# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:55:25 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (1R,2R,3R,4R,5R,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-4-fluoro-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@]2(O[C@H]([C@H](O)CO)[C@@H]1O2)C(O)=O
#
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
 19D  19D  '(1R,2R,3R,4R,5R,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-4-fluoro-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid (non-preferred name)'  ligand  36  21  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_19D
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
 19D  C1   C  C      0   0.389  -1.0328   2.5110   0.5471
 19D  O1A  O  OC    -1  -0.597  -0.2168   3.2481   1.1274
 19D  O1B  O  O      0  -0.572  -2.2426   2.6882   0.3624
 19D  C2   C  CT     0   0.297  -0.4158   1.1904   0.0153
 19D  C3   C  CH1    0   0.199   0.8310   1.4269  -0.8349
 19D  C4   C  CH1    0  -0.035   1.4350   0.1328  -1.3849
 19D  O4   O  OH1    0  -0.660   0.7419  -0.3727  -2.4965
 19D  C5   C  CH1    0  -0.067   1.4098  -0.9515  -0.2859
 19D  N5   N  NH1    0  -0.641   2.5315  -0.8096   0.6151
 19D  C6   C  CH1    0  -0.137   0.1222  -0.8892   0.5343
 19D  O6   O  O2     0  -0.501   0.0105   0.4066   1.1071
 19D  C7   C  CH1    0   0.024  -1.1605  -0.9504  -0.2947
 19D  O7   O  O2     0  -0.507  -1.3499   0.4029  -0.6696
 19D  C8   C  CH1    0  -0.019  -2.3464  -1.4557   0.5335
 19D  O8   O  OH1    0  -0.661  -2.1454  -2.8116   0.8638
 19D  C9   C  CH2    0  -0.163  -3.6631  -1.2239  -0.1875
 19D  O9   O  OH1    0  -0.671  -4.7125  -1.6847   0.6322
 19D  C10  C  C      0   0.529   3.7423  -1.3441   0.3690
 19D  O10  O  O      0  -0.505   3.9784  -2.0101  -0.6299
 19D  C11  C  CH3    0  -0.778   4.7950  -1.0722   1.4128
 19D  F1   F  F      0  -0.376   0.5124   2.2661  -1.9025
 19D  H2   H  HCH1   0   0.226   1.5721   1.9405  -0.2203
 19D  H3   H  HCH1   0   0.243   2.4825   0.3295  -1.6514
 19D  H4   H  HOH1   0   0.453   0.5247   0.3547  -3.0884
 19D  H5   H  HCH1   0   0.283   1.4787  -1.9276  -0.7716
 19D  H6   H  HNH1   0   0.403   2.4136  -0.2294   1.4310
 19D  H7   H  HCH1   0   0.280   0.1520  -1.6304   1.3345
 19D  H8   H  HCH1   0   0.248  -1.0538  -1.5741  -1.1889
 19D  H9   H  HCH1   0   0.233  -2.3712  -0.9157   1.4864
 19D  H10  H  HOH1   0   0.445  -2.1833  -3.3356   0.0554
 19D  H11  H  HCH2   0   0.214  -3.7597  -0.1551  -0.4041
 19D  H12  H  HCH2   0   0.186  -3.6424  -1.7527  -1.1536
 19D  H13  H  HOH1   0   0.455  -5.5424  -1.4562   0.2050
 19D  H14  H  HCH3   0   0.250   4.4340  -0.4909   2.2589
 19D  H15  H  HCH3   0   0.267   5.1865  -2.0188   1.7845
 19D  H16  H  HCH3   0   0.267   5.6253  -0.5345   0.9553

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
 19D  C11  C10  single  1.507  0.020  1.507
 19D  O10  C10  double  1.224  0.020  1.224
 19D  C10  N5   single  1.346  0.020  1.346
 19D  N5   C5   single  1.446  0.020  1.446
 19D  C9   O9   single  1.409  0.020  1.409
 19D  C9   C8   single  1.519  0.020  1.519
 19D  C5   C4   single  1.544  0.020  1.544
 19D  C5   C6   single  1.528  0.020  1.528
 19D  O4   C4   single  1.404  0.020  1.404
 19D  C7   C6   single  1.529  0.020  1.529
 19D  C7   C8   single  1.532  0.020  1.532
 19D  C7   O7   single  1.417  0.020  1.417
 19D  C4   C3   single  1.530  0.020  1.530
 19D  C6   O6   single  1.421  0.020  1.421
 19D  C8   O8   single  1.410  0.020  1.410
 19D  F1   C3   single  1.395  0.020  1.395
 19D  O7   C2   single  1.401  0.020  1.401
 19D  C3   C2   single  1.528  0.020  1.528
 19D  O6   C2   single  1.410  0.020  1.410
 19D  C2   C1   single  1.552  0.020  1.552
 19D  C1   O1B  deloc   1.237  0.020  1.237
 19D  C1   O1A  deloc   1.243  0.020  1.243
 19D  C3   H2   single  0.970  0.020  1.090
 19D  C4   H3   single  0.970  0.020  1.090
 19D  O4   H4   single  0.850  0.020  0.980
 19D  C5   H5   single  0.970  0.020  1.090
 19D  N5   H6   single  0.860  0.020  1.020
 19D  C6   H7   single  0.970  0.020  1.090
 19D  C7   H8   single  0.970  0.020  1.090
 19D  C8   H9   single  0.970  0.020  1.090
 19D  O8   H10  single  0.850  0.020  0.980
 19D  C9   H11  single  0.970  0.020  1.090
 19D  C9   H12  single  0.970  0.020  1.090
 19D  O9   H13  single  0.850  0.020  0.980
 19D  C11  H14  single  0.970  0.020  1.090
 19D  C11  H15  single  0.970  0.020  1.090
 19D  C11  H16  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
 19D  C2   C1   O1B  117.38  3.000
 19D  O1B  C1   O1A  128.82  3.000
 19D  C2   C1   O1A  113.80  3.000
 19D  O7   C2   O6   105.52  3.000
 19D  O6   C2   C3   105.68  3.000
 19D  O7   C2   C3   111.05  3.000
 19D  O6   C2   C1   109.15  3.000
 19D  C3   C2   C1   112.56  3.000
 19D  O7   C2   C1   112.40  3.000
 19D  H2   C3   F1   107.64  3.000
 19D  H2   C3   C4   109.41  3.000
 19D  F1   C3   C4   108.90  3.000
 19D  H2   C3   C2   108.28  3.000
 19D  F1   C3   C2   109.43  3.000
 19D  C4   C3   C2   113.03  3.000
 19D  H3   C4   C5   108.30  3.000
 19D  H3   C4   O4   110.06  3.000
 19D  C5   C4   O4   107.61  3.000
 19D  H3   C4   C3   108.18  3.000
 19D  O4   C4   C3   113.21  3.000
 19D  C5   C4   C3   109.37  3.000
 19D  H4   O4   C4   109.03  3.000
 19D  H5   C5   C6   109.16  3.000
 19D  H5   C5   N5   108.41  3.000
 19D  C6   C5   N5   108.38  3.000
 19D  H5   C5   C4   108.06  3.000
 19D  C6   C5   C4   111.54  3.000
 19D  N5   C5   C4   111.22  3.000
 19D  H6   N5   C10  118.79  3.000
 19D  H6   N5   C5   118.05  3.000
 19D  C10  N5   C5   123.02  3.000
 19D  H7   C6   C7   113.17  3.000
 19D  H7   C6   O6   109.02  3.000
 19D  C7   C6   O6   100.90  3.000
 19D  H7   C6   C5   110.06  3.000
 19D  O6   C6   C5   108.65  3.000
 19D  C7   C6   C5   114.48  3.000
 19D  C6   O6   C2   102.63  3.000
 19D  H8   C7   C8   109.20  3.000
 19D  H8   C7   O7   109.93  3.000
 19D  C8   C7   O7   110.77  3.000
 19D  H8   C7   C6   112.57  3.000
 19D  O7   C7   C6   102.56  3.000
 19D  C8   C7   C6   111.69  3.000
 19D  C7   O7   C2   108.58  3.000
 19D  H9   C8   C9   108.54  3.000
 19D  H9   C8   O8   105.87  3.000
 19D  C9   C8   O8   112.43  3.000
 19D  H9   C8   C7   108.97  3.000
 19D  O8   C8   C7   109.48  3.000
 19D  C9   C8   C7   111.35  3.000
 19D  H10  O8   C8   108.70  3.000
 19D  H12  C9   H11  107.27  3.000
 19D  H12  C9   O9   111.54  3.000
 19D  H11  C9   O9   111.63  3.000
 19D  H12  C9   C8   109.07  3.000
 19D  H11  C9   C8   108.62  3.000
 19D  O9   C9   C8   108.63  3.000
 19D  H13  O9   C9   107.86  3.000
 19D  C11  C10  O10  121.92  3.000
 19D  O10  C10  N5   122.61  3.000
 19D  C11  C10  N5   115.47  3.000
 19D  H16  C11  H15  107.34  3.000
 19D  H16  C11  H14  108.39  3.000
 19D  H15  C11  H14  108.54  3.000
 19D  H16  C11  C10  109.30  3.000
 19D  H15  C11  C10  109.30  3.000
 19D  H14  C11  C10  113.77  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
 19D  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 19D  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 19D  CONST_03  H6   N5   C10  O10  180.00   0.0  0
 19D  Var_01    H14  C11  C10  N5     1.46  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
 19D  chir_01  C2  C3  O6  C1  negativ
 19D  chir_02  C3  F1  C2  C4  negativ
 19D  chir_03  C4  O4  C3  C5  negativ
 19D  chir_04  C5  N5  C6  C4  negativ
 19D  chir_05  C6  O6  C7  C5  negativ
 19D  chir_06  C7  O7  C8  C6  positiv
 19D  chir_07  C8  O8  C7  C9  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
 19D  plan-1  C5   0.020
 19D  plan-1  N5   0.020
 19D  plan-1  C10  0.020
 19D  plan-1  O10  0.020
 19D  plan-1  C11  0.020
 19D  plan-1  H6   0.020
 19D  plan-2  C1   0.020
 19D  plan-2  O1A  0.020
 19D  plan-2  O1B  0.020
 19D  plan-2  C2   0.020

