# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:17:27 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]12C[C@@H]1[C@H](O)[C@H](O)[C@@H](O)[C@H]2O
#
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
 7D2  7D2  (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol  ligand  27  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_7D2
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
 7D2  OAJ  O  OH1   0  -0.675   1.0697   1.7485   0.6820
 7D2  CAL  C  CH1   0   0.031   0.7368   0.9086  -0.4017
 7D2  CAI  C  CH1   0   0.004  -0.7714   0.9621  -0.6584
 7D2  OAA  O  OH1   0  -0.685  -1.1097   2.3238  -0.8041
 7D2  CAG  C  CH1   0  -0.014  -1.5124   0.3174   0.5046
 7D2  OAD  O  OH1   0  -0.681  -2.8942   0.5893   0.3469
 7D2  CAM  C  CH1   0   0.016  -1.2610  -1.1931   0.5526
 7D2  OAE  O  OH1   0  -0.668  -2.0018  -1.8653  -0.4414
 7D2  CAB  C  CH1   0  -0.295   0.2084  -1.5260   0.3890
 7D2  CAH  C  CH2   0  -0.464   0.8129  -1.6063  -0.9826
 7D2  CAC  C  CT    0  -0.073   1.2090  -0.4934  -0.0688
 7D2  CAF  C  CH2   0  -0.145   2.5868  -0.5853   0.5320
 7D2  OAK  O  OH1   0  -0.673   3.5234  -0.0983  -0.4046
 7D2  H1   H  HOH1  0   0.447   0.6455   2.5998   0.5246
 7D2  H2   H  HCH1  0   0.225   1.2540   1.2452  -1.3124
 7D2  H3   H  HCH1  0   0.215  -1.0082   0.4188  -1.5837
 7D2  H4   H  HOH1  0   0.451  -2.0627   2.4038  -0.6816
 7D2  H5   H  HCH1  0   0.230  -1.1415   0.7523   1.4399
 7D2  H6   H  HOH1  0   0.464  -3.3028   0.6410   1.2161
 7D2  H7   H  HCH1  0   0.218  -1.5706  -1.5396   1.5489
 7D2  H8   H  HOH1  0   0.442  -2.9036  -1.5262  -0.3986
 7D2  H9   H  HCH1  0   0.262   0.5846  -2.2499   1.1038
 7D2  H10  H  HCH2  0   0.257   1.5419  -2.3869  -1.1652
 7D2  H11  H  HCH2  0   0.256   0.1856  -1.3947  -1.8384
 7D2  H12  H  HCH2  0   0.208   2.6271  -0.0213   1.4699
 7D2  H13  H  HCH2  0   0.194   2.7851  -1.6357   0.7850
 7D2  H14  H  HOH1  0   0.453   4.3825  -0.0623   0.0255

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
 7D2  OAJ  CAL  single  1.411  0.020  1.411
 7D2  OAK  CAF  single  1.411  0.020  1.411
 7D2  CAF  CAC  single  1.506  0.020  1.506
 7D2  CAC  CAL  single  1.516  0.020  1.516
 7D2  CAC  CAB  single  1.509  0.020  1.509
 7D2  CAC  CAH  single  1.494  0.020  1.494
 7D2  CAL  CAI  single  1.531  0.020  1.531
 7D2  CAB  CAM  single  1.515  0.020  1.515
 7D2  CAB  CAH  single  1.501  0.020  1.501
 7D2  CAG  CAM  single  1.532  0.020  1.532
 7D2  CAG  CAI  single  1.522  0.020  1.522
 7D2  CAG  OAD  single  1.417  0.020  1.417
 7D2  CAM  OAE  single  1.410  0.020  1.410
 7D2  OAA  CAI  single  1.411  0.020  1.411
 7D2  OAJ  H1   single  0.850  0.020  0.980
 7D2  CAL  H2   single  0.970  0.020  1.090
 7D2  CAI  H3   single  0.970  0.020  1.090
 7D2  OAA  H4   single  0.850  0.020  0.980
 7D2  CAG  H5   single  0.970  0.020  1.090
 7D2  OAD  H6   single  0.850  0.020  0.980
 7D2  CAM  H7   single  0.970  0.020  1.090
 7D2  OAE  H8   single  0.850  0.020  0.980
 7D2  CAB  H9   single  0.970  0.020  1.090
 7D2  CAH  H10  single  0.970  0.020  1.090
 7D2  CAH  H11  single  0.970  0.020  1.090
 7D2  CAF  H12  single  0.970  0.020  1.090
 7D2  CAF  H13  single  0.970  0.020  1.090
 7D2  OAK  H14  single  0.850  0.020  0.980

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
 7D2  H1   OAJ  CAL  107.24  3.000
 7D2  H2   CAL  CAC  108.56  3.000
 7D2  H2   CAL  CAI  108.29  3.000
 7D2  CAC  CAL  CAI  112.08  3.000
 7D2  H2   CAL  OAJ  110.05  3.000
 7D2  CAI  CAL  OAJ  109.90  3.000
 7D2  CAC  CAL  OAJ  107.95  3.000
 7D2  H3   CAI  CAG  109.21  3.000
 7D2  H3   CAI  OAA  109.80  3.000
 7D2  CAG  CAI  OAA  111.78  3.000
 7D2  H3   CAI  CAL  109.64  3.000
 7D2  OAA  CAI  CAL  106.70  3.000
 7D2  CAG  CAI  CAL  109.67  3.000
 7D2  H4   OAA  CAI  107.70  3.000
 7D2  H5   CAG  CAM  108.00  3.000
 7D2  H5   CAG  OAD  110.42  3.000
 7D2  CAM  CAG  OAD  110.65  3.000
 7D2  H5   CAG  CAI  108.61  3.000
 7D2  OAD  CAG  CAI  107.96  3.000
 7D2  CAM  CAG  CAI  111.20  3.000
 7D2  H6   OAD  CAG  108.90  3.000
 7D2  H7   CAM  CAB  107.56  3.000
 7D2  H7   CAM  OAE  109.91  3.000
 7D2  CAB  CAM  OAE  109.18  3.000
 7D2  H7   CAM  CAG  107.03  3.000
 7D2  OAE  CAM  CAG  111.20  3.000
 7D2  CAB  CAM  CAG  111.86  3.000
 7D2  H8   OAE  CAM  107.00  3.000
 7D2  H9   CAB  CAC  115.26  3.000
 7D2  H9   CAB  CAH  115.27  3.000
 7D2  CAC  CAB  CAH   59.49  3.000
 7D2  H9   CAB  CAM  114.31  3.000
 7D2  CAH  CAB  CAM  120.06  3.000
 7D2  CAC  CAB  CAM  121.69  3.000
 7D2  H11  CAH  H10  113.43  3.000
 7D2  H11  CAH  CAC  119.47  3.000
 7D2  H10  CAH  CAC  117.48  3.000
 7D2  H11  CAH  CAB  118.61  3.000
 7D2  H10  CAH  CAB  117.61  3.000
 7D2  CAC  CAH  CAB   60.52  3.000
 7D2  CAF  CAC  CAH  116.18  3.000
 7D2  CAH  CAC  CAB   59.99  3.000
 7D2  CAF  CAC  CAB  116.35  3.000
 7D2  CAH  CAC  CAL  118.17  3.000
 7D2  CAB  CAC  CAL  119.53  3.000
 7D2  CAF  CAC  CAL  115.40  3.000
 7D2  H13  CAF  H12  106.77  3.000
 7D2  H13  CAF  OAK  111.29  3.000
 7D2  H12  CAF  OAK  111.48  3.000
 7D2  H13  CAF  CAC  108.39  3.000
 7D2  H12  CAF  CAC  110.11  3.000
 7D2  OAK  CAF  CAC  108.75  3.000
 7D2  H14  OAK  CAF  108.00  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
 7D2  Var_01  CAM  CAB  CAC  CAL   -1.21  30.0  1
 7D2  Var_02  OAK  CAF  CAC  CAL  -62.42  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
 7D2  chir_01  CAL  OAJ  CAC  CAI  negativ
 7D2  chir_02  CAI  OAA  CAL  CAG  negativ
 7D2  chir_03  CAG  OAD  CAI  CAM  positiv
 7D2  chir_04  CAM  OAE  CAG  CAB  positiv
 7D2  chir_05  CAB  CAC  CAM  CAH  both
 7D2  chir_06  CAC  CAB  CAL  CAF  both

