# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:24:21 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: ~{N}-[[3-(4-methoxyphenyl)-1,2,4-oxadiazol-5-yl]methyl]-2-(4-nitrophenyl)-~{N}-propan-2-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2noc(CN(C(C)C)C(=O)Cc3ccc(cc3)[N](=O)=O)n2
#
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
 6XF  6XF  ~{N}-[[3-(4-methoxyphenyl)-1,2,4-oxadiazol-5-yl]methyl]-2-(4-nitrophenyl)-~{N}-propan-2-yl-ethanamide  ligand  52  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 PERFECT
;

data_comp_6XF
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
 6XF  CAA  C  CH3    0  -0.440   7.5059   3.9604  -0.1510
 6XF  OAS  O  O2     0  -0.463   6.9381   3.1766   0.8824
 6XF  CAW  C  CR6    0   0.391   5.9328   2.3429   0.5808
 6XF  CAJ  C  CR16   0  -0.328   5.4140   1.5880   1.6366
 6XF  CAL  C  CR16   0  -0.270   4.3786   0.7038   1.4161
 6XF  CAI  C  CR16   0  -0.368   5.3921   2.1934  -0.6971
 6XF  CAK  C  CR16   0  -0.266   4.3540   1.3010  -0.9058
 6XF  CAX  C  CR6    0  -0.021   3.8329   0.5451   0.1407
 6XF  CBA  C  CR5    0   0.318   2.7402  -0.3956  -0.0743
 6XF  NAR  N  N      0  -0.472   2.1564  -1.1052   0.9383
 6XF  NAQ  N  N      0  -0.168   2.2196  -0.6390  -1.2418
 6XF  OAT  O  O      0  -0.322   1.2427  -1.5645  -0.9803
 6XF  CAZ  C  CR5    0   0.564   1.2547  -1.7885   0.3220
 6XF  CAP  C  CH2    0  -0.441   0.3245  -2.7959   0.9049
 6XF  NBC  N  NT     0  -0.460  -0.9209  -2.9069   0.1819
 6XF  CBB  C  CH1    0  -0.146  -1.2839  -4.2029  -0.3977
 6XF  CAC  C  CH3    0  -0.649  -0.2964  -4.6235  -1.4779
 6XF  CAB  C  CH3    0  -0.649  -1.4451  -5.2684   0.6801
 6XF  CAU  C  C      0   0.604  -1.6827  -1.7911   0.1471
 6XF  OAD  O  O      0  -0.478  -1.2985  -0.7581   0.6738
 6XF  CAO  C  CH2    0  -0.727  -3.0228  -1.8569  -0.5684
 6XF  CAV  C  CR6    0   0.189  -3.6841  -0.5132  -0.5895
 6XF  CAG  C  CR16   0  -0.298  -4.5929  -0.1525   0.4000
 6XF  CAM  C  CR16   0  -0.252  -5.2022   1.0899   0.3903
 6XF  CAY  C  CR6    0   0.236  -4.8906   1.9773  -0.6295
 6XF  NBD  N  N      1   0.330  -5.5253   3.2844  -0.6527
 6XF  OAF  O  O     -1  -0.381  -6.2943   3.5601   0.2383
 6XF  OAE  O  O      0  -0.381  -5.2528   4.0336  -1.5616
 6XF  CAN  C  CR16   0  -0.253  -3.9888   1.6445  -1.6306
 6XF  CAH  C  CR16   0  -0.289  -3.3917   0.3977  -1.6005
 6XF  H1   H  HCH3   0   0.233   6.7752   4.6433  -0.5915
 6XF  H2   H  HCH3   0   0.263   8.2993   4.5450   0.3071
 6XF  H3   H  HCH3   0   0.233   7.9345   3.3407  -0.9423
 6XF  H4   H  HCR6   0   0.270   5.8315   1.7016   2.6289
 6XF  H5   H  HCR6   0   0.262   3.9910   0.1261   2.2447
 6XF  H6   H  HCR6   0   0.287   5.7643   2.7637  -1.5368
 6XF  H7   H  HCR6   0   0.264   3.9483   1.2020  -1.9043
 6XF  H8   H  HCH2   0   0.311   0.8307  -3.7630   0.9027
 6XF  H9   H  HCH2   0   0.308   0.1688  -2.5342   1.9530
 6XF  H10  H  HCH1   0   0.278  -2.2537  -4.0752  -0.8731
 6XF  H11  H  HCH3   0   0.228   0.6988  -4.8141  -1.0724
 6XF  H12  H  HCH3   0   0.244  -0.6362  -5.5484  -1.9440
 6XF  H13  H  HCH3   0   0.243  -0.2112  -3.8650  -2.2554
 6XF  H14  H  HCH3   0   0.243  -2.1333  -4.9402   1.4593
 6XF  H15  H  HCH3   0   0.246  -1.8474  -6.1794   0.2375
 6XF  H16  H  HCH3   0   0.228  -0.4944  -5.5296   1.1476
 6XF  H17  H  HCH2   0   0.306  -2.8828  -2.2170  -1.5905
 6XF  H18  H  HCH2   0   0.310  -3.6644  -2.5871  -0.0682
 6XF  H19  H  HCR6   0   0.271  -4.8349  -0.8522   1.1894
 6XF  H20  H  HCR6   0   0.297  -5.9067   1.3496   1.1669
 6XF  H21  H  HCR6   0   0.297  -3.7505   2.3381  -2.4234
 6XF  H22  H  HCR6   0   0.270  -2.6910   0.1322  -2.3818

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
 6XF  CAO  CAU  single    1.521  0.020  1.521
 6XF  CAO  CAV  single    1.498  0.020  1.498
 6XF  CAB  CBB  single    1.524  0.020  1.524
 6XF  CAG  CAV  aromatic  1.391  0.020  1.391
 6XF  CAG  CAM  aromatic  1.384  0.020  1.384
 6XF  OAD  CAU  double    1.221  0.020  1.221
 6XF  CAU  NBC  single    1.352  0.020  1.352
 6XF  CAV  CAH  aromatic  1.392  0.020  1.392
 6XF  CAM  CAY  aromatic  1.387  0.020  1.387
 6XF  NBC  CBB  single    1.465  0.020  1.465
 6XF  NBC  CAP  single    1.444  0.020  1.444
 6XF  CBB  CAC  single    1.523  0.020  1.523
 6XF  CAH  CAN  aromatic  1.383  0.020  1.383
 6XF  CAP  CAZ  single    1.490  0.020  1.490
 6XF  CAY  CAN  aromatic  1.388  0.020  1.388
 6XF  CAY  NBD  single    1.453  0.020  1.453
 6XF  NBD  OAF  single    1.209  0.020  1.209
 6XF  NBD  OAE  double    1.209  0.020  1.209
 6XF  CAZ  OAT  aromatic  1.321  0.020  1.321
 6XF  CAZ  NAR  aromatic  1.288  0.020  1.288
 6XF  OAT  NAQ  aromatic  1.371  0.020  1.371
 6XF  NAR  CBA  aromatic  1.367  0.020  1.367
 6XF  NAQ  CBA  aromatic  1.301  0.020  1.301
 6XF  CBA  CAX  single    1.458  0.020  1.458
 6XF  CAX  CAK  aromatic  1.392  0.020  1.392
 6XF  CAX  CAL  aromatic  1.396  0.020  1.396
 6XF  CAK  CAI  aromatic  1.385  0.020  1.385
 6XF  CAL  CAJ  aromatic  1.379  0.020  1.379
 6XF  CAI  CAW  aromatic  1.396  0.020  1.396
 6XF  CAJ  CAW  aromatic  1.398  0.020  1.398
 6XF  CAW  OAS  single    1.340  0.020  1.340
 6XF  OAS  CAA  single    1.416  0.020  1.416
 6XF  CAA  H1   single    0.970  0.020  1.090
 6XF  CAA  H2   single    0.970  0.020  1.090
 6XF  CAA  H3   single    0.970  0.020  1.090
 6XF  CAJ  H4   single    0.930  0.020  1.080
 6XF  CAL  H5   single    0.930  0.020  1.080
 6XF  CAI  H6   single    0.930  0.020  1.080
 6XF  CAK  H7   single    0.930  0.020  1.080
 6XF  CAP  H8   single    0.970  0.020  1.090
 6XF  CAP  H9   single    0.970  0.020  1.090
 6XF  CBB  H10  single    0.970  0.020  1.090
 6XF  CAC  H11  single    0.970  0.020  1.090
 6XF  CAC  H12  single    0.970  0.020  1.090
 6XF  CAC  H13  single    0.970  0.020  1.090
 6XF  CAB  H14  single    0.970  0.020  1.090
 6XF  CAB  H15  single    0.970  0.020  1.090
 6XF  CAB  H16  single    0.970  0.020  1.090
 6XF  CAO  H17  single    0.970  0.020  1.090
 6XF  CAO  H18  single    0.970  0.020  1.090
 6XF  CAG  H19  single    0.930  0.020  1.080
 6XF  CAM  H20  single    0.930  0.020  1.080
 6XF  CAN  H21  single    0.930  0.020  1.080
 6XF  CAH  H22  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
 6XF  H3   CAA  H2   108.90  3.000
 6XF  H3   CAA  H1   108.96  3.000
 6XF  H2   CAA  H1   108.78  3.000
 6XF  H3   CAA  OAS  111.83  3.000
 6XF  H2   CAA  OAS  106.43  3.000
 6XF  H1   CAA  OAS  111.84  3.000
 6XF  CAW  OAS  CAA  118.75  3.000
 6XF  CAI  CAW  CAJ  119.34  3.000
 6XF  CAJ  CAW  OAS  116.38  3.000
 6XF  CAI  CAW  OAS  124.27  3.000
 6XF  H4   CAJ  CAL  120.22  3.000
 6XF  H4   CAJ  CAW  119.51  3.000
 6XF  CAL  CAJ  CAW  120.27  3.000
 6XF  H5   CAL  CAX  119.93  3.000
 6XF  H5   CAL  CAJ  119.26  3.000
 6XF  CAX  CAL  CAJ  120.81  3.000
 6XF  H6   CAI  CAK  118.75  3.000
 6XF  H6   CAI  CAW  121.42  3.000
 6XF  CAK  CAI  CAW  119.83  3.000
 6XF  H7   CAK  CAX  120.23  3.000
 6XF  H7   CAK  CAI  118.62  3.000
 6XF  CAX  CAK  CAI  121.15  3.000
 6XF  CBA  CAX  CAK  121.34  3.000
 6XF  CAK  CAX  CAL  118.60  3.000
 6XF  CBA  CAX  CAL  120.07  3.000
 6XF  NAQ  CBA  NAR  113.36  3.000
 6XF  NAQ  CBA  CAX  123.57  3.000
 6XF  NAR  CBA  CAX  123.07  3.000
 6XF  CAZ  NAR  CBA  102.70  3.000
 6XF  OAT  NAQ  CBA  103.90  3.000
 6XF  CAZ  OAT  NAQ  107.21  3.000
 6XF  CAP  CAZ  OAT  119.63  3.000
 6XF  OAT  CAZ  NAR  112.82  3.000
 6XF  CAP  CAZ  NAR  127.48  3.000
 6XF  H9   CAP  H8   106.29  3.000
 6XF  H9   CAP  NBC  112.10  3.000
 6XF  H8   CAP  NBC  109.32  3.000
 6XF  H9   CAP  CAZ  107.61  3.000
 6XF  H8   CAP  CAZ  107.98  3.000
 6XF  NBC  CAP  CAZ  113.24  3.000
 6XF  CAU  NBC  CBB  125.48  3.000
 6XF  CBB  NBC  CAP  118.66  3.000
 6XF  CAU  NBC  CAP  115.82  3.000
 6XF  H10  CBB  CAB  107.27  3.000
 6XF  H10  CBB  CAC  107.49  3.000
 6XF  CAB  CBB  CAC  112.16  3.000
 6XF  H10  CBB  NBC  106.86  3.000
 6XF  CAC  CBB  NBC  111.36  3.000
 6XF  CAB  CBB  NBC  111.40  3.000
 6XF  H13  CAC  H12  108.06  3.000
 6XF  H13  CAC  H11  108.38  3.000
 6XF  H12  CAC  H11  107.15  3.000
 6XF  H13  CAC  CBB  111.38  3.000
 6XF  H12  CAC  CBB  109.61  3.000
 6XF  H11  CAC  CBB  112.08  3.000
 6XF  H16  CAB  H15  107.19  3.000
 6XF  H16  CAB  H14  108.41  3.000
 6XF  H15  CAB  H14  108.00  3.000
 6XF  H16  CAB  CBB  112.22  3.000
 6XF  H15  CAB  CBB  109.65  3.000
 6XF  H14  CAB  CBB  111.21  3.000
 6XF  CAO  CAU  OAD  121.11  3.000
 6XF  OAD  CAU  NBC  120.65  3.000
 6XF  CAO  CAU  NBC  118.24  3.000
 6XF  H18  CAO  H17  106.44  3.000
 6XF  H18  CAO  CAV  110.27  3.000
 6XF  H17  CAO  CAV  109.82  3.000
 6XF  H18  CAO  CAU  109.32  3.000
 6XF  H17  CAO  CAU  109.97  3.000
 6XF  CAV  CAO  CAU  110.91  3.000
 6XF  CAH  CAV  CAG  118.96  3.000
 6XF  CAH  CAV  CAO  120.30  3.000
 6XF  CAG  CAV  CAO  120.74  3.000
 6XF  H19  CAG  CAM  119.15  3.000
 6XF  H19  CAG  CAV  119.82  3.000
 6XF  CAM  CAG  CAV  121.03  3.000
 6XF  H20  CAM  CAY  121.41  3.000
 6XF  H20  CAM  CAG  119.87  3.000
 6XF  CAY  CAM  CAG  118.72  3.000
 6XF  CAN  CAY  NBD  119.21  3.000
 6XF  NBD  CAY  CAM  119.28  3.000
 6XF  CAN  CAY  CAM  121.52  3.000
 6XF  OAE  NBD  OAF  123.79  3.000
 6XF  OAE  NBD  CAY  118.10  3.000
 6XF  OAF  NBD  CAY  118.11  3.000
 6XF  H21  CAN  CAH  119.98  3.000
 6XF  H21  CAN  CAY  121.26  3.000
 6XF  CAH  CAN  CAY  118.76  3.000
 6XF  H22  CAH  CAN  119.01  3.000
 6XF  H22  CAH  CAV  119.98  3.000
 6XF  CAN  CAH  CAV  121.01  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
 6XF  CONST_01  CAX  CAK  CAI  CAW     0.00   0.0  0
 6XF  CONST_02  CAX  CAL  CAJ  CAW     0.00   0.0  0
 6XF  CONST_03  CBA  CAX  CAL  CAJ   180.00   0.0  0
 6XF  CONST_04  CAK  CAX  CAL  CAJ     0.00   0.0  0
 6XF  CONST_05  CAK  CAI  CAW  CAJ     0.00   0.0  0
 6XF  CONST_06  NAR  CBA  CAX  CAL     0.00   0.0  0
 6XF  CONST_07  NAQ  CBA  CAX  CAL   180.00   0.0  0
 6XF  CONST_08  CAI  CAK  CAX  CAL     0.00   0.0  0
 6XF  CONST_09  CAI  CAW  CAJ  CAL     0.00   0.0  0
 6XF  CONST_10  CBA  CAX  CAK  CAI   180.00   0.0  0
 6XF  CONST_11  NAR  CBA  CAX  CAK   180.00   0.0  0
 6XF  CONST_12  NAQ  CBA  CAX  CAK     0.00   0.0  0
 6XF  CONST_13  CAZ  NAR  CBA  CAX   180.00   0.0  0
 6XF  CONST_14  OAT  NAQ  CBA  CAX   180.00   0.0  0
 6XF  CONST_15  OAT  CAZ  NAR  CBA     0.00   0.0  0
 6XF  CONST_16  CAZ  OAT  NAQ  CBA     0.00   0.0  0
 6XF  CONST_17  NAQ  OAT  CAZ  NAR     0.00   0.0  0
 6XF  CONST_18  OAT  NAQ  CBA  NAR     0.00   0.0  0
 6XF  CONST_19  CAZ  NAR  CBA  NAQ     0.00   0.0  0
 6XF  CONST_20  CAY  CAM  CAG  CAV     0.00   0.0  0
 6XF  CONST_21  CAY  CAN  CAH  CAV     0.00   0.0  0
 6XF  CONST_22  CAN  CAH  CAV  CAG     0.00   0.0  0
 6XF  CONST_23  CAN  CAY  CAM  CAG     0.00   0.0  0
 6XF  CONST_24  CAH  CAV  CAG  CAM     0.00   0.0  0
 6XF  CONST_25  CAH  CAN  CAY  CAM     0.00   0.0  0
 6XF  CONST_26  CAK  CAI  CAW  OAS   180.00   0.0  0
 6XF  CONST_27  CAL  CAJ  CAW  OAS   180.00   0.0  0
 6XF  CONST_28  CAP  CAZ  NAR  CBA   180.00   0.0  0
 6XF  CONST_29  CAP  CAZ  OAT  NAQ   180.00   0.0  0
 6XF  CONST_30  CAM  CAG  CAV  CAO   180.00   0.0  0
 6XF  CONST_31  CAN  CAH  CAV  CAO   180.00   0.0  0
 6XF  CONST_32  NBD  CAY  CAM  CAG   180.00   0.0  0
 6XF  CONST_33  CAH  CAN  CAY  NBD   180.00   0.0  0
 6XF  CONST_34  H7   CAK  CAI  CAW   180.00   0.0  0
 6XF  CONST_35  H5   CAL  CAJ  CAW   180.00   0.0  0
 6XF  CONST_36  H6   CAI  CAW  CAJ   180.00   0.0  0
 6XF  CONST_37  H4   CAJ  CAW  CAI   180.00   0.0  0
 6XF  CONST_38  H20  CAM  CAG  CAV   180.00   0.0  0
 6XF  CONST_39  H21  CAN  CAH  CAV   180.00   0.0  0
 6XF  CONST_40  H22  CAH  CAV  CAG   180.00   0.0  0
 6XF  CONST_41  H19  CAG  CAM  CAY   180.00   0.0  0
 6XF  CONST_42  OAF  NBD  CAY  CAM     0.00   0.0  0
 6XF  CONST_43  OAE  NBD  CAY  CAM   180.00   0.0  0
 6XF  CONST_44  CAN  CAY  NBD  OAF   180.00   0.0  0
 6XF  CONST_45  CAN  CAY  NBD  OAE     0.00   0.0  0
 6XF  CONST_46  CAO  CAU  NBC  CAP   180.00   0.0  0
 6XF  CONST_47  OAD  CAU  NBC  CAP     0.00   0.0  0
 6XF  CONST_48  CAO  CAU  NBC  CBB     0.00   0.0  0
 6XF  CONST_49  OAD  CAU  NBC  CBB   180.00   0.0  0
 6XF  Var_01    CAI  CAW  OAS  CAA    -0.32  30.0  3
 6XF  Var_02    NBC  CAP  CAZ  NAR   151.97  30.0  1
 6XF  Var_03    CAG  CAV  CAO  CAU   -93.39  30.0  2
 6XF  Var_04    CAU  NBC  CAP  CAZ   -62.01  30.0  2
 6XF  Var_05    CAV  CAO  CAU  NBC  -176.09  30.0  1
 6XF  Var_06    H1   CAA  OAS  CAW    61.98  30.0  3
 6XF  Var_07    CAB  CBB  NBC  CAP    61.97  30.0  3
 6XF  Var_08    H14  CAB  CBB  NBC    52.82  30.0  3
 6XF  Var_09    H11  CAC  CBB  NBC    65.69  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
 6XF  plan-1  CAX  0.020
 6XF  plan-1  CBA  0.020
 6XF  plan-1  NAR  0.020
 6XF  plan-1  NAQ  0.020
 6XF  plan-1  OAT  0.020
 6XF  plan-1  CAZ  0.020
 6XF  plan-1  CAP  0.020
 6XF  plan-2  OAS  0.020
 6XF  plan-2  CAW  0.020
 6XF  plan-2  CAJ  0.020
 6XF  plan-2  CAL  0.020
 6XF  plan-2  CAI  0.020
 6XF  plan-2  CAK  0.020
 6XF  plan-2  CAX  0.020
 6XF  plan-2  CBA  0.020
 6XF  plan-2  H4   0.020
 6XF  plan-2  H5   0.020
 6XF  plan-2  H6   0.020
 6XF  plan-2  H7   0.020
 6XF  plan-3  CAO  0.020
 6XF  plan-3  CAV  0.020
 6XF  plan-3  CAG  0.020
 6XF  plan-3  CAM  0.020
 6XF  plan-3  CAY  0.020
 6XF  plan-3  NBD  0.020
 6XF  plan-3  CAN  0.020
 6XF  plan-3  CAH  0.020
 6XF  plan-3  H19  0.020
 6XF  plan-3  H20  0.020
 6XF  plan-3  H21  0.020
 6XF  plan-3  H22  0.020
 6XF  plan-4  CAP  0.020
 6XF  plan-4  NBC  0.020
 6XF  plan-4  CBB  0.020
 6XF  plan-4  CAU  0.020
 6XF  plan-4  OAD  0.020
 6XF  plan-4  CAO  0.020
 6XF  plan-5  CAY  0.020
 6XF  plan-5  NBD  0.020
 6XF  plan-5  OAF  0.020
 6XF  plan-5  OAE  0.020

