# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:42:56 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-(4-aminobenzyl)-3-{2-[(2R)-2-(2,5-dimethoxyphenyl)pyrrolidin-1-yl]-2-oxoethyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(c1)[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
 67Z  67Z  1-(4-aminobenzyl)-3-{2-[(2R)-2-(2,5-dimethoxyphenyl)pyrrolidin-1-yl]-2-oxoethyl}urea  ligand  58  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 GRAND
;

data_comp_67Z
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
 67Z  CAB  C  CH3   0  -0.433   5.6722  -1.1431   3.2834
 67Z  OAU  O  O2    0  -0.475   4.9544  -0.3965   2.3255
 67Z  CBA  C  CR6   0   0.328   4.6043  -1.0018   1.1662
 67Z  CAK  C  CR16  0  -0.370   4.9400  -2.3061   0.8361
 67Z  CAJ  C  CR16  0  -0.384   4.5569  -2.8567  -0.3854
 67Z  CAZ  C  CR6   0   0.374   3.8332  -2.0936  -1.2886
 67Z  OAT  O  O2    0  -0.479   3.4140  -2.5253  -2.5003
 67Z  CAA  C  CH3   0  -0.435   3.7383  -3.8444  -2.8825
 67Z  CAL  C  CR16  0  -0.387   3.4958  -0.7818  -0.9507
 67Z  CBB  C  CR6   0   0.054   3.8613  -0.2286   0.2610
 67Z  CBC  C  CH1   0  -0.084   3.5399   1.2079   0.5943
 67Z  CAP  C  CH2   0  -0.467   4.6554   2.1659   0.1442
 67Z  CAM  C  CH2   0  -0.468   3.9197   3.4500  -0.2123
 67Z  CAQ  C  CH2   0  -0.286   2.6447   2.9344  -0.8641
 67Z  NBD  N  NT    0  -0.492   2.3601   1.7233  -0.0989
 67Z  C    C  C     0   0.526   1.1436   1.2201   0.1515
 67Z  O    O  O     0  -0.490   0.9627   0.2897   0.9261
 67Z  CA   C  CH2   0  -0.364  -0.0123   1.8675  -0.5930
 67Z  N    N  NH1   0  -0.695  -1.2021   1.0983  -0.3799
 67Z  CAV  C  C     0   0.748  -2.3873   1.4678  -0.9247
 67Z  OAD  O  O     0  -0.553  -2.4865   2.4223  -1.6910
 67Z  NAS  N  NH1   0  -0.675  -3.4536   0.7105  -0.5490
 67Z  CAO  C  CH2   0  -0.318  -4.7389   0.8421  -1.2075
 67Z  CAY  C  CR6   0   0.039  -5.8113   0.1625  -0.4043
 67Z  CAH  C  CR16  0  -0.279  -6.2870   0.7249   0.7792
 67Z  CAF  C  CR16  0  -0.313  -7.2623   0.1011   1.5358
 67Z  CAX  C  CR6   0   0.291  -7.8024  -1.1283   1.1327
 67Z  NAC  N  NH2   0  -0.859  -8.8154  -1.7265   1.8521
 67Z  CAG  C  CR16  0  -0.314  -7.3229  -1.6987  -0.0507
 67Z  CAI  C  CR16  0  -0.294  -6.3456  -1.0592  -0.7981
 67Z  H1   H  HCH3  0   0.258   5.8259  -0.4874   4.1371
 67Z  H2   H  HCH3  0   0.225   5.1179  -2.0255   3.6142
 67Z  H3   H  HCH3  0   0.224   6.6478  -1.4630   2.9071
 67Z  H4   H  HCR6  0   0.280   5.5092  -2.9259   1.5156
 67Z  H5   H  HCR6  0   0.277   4.8420  -3.8776  -0.5988
 67Z  H6   H  HCH3  0   0.257   3.3179  -3.9948  -3.8741
 67Z  H7   H  HCH3  0   0.224   4.8194  -4.0035  -2.9324
 67Z  H8   H  HCH3  0   0.224   3.3076  -4.5862  -2.2037
 67Z  H9   H  HCR6  0   0.251   2.9273  -0.1930  -1.6615
 67Z  H10  H  HCH1  0   0.264   3.3818   1.3060   1.6710
 67Z  H11  H  HCH2  0   0.262   5.4100   2.2920   0.9192
 67Z  H12  H  HCH2  0   0.242   5.1542   1.7649  -0.7410
 67Z  H13  H  HCH2  0   0.243   3.6734   4.0175   0.6871
 67Z  H14  H  HCH2  0   0.256   4.4897   4.0981  -0.8765
 67Z  H15  H  HCH2  0   0.264   1.8279   3.6514  -0.7984
 67Z  H16  H  HCH2  0   0.248   2.8050   2.7000  -1.9207
 67Z  H17  H  HCH2  0   0.268  -0.1247   2.8998  -0.2380
 67Z  H18  H  HCH2  0   0.269   0.2311   1.9338  -1.6577
 67Z  H19  H  HNH1  0   0.391  -1.1573   0.3853   0.3315
 67Z  H20  H  HNH1  0   0.388  -3.2770  -0.1696  -0.0902
 67Z  H21  H  HCH2  0   0.247  -4.9642   1.9036  -1.3141
 67Z  H22  H  HCH2  0   0.235  -4.7149   0.4215  -2.2189
 67Z  H23  H  HCR6  0   0.246  -5.8899   1.6761   1.1154
 67Z  H24  H  HCR6  0   0.254  -7.6161   0.5688   2.4476
 67Z  H25  H  HNH2  0   0.378  -8.8602  -1.4834   2.8286
 67Z  H26  H  HNH2  0   0.378  -8.9214  -2.7184   1.7121
 67Z  H27  H  HCR6  0   0.253  -7.7197  -2.6503  -0.3849
 67Z  H28  H  HCR6  0   0.246  -5.9944  -1.5288  -1.7103

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
 67Z  CAB  OAU  single    1.411  0.020  1.411
 67Z  OAU  CBA  single    1.354  0.020  1.354
 67Z  CAK  CBA  aromatic  1.387  0.020  1.387
 67Z  CAK  CAJ  aromatic  1.394  0.020  1.394
 67Z  CBA  CBB  aromatic  1.403  0.020  1.403
 67Z  CAJ  CAZ  aromatic  1.386  0.020  1.386
 67Z  CBB  CBC  single    1.509  0.020  1.509
 67Z  CBB  CAL  aromatic  1.381  0.020  1.381
 67Z  CBC  CAP  single    1.538  0.020  1.538
 67Z  CBC  NBD  single    1.462  0.020  1.462
 67Z  CAZ  CAL  aromatic  1.396  0.020  1.396
 67Z  CAZ  OAT  single    1.353  0.020  1.353
 67Z  CAP  CAM  single    1.522  0.020  1.522
 67Z  OAD  CAV  double    1.228  0.020  1.228
 67Z  CAA  OAT  single    1.411  0.020  1.411
 67Z  CA   N    single    1.433  0.020  1.433
 67Z  CA   C    single    1.520  0.020  1.520
 67Z  CAV  N    single    1.356  0.020  1.356
 67Z  CAV  NAS  single    1.361  0.020  1.361
 67Z  NBD  C    single    1.340  0.020  1.340
 67Z  NBD  CAQ  single    1.461  0.020  1.461
 67Z  CAO  NAS  single    1.450  0.020  1.450
 67Z  CAO  CAY  single    1.502  0.020  1.502
 67Z  CAM  CAQ  single    1.522  0.020  1.522
 67Z  C    O    double    1.224  0.020  1.224
 67Z  CAY  CAH  aromatic  1.394  0.020  1.394
 67Z  CAY  CAI  aromatic  1.390  0.020  1.390
 67Z  CAH  CAF  aromatic  1.383  0.020  1.383
 67Z  CAI  CAG  aromatic  1.387  0.020  1.387
 67Z  CAF  CAX  aromatic  1.402  0.020  1.402
 67Z  CAG  CAX  aromatic  1.398  0.020  1.398
 67Z  CAX  NAC  single    1.379  0.020  1.379
 67Z  CAB  H1   single    0.970  0.020  1.090
 67Z  CAB  H2   single    0.970  0.020  1.090
 67Z  CAB  H3   single    0.970  0.020  1.090
 67Z  CAK  H4   single    0.930  0.020  1.080
 67Z  CAJ  H5   single    0.930  0.020  1.080
 67Z  CAA  H6   single    0.970  0.020  1.090
 67Z  CAA  H7   single    0.970  0.020  1.090
 67Z  CAA  H8   single    0.970  0.020  1.090
 67Z  CAL  H9   single    0.930  0.020  1.080
 67Z  CBC  H10  single    0.970  0.020  1.090
 67Z  CAP  H11  single    0.970  0.020  1.090
 67Z  CAP  H12  single    0.970  0.020  1.090
 67Z  CAM  H13  single    0.970  0.020  1.090
 67Z  CAM  H14  single    0.970  0.020  1.090
 67Z  CAQ  H15  single    0.970  0.020  1.090
 67Z  CAQ  H16  single    0.970  0.020  1.090
 67Z  CA   H17  single    0.970  0.020  1.090
 67Z  CA   H18  single    0.970  0.020  1.090
 67Z  N    H19  single    0.860  0.020  1.020
 67Z  NAS  H20  single    0.890  0.020  1.040
 67Z  CAO  H21  single    0.970  0.020  1.090
 67Z  CAO  H22  single    0.970  0.020  1.090
 67Z  CAH  H23  single    0.930  0.020  1.080
 67Z  CAF  H24  single    0.930  0.020  1.080
 67Z  NAC  H25  single    0.890  0.020  1.040
 67Z  NAC  H26  single    0.890  0.020  1.040
 67Z  CAG  H27  single    0.930  0.020  1.080
 67Z  CAI  H28  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
 67Z  H3   CAB  H2   108.68  3.000
 67Z  H3   CAB  H1   108.69  3.000
 67Z  H2   CAB  H1   108.71  3.000
 67Z  H3   CAB  OAU  112.04  3.000
 67Z  H2   CAB  OAU  112.00  3.000
 67Z  H1   CAB  OAU  106.61  3.000
 67Z  CBA  OAU  CAB  118.45  3.000
 67Z  CBB  CBA  CAK  119.53  3.000
 67Z  CBB  CBA  OAU  116.29  3.000
 67Z  CAK  CBA  OAU  124.18  3.000
 67Z  H4   CAK  CAJ  117.96  3.000
 67Z  H4   CAK  CBA  121.12  3.000
 67Z  CAJ  CAK  CBA  120.91  3.000
 67Z  H5   CAJ  CAZ  121.92  3.000
 67Z  H5   CAJ  CAK  118.27  3.000
 67Z  CAZ  CAJ  CAK  119.81  3.000
 67Z  CAL  CAZ  OAT  116.21  3.000
 67Z  OAT  CAZ  CAJ  124.73  3.000
 67Z  CAL  CAZ  CAJ  119.06  3.000
 67Z  CAA  OAT  CAZ  118.01  3.000
 67Z  H8   CAA  H7   108.59  3.000
 67Z  H8   CAA  H6   108.65  3.000
 67Z  H7   CAA  H6   108.69  3.000
 67Z  H8   CAA  OAT  112.05  3.000
 67Z  H7   CAA  OAT  112.05  3.000
 67Z  H6   CAA  OAT  106.70  3.000
 67Z  H9   CAL  CBB  119.77  3.000
 67Z  H9   CAL  CAZ  118.58  3.000
 67Z  CBB  CAL  CAZ  121.65  3.000
 67Z  CBC  CBB  CAL  121.24  3.000
 67Z  CAL  CBB  CBA  119.03  3.000
 67Z  CBC  CBB  CBA  119.65  3.000
 67Z  H10  CBC  NBD  108.59  3.000
 67Z  H10  CBC  CAP  109.72  3.000
 67Z  NBD  CBC  CAP  103.12  3.000
 67Z  H10  CBC  CBB  109.50  3.000
 67Z  NBD  CBC  CBB  113.74  3.000
 67Z  CAP  CBC  CBB  111.96  3.000
 67Z  H12  CAP  H11  107.62  3.000
 67Z  H12  CAP  CAM  109.91  3.000
 67Z  H11  CAP  CAM  113.82  3.000
 67Z  H12  CAP  CBC  109.86  3.000
 67Z  H11  CAP  CBC  111.50  3.000
 67Z  CAM  CAP  CBC  104.09  3.000
 67Z  H14  CAM  H13  108.13  3.000
 67Z  H14  CAM  CAQ  112.26  3.000
 67Z  H13  CAM  CAQ  109.87  3.000
 67Z  H14  CAM  CAP  113.07  3.000
 67Z  H13  CAM  CAP  110.77  3.000
 67Z  CAQ  CAM  CAP  102.67  3.000
 67Z  H16  CAQ  H15  108.02  3.000
 67Z  H16  CAQ  NBD  110.91  3.000
 67Z  H15  CAQ  NBD  111.61  3.000
 67Z  H16  CAQ  CAM  111.31  3.000
 67Z  H15  CAQ  CAM  112.30  3.000
 67Z  NBD  CAQ  CAM  102.69  3.000
 67Z  C    NBD  CAQ  125.88  3.000
 67Z  CAQ  NBD  CBC  112.55  3.000
 67Z  C    NBD  CBC  120.77  3.000
 67Z  CA   C    O    121.43  3.000
 67Z  O    C    NBD  122.53  3.000
 67Z  CA   C    NBD  116.04  3.000
 67Z  H18  CA   H17  106.30  3.000
 67Z  H18  CA   N    111.23  3.000
 67Z  H17  CA   N    111.83  3.000
 67Z  H18  CA   C    109.47  3.000
 67Z  H17  CA   C    108.67  3.000
 67Z  N    CA   C    109.27  3.000
 67Z  H19  N    CAV  121.00  3.000
 67Z  H19  N    CA   116.60  3.000
 67Z  CAV  N    CA   121.32  3.000
 67Z  NAS  CAV  OAD  122.79  3.000
 67Z  NAS  CAV  N    114.99  3.000
 67Z  OAD  CAV  N    122.22  3.000
 67Z  H20  NAS  CAO  116.18  3.000
 67Z  H20  NAS  CAV  118.31  3.000
 67Z  CAO  NAS  CAV  121.24  3.000
 67Z  H22  CAO  H21  106.74  3.000
 67Z  H22  CAO  CAY  109.61  3.000
 67Z  H21  CAO  CAY  110.19  3.000
 67Z  H22  CAO  NAS  111.40  3.000
 67Z  H21  CAO  NAS  108.41  3.000
 67Z  CAY  CAO  NAS  110.42  3.000
 67Z  CAI  CAY  CAH  117.64  3.000
 67Z  CAI  CAY  CAO  121.35  3.000
 67Z  CAH  CAY  CAO  121.00  3.000
 67Z  H23  CAH  CAF  118.97  3.000
 67Z  H23  CAH  CAY  119.49  3.000
 67Z  CAF  CAH  CAY  121.54  3.000
 67Z  H24  CAF  CAX  119.63  3.000
 67Z  H24  CAF  CAH  119.71  3.000
 67Z  CAX  CAF  CAH  120.66  3.000
 67Z  CAG  CAX  NAC  121.09  3.000
 67Z  NAC  CAX  CAF  120.89  3.000
 67Z  CAG  CAX  CAF  117.96  3.000
 67Z  H26  NAC  H25  111.57  3.000
 67Z  H26  NAC  CAX  115.59  3.000
 67Z  H25  NAC  CAX  115.71  3.000
 67Z  H27  CAG  CAI  119.78  3.000
 67Z  H27  CAG  CAX  119.58  3.000
 67Z  CAI  CAG  CAX  120.64  3.000
 67Z  H28  CAI  CAG  118.81  3.000
 67Z  H28  CAI  CAY  119.63  3.000
 67Z  CAG  CAI  CAY  121.56  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
 67Z  CONST_01  CAZ  CAJ  CAK  CBA     0.00   0.0  0
 67Z  CONST_02  CAZ  CAL  CBB  CBA     0.00   0.0  0
 67Z  CONST_03  CAL  CBB  CBA  CAK     0.00   0.0  0
 67Z  CONST_04  CAL  CAZ  CAJ  CAK     0.00   0.0  0
 67Z  CONST_05  CBB  CBA  CAK  CAJ     0.00   0.0  0
 67Z  CONST_06  CBB  CAL  CAZ  CAJ     0.00   0.0  0
 67Z  CONST_07  CAX  CAF  CAH  CAY     0.00   0.0  0
 67Z  CONST_08  CAX  CAG  CAI  CAY     0.00   0.0  0
 67Z  CONST_09  CAG  CAI  CAY  CAH     0.00   0.0  0
 67Z  CONST_10  CAG  CAX  CAF  CAH     0.00   0.0  0
 67Z  CONST_11  CAI  CAY  CAH  CAF     0.00   0.0  0
 67Z  CONST_12  CAI  CAG  CAX  CAF     0.00   0.0  0
 67Z  CONST_13  CBC  CBB  CBA  CAK   180.00   0.0  0
 67Z  CONST_14  CBC  CBB  CAL  CAZ   180.00   0.0  0
 67Z  CONST_15  CAJ  CAK  CBA  OAU   180.00   0.0  0
 67Z  CONST_16  CBC  CBB  CBA  OAU     0.00   0.0  0
 67Z  CONST_17  CAL  CBB  CBA  OAU   180.00   0.0  0
 67Z  CONST_18  OAT  CAZ  CAJ  CAK   180.00   0.0  0
 67Z  CONST_19  CBB  CAL  CAZ  OAT   180.00   0.0  0
 67Z  CONST_20  CAF  CAH  CAY  CAO   180.00   0.0  0
 67Z  CONST_21  CAG  CAI  CAY  CAO   180.00   0.0  0
 67Z  CONST_22  NAC  CAX  CAF  CAH   180.00   0.0  0
 67Z  CONST_23  CAI  CAG  CAX  NAC   180.00   0.0  0
 67Z  CONST_24  H5   CAJ  CAK  CBA   180.00   0.0  0
 67Z  CONST_25  H9   CAL  CBB  CBA   180.00   0.0  0
 67Z  CONST_26  H4   CAK  CAJ  CAZ   180.00   0.0  0
 67Z  CONST_27  H24  CAF  CAH  CAY   180.00   0.0  0
 67Z  CONST_28  H27  CAG  CAI  CAY   180.00   0.0  0
 67Z  CONST_29  H28  CAI  CAY  CAH   180.00   0.0  0
 67Z  CONST_30  H23  CAH  CAF  CAX   180.00   0.0  0
 67Z  CONST_31  CA   C    NBD  CBC   180.00   0.0  0
 67Z  CONST_32  O    C    NBD  CBC     0.00   0.0  0
 67Z  CONST_33  CA   C    NBD  CAQ     0.00   0.0  0
 67Z  CONST_34  O    C    NBD  CAQ   180.00   0.0  0
 67Z  CONST_37  OAD  CAV  N    CA      0.00   0.0  0
 67Z  CONST_38  CAO  NAS  CAV  OAD     0.00   0.0  0
 67Z  CONST_39  NAS  CAV  N    CA    180.00   0.0  0
 67Z  CONST_40  CAO  NAS  CAV  N     180.00   0.0  0
 67Z  CONST_41  H19  N    CAV  OAD   180.00   0.0  0
 67Z  CONST_42  H20  NAS  CAV  OAD   180.00   0.0  0
 67Z  Var_01    CAQ  CAM  CAP  CBC   -37.88  30.0  1
 67Z  Var_02    CAM  CAQ  NBD  CBC   -20.52  30.0  1
 67Z  Var_03    NBD  CAQ  CAM  CAP    35.36  30.0  1
 67Z  Var_04    CAK  CBA  OAU  CAB    -1.99  30.0  2
 67Z  Var_05    CAL  CAZ  OAT  CAA   179.79  30.0  2
 67Z  Var_06    CAH  CAY  CAO  NAS    73.65  30.0  2
 67Z  Var_07    N    CA   C    NBD   171.29  30.0  2
 67Z  Var_08    CAY  CAO  NAS  CAV  -166.10  30.0  1
 67Z  Var_09    H1   CAB  OAU  CBA  -178.49  30.0  3
 67Z  Var_10    H6   CAA  OAT  CAZ  -179.95  30.0  3
 67Z  Var_11    CAV  N    CA   C     179.29  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
 67Z  chir_01  CBC  CBB  CAP  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
 67Z  plan-1  OAU  0.020
 67Z  plan-1  CBA  0.020
 67Z  plan-1  CAK  0.020
 67Z  plan-1  CAJ  0.020
 67Z  plan-1  CAZ  0.020
 67Z  plan-1  OAT  0.020
 67Z  plan-1  CAL  0.020
 67Z  plan-1  CBB  0.020
 67Z  plan-1  CBC  0.020
 67Z  plan-1  H4   0.020
 67Z  plan-1  H5   0.020
 67Z  plan-1  H9   0.020
 67Z  plan-2  CAO  0.020
 67Z  plan-2  CAY  0.020
 67Z  plan-2  CAH  0.020
 67Z  plan-2  CAF  0.020
 67Z  plan-2  CAX  0.020
 67Z  plan-2  NAC  0.020
 67Z  plan-2  CAG  0.020
 67Z  plan-2  CAI  0.020
 67Z  plan-2  H23  0.020
 67Z  plan-2  H24  0.020
 67Z  plan-2  H27  0.020
 67Z  plan-2  H28  0.020
 67Z  plan-3  CA   0.020
 67Z  plan-3  N    0.020
 67Z  plan-3  CAV  0.020
 67Z  plan-3  OAD  0.020
 67Z  plan-3  NAS  0.020
 67Z  plan-3  CAO  0.020
 67Z  plan-3  H19  0.020
 67Z  plan-3  H20  0.020
 67Z  plan-4  CAX  0.020
 67Z  plan-4  NAC  0.020
 67Z  plan-4  H25  0.020
 67Z  plan-4  H26  0.020
 67Z  plan-5  CBC  0.020
 67Z  plan-5  CAQ  0.020
 67Z  plan-5  NBD  0.020
 67Z  plan-5  C    0.020
 67Z  plan-5  O    0.020
 67Z  plan-5  CA   0.020

