# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:07:15 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-[5-(2-ethoxyphenyl)-1,2,4-oxadiazol-3-yl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccccc1c2onc(n2)c3ccncc3
#
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
 3M4  3M4  4-[5-(2-ethoxyphenyl)-1,2,4-oxadiazol-3-yl]pyridine  ligand  33  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 PERFECT
;

data_comp_3M4
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
 3M4  CAA   C  CH3   0  -0.678  -3.7614   3.3624  -0.1593
 3M4  CAB   C  CR16  0  -0.226  -4.1277  -2.2968   0.0319
 3M4  CAC   C  CR16  0  -0.269  -2.9218  -2.9847   0.0795
 3M4  CAD   C  CR16  0  -0.054   5.2436   0.9853   0.0802
 3M4  CAE   C  CR16  0  -0.053   4.9635  -1.2259  -0.3568
 3M4  CAF   C  CR16  0  -0.385  -4.1580  -0.9123   0.0198
 3M4  CAG   C  CR16  0  -0.263  -1.7422  -2.2682   0.1152
 3M4  CAH   C  CR16  0  -0.351   3.8798   1.1963   0.1923
 3M4  CAI   C  CR16  0  -0.362   3.5833  -1.1275  -0.2650
 3M4  CAJ   C  CH2   0  -0.197  -4.1270   1.8988  -0.1208
 3M4  NAK   N  N     0  -0.399   5.7853  -0.1978  -0.1893
 3M4  NAL   N  N     0  -0.145   0.9913   1.4062   0.3182
 3M4  NAM   N  N     0  -0.474   0.7072  -0.7764  -0.0071
 3M4  OAN   O  O2    0  -0.452  -2.9241   1.1517   0.0461
 3M4  OAO   O  O     0  -0.321  -0.3358   1.1018   0.3330
 3M4  CAP   C  CR6   0   0.092   3.0243   0.1132   0.0153
 3M4  CAQ   C  CR6   0   0.411  -2.9702  -0.1802   0.0600
 3M4  CAR   C  CR5   0   0.346   1.5722   0.2616   0.1144
 3M4  CAS   C  CR6   0  -0.186  -1.7432  -0.8708   0.1086
 3M4  CAT   C  CR5   0   0.588  -0.4509  -0.2075   0.1356
 3M4  HAA   H  HCH3  0   0.239  -4.6645   3.9523  -0.3117
 3M4  HAAA  H  HCH3  0   0.237  -3.3037   3.6839   0.7759
 3M4  HAAB  H  HCH3  0   0.237  -3.0749   3.5803  -0.9771
 3M4  HAB   H  HCR6  0   0.273  -5.0620  -2.8421   0.0029
 3M4  HAC   H  HCR6  0   0.265  -2.9027  -4.0653   0.0893
 3M4  HAE   H  HCR6  0   0.272   5.4205  -2.1837  -0.5777
 3M4  HAF   H  HCR6  0   0.292  -5.1138  -0.4090  -0.0198
 3M4  HAG   H  HCR6  0   0.271  -0.7959  -2.7907   0.1527
 3M4  HAH   H  HCR6  0   0.276   3.5031   2.1850   0.4150
 3M4  HAI   H  HCR6  0   0.277   2.9640  -2.0011  -0.4130
 3M4  HAJ   H  HCH2  0   0.233  -4.8147   1.6972   0.7061
 3M4  HAJA  H  HCH2  0   0.233  -4.6230   1.5990  -1.0490
 3M4  HAD   H  HCR6  0   0.272   5.9292   1.8136   0.2161

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
 3M4  CAJ  CAA   single    1.509  0.020  1.509
 3M4  CAA  HAA   single    0.970  0.020  1.090
 3M4  CAA  HAAA  single    0.970  0.020  1.090
 3M4  CAA  HAAB  single    0.970  0.020  1.090
 3M4  CAC  CAB   aromatic  1.389  0.020  1.389
 3M4  CAF  CAB   aromatic  1.385  0.020  1.385
 3M4  CAB  HAB   single    0.930  0.020  1.080
 3M4  CAG  CAC   aromatic  1.381  0.020  1.381
 3M4  CAC  HAC   single    0.930  0.020  1.080
 3M4  NAK  CAD   aromatic  1.329  0.020  1.329
 3M4  CAD  CAH   aromatic  1.385  0.020  1.385
 3M4  CAD  HAD   single    0.930  0.020  1.080
 3M4  NAK  CAE   aromatic  1.327  0.020  1.327
 3M4  CAE  CAI   aromatic  1.387  0.020  1.387
 3M4  CAE  HAE   single    0.930  0.020  1.080
 3M4  CAQ  CAF   aromatic  1.396  0.020  1.396
 3M4  CAF  HAF   single    0.930  0.020  1.080
 3M4  CAS  CAG   aromatic  1.397  0.020  1.397
 3M4  CAG  HAG   single    0.930  0.020  1.080
 3M4  CAH  CAP   aromatic  1.392  0.020  1.392
 3M4  CAH  HAH   single    0.930  0.020  1.080
 3M4  CAI  CAP   aromatic  1.389  0.020  1.389
 3M4  CAI  HAI   single    0.930  0.020  1.080
 3M4  CAJ  OAN   single    1.426  0.020  1.426
 3M4  CAJ  HAJ   single    0.970  0.020  1.090
 3M4  CAJ  HAJA  single    0.970  0.020  1.090
 3M4  CAR  NAL   aromatic  1.300  0.020  1.300
 3M4  NAL  OAO   aromatic  1.362  0.020  1.362
 3M4  CAR  NAM   aromatic  1.357  0.020  1.357
 3M4  NAM  CAT   aromatic  1.298  0.020  1.298
 3M4  OAN  CAQ   single    1.333  0.020  1.333
 3M4  OAO  CAT   aromatic  1.329  0.020  1.329
 3M4  CAP  CAR   single    1.463  0.020  1.463
 3M4  CAS  CAQ   aromatic  1.409  0.020  1.409
 3M4  CAT  CAS   single    1.453  0.020  1.453

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
 3M4  HAAB  CAA  HAAA  108.69  3.000
 3M4  HAAB  CAA  HAA   108.00  3.000
 3M4  HAAA  CAA  HAA   107.97  3.000
 3M4  HAAB  CAA  CAJ   111.45  3.000
 3M4  HAAA  CAA  CAJ   111.47  3.000
 3M4  HAA   CAA  CAJ   109.14  3.000
 3M4  HAB   CAB  CAF   118.99  3.000
 3M4  HAB   CAB  CAC   120.06  3.000
 3M4  CAF   CAB  CAC   120.95  3.000
 3M4  HAC   CAC  CAG   120.23  3.000
 3M4  HAC   CAC  CAB   120.71  3.000
 3M4  CAG   CAC  CAB   119.05  3.000
 3M4  HAD   CAD  NAK   116.62  3.000
 3M4  HAD   CAD  CAH   119.77  3.000
 3M4  NAK   CAD  CAH   123.61  3.000
 3M4  HAE   CAE  NAK   116.69  3.000
 3M4  HAE   CAE  CAI   119.73  3.000
 3M4  NAK   CAE  CAI   123.58  3.000
 3M4  HAF   CAF  CAQ   120.61  3.000
 3M4  HAF   CAF  CAB   119.02  3.000
 3M4  CAQ   CAF  CAB   120.37  3.000
 3M4  HAG   CAG  CAS   118.93  3.000
 3M4  HAG   CAG  CAC   119.85  3.000
 3M4  CAS   CAG  CAC   121.22  3.000
 3M4  HAH   CAH  CAP   121.59  3.000
 3M4  HAH   CAH  CAD   119.94  3.000
 3M4  CAP   CAH  CAD   118.47  3.000
 3M4  HAI   CAI  CAP   121.25  3.000
 3M4  HAI   CAI  CAE   120.25  3.000
 3M4  CAP   CAI  CAE   118.50  3.000
 3M4  HAJA  CAJ  HAJ   107.80  3.000
 3M4  HAJA  CAJ  OAN   109.76  3.000
 3M4  HAJ   CAJ  OAN   110.20  3.000
 3M4  HAJA  CAJ  CAA   110.73  3.000
 3M4  HAJ   CAJ  CAA   110.50  3.000
 3M4  OAN   CAJ  CAA   107.86  3.000
 3M4  CAE   NAK  CAD   117.58  3.000
 3M4  CAR   NAL  OAO   103.91  3.000
 3M4  CAT   NAM  CAR   102.93  3.000
 3M4  CAQ   OAN  CAJ   119.72  3.000
 3M4  CAT   OAO  NAL   107.64  3.000
 3M4  CAR   CAP  CAI   120.24  3.000
 3M4  CAR   CAP  CAH   121.51  3.000
 3M4  CAI   CAP  CAH   118.25  3.000
 3M4  CAS   CAQ  OAN   117.40  3.000
 3M4  CAS   CAQ  CAF   119.01  3.000
 3M4  OAN   CAQ  CAF   123.59  3.000
 3M4  CAP   CAR  NAM   123.32  3.000
 3M4  CAP   CAR  NAL   122.93  3.000
 3M4  NAM   CAR  NAL   113.76  3.000
 3M4  CAT   CAS  CAQ   123.47  3.000
 3M4  CAT   CAS  CAG   117.12  3.000
 3M4  CAQ   CAS  CAG   119.40  3.000
 3M4  CAS   CAT  OAO   121.98  3.000
 3M4  CAS   CAT  NAM   126.26  3.000
 3M4  OAO   CAT  NAM   111.76  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
 3M4  CONST_01  CAS  CAG  CAC  CAB    0.00   0.0  0
 3M4  CONST_02  CAS  CAQ  CAF  CAB    0.00   0.0  0
 3M4  CONST_03  CAQ  CAF  CAB  CAC    0.00   0.0  0
 3M4  CONST_04  CAQ  CAS  CAG  CAC    0.00   0.0  0
 3M4  CONST_05  CAT  CAS  CAG  CAC  180.00   0.0  0
 3M4  CONST_06  CAI  CAE  NAK  CAD    0.00   0.0  0
 3M4  CONST_07  CAI  CAP  CAH  CAD    0.00   0.0  0
 3M4  CONST_08  CAR  CAP  CAH  CAD  180.00   0.0  0
 3M4  CONST_09  CAH  CAD  NAK  CAE    0.00   0.0  0
 3M4  CONST_10  CAH  CAP  CAI  CAE    0.00   0.0  0
 3M4  CONST_11  CAR  CAP  CAI  CAE  180.00   0.0  0
 3M4  CONST_12  CAG  CAC  CAB  CAF    0.00   0.0  0
 3M4  CONST_13  CAG  CAS  CAQ  CAF    0.00   0.0  0
 3M4  CONST_14  CAT  CAS  CAQ  CAF  180.00   0.0  0
 3M4  CONST_15  NAM  CAT  CAS  CAG    0.00   0.0  0
 3M4  CONST_16  OAO  CAT  CAS  CAG  180.00   0.0  0
 3M4  CONST_17  NAL  CAR  CAP  CAH    0.00   0.0  0
 3M4  CONST_18  NAM  CAR  CAP  CAH  180.00   0.0  0
 3M4  CONST_19  NAL  CAR  CAP  CAI  180.00   0.0  0
 3M4  CONST_20  NAM  CAR  CAP  CAI    0.00   0.0  0
 3M4  CONST_21  CAP  CAH  CAD  NAK    0.00   0.0  0
 3M4  CONST_22  CAP  CAI  CAE  NAK    0.00   0.0  0
 3M4  CONST_23  CAT  NAM  CAR  NAL    0.00   0.0  0
 3M4  CONST_24  NAM  CAT  OAO  NAL    0.00   0.0  0
 3M4  CONST_25  CAS  CAT  OAO  NAL  180.00   0.0  0
 3M4  CONST_26  OAO  NAL  CAR  NAM    0.00   0.0  0
 3M4  CONST_27  CAQ  CAS  CAT  NAM  180.00   0.0  0
 3M4  CONST_28  CAP  CAR  NAL  OAO  180.00   0.0  0
 3M4  CONST_29  CAR  NAM  CAT  OAO    0.00   0.0  0
 3M4  CONST_30  CAQ  CAS  CAT  OAO    0.00   0.0  0
 3M4  CONST_31  CAT  NAM  CAR  CAP  180.00   0.0  0
 3M4  CONST_32  CAT  OAO  NAL  CAR    0.00   0.0  0
 3M4  CONST_33  CAS  CAT  NAM  CAR  180.00   0.0  0
 3M4  CONST_34  OAN  CAQ  CAF  CAB  180.00   0.0  0
 3M4  CONST_35  OAN  CAQ  CAS  CAG  180.00   0.0  0
 3M4  CONST_36  CAT  CAS  CAQ  OAN    0.00   0.0  0
 3M4  CONST_37  HAG  CAG  CAC  CAB  180.00   0.0  0
 3M4  CONST_38  HAF  CAF  CAB  CAC  180.00   0.0  0
 3M4  CONST_39  HAE  CAE  NAK  CAD  180.00   0.0  0
 3M4  CONST_40  HAD  CAD  NAK  CAE  180.00   0.0  0
 3M4  CONST_41  HAC  CAC  CAB  CAF  180.00   0.0  0
 3M4  CONST_42  HAB  CAB  CAC  CAG  180.00   0.0  0
 3M4  CONST_43  HAI  CAI  CAP  CAH  180.00   0.0  0
 3M4  CONST_44  HAH  CAH  CAP  CAI  180.00   0.0  0
 3M4  Var_01    CAS  CAQ  OAN  CAJ  174.52  30.0  2
 3M4  Var_02    HAJ  CAJ  OAN  CAQ   61.83  30.0  2
 3M4  Var_03    HAA  CAA  CAJ  OAN  178.59  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
 3M4  plan-1  NAL  0.020
 3M4  plan-1  NAM  0.020
 3M4  plan-1  OAO  0.020
 3M4  plan-1  CAP  0.020
 3M4  plan-1  CAR  0.020
 3M4  plan-1  CAS  0.020
 3M4  plan-1  CAT  0.020
 3M4  plan-2  CAB  0.020
 3M4  plan-2  CAC  0.020
 3M4  plan-2  CAF  0.020
 3M4  plan-2  CAG  0.020
 3M4  plan-2  OAN  0.020
 3M4  plan-2  CAQ  0.020
 3M4  plan-2  CAS  0.020
 3M4  plan-2  CAT  0.020
 3M4  plan-2  HAB  0.020
 3M4  plan-2  HAC  0.020
 3M4  plan-2  HAF  0.020
 3M4  plan-2  HAG  0.020
 3M4  plan-3  CAD  0.020
 3M4  plan-3  CAE  0.020
 3M4  plan-3  CAH  0.020
 3M4  plan-3  CAI  0.020
 3M4  plan-3  NAK  0.020
 3M4  plan-3  CAP  0.020
 3M4  plan-3  CAR  0.020
 3M4  plan-3  HAE  0.020
 3M4  plan-3  HAH  0.020
 3M4  plan-3  HAI  0.020
 3M4  plan-3  HAD  0.020

