# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:58:39 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-(4-aminobenzyl)-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(CNC(=O)NCC(=O)N2CCCC2)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
 53Z  53Z  1-(4-aminobenzyl)-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea  ligand  40  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_53Z
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
 53Z  CAJ  C  CH2   0  -0.279  -5.2022   0.8691  -0.2587
 53Z  CAH  C  CH2   0  -0.472  -6.6729   0.6283   0.0572
 53Z  CAI  C  CH2   0  -0.487  -6.8551  -0.8522  -0.2631
 53Z  CAK  C  CH2   0  -0.259  -5.5581  -1.4819   0.2328
 53Z  NAT  N  NT    0  -0.472  -4.5798  -0.4098   0.0723
 53Z  C    C  C     0   0.525  -3.2697  -0.6296   0.2044
 53Z  O    O  O     0  -0.507  -2.8058  -1.7296   0.4881
 53Z  CA   C  CH2   0  -0.359  -2.3743   0.5783  -0.0173
 53Z  N    N  NH1   0  -0.696  -1.0016   0.1792   0.0696
 53Z  CAP  C  C     0   0.748   0.0009   1.0899   0.0268
 53Z  OAB  O  O     0  -0.554  -0.2080   2.2834  -0.1758
 53Z  NAO  N  NH1   0  -0.676   1.2511   0.5788   0.1902
 53Z  CAM  C  CH2   0  -0.316   2.4059   1.4419   0.3434
 53Z  CAS  C  CR6   0   0.038   3.6739   0.6518   0.1820
 53Z  CAF  C  CR16  0  -0.294   4.4744   0.3403   1.2750
 53Z  CAD  C  CR16  0  -0.314   5.6381  -0.4009   1.1361
 53Z  CAR  C  CR6   0   0.292   6.0403  -0.8661  -0.1199
 53Z  NAA  N  NH2   0  -0.859   7.1647  -1.6508  -0.2629
 53Z  CAE  C  CR16  0  -0.312   5.2353  -0.5542  -1.2246
 53Z  CAG  C  CR16  0  -0.279   4.0777   0.1867  -1.0685
 53Z  H1   H  HCH2  0   0.247  -5.0603   1.1064  -1.3174
 53Z  H2   H  HCH2  0   0.258  -4.7789   1.6857   0.3273
 53Z  H3   H  HCH2  0   0.242  -6.8629   0.8146   1.1161
 53Z  H4   H  HCH2  0   0.255  -7.3269   1.2802  -0.5199
 53Z  H5   H  HCH2  0   0.255  -7.7312  -1.2902   0.2127
 53Z  H6   H  HCH2  0   0.241  -6.9550  -0.9944  -1.3413
 53Z  H7   H  HCH2  0   0.240  -5.6312  -1.7758   1.2834
 53Z  H8   H  HCH2  0   0.249  -5.2689  -2.3639  -0.3389
 53Z  H9   H  HCH2  0   0.266  -2.6072   1.0209  -0.9917
 53Z  H10  H  HCH2  0   0.268  -2.6180   1.3410   0.7313
 53Z  H11  H  HNH1  0   0.391  -0.8219  -0.7879   0.2914
 53Z  H12  H  HNH1  0   0.388   1.3426  -0.3569   0.5532
 53Z  H13  H  HCH2  0   0.247   2.3536   2.2273  -0.4117
 53Z  H14  H  HCH2  0   0.235   2.4069   1.9417   1.3188
 53Z  H15  H  HCR6  0   0.246   4.1879   0.6846   2.2623
 53Z  H16  H  HCR6  0   0.253   6.2410  -0.6219   2.0092
 53Z  H17  H  HNH2  0   0.378   7.8600  -1.5540   0.4596
 53Z  H18  H  HNH2  0   0.378   7.5801  -1.6564  -1.1806
 53Z  H19  H  HCR6  0   0.254   5.5271  -0.8943  -2.2115
 53Z  H20  H  HCR6  0   0.246   3.4794   0.4137  -1.9438

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
 53Z  OAB  CAP  double    1.228  0.020  1.228
 53Z  CAK  CAI  single    1.525  0.020  1.525
 53Z  CAK  NAT  single    1.460  0.020  1.460
 53Z  CAI  CAH  single    1.526  0.020  1.526
 53Z  CA   N    single    1.432  0.020  1.432
 53Z  CA   C    single    1.520  0.020  1.520
 53Z  CAP  N    single    1.355  0.020  1.355
 53Z  CAP  NAO  single    1.361  0.020  1.361
 53Z  CAM  NAO  single    1.450  0.020  1.450
 53Z  CAM  CAS  single    1.503  0.020  1.503
 53Z  NAT  C    single    1.335  0.020  1.335
 53Z  NAT  CAJ  single    1.460  0.020  1.460
 53Z  CAH  CAJ  single    1.523  0.020  1.523
 53Z  C    O    double    1.227  0.020  1.227
 53Z  CAS  CAG  aromatic  1.394  0.020  1.394
 53Z  CAS  CAF  aromatic  1.390  0.020  1.390
 53Z  CAG  CAE  aromatic  1.383  0.020  1.383
 53Z  CAF  CAD  aromatic  1.387  0.020  1.387
 53Z  CAE  CAR  aromatic  1.402  0.020  1.402
 53Z  CAD  CAR  aromatic  1.398  0.020  1.398
 53Z  CAR  NAA  single    1.379  0.020  1.379
 53Z  CAJ  H1   single    0.970  0.020  1.090
 53Z  CAJ  H2   single    0.970  0.020  1.090
 53Z  CAH  H3   single    0.970  0.020  1.090
 53Z  CAH  H4   single    0.970  0.020  1.090
 53Z  CAI  H5   single    0.970  0.020  1.090
 53Z  CAI  H6   single    0.970  0.020  1.090
 53Z  CAK  H7   single    0.970  0.020  1.090
 53Z  CAK  H8   single    0.970  0.020  1.090
 53Z  CA   H9   single    0.970  0.020  1.090
 53Z  CA   H10  single    0.970  0.020  1.090
 53Z  N    H11  single    0.860  0.020  1.020
 53Z  NAO  H12  single    0.890  0.020  1.040
 53Z  CAM  H13  single    0.970  0.020  1.090
 53Z  CAM  H14  single    0.970  0.020  1.090
 53Z  CAF  H15  single    0.930  0.020  1.080
 53Z  CAD  H16  single    0.930  0.020  1.080
 53Z  NAA  H17  single    0.890  0.020  1.040
 53Z  NAA  H18  single    0.890  0.020  1.040
 53Z  CAE  H19  single    0.930  0.020  1.080
 53Z  CAG  H20  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
 53Z  H2   CAJ  H1   107.89  3.000
 53Z  H2   CAJ  NAT  111.62  3.000
 53Z  H1   CAJ  NAT  110.73  3.000
 53Z  H2   CAJ  CAH  112.44  3.000
 53Z  H1   CAJ  CAH  111.11  3.000
 53Z  NAT  CAJ  CAH  103.07  3.000
 53Z  H4   CAH  H3   107.90  3.000
 53Z  H4   CAH  CAI  113.45  3.000
 53Z  H3   CAH  CAI  110.39  3.000
 53Z  H4   CAH  CAJ  112.05  3.000
 53Z  H3   CAH  CAJ  110.01  3.000
 53Z  CAI  CAH  CAJ  103.01  3.000
 53Z  H6   CAI  H5   107.78  3.000
 53Z  H6   CAI  CAK  110.19  3.000
 53Z  H5   CAI  CAK  112.09  3.000
 53Z  H6   CAI  CAH  110.16  3.000
 53Z  H5   CAI  CAH  113.25  3.000
 53Z  CAK  CAI  CAH  103.35  3.000
 53Z  H8   CAK  H7   107.70  3.000
 53Z  H8   CAK  NAT  111.02  3.000
 53Z  H7   CAK  NAT  110.35  3.000
 53Z  H8   CAK  CAI  112.91  3.000
 53Z  H7   CAK  CAI  111.51  3.000
 53Z  NAT  CAK  CAI  103.36  3.000
 53Z  C    NAT  CAK  121.72  3.000
 53Z  C    NAT  CAJ  125.80  3.000
 53Z  CAK  NAT  CAJ  112.47  3.000
 53Z  CA   C    O    121.57  3.000
 53Z  O    C    NAT  122.78  3.000
 53Z  CA   C    NAT  115.65  3.000
 53Z  H10  CA   H9   106.21  3.000
 53Z  H10  CA   N    111.44  3.000
 53Z  H9   CA   N    111.74  3.000
 53Z  H10  CA   C    108.81  3.000
 53Z  H9   CA   C    109.01  3.000
 53Z  N    CA   C    109.53  3.000
 53Z  H11  N    CAP  121.31  3.000
 53Z  H11  N    CA   116.84  3.000
 53Z  CAP  N    CA   121.32  3.000
 53Z  NAO  CAP  OAB  122.75  3.000
 53Z  NAO  CAP  N    115.06  3.000
 53Z  OAB  CAP  N    122.17  3.000
 53Z  H12  NAO  CAM  116.25  3.000
 53Z  H12  NAO  CAP  118.39  3.000
 53Z  CAM  NAO  CAP  121.40  3.000
 53Z  H14  CAM  H13  106.72  3.000
 53Z  H14  CAM  CAS  109.55  3.000
 53Z  H13  CAM  CAS  110.16  3.000
 53Z  H14  CAM  NAO  111.49  3.000
 53Z  H13  CAM  NAO  108.50  3.000
 53Z  CAS  CAM  NAO  110.35  3.000
 53Z  CAG  CAS  CAF  117.63  3.000
 53Z  CAF  CAS  CAM  121.28  3.000
 53Z  CAG  CAS  CAM  121.08  3.000
 53Z  H15  CAF  CAD  118.86  3.000
 53Z  H15  CAF  CAS  119.52  3.000
 53Z  CAD  CAF  CAS  121.62  3.000
 53Z  H16  CAD  CAR  119.72  3.000
 53Z  H16  CAD  CAF  119.67  3.000
 53Z  CAR  CAD  CAF  120.61  3.000
 53Z  CAE  CAR  NAA  120.88  3.000
 53Z  NAA  CAR  CAD  121.14  3.000
 53Z  CAE  CAR  CAD  117.94  3.000
 53Z  H18  NAA  H17  111.68  3.000
 53Z  H18  NAA  CAR  115.72  3.000
 53Z  H17  NAA  CAR  115.71  3.000
 53Z  H19  CAE  CAG  119.74  3.000
 53Z  H19  CAE  CAR  119.54  3.000
 53Z  CAG  CAE  CAR  120.72  3.000
 53Z  H20  CAG  CAE  118.88  3.000
 53Z  H20  CAG  CAS  119.63  3.000
 53Z  CAE  CAG  CAS  121.49  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
 53Z  CONST_01  CAR  CAE  CAG  CAS     0.00   0.0  0
 53Z  CONST_02  CAR  CAD  CAF  CAS     0.00   0.0  0
 53Z  CONST_03  CAE  CAG  CAS  CAF     0.00   0.0  0
 53Z  CONST_04  CAE  CAR  CAD  CAF     0.00   0.0  0
 53Z  CONST_05  CAG  CAS  CAF  CAD     0.00   0.0  0
 53Z  CONST_06  CAG  CAE  CAR  CAD     0.00   0.0  0
 53Z  CONST_07  CAE  CAG  CAS  CAM   180.00   0.0  0
 53Z  CONST_08  CAD  CAF  CAS  CAM   180.00   0.0  0
 53Z  CONST_09  NAA  CAR  CAD  CAF   180.00   0.0  0
 53Z  CONST_10  CAG  CAE  CAR  NAA   180.00   0.0  0
 53Z  CONST_11  H19  CAE  CAG  CAS   180.00   0.0  0
 53Z  CONST_12  H16  CAD  CAF  CAS   180.00   0.0  0
 53Z  CONST_13  H20  CAG  CAS  CAF   180.00   0.0  0
 53Z  CONST_14  H15  CAF  CAD  CAR   180.00   0.0  0
 53Z  CONST_15  CA   C    NAT  CAJ     0.00   0.0  0
 53Z  CONST_16  O    C    NAT  CAJ   180.00   0.0  0
 53Z  CONST_17  CA   C    NAT  CAK   180.00   0.0  0
 53Z  CONST_18  O    C    NAT  CAK     0.00   0.0  0
 53Z  CONST_21  OAB  CAP  N    CA      0.00   0.0  0
 53Z  CONST_22  CAM  NAO  CAP  OAB     0.00   0.0  0
 53Z  CONST_23  NAO  CAP  N    CA    180.00   0.0  0
 53Z  CONST_24  CAM  NAO  CAP  N     180.00   0.0  0
 53Z  CONST_25  H11  N    CAP  OAB   180.00   0.0  0
 53Z  CONST_26  H12  NAO  CAP  OAB   180.00   0.0  0
 53Z  Var_01    CAI  CAK  NAT  CAJ     9.66  30.0  1
 53Z  Var_02    CAK  CAI  CAH  CAJ    38.64  30.0  1
 53Z  Var_03    NAT  CAK  CAI  CAH   -29.65  30.0  1
 53Z  Var_04    CAK  NAT  CAJ  CAH    14.34  30.0  1
 53Z  Var_05    NAT  CAJ  CAH  CAI   -32.30  30.0  1
 53Z  Var_06    CAG  CAS  CAM  NAO    72.45  30.0  2
 53Z  Var_07    N    CA   C    NAT  -176.27  30.0  1
 53Z  Var_08    CAS  CAM  NAO  CAP  -166.71  30.0  2
 53Z  Var_09    CAP  N    CA   C    -174.07  30.0  3

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
 53Z  plan-1  CAM  0.020
 53Z  plan-1  CAS  0.020
 53Z  plan-1  CAF  0.020
 53Z  plan-1  CAD  0.020
 53Z  plan-1  CAR  0.020
 53Z  plan-1  NAA  0.020
 53Z  plan-1  CAE  0.020
 53Z  plan-1  CAG  0.020
 53Z  plan-1  H15  0.020
 53Z  plan-1  H16  0.020
 53Z  plan-1  H19  0.020
 53Z  plan-1  H20  0.020
 53Z  plan-2  CA   0.020
 53Z  plan-2  N    0.020
 53Z  plan-2  CAP  0.020
 53Z  plan-2  OAB  0.020
 53Z  plan-2  NAO  0.020
 53Z  plan-2  CAM  0.020
 53Z  plan-2  H11  0.020
 53Z  plan-2  H12  0.020
 53Z  plan-3  CAR  0.020
 53Z  plan-3  NAA  0.020
 53Z  plan-3  H17  0.020
 53Z  plan-3  H18  0.020
 53Z  plan-4  CAJ  0.020
 53Z  plan-4  CAK  0.020
 53Z  plan-4  NAT  0.020
 53Z  plan-4  C    0.020
 53Z  plan-4  O    0.020
 53Z  plan-4  CA   0.020

