# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:30:06 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-(4-aminobenzyl)-3-{2-[(2R)-2-(2-methoxyphenyl)pyrrolidin-1-yl]-2-oxoethyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1[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
 7B7  7B7  1-(4-aminobenzyl)-3-{2-[(2R)-2-(2-methoxyphenyl)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_7B7
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
 7B7  CAA  C  CH3   0  -0.435   5.8564   2.7062  -2.0936
 7B7  OAT  O  O2    0  -0.471   5.1660   1.6116  -1.5273
 7B7  CAY  C  CR6   0   0.351   4.8814   1.6309  -0.2086
 7B7  CAG  C  CR16  0  -0.383   5.2711   2.6555   0.6506
 7B7  CAE  C  CR16  0  -0.256   4.9564   2.5851   2.0025
 7B7  CAF  C  CR16  0  -0.272   4.2566   1.5001   2.5021
 7B7  CAH  C  CR16  0  -0.291   3.8665   0.4856   1.6357
 7B7  CAZ  C  CR6   0   0.034   4.1590   0.5337   0.2816
 7B7  CBA  C  CH1   0  -0.086   3.7828  -0.5939  -0.6493
 7B7  CAP  C  CH2   0  -0.469   4.8962  -1.6527  -0.7526
 7B7  CAM  C  CH2   0  -0.464   4.1522  -2.9742  -0.8936
 7B7  CAQ  C  CH2   0  -0.289   2.9422  -2.7766   0.0063
 7B7  NBB  N  NT    0  -0.489   2.6292  -1.3650  -0.1862
 7B7  C    C  C     0   0.526   1.4106  -0.8114  -0.1328
 7B7  O    O  O     0  -0.492   1.2074   0.3615  -0.4197
 7B7  CA   C  CH2   0  -0.363   0.2790  -1.7250   0.3101
 7B7  N    N  NH1   0  -0.696  -0.9133  -0.9498   0.4851
 7B7  CAU  C  C     0   0.746  -2.1106  -1.5439   0.7191
 7B7  OAC  O  O     0  -0.553  -2.2147  -2.7545   0.8986
 7B7  NAS  N  NH1   0  -0.676  -3.1727  -0.6970   0.7308
 7B7  CAO  C  CH2   0  -0.324  -4.5079  -1.1182   1.0938
 7B7  CAX  C  CR6   0   0.050  -5.5423  -0.2746   0.4004
 7B7  CAK  C  CR16  0  -0.279  -5.6599  -0.2799  -0.9890
 7B7  CAI  C  CR16  0  -0.311  -6.6000   0.4998  -1.6374
 7B7  CAW  C  CR6   0   0.288  -7.4675   1.3284  -0.9114
 7B7  NAB  N  NH2   0  -0.858  -8.4414   2.0672  -1.5516
 7B7  CAJ  C  CR16  0  -0.313  -7.3495   1.3392   0.4814
 7B7  CAL  C  CR16  0  -0.300  -6.4011   0.5507   1.1163
 7B7  H1   H  HCH3  0   0.227   6.8545   2.8278  -1.6643
 7B7  H2   H  HCH3  0   0.259   5.9568   2.4915  -3.1547
 7B7  H3   H  HCH3  0   0.228   5.3059   3.6434  -1.9753
 7B7  H4   H  HCR6  0   0.277   5.8203   3.5124   0.2848
 7B7  H5   H  HCR6  0   0.255   5.2672   3.3872   2.6595
 7B7  H6   H  HCR6  0   0.249   4.0116   1.4397   3.5541
 7B7  H7   H  HCR6  0   0.245   3.3178  -0.3619   2.0286
 7B7  H8   H  HCH1  0   0.263   3.5555  -0.1934  -1.6401
 7B7  H9   H  HCH2  0   0.261   5.5712  -1.4465  -1.5818
 7B7  H10  H  HCH2  0   0.242   5.4909  -1.6541   0.1631
 7B7  H11  H  HCH2  0   0.243   3.8259  -3.1287  -1.9240
 7B7  H12  H  HCH2  0   0.255   4.7513  -3.8341  -0.5971
 7B7  H13  H  HCH2  0   0.265   2.1085  -3.4174  -0.2763
 7B7  H14  H  HCH2  0   0.248   3.1876  -2.9806   1.0529
 7B7  H15  H  HCH2  0   0.269   0.1453  -2.5062  -0.4473
 7B7  H16  H  HCH2  0   0.266   0.5648  -2.2368   1.2341
 7B7  H17  H  HNH1  0   0.391  -0.8618   0.0208   0.2155
 7B7  H18  H  HNH1  0   0.389  -3.0020   0.2960   0.7165
 7B7  H19  H  HCH2  0   0.252  -4.6193  -2.1656   0.8121
 7B7  H20  H  HCH2  0   0.238  -4.6625  -1.0659   2.1773
 7B7  H21  H  HCR6  0   0.246  -5.0016  -0.9061  -1.5805
 7B7  H22  H  HCR6  0   0.254  -6.6696   0.4700  -2.7188
 7B7  H23  H  HNH2  0   0.377  -8.2471   2.2997  -2.5124
 7B7  H24  H  HNH2  0   0.377  -8.7831   2.8667  -1.0424
 7B7  H25  H  HCR6  0   0.253  -8.0020   1.9725   1.0708
 7B7  H26  H  HCR6  0   0.246  -6.3296   0.5859   2.1978

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
 7B7  CAA  OAT  single    1.413  0.020  1.413
 7B7  OAT  CAY  single    1.349  0.020  1.349
 7B7  CAG  CAY  aromatic  1.393  0.020  1.393
 7B7  CAG  CAE  aromatic  1.390  0.020  1.390
 7B7  CAY  CAZ  aromatic  1.402  0.020  1.402
 7B7  CAE  CAF  aromatic  1.384  0.020  1.384
 7B7  CAZ  CBA  single    1.510  0.020  1.510
 7B7  CAZ  CAH  aromatic  1.386  0.020  1.386
 7B7  CBA  CAP  single    1.540  0.020  1.540
 7B7  CBA  NBB  single    1.463  0.020  1.463
 7B7  CAP  CAM  single    1.523  0.020  1.523
 7B7  OAC  CAU  double    1.228  0.020  1.228
 7B7  CAF  CAH  aromatic  1.390  0.020  1.390
 7B7  CA   N    single    1.433  0.020  1.433
 7B7  CA   C    single    1.520  0.020  1.520
 7B7  CAU  N    single    1.357  0.020  1.357
 7B7  CAU  NAS  single    1.358  0.020  1.358
 7B7  NAS  CAO  single    1.446  0.020  1.446
 7B7  CAO  CAX  single    1.504  0.020  1.504
 7B7  NBB  C    single    1.340  0.020  1.340
 7B7  NBB  CAQ  single    1.459  0.020  1.459
 7B7  CAM  CAQ  single    1.521  0.020  1.521
 7B7  C    O    double    1.224  0.020  1.224
 7B7  CAX  CAK  aromatic  1.394  0.020  1.394
 7B7  CAX  CAL  aromatic  1.390  0.020  1.390
 7B7  CAK  CAI  aromatic  1.383  0.020  1.383
 7B7  CAL  CAJ  aromatic  1.387  0.020  1.387
 7B7  CAI  CAW  aromatic  1.402  0.020  1.402
 7B7  CAJ  CAW  aromatic  1.398  0.020  1.398
 7B7  CAW  NAB  single    1.380  0.020  1.380
 7B7  CAA  H1   single    0.970  0.020  1.090
 7B7  CAA  H2   single    0.970  0.020  1.090
 7B7  CAA  H3   single    0.970  0.020  1.090
 7B7  CAG  H4   single    0.930  0.020  1.080
 7B7  CAE  H5   single    0.930  0.020  1.080
 7B7  CAF  H6   single    0.930  0.020  1.080
 7B7  CAH  H7   single    0.930  0.020  1.080
 7B7  CBA  H8   single    0.970  0.020  1.090
 7B7  CAP  H9   single    0.970  0.020  1.090
 7B7  CAP  H10  single    0.970  0.020  1.090
 7B7  CAM  H11  single    0.970  0.020  1.090
 7B7  CAM  H12  single    0.970  0.020  1.090
 7B7  CAQ  H13  single    0.970  0.020  1.090
 7B7  CAQ  H14  single    0.970  0.020  1.090
 7B7  CA   H15  single    0.970  0.020  1.090
 7B7  CA   H16  single    0.970  0.020  1.090
 7B7  N    H17  single    0.860  0.020  1.020
 7B7  NAS  H18  single    0.860  0.020  1.020
 7B7  CAO  H19  single    0.970  0.020  1.090
 7B7  CAO  H20  single    0.970  0.020  1.090
 7B7  CAK  H21  single    0.930  0.020  1.080
 7B7  CAI  H22  single    0.930  0.020  1.080
 7B7  NAB  H23  single    0.890  0.020  1.040
 7B7  NAB  H24  single    0.890  0.020  1.040
 7B7  CAJ  H25  single    0.930  0.020  1.080
 7B7  CAL  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
 7B7  H3   CAA  H2   108.74  3.000
 7B7  H3   CAA  H1   108.77  3.000
 7B7  H2   CAA  H1   108.72  3.000
 7B7  H3   CAA  OAT  112.01  3.000
 7B7  H2   CAA  OAT  106.46  3.000
 7B7  H1   CAA  OAT  112.02  3.000
 7B7  CAY  OAT  CAA  118.93  3.000
 7B7  CAZ  CAY  CAG  120.27  3.000
 7B7  CAZ  CAY  OAT  116.05  3.000
 7B7  CAG  CAY  OAT  123.68  3.000
 7B7  H4   CAG  CAE  118.95  3.000
 7B7  H4   CAG  CAY  121.08  3.000
 7B7  CAE  CAG  CAY  119.96  3.000
 7B7  H5   CAE  CAF  120.45  3.000
 7B7  H5   CAE  CAG  119.21  3.000
 7B7  CAF  CAE  CAG  120.34  3.000
 7B7  H6   CAF  CAH  120.12  3.000
 7B7  H6   CAF  CAE  120.61  3.000
 7B7  CAH  CAF  CAE  119.27  3.000
 7B7  H7   CAH  CAZ  119.23  3.000
 7B7  H7   CAH  CAF  119.15  3.000
 7B7  CAZ  CAH  CAF  121.62  3.000
 7B7  CBA  CAZ  CAH  121.59  3.000
 7B7  CAH  CAZ  CAY  118.51  3.000
 7B7  CBA  CAZ  CAY  119.82  3.000
 7B7  H8   CBA  NBB  108.44  3.000
 7B7  H8   CBA  CAP  109.97  3.000
 7B7  NBB  CBA  CAP  103.24  3.000
 7B7  H8   CBA  CAZ  109.71  3.000
 7B7  NBB  CBA  CAZ  113.27  3.000
 7B7  CAP  CBA  CAZ  112.01  3.000
 7B7  H10  CAP  H9   107.54  3.000
 7B7  H10  CAP  CAM  110.03  3.000
 7B7  H9   CAP  CAM  113.37  3.000
 7B7  H10  CAP  CBA  109.78  3.000
 7B7  H9   CAP  CBA  111.66  3.000
 7B7  CAM  CAP  CBA  104.45  3.000
 7B7  H12  CAM  H11  108.04  3.000
 7B7  H12  CAM  CAQ  112.28  3.000
 7B7  H11  CAM  CAQ  109.82  3.000
 7B7  H12  CAM  CAP  113.02  3.000
 7B7  H11  CAM  CAP  110.86  3.000
 7B7  CAQ  CAM  CAP  102.78  3.000
 7B7  H14  CAQ  H13  108.08  3.000
 7B7  H14  CAQ  NBB  110.78  3.000
 7B7  H13  CAQ  NBB  111.77  3.000
 7B7  H14  CAQ  CAM  111.31  3.000
 7B7  H13  CAQ  CAM  112.28  3.000
 7B7  NBB  CAQ  CAM  102.61  3.000
 7B7  C    NBB  CAQ  126.15  3.000
 7B7  CAQ  NBB  CBA  112.50  3.000
 7B7  C    NBB  CBA  120.81  3.000
 7B7  CA   C    O    121.36  3.000
 7B7  O    C    NBB  122.51  3.000
 7B7  CA   C    NBB  116.13  3.000
 7B7  H16  CA   H15  106.38  3.000
 7B7  H16  CA   N    111.54  3.000
 7B7  H15  CA   N    111.62  3.000
 7B7  H16  CA   C    109.43  3.000
 7B7  H15  CA   C    108.53  3.000
 7B7  N    CA   C    109.26  3.000
 7B7  H17  N    CAU  120.83  3.000
 7B7  H17  N    CA   116.45  3.000
 7B7  CAU  N    CA   121.22  3.000
 7B7  NAS  CAU  OAC  123.16  3.000
 7B7  NAS  CAU  N    114.73  3.000
 7B7  OAC  CAU  N    122.11  3.000
 7B7  H18  NAS  CAO  116.55  3.000
 7B7  H18  NAS  CAU  118.81  3.000
 7B7  CAO  NAS  CAU  122.84  3.000
 7B7  H20  CAO  H19  106.68  3.000
 7B7  H20  CAO  CAX  109.39  3.000
 7B7  H19  CAO  CAX  110.45  3.000
 7B7  H20  CAO  NAS  111.38  3.000
 7B7  H19  CAO  NAS  108.01  3.000
 7B7  CAX  CAO  NAS  110.84  3.000
 7B7  CAL  CAX  CAK  117.62  3.000
 7B7  CAL  CAX  CAO  121.37  3.000
 7B7  CAK  CAX  CAO  121.01  3.000
 7B7  H21  CAK  CAI  118.86  3.000
 7B7  H21  CAK  CAX  119.65  3.000
 7B7  CAI  CAK  CAX  121.49  3.000
 7B7  H22  CAI  CAW  119.54  3.000
 7B7  H22  CAI  CAK  119.73  3.000
 7B7  CAW  CAI  CAK  120.73  3.000
 7B7  CAJ  CAW  NAB  121.18  3.000
 7B7  NAB  CAW  CAI  120.85  3.000
 7B7  CAJ  CAW  CAI  117.92  3.000
 7B7  H24  NAB  H23  111.36  3.000
 7B7  H24  NAB  CAW  115.45  3.000
 7B7  H23  NAB  CAW  115.46  3.000
 7B7  H25  CAJ  CAL  119.66  3.000
 7B7  H25  CAJ  CAW  119.71  3.000
 7B7  CAL  CAJ  CAW  120.63  3.000
 7B7  H26  CAL  CAJ  118.89  3.000
 7B7  H26  CAL  CAX  119.50  3.000
 7B7  CAJ  CAL  CAX  121.61  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
 7B7  CONST_01  CAF  CAE  CAG  CAY     0.00   0.0  0
 7B7  CONST_02  CAF  CAH  CAZ  CAY     0.00   0.0  0
 7B7  CONST_03  CAH  CAZ  CAY  CAG     0.00   0.0  0
 7B7  CONST_04  CAH  CAF  CAE  CAG     0.00   0.0  0
 7B7  CONST_05  CAZ  CAY  CAG  CAE     0.00   0.0  0
 7B7  CONST_06  CAZ  CAH  CAF  CAE     0.00   0.0  0
 7B7  CONST_07  CAW  CAI  CAK  CAX     0.00   0.0  0
 7B7  CONST_08  CAW  CAJ  CAL  CAX     0.00   0.0  0
 7B7  CONST_09  CAJ  CAL  CAX  CAK     0.00   0.0  0
 7B7  CONST_10  CAJ  CAW  CAI  CAK     0.00   0.0  0
 7B7  CONST_11  CAL  CAX  CAK  CAI     0.00   0.0  0
 7B7  CONST_12  CAL  CAJ  CAW  CAI     0.00   0.0  0
 7B7  CONST_13  CBA  CAZ  CAY  CAG   180.00   0.0  0
 7B7  CONST_14  CBA  CAZ  CAH  CAF   180.00   0.0  0
 7B7  CONST_15  CAE  CAG  CAY  OAT   180.00   0.0  0
 7B7  CONST_16  CBA  CAZ  CAY  OAT     0.00   0.0  0
 7B7  CONST_17  CAH  CAZ  CAY  OAT   180.00   0.0  0
 7B7  CONST_18  CAI  CAK  CAX  CAO   180.00   0.0  0
 7B7  CONST_19  CAJ  CAL  CAX  CAO   180.00   0.0  0
 7B7  CONST_20  NAB  CAW  CAI  CAK   180.00   0.0  0
 7B7  CONST_21  CAL  CAJ  CAW  NAB   180.00   0.0  0
 7B7  CONST_22  H5   CAE  CAG  CAY   180.00   0.0  0
 7B7  CONST_23  H7   CAH  CAZ  CAY   180.00   0.0  0
 7B7  CONST_24  H6   CAF  CAE  CAG   180.00   0.0  0
 7B7  CONST_25  H4   CAG  CAE  CAF   180.00   0.0  0
 7B7  CONST_26  H22  CAI  CAK  CAX   180.00   0.0  0
 7B7  CONST_27  H25  CAJ  CAL  CAX   180.00   0.0  0
 7B7  CONST_28  H26  CAL  CAX  CAK   180.00   0.0  0
 7B7  CONST_29  H21  CAK  CAI  CAW   180.00   0.0  0
 7B7  CONST_30  CA   C    NBB  CBA   180.00   0.0  0
 7B7  CONST_31  O    C    NBB  CBA     0.00   0.0  0
 7B7  CONST_32  CA   C    NBB  CAQ     0.00   0.0  0
 7B7  CONST_33  O    C    NBB  CAQ   180.00   0.0  0
 7B7  CONST_36  OAC  CAU  N    CA      0.00   0.0  0
 7B7  CONST_37  CAO  NAS  CAU  OAC     0.00   0.0  0
 7B7  CONST_38  NAS  CAU  N    CA    180.00   0.0  0
 7B7  CONST_39  CAO  NAS  CAU  N     180.00   0.0  0
 7B7  CONST_40  H17  N    CAU  OAC   180.00   0.0  0
 7B7  CONST_41  H18  NAS  CAU  OAC   180.00   0.0  0
 7B7  Var_01    CAQ  CAM  CAP  CBA   -36.47  30.0  1
 7B7  Var_02    CAM  CAQ  NBB  CBA   -23.02  30.0  1
 7B7  Var_03    NBB  CAQ  CAM  CAP    35.90  30.0  1
 7B7  Var_04    CAG  CAY  OAT  CAA    -2.32  30.0  2
 7B7  Var_05    CAK  CAX  CAO  NAS    63.74  30.0  2
 7B7  Var_06    N    CA   C    NBB   172.44  30.0  1
 7B7  Var_07    CAX  CAO  NAS  CAU  -151.55  30.0  3
 7B7  Var_08    H1   CAA  OAT  CAY    62.53  30.0  3
 7B7  Var_09    CAU  N    CA   C     171.85  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
 7B7  chir_01  CBA  CAZ  CAP  NBB  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
 7B7  plan-1  OAT  0.020
 7B7  plan-1  CAY  0.020
 7B7  plan-1  CAG  0.020
 7B7  plan-1  CAE  0.020
 7B7  plan-1  CAF  0.020
 7B7  plan-1  CAH  0.020
 7B7  plan-1  CAZ  0.020
 7B7  plan-1  CBA  0.020
 7B7  plan-1  H4   0.020
 7B7  plan-1  H5   0.020
 7B7  plan-1  H6   0.020
 7B7  plan-1  H7   0.020
 7B7  plan-2  CAO  0.020
 7B7  plan-2  CAX  0.020
 7B7  plan-2  CAK  0.020
 7B7  plan-2  CAI  0.020
 7B7  plan-2  CAW  0.020
 7B7  plan-2  NAB  0.020
 7B7  plan-2  CAJ  0.020
 7B7  plan-2  CAL  0.020
 7B7  plan-2  H21  0.020
 7B7  plan-2  H22  0.020
 7B7  plan-2  H25  0.020
 7B7  plan-2  H26  0.020
 7B7  plan-3  CA   0.020
 7B7  plan-3  N    0.020
 7B7  plan-3  CAU  0.020
 7B7  plan-3  OAC  0.020
 7B7  plan-3  NAS  0.020
 7B7  plan-3  CAO  0.020
 7B7  plan-3  H17  0.020
 7B7  plan-3  H18  0.020
 7B7  plan-4  CAW  0.020
 7B7  plan-4  NAB  0.020
 7B7  plan-4  H23  0.020
 7B7  plan-4  H24  0.020
 7B7  plan-5  CBA  0.020
 7B7  plan-5  CAQ  0.020
 7B7  plan-5  NBB  0.020
 7B7  plan-5  C    0.020
 7B7  plan-5  O    0.020
 7B7  plan-5  CA   0.020

