# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:21:41 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (1~{R},2~{S},3~{S},4~{S},6~{R})-4-fluoranyl-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]12C[C@@H]1C[C@H](F)[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
 7D8  7D8  (1~{R},2~{S},3~{S},4~{S},6~{R})-4-fluoranyl-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3-diol  ligand  25  12  .  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_7D8
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
 7D8  OAJ  O  OH1   0  -0.672  -0.4917  -1.5873   0.8993
 7D8  CAA  C  CH1   0   0.025  -0.3938  -0.8549  -0.3030
 7D8  CAB  C  CH1   0  -0.039   1.0790  -0.6005  -0.6422
 7D8  OAK  O  OH1   0  -0.679   1.7045  -1.8625  -0.6650
 7D8  CAC  C  CH1   0   0.203   1.6777   0.3239   0.4014
 7D8  FAF  F  F     0  -0.387   3.0621   0.4106   0.1880
 7D8  CAD  C  CH2   0  -0.516   1.0854   1.7165   0.3238
 7D8  CAG  C  CH1   0  -0.269  -0.4277   1.7043   0.1879
 7D8  CAI  C  CH2   0  -0.478  -1.0509   1.5011  -1.1620
 7D8  CAH  C  CT    0  -0.073  -1.1730   0.4317  -0.1212
 7D8  CAL  C  CH2   0  -0.145  -2.5346   0.2751   0.5025
 7D8  OAM  O  OH1   0  -0.673  -3.3300  -0.5284  -0.3422
 7D8  H1   H  HOH1  0   0.450   0.0477  -2.3804   0.8071
 7D8  H2   H  HCH1  0   0.229  -0.8370  -1.4253  -1.1318
 7D8  H3   H  HCH1  0   0.223   1.1489  -0.1209  -1.6293
 7D8  H4   H  HOH1  0   0.456   2.6520  -1.7395  -0.7806
 7D8  H5   H  HCH1  0   0.211   1.5426  -0.1029   1.3978
 7D8  H6   H  HCH2  0   0.258   1.3686   2.2746   1.2173
 7D8  H7   H  HCH2  0   0.247   1.5307   2.2370  -0.5286
 7D8  H8   H  HCH1  0   0.262  -0.9415   2.3985   0.8438
 7D8  H9   H  HCH2  0   0.259  -1.9430   2.0638  -1.4098
 7D8  H10  H  HCH2  0   0.253  -0.3902   1.3478  -2.0071
 7D8  H11  H  HCH2  0   0.211  -2.4450  -0.1603   1.5029
 7D8  H12  H  HCH2  0   0.194  -2.9749   1.2733   0.6337
 7D8  H13  H  HOH1  0   0.454  -4.1181  -0.7856   0.1440

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
 7D8  OAK  CAB  single  1.409  0.020  1.409
 7D8  CAI  CAH  single  1.497  0.020  1.497
 7D8  CAI  CAG  single  1.501  0.020  1.501
 7D8  CAB  CAA  single  1.533  0.020  1.533
 7D8  CAB  CAC  single  1.517  0.020  1.517
 7D8  FAF  CAC  single  1.403  0.020  1.403
 7D8  CAA  CAH  single  1.515  0.020  1.515
 7D8  CAA  OAJ  single  1.411  0.020  1.411
 7D8  CAH  CAG  single  1.507  0.020  1.507
 7D8  CAH  CAL  single  1.506  0.020  1.506
 7D8  CAC  CAD  single  1.515  0.020  1.515
 7D8  CAG  CAD  single  1.519  0.020  1.519
 7D8  CAL  OAM  single  1.411  0.020  1.411
 7D8  OAJ  H1   single  0.850  0.020  0.980
 7D8  CAA  H2   single  0.970  0.020  1.090
 7D8  CAB  H3   single  0.970  0.020  1.090
 7D8  OAK  H4   single  0.850  0.020  0.980
 7D8  CAC  H5   single  0.970  0.020  1.090
 7D8  CAD  H6   single  0.970  0.020  1.090
 7D8  CAD  H7   single  0.970  0.020  1.090
 7D8  CAG  H8   single  0.970  0.020  1.090
 7D8  CAI  H9   single  0.970  0.020  1.090
 7D8  CAI  H10  single  0.970  0.020  1.090
 7D8  CAL  H11  single  0.970  0.020  1.090
 7D8  CAL  H12  single  0.970  0.020  1.090
 7D8  OAM  H13  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
 7D8  H1   OAJ  CAA  107.87  3.000
 7D8  H2   CAA  CAH  108.89  3.000
 7D8  H2   CAA  CAB  107.86  3.000
 7D8  CAH  CAA  CAB  112.32  3.000
 7D8  H2   CAA  OAJ  110.18  3.000
 7D8  CAH  CAA  OAJ  107.63  3.000
 7D8  CAB  CAA  OAJ  109.96  3.000
 7D8  H3   CAB  CAC  109.06  3.000
 7D8  H3   CAB  OAK  110.36  3.000
 7D8  CAC  CAB  OAK  112.44  3.000
 7D8  H3   CAB  CAA  109.40  3.000
 7D8  CAC  CAB  CAA  109.15  3.000
 7D8  OAK  CAB  CAA  106.36  3.000
 7D8  H4   OAK  CAB  108.94  3.000
 7D8  H5   CAC  CAD  110.95  3.000
 7D8  H5   CAC  FAF  106.55  3.000
 7D8  CAD  CAC  FAF  108.73  3.000
 7D8  H5   CAC  CAB  109.91  3.000
 7D8  CAD  CAC  CAB  111.74  3.000
 7D8  FAF  CAC  CAB  108.80  3.000
 7D8  H7   CAD  H6   106.81  3.000
 7D8  H7   CAD  CAG  109.85  3.000
 7D8  H6   CAD  CAG  109.63  3.000
 7D8  H7   CAD  CAC  108.56  3.000
 7D8  H6   CAD  CAC  109.07  3.000
 7D8  CAG  CAD  CAC  112.74  3.000
 7D8  H8   CAG  CAH  115.49  3.000
 7D8  H8   CAG  CAI  115.72  3.000
 7D8  CAH  CAG  CAI   59.71  3.000
 7D8  H8   CAG  CAD  114.37  3.000
 7D8  CAH  CAG  CAD  121.18  3.000
 7D8  CAI  CAG  CAD  119.68  3.000
 7D8  H10  CAI  H9   113.40  3.000
 7D8  H10  CAI  CAH  119.40  3.000
 7D8  H9   CAI  CAH  117.57  3.000
 7D8  H10  CAI  CAG  117.87  3.000
 7D8  H9   CAI  CAG  118.51  3.000
 7D8  CAH  CAI  CAG   60.35  3.000
 7D8  CAL  CAH  CAI  115.85  3.000
 7D8  CAL  CAH  CAG  116.75  3.000
 7D8  CAI  CAH  CAG   59.94  3.000
 7D8  CAL  CAH  CAA  115.24  3.000
 7D8  CAG  CAH  CAA  119.17  3.000
 7D8  CAI  CAH  CAA  118.76  3.000
 7D8  H12  CAL  H11  106.56  3.000
 7D8  H12  CAL  OAM  111.27  3.000
 7D8  H11  CAL  OAM  111.51  3.000
 7D8  H12  CAL  CAH  108.50  3.000
 7D8  H11  CAL  CAH  110.23  3.000
 7D8  OAM  CAL  CAH  108.72  3.000
 7D8  H13  OAM  CAL  108.17  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
 7D8  Var_01  CAG  CAI  CAH  CAA  -108.95  30.0  1
 7D8  Var_02  CAI  CAG  CAD  CAC   -82.29  30.0  1
 7D8  Var_03  CAH  CAI  CAG  CAD   110.93  30.0  1
 7D8  Var_04  OAM  CAL  CAH  CAA   -62.00  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
 7D8  chir_01  CAA  CAB  CAH  OAJ  positiv
 7D8  chir_02  CAB  OAK  CAA  CAC  negativ
 7D8  chir_03  CAC  FAF  CAD  CAB  negativ
 7D8  chir_04  CAG  CAI  CAH  CAD  both
 7D8  chir_05  CAH  CAA  CAG  CAL  both

