# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 19:09:12 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO/N=C/c1ccc(OCC[C@@H](C)CCN2CCN(C2=O)c3ccnc(N)c3)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
 906  906  1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one  ligand  62  31  .  2022-07-24  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_906
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
 906  CAA   C  CH3   0  -0.674   12.6511   1.0198   1.0220
 906  CAB   C  CH3   0  -0.653   -0.1892   0.6733   1.7309
 906  CAE   C  C1    0  -0.051    8.5341   0.0777  -0.7010
 906  CAF   C  CR16  0  -0.051   -9.4641   0.0416  -0.9542
 906  CAG   C  CR16  0  -0.431   -8.3380  -0.6953  -0.6648
 906  CAH   C  CR16  0  -0.257    6.4421  -0.4278  -1.8898
 906  CAI   C  CR16  0  -0.253    6.3135   0.0171   0.4575
 906  CAJ   C  CR16  0  -0.315    5.0748  -0.6083  -1.9395
 906  CAK   C  CR16  0  -0.340    4.9422  -0.1644   0.4242
 906  CAL   C  CR16  0  -0.466   -7.2438   1.3778  -0.1825
 906  CAM   C  CH2   0  -0.124   11.1740   0.9304   1.3212
 906  CAN   C  CH2   0  -0.162    2.1419  -0.4628   0.2092
 906  CAO   C  CH2   0  -0.435    0.7081  -0.6198  -0.2539
 906  CAP   C  CH2   0  -0.419   -1.7201  -0.7683   0.3259
 906  CAQ   C  CH2   0  -0.271   -2.7435  -1.1529   1.3906
 906  CAR   C  CH2   0  -0.263   -4.4878  -2.4652   0.1095
 906  CAS   C  CH2   0  -0.290   -5.9609  -2.1696  -0.1547
 906  NAT   N  N     0  -0.112    9.1699   0.4011   0.3493
 906  NAU   N  N     0  -0.484   -9.5474   1.3658  -0.8845
 906  OAV   O  O2    0  -0.409   10.5124   0.5175   0.1320
 906  OAW   O  O2    0  -0.473    2.9863  -0.6666  -0.9139
 906  CAX   C  CR5   0   0.754   -4.9167  -0.2618   0.7115
 906  CAY   C  CR6   0   0.470   -8.4462   2.0146  -0.5063
 906  CAZ   C  CR6   0   0.032    7.0884  -0.1088  -0.6941
 906  CBA   C  CR6   0   0.387    4.3093  -0.4766  -0.7806
 906  CBB   C  CR6   0   0.481   -7.1774  -0.0106  -0.2580
 906  CBC   C  CH1   0  -0.240   -0.3073  -0.5959   0.8895
 906  NBD   N  NR5   0  -0.512   -4.0792  -1.3160   0.8780
 906  NBE   N  NR5   0  -0.634   -6.0359  -0.7286   0.0224
 906  HAA   H  HCH3  0   0.224   12.8590   1.7434   0.2341
 906  HAAA  H  HCH3  0   0.231   13.1793   1.3436   1.9175
 906  HAAB  H  HCH3  0   0.228   13.0613   0.0553   0.7238
 906  HAB   H  HCH3  0   0.216   -0.2704   1.5658   1.1062
 906  HABA  H  HCH3  0   0.235   -0.9682   0.7337   2.4908
 906  HABB  H  HCH3  0   0.222    0.7630   0.7264   2.2600
 906  HNAC  H  HNH2  0   0.364   -7.8354   3.8829   0.0460
 906  HNAA  H  HNH2  0   0.357   -9.4480   3.7727  -0.4677
 906  HAE   H  H     0   0.220    9.0483  -0.0725  -1.6510
 906  HAF   H  HCR6  0   0.240  -10.3671  -0.4757  -1.2602
 906  HAG   H  HCR6  0   0.252   -8.3788  -1.7710  -0.7417
 906  HAH   H  HCR6  0   0.231    7.0175  -0.5342  -2.8014
 906  HAI   H  HCR6  0   0.245    6.7831   0.2610   1.4010
 906  HAJ   H  HCR6  0   0.247    4.5902  -0.8551  -2.8748
 906  HAK   H  HCR6  0   0.260    4.3852  -0.0633   1.3450
 906  HAL   H  HCR6  0   0.287   -6.3898   1.9613   0.1205
 906  HAM   H  HCH2  0   0.208   10.9862   0.2116   2.1244
 906  HAMA  H  HCH2  0   0.207   10.7892   1.9015   1.6465
 906  HAN   H  HCH2  0   0.216    2.3117   0.5371   0.6215
 906  HANA  H  HCH2  0   0.211    2.3712  -1.1924   0.9957
 906  HAO   H  HCH2  0   0.222    0.4737   0.1738  -0.9708
 906  HAOA  H  HCH2  0   0.232    0.6149  -1.5689  -0.7893
 906  HAP   H  HCH2  0   0.218   -1.7050  -1.5413  -0.4491
 906  HAPA  H  HCH2  0   0.229   -2.0370   0.1589  -0.1615
 906  HAQ   H  HCH2  0   0.227   -2.4493  -2.0942   1.8614
 906  HAQA  H  HCH2  0   0.251   -2.7820  -0.4048   2.1823
 906  HAR   H  HCH2  0   0.245   -4.3541  -3.3918   0.6662
 906  HARA  H  HCH2  0   0.235   -3.9272  -2.5496  -0.8261
 906  HAS   H  HCH2  0   0.256   -6.2538  -2.4678  -1.1594
 906  HASA  H  HCH2  0   0.250   -6.6050  -2.6868   0.5608
 906  HBC   H  HCH1  0   0.214   -0.0993  -1.4556   1.5396
 906  OAD   O  O     0  -0.461   -4.7281   0.8689   1.1024
 906  NAC   N  NH2   0  -0.822   -8.5233   3.3801  -0.4855

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
 906  CAA  CAM   single    1.510  0.020  1.510
 906  CAB  CBC   single    1.527  0.020  1.527
 906  NAC  CAY   single    1.368  0.020  1.368
 906  OAD  CAX   double    1.211  0.020  1.211
 906  CAE  NAT   double    1.270  0.020  1.270
 906  CAE  CAZ   single    1.458  0.020  1.458
 906  CAF  CAG   aromatic  1.377  0.020  1.377
 906  CAF  NAU   aromatic  1.329  0.020  1.329
 906  CAG  CBB   aromatic  1.408  0.020  1.408
 906  CAH  CAJ   aromatic  1.380  0.020  1.380
 906  CAH  CAZ   aromatic  1.396  0.020  1.396
 906  CAI  CAK   aromatic  1.384  0.020  1.384
 906  CAI  CAZ   aromatic  1.394  0.020  1.394
 906  CAJ  CBA   aromatic  1.395  0.020  1.395
 906  CAK  CBA   aromatic  1.396  0.020  1.396
 906  CAL  CAY   aromatic  1.399  0.020  1.399
 906  CAL  CBB   aromatic  1.392  0.020  1.392
 906  CAM  OAV   single    1.422  0.020  1.422
 906  CAN  CAO   single    1.515  0.020  1.515
 906  CAN  OAW   single    1.420  0.020  1.420
 906  CAO  CBC   single    1.529  0.020  1.529
 906  CAP  CAQ   single    1.526  0.020  1.526
 906  CAP  CBC   single    1.531  0.020  1.531
 906  CAQ  NBD   single    1.440  0.020  1.440
 906  CAR  CAS   single    1.526  0.020  1.526
 906  CAR  NBD   single    1.442  0.020  1.442
 906  CAS  NBE   single    1.454  0.020  1.454
 906  NAT  OAV   single    1.365  0.020  1.365
 906  NAU  CAY   aromatic  1.333  0.020  1.333
 906  OAW  CBA   single    1.343  0.020  1.343
 906  CAX  NBD   single    1.357  0.020  1.357
 906  CAX  NBE   single    1.395  0.020  1.395
 906  CBB  NBE   single    1.377  0.020  1.377
 906  CAA  HAA   single    0.970  0.020  1.090
 906  CAA  HAAA  single    0.970  0.020  1.090
 906  CAA  HAAB  single    0.970  0.020  1.090
 906  CAB  HAB   single    0.970  0.020  1.090
 906  CAB  HABA  single    0.970  0.020  1.090
 906  CAB  HABB  single    0.970  0.020  1.090
 906  NAC  HNAC  single    0.890  0.020  1.040
 906  NAC  HNAA  single    0.890  0.020  1.040
 906  CAE  HAE   single    0.930  0.020  1.080
 906  CAF  HAF   single    0.930  0.020  1.080
 906  CAG  HAG   single    0.930  0.020  1.080
 906  CAH  HAH   single    0.930  0.020  1.080
 906  CAI  HAI   single    0.930  0.020  1.080
 906  CAJ  HAJ   single    0.930  0.020  1.080
 906  CAK  HAK   single    0.930  0.020  1.080
 906  CAL  HAL   single    0.930  0.020  1.080
 906  CAM  HAM   single    0.970  0.020  1.090
 906  CAM  HAMA  single    0.970  0.020  1.090
 906  CAN  HAN   single    0.970  0.020  1.090
 906  CAN  HANA  single    0.970  0.020  1.090
 906  CAO  HAO   single    0.970  0.020  1.090
 906  CAO  HAOA  single    0.970  0.020  1.090
 906  CAP  HAP   single    0.970  0.020  1.090
 906  CAP  HAPA  single    0.970  0.020  1.090
 906  CAQ  HAQ   single    0.970  0.020  1.090
 906  CAQ  HAQA  single    0.970  0.020  1.090
 906  CAR  HAR   single    0.970  0.020  1.090
 906  CAR  HARA  single    0.970  0.020  1.090
 906  CAS  HAS   single    0.970  0.020  1.090
 906  CAS  HASA  single    0.970  0.020  1.090
 906  CBC  HBC   single    0.970  0.020  1.090

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
 906  HAAB  CAA  HAAA  107.80  3.000
 906  HAAB  CAA  HAA   108.54  3.000
 906  HAAA  CAA  HAA   107.73  3.000
 906  HAAB  CAA  CAM   111.73  3.000
 906  HAAA  CAA  CAM   109.22  3.000
 906  HAA   CAA  CAM   111.67  3.000
 906  HABB  CAB  HABA  106.45  3.000
 906  HABB  CAB  HAB   107.62  3.000
 906  HABA  CAB  HAB   107.48  3.000
 906  HABB  CAB  CBC   112.03  3.000
 906  HABA  CAB  CBC   112.02  3.000
 906  HAB   CAB  CBC   110.98  3.000
 906  HAE   CAE  CAZ   117.01  3.000
 906  HAE   CAE  NAT   121.30  3.000
 906  CAZ   CAE  NAT   121.69  3.000
 906  HAF   CAF  NAU   115.97  3.000
 906  HAF   CAF  CAG   119.02  3.000
 906  NAU   CAF  CAG   125.01  3.000
 906  HAG   CAG  CBB   122.46  3.000
 906  HAG   CAG  CAF   119.18  3.000
 906  CBB   CAG  CAF   118.35  3.000
 906  HAH   CAH  CAZ   119.82  3.000
 906  HAH   CAH  CAJ   118.89  3.000
 906  CAZ   CAH  CAJ   121.29  3.000
 906  HAI   CAI  CAZ   119.98  3.000
 906  HAI   CAI  CAK   118.74  3.000
 906  CAZ   CAI  CAK   121.29  3.000
 906  HAJ   CAJ  CBA   119.60  3.000
 906  HAJ   CAJ  CAH   120.31  3.000
 906  CBA   CAJ  CAH   120.09  3.000
 906  HAK   CAK  CBA   121.49  3.000
 906  HAK   CAK  CAI   118.55  3.000
 906  CBA   CAK  CAI   119.96  3.000
 906  HAL   CAL  CBB   121.16  3.000
 906  HAL   CAL  CAY   119.99  3.000
 906  CBB   CAL  CAY   118.85  3.000
 906  HAMA  CAM  HAM   107.73  3.000
 906  HAMA  CAM  OAV   110.04  3.000
 906  HAM   CAM  OAV   110.08  3.000
 906  HAMA  CAM  CAA   110.52  3.000
 906  HAM   CAM  CAA   110.63  3.000
 906  OAV   CAM  CAA   107.85  3.000
 906  HANA  CAN  HAN   107.76  3.000
 906  HANA  CAN  OAW   110.32  3.000
 906  HAN   CAN  OAW   109.68  3.000
 906  HANA  CAN  CAO   110.37  3.000
 906  HAN   CAN  CAO   110.89  3.000
 906  OAW   CAN  CAO   107.83  3.000
 906  HAOA  CAO  HAO   106.87  3.000
 906  HAOA  CAO  CBC   108.85  3.000
 906  HAO   CAO  CBC   109.64  3.000
 906  HAOA  CAO  CAN   108.68  3.000
 906  HAO   CAO  CAN   109.13  3.000
 906  CBC   CAO  CAN   113.46  3.000
 906  HAPA  CAP  HAP   106.68  3.000
 906  HAPA  CAP  CBC   109.62  3.000
 906  HAP   CAP  CBC   109.11  3.000
 906  HAPA  CAP  CAQ   109.27  3.000
 906  HAP   CAP  CAQ   108.98  3.000
 906  CBC   CAP  CAQ   112.98  3.000
 906  HAQA  CAQ  HAQ   106.73  3.000
 906  HAQA  CAQ  NBD   107.67  3.000
 906  HAQ   CAQ  NBD   107.79  3.000
 906  HAQA  CAQ  CAP   110.94  3.000
 906  HAQ   CAQ  CAP   109.70  3.000
 906  NBD   CAQ  CAP   113.72  3.000
 906  HARA  CAR  HAR   107.98  3.000
 906  HARA  CAR  NBD   111.85  3.000
 906  HAR   CAR  NBD   111.77  3.000
 906  HARA  CAR  CAS   111.20  3.000
 906  HAR   CAR  CAS   111.83  3.000
 906  NBD   CAR  CAS   102.21  3.000
 906  HASA  CAS  HAS   108.43  3.000
 906  HASA  CAS  NBE   111.04  3.000
 906  HAS   CAS  NBE   111.73  3.000
 906  HASA  CAS  CAR   111.35  3.000
 906  HAS   CAS  CAR   111.51  3.000
 906  NBE   CAS  CAR   102.76  3.000
 906  OAV   NAT  CAE   112.49  3.000
 906  CAY   NAU  CAF   116.63  3.000
 906  NAT   OAV  CAM   110.44  3.000
 906  CBA   OAW  CAN   119.14  3.000
 906  NBE   CAX  NBD   107.21  3.000
 906  NBE   CAX  OAD   126.65  3.000
 906  NBD   CAX  OAD   126.14  3.000
 906  NAU   CAY  CAL   123.67  3.000
 906  NAU   CAY  NAC   116.34  3.000
 906  CAL   CAY  NAC   119.96  3.000
 906  CAI   CAZ  CAH   118.09  3.000
 906  CAI   CAZ  CAE   122.94  3.000
 906  CAH   CAZ  CAE   118.96  3.000
 906  OAW   CBA  CAK   124.32  3.000
 906  OAW   CBA  CAJ   116.40  3.000
 906  CAK   CBA  CAJ   119.28  3.000
 906  NBE   CBB  CAL   123.26  3.000
 906  NBE   CBB  CAG   119.25  3.000
 906  CAL   CBB  CAG   117.49  3.000
 906  HBC   CBC  CAP   107.74  3.000
 906  HBC   CBC  CAO   107.74  3.000
 906  CAP   CBC  CAO   109.61  3.000
 906  HBC   CBC  CAB   108.05  3.000
 906  CAP   CBC  CAB   111.58  3.000
 906  CAO   CBC  CAB   111.93  3.000
 906  CAX   NBD  CAR   112.28  3.000
 906  CAX   NBD  CAQ   121.89  3.000
 906  CAR   NBD  CAQ   122.89  3.000
 906  CBB   NBE  CAX   126.24  3.000
 906  CBB   NBE  CAS   122.32  3.000
 906  CAX   NBE  CAS   110.52  3.000
 906  HNAA  NAC  HNAC  115.17  3.000
 906  HNAA  NAC  CAY   116.25  3.000
 906  HNAC  NAC  CAY   117.99  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
 906  CONST_01  CAL  CBB  CAG  CAF     0.00   0.0  0
 906  CONST_02  CAL  CAY  NAU  CAF     0.00   0.0  0
 906  CONST_03  CAY  NAU  CAF  CAG     0.00   0.0  0
 906  CONST_04  CAY  CAL  CBB  CAG     0.00   0.0  0
 906  CONST_05  CAK  CBA  CAJ  CAH     0.00   0.0  0
 906  CONST_06  CAK  CAI  CAZ  CAH     0.00   0.0  0
 906  CONST_07  CAJ  CBA  CAK  CAI     0.00   0.0  0
 906  CONST_08  CAJ  CAH  CAZ  CAI     0.00   0.0  0
 906  CONST_09  CBB  CAG  CAF  NAU     0.00   0.0  0
 906  CONST_10  CBB  CAL  CAY  NAU     0.00   0.0  0
 906  CONST_11  CBA  CAJ  CAH  CAZ     0.00   0.0  0
 906  CONST_12  CBA  CAK  CAI  CAZ     0.00   0.0  0
 906  CONST_13  NBE  CBB  CAG  CAF   180.00   0.0  0
 906  CONST_14  NBE  CBB  CAL  CAY   180.00   0.0  0
 906  CONST_16  CBB  NBE  CAS  CAR   180.00   0.0  0
 906  CONST_17  NBE  CAX  NBD  CAR     0.00   0.0  0
 906  CONST_19  NBD  CAX  NBE  CAS     0.00   0.0  0
 906  CONST_20  NBD  CAX  NBE  CBB   180.00   0.0  0
 906  CONST_22  CBB  CAL  CAY  NAC   180.00   0.0  0
 906  CONST_23  CAF  NAU  CAY  NAC   180.00   0.0  0
 906  CONST_24  CAJ  CAH  CAZ  CAE   180.00   0.0  0
 906  CONST_25  CAK  CAI  CAZ  CAE   180.00   0.0  0
 906  CONST_26  OAW  CBA  CAJ  CAH   180.00   0.0  0
 906  CONST_27  OAW  CBA  CAK  CAI   180.00   0.0  0
 906  CONST_28  CAR  NBD  CAX  OAD   180.00   0.0  0
 906  CONST_29  CAS  NBE  CAX  OAD   180.00   0.0  0
 906  CONST_30  CBB  NBE  CAX  OAD     0.00   0.0  0
 906  CONST_31  CAS  CAR  NBD  CAQ   180.00   0.0  0
 906  CONST_32  NBE  CAX  NBD  CAQ   180.00   0.0  0
 906  CONST_33  HAL  CAL  CBB  CAG   180.00   0.0  0
 906  CONST_34  HAI  CAI  CAZ  CAH   180.00   0.0  0
 906  CONST_35  HAH  CAH  CAZ  CAI   180.00   0.0  0
 906  CONST_36  HAK  CAK  CBA  CAJ   180.00   0.0  0
 906  CONST_37  HAJ  CAJ  CBA  CAK   180.00   0.0  0
 906  CONST_38  HAG  CAG  CBB  CAL   180.00   0.0  0
 906  CONST_39  HAF  CAF  NAU  CAY   180.00   0.0  0
 906  CONST_40  CAQ  NBD  CAX  OAD     0.00   0.0  0
 906  CONST_43  CAZ  CAE  NAT  OAV   180.00   0.0  0
 906  CONST_44  HAE  CAE  NAT  OAV     0.00   0.0  0
 906  Var_01    CAS  NBE  CBB  CAG     3.36  30.0  2
 906  Var_02    HAR  CAR  NBD  CAX  -140.07  30.0  1
 906  Var_03    HAS  CAS  NBE  CAX  -136.79  30.0  1
 906  Var_04    NAT  CAE  CAZ  CAH   178.23  30.0  3
 906  Var_05    CAR  NBD  CAQ  CAP    74.97  30.0  3
 906  Var_06    NBD  CAQ  CAP  CBC   179.85  30.0  3
 906  Var_07    HAN  CAN  OAW  CBA    54.01  30.0  1
 906  Var_08    CBC  CAO  CAN  OAW   172.91  30.0  3
 906  Var_09    HAM  CAM  OAV  NAT    58.36  30.0  1
 906  Var_10    HAA  CAA  CAM  OAV    60.45  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
 906  chir_01  CBC  CAB  CAO  CAP  positiv

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
 906  plan-1  CAE   0.020
 906  plan-1  NAT   0.020
 906  plan-1  OAV   0.020
 906  plan-1  CAZ   0.020
 906  plan-1  HAE   0.020
 906  plan-2  CAF   0.020
 906  plan-2  CAG   0.020
 906  plan-2  CAL   0.020
 906  plan-2  NAU   0.020
 906  plan-2  CAY   0.020
 906  plan-2  CBB   0.020
 906  plan-2  NBE   0.020
 906  plan-2  HAF   0.020
 906  plan-2  HAG   0.020
 906  plan-2  HAL   0.020
 906  plan-2  NAC   0.020
 906  plan-3  CAE   0.020
 906  plan-3  CAH   0.020
 906  plan-3  CAI   0.020
 906  plan-3  CAJ   0.020
 906  plan-3  CAK   0.020
 906  plan-3  OAW   0.020
 906  plan-3  CAZ   0.020
 906  plan-3  CBA   0.020
 906  plan-3  HAH   0.020
 906  plan-3  HAI   0.020
 906  plan-3  HAJ   0.020
 906  plan-3  HAK   0.020
 906  plan-4  CAY   0.020
 906  plan-4  HNAC  0.020
 906  plan-4  HNAA  0.020
 906  plan-4  NAC   0.020
 906  plan-5  CAQ   0.020
 906  plan-5  CAR   0.020
 906  plan-5  CAS   0.020
 906  plan-5  CAX   0.020
 906  plan-5  CBB   0.020
 906  plan-5  NBD   0.020
 906  plan-5  NBE   0.020
 906  plan-5  OAD   0.020

