# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:36:48 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-[4-[(4-cyclopentyl-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)C3CCCC3)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
 XT0  XT0  2-[4-[(4-cyclopentyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile  ligand  47  27  .  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_XT0
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
 XT0  NAA  N  NS    0  -0.251   6.8526   0.5220  -0.2798
 XT0  CAC  C  CSP   0   0.067   5.9808  -0.2261  -0.1865
 XT0  CAV  C  CR6   0  -0.087   4.9200  -1.1676  -0.0664
 XT0  CAF  C  CR16  0  -0.236   5.1967  -2.5155   0.1634
 XT0  CAD  C  CR16  0  -0.267   4.1594  -3.4210   0.2845
 XT0  CAE  C  CR16  0  -0.231   2.8479  -2.9742   0.1711
 XT0  CAG  C  CR16  0  -0.335   2.5574  -1.6380  -0.0600
 XT0  CAY  C  CR6   0   0.411   3.5968  -0.7263  -0.1791
 XT0  OAS  O  O2    0  -0.494   3.4359   0.5899  -0.4281
 XT0  CAX  C  CR6   0   0.230   2.1797   1.1414  -0.3462
 XT0  CAT  C  CR6   0   0.337   1.6325   1.4021   0.9103
 XT0  CAJ  C  CR16  0  -0.431   0.3837   2.0104   0.9786
 XT0  OAB  O  OH1   0  -0.611   2.3475   1.0418   1.9859
 XT0  CAI  C  CR16  0  -0.291   1.5021   1.4831  -1.5015
 XT0  CAH  C  CR16  0  -0.310   0.2606   2.0950  -1.4219
 XT0  CAU  C  CR6   0   0.138  -0.3022   2.3573  -0.1783
 XT0  CAP  C  CH2   0  -0.425  -1.6658   2.9889  -0.0827
 XT0  NBA  N  NR5   0  -0.246  -2.7088   2.0464  -0.4413
 XT0  CAK  C  CR15  0  -0.091  -3.2092   1.0411   0.2991
 XT0  NAR  N  N     0  -0.102  -3.2165   2.0333  -1.6586
 XT0  NAQ  N  N     0  -0.325  -4.0462   1.0494  -1.7311
 XT0  CAW  C  CR5   0   0.196  -4.0814   0.3996  -0.5443
 XT0  CAZ  C  CR15  0  -0.312  -4.9556  -0.7783  -0.2970
 XT0  CAN  C  CH2   0  -0.434  -6.4589  -0.4857  -0.4218
 XT0  CAL  C  CH2   0  -0.444  -7.1528  -1.6236   0.3541
 XT0  CAM  C  CH2   0  -0.453  -6.0403  -2.3288   1.1600
 XT0  CAO  C  CH2   0  -0.436  -4.8443  -1.3800   1.1016
 XT0  H1   H  HCR6  0   0.286   6.2253  -2.8385   0.2485
 XT0  H2   H  HCR6  0   0.273   4.3694  -4.4662   0.4623
 XT0  H3   H  HCR6  0   0.280   2.0308  -3.6774   0.2606
 XT0  H4   H  HCR6  0   0.293   1.5278  -1.3206  -0.1560
 XT0  H5   H  HCR6  0   0.283  -0.0524   2.2194   1.9495
 XT0  H6   H  HOH1  0   0.484   1.8675   1.2480   2.7966
 XT0  H7   H  HCR6  0   0.280   1.9538   1.2756  -2.4630
 XT0  H8   H  HCR6  0   0.262  -0.2640   2.3618  -2.3301
 XT0  H9   H  HCH2  0   0.299  -1.8628   3.3490   0.9261
 XT0  H10  H  HCH2  0   0.304  -1.7557   3.8349  -0.7623
 XT0  H11  H  HCR5  0   0.302  -2.9212   0.8703   1.3225
 XT0  H12  H  HCR5  0   0.248  -4.6984  -1.5594  -1.0230
 XT0  H13  H  HCH2  0   0.224  -6.6767   0.4801   0.0404
 XT0  H14  H  HCH2  0   0.238  -6.7817  -0.4210  -1.4611
 XT0  H15  H  HCH2  0   0.229  -7.9269  -1.2238   1.0102
 XT0  H16  H  HCH2  0   0.230  -7.6489  -2.3225  -0.3202
 XT0  H17  H  HCH2  0   0.233  -6.3425  -2.5596   2.1817
 XT0  H18  H  HCH2  0   0.225  -5.7751  -3.2761   0.6854
 XT0  H19  H  HCH2  0   0.239  -3.8903  -1.8795   1.2795
 XT0  H20  H  HCH2  0   0.220  -4.9505  -0.5916   1.8538

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
 XT0  NAA  CAC  triple    1.153  0.020  1.153
 XT0  CAC  CAV  single    1.423  0.020  1.423
 XT0  CAI  CAH  aromatic  1.386  0.020  1.386
 XT0  CAI  CAX  aromatic  1.382  0.020  1.382
 XT0  CAV  CAF  aromatic  1.395  0.020  1.395
 XT0  CAV  CAY  aromatic  1.399  0.020  1.399
 XT0  CAF  CAD  aromatic  1.382  0.020  1.382
 XT0  OAS  CAY  single    1.349  0.020  1.349
 XT0  OAS  CAX  single    1.374  0.020  1.374
 XT0  CAY  CAG  aromatic  1.388  0.020  1.388
 XT0  CAH  CAU  aromatic  1.390  0.020  1.390
 XT0  CAX  CAT  aromatic  1.395  0.020  1.395
 XT0  CAD  CAE  aromatic  1.390  0.020  1.390
 XT0  CAG  CAE  aromatic  1.387  0.020  1.387
 XT0  NAR  NAQ  aromatic  1.289  0.020  1.289
 XT0  NAR  NBA  aromatic  1.319  0.020  1.319
 XT0  NAQ  CAW  aromatic  1.354  0.020  1.354
 XT0  CAU  CAP  single    1.506  0.020  1.506
 XT0  CAU  CAJ  aromatic  1.389  0.020  1.389
 XT0  CAT  CAJ  aromatic  1.391  0.020  1.391
 XT0  CAT  OAB  single    1.341  0.020  1.341
 XT0  CAP  NBA  single    1.451  0.020  1.451
 XT0  NBA  CAK  aromatic  1.345  0.020  1.345
 XT0  CAW  CAK  aromatic  1.372  0.020  1.372
 XT0  CAW  CAZ  single    1.488  0.020  1.488
 XT0  CAO  CAZ  single    1.527  0.020  1.527
 XT0  CAO  CAM  single    1.528  0.020  1.528
 XT0  CAZ  CAN  single    1.537  0.020  1.537
 XT0  CAM  CAL  single    1.544  0.020  1.544
 XT0  CAN  CAL  single    1.542  0.020  1.542
 XT0  CAF  H1   single    0.930  0.020  1.080
 XT0  CAD  H2   single    0.930  0.020  1.080
 XT0  CAE  H3   single    0.930  0.020  1.080
 XT0  CAG  H4   single    0.930  0.020  1.080
 XT0  CAJ  H5   single    0.930  0.020  1.080
 XT0  OAB  H6   single    0.850  0.020  0.980
 XT0  CAI  H7   single    0.930  0.020  1.080
 XT0  CAH  H8   single    0.930  0.020  1.080
 XT0  CAP  H9   single    0.970  0.020  1.090
 XT0  CAP  H10  single    0.970  0.020  1.090
 XT0  CAK  H11  single    0.930  0.020  1.080
 XT0  CAZ  H12  single    0.970  0.020  1.090
 XT0  CAN  H13  single    0.970  0.020  1.090
 XT0  CAN  H14  single    0.970  0.020  1.090
 XT0  CAL  H15  single    0.970  0.020  1.090
 XT0  CAL  H16  single    0.970  0.020  1.090
 XT0  CAM  H17  single    0.970  0.020  1.090
 XT0  CAM  H18  single    0.970  0.020  1.090
 XT0  CAO  H19  single    0.970  0.020  1.090
 XT0  CAO  H20  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
 XT0  CAV  CAC  NAA  180.00  3.000
 XT0  CAY  CAV  CAF  120.36  3.000
 XT0  CAY  CAV  CAC  119.30  3.000
 XT0  CAF  CAV  CAC  120.34  3.000
 XT0  H1   CAF  CAD  120.74  3.000
 XT0  H1   CAF  CAV  119.35  3.000
 XT0  CAD  CAF  CAV  119.90  3.000
 XT0  H2   CAD  CAE  120.50  3.000
 XT0  H2   CAD  CAF  120.14  3.000
 XT0  CAE  CAD  CAF  119.36  3.000
 XT0  H3   CAE  CAG  118.81  3.000
 XT0  H3   CAE  CAD  119.80  3.000
 XT0  CAG  CAE  CAD  121.39  3.000
 XT0  H4   CAG  CAY  120.83  3.000
 XT0  H4   CAG  CAE  119.80  3.000
 XT0  CAY  CAG  CAE  119.37  3.000
 XT0  OAS  CAY  CAG  124.57  3.000
 XT0  CAG  CAY  CAV  119.61  3.000
 XT0  OAS  CAY  CAV  115.80  3.000
 XT0  CAX  OAS  CAY  119.30  3.000
 XT0  CAI  CAX  CAT  120.95  3.000
 XT0  CAT  CAX  OAS  119.15  3.000
 XT0  CAI  CAX  OAS  119.84  3.000
 XT0  OAB  CAT  CAJ  123.85  3.000
 XT0  OAB  CAT  CAX  117.59  3.000
 XT0  CAJ  CAT  CAX  118.56  3.000
 XT0  H5   CAJ  CAU  119.92  3.000
 XT0  H5   CAJ  CAT  119.29  3.000
 XT0  CAU  CAJ  CAT  120.79  3.000
 XT0  H6   OAB  CAT  110.58  3.000
 XT0  H7   CAI  CAH  120.62  3.000
 XT0  H7   CAI  CAX  119.37  3.000
 XT0  CAH  CAI  CAX  120.01  3.000
 XT0  H8   CAH  CAU  120.53  3.000
 XT0  H8   CAH  CAI  119.65  3.000
 XT0  CAU  CAH  CAI  119.82  3.000
 XT0  CAP  CAU  CAH  120.18  3.000
 XT0  CAP  CAU  CAJ  119.94  3.000
 XT0  CAH  CAU  CAJ  119.87  3.000
 XT0  H10  CAP  H9   107.84  3.000
 XT0  H10  CAP  NBA  106.92  3.000
 XT0  H9   CAP  NBA  108.28  3.000
 XT0  H10  CAP  CAU  111.16  3.000
 XT0  H9   CAP  CAU  111.18  3.000
 XT0  NBA  CAP  CAU  111.28  3.000
 XT0  NAR  NBA  CAK  110.94  3.000
 XT0  CAK  NBA  CAP  128.09  3.000
 XT0  NAR  NBA  CAP  120.75  3.000
 XT0  H11  CAK  CAW  132.84  3.000
 XT0  H11  CAK  NBA  122.83  3.000
 XT0  CAW  CAK  NBA  104.33  3.000
 XT0  NAQ  NAR  NBA  107.90  3.000
 XT0  CAW  NAQ  NAR  109.50  3.000
 XT0  CAZ  CAW  NAQ  122.77  3.000
 XT0  CAZ  CAW  CAK  129.90  3.000
 XT0  NAQ  CAW  CAK  107.33  3.000
 XT0  H12  CAZ  CAO  107.98  3.000
 XT0  H12  CAZ  CAN  108.13  3.000
 XT0  CAO  CAZ  CAN  102.75  3.000
 XT0  H12  CAZ  CAW  108.42  3.000
 XT0  CAN  CAZ  CAW  114.24  3.000
 XT0  CAO  CAZ  CAW  114.94  3.000
 XT0  H14  CAN  H13  106.97  3.000
 XT0  H14  CAN  CAL  112.96  3.000
 XT0  H13  CAN  CAL  110.47  3.000
 XT0  H14  CAN  CAZ  112.24  3.000
 XT0  H13  CAN  CAZ  109.21  3.000
 XT0  CAL  CAN  CAZ  105.00  3.000
 XT0  H16  CAL  H15  106.50  3.000
 XT0  H16  CAL  CAM  110.96  3.000
 XT0  H15  CAL  CAM  111.39  3.000
 XT0  H16  CAL  CAN  111.50  3.000
 XT0  H15  CAL  CAN  110.58  3.000
 XT0  CAM  CAL  CAN  105.99  3.000
 XT0  H18  CAM  H17  106.91  3.000
 XT0  H18  CAM  CAO  109.39  3.000
 XT0  H17  CAM  CAO  112.60  3.000
 XT0  H18  CAM  CAL  110.14  3.000
 XT0  H17  CAM  CAL  112.71  3.000
 XT0  CAO  CAM  CAL  105.09  3.000
 XT0  H20  CAO  H19  107.60  3.000
 XT0  H20  CAO  CAM  110.18  3.000
 XT0  H19  CAO  CAM  113.19  3.000
 XT0  H20  CAO  CAZ  109.79  3.000
 XT0  H19  CAO  CAZ  113.17  3.000
 XT0  CAM  CAO  CAZ  102.87  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
 XT0  CONST_01  CAE  CAD  CAF  CAV     0.00   0.0  0
 XT0  CONST_02  CAE  CAG  CAY  CAV     0.00   0.0  0
 XT0  CONST_03  CAG  CAY  CAV  CAF     0.00   0.0  0
 XT0  CONST_04  CAG  CAE  CAD  CAF     0.00   0.0  0
 XT0  CONST_05  CAY  CAV  CAF  CAD     0.00   0.0  0
 XT0  CONST_06  CAY  CAG  CAE  CAD     0.00   0.0  0
 XT0  CONST_07  CAU  CAH  CAI  CAX     0.00   0.0  0
 XT0  CONST_08  CAU  CAJ  CAT  CAX     0.00   0.0  0
 XT0  CONST_09  CAH  CAI  CAX  CAT     0.00   0.0  0
 XT0  CONST_10  CAH  CAU  CAJ  CAT     0.00   0.0  0
 XT0  CONST_11  CAI  CAH  CAU  CAJ     0.00   0.0  0
 XT0  CONST_12  CAI  CAX  CAT  CAJ     0.00   0.0  0
 XT0  CONST_13  CAW  NAQ  NAR  NBA     0.00   0.0  0
 XT0  CONST_14  NAQ  CAW  CAK  NBA     0.00   0.0  0
 XT0  CONST_15  NAQ  NAR  NBA  CAK     0.00   0.0  0
 XT0  CONST_16  NAR  NAQ  CAW  CAK     0.00   0.0  0
 XT0  CONST_17  CAW  CAK  NBA  NAR     0.00   0.0  0
 XT0  CONST_18  CAZ  CAW  CAK  NBA   180.00   0.0  0
 XT0  CONST_19  CAZ  CAW  NAQ  NAR   180.00   0.0  0
 XT0  CONST_20  CAD  CAF  CAV  CAC   180.00   0.0  0
 XT0  CONST_21  CAG  CAY  CAV  CAC   180.00   0.0  0
 XT0  CONST_22  OAS  CAY  CAV  CAF   180.00   0.0  0
 XT0  CONST_23  OAS  CAY  CAG  CAE   180.00   0.0  0
 XT0  CONST_24  CAH  CAI  CAX  OAS   180.00   0.0  0
 XT0  CONST_25  CAJ  CAT  CAX  OAS   180.00   0.0  0
 XT0  CONST_26  CAP  CAU  CAJ  CAT   180.00   0.0  0
 XT0  CONST_27  CAI  CAX  CAT  OAB   180.00   0.0  0
 XT0  CONST_28  CAU  CAJ  CAT  OAB   180.00   0.0  0
 XT0  CONST_29  CAP  CAU  CAH  CAI   180.00   0.0  0
 XT0  CONST_30  NAQ  NAR  NBA  CAP   180.00   0.0  0
 XT0  CONST_31  CAW  CAK  NBA  CAP   180.00   0.0  0
 XT0  CONST_32  H2   CAD  CAF  CAV   180.00   0.0  0
 XT0  CONST_33  H4   CAG  CAY  CAV   180.00   0.0  0
 XT0  CONST_34  H3   CAE  CAD  CAF   180.00   0.0  0
 XT0  CONST_35  H1   CAF  CAD  CAE   180.00   0.0  0
 XT0  CONST_36  H8   CAH  CAI  CAX   180.00   0.0  0
 XT0  CONST_37  H5   CAJ  CAT  CAX   180.00   0.0  0
 XT0  CONST_38  H7   CAI  CAX  CAT   180.00   0.0  0
 XT0  CONST_39  H11  CAK  NBA  NAR   180.00   0.0  0
 XT0  Var_01    CAL  CAM  CAO  CAZ   -35.25  30.0  1
 XT0  Var_02    CAM  CAL  CAN  CAZ    12.81  30.0  1
 XT0  Var_03    CAO  CAM  CAL  CAN    13.78  30.0  1
 XT0  Var_04    CAI  CAX  OAS  CAY  -106.14  30.0  2
 XT0  Var_05    NBA  CAP  CAU  CAJ  -105.63  30.0  2
 XT0  Var_06    NAR  NBA  CAP  CAU   -97.19  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
 XT0  chir_01  CAZ  CAW  CAO  CAN  negativ

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
 XT0  plan-1  CAP  0.020
 XT0  plan-1  NBA  0.020
 XT0  plan-1  CAK  0.020
 XT0  plan-1  NAR  0.020
 XT0  plan-1  NAQ  0.020
 XT0  plan-1  CAW  0.020
 XT0  plan-1  CAZ  0.020
 XT0  plan-1  H11  0.020
 XT0  plan-2  NAA  0.020
 XT0  plan-2  CAC  0.020
 XT0  plan-2  CAV  0.020
 XT0  plan-2  CAF  0.020
 XT0  plan-2  CAD  0.020
 XT0  plan-2  CAE  0.020
 XT0  plan-2  CAG  0.020
 XT0  plan-2  CAY  0.020
 XT0  plan-2  OAS  0.020
 XT0  plan-2  H1   0.020
 XT0  plan-2  H2   0.020
 XT0  plan-2  H3   0.020
 XT0  plan-2  H4   0.020
 XT0  plan-3  OAS  0.020
 XT0  plan-3  CAX  0.020
 XT0  plan-3  CAT  0.020
 XT0  plan-3  CAJ  0.020
 XT0  plan-3  OAB  0.020
 XT0  plan-3  CAI  0.020
 XT0  plan-3  CAH  0.020
 XT0  plan-3  CAU  0.020
 XT0  plan-3  CAP  0.020
 XT0  plan-3  H5   0.020
 XT0  plan-3  H7   0.020
 XT0  plan-3  H8   0.020

