# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:32:21 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(1R,2R)-1,2-dihydroxypropyl]-5-fluoro-4-hydroxy-2,3,4,5-tetrahydropyranium (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](O)[C@@H]1[O+]=C([C@H](F)[C@H](O)[C@H]1NC(C)=O)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
 9TM  9TM  '(2R,3R,4R,5R)-3-(acetylamino)-6-carboxy-2-[(1R,2R)-1,2-dihydroxypropyl]-5-fluoro-4-hydroxy-2,3,4,5-tetrahydropyranium (non-preferred name)'  ligand  37  20  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9TM
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
 9TM  O1B  O  O     0  -0.349  24.7714  20.7464  65.0523
 9TM  C1   C  C     0   0.546  23.9204  20.0045  64.6706
 9TM  O1A  O  OH1   0  -0.549  22.6591  19.9476  64.9876
 9TM  C2   C  C     0   0.398  24.2553  18.9097  63.6548
 9TM  C3   C  CH1   0   0.084  23.4113  17.6765  63.4981
 9TM  F1   F  F     0  -0.331  23.5102  17.0906  64.7431
 9TM  O6   O  OC2   1  -0.273  25.3111  19.1020  63.0538
 9TM  C6   C  CH1   0  -0.016  25.9547  18.1341  62.1159
 9TM  C7   C  CH1   0  -0.016  27.4598  18.3409  62.2859
 9TM  C8   C  CH1   0   0.042  27.8851  19.8052  62.1300
 9TM  C9   C  CH3   0  -0.690  29.3959  19.9203  62.0110
 9TM  O8   O  OH1   0  -0.672  27.2275  20.2926  60.9810
 9TM  O7   O  OH1   0  -0.676  27.8981  17.8840  63.5283
 9TM  C5   C  CH1   0  -0.187  25.4487  16.7256  62.4336
 9TM  C4   C  CH1   0   0.021  23.9212  16.7406  62.4032
 9TM  O4   O  OH1   0  -0.640  23.4314  15.4583  62.6009
 9TM  N5   N  NH1   0  -0.630  25.9705  15.7984  61.4716
 9TM  C10  C  C     0   0.561  27.0745  15.0552  61.6903
 9TM  O10  O  O     0  -0.505  27.7691  15.1926  62.6927
 9TM  C11  C  CH3   0  -0.773  27.4120  14.0542  60.6246
 9TM  H1   H  HOH1  0   0.524  22.4149  20.6305  65.6360
 9TM  H3   H  HCH1  0   0.337  22.3737  17.9684  63.3129
 9TM  H4   H  HCH1  0   0.353  25.6219  18.4625  61.1297
 9TM  H5   H  HCH1  0   0.260  27.9062  17.7803  61.4520
 9TM  H6   H  HCH1  0   0.219  27.5649  20.3546  63.0255
 9TM  H7   H  HCH3  0   0.238  29.8932  19.5480  62.9053
 9TM  H8   H  HCH3  0   0.229  29.7655  19.3589  61.1509
 9TM  H9   H  HCH3  0   0.241  29.6854  20.9651  61.8867
 9TM  H10  H  HOH1  0   0.462  27.4156  21.2326  60.8975
 9TM  H11  H  HOH1  0   0.466  27.9913  16.9183  63.4688
 9TM  H12  H  HCH1  0   0.319  25.7840  16.4208  63.4299
 9TM  H13  H  HCH1  0   0.289  23.5930  17.1685  61.4464
 9TM  H14  H  HOH1  0   0.478  22.5983  15.3592  62.1285
 9TM  H15  H  HNH1  0   0.422  25.4532  15.6574  60.6172
 9TM  H16  H  HCH3  0   0.279  28.3767  14.3103  60.1867
 9TM  H17  H  HCH3  0   0.279  27.5121  13.0694  61.0793
 9TM  H18  H  HCH3  0   0.260  26.6725  13.9988  59.8293

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
 9TM  C11  C10  single  1.500  0.020  1.500
 9TM  O8   C8   single  1.411  0.020  1.411
 9TM  N5   C10  single  1.349  0.020  1.349
 9TM  N5   C5   single  1.434  0.020  1.434
 9TM  C10  O10  double  1.227  0.020  1.227
 9TM  C8   C9   single  1.520  0.020  1.520
 9TM  C8   C7   single  1.533  0.020  1.533
 9TM  C6   C7   single  1.529  0.020  1.529
 9TM  C6   C5   single  1.530  0.020  1.530
 9TM  C6   O6   single  1.494  0.020  1.494
 9TM  C7   O7   single  1.394  0.020  1.394
 9TM  C4   O4   single  1.387  0.020  1.387
 9TM  C4   C5   single  1.528  0.020  1.528
 9TM  C4   C3   single  1.528  0.020  1.528
 9TM  O6   C2   double  1.230  0.020  1.230
 9TM  C3   C2   single  1.502  0.020  1.502
 9TM  C3   F1   single  1.380  0.020  1.380
 9TM  C2   C1   single  1.531  0.020  1.531
 9TM  C1   O1B  double  1.192  0.020  1.192
 9TM  C1   O1A  single  1.302  0.020  1.302
 9TM  O1A  H1   single  0.850  0.020  0.980
 9TM  C3   H3   single  0.970  0.020  1.090
 9TM  C6   H4   single  0.970  0.020  1.090
 9TM  C7   H5   single  0.970  0.020  1.090
 9TM  C8   H6   single  0.970  0.020  1.090
 9TM  C9   H7   single  0.970  0.020  1.090
 9TM  C9   H8   single  0.970  0.020  1.090
 9TM  C9   H9   single  0.970  0.020  1.090
 9TM  O8   H10  single  0.850  0.020  0.980
 9TM  O7   H11  single  0.850  0.020  0.980
 9TM  C5   H12  single  0.970  0.020  1.090
 9TM  C4   H13  single  0.970  0.020  1.090
 9TM  O4   H14  single  0.850  0.020  0.980
 9TM  N5   H15  single  0.860  0.020  1.020
 9TM  C11  H16  single  0.970  0.020  1.090
 9TM  C11  H17  single  0.970  0.020  1.090
 9TM  C11  H18  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
 9TM  C2   C1   O1A  110.02  3.000
 9TM  O1A  C1   O1B  129.87  3.000
 9TM  C2   C1   O1B  120.11  3.000
 9TM  H1   O1A  C1   112.01  3.000
 9TM  O6   C2   C3   124.02  3.000
 9TM  C3   C2   C1   122.24  3.000
 9TM  O6   C2   C1   113.59  3.000
 9TM  H3   C3   C4   111.02  3.000
 9TM  H3   C3   F1   109.52  3.000
 9TM  C4   C3   F1   111.26  3.000
 9TM  H3   C3   C2   109.36  3.000
 9TM  F1   C3   C2   102.37  3.000
 9TM  C4   C3   C2   112.96  3.000
 9TM  C6   O6   C2   125.13  3.000
 9TM  H4   C6   C5   111.33  3.000
 9TM  H4   C6   C7   111.10  3.000
 9TM  C5   C6   C7   115.28  3.000
 9TM  H4   C6   O6   103.94  3.000
 9TM  C5   C6   O6   108.88  3.000
 9TM  C7   C6   O6   105.47  3.000
 9TM  H5   C7   O7   112.40  3.000
 9TM  H5   C7   C8   107.30  3.000
 9TM  O7   C7   C8   108.45  3.000
 9TM  H5   C7   C6   104.27  3.000
 9TM  O7   C7   C6   111.35  3.000
 9TM  C8   C7   C6   113.02  3.000
 9TM  H6   C8   O8   110.82  3.000
 9TM  H6   C8   C9   108.41  3.000
 9TM  O8   C8   C9   111.93  3.000
 9TM  H6   C8   C7   108.30  3.000
 9TM  C9   C8   C7   110.86  3.000
 9TM  O8   C8   C7   106.47  3.000
 9TM  H9   C9   H8   108.23  3.000
 9TM  H9   C9   H7   107.44  3.000
 9TM  H8   C9   H7   108.46  3.000
 9TM  H9   C9   C8   110.19  3.000
 9TM  H8   C9   C8   111.06  3.000
 9TM  H7   C9   C8   111.34  3.000
 9TM  H10  O8   C8   108.48  3.000
 9TM  H11  O7   C7   107.53  3.000
 9TM  H12  C5   N5   108.61  3.000
 9TM  H12  C5   C4   109.10  3.000
 9TM  N5   C5   C4   110.90  3.000
 9TM  H12  C5   C6   110.12  3.000
 9TM  C4   C5   C6   108.51  3.000
 9TM  N5   C5   C6   109.60  3.000
 9TM  H13  C4   O4   112.27  3.000
 9TM  H13  C4   C5   108.66  3.000
 9TM  O4   C4   C5   109.94  3.000
 9TM  H13  C4   C3   106.61  3.000
 9TM  C5   C4   C3   108.98  3.000
 9TM  O4   C4   C3   110.26  3.000
 9TM  H14  O4   C4   109.31  3.000
 9TM  H15  N5   C10  118.69  3.000
 9TM  H15  N5   C5   118.16  3.000
 9TM  C10  N5   C5   123.04  3.000
 9TM  C11  C10  O10  121.84  3.000
 9TM  O10  C10  N5   122.27  3.000
 9TM  C11  C10  N5   115.88  3.000
 9TM  H18  C11  H17  108.77  3.000
 9TM  H18  C11  H16  108.66  3.000
 9TM  H17  C11  H16  107.38  3.000
 9TM  H18  C11  C10  113.61  3.000
 9TM  H17  C11  C10  109.11  3.000
 9TM  H16  C11  C10  109.13  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
 9TM  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 9TM  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 9TM  CONST_03  H1   O1A  C1   C2   180.00   0.0  0
 9TM  CONST_04  H15  N5   C10  O10  180.00   0.0  0
 9TM  Var_01    O6   C2   C1   O1B  -17.87  30.0  2
 9TM  Var_02    H16  C11  C10  N5   117.08  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
 9TM  chir_01  C3  C4  C2  F1  positiv
 9TM  chir_02  C6  O6  C5  C7  positiv
 9TM  chir_03  C7  O7  C6  C8  negativ
 9TM  chir_04  C8  O8  C7  C9  negativ
 9TM  chir_05  C5  N5  C4  C6  positiv
 9TM  chir_06  C4  O4  C5  C3  positiv

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
 9TM  plan-1  C5   0.020
 9TM  plan-1  N5   0.020
 9TM  plan-1  C10  0.020
 9TM  plan-1  O10  0.020
 9TM  plan-1  C11  0.020
 9TM  plan-1  H15  0.020
 9TM  plan-2  O1B  0.020
 9TM  plan-2  C1   0.020
 9TM  plan-2  O1A  0.020
 9TM  plan-2  C2   0.020
 9TM  plan-2  H1   0.020

