# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:01:46 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: [(1~{R},2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-tris(oxidanyl)-7-oxabicyclo[4.1.0]heptan-2-yl]methanediazonium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](C[N+]#N)[C@H]2O[C@H]2[C@@H]1O
#
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
 8P2  8P2  '[(1~{R},2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-tris(oxidanyl)-7-oxabicyclo[4.1.0]heptan-2-yl]methanediazonium'  ligand  24  13  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8P2
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
 8P2  N1   N  N     1   0.276  -3.1217  -0.0965   0.1653
 8P2  OAE  O  OH1   0  -0.675  -1.1397   1.7005  -0.0816
 8P2  CAC  C  CH1   0   0.044  -0.2185   0.6627  -0.3103
 8P2  CAK  C  CH1   0  -0.009   1.1852   1.0094   0.1855
 8P2  OAF  O  OH1   0  -0.673   1.6439   2.2189  -0.3679
 8P2  CAJ  C  CH1   0   0.031   2.1742  -0.0806  -0.2148
 8P2  OAG  O  OH1   0  -0.671   3.3984   0.0604   0.4603
 8P2  CAB  C  CH1   0  -0.043   1.6454  -1.4632   0.1137
 8P2  OAI  O  O2    0  -0.472   0.7616  -2.0349  -0.8387
 8P2  CAA  C  CH1   0  -0.004   0.2385  -1.6996   0.4308
 8P2  CAD  C  CH1   0  -0.385  -0.7288  -0.5437   0.4655
 8P2  CAH  C  CH2   0  -0.297  -2.0689  -1.0453  -0.0758
 8P2  H4   H  HOH1  0   0.468  -1.0505   2.3572  -0.7793
 8P2  H5   H  HCH1  0   0.245  -0.1744   0.4207  -1.3809
 8P2  H6   H  HCH1  0   0.236   1.1622   1.0635   1.2841
 8P2  H7   H  HOH1  0   0.463   1.3580   2.9484   0.1895
 8P2  H8   H  HCH1  0   0.236   2.3189  -0.0284  -1.3050
 8P2  H9   H  HOH1  0   0.457   3.7584   0.9277   0.2475
 8P2  H10  H  HCH1  0   0.279   2.3833  -2.1530   0.5190
 8P2  H11  H  HCH1  0   0.290  -0.0238  -2.5422   1.0679
 8P2  H12  H  HCH1  0   0.329  -0.8595  -0.2720   1.5181
 8P2  H13  H  HCH2  0   0.394  -2.4200  -1.9471   0.4290
 8P2  H14  H  HCH2  0   0.382  -2.0807  -1.2013  -1.1554
 8P2  N2   N  N     0   0.100  -3.9468   0.5821   0.3708

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
 8P2  OAE  CAC  single  1.406  0.020  1.406
 8P2  OAF  CAK  single  1.407  0.020  1.407
 8P2  CAC  CAK  single  1.528  0.020  1.528
 8P2  CAC  CAD  single  1.522  0.020  1.522
 8P2  CAH  N1   single  1.438  0.020  1.438
 8P2  CAH  CAD  single  1.530  0.020  1.530
 8P2  CAK  CAJ  single  1.525  0.020  1.525
 8P2  CAD  CAA  single  1.508  0.020  1.508
 8P2  CAJ  OAG  single  1.405  0.020  1.405
 8P2  CAJ  CAB  single  1.516  0.020  1.516
 8P2  CAA  OAI  single  1.413  0.020  1.413
 8P2  CAA  CAB  single  1.461  0.020  1.461
 8P2  OAI  CAB  single  1.419  0.020  1.419
 8P2  OAE  H4   single  0.850  0.020  0.980
 8P2  CAC  H5   single  0.970  0.020  1.090
 8P2  CAK  H6   single  0.970  0.020  1.090
 8P2  OAF  H7   single  0.850  0.020  0.980
 8P2  CAJ  H8   single  0.970  0.020  1.090
 8P2  OAG  H9   single  0.850  0.020  0.980
 8P2  CAB  H10  single  0.970  0.020  1.090
 8P2  CAA  H11  single  0.970  0.020  1.090
 8P2  CAD  H12  single  0.970  0.020  1.090
 8P2  CAH  H13  single  0.970  0.020  1.090
 8P2  CAH  H14  single  0.970  0.020  1.090
 8P2  N1   N2   triple  1.088  0.020  1.088

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
 8P2  N2   N1   CAH  180.00  3.000
 8P2  H4   OAE  CAC  108.96  3.000
 8P2  H5   CAC  CAD  109.60  3.000
 8P2  H5   CAC  CAK  109.22  3.000
 8P2  CAD  CAC  CAK  108.80  3.000
 8P2  H5   CAC  OAE  110.33  3.000
 8P2  CAD  CAC  OAE  106.40  3.000
 8P2  CAK  CAC  OAE  112.43  3.000
 8P2  H6   CAK  CAJ  108.11  3.000
 8P2  H6   CAK  OAF  110.93  3.000
 8P2  CAJ  CAK  OAF  107.44  3.000
 8P2  H6   CAK  CAC  108.41  3.000
 8P2  CAJ  CAK  CAC  110.38  3.000
 8P2  OAF  CAK  CAC  111.51  3.000
 8P2  H7   OAF  CAK  109.10  3.000
 8P2  H8   CAJ  CAB  107.67  3.000
 8P2  H8   CAJ  OAG  110.89  3.000
 8P2  CAB  CAJ  OAG  106.93  3.000
 8P2  H8   CAJ  CAK  108.13  3.000
 8P2  CAB  CAJ  CAK  111.63  3.000
 8P2  OAG  CAJ  CAK  111.54  3.000
 8P2  H9   OAG  CAJ  108.05  3.000
 8P2  H10  CAB  CAA  117.99  3.000
 8P2  H10  CAB  OAI  114.63  3.000
 8P2  CAA  CAB  OAI   58.74  3.000
 8P2  H10  CAB  CAJ  114.97  3.000
 8P2  OAI  CAB  CAJ  116.04  3.000
 8P2  CAA  CAB  CAJ  122.02  3.000
 8P2  CAA  OAI  CAB   62.11  3.000
 8P2  H11  CAA  CAD  115.18  3.000
 8P2  H11  CAA  OAI  115.55  3.000
 8P2  CAD  CAA  OAI  116.10  3.000
 8P2  H11  CAA  CAB  118.96  3.000
 8P2  OAI  CAA  CAB   59.15  3.000
 8P2  CAD  CAA  CAB  119.91  3.000
 8P2  H12  CAD  CAH  108.47  3.000
 8P2  H12  CAD  CAA  106.79  3.000
 8P2  CAH  CAD  CAA  107.61  3.000
 8P2  H12  CAD  CAC  109.47  3.000
 8P2  CAA  CAD  CAC  112.38  3.000
 8P2  CAH  CAD  CAC  111.91  3.000
 8P2  H14  CAH  H13  109.64  3.000
 8P2  H14  CAH  CAD  113.98  3.000
 8P2  H13  CAH  CAD  112.90  3.000
 8P2  H14  CAH  N1   104.62  3.000
 8P2  H13  CAH  N1   103.43  3.000
 8P2  CAD  CAH  N1   111.45  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
 8P2  Var_01  CAD  CAA  CAB  CAJ  -1.27  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
 8P2  chir_01  CAC  OAE  CAK  CAD  negativ
 8P2  chir_02  CAK  OAF  CAC  CAJ  negativ
 8P2  chir_03  CAJ  OAG  CAK  CAB  positiv
 8P2  chir_06  CAD  CAC  CAH  CAA  negativ
 8P2  chir_07  CAB  CAJ  CAA  OAI  both
 8P2  chir_08  CAA  OAI  CAB  CAD  both

