# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 09:46:46 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-(4-aminobenzyl)-3-{2-[(2R)-2-(2-bromophenyl)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]2c3ccccc3Br)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
 728  728  1-(4-aminobenzyl)-3-{2-[(2R)-2-(2-bromophenyl)pyrrolidin-1-yl]-2-oxoethyl}urea  ligand  50  27  .  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_728
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
 728  CAA  C   CR16  0  -0.299  -7.0500  -0.3205  -1.1231
 728  CAB  C   CR16  0  -0.314  -7.9585  -1.2988  -0.7476
 728  CAC  C   CR6   0   0.292  -8.0846  -1.6769   0.5928
 728  NAG  N   NH2   0  -0.859  -9.0248  -2.6061   0.9843
 728  CAD  C   CR16  0  -0.312  -7.2644  -1.0402   1.5348
 728  CAE  C   CR16  0  -0.277  -6.3652  -0.0646   1.1439
 728  CAF  C   CR6   0   0.037  -6.2414   0.3189  -0.1908
 728  CAH  C   CH2   0  -0.314  -5.2586   1.3787  -0.6047
 728  NAI  N   NH1   0  -0.678  -3.9002   0.9210  -0.3928
 728  CAJ  C   C     0   0.748  -2.8484   1.7823  -0.4080
 728  OAL  O   O     0  -0.552  -2.9872   3.0016  -0.4480
 728  N    N   NH1   0  -0.696  -1.6262   1.1937  -0.3677
 728  CA   C   CH2   0  -0.364  -0.4323   1.9767  -0.2403
 728  C    C   C     0   0.529   0.7444   1.0577   0.0374
 728  O    O   O     0  -0.486   0.5854  -0.1304   0.2831
 728  NAP  N   NT    0  -0.492   1.9595   1.6236  -0.0082
 728  CAQ  C   CH2   0  -0.286   2.2398   3.0509  -0.1415
 728  CAR  C   CH2   0  -0.470   3.5622   3.2046   0.5953
 728  CAS  C   CH2   0  -0.464   4.2750   1.8952   0.2865
 728  CAT  C   CH1   0  -0.113   3.1515   0.8455   0.3167
 728  CAU  C   CR6   0   0.222   3.4126  -0.2828  -0.6528
 728  CAX  C   CR16  0  -0.303   3.0134  -0.1652  -1.9835
 728  CAW  C   CR16  0  -0.236   3.2821  -1.1510  -2.9173
 728  CAV  C   CR16  0  -0.270   3.9718  -2.2942  -2.5379
 728  CAY  C   CR16  0  -0.216   4.3930  -2.4360  -1.2262
 728  CAZ  C   CR6   0  -0.200   4.1149  -1.4334  -0.3042
 728  BR   BR  BR    0  -0.054   4.7544  -1.6879   1.4646
 728  H1   H   HCR6  0   0.247  -6.9758  -0.0502  -2.1702
 728  H2   H   HCR6  0   0.253  -8.5783  -1.7734  -1.4993
 728  H3   H   HNH2  0   0.378  -9.3066  -3.2673   0.2785
 728  H4   H   HNH2  0   0.378  -8.8552  -3.0551   1.8698
 728  H5   H   HCR6  0   0.254  -7.3379  -1.3154   2.5807
 728  H6   H   HCR6  0   0.247  -5.7442   0.4073   1.8968
 728  H7   H   HCH2  0   0.236  -5.4335   1.6481  -1.6521
 728  H8   H   HCH2  0   0.247  -5.4135   2.2841  -0.0162
 728  H9   H   HNH1  0   0.389  -3.7258  -0.0568  -0.5642
 728  H10  H   HNH1  0   0.392  -1.5374   0.2060  -0.1829
 728  H11  H   HCH2  0   0.268  -0.2369   2.5613  -1.1446
 728  H12  H   HCH2  0   0.271  -0.5112   2.6994   0.5804
 728  H13  H   HCH2  0   0.250   2.3392   3.3302  -1.1946
 728  H14  H   HCH2  0   0.266   1.4486   3.6580   0.2959
 728  H15  H   HCH2  0   0.259   4.1181   4.0801   0.2632
 728  H16  H   HCH2  0   0.246   3.3847   3.3040   1.6679
 728  H17  H   HCH2  0   0.248   4.7177   1.9365  -0.7111
 728  H18  H   HCH2  0   0.263   5.0677   1.6542   0.9928
 728  H19  H   HCH1  0   0.271   3.0382   0.4485   1.3287
 728  H20  H   HCR6  0   0.256   2.4755   0.7221  -2.2939
 728  H21  H   HCR6  0   0.263   2.9526  -1.0263  -3.9402
 728  H22  H   HCR6  0   0.267   4.1875  -3.0731  -3.2568
 728  H23  H   HCR6  0   0.278   4.9362  -3.3226  -0.9271

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
 728  BR   CAZ  single    1.898  0.020  1.898
 728  CAY  CAZ  aromatic  1.390  0.020  1.390
 728  CAY  CAV  aromatic  1.385  0.020  1.385
 728  CAZ  CAU  aromatic  1.392  0.020  1.392
 728  CAV  CAW  aromatic  1.388  0.020  1.388
 728  CAU  CAT  single    1.510  0.020  1.510
 728  CAU  CAX  aromatic  1.394  0.020  1.394
 728  CAT  CAS  single    1.538  0.020  1.538
 728  CAT  NAP  single    1.460  0.020  1.460
 728  CAS  CAR  single    1.522  0.020  1.522
 728  OAL  CAJ  double    1.228  0.020  1.228
 728  CA   N    single    1.433  0.020  1.433
 728  CA   C    single    1.519  0.020  1.519
 728  CAW  CAX  aromatic  1.384  0.020  1.384
 728  CAJ  N    single    1.357  0.020  1.357
 728  CAJ  NAI  single    1.360  0.020  1.360
 728  CAH  NAI  single    1.449  0.020  1.449
 728  CAH  CAF  single    1.503  0.020  1.503
 728  NAP  C    single    1.341  0.020  1.341
 728  NAP  CAQ  single    1.461  0.020  1.461
 728  CAR  CAQ  single    1.522  0.020  1.522
 728  C    O    double    1.224  0.020  1.224
 728  CAF  CAE  aromatic  1.394  0.020  1.394
 728  CAF  CAA  aromatic  1.390  0.020  1.390
 728  CAE  CAD  aromatic  1.383  0.020  1.383
 728  CAA  CAB  aromatic  1.387  0.020  1.387
 728  CAD  CAC  aromatic  1.402  0.020  1.402
 728  CAB  CAC  aromatic  1.398  0.020  1.398
 728  CAC  NAG  single    1.379  0.020  1.379
 728  CAA  H1   single    0.930  0.020  1.080
 728  CAB  H2   single    0.930  0.020  1.080
 728  NAG  H3   single    0.890  0.020  1.040
 728  NAG  H4   single    0.890  0.020  1.040
 728  CAD  H5   single    0.930  0.020  1.080
 728  CAE  H6   single    0.930  0.020  1.080
 728  CAH  H7   single    0.970  0.020  1.090
 728  CAH  H8   single    0.970  0.020  1.090
 728  NAI  H9   single    0.890  0.020  1.040
 728  N    H10  single    0.860  0.020  1.020
 728  CA   H11  single    0.970  0.020  1.090
 728  CA   H12  single    0.970  0.020  1.090
 728  CAQ  H13  single    0.970  0.020  1.090
 728  CAQ  H14  single    0.970  0.020  1.090
 728  CAR  H15  single    0.970  0.020  1.090
 728  CAR  H16  single    0.970  0.020  1.090
 728  CAS  H17  single    0.970  0.020  1.090
 728  CAS  H18  single    0.970  0.020  1.090
 728  CAT  H19  single    0.970  0.020  1.090
 728  CAX  H20  single    0.930  0.020  1.080
 728  CAW  H21  single    0.930  0.020  1.080
 728  CAV  H22  single    0.930  0.020  1.080
 728  CAY  H23  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
 728  H1   CAA  CAF  119.56  3.000
 728  H1   CAA  CAB  118.83  3.000
 728  CAF  CAA  CAB  121.60  3.000
 728  H2   CAB  CAC  119.66  3.000
 728  H2   CAB  CAA  119.72  3.000
 728  CAC  CAB  CAA  120.62  3.000
 728  CAD  CAC  NAG  120.95  3.000
 728  NAG  CAC  CAB  121.06  3.000
 728  CAD  CAC  CAB  117.94  3.000
 728  H4   NAG  H3   111.75  3.000
 728  H4   NAG  CAC  115.81  3.000
 728  H3   NAG  CAC  115.73  3.000
 728  H5   CAD  CAE  119.73  3.000
 728  H5   CAD  CAC  119.56  3.000
 728  CAE  CAD  CAC  120.71  3.000
 728  H6   CAE  CAF  119.62  3.000
 728  H6   CAE  CAD  118.89  3.000
 728  CAF  CAE  CAD  121.49  3.000
 728  CAH  CAF  CAE  121.03  3.000
 728  CAE  CAF  CAA  117.64  3.000
 728  CAH  CAF  CAA  121.33  3.000
 728  H8   CAH  H7   106.80  3.000
 728  H8   CAH  NAI  108.45  3.000
 728  H7   CAH  NAI  111.54  3.000
 728  H8   CAH  CAF  110.10  3.000
 728  H7   CAH  CAF  109.40  3.000
 728  NAI  CAH  CAF  110.48  3.000
 728  H9   NAI  CAJ  118.61  3.000
 728  H9   NAI  CAH  116.35  3.000
 728  CAJ  NAI  CAH  121.57  3.000
 728  N    CAJ  OAL  122.25  3.000
 728  N    CAJ  NAI  114.94  3.000
 728  OAL  CAJ  NAI  122.82  3.000
 728  H10  N    CA   116.44  3.000
 728  H10  N    CAJ  120.62  3.000
 728  CA   N    CAJ  121.05  3.000
 728  H12  CA   H11  106.21  3.000
 728  H12  CA   C    108.53  3.000
 728  H11  CA   C    109.63  3.000
 728  H12  CA   N    111.51  3.000
 728  H11  CA   N    111.53  3.000
 728  C    CA   N    109.34  3.000
 728  NAP  C    O    122.29  3.000
 728  O    C    CA   121.57  3.000
 728  NAP  C    CA   116.13  3.000
 728  CAT  NAP  CAQ  112.61  3.000
 728  CAQ  NAP  C    126.10  3.000
 728  CAT  NAP  C    120.48  3.000
 728  H14  CAQ  H13  108.08  3.000
 728  H14  CAQ  CAR  112.37  3.000
 728  H13  CAQ  CAR  111.18  3.000
 728  H14  CAQ  NAP  111.64  3.000
 728  H13  CAQ  NAP  110.78  3.000
 728  CAR  CAQ  NAP  102.78  3.000
 728  H16  CAR  H15  108.02  3.000
 728  H16  CAR  CAS  110.72  3.000
 728  H15  CAR  CAS  112.99  3.000
 728  H16  CAR  CAQ  110.10  3.000
 728  H15  CAR  CAQ  112.16  3.000
 728  CAS  CAR  CAQ  102.82  3.000
 728  H18  CAS  H17  107.81  3.000
 728  H18  CAS  CAT  111.60  3.000
 728  H17  CAS  CAT  109.87  3.000
 728  H18  CAS  CAR  113.55  3.000
 728  H17  CAS  CAR  110.03  3.000
 728  CAT  CAS  CAR  103.95  3.000
 728  H19  CAT  CAU  109.94  3.000
 728  H19  CAT  CAS  109.99  3.000
 728  CAU  CAT  CAS  111.78  3.000
 728  H19  CAT  NAP  108.36  3.000
 728  CAS  CAT  NAP  103.19  3.000
 728  CAU  CAT  NAP  113.35  3.000
 728  CAZ  CAU  CAX  116.94  3.000
 728  CAX  CAU  CAT  120.01  3.000
 728  CAZ  CAU  CAT  122.94  3.000
 728  H20  CAX  CAW  119.12  3.000
 728  H20  CAX  CAU  119.00  3.000
 728  CAW  CAX  CAU  121.88  3.000
 728  H21  CAW  CAV  120.31  3.000
 728  H21  CAW  CAX  119.78  3.000
 728  CAV  CAW  CAX  119.91  3.000
 728  H22  CAV  CAY  119.67  3.000
 728  H22  CAV  CAW  120.70  3.000
 728  CAY  CAV  CAW  119.63  3.000
 728  H23  CAY  CAZ  120.53  3.000
 728  H23  CAY  CAV  119.90  3.000
 728  CAZ  CAY  CAV  119.56  3.000
 728  BR   CAZ  CAY  117.00  3.000
 728  CAY  CAZ  CAU  122.06  3.000
 728  BR   CAZ  CAU  120.94  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
 728  CONST_01  CAD  CAE  CAF  CAA     0.00   0.0  0
 728  CONST_02  CAD  CAC  CAB  CAA     0.00   0.0  0
 728  CONST_03  CAE  CAF  CAA  CAB     0.00   0.0  0
 728  CONST_04  CAE  CAD  CAC  CAB     0.00   0.0  0
 728  CONST_05  CAF  CAE  CAD  CAC     0.00   0.0  0
 728  CONST_06  CAF  CAA  CAB  CAC     0.00   0.0  0
 728  CONST_07  CAV  CAY  CAZ  CAU     0.00   0.0  0
 728  CONST_08  CAV  CAW  CAX  CAU     0.00   0.0  0
 728  CONST_09  CAY  CAZ  CAU  CAX     0.00   0.0  0
 728  CONST_10  CAY  CAV  CAW  CAX     0.00   0.0  0
 728  CONST_11  CAZ  CAY  CAV  CAW     0.00   0.0  0
 728  CONST_12  CAZ  CAU  CAX  CAW     0.00   0.0  0
 728  CONST_13  CAY  CAZ  CAU  CAT   180.00   0.0  0
 728  CONST_14  CAW  CAX  CAU  CAT   180.00   0.0  0
 728  CONST_15  NAG  CAC  CAB  CAA   180.00   0.0  0
 728  CONST_16  CAH  CAF  CAA  CAB   180.00   0.0  0
 728  CONST_17  CAE  CAD  CAC  NAG   180.00   0.0  0
 728  CONST_18  CAH  CAF  CAE  CAD   180.00   0.0  0
 728  CONST_19  BR   CAZ  CAU  CAT     0.00   0.0  0
 728  CONST_20  BR   CAZ  CAU  CAX   180.00   0.0  0
 728  CONST_21  BR   CAZ  CAY  CAV   180.00   0.0  0
 728  CONST_22  H6   CAE  CAF  CAA   180.00   0.0  0
 728  CONST_23  H5   CAD  CAC  CAB   180.00   0.0  0
 728  CONST_24  H1   CAA  CAB  CAC   180.00   0.0  0
 728  CONST_25  H2   CAB  CAC  CAD   180.00   0.0  0
 728  CONST_26  H20  CAX  CAU  CAT     0.00   0.0  0
 728  CONST_27  H23  CAY  CAZ  CAU   180.00   0.0  0
 728  CONST_28  H21  CAW  CAX  CAU   180.00   0.0  0
 728  CONST_29  H22  CAV  CAW  CAX   180.00   0.0  0
 728  CONST_30  CAT  NAP  C    CA    180.00   0.0  0
 728  CONST_31  CAQ  NAP  C    CA      0.00   0.0  0
 728  CONST_32  CAT  NAP  C    O       0.00   0.0  0
 728  CONST_33  CAQ  NAP  C    O     180.00   0.0  0
 728  CONST_36  OAL  CAJ  NAI  CAH     0.00   0.0  0
 728  CONST_37  CA   N    CAJ  OAL     0.00   0.0  0
 728  CONST_38  N    CAJ  NAI  CAH   180.00   0.0  0
 728  CONST_39  CA   N    CAJ  NAI   180.00   0.0  0
 728  CONST_40  H10  N    CAJ  OAL   180.00   0.0  0
 728  CONST_41  H9   NAI  CAJ  OAL   180.00   0.0  0
 728  Var_01    CAS  CAR  CAQ  NAP    34.77  30.0  1
 728  Var_02    CAT  CAS  CAR  CAQ   -37.80  30.0  1
 728  Var_03    CAT  NAP  CAQ  CAR   -19.53  30.0  1
 728  Var_04    NAI  CAH  CAF  CAA  -113.28  30.0  2
 728  Var_05    CAJ  NAI  CAH  CAF  -165.35  30.0  3
 728  Var_06    NAP  C    CA   N     170.79  30.0  3
 728  Var_07    C    CA   N    CAJ   169.52  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
 728  chir_01  CAT  CAU  CAS  NAP  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
 728  plan-1  CAA  0.020
 728  plan-1  CAB  0.020
 728  plan-1  CAC  0.020
 728  plan-1  NAG  0.020
 728  plan-1  CAD  0.020
 728  plan-1  CAE  0.020
 728  plan-1  CAF  0.020
 728  plan-1  CAH  0.020
 728  plan-1  H1   0.020
 728  plan-1  H2   0.020
 728  plan-1  H5   0.020
 728  plan-1  H6   0.020
 728  plan-2  CAT  0.020
 728  plan-2  CAU  0.020
 728  plan-2  CAX  0.020
 728  plan-2  CAW  0.020
 728  plan-2  CAV  0.020
 728  plan-2  CAY  0.020
 728  plan-2  CAZ  0.020
 728  plan-2  BR   0.020
 728  plan-2  H20  0.020
 728  plan-2  H21  0.020
 728  plan-2  H22  0.020
 728  plan-2  H23  0.020
 728  plan-3  CAH  0.020
 728  plan-3  NAI  0.020
 728  plan-3  CAJ  0.020
 728  plan-3  OAL  0.020
 728  plan-3  N    0.020
 728  plan-3  CA   0.020
 728  plan-3  H9   0.020
 728  plan-3  H10  0.020
 728  plan-4  CA   0.020
 728  plan-4  C    0.020
 728  plan-4  O    0.020
 728  plan-4  NAP  0.020
 728  plan-4  CAQ  0.020
 728  plan-4  CAT  0.020
 728  plan-5  CAC  0.020
 728  plan-5  NAG  0.020
 728  plan-5  H3   0.020
 728  plan-5  H4   0.020

