# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:41:03 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-(2-methylphenoxy)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1Oc2ccc(Cn3cc(nn3)C4CC4)cc2O
#
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
 XT5  XT5  5-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-(2-methylphenoxy)phenol  ligand  43  24  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XT5
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
 XT5  CAK  C  CH2   0  -0.452  -5.9434  -1.5884   0.9571
 XT5  CAL  C  CH2   0  -0.460  -4.7422  -2.3937   0.5939
 XT5  CAW  C  CH1   0  -0.347  -5.2527  -1.3528  -0.3605
 XT5  CAT  C  CR5   0   0.195  -4.4956  -0.1152  -0.5962
 XT5  CAJ  C  CR15  0  -0.086  -3.5597   0.5221   0.1804
 XT5  NAN  N  N     0  -0.300  -4.6696   0.6247  -1.7160
 XT5  NAO  N  N     0  -0.067  -3.9095   1.6618  -1.6667
 XT5  NAX  N  NR5   0  -0.247  -3.2415   1.6206  -0.5294
 XT5  CAM  C  CH2   0  -0.396  -2.2597   2.6378  -0.2156
 XT5  CAR  C  CR6   0   0.138  -0.8543   2.1117  -0.3200
 XT5  CAI  C  CR16  0  -0.425  -0.0668   1.9830   0.8177
 XT5  CAS  C  CR6   0   0.342   1.2298   1.4900   0.7375
 XT5  OAB  O  OH1   0  -0.585   2.0432   1.3512   1.7970
 XT5  CAG  C  CR16  0  -0.284  -0.3409   1.7400  -1.5542
 XT5  CAH  C  CR16  0  -0.285   0.9477   1.2361  -1.6414
 XT5  CAV  C  CR6   0   0.265   1.7329   1.1099  -0.5099
 XT5  OAP  O  O2    0  -0.495   3.0143   0.6658  -0.6137
 XT5  CAU  C  CR6   0   0.345   3.3341  -0.5617  -0.0979
 XT5  CAF  C  CR16  0  -0.304   2.3958  -1.5683   0.0676
 XT5  CAD  C  CR16  0  -0.235   2.7958  -2.8020   0.5619
 XT5  CAC  C  CR16  0  -0.226   4.1236  -3.0257   0.8810
 XT5  CAE  C  CR16  0  -0.269   5.0484  -2.0053   0.7049
 XT5  CAQ  C  CR6   0   0.038   4.6784  -0.7577   0.2204
 XT5  CAA  C  CH3   0  -0.694   5.6742   0.3500   0.0538
 XT5  H1   H  HCH2  0   0.254  -6.9113  -2.0716   0.9402
 XT5  H2   H  HCH2  0   0.244  -5.8399  -0.8274   1.7195
 XT5  H3   H  HCH2  0   0.238  -3.8120  -2.1950   1.1116
 XT5  H4   H  HCH2  0   0.253  -4.8800  -3.4324   0.3243
 XT5  H5   H  HCH1  0   0.259  -5.7688  -1.7144  -1.2420
 XT5  H6   H  HCR5  0   0.266  -3.1192   0.2938   1.1357
 XT5  H7   H  HCH2  0   0.290  -2.4301   3.4509  -0.9202
 XT5  H8   H  HCH2  0   0.259  -2.4615   3.0220   0.7850
 XT5  H9   H  HCR6  0   0.223  -0.4652   2.2818   1.7828
 XT5  H10  H  HOH1  0   0.445   1.5957   1.6178   2.6044
 XT5  H11  H  HCR6  0   0.243  -0.9456   1.8333  -2.4474
 XT5  H12  H  HCR6  0   0.252   1.3608   0.9433  -2.5977
 XT5  H13  H  HCR6  0   0.244   1.3578  -1.4034  -0.1919
 XT5  H14  H  HCR6  0   0.223   2.0614  -3.5859   0.6904
 XT5  H15  H  HCR6  0   0.221   4.4425  -3.9853   1.2644
 XT5  H16  H  HCR6  0   0.217   6.0878  -2.1772   0.9567
 XT5  H17  H  HCH3  0   0.238   5.7775   0.6522  -0.9893
 XT5  H18  H  HCH3  0   0.242   5.3795   1.2374   0.6153
 XT5  H19  H  HCH3  0   0.224   6.6564   0.0397   0.4069

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
 XT5  CAC  CAD  aromatic  1.384  0.020  1.384
 XT5  CAC  CAE  aromatic  1.388  0.020  1.388
 XT5  CAD  CAF  aromatic  1.388  0.020  1.388
 XT5  CAE  CAQ  aromatic  1.389  0.020  1.389
 XT5  CAK  CAL  single    1.491  0.020  1.491
 XT5  CAK  CAW  single    1.506  0.020  1.506
 XT5  CAF  CAU  aromatic  1.386  0.020  1.386
 XT5  CAL  CAW  single    1.502  0.020  1.502
 XT5  CAW  CAT  single    1.470  0.020  1.470
 XT5  CAQ  CAU  aromatic  1.395  0.020  1.395
 XT5  CAQ  CAA  single    1.499  0.020  1.499
 XT5  CAU  OAP  single    1.369  0.020  1.369
 XT5  CAT  CAJ  aromatic  1.373  0.020  1.373
 XT5  CAT  NAN  aromatic  1.353  0.020  1.353
 XT5  CAJ  NAX  aromatic  1.346  0.020  1.346
 XT5  OAB  CAS  single    1.343  0.020  1.343
 XT5  OAP  CAV  single    1.360  0.020  1.360
 XT5  NAN  NAO  aromatic  1.287  0.020  1.287
 XT5  CAS  CAV  aromatic  1.398  0.020  1.398
 XT5  CAS  CAI  aromatic  1.389  0.020  1.389
 XT5  CAV  CAH  aromatic  1.383  0.020  1.383
 XT5  CAI  CAR  aromatic  1.390  0.020  1.390
 XT5  CAH  CAG  aromatic  1.386  0.020  1.386
 XT5  NAX  NAO  aromatic  1.320  0.020  1.320
 XT5  NAX  CAM  single    1.448  0.020  1.448
 XT5  CAR  CAG  aromatic  1.387  0.020  1.387
 XT5  CAR  CAM  single    1.504  0.020  1.504
 XT5  CAK  H1   single    0.970  0.020  1.090
 XT5  CAK  H2   single    0.970  0.020  1.090
 XT5  CAL  H3   single    0.970  0.020  1.090
 XT5  CAL  H4   single    0.970  0.020  1.090
 XT5  CAW  H5   single    0.970  0.020  1.090
 XT5  CAJ  H6   single    0.930  0.020  1.080
 XT5  CAM  H7   single    0.970  0.020  1.090
 XT5  CAM  H8   single    0.970  0.020  1.090
 XT5  CAI  H9   single    0.930  0.020  1.080
 XT5  OAB  H10  single    0.850  0.020  0.980
 XT5  CAG  H11  single    0.930  0.020  1.080
 XT5  CAH  H12  single    0.930  0.020  1.080
 XT5  CAF  H13  single    0.930  0.020  1.080
 XT5  CAD  H14  single    0.930  0.020  1.080
 XT5  CAC  H15  single    0.930  0.020  1.080
 XT5  CAE  H16  single    0.930  0.020  1.080
 XT5  CAA  H17  single    0.970  0.020  1.090
 XT5  CAA  H18  single    0.970  0.020  1.090
 XT5  CAA  H19  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
 XT5  H2   CAK  H1   114.25  3.000
 XT5  H2   CAK  CAW  117.54  3.000
 XT5  H1   CAK  CAW  117.80  3.000
 XT5  H2   CAK  CAL  118.31  3.000
 XT5  H1   CAK  CAL  118.40  3.000
 XT5  CAW  CAK  CAL   60.13  3.000
 XT5  H4   CAL  H3   113.88  3.000
 XT5  H4   CAL  CAW  117.63  3.000
 XT5  H3   CAL  CAW  117.95  3.000
 XT5  H4   CAL  CAK  118.46  3.000
 XT5  H3   CAL  CAK  118.45  3.000
 XT5  CAW  CAL  CAK   60.43  3.000
 XT5  H5   CAW  CAT  113.32  3.000
 XT5  H5   CAW  CAL  116.59  3.000
 XT5  CAT  CAW  CAL  120.69  3.000
 XT5  H5   CAW  CAK  116.16  3.000
 XT5  CAT  CAW  CAK  120.54  3.000
 XT5  CAL  CAW  CAK   59.43  3.000
 XT5  NAN  CAT  CAJ  107.57  3.000
 XT5  NAN  CAT  CAW  121.79  3.000
 XT5  CAJ  CAT  CAW  130.64  3.000
 XT5  H6   CAJ  NAX  122.98  3.000
 XT5  H6   CAJ  CAT  133.03  3.000
 XT5  NAX  CAJ  CAT  103.99  3.000
 XT5  NAO  NAN  CAT  109.45  3.000
 XT5  NAX  NAO  NAN  107.87  3.000
 XT5  CAM  NAX  NAO  120.53  3.000
 XT5  CAM  NAX  CAJ  128.27  3.000
 XT5  NAO  NAX  CAJ  111.11  3.000
 XT5  H8   CAM  H7   107.55  3.000
 XT5  H8   CAM  CAR  111.09  3.000
 XT5  H7   CAM  CAR  111.25  3.000
 XT5  H8   CAM  NAX  108.71  3.000
 XT5  H7   CAM  NAX  106.14  3.000
 XT5  CAR  CAM  NAX  111.88  3.000
 XT5  CAG  CAR  CAI  119.59  3.000
 XT5  CAG  CAR  CAM  120.08  3.000
 XT5  CAI  CAR  CAM  120.33  3.000
 XT5  H9   CAI  CAS  119.43  3.000
 XT5  H9   CAI  CAR  119.61  3.000
 XT5  CAS  CAI  CAR  120.95  3.000
 XT5  CAV  CAS  OAB  117.26  3.000
 XT5  CAV  CAS  CAI  118.94  3.000
 XT5  OAB  CAS  CAI  123.80  3.000
 XT5  H10  OAB  CAS  110.62  3.000
 XT5  H11  CAG  CAH  119.91  3.000
 XT5  H11  CAG  CAR  120.27  3.000
 XT5  CAH  CAG  CAR  119.82  3.000
 XT5  H12  CAH  CAV  118.79  3.000
 XT5  H12  CAH  CAG  120.58  3.000
 XT5  CAV  CAH  CAG  120.62  3.000
 XT5  OAP  CAV  CAH  120.15  3.000
 XT5  CAH  CAV  CAS  120.07  3.000
 XT5  OAP  CAV  CAS  119.74  3.000
 XT5  CAU  OAP  CAV  118.94  3.000
 XT5  CAQ  CAU  CAF  121.53  3.000
 XT5  CAQ  CAU  OAP  115.90  3.000
 XT5  CAF  CAU  OAP  122.54  3.000
 XT5  H13  CAF  CAD  119.81  3.000
 XT5  H13  CAF  CAU  120.65  3.000
 XT5  CAD  CAF  CAU  119.53  3.000
 XT5  H14  CAD  CAC  120.45  3.000
 XT5  H14  CAD  CAF  119.39  3.000
 XT5  CAC  CAD  CAF  120.16  3.000
 XT5  H15  CAC  CAE  120.05  3.000
 XT5  H15  CAC  CAD  120.54  3.000
 XT5  CAE  CAC  CAD  119.41  3.000
 XT5  H16  CAE  CAQ  118.64  3.000
 XT5  H16  CAE  CAC  119.54  3.000
 XT5  CAQ  CAE  CAC  121.82  3.000
 XT5  CAA  CAQ  CAE  121.72  3.000
 XT5  CAA  CAQ  CAU  120.73  3.000
 XT5  CAE  CAQ  CAU  117.55  3.000
 XT5  H19  CAA  H18  107.97  3.000
 XT5  H19  CAA  H17  107.68  3.000
 XT5  H18  CAA  H17  107.00  3.000
 XT5  H19  CAA  CAQ  110.65  3.000
 XT5  H18  CAA  CAQ  111.38  3.000
 XT5  H17  CAA  CAQ  111.96  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
 XT5  CONST_01  NAO  NAX  CAJ  CAT     0.00   0.0  0
 XT5  CONST_02  NAX  NAO  NAN  CAT     0.00   0.0  0
 XT5  CONST_03  NAO  NAN  CAT  CAJ     0.00   0.0  0
 XT5  CONST_04  NAN  NAO  NAX  CAJ     0.00   0.0  0
 XT5  CONST_05  NAX  CAJ  CAT  NAN     0.00   0.0  0
 XT5  CONST_06  CAV  CAS  CAI  CAR     0.00   0.0  0
 XT5  CONST_07  CAV  CAH  CAG  CAR     0.00   0.0  0
 XT5  CONST_08  CAH  CAV  CAS  CAI     0.00   0.0  0
 XT5  CONST_09  CAH  CAG  CAR  CAI     0.00   0.0  0
 XT5  CONST_10  CAG  CAH  CAV  CAS     0.00   0.0  0
 XT5  CONST_11  CAG  CAR  CAI  CAS     0.00   0.0  0
 XT5  CONST_12  CAC  CAD  CAF  CAU     0.00   0.0  0
 XT5  CONST_13  CAC  CAE  CAQ  CAU     0.00   0.0  0
 XT5  CONST_14  CAE  CAC  CAD  CAF     0.00   0.0  0
 XT5  CONST_15  CAE  CAQ  CAU  CAF     0.00   0.0  0
 XT5  CONST_16  CAQ  CAE  CAC  CAD     0.00   0.0  0
 XT5  CONST_17  CAQ  CAU  CAF  CAD     0.00   0.0  0
 XT5  CONST_18  NAX  CAJ  CAT  CAW   180.00   0.0  0
 XT5  CONST_19  NAO  NAN  CAT  CAW   180.00   0.0  0
 XT5  CONST_20  CAM  NAX  CAJ  CAT   180.00   0.0  0
 XT5  CONST_21  CAM  NAX  NAO  NAN   180.00   0.0  0
 XT5  CONST_22  CAS  CAI  CAR  CAM   180.00   0.0  0
 XT5  CONST_23  CAH  CAG  CAR  CAM   180.00   0.0  0
 XT5  CONST_24  OAB  CAS  CAI  CAR   180.00   0.0  0
 XT5  CONST_25  OAP  CAV  CAS  CAI   180.00   0.0  0
 XT5  CONST_26  CAH  CAV  CAS  OAB   180.00   0.0  0
 XT5  CONST_27  OAP  CAV  CAH  CAG   180.00   0.0  0
 XT5  CONST_28  CAD  CAF  CAU  OAP   180.00   0.0  0
 XT5  CONST_29  CAE  CAQ  CAU  OAP   180.00   0.0  0
 XT5  CONST_30  CAA  CAQ  CAU  CAF   180.00   0.0  0
 XT5  CONST_31  CAA  CAQ  CAE  CAC   180.00   0.0  0
 XT5  CONST_32  H6   CAJ  CAT  CAW     0.00   0.0  0
 XT5  CONST_33  H12  CAH  CAG  CAR   180.00   0.0  0
 XT5  CONST_34  H11  CAG  CAR  CAI   180.00   0.0  0
 XT5  CONST_35  H9   CAI  CAR  CAG   180.00   0.0  0
 XT5  CONST_36  H14  CAD  CAF  CAU   180.00   0.0  0
 XT5  CONST_37  H16  CAE  CAQ  CAU   180.00   0.0  0
 XT5  CONST_38  H15  CAC  CAD  CAF   180.00   0.0  0
 XT5  CONST_39  H13  CAF  CAD  CAC   180.00   0.0  0
 XT5  Var_01    CAT  CAW  CAL  CAK   109.62  30.0  1
 XT5  Var_02    CAJ  CAT  CAW  CAK    47.61  30.0  2
 XT5  Var_03    CAR  CAM  NAX  CAJ    69.19  30.0  2
 XT5  Var_04    CAI  CAR  CAM  NAX  -112.64  30.0  2
 XT5  Var_05    CAF  CAU  OAP  CAV    24.72  30.0  1
 XT5  Var_06    H17  CAA  CAQ  CAU   -63.41  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
 XT5  chir_01  CAW  CAK  CAL  CAT  both

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
 XT5  plan-1  CAW  0.020
 XT5  plan-1  CAT  0.020
 XT5  plan-1  CAJ  0.020
 XT5  plan-1  NAN  0.020
 XT5  plan-1  NAO  0.020
 XT5  plan-1  NAX  0.020
 XT5  plan-1  CAM  0.020
 XT5  plan-1  H6   0.020
 XT5  plan-2  CAM  0.020
 XT5  plan-2  CAR  0.020
 XT5  plan-2  CAI  0.020
 XT5  plan-2  CAS  0.020
 XT5  plan-2  OAB  0.020
 XT5  plan-2  CAG  0.020
 XT5  plan-2  CAH  0.020
 XT5  plan-2  CAV  0.020
 XT5  plan-2  OAP  0.020
 XT5  plan-2  H9   0.020
 XT5  plan-2  H11  0.020
 XT5  plan-2  H12  0.020
 XT5  plan-3  OAP  0.020
 XT5  plan-3  CAU  0.020
 XT5  plan-3  CAF  0.020
 XT5  plan-3  CAD  0.020
 XT5  plan-3  CAC  0.020
 XT5  plan-3  CAE  0.020
 XT5  plan-3  CAQ  0.020
 XT5  plan-3  CAA  0.020
 XT5  plan-3  H13  0.020
 XT5  plan-3  H14  0.020
 XT5  plan-3  H15  0.020
 XT5  plan-3  H16  0.020

