# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 04:41:06 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 1-(5-{4-[(E)-(ethoxyimino)methyl]phenoxy}pentyl)-3-(pyridin-4-yl)imidazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO\N=C\c1ccc(OCCCCCN2CCN(C2=O)c3ccncc3)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
 7VR  7VR  1-(5-{4-[(E)-(ethoxyimino)methyl]phenoxy}pentyl)-3-(pyridin-4-yl)imidazolidin-2-one  ligand  57  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7VR
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
 7VR  CAA   C  CH3   0  -0.702   12.3207   1.3115   0.7473
 7VR  CAL   C  CH2   0  -0.139   10.8238   1.4956   0.8327
 7VR  OAV   O  O2    0  -0.401   10.2105   0.3163   0.3275
 7VR  NAT   N  N     0  -0.102    8.8534   0.4358   0.3604
 7VR  CAC   C  C1    0  -0.079    8.2620  -0.5928  -0.0928
 7VR  CAY   C  CR6   0   0.026    6.8062  -0.6674  -0.1527
 7VR  CAI   C  CR16  0  -0.284    6.2072  -1.8171  -0.6722
 7VR  CAK   C  CR16  0  -0.338    4.8339  -1.9314  -0.7631
 7VR  CAH   C  CR16  0  -0.272    5.9756   0.3647   0.2819
 7VR  CAJ   C  CR16  0  -0.364    4.5975   0.2651   0.1979
 7VR  CAZ   C  CR6   0   0.387    4.0126  -0.8874  -0.3330
 7VR  OAW   O  O2    0  -0.471    2.6900  -1.0721  -0.4681
 7VR  CAP   C  CH2   0  -0.172    1.8046  -0.0229  -0.1008
 7VR  CAN   C  CH2   0  -0.456    0.3944  -0.4415  -0.4569
 7VR  CAM   C  CH2   0  -0.435   -0.6101   0.6509  -0.1094
 7VR  CAO   C  CH2   0  -0.425   -2.0371   0.2660  -0.4747
 7VR  CAQ   C  CH2   0  -0.283   -3.0305   1.3667  -0.1212
 7VR  NBB   N  NR5   0  -0.510   -4.3829   1.0426  -0.5011
 7VR  CAX   C  CR5   0   0.749   -5.3245   0.6156   0.3634
 7VR  OAB   O  O     0  -0.505   -5.1693   0.4027   1.5517
 7VR  CAR   C  CH2   0  -0.286   -4.9023   1.2961  -1.8233
 7VR  CAS   C  CH2   0  -0.322   -6.2665   0.6110  -1.7795
 7VR  NBC   N  NR5   0  -0.626   -6.5075   0.4551  -0.3530
 7VR  CBA   C  CR6   0   0.465   -7.7018  -0.0269   0.1367
 7VR  CAF   C  CR16  0  -0.379   -8.0230  -0.0776   1.5003
 7VR  CAD   C  CR16  0  -0.074   -9.2647  -0.5567   1.8730
 7VR  NAU   N  N     0  -0.421  -10.2030  -0.9798   1.0308
 7VR  CAE   C  CR16  0  -0.070   -9.8951  -0.9243  -0.2591
 7VR  CAG   C  CR16  0  -0.418   -8.6872  -0.4676  -0.7549
 7VR  HAA1  H  HCH3  0   0.239   12.8155   2.2085   1.1186
 7VR  HAA2  H  HCH3  0   0.234   12.6579   0.4698   1.3526
 7VR  HAA3  H  HCH3  0   0.234   12.6481   1.1533  -0.2807
 7VR  HAL1  H  HCH2  0   0.213   10.5158   1.6662   1.8691
 7VR  HAL2  H  HCH2  0   0.213   10.5088   2.3631   0.2444
 7VR  HAC   H  H     0   0.245    8.8182  -1.4569  -0.4585
 7VR  HAI   H  HCR6  0   0.258    6.8262  -2.6377  -1.0151
 7VR  HAH   H  HCR6  0   0.259    6.4083   1.2672   0.6935
 7VR  HAK   H  HCR6  0   0.265    4.3868  -2.8282  -1.1727
 7VR  HAJ   H  HCR6  0   0.283    3.9970   1.0931   0.5489
 7VR  HAP1  H  HCH2  0   0.224    1.8851   0.1804   0.9732
 7VR  HAP2  H  HCH2  0   0.223    2.0700   0.8976  -0.6332
 7VR  HAN1  H  HCH2  0   0.232    0.3401  -0.6615  -1.5268
 7VR  HAN2  H  HCH2  0   0.233    0.1351  -1.3622   0.0735
 7VR  HAM1  H  HCH2  0   0.225   -0.5540   0.8739   0.9611
 7VR  HAM2  H  HCH2  0   0.224   -0.3366   1.5753  -0.6289
 7VR  HAO1  H  HCH2  0   0.225   -2.0951   0.0479  -1.5454
 7VR  HAO2  H  HCH2  0   0.228   -2.3221  -0.6519   0.0475
 7VR  HAQ1  H  HCH2  0   0.252   -3.0058   1.5637   0.9512
 7VR  HAQ2  H  HCH2  0   0.244   -2.7508   2.2991  -0.6196
 7VR  HAR1  H  HCH2  0   0.256   -4.9900   2.3707  -2.0067
 7VR  HAR2  H  HCH2  0   0.263   -4.2643   0.8709  -2.5976
 7VR  HAS1  H  HCH2  0   0.275   -7.0415   1.2156  -2.2481
 7VR  HAS2  H  HCH2  0   0.266   -6.2419  -0.3619  -2.2771
 7VR  HAF   H  HCR6  0   0.284   -7.3362   0.2501   2.2619
 7VR  HAG   H  HCR6  0   0.286   -8.5315  -0.4668  -1.8242
 7VR  HAD   H  HCR6  0   0.261   -9.5121  -0.5936   2.9286
 7VR  HAE   H  HCR6  0   0.262  -10.6532  -1.2660  -0.9556

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
 7VR  CAA  CAL   single    1.511  0.020  1.511
 7VR  CAL  OAV   single    1.422  0.020  1.422
 7VR  OAV  NAT   single    1.363  0.020  1.363
 7VR  NAT  CAC   double    1.270  0.020  1.270
 7VR  CAC  CAY   single    1.459  0.020  1.459
 7VR  CAY  CAI   aromatic  1.397  0.020  1.397
 7VR  CAY  CAH   aromatic  1.394  0.020  1.394
 7VR  CAI  CAK   aromatic  1.381  0.020  1.381
 7VR  CAK  CAZ   aromatic  1.396  0.020  1.396
 7VR  CAH  CAJ   aromatic  1.384  0.020  1.384
 7VR  CAJ  CAZ   aromatic  1.397  0.020  1.397
 7VR  CAZ  OAW   single    1.342  0.020  1.342
 7VR  OAW  CAP   single    1.421  0.020  1.421
 7VR  CAP  CAN   single    1.513  0.020  1.513
 7VR  CAN  CAM   single    1.524  0.020  1.524
 7VR  CAM  CAO   single    1.522  0.020  1.522
 7VR  CAO  CAQ   single    1.524  0.020  1.524
 7VR  CAQ  NBB   single    1.442  0.020  1.442
 7VR  NBB  CAX   single    1.348  0.020  1.348
 7VR  NBB  CAR   single    1.443  0.020  1.443
 7VR  CAX  OAB   double    1.217  0.020  1.217
 7VR  CAX  NBC   single    1.392  0.020  1.392
 7VR  CAR  CAS   single    1.527  0.020  1.527
 7VR  CAS  NBC   single    1.455  0.020  1.455
 7VR  NBC  CBA   single    1.378  0.020  1.378
 7VR  CBA  CAF   aromatic  1.402  0.020  1.402
 7VR  CBA  CAG   aromatic  1.400  0.020  1.400
 7VR  CAF  CAD   aromatic  1.382  0.020  1.382
 7VR  CAD  NAU   aromatic  1.330  0.020  1.330
 7VR  NAU  CAE   aromatic  1.327  0.020  1.327
 7VR  CAE  CAG   aromatic  1.383  0.020  1.383
 7VR  CAA  HAA1  single    0.970  0.020  1.090
 7VR  CAA  HAA2  single    0.970  0.020  1.090
 7VR  CAA  HAA3  single    0.970  0.020  1.090
 7VR  CAL  HAL1  single    0.970  0.020  1.090
 7VR  CAL  HAL2  single    0.970  0.020  1.090
 7VR  CAC  HAC   single    0.930  0.020  1.080
 7VR  CAI  HAI   single    0.930  0.020  1.080
 7VR  CAH  HAH   single    0.930  0.020  1.080
 7VR  CAK  HAK   single    0.930  0.020  1.080
 7VR  CAJ  HAJ   single    0.930  0.020  1.080
 7VR  CAP  HAP1  single    0.970  0.020  1.090
 7VR  CAP  HAP2  single    0.970  0.020  1.090
 7VR  CAN  HAN1  single    0.970  0.020  1.090
 7VR  CAN  HAN2  single    0.970  0.020  1.090
 7VR  CAM  HAM1  single    0.970  0.020  1.090
 7VR  CAM  HAM2  single    0.970  0.020  1.090
 7VR  CAO  HAO1  single    0.970  0.020  1.090
 7VR  CAO  HAO2  single    0.970  0.020  1.090
 7VR  CAQ  HAQ1  single    0.970  0.020  1.090
 7VR  CAQ  HAQ2  single    0.970  0.020  1.090
 7VR  CAR  HAR1  single    0.970  0.020  1.090
 7VR  CAR  HAR2  single    0.970  0.020  1.090
 7VR  CAS  HAS1  single    0.970  0.020  1.090
 7VR  CAS  HAS2  single    0.970  0.020  1.090
 7VR  CAF  HAF   single    0.930  0.020  1.080
 7VR  CAG  HAG   single    0.930  0.020  1.080
 7VR  CAD  HAD   single    0.930  0.020  1.080
 7VR  CAE  HAE   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
 7VR  HAA3  CAA  HAA2  108.57  3.000
 7VR  HAA3  CAA  HAA1  107.72  3.000
 7VR  HAA2  CAA  HAA1  107.80  3.000
 7VR  HAA3  CAA  CAL   111.63  3.000
 7VR  HAA2  CAA  CAL   111.67  3.000
 7VR  HAA1  CAA  CAL   109.29  3.000
 7VR  HAL2  CAL  HAL1  107.72  3.000
 7VR  HAL2  CAL  OAV   110.01  3.000
 7VR  HAL1  CAL  OAV   110.13  3.000
 7VR  HAL2  CAL  CAA   110.57  3.000
 7VR  HAL1  CAL  CAA   110.57  3.000
 7VR  OAV   CAL  CAA   107.83  3.000
 7VR  NAT   OAV  CAL   110.38  3.000
 7VR  CAC   NAT  OAV   112.59  3.000
 7VR  HAC   CAC  CAY   117.04  3.000
 7VR  HAC   CAC  NAT   121.58  3.000
 7VR  CAY   CAC  NAT   121.38  3.000
 7VR  CAH   CAY  CAI   118.02  3.000
 7VR  CAH   CAY  CAC   122.94  3.000
 7VR  CAI   CAY  CAC   119.03  3.000
 7VR  HAI   CAI  CAK   118.98  3.000
 7VR  HAI   CAI  CAY   119.75  3.000
 7VR  CAK   CAI  CAY   121.27  3.000
 7VR  HAK   CAK  CAZ   119.54  3.000
 7VR  HAK   CAK  CAI   120.28  3.000
 7VR  CAZ   CAK  CAI   120.18  3.000
 7VR  HAH   CAH  CAJ   118.76  3.000
 7VR  HAH   CAH  CAY   119.85  3.000
 7VR  CAJ   CAH  CAY   121.39  3.000
 7VR  HAJ   CAJ  CAZ   121.50  3.000
 7VR  HAJ   CAJ  CAH   118.56  3.000
 7VR  CAZ   CAJ  CAH   119.94  3.000
 7VR  OAW   CAZ  CAJ   124.35  3.000
 7VR  OAW   CAZ  CAK   116.47  3.000
 7VR  CAJ   CAZ  CAK   119.18  3.000
 7VR  CAP   OAW  CAZ   119.10  3.000
 7VR  HAP2  CAP  HAP1  107.60  3.000
 7VR  HAP2  CAP  CAN   110.10  3.000
 7VR  HAP1  CAP  CAN   110.50  3.000
 7VR  HAP2  CAP  OAW   110.10  3.000
 7VR  HAP1  CAP  OAW   110.14  3.000
 7VR  CAN   CAP  OAW   108.39  3.000
 7VR  HAN2  CAN  HAN1  107.06  3.000
 7VR  HAN2  CAN  CAM   109.66  3.000
 7VR  HAN1  CAN  CAM   109.54  3.000
 7VR  HAN2  CAN  CAP   109.85  3.000
 7VR  HAN1  CAN  CAP   109.39  3.000
 7VR  CAM   CAN  CAP   111.24  3.000
 7VR  HAM2  CAM  HAM1  106.21  3.000
 7VR  HAM2  CAM  CAO   109.49  3.000
 7VR  HAM1  CAM  CAO   109.52  3.000
 7VR  HAM2  CAM  CAN   109.40  3.000
 7VR  HAM1  CAM  CAN   109.58  3.000
 7VR  CAO   CAM  CAN   112.45  3.000
 7VR  HAO2  CAO  HAO1  106.62  3.000
 7VR  HAO2  CAO  CAQ   108.99  3.000
 7VR  HAO1  CAO  CAQ   109.65  3.000
 7VR  HAO2  CAO  CAM   109.99  3.000
 7VR  HAO1  CAO  CAM   109.57  3.000
 7VR  CAQ   CAO  CAM   111.88  3.000
 7VR  HAQ2  CAQ  HAQ1  106.76  3.000
 7VR  HAQ2  CAQ  NBB   108.15  3.000
 7VR  HAQ1  CAQ  NBB   108.73  3.000
 7VR  HAQ2  CAQ  CAO   110.07  3.000
 7VR  HAQ1  CAQ  CAO   110.10  3.000
 7VR  NBB   CAQ  CAO   112.83  3.000
 7VR  CAR   NBB  CAX   113.08  3.000
 7VR  CAR   NBB  CAQ   122.66  3.000
 7VR  CAX   NBB  CAQ   123.89  3.000
 7VR  NBC   CAX  OAB   126.19  3.000
 7VR  NBC   CAX  NBB   107.46  3.000
 7VR  OAB   CAX  NBB   126.34  3.000
 7VR  HAR2  CAR  HAR1  108.13  3.000
 7VR  HAR2  CAR  CAS   111.61  3.000
 7VR  HAR1  CAR  CAS   111.96  3.000
 7VR  HAR2  CAR  NBB   111.83  3.000
 7VR  HAR1  CAR  NBB   110.81  3.000
 7VR  CAS   CAR  NBB   102.50  3.000
 7VR  HAS2  CAS  HAS1  108.32  3.000
 7VR  HAS2  CAS  NBC   110.78  3.000
 7VR  HAS1  CAS  NBC   111.31  3.000
 7VR  HAS2  CAS  CAR   111.48  3.000
 7VR  HAS1  CAS  CAR   111.98  3.000
 7VR  NBC   CAS  CAR   102.95  3.000
 7VR  CBA   NBC  CAS   121.97  3.000
 7VR  CBA   NBC  CAX   126.44  3.000
 7VR  CAS   NBC  CAX   110.57  3.000
 7VR  CAG   CBA  CAF   116.54  3.000
 7VR  CAG   CBA  NBC   119.59  3.000
 7VR  CAF   CBA  NBC   123.85  3.000
 7VR  HAF   CAF  CAD   119.20  3.000
 7VR  HAF   CAF  CBA   122.07  3.000
 7VR  CAD   CAF  CBA   118.74  3.000
 7VR  HAD   CAD  NAU   116.39  3.000
 7VR  HAD   CAD  CAF   118.63  3.000
 7VR  NAU   CAD  CAF   124.98  3.000
 7VR  CAE   NAU  CAD   116.00  3.000
 7VR  HAE   CAE  CAG   118.96  3.000
 7VR  HAE   CAE  NAU   116.66  3.000
 7VR  CAG   CAE  NAU   124.38  3.000
 7VR  HAG   CAG  CAE   118.74  3.000
 7VR  HAG   CAG  CBA   121.91  3.000
 7VR  CAE   CAG  CBA   119.36  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
 7VR  CONST_01  CAZ   CAK  CAI  CAY     0.00   0.0  0
 7VR  CONST_02  CAZ   CAJ  CAH  CAY     0.00   0.0  0
 7VR  CONST_03  CAJ   CAH  CAY  CAI     0.00   0.0  0
 7VR  CONST_04  CAJ   CAZ  CAK  CAI     0.00   0.0  0
 7VR  CONST_05  CAH   CAY  CAI  CAK     0.00   0.0  0
 7VR  CONST_06  CAH   CAJ  CAZ  CAK     0.00   0.0  0
 7VR  CONST_07  NAU   CAD  CAF  CBA     0.00   0.0  0
 7VR  CONST_08  NAU   CAE  CAG  CBA     0.00   0.0  0
 7VR  CONST_09  CAE   CAG  CBA  CAF     0.00   0.0  0
 7VR  CONST_10  CAE   NAU  CAD  CAF     0.00   0.0  0
 7VR  CONST_11  CAG   CBA  CAF  CAD     0.00   0.0  0
 7VR  CONST_12  CAG   CAE  NAU  CAD     0.00   0.0  0
 7VR  CONST_13  CAD   CAF  CBA  NBC   180.00   0.0  0
 7VR  CONST_14  CAE   CAG  CBA  NBC   180.00   0.0  0
 7VR  CONST_15  CAS   NBC  CAX  NBB     0.00   0.0  0
 7VR  CONST_16  CBA   NBC  CAX  NBB   180.00   0.0  0
 7VR  CONST_18  CAS   CAR  NBB  CAX     0.00   0.0  0
 7VR  CONST_20  NBC   CAX  NBB  CAR     0.00   0.0  0
 7VR  CONST_21  CBA   NBC  CAS  CAR   180.00   0.0  0
 7VR  CONST_22  CAK   CAI  CAY  CAC   180.00   0.0  0
 7VR  CONST_23  CAJ   CAH  CAY  CAC   180.00   0.0  0
 7VR  CONST_24  OAW   CAZ  CAK  CAI   180.00   0.0  0
 7VR  CONST_25  OAW   CAZ  CAJ  CAH   180.00   0.0  0
 7VR  CONST_26  NBC   CAX  NBB  CAQ   180.00   0.0  0
 7VR  CONST_27  CAS   CAR  NBB  CAQ   180.00   0.0  0
 7VR  CONST_28  CAR   NBB  CAX  OAB   180.00   0.0  0
 7VR  CONST_29  CAS   NBC  CAX  OAB   180.00   0.0  0
 7VR  CONST_30  CBA   NBC  CAX  OAB     0.00   0.0  0
 7VR  CONST_31  HAK   CAK  CAI  CAY   180.00   0.0  0
 7VR  CONST_32  HAJ   CAJ  CAH  CAY   180.00   0.0  0
 7VR  CONST_33  HAH   CAH  CAY  CAI   180.00   0.0  0
 7VR  CONST_34  HAI   CAI  CAY  CAH   180.00   0.0  0
 7VR  CONST_35  HAF   CAF  CBA  NBC     0.00   0.0  0
 7VR  CONST_36  HAG   CAG  CBA  NBC     0.00   0.0  0
 7VR  CONST_37  HAD   CAD  CAF  CBA   180.00   0.0  0
 7VR  CONST_38  HAE   CAE  CAG  CBA   180.00   0.0  0
 7VR  CONST_39  OAB   CAX  NBB  CAQ     0.00   0.0  0
 7VR  CONST_40  CAY   CAC  NAT  OAV   180.00   0.0  0
 7VR  CONST_41  HAC   CAC  NAT  OAV     0.00   0.0  0
 7VR  Var_01    CAF   CBA  NBC  CAX    18.81  30.0  2
 7VR  Var_02    HAS1  CAS  CAR  NBB   137.46  30.0  1
 7VR  Var_03    HAR1  CAR  NBB  CAX   105.07  30.0  1
 7VR  Var_04    CAI   CAY  CAC  NAT   179.39  30.0  2
 7VR  Var_05    CAX   NBB  CAQ  CAO   102.00  30.0  3
 7VR  Var_06    CAN   CAP  OAW  CAZ   175.33  30.0  3
 7VR  Var_07    NBB   CAQ  CAO  CAM   177.97  30.0  3
 7VR  Var_08    CAM   CAN  CAP  OAW  -179.09  30.0  3
 7VR  Var_09    CAO   CAM  CAN  CAP   179.19  30.0  3
 7VR  Var_10    CAQ   CAO  CAM  CAN   179.97  30.0  3
 7VR  Var_11    HAA1  CAA  CAL  OAV   179.35  30.0  3
 7VR  Var_12    HAL1  CAL  OAV  NAT    60.26  30.0  1

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
 7VR  plan-1  CAC  0.020
 7VR  plan-1  CAY  0.020
 7VR  plan-1  CAI  0.020
 7VR  plan-1  CAK  0.020
 7VR  plan-1  CAH  0.020
 7VR  plan-1  CAJ  0.020
 7VR  plan-1  CAZ  0.020
 7VR  plan-1  OAW  0.020
 7VR  plan-1  HAI  0.020
 7VR  plan-1  HAH  0.020
 7VR  plan-1  HAK  0.020
 7VR  plan-1  HAJ  0.020
 7VR  plan-2  NBC  0.020
 7VR  plan-2  CBA  0.020
 7VR  plan-2  CAF  0.020
 7VR  plan-2  CAD  0.020
 7VR  plan-2  NAU  0.020
 7VR  plan-2  CAE  0.020
 7VR  plan-2  CAG  0.020
 7VR  plan-2  HAF  0.020
 7VR  plan-2  HAG  0.020
 7VR  plan-2  HAD  0.020
 7VR  plan-2  HAE  0.020
 7VR  plan-3  CAQ  0.020
 7VR  plan-3  NBB  0.020
 7VR  plan-3  CAX  0.020
 7VR  plan-3  OAB  0.020
 7VR  plan-3  CAR  0.020
 7VR  plan-3  CAS  0.020
 7VR  plan-3  NBC  0.020
 7VR  plan-3  CBA  0.020
 7VR  plan-4  OAV  0.020
 7VR  plan-4  NAT  0.020
 7VR  plan-4  CAC  0.020
 7VR  plan-4  CAY  0.020
 7VR  plan-4  HAC  0.020

