# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 16:45:23 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-bis(fluoranyl)phenoxy]-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]12C[C@@H]1[C@H](Oc3cc(F)cc(F)c3)[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
 7D0  7D0  (1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-bis(fluoranyl)phenoxy]-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4-triol  ligand  37  21  .  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_7D0
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
 7D0  CAN  C  CR16  0  -0.530   2.6272   1.1228  -0.8155
 7D0  CAP  C  CR6   0   0.552   3.9860   0.9144  -0.7452
 7D0  FAE  F  F     0  -0.310   4.7734   1.5466  -1.6253
 7D0  CAO  C  CR16  0  -0.590   4.5827   0.0836   0.1860
 7D0  CAS  C  CR6   0   0.565   3.7248  -0.5413   1.0678
 7D0  FAF  F  F     0  -0.311   4.2508  -1.3595   1.9893
 7D0  CAR  C  CR16  0  -0.555   2.3527  -0.3801   1.0566
 7D0  CAM  C  CR6   0   0.461   1.7965   0.4672   0.0979
 7D0  OAL  O  O2    0  -0.478   0.4951   0.7604  -0.0131
 7D0  CAD  C  CH1   0  -0.044  -0.5093   0.0483   0.7031
 7D0  CAH  C  CH1   0  -0.285  -1.6609   0.9997   0.9488
 7D0  CAI  C  CH2   0  -0.470  -2.1248   1.9293  -0.1353
 7D0  CAG  C  CT    0  -0.069  -3.0065   0.8052   0.2959
 7D0  CAQ  C  CH2   0  -0.146  -4.2146   1.1760   1.1152
 7D0  OAT  O  OH1   0  -0.673  -5.2371   1.5939   0.2376
 7D0  CAA  C  CH1   0   0.030  -3.2041  -0.3494  -0.6645
 7D0  OAU  O  OH1   0  -0.673  -3.8740  -1.3791   0.0277
 7D0  CAB  C  CH1   0  -0.000  -1.8760  -0.8655  -1.2188
 7D0  OAJ  O  OH1   0  -0.684  -2.1719  -2.0065  -1.9906
 7D0  CAC  C  CH1   0   0.018  -0.9284  -1.2066  -0.0735
 7D0  OAK  O  OH1   0  -0.668   0.1775  -1.8782  -0.6315
 7D0  H1   H  HCR6  0   0.288   2.2058   1.7820  -1.5631
 7D0  H2   H  HCR6  0   0.298   5.6527  -0.0689   0.2193
 7D0  H3   H  HCR6  0   0.297   1.7622  -0.9129   1.7879
 7D0  H4   H  HCH1  0   0.267  -0.1255  -0.2592   1.6793
 7D0  H5   H  HCH1  0   0.272  -1.6818   1.4097   1.9524
 7D0  H6   H  HCH2  0   0.265  -2.4084   2.9322   0.1597
 7D0  H7   H  HCH2  0   0.262  -1.6427   1.8875  -1.1036
 7D0  H8   H  HCH2  0   0.213  -4.5323   0.3247   1.7257
 7D0  H9   H  HCH2  0   0.195  -3.9356   1.9781   1.8130
 7D0  H10  H  HOH1  0   0.455  -6.0599   1.6323   0.7330
 7D0  H11  H  HCH1  0   0.229  -3.8156  -0.0005  -1.5095
 7D0  H12  H  HOH1  0   0.448  -3.9143  -2.1436  -0.5578
 7D0  H13  H  HCH1  0   0.220  -1.4166  -0.0939  -1.8527
 7D0  H14  H  HOH1  0   0.451  -1.3532  -2.5047  -2.0988
 7D0  H15  H  HCH1  0   0.237  -1.4614  -1.8544   0.6328
 7D0  H16  H  HOH1  0   0.463   0.5329  -2.4998   0.0103

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
 7D0  FAF  CAS  single    1.340  0.020  1.340
 7D0  CAS  CAO  aromatic  1.380  0.020  1.380
 7D0  CAS  CAR  aromatic  1.382  0.020  1.382
 7D0  CAO  CAP  aromatic  1.383  0.020  1.383
 7D0  CAR  CAM  aromatic  1.395  0.020  1.395
 7D0  CAP  FAE  single    1.339  0.020  1.339
 7D0  CAP  CAN  aromatic  1.377  0.020  1.377
 7D0  CAM  CAN  aromatic  1.398  0.020  1.398
 7D0  CAM  OAL  single    1.339  0.020  1.339
 7D0  OAL  CAD  single    1.424  0.020  1.424
 7D0  CAI  CAH  single    1.502  0.020  1.502
 7D0  CAI  CAG  single    1.492  0.020  1.492
 7D0  OAK  CAC  single    1.409  0.020  1.409
 7D0  CAB  OAJ  single    1.409  0.020  1.409
 7D0  CAB  CAC  single    1.525  0.020  1.525
 7D0  CAB  CAA  single    1.529  0.020  1.529
 7D0  CAD  CAC  single    1.534  0.020  1.534
 7D0  CAD  CAH  single    1.514  0.020  1.514
 7D0  CAH  CAG  single    1.508  0.020  1.508
 7D0  CAA  CAG  single    1.515  0.020  1.515
 7D0  CAA  OAU  single    1.410  0.020  1.410
 7D0  CAG  CAQ  single    1.506  0.020  1.506
 7D0  CAQ  OAT  single    1.411  0.020  1.411
 7D0  CAN  H1   single    0.930  0.020  1.080
 7D0  CAO  H2   single    0.930  0.020  1.080
 7D0  CAR  H3   single    0.930  0.020  1.080
 7D0  CAD  H4   single    0.970  0.020  1.090
 7D0  CAH  H5   single    0.970  0.020  1.090
 7D0  CAI  H6   single    0.970  0.020  1.090
 7D0  CAI  H7   single    0.970  0.020  1.090
 7D0  CAQ  H8   single    0.970  0.020  1.090
 7D0  CAQ  H9   single    0.970  0.020  1.090
 7D0  OAT  H10  single    0.850  0.020  0.980
 7D0  CAA  H11  single    0.970  0.020  1.090
 7D0  OAU  H12  single    0.850  0.020  0.980
 7D0  CAB  H13  single    0.970  0.020  1.090
 7D0  OAJ  H14  single    0.850  0.020  0.980
 7D0  CAC  H15  single    0.970  0.020  1.090
 7D0  OAK  H16  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
 7D0  H1   CAN  CAM  120.38  3.000
 7D0  H1   CAN  CAP  120.79  3.000
 7D0  CAM  CAN  CAP  118.84  3.000
 7D0  CAO  CAP  FAE  118.18  3.000
 7D0  FAE  CAP  CAN  118.38  3.000
 7D0  CAO  CAP  CAN  123.44  3.000
 7D0  H2   CAO  CAS  122.12  3.000
 7D0  H2   CAO  CAP  122.16  3.000
 7D0  CAS  CAO  CAP  115.72  3.000
 7D0  CAR  CAS  FAF  117.82  3.000
 7D0  CAR  CAS  CAO  124.02  3.000
 7D0  FAF  CAS  CAO  118.16  3.000
 7D0  H3   CAR  CAM  123.14  3.000
 7D0  H3   CAR  CAS  118.67  3.000
 7D0  CAM  CAR  CAS  118.19  3.000
 7D0  OAL  CAM  CAR  125.28  3.000
 7D0  OAL  CAM  CAN  114.89  3.000
 7D0  CAR  CAM  CAN  119.80  3.000
 7D0  CAD  OAL  CAM  122.30  3.000
 7D0  H4   CAD  CAC  108.54  3.000
 7D0  H4   CAD  CAH  107.40  3.000
 7D0  CAC  CAD  CAH  112.86  3.000
 7D0  H4   CAD  OAL  110.00  3.000
 7D0  CAH  CAD  OAL  107.69  3.000
 7D0  CAC  CAD  OAL  110.30  3.000
 7D0  H5   CAH  CAG  115.60  3.000
 7D0  H5   CAH  CAI  115.35  3.000
 7D0  CAG  CAH  CAI   59.45  3.000
 7D0  H5   CAH  CAD  113.74  3.000
 7D0  CAG  CAH  CAD  121.83  3.000
 7D0  CAI  CAH  CAD  120.46  3.000
 7D0  H7   CAI  H6   113.33  3.000
 7D0  H7   CAI  CAG  119.50  3.000
 7D0  H6   CAI  CAG  117.65  3.000
 7D0  H7   CAI  CAH  118.97  3.000
 7D0  H6   CAI  CAH  117.22  3.000
 7D0  CAG  CAI  CAH   60.50  3.000
 7D0  CAA  CAG  CAQ  115.34  3.000
 7D0  CAQ  CAG  CAI  116.47  3.000
 7D0  CAA  CAG  CAI  117.90  3.000
 7D0  CAQ  CAG  CAH  116.64  3.000
 7D0  CAA  CAG  CAH  119.28  3.000
 7D0  CAI  CAG  CAH   60.05  3.000
 7D0  H9   CAQ  H8   106.68  3.000
 7D0  H9   CAQ  OAT  111.26  3.000
 7D0  H8   CAQ  OAT  111.53  3.000
 7D0  H9   CAQ  CAG  108.75  3.000
 7D0  H8   CAQ  CAG  110.17  3.000
 7D0  OAT  CAQ  CAG  108.42  3.000
 7D0  H10  OAT  CAQ  108.16  3.000
 7D0  H11  CAA  CAB  108.15  3.000
 7D0  H11  CAA  OAU  110.16  3.000
 7D0  CAB  CAA  OAU  110.13  3.000
 7D0  H11  CAA  CAG  108.53  3.000
 7D0  OAU  CAA  CAG  107.90  3.000
 7D0  CAB  CAA  CAG  111.95  3.000
 7D0  H12  OAU  CAA  107.51  3.000
 7D0  H13  CAB  CAC  109.29  3.000
 7D0  H13  CAB  OAJ  109.89  3.000
 7D0  CAC  CAB  OAJ  111.15  3.000
 7D0  H13  CAB  CAA  109.58  3.000
 7D0  CAC  CAB  CAA  110.06  3.000
 7D0  OAJ  CAB  CAA  106.83  3.000
 7D0  H14  OAJ  CAB  107.55  3.000
 7D0  H15  CAC  OAK  110.79  3.000
 7D0  H15  CAC  CAB  108.29  3.000
 7D0  OAK  CAC  CAB  107.27  3.000
 7D0  H15  CAC  CAD  106.85  3.000
 7D0  CAB  CAC  CAD  111.53  3.000
 7D0  OAK  CAC  CAD  112.09  3.000
 7D0  H16  OAK  CAC  109.51  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
 7D0  CONST_01  CAS  CAO  CAP  CAN    0.00   0.0  0
 7D0  CONST_02  CAS  CAR  CAM  CAN    0.00   0.0  0
 7D0  CONST_03  CAR  CAS  CAO  CAP    0.00   0.0  0
 7D0  CONST_04  CAR  CAM  CAN  CAP    0.00   0.0  0
 7D0  CONST_05  CAM  CAR  CAS  CAO    0.00   0.0  0
 7D0  CONST_06  CAM  CAN  CAP  CAO    0.00   0.0  0
 7D0  CONST_07  FAF  CAS  CAO  CAP  180.00   0.0  0
 7D0  CONST_08  OAL  CAM  CAN  CAP  180.00   0.0  0
 7D0  CONST_09  CAS  CAO  CAP  FAE  180.00   0.0  0
 7D0  CONST_10  CAM  CAN  CAP  FAE  180.00   0.0  0
 7D0  CONST_11  OAL  CAM  CAR  CAS  180.00   0.0  0
 7D0  CONST_12  CAM  CAR  CAS  FAF  180.00   0.0  0
 7D0  CONST_13  H2   CAO  CAP  CAN  180.00   0.0  0
 7D0  CONST_14  H3   CAR  CAM  CAN  180.00   0.0  0
 7D0  CONST_15  H1   CAN  CAP  CAO  180.00   0.0  0
 7D0  Var_01    CAG  CAI  CAH  CAD  111.31  30.0  1
 7D0  Var_02    OAT  CAQ  CAG  CAH  150.22  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
 7D0  chir_01  CAD  OAL  CAC  CAH  positiv
 7D0  chir_04  CAA  CAB  CAG  OAU  positiv
 7D0  chir_05  CAB  OAJ  CAA  CAC  negativ
 7D0  chir_06  CAC  OAK  CAD  CAB  negativ
 7D0  chir_07  CAH  CAI  CAD  CAG  both
 7D0  chir_08  CAG  CAH  CAA  CAQ  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
 7D0  plan-1  CAN  0.020
 7D0  plan-1  CAP  0.020
 7D0  plan-1  FAE  0.020
 7D0  plan-1  CAO  0.020
 7D0  plan-1  CAS  0.020
 7D0  plan-1  FAF  0.020
 7D0  plan-1  CAR  0.020
 7D0  plan-1  CAM  0.020
 7D0  plan-1  OAL  0.020
 7D0  plan-1  H1   0.020
 7D0  plan-1  H2   0.020
 7D0  plan-1  H3   0.020

