# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 19:02:28 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: 6-[(1~{R},2~{S},6~{R},7~{S})-1,7,8,9,10,10-hexakis(chloranyl)-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]dec-8-en-4-yl]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCN1C(=O)[C@@H]2[C@H](C1=O)[C@]3(Cl)C(=C(Cl)[C@@]2(Cl)C3(Cl)Cl)Cl
#
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
 Q5E  Q5E  '6-[(1~{R},2~{S},6~{R},7~{S})-1,7,8,9,10,10-hexakis(chloranyl)-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]dec-8-en-4-yl]hexanoic acid'  ligand  38  26  .  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_Q5E
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
 Q5E  OAQ  O   O      0  -0.390  -6.8172   4.5793  31.6811
 Q5E  CAO  C   CR5    0   0.590  -5.7893   4.3280  31.1102
 Q5E  CAC  C   CR15   0  -0.365  -5.5776   4.2859  29.6143
 Q5E  CAD  C   CT     0  -0.117  -5.6729   5.6587  28.9072
 Q5E  CAJ  C   CT     0  -0.145  -4.7349   5.4186  27.6985
 Q5E  CL2  CL  CL     0   0.029  -5.2337   4.0861  26.6653
 Q5E  CL1  CL  CL     0   0.032  -4.4934   6.8409  26.6970
 Q5E  CL6  CL  CL     0  -0.006  -7.2844   6.1953  28.5285
 Q5E  CAE  C   C      0   0.088  -4.8204   6.6389  29.6909
 Q5E  CL5  CL  CL     0  -0.012  -5.4526   7.8383  30.6910
 Q5E  CAF  C   C      0   0.092  -3.5459   6.3114  29.4949
 Q5E  CL4  CL  CL     0  -0.014  -2.1621   7.0288  30.1325
 Q5E  CAA  C   CT     0  -0.116  -3.5265   5.0847  28.6065
 Q5E  CL3  CL  CL     0  -0.007  -2.0232   4.7668  27.7910
 Q5E  CAB  C   CR15   0  -0.361  -4.1049   3.9055  29.4331
 Q5E  CAN  C   CR5    0   0.591  -3.5601   3.7890  30.8413
 Q5E  OAR  O   O      0  -0.389  -2.4255   3.5351  31.1455
 Q5E  NAP  N   NR5    0  -0.519  -4.5997   4.0025  31.7230
 Q5E  CAS  C   CH2    0  -0.327  -4.4915   3.8387  33.1683
 Q5E  CAT  C   CH2    0  -0.434  -4.3994   5.1445  33.9449
 Q5E  CAU  C   CH2    0  -0.426  -3.1353   5.9455  33.6702
 Q5E  CAV  C   CH2    0  -0.408  -2.9451   7.1442  34.5974
 Q5E  CAW  C   CH2    0  -0.583  -4.0180   8.2130  34.4560
 Q5E  CAX  C   C      0   0.410  -3.8101   9.5028  35.2778
 Q5E  OAZ  O   OC    -1  -0.604  -2.7532   9.6188  35.9296
 Q5E  OAY  O   O      0  -0.626  -4.7337  10.3415  35.2106
 Q5E  H1   H   HCR5   0   0.373  -6.2674   3.5692  29.1676
 Q5E  H2   H   HCR5   0   0.373  -3.9694   2.9586  28.9088
 Q5E  H3   H   HCH2   0   0.276  -5.3615   3.2677  33.4931
 Q5E  H4   H   HCH2   0   0.268  -3.6131   3.2216  33.3540
 Q5E  H5   H   HCH2   0   0.237  -5.2892   5.7484  33.7549
 Q5E  H6   H   HCH2   0   0.234  -4.4364   4.8755  35.0050
 Q5E  H7   H   HCH2   0   0.217  -2.2680   5.2845  33.7633
 Q5E  H8   H   HCH2   0   0.204  -3.1433   6.2987  32.6360
 Q5E  H9   H   HCH2   0   0.200  -2.9018   6.7938  35.6337
 Q5E  H10  H   HCH2   0   0.210  -1.9683   7.5870  34.3900
 Q5E  H11  H   HCH2   0   0.208  -4.1037   8.4995  33.4007
 Q5E  H12  H   HCH2   0   0.216  -5.0009   7.8065  34.7161

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
 Q5E  CL2  CAJ  single  1.758  0.020  1.758
 Q5E  CL1  CAJ  single  1.756  0.020  1.756
 Q5E  CAJ  CAA  single  1.548  0.020  1.548
 Q5E  CAJ  CAD  single  1.549  0.020  1.549
 Q5E  CL3  CAA  single  1.740  0.020  1.740
 Q5E  CL6  CAD  single  1.740  0.020  1.740
 Q5E  CAA  CAF  single  1.515  0.020  1.515
 Q5E  CAA  CAB  single  1.552  0.020  1.552
 Q5E  CAD  CAE  single  1.517  0.020  1.517
 Q5E  CAD  CAC  single  1.547  0.020  1.547
 Q5E  CAF  CAE  double  1.330  0.020  1.330
 Q5E  CAF  CL4  single  1.684  0.020  1.684
 Q5E  CAB  CAC  single  1.532  0.020  1.532
 Q5E  CAB  CAN  single  1.514  0.020  1.514
 Q5E  CAE  CL5  single  1.685  0.020  1.685
 Q5E  CAC  CAO  single  1.511  0.020  1.511
 Q5E  CAN  OAR  double  1.202  0.020  1.202
 Q5E  CAN  NAP  single  1.380  0.020  1.380
 Q5E  CAO  OAQ  double  1.202  0.020  1.202
 Q5E  CAO  NAP  single  1.377  0.020  1.377
 Q5E  NAP  CAS  single  1.459  0.020  1.459
 Q5E  CAS  CAT  single  1.522  0.020  1.522
 Q5E  CAU  CAT  single  1.521  0.020  1.521
 Q5E  CAU  CAV  single  1.527  0.020  1.527
 Q5E  CAV  CAW  single  1.521  0.020  1.521
 Q5E  CAW  CAX  single  1.543  0.020  1.543
 Q5E  CAX  OAY  deloc   1.249  0.020  1.249
 Q5E  CAX  OAZ  deloc   1.247  0.020  1.247
 Q5E  CAC  H1   single  0.970  0.020  1.090
 Q5E  CAB  H2   single  0.970  0.020  1.090
 Q5E  CAS  H3   single  0.970  0.020  1.090
 Q5E  CAS  H4   single  0.970  0.020  1.090
 Q5E  CAT  H5   single  0.970  0.020  1.090
 Q5E  CAT  H6   single  0.970  0.020  1.090
 Q5E  CAU  H7   single  0.970  0.020  1.090
 Q5E  CAU  H8   single  0.970  0.020  1.090
 Q5E  CAV  H9   single  0.970  0.020  1.090
 Q5E  CAV  H10  single  0.970  0.020  1.090
 Q5E  CAW  H11  single  0.970  0.020  1.090
 Q5E  CAW  H12  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
 Q5E  NAP  CAO  CAC  108.23  3.000
 Q5E  NAP  CAO  OAQ  125.21  3.000
 Q5E  CAC  CAO  OAQ  126.55  3.000
 Q5E  H1   CAC  CAB  113.36  3.000
 Q5E  H1   CAC  CAD  110.92  3.000
 Q5E  CAB  CAC  CAD  103.03  3.000
 Q5E  H1   CAC  CAO  109.58  3.000
 Q5E  CAB  CAC  CAO  104.99  3.000
 Q5E  CAD  CAC  CAO  114.77  3.000
 Q5E  CAE  CAD  CL6  115.70  3.000
 Q5E  CAE  CAD  CAJ   99.38  3.000
 Q5E  CL6  CAD  CAJ  116.03  3.000
 Q5E  CAE  CAD  CAC  107.62  3.000
 Q5E  CL6  CAD  CAC  115.47  3.000
 Q5E  CAJ  CAD  CAC  100.48  3.000
 Q5E  CAA  CAJ  CL1  113.70  3.000
 Q5E  CAA  CAJ  CL2  113.74  3.000
 Q5E  CL1  CAJ  CL2  108.52  3.000
 Q5E  CAA  CAJ  CAD   92.77  3.000
 Q5E  CL1  CAJ  CAD  113.75  3.000
 Q5E  CL2  CAJ  CAD  113.85  3.000
 Q5E  CAF  CAE  CL5  128.47  3.000
 Q5E  CL5  CAE  CAD  123.76  3.000
 Q5E  CAF  CAE  CAD  107.65  3.000
 Q5E  CAA  CAF  CL4  123.82  3.000
 Q5E  CL4  CAF  CAE  128.80  3.000
 Q5E  CAA  CAF  CAE  107.33  3.000
 Q5E  CAB  CAA  CL3  115.66  3.000
 Q5E  CAB  CAA  CAF  107.35  3.000
 Q5E  CL3  CAA  CAF  115.72  3.000
 Q5E  CAB  CAA  CAJ  100.69  3.000
 Q5E  CAF  CAA  CAJ   99.17  3.000
 Q5E  CL3  CAA  CAJ  116.04  3.000
 Q5E  H2   CAB  CAN  109.60  3.000
 Q5E  H2   CAB  CAA  110.93  3.000
 Q5E  CAN  CAB  CAA  114.82  3.000
 Q5E  H2   CAB  CAC  113.07  3.000
 Q5E  CAN  CAB  CAC  104.77  3.000
 Q5E  CAA  CAB  CAC  103.45  3.000
 Q5E  NAP  CAN  OAR  125.61  3.000
 Q5E  NAP  CAN  CAB  108.14  3.000
 Q5E  OAR  CAN  CAB  126.24  3.000
 Q5E  CAS  NAP  CAN  124.05  3.000
 Q5E  CAS  NAP  CAO  122.11  3.000
 Q5E  CAN  NAP  CAO  113.77  3.000
 Q5E  H4   CAS  H3   107.21  3.000
 Q5E  H4   CAS  CAT  110.50  3.000
 Q5E  H3   CAS  CAT  110.22  3.000
 Q5E  H4   CAS  NAP  107.00  3.000
 Q5E  H3   CAS  NAP  107.15  3.000
 Q5E  CAT  CAS  NAP  114.44  3.000
 Q5E  H6   CAT  H5   106.08  3.000
 Q5E  H6   CAT  CAU  109.41  3.000
 Q5E  H5   CAT  CAU  110.76  3.000
 Q5E  H6   CAT  CAS  106.34  3.000
 Q5E  H5   CAT  CAS  109.65  3.000
 Q5E  CAU  CAT  CAS  114.20  3.000
 Q5E  H8   CAU  H7   106.34  3.000
 Q5E  H8   CAU  CAV  108.77  3.000
 Q5E  H7   CAU  CAV  108.89  3.000
 Q5E  H8   CAU  CAT  109.57  3.000
 Q5E  H7   CAU  CAT  108.97  3.000
 Q5E  CAV  CAU  CAT  114.02  3.000
 Q5E  H10  CAV  H9   105.90  3.000
 Q5E  H10  CAV  CAW  109.17  3.000
 Q5E  H9   CAV  CAW  109.93  3.000
 Q5E  H10  CAV  CAU  108.32  3.000
 Q5E  H9   CAV  CAU  109.17  3.000
 Q5E  CAW  CAV  CAU  114.03  3.000
 Q5E  H12  CAW  H11  104.79  3.000
 Q5E  H12  CAW  CAX  107.74  3.000
 Q5E  H11  CAW  CAX  107.73  3.000
 Q5E  H12  CAW  CAV  110.50  3.000
 Q5E  H11  CAW  CAV  109.15  3.000
 Q5E  CAX  CAW  CAV  116.28  3.000
 Q5E  OAY  CAX  OAZ  126.31  3.000
 Q5E  OAZ  CAX  CAW  118.04  3.000
 Q5E  OAY  CAX  CAW  115.65  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
 Q5E  CONST_01  CAN  NAP  CAO  CAC     0.00   0.0  0
 Q5E  CONST_02  CAN  NAP  CAO  OAQ   180.00   0.0  0
 Q5E  CONST_03  CAS  NAP  CAO  CAC   180.00   0.0  0
 Q5E  CONST_04  CAS  NAP  CAO  OAQ     0.00   0.0  0
 Q5E  Var_01    CAB  CAN  NAP  CAO    -3.43  30.0  1
 Q5E  Var_02    CAA  CAF  CAE  CAD    -1.46  30.0  2
 Q5E  Var_03    CAT  CAS  NAP  CAO   -79.29  30.0  3
 Q5E  Var_04    CAU  CAT  CAS  NAP   -65.38  30.0  3
 Q5E  Var_05    CAV  CAU  CAT  CAS  -171.38  30.0  1
 Q5E  Var_06    CAW  CAV  CAU  CAT   -64.05  30.0  3
 Q5E  Var_07    CAX  CAW  CAV  CAU  -174.81  30.0  3
 Q5E  Var_08    OAY  CAX  CAW  CAV  -176.21  30.0  3

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
 Q5E  chir_01  CAC  CAD  CAB  CAO  negativ
 Q5E  chir_02  CAD  CAJ  CAE  CAC  positiv
 Q5E  chir_03  CAA  CAB  CAF  CAJ  positiv
 Q5E  chir_04  CAB  CAN  CAC  CAA  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
 Q5E  plan-1  CAB  0.020
 Q5E  plan-1  CAN  0.020
 Q5E  plan-1  OAR  0.020
 Q5E  plan-1  NAP  0.020
 Q5E  plan-2  OAQ  0.020
 Q5E  plan-2  CAO  0.020
 Q5E  plan-2  CAC  0.020
 Q5E  plan-2  CAN  0.020
 Q5E  plan-2  NAP  0.020
 Q5E  plan-2  CAS  0.020
 Q5E  plan-3  CAW  0.020
 Q5E  plan-3  CAX  0.020
 Q5E  plan-3  OAZ  0.020
 Q5E  plan-3  OAY  0.020

