# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:13:17 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: ~{N}-[2-(1,2,3-triazol-1-yl)ethyl]cubane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCn1ccnn1)C23C4C5C6C4C2C6C35
#
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
 O0Q  O0Q  ~{N}-[2-(1,2,3-triazol-1-yl)ethyl]cubane-1-carboxamide  ligand  32  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O0Q
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
 O0Q  CAS  C  CR15  0  -0.184  12.4244  29.1073  -67.2938
 O0Q  CAT  C  CR15  0  -0.059  11.0971  29.3834  -67.4861
 O0Q  CAX  C  CH2   0  -0.318   9.0681  27.9222  -67.2344
 O0Q  CAZ  C  CH2   0  -0.303   8.5152  28.0597  -65.8152
 O0Q  CBB  C  C     0   0.500   6.1066  28.7183  -65.6498
 O0Q  CBD  C  C     0  -0.179   6.4940  30.1473  -65.4866
 O0Q  CBE  C  C     0  -0.184   5.4553  31.2876  -65.3479
 O0Q  CBF  C  C     0  -0.196   6.2692  32.1582  -66.3458
 O0Q  CBG  C  C     0  -0.204   7.3208  31.0240  -66.4855
 O0Q  CBH  C  C     0  -0.213   7.0786  32.7629  -65.1628
 O0Q  CBI  C  C     0  -0.202   6.2639  31.8905  -64.1650
 O0Q  CBJ  C  C     0  -0.211   8.1297  31.6230  -65.3001
 O0Q  CBK  C  C     0  -0.197   7.3152  30.7553  -64.2984
 O0Q  NAU  N  NR5   0  -0.245  10.4859  28.2070  -67.2620
 O0Q  NAV  N  N     0  -0.294  12.5380  27.8038  -66.9634
 O0Q  NAW  N  N     0  -0.101  11.3648  27.2720  -66.9419
 O0Q  NBA  N  NH1   0  -0.624   7.0994  27.8106  -65.7715
 O0Q  OBC  O  O     0  -0.483   4.9303  28.3803  -65.6557
 O0Q  H1   H  HCR5  0   0.279  13.2768  29.7600  -67.3815
 O0Q  H2   H  HCR5  0   0.312  10.5712  30.2798  -67.7676
 O0Q  H3   H  HCH2  0   0.281   8.5704  28.6085  -67.9170
 O0Q  H4   H  HCH2  0   0.293   8.9165  26.9116  -67.6109
 O0Q  H5   H  HCH2  0   0.280   9.0248  27.3500  -65.1611
 O0Q  H6   H  HCH2  0   0.271   8.7408  29.0515  -65.4269
 O0Q  H7   H  H     0   0.221   4.3778  31.1432  -65.3683
 O0Q  H8   H  H     0   0.224   5.8463  32.7181  -67.1767
 O0Q  H9   H  H     0   0.232   7.7344  30.6751  -67.4299
 O0Q  H10  H  H     0   0.221   7.3129  33.8167  -65.0313
 O0Q  H11  H  H     0   0.223   5.8393  32.2347  -63.2249
 O0Q  H12  H  H     0   0.227   9.2094  31.7559  -65.2794
 O0Q  H13  H  H     0   0.235   7.7312  30.1782  -63.4748
 O0Q  H14  H  HNH1  0   0.397   6.8066  26.8485  -65.8662

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
 O0Q  CAS  NAV  aromatic  1.349  0.020  1.349
 O0Q  CAS  CAT  aromatic  1.369  0.020  1.369
 O0Q  NAV  NAW  aromatic  1.288  0.020  1.288
 O0Q  CAT  NAU  aromatic  1.345  0.020  1.345
 O0Q  NAW  NAU  aromatic  1.323  0.020  1.323
 O0Q  NAU  CAX  single    1.446  0.020  1.446
 O0Q  CAX  CAZ  single    1.529  0.020  1.529
 O0Q  CBG  CBF  single    1.553  0.020  1.553
 O0Q  CBG  CBD  single    1.565  0.020  1.565
 O0Q  CBG  CBJ  single    1.555  0.020  1.555
 O0Q  OBC  CBB  double    1.224  0.020  1.224
 O0Q  CBF  CBE  single    1.554  0.020  1.554
 O0Q  CBF  CBH  single    1.556  0.020  1.556
 O0Q  CBB  NBA  single    1.351  0.020  1.351
 O0Q  CBB  CBD  single    1.489  0.020  1.489
 O0Q  NBA  CAZ  single    1.438  0.020  1.438
 O0Q  CBD  CBE  single    1.549  0.020  1.549
 O0Q  CBD  CBK  single    1.567  0.020  1.567
 O0Q  CBE  CBI  single    1.555  0.020  1.555
 O0Q  CBJ  CBH  single    1.557  0.020  1.557
 O0Q  CBJ  CBK  single    1.556  0.020  1.556
 O0Q  CBH  CBI  single    1.556  0.020  1.556
 O0Q  CBK  CBI  single    1.553  0.020  1.553
 O0Q  CAS  H1   single    0.930  0.020  1.080
 O0Q  CAT  H2   single    0.930  0.020  1.080
 O0Q  CAX  H3   single    0.970  0.020  1.090
 O0Q  CAX  H4   single    0.970  0.020  1.090
 O0Q  CAZ  H5   single    0.970  0.020  1.090
 O0Q  CAZ  H6   single    0.970  0.020  1.090
 O0Q  CBE  H7   single    0.970  0.020  1.090
 O0Q  CBF  H8   single    0.970  0.020  1.090
 O0Q  CBG  H9   single    0.970  0.020  1.090
 O0Q  CBH  H10  single    0.970  0.020  1.090
 O0Q  CBI  H11  single    0.970  0.020  1.090
 O0Q  CBJ  H12  single    0.970  0.020  1.090
 O0Q  CBK  H13  single    0.970  0.020  1.090
 O0Q  NBA  H14  single    0.860  0.020  1.020

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
 O0Q  H1   CAS  NAV  122.59  3.000
 O0Q  H1   CAS  CAT  129.31  3.000
 O0Q  NAV  CAS  CAT  108.10  3.000
 O0Q  H2   CAT  NAU  123.36  3.000
 O0Q  H2   CAT  CAS  132.69  3.000
 O0Q  NAU  CAT  CAS  103.94  3.000
 O0Q  H4   CAX  H3   107.74  3.000
 O0Q  H4   CAX  NAU  108.21  3.000
 O0Q  H3   CAX  NAU  108.19  3.000
 O0Q  H4   CAX  CAZ  110.73  3.000
 O0Q  H3   CAX  CAZ  111.10  3.000
 O0Q  NAU  CAX  CAZ  110.76  3.000
 O0Q  H6   CAZ  H5   106.37  3.000
 O0Q  H6   CAZ  NBA  110.54  3.000
 O0Q  H5   CAZ  NBA  109.20  3.000
 O0Q  H6   CAZ  CAX  109.75  3.000
 O0Q  H5   CAZ  CAX  109.21  3.000
 O0Q  NBA  CAZ  CAX  111.62  3.000
 O0Q  OBC  CBB  NBA  121.36  3.000
 O0Q  NBA  CBB  CBD  117.61  3.000
 O0Q  OBC  CBB  CBD  121.03  3.000
 O0Q  CBK  CBD  CBG   89.41  3.000
 O0Q  CBK  CBD  CBE   89.88  3.000
 O0Q  CBG  CBD  CBE   89.95  3.000
 O0Q  CBK  CBD  CBB  126.27  3.000
 O0Q  CBE  CBD  CBB  122.80  3.000
 O0Q  CBG  CBD  CBB  127.21  3.000
 O0Q  H7   CBE  CBI  125.54  3.000
 O0Q  H7   CBE  CBF  125.53  3.000
 O0Q  CBI  CBE  CBF   89.94  3.000
 O0Q  H7   CBE  CBD  124.42  3.000
 O0Q  CBI  CBE  CBD   90.28  3.000
 O0Q  CBF  CBE  CBD   90.21  3.000
 O0Q  H8   CBF  CBH  125.67  3.000
 O0Q  H8   CBF  CBG  124.79  3.000
 O0Q  CBH  CBF  CBG   90.00  3.000
 O0Q  H8   CBF  CBE  125.12  3.000
 O0Q  CBH  CBF  CBE   90.11  3.000
 O0Q  CBG  CBF  CBE   90.19  3.000
 O0Q  H9   CBG  CBJ  125.96  3.000
 O0Q  H9   CBG  CBF  124.71  3.000
 O0Q  CBJ  CBG  CBF   90.13  3.000
 O0Q  H9   CBG  CBD  125.10  3.000
 O0Q  CBJ  CBG  CBD   90.23  3.000
 O0Q  CBF  CBG  CBD   89.65  3.000
 O0Q  H10  CBH  CBJ  125.08  3.000
 O0Q  H10  CBH  CBI  125.35  3.000
 O0Q  CBJ  CBH  CBI   89.97  3.000
 O0Q  H10  CBH  CBF  125.50  3.000
 O0Q  CBI  CBH  CBF   89.85  3.000
 O0Q  CBJ  CBH  CBF   89.98  3.000
 O0Q  H11  CBI  CBK  124.75  3.000
 O0Q  H11  CBI  CBH  125.55  3.000
 O0Q  CBK  CBI  CBH   90.02  3.000
 O0Q  H11  CBI  CBE  125.27  3.000
 O0Q  CBK  CBI  CBE   90.19  3.000
 O0Q  CBH  CBI  CBE   90.10  3.000
 O0Q  H12  CBJ  CBK  125.13  3.000
 O0Q  H12  CBJ  CBH  125.38  3.000
 O0Q  CBK  CBJ  CBH   89.89  3.000
 O0Q  H12  CBJ  CBG  125.29  3.000
 O0Q  CBK  CBJ  CBG   90.21  3.000
 O0Q  CBH  CBJ  CBG   89.89  3.000
 O0Q  H13  CBK  CBJ  125.66  3.000
 O0Q  H13  CBK  CBI  125.54  3.000
 O0Q  CBJ  CBK  CBI   90.12  3.000
 O0Q  H13  CBK  CBD  124.63  3.000
 O0Q  CBI  CBK  CBD   89.66  3.000
 O0Q  CBJ  CBK  CBD   90.15  3.000
 O0Q  NAW  NAU  CAX  120.51  3.000
 O0Q  CAX  NAU  CAT  128.39  3.000
 O0Q  NAW  NAU  CAT  110.90  3.000
 O0Q  NAW  NAV  CAS  109.04  3.000
 O0Q  NAV  NAW  NAU  108.02  3.000
 O0Q  H14  NBA  CBB  115.82  3.000
 O0Q  H14  NBA  CAZ  116.58  3.000
 O0Q  CBB  NBA  CAZ  127.59  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
 O0Q  CONST_01  NAU  NAW  NAV  CAS     0.00   0.0  0
 O0Q  CONST_02  NAW  NAU  CAT  CAS     0.00   0.0  0
 O0Q  CONST_03  NAW  NAV  CAS  CAT     0.00   0.0  0
 O0Q  CONST_04  NAV  NAW  NAU  CAT     0.00   0.0  0
 O0Q  CONST_05  NAV  CAS  CAT  NAU     0.00   0.0  0
 O0Q  CONST_06  CAX  NAU  CAT  CAS   180.00   0.0  0
 O0Q  CONST_07  NAV  NAW  NAU  CAX   180.00   0.0  0
 O0Q  CONST_08  H1   CAS  CAT  NAU   180.00   0.0  0
 O0Q  CONST_09  H2   CAT  CAS  NAV   180.00   0.0  0
 O0Q  CONST_10  CBD  CBB  NBA  CAZ     0.00   0.0  0
 O0Q  CONST_11  H14  NBA  CBB  CBD   180.00   0.0  0
 O0Q  CONST_12  OBC  CBB  NBA  CAZ   180.00   0.0  0
 O0Q  Var_01    CAZ  CAX  NAU  CAT   -91.59  30.0  2
 O0Q  Var_02    NBA  CAZ  CAX  NAU   178.66  30.0  3
 O0Q  Var_03    CBB  NBA  CAZ  CAX  -104.54  30.0  1

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
 O0Q  chir_01  CBD  CBG  CBE  CBK  positiv
 O0Q  chir_02  CBE  CBF  CBD  CBI  negativ
 O0Q  chir_03  CBF  CBG  CBE  CBH  negativ
 O0Q  chir_04  CBG  CBF  CBD  CBJ  positiv
 O0Q  chir_05  CBH  CBI  CBJ  CBF  negativ
 O0Q  chir_06  CBI  CBE  CBH  CBK  positiv
 O0Q  chir_07  CBJ  CBK  CBH  CBG  positiv
 O0Q  chir_08  CBK  CBD  CBJ  CBI  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
 O0Q  plan-1  CAS  0.020
 O0Q  plan-1  CAT  0.020
 O0Q  plan-1  CAX  0.020
 O0Q  plan-1  NAU  0.020
 O0Q  plan-1  NAV  0.020
 O0Q  plan-1  NAW  0.020
 O0Q  plan-1  H1   0.020
 O0Q  plan-1  H2   0.020
 O0Q  plan-2  CAZ  0.020
 O0Q  plan-2  CBB  0.020
 O0Q  plan-2  CBD  0.020
 O0Q  plan-2  NBA  0.020
 O0Q  plan-2  OBC  0.020
 O0Q  plan-2  H14  0.020

