423  0.020  1.423
 671  CBA  CAM  aromatic  1.414  0.020  1.414
 671  CBB  CAZ  aromatic  1.426  0.020  1.426
 671  CAM  CAF  aromatic  1.366  0.020  1.366
 671  CAZ  CBC  single    1.511  0.020  1.511
 671  CAZ  CAG  aromatic  1.371  0.020  1.371
 671  CBC  CAQ  single    1.541  0.020  1.541
 671  CBC  NBD  single    1.460  0.020  1.460
 671  CAQ  CAO  single    1.523  0.020  1.523
 671  OAB  CAV  double    1.228  0.020  1.228
 671  CAF  CAG  aromatic  1.408  0.020  1.408
 671  CA   N    single    1.432  0.020  1.432
 671  CA   C    single    1.520  0.020  1.520
 671  CAV  N    single    1.355  0.020  1.355
 671  CAV  NAU  single    1.360  0.020  1.360
 671  NBD  C    single    1.341  0.020  1.341
 671  NBD  CAS  single    1.459  0.020  1.459
 671  CAR  NAU  single    1.449  0.020  1.449
 671  CAR  CAY  single    1.503  0.020  1.503
 671  CAO  CAS  single    1.521  0.020  1.521
 671  C    O    double    1.224  0.020  1.224
 671  CAY  CAK  aromatic  1.390  0.020  1.390
 671  CAY  CAJ  aromatic  1.394  0.020  1.394
 671  CAK  CAI  aromatic  1.387  0.020  1.387
 671  CAJ  CAH  aromatic  1.383  0.020  1.383
 671  CAI  CAX  aromatic  1.398  0.020  1.398
 671  CAH  CAX  aromatic  1.402  0.020  1.402
 671  CAX  NAA  single    1.379  0.020  1.379
 671  CAJ  H1   single    0.930  0.020  1.080
 671  CAH  H2   single    0.930  0.020  1.080
 671  NAA  H3   single    0.890  0.020  1.040
 671  NAA  H4   single    0.890  0.020  1.040
 671  CAI  H5   single    0.930  0.020  1.080
 671  CAK  H6   single    0.930  0.020  1.080
 671  CAR  H7   single    0.970  0.020  1.090
 671  CAR  H8   single    0.970  0.020  1.090
 671  NAU  H9   single    0.890  0.020  1.040
 671  N    H10  single    0.860  0.020  1.020
 671  CA   H11  single    0.970  0.020  1.090
 671  CA   H12  single    0.970  0.020  1.090
 671  CAS  H13  single    0.970  0.020  1.090
 671  CAS  H14  single    0.970  0.020  1.090
 671  CAO  H15  single    0.970  0.020  1.090
 671  CAO  H16  single    0.970  0.020  1.090
 671  CAQ  H17  single    0.970  0.020  1.090
 671  CAQ  H18  single    0.970  0.020  1.090
 671  CBC  H19  single    0.970  0.020  1.090
 671  CAN  H20  single    0.930  0.020  1.080
 671  CAE  H21  single    0.930  0.020  1.080
 671  CAD  H22  single    0.930  0.020  1.080
 671  CAL  H23  single    0.930  0.020  1.080
 671  CAM  H24  single    0.930  0.020  1.080
 671  CAF  H25  single    0.930  0.020  1.080
 671  CAG  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
 671  H1   CAJ  CAY  119.63  3.000
 671  H1   CAJ  CAH  118.86  3.000
 671  CAY  CAJ  CAH  121.52  3.000
 671  H2   CAH  CAX  119.62  3.000
 671  H2   CAH  CAJ  119.64  3.000
 671  CAX  CAH  CAJ  120.74  3.000
 671  CAI  CAX  NAA  121.14  3.000
 671  NAA  CAX  CAH  120.93  3.000
 671  CAI  CAX  CAH  117.88  3.000
 671  H4   NAA  H3   111.44  3.000
 671  H4   NAA  CAX  115.49  3.000
 671  H3   NAA  CAX  115.54  3.000
 671  H5   CAI  CAK  119.65  3.000
 671  H5   CAI  CAX  119.69  3.000
 671  CAK  CAI  CAX  120.66  3.000
 671  H6   CAK  CAY  119.61  3.000
 671  H6   CAK  CAI  118.77  3.000
 671  CAY  CAK  CAI  121.62  3.000
 671  CAR  CAY  CAK  121.40  3.000
 671  CAK  CAY  CAJ  117.58  3.000
 671  CAR  CAY  CAJ  121.01  3.000
 671  H8   CAR  H7   106.69  3.000
 671  H8   CAR  NAU  111.49  3.000
 671  H7   CAR  NAU  108.44  3.000
 671  H8   CAR  CAY  109.56  3.000
 671  H7   CAR  CAY  110.12  3.000
 671  NAU  CAR  CAY  110.46  3.000
 671  H9   NAU  CAV  118.65  3.000
 671  H9   NAU  CAR  116.50  3.000
 671  CAV  NAU  CAR  121.29  3.000
 671  N    CAV  OAB  122.26  3.000
 671  N    CAV  NAU  115.09  3.000
 671  OAB  CAV  NAU  122.64  3.000
 671  H10  N    CA   117.07  3.000
 671  H10  N    CAV  121.39  3.000
 671  CA   N    CAV  121.53  3.000
 671  H12  CA   H11  106.36  3.000
 671  H12  CA   C    108.65  3.000
 671  H11  CA   C    109.37  3.000
 671  H12  CA   N    111.75  3.000
 671  H11  CA   N    111.23  3.000
 671  C    CA   N    109.40  3.000
 671  NBD  C    O    122.43  3.000
 671  O    C    CA   121.49  3.000
 671  NBD  C    CA   116.08  3.000
 671  CBC  NBD  CAS  112.57  3.000
 671  CAS  NBD  C    126.15  3.000
 671  CBC  NBD  C    120.68  3.000
 671  H14  CAS  H13  108.02  3.000
 671  H14  CAS  CAO  112.30  3.000
 671  H13  CAS  CAO  111.39  3.000
 671  H14  CAS  NBD  111.60  3.000
 671  H13  CAS  NBD  110.90  3.000
 671  CAO  CAS  NBD  102.62  3.000
 671  H16  CAO  H15  108.10  3.000
 671  H16  CAO  CAQ  110.73  3.000
 671  H15  CAO  CAQ  112.90  3.000
 671  H16  CAO  CAS  109.88  3.000
 671  H15  CAO  CAS  112.26  3.000
 671  CAQ  CAO  CAS  102.93  3.000
 671  H18  CAQ  H17  107.65  3.000
 671  H18  CAQ  CBC  111.58  3.000
 671  H17  CAQ  CBC  109.79  3.000
 671  H18  CAQ  CAO  113.20  3.000
 671  H17  CAQ  CAO  110.20  3.000
 671  CBC  CAQ  CAO  104.41  3.000
 671  H19  CBC  CAZ  109.72  3.000
 671  H19  CBC  CAQ  110.08  3.000
 671  CAZ  CBC  CAQ  111.69  3.000
 671  H19  CBC  NBD  108.11  3.000
 671  CAQ  CBC  NBD  103.38  3.000
 671  CAZ  CBC  NBD  113.65  3.000
 671  CAG  CAZ  CBB  119.20  3.000
 671  CAG  CAZ  CBC  120.83  3.000
 671  CBB  CAZ  CBC  119.87  3.000
 671  CBA  CBB  CAN  117.87  3.000
 671  CBA  CBB  CAZ  119.12  3.000
 671  CAN  CBB  CAZ  123.01  3.000
 671  H20  CAN  CAE  118.26  3.000
 671  H20  CAN  CBB  120.51  3.000
 671  CAE  CAN  CBB  121.23  3.000
 671  H21  CAE  CAD  119.69  3.000
 671  H21  CAE  CAN  119.71  3.000
 671  CAD  CAE  CAN  120.60  3.000
 671  H22  CAD  CAL  120.37  3.000
 671  H22  CAD  CAE  119.87  3.000
 671  CAL  CAD  CAE  119.76  3.000
 671  H23  CAL  CBA  118.58  3.000
 671  H23  CAL  CAD  120.45  3.000
 671  CBA  CAL  CAD  120.97  3.000
 671  CAM  CBA  CAL  120.82  3.000
 671  CAM  CBA  CBB  119.62  3.000
 671  CAL  CBA  CBB  119.57  3.000
 671  H24  CAM  CAF  120.65  3.000
 671  H24  CAM  CBA  119.19  3.000
 671  CAF  CAM  CBA  120.16  3.000
 671  H25  CAF  CAG  119.33  3.000
 671  H25  CAF  CAM  120.32  3.000
 671  CAG  CAF  CAM  120.35  3.000
 671  H26  CAG  CAF  118.47  3.000
 671  H26  CAG  CAZ  119.98  3.000
 671  CAF  CAG  CAZ  121.55  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
 671  CONST_01  CAI  CAK  CAY  CAJ     0.00   0.0  0
 671  CONST_02  CAI  CAX  CAH  CAJ     0.00   0.0  0
 671  CONST_03  CAK  CAY  CAJ  CAH     0.00   0.0  0
 671  CONST_04  CAK  CAI  CAX  CAH     0.00   0.0  0
 671  CONST_05  CAY  CAK  CAI  CAX     0.00   0.0  0
 671  CONST_06  CAY  CAJ  CAH  CAX     0.00   0.0  0
 671  CONST_07  CAE  CAN  CBB  CAZ   180.00   0.0  0
 671  CONST_08  CAL  CBA  CBB  CAZ   180.00   0.0  0
 671  CONST_09  CAM  CBA  CBB  CAZ     0.00   0.0  0
 671  CONST_10  CAM  CAF  CAG  CAZ     0.00   0.0  0
 671  CONST_11  CAD  CAE  CAN  CBB     0.00   0.0  0
 671  CONST_12  CAD  CAL  CBA  CBB     0.00   0.0  0
 671  CONST_13  CAF  CAM  CBA  CBB     0.00   0.0  0
 671  CONST_14  CAF  CAG  CAZ  CBB     0.00   0.0  0
 671  CONST_15  CAL  CAD  CAE  CAN     0.00   0.0  0
 671  CONST_16  CAL  CBA  CBB  CAN     0.00   0.0  0
 671  CONST_17  CAM  CBA  CBB  CAN   180.00   0.0  0
 671  CONST_18  CAG  CAZ  CBB  CAN   180.00   0.0  0
 671  CONST_19  CBA  CAL  CAD  CAE     0.00   0.0  0
 671  CONST_20  CBA  CBB  CAN  CAE     0.00   0.0  0
 671  CONST_21  CAM  CBA  CAL  CAD   180.00   0.0  0
 671  CONST_22  CAF  CAM  CBA  CAL   180.00   0.0  0
 671  CONST_23  CAG  CAZ  CBB  CBA     0.00   0.0  0
 671  CONST_24  CAG  CAF  CAM  CBA     0.00   0.0  0
 671  CONST_25  CAN  CBB  CAZ  CBC     0.00   0.0  0
 671  CONST_26  CBA  CBB  CAZ  CBC   180.00   0.0  0
 671  CONST_27  CAF  CAG  CAZ  CBC   180.00   0.0  0
 671  CONST_28  NAA  CAX  CAH  CAJ   180.00   0.0  0
 671  CONST_29  CAR  CAY  CAJ  CAH   180.00   0.0  0
 671  CONST_30  CAK  CAI  CAX  NAA   180.00   0.0  0
 671  CONST_31  CAR  CAY  CAK  CAI   180.00   0.0  0
 671  CONST_32  H6   CAK  CAY  CAJ   180.00   0.0  0
 671  CONST_33  H5   CAI  CAX  CAH   180.00   0.0  0
 671  CONST_34  H1   CAJ  CAH  CAX   180.00   0.0  0
 671  CONST_35  H2   CAH  CAX  CAI   180.00   0.0  0
 671  CONST_36  H26  CAG  CAZ  CBC     0.00   0.0  0
 671  CONST_37  H20  CAN  CBB  CAZ     0.00   0.0  0
 671  CONST_38  H25  CAF  CAG  CAZ   180.00   0.0  0
 671  CONST_39  H21  CAE  CAN  CBB   180.00   0.0  0
 671  CONST_40  H23  CAL  CBA  CBB   180.00   0.0  0
 671  CONST_41  H24  CAM  CBA  CBB   180.00   0.0  0
 671  CONST_42  H22  CAD  CAE  CAN   180.00   0.0  0
 671  CONST_43  CBC  NBD  C    CA    180.00   0.0  0
 671  CONST_44  CAS  NBD  C    CA      0.00   0.0  0
 671  CONST_45  CBC  NBD  C    O       0.00   0.0  0
 671  CONST_46  CAS  NBD  C    O     180.00   0.0  0
 671  CONST_49  OAB  CAV  NAU  CAR     0.00   0.0  0
 671  CONST_50  CA   N    CAV  OAB     0.00   0.0  0
 671  CONST_51  N    CAV  NAU  CAR   180.00   0.0  0
 671  CONST_52  CA   N    CAV  NAU   180.00   0.0  0
 671  CONST_53  H10  N    CAV  OAB   180.00   0.0  0
 671  CONST_54  H9   NAU  CAV  OAB   180.00   0.0  0
 671  Var_01    CAQ  CAO  CAS  NBD    35.57  30.0  1
 671  Var_02    CBC  CAQ  CAO  CAS   -35.95  30.0  1
 671  Var_03    CBC  NBD  CAS  CAO   -22.94  30.0  1
 671  Var_04    NAU  CAR  CAY  CAJ   -67.62  30.0  2
 671  Var_05    CAV  NAU  CAR  CAY   167.57  30.0  3
 671  Var_06    NBD  C    CA   N     172.45  30.0  3
 671  Var_07    C    CA   N    CAV  -171.23  30.0  1

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
 671  chir_01  CBC  CAZ  CAQ  NBD  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
 671  plan-1  CAJ  0.020
 671  plan-1  CAH  0.020
 671  plan-1  CAX  0.020
 671  plan-1  NAA  0.020
 671  plan-1  CAI  0.020
 671  plan-1  CAK  0.020
 671  plan-1  CAY  0.020
 671  plan-1  CAR  0.020
 671  plan-1  H1   0.020
 671  plan-1  H2   0.020
 671  plan-1  H5   0.020
 671  plan-1  H6   0.020
 671  plan-2  CBC  0.020
 671  plan-2  CAZ  0.020
 671  plan-2  CBB  0.020
 671  plan-2  CAN  0.020
 671  plan-2  CAE  0.020
 671  plan-2  CAD  0.020
 671  plan-2  CAL  0.020
 671  plan-2  CBA  0.020
 671  plan-2  CAM  0.020
 671  plan-2  CAF  0.020
 671  plan-2  CAG  0.020
 671  plan-2  H20  0.020
 671  plan-2  H21  0.020
 671  plan-2  H22  0.020
 671  plan-2  H23  0.020
 671  plan-2  H24  0.020
 671  plan-2  H25  0.020
 671  plan-2  H26  0.020
 671  plan-3  CAR  0.020
 671  plan-3  NAU  0.020
 671  plan-3  CAV  0.020
 671  plan-3  OAB  0.020
 671  plan-3  N    0.020
 671  plan-3  CA   0.020
 671  plan-3  H9   0.020
 671  plan-3  H10  0.020
 671  plan-4  CA   0.020
 671  plan-4  C    0.020
 671  plan-4  O    0.020
 671  plan-4  NBD  0.020
 671  plan-4  CAS  0.020
 671  plan-4  CBC  0.020
 671  plan-5  CAX  0.020
 671  plan-5  NAA  0.020
 671  plan-5  H3   0.020
 671  plan-5  H4   0.020

