# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:05:04 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[4-[(4-cyclohexyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(Cn2cc(nn2)C3CCCCC3)ccc1Oc4ccccc4C#N
#
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
 XT3  XT3  2-[4-[(4-cyclohexyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile  ligand  50  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XT3
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
 XT3  NAA  N  NS    0  -0.247  -4.6184  -3.8557  -0.2467
 XT3  CAC  C  CSP   0   0.069  -4.9131  -2.7430  -0.3008
 XT3  CAW  C  CR6   0  -0.077  -5.2920  -1.3725  -0.3698
 XT3  CAF  C  CR16  0  -0.237  -6.6364  -1.0158  -0.4693
 XT3  CAD  C  CR16  0  -0.263  -6.9929   0.3184  -0.5367
 XT3  CAE  C  CR16  0  -0.228  -6.0023   1.2918  -0.5033
 XT3  CAG  C  CR16  0  -0.329  -4.6603   0.9524  -0.4035
 XT3  CAZ  C  CR6   0   0.394  -4.3018  -0.3849  -0.3341
 XT3  OAT  O  O2    0  -0.511  -3.0293  -0.8347  -0.2187
 XT3  CAY  C  CR6   0   0.193  -1.9851   0.0589  -0.3224
 XT3  CAU  C  CR6   0   0.332  -1.3596   0.4719   0.8559
 XT3  CAJ  C  CR16  0  -0.369  -0.2785   1.3393   0.7645
 XT3  OAB  O  OH1   0  -0.616  -1.7647   0.0697   2.0705
 XT3  CAI  C  CR16  0  -0.281  -1.5446   0.4947  -1.5569
 XT3  CAH  C  CR16  0  -0.328  -0.4642   1.3613  -1.6347
 XT3  CAV  C  CR6   0   0.117   0.1666   1.7880  -0.4728
 XT3  CAQ  C  CH2   0  -0.400   1.3468   2.7211  -0.5456
 XT3  NBB  N  NR5   0  -0.247   2.5412   2.1116   0.0040
 XT3  CAK  C  CR15  0  -0.084   3.2651   1.1023  -0.5105
 XT3  NAS  N  N     0  -0.106   2.9952   2.4610   1.1927
 XT3  NAR  N  N     0  -0.323   4.0075   1.7095   1.4643
 XT3  CAX  C  CR5   0   0.204   4.2189   0.8471   0.4443
 XT3  CBA  C  CH1   0  -0.330   5.3355  -0.1421   0.4383
 XT3  CAO  C  CH2   0  -0.414   6.5630   0.4028  -0.3043
 XT3  CAM  C  CH2   0  -0.436   7.7073  -0.6054  -0.3041
 XT3  CAL  C  CH2   0  -0.431   7.2695  -1.9466  -0.8832
 XT3  CAN  C  CH2   0  -0.433   6.0487  -2.4927  -0.1501
 XT3  CAP  C  CH2   0  -0.422   4.9029  -1.4867  -0.1514
 XT3  H1   H  HCR6  0   0.288  -7.3899  -1.7908  -0.4945
 XT3  H2   H  HCR6  0   0.275  -8.0341   0.5971  -0.6152
 XT3  H3   H  HCR6  0   0.282  -6.2718   2.3382  -0.5545
 XT3  H4   H  HCR6  0   0.298  -3.9108   1.7311  -0.3820
 XT3  H5   H  HCR6  0   0.272   0.2112   1.6607   1.6768
 XT3  H6   H  HOH1  0   0.478  -2.4244  -0.6308   2.0033
 XT3  H7   H  HCR6  0   0.287  -2.0406   0.1519  -2.4561
 XT3  H8   H  HCR6  0   0.267  -0.1142   1.6969  -2.6021
 XT3  H9   H  HCH2  0   0.297   1.5475   3.0120  -1.5760
 XT3  H10  H  HCH2  0   0.302   1.1655   3.6307   0.0263
 XT3  H11  H  HCR5  0   0.303   3.0513   0.6673  -1.4721
 XT3  H12  H  HCH1  0   0.237   5.6257  -0.3040   1.4834
 XT3  H13  H  HCH2  0   0.215   6.2792   0.6370  -1.3361
 XT3  H14  H  HCH2  0   0.234   6.8822   1.3427   0.1531
 XT3  H15  H  HCH2  0   0.230   8.5537  -0.2070  -0.8687
 XT3  H16  H  HCH2  0   0.212   8.0615  -0.7512   0.7226
 XT3  H17  H  HCH2  0   0.210   7.0259  -1.8209  -1.9439
 XT3  H18  H  HCH2  0   0.229   8.0913  -2.6650  -0.8363
 XT3  H19  H  HCH2  0   0.230   5.7213  -3.4302  -0.6054
 XT3  H20  H  HCH2  0   0.212   6.3220  -2.7292   0.8838
 XT3  H21  H  HCH2  0   0.236   4.0508  -1.8784   0.4098
 XT3  H22  H  HCH2  0   0.214   4.5567  -1.3395  -1.1809

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
 XT3  CAD  CAF  aromatic  1.383  0.020  1.383
 XT3  CAD  CAE  aromatic  1.389  0.020  1.389
 XT3  CAF  CAW  aromatic  1.394  0.020  1.394
 XT3  CAE  CAG  aromatic  1.388  0.020  1.388
 XT3  CAW  CAC  single    1.424  0.020  1.424
 XT3  CAW  CAZ  aromatic  1.399  0.020  1.399
 XT3  CAG  CAZ  aromatic  1.386  0.020  1.386
 XT3  CAC  NAA  triple    1.152  0.020  1.152
 XT3  CAZ  OAT  single    1.355  0.020  1.355
 XT3  OAB  CAU  single    1.342  0.020  1.342
 XT3  OAT  CAY  single    1.378  0.020  1.378
 XT3  CAU  CAY  aromatic  1.396  0.020  1.396
 XT3  CAU  CAJ  aromatic  1.389  0.020  1.389
 XT3  CAO  CBA  single    1.535  0.020  1.535
 XT3  CAO  CAM  single    1.525  0.020  1.525
 XT3  CBA  CAP  single    1.531  0.020  1.531
 XT3  CBA  CAX  single    1.492  0.020  1.492
 XT3  CAY  CAI  aromatic  1.381  0.020  1.381
 XT3  CAJ  CAV  aromatic  1.389  0.020  1.389
 XT3  CAP  CAN  single    1.525  0.020  1.525
 XT3  CAX  CAK  aromatic  1.374  0.020  1.374
 XT3  CAX  NAR  aromatic  1.352  0.020  1.352
 XT3  CAK  NBB  aromatic  1.344  0.020  1.344
 XT3  CAN  CAL  single    1.525  0.020  1.525
 XT3  CAI  CAH  aromatic  1.387  0.020  1.387
 XT3  CAM  CAL  single    1.525  0.020  1.525
 XT3  CAV  CAH  aromatic  1.389  0.020  1.389
 XT3  CAV  CAQ  single    1.506  0.020  1.506
 XT3  NAR  NAS  aromatic  1.290  0.020  1.290
 XT3  NBB  NAS  aromatic  1.320  0.020  1.320
 XT3  NBB  CAQ  single    1.449  0.020  1.449
 XT3  CAF  H1   single    0.930  0.020  1.080
 XT3  CAD  H2   single    0.930  0.020  1.080
 XT3  CAE  H3   single    0.930  0.020  1.080
 XT3  CAG  H4   single    0.930  0.020  1.080
 XT3  CAJ  H5   single    0.930  0.020  1.080
 XT3  OAB  H6   single    0.850  0.020  0.980
 XT3  CAI  H7   single    0.930  0.020  1.080
 XT3  CAH  H8   single    0.930  0.020  1.080
 XT3  CAQ  H9   single    0.970  0.020  1.090
 XT3  CAQ  H10  single    0.970  0.020  1.090
 XT3  CAK  H11  single    0.930  0.020  1.080
 XT3  CBA  H12  single    0.970  0.020  1.090
 XT3  CAO  H13  single    0.970  0.020  1.090
 XT3  CAO  H14  single    0.970  0.020  1.090
 XT3  CAM  H15  single    0.970  0.020  1.090
 XT3  CAM  H16  single    0.970  0.020  1.090
 XT3  CAL  H17  single    0.970  0.020  1.090
 XT3  CAL  H18  single    0.970  0.020  1.090
 XT3  CAN  H19  single    0.970  0.020  1.090
 XT3  CAN  H20  single    0.970  0.020  1.090
 XT3  CAP  H21  single    0.970  0.020  1.090
 XT3  CAP  H22  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
 XT3  CAW  CAC  NAA  180.00  3.000
 XT3  CAZ  CAW  CAF  120.24  3.000
 XT3  CAZ  CAW  CAC  119.34  3.000
 XT3  CAF  CAW  CAC  120.42  3.000
 XT3  H1   CAF  CAD  120.72  3.000
 XT3  H1   CAF  CAW  119.35  3.000
 XT3  CAD  CAF  CAW  119.93  3.000
 XT3  H2   CAD  CAE  120.54  3.000
 XT3  H2   CAD  CAF  120.05  3.000
 XT3  CAE  CAD  CAF  119.41  3.000
 XT3  H3   CAE  CAG  118.74  3.000
 XT3  H3   CAE  CAD  119.93  3.000
 XT3  CAG  CAE  CAD  121.33  3.000
 XT3  H4   CAG  CAZ  120.97  3.000
 XT3  H4   CAG  CAE  119.72  3.000
 XT3  CAZ  CAG  CAE  119.31  3.000
 XT3  OAT  CAZ  CAG  124.58  3.000
 XT3  OAT  CAZ  CAW  115.64  3.000
 XT3  CAG  CAZ  CAW  119.78  3.000
 XT3  CAY  OAT  CAZ  119.34  3.000
 XT3  CAI  CAY  CAU  121.19  3.000
 XT3  CAI  CAY  OAT  120.89  3.000
 XT3  CAU  CAY  OAT  117.88  3.000
 XT3  OAB  CAU  CAJ  118.79  3.000
 XT3  CAJ  CAU  CAY  118.54  3.000
 XT3  OAB  CAU  CAY  122.67  3.000
 XT3  H5   CAJ  CAV  120.60  3.000
 XT3  H5   CAJ  CAU  118.76  3.000
 XT3  CAV  CAJ  CAU  120.64  3.000
 XT3  H6   OAB  CAU  111.16  3.000
 XT3  H7   CAI  CAH  120.53  3.000
 XT3  H7   CAI  CAY  119.76  3.000
 XT3  CAH  CAI  CAY  119.71  3.000
 XT3  H8   CAH  CAV  120.37  3.000
 XT3  H8   CAH  CAI  119.72  3.000
 XT3  CAV  CAH  CAI  119.91  3.000
 XT3  CAQ  CAV  CAH  120.37  3.000
 XT3  CAQ  CAV  CAJ  119.61  3.000
 XT3  CAH  CAV  CAJ  120.01  3.000
 XT3  H10  CAQ  H9   107.71  3.000
 XT3  H10  CAQ  NBB  106.81  3.000
 XT3  H9   CAQ  NBB  108.61  3.000
 XT3  H10  CAQ  CAV  111.19  3.000
 XT3  H9   CAQ  CAV  110.83  3.000
 XT3  NBB  CAQ  CAV  111.52  3.000
 XT3  NAS  NBB  CAK  111.00  3.000
 XT3  NAS  NBB  CAQ  120.92  3.000
 XT3  CAK  NBB  CAQ  127.91  3.000
 XT3  H11  CAK  CAX  133.12  3.000
 XT3  H11  CAK  NBB  122.55  3.000
 XT3  CAX  CAK  NBB  104.32  3.000
 XT3  NAR  NAS  NBB  107.79  3.000
 XT3  CAX  NAR  NAS  109.60  3.000
 XT3  CBA  CAX  NAR  122.88  3.000
 XT3  NAR  CAX  CAK  107.30  3.000
 XT3  CBA  CAX  CAK  129.80  3.000
 XT3  H12  CBA  CAP  108.20  3.000
 XT3  H12  CBA  CAO  107.57  3.000
 XT3  CAP  CBA  CAO  110.58  3.000
 XT3  H12  CBA  CAX  106.99  3.000
 XT3  CAP  CBA  CAX  111.88  3.000
 XT3  CAO  CBA  CAX  111.42  3.000
 XT3  H14  CAO  H13  106.62  3.000
 XT3  H14  CAO  CAM  110.45  3.000
 XT3  H13  CAO  CAM  109.62  3.000
 XT3  H14  CAO  CBA  109.66  3.000
 XT3  H13  CAO  CBA  108.93  3.000
 XT3  CAM  CAO  CBA  111.43  3.000
 XT3  H16  CAM  H15  106.40  3.000
 XT3  H16  CAM  CAL  109.36  3.000
 XT3  H15  CAM  CAL  110.29  3.000
 XT3  H16  CAM  CAO  109.30  3.000
 XT3  H15  CAM  CAO  109.88  3.000
 XT3  CAL  CAM  CAO  111.47  3.000
 XT3  H18  CAL  H17  106.51  3.000
 XT3  H18  CAL  CAN  110.24  3.000
 XT3  H17  CAL  CAN  109.18  3.000
 XT3  H18  CAL  CAM  110.25  3.000
 XT3  H17  CAL  CAM  109.30  3.000
 XT3  CAN  CAL  CAM  111.23  3.000
 XT3  H20  CAN  H19  106.43  3.000
 XT3  H20  CAN  CAP  109.32  3.000
 XT3  H19  CAN  CAP  109.91  3.000
 XT3  H20  CAN  CAL  109.35  3.000
 XT3  H19  CAN  CAL  110.30  3.000
 XT3  CAP  CAN  CAL  111.40  3.000
 XT3  H22  CAP  H21  106.50  3.000
 XT3  H22  CAP  CAN  109.07  3.000
 XT3  H21  CAP  CAN  110.43  3.000
 XT3  H22  CAP  CBA  109.46  3.000
 XT3  H21  CAP  CBA  109.71  3.000
 XT3  CAN  CAP  CBA  111.52  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
 XT3  CONST_01  CAE  CAD  CAF  CAW    0.00   0.0  0
 XT3  CONST_02  CAE  CAG  CAZ  CAW    0.00   0.0  0
 XT3  CONST_03  CAG  CAE  CAD  CAF    0.00   0.0  0
 XT3  CONST_04  CAG  CAZ  CAW  CAF    0.00   0.0  0
 XT3  CONST_05  CAZ  CAW  CAF  CAD    0.00   0.0  0
 XT3  CONST_06  CAZ  CAG  CAE  CAD    0.00   0.0  0
 XT3  CONST_07  CAV  CAJ  CAU  CAY    0.00   0.0  0
 XT3  CONST_08  CAV  CAH  CAI  CAY    0.00   0.0  0
 XT3  CONST_09  CAH  CAI  CAY  CAU    0.00   0.0  0
 XT3  CONST_10  CAH  CAV  CAJ  CAU    0.00   0.0  0
 XT3  CONST_11  CAI  CAY  CAU  CAJ    0.00   0.0  0
 XT3  CONST_12  CAI  CAH  CAV  CAJ    0.00   0.0  0
 XT3  CONST_13  NAR  CAX  CAK  NBB    0.00   0.0  0
 XT3  CONST_14  CAX  NAR  NAS  NBB    0.00   0.0  0
 XT3  CONST_15  NAS  NAR  CAX  CAK    0.00   0.0  0
 XT3  CONST_16  NAR  NAS  NBB  CAK    0.00   0.0  0
 XT3  CONST_17  CAX  CAK  NBB  NAS    0.00   0.0  0
 XT3  CONST_18  CBA  CAX  CAK  NBB  180.00   0.0  0
 XT3  CONST_19  CBA  CAX  NAR  NAS  180.00   0.0  0
 XT3  CONST_20  CAD  CAF  CAW  CAC  180.00   0.0  0
 XT3  CONST_21  CAG  CAZ  CAW  CAC  180.00   0.0  0
 XT3  CONST_22  OAT  CAZ  CAW  CAF  180.00   0.0  0
 XT3  CONST_23  OAT  CAZ  CAG  CAE  180.00   0.0  0
 XT3  CONST_24  CAJ  CAU  CAY  OAT  180.00   0.0  0
 XT3  CONST_25  CAH  CAI  CAY  OAT  180.00   0.0  0
 XT3  CONST_26  CAQ  CAV  CAJ  CAU  180.00   0.0  0
 XT3  CONST_27  CAI  CAY  CAU  OAB  180.00   0.0  0
 XT3  CONST_28  CAV  CAJ  CAU  OAB  180.00   0.0  0
 XT3  CONST_29  CAQ  CAV  CAH  CAI  180.00   0.0  0
 XT3  CONST_30  CAX  CAK  NBB  CAQ  180.00   0.0  0
 XT3  CONST_31  NAR  NAS  NBB  CAQ  180.00   0.0  0
 XT3  CONST_32  H2   CAD  CAF  CAW  180.00   0.0  0
 XT3  CONST_33  H4   CAG  CAZ  CAW  180.00   0.0  0
 XT3  CONST_34  H3   CAE  CAD  CAF  180.00   0.0  0
 XT3  CONST_35  H1   CAF  CAD  CAE  180.00   0.0  0
 XT3  CONST_36  H5   CAJ  CAU  CAY  180.00   0.0  0
 XT3  CONST_37  H8   CAH  CAI  CAY  180.00   0.0  0
 XT3  CONST_38  H7   CAI  CAY  CAU  180.00   0.0  0
 XT3  CONST_39  H11  CAK  NBB  NAS  180.00   0.0  0
 XT3  Var_01    CAL  CAM  CAO  CBA   55.40  30.0  1
 XT3  Var_02    CAL  CAN  CAP  CBA  -55.59  30.0  1
 XT3  Var_03    CAN  CAL  CAM  CAO  -55.09  30.0  1
 XT3  Var_04    CAP  CAN  CAL  CAM   55.12  30.0  1
 XT3  Var_05    CAU  CAY  OAT  CAZ  102.38  30.0  2
 XT3  Var_06    NBB  CAQ  CAV  CAJ   61.11  30.0  2
 XT3  Var_07    CAK  NBB  CAQ  CAV   70.08  30.0  2

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
 XT3  chir_01  CBA  CAO  CAP  CAX  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
 XT3  plan-1  CAQ  0.020
 XT3  plan-1  NBB  0.020
 XT3  plan-1  CAK  0.020
 XT3  plan-1  NAS  0.020
 XT3  plan-1  NAR  0.020
 XT3  plan-1  CAX  0.020
 XT3  plan-1  CBA  0.020
 XT3  plan-1  H11  0.020
 XT3  plan-2  NAA  0.020
 XT3  plan-2  CAC  0.020
 XT3  plan-2  CAW  0.020
 XT3  plan-2  CAF  0.020
 XT3  plan-2  CAD  0.020
 XT3  plan-2  CAE  0.020
 XT3  plan-2  CAG  0.020
 XT3  plan-2  CAZ  0.020
 XT3  plan-2  OAT  0.020
 XT3  plan-2  H1   0.020
 XT3  plan-2  H2   0.020
 XT3  plan-2  H3   0.020
 XT3  plan-2  H4   0.020
 XT3  plan-3  OAT  0.020
 XT3  plan-3  CAY  0.020
 XT3  plan-3  CAU  0.020
 XT3  plan-3  CAJ  0.020
 XT3  plan-3  OAB  0.020
 XT3  plan-3  CAI  0.020
 XT3  plan-3  CAH  0.020
 XT3  plan-3  CAV  0.020
 XT3  plan-3  CAQ  0.020
 XT3  plan-3  H5   0.020
 XT3  plan-3  H7   0.020
 XT3  plan-3  H8   0.020

