# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:14:57 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-{[(4-chlorophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)NC(=O)c2ccc(Cl)cc2)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 F55  F55  N-{[(4-chlorophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine  D-saccharide  41  24  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F55
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
 F55  C14  C   CR16  0  -0.263  -4.6370  -1.1373  -0.6369
 F55  C13  C   CR16  0  -0.197  -5.8787  -0.7968  -0.1308
 F55  C12  C   CR6   0  -0.038  -6.0256   0.4069   0.5436
 F55  CL1  CL  CL    0  -0.109  -7.5756   0.8456   1.1682
 F55  C11  C   CR16  0  -0.193  -4.9532   1.2668   0.7190
 F55  C10  C   CR16  0  -0.292  -3.7120   0.9076   0.2185
 F55  C9   C   CR6   0  -0.045  -3.5392  -0.2977  -0.4587
 F55  C8   C   C     0   0.553  -2.2366  -0.7191  -1.0546
 F55  O8   O   O     0  -0.417  -2.1899  -1.4821  -1.9921
 F55  N2   N   NH1   0  -0.762  -1.1277  -0.1877  -0.4392
 F55  C7   C   C     0   0.768   0.1873  -0.2859  -0.8898
 F55  O7   O   O     0  -0.470   0.4977  -0.7683  -1.9547
 F55  N1   N   NH1   0  -0.737   1.0712   0.2609  -0.0119
 F55  C1   C   CH1   0   0.209   2.4767   0.2586  -0.2447
 F55  O5   O   O2    0  -0.487   3.0427  -0.8545   0.4051
 F55  C5   C   CH1   0  -0.015   4.4249  -1.0070   0.1552
 F55  C6   C   CH2   0  -0.157   4.8772  -2.2908   0.8180
 F55  O6   O   OH1   0  -0.670   4.2105  -3.3727   0.2134
 F55  C4   C   CH1   0   0.036   5.1828   0.2082   0.6924
 F55  O4   O   OH1   0  -0.672   6.5431   0.0532   0.3748
 F55  C3   C   CH1   0  -0.007   4.6134   1.4823   0.0790
 F55  O3   O   OH1   0  -0.671   5.2767   2.5710   0.6752
 F55  C2   C   CH1   0  -0.026   3.1064   1.5503   0.2829
 F55  O2   O   OH1   0  -0.663   2.6318   2.6744  -0.4118
 F55  H14  H   HCR6  0   0.276  -4.5247  -2.0727  -1.1681
 F55  H13  H   HCR6  0   0.289  -6.7221  -1.4601  -0.2633
 F55  H11  H   HCR6  0   0.291  -5.0787   2.2091   1.2341
 F55  H10  H   HCR6  0   0.274  -2.8956   1.6066   0.3484
 F55  HN2  H   HNH1  0   0.427  -1.2804   0.3093   0.4249
 F55  HN1  H   HNH1  0   0.410   0.7570   0.5186   0.9131
 F55  H1   H   HCH1  0   0.236   2.6462   0.1975  -1.3267
 F55  H5   H   HCH1  0   0.224   4.6052  -1.0820  -0.9300
 F55  H6   H   HCH2  0   0.213   5.9636  -2.3710   0.7080
 F55  H6A  H   HCH2  0   0.197   4.6657  -2.2288   1.8947
 F55  HO6  H   HOH1  0   0.457   4.5439  -4.1838   0.6071
 F55  H4   H   HCH1  0   0.213   5.0335   0.2523   1.7835
 F55  HO4  H   HOH1  0   0.455   7.0164   0.8254   0.7022
 F55  H3   H   HCH1  0   0.219   4.8097   1.4525  -1.0049
 F55  HO3  H   HOH1  0   0.458   5.0895   3.3632   0.1622
 F55  H2   H   HCH1  0   0.227   2.8990   1.6259   1.3620
 F55  HO2  H   HOH1  0   0.457   1.7201   2.8406  -0.1520

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
 F55  C14  C13  aromatic  1.383  0.020  1.383
 F55  C14  C9   aromatic  1.393  0.020  1.393
 F55  C13  C12  aromatic  1.388  0.020  1.388
 F55  C12  CL1  single    1.728  0.020  1.728
 F55  C12  C11  aromatic  1.386  0.020  1.386
 F55  C11  C10  aromatic  1.386  0.020  1.386
 F55  C10  C9   aromatic  1.393  0.020  1.393
 F55  C9   C8   single    1.493  0.020  1.493
 F55  C8   O8   double    1.210  0.020  1.210
 F55  C8   N2   single    1.375  0.020  1.375
 F55  N2   C7   single    1.394  0.020  1.394
 F55  C7   O7   double    1.210  0.020  1.210
 F55  C7   N1   single    1.360  0.020  1.360
 F55  N1   C1   single    1.425  0.020  1.425
 F55  C1   O5   single    1.408  0.020  1.408
 F55  C1   C2   single    1.531  0.020  1.531
 F55  O5   C5   single    1.413  0.020  1.413
 F55  C5   C6   single    1.514  0.020  1.514
 F55  C5   C4   single    1.530  0.020  1.530
 F55  C6   O6   single    1.407  0.020  1.407
 F55  C4   O4   single    1.406  0.020  1.406
 F55  C4   C3   single    1.524  0.020  1.524
 F55  C3   O3   single    1.407  0.020  1.407
 F55  C3   C2   single    1.522  0.020  1.522
 F55  C2   O2   single    1.404  0.020  1.404
 F55  C14  H14  single    0.930  0.020  1.080
 F55  C13  H13  single    0.930  0.020  1.080
 F55  C11  H11  single    0.930  0.020  1.080
 F55  C10  H10  single    0.930  0.020  1.080
 F55  N2   HN2  single    0.860  0.020  1.020
 F55  N1   HN1  single    0.860  0.020  1.020
 F55  C1   H1   single    0.970  0.020  1.090
 F55  C5   H5   single    0.970  0.020  1.090
 F55  C6   H6   single    0.970  0.020  1.090
 F55  C6   H6A  single    0.970  0.020  1.090
 F55  O6   HO6  single    0.850  0.020  0.980
 F55  C4   H4   single    0.970  0.020  1.090
 F55  O4   HO4  single    0.850  0.020  0.980
 F55  C3   H3   single    0.970  0.020  1.090
 F55  O3   HO3  single    0.850  0.020  0.980
 F55  C2   H2   single    0.970  0.020  1.090
 F55  O2   HO2  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
 F55  H14  C14  C9   120.14  3.000
 F55  H14  C14  C13  119.06  3.000
 F55  C9   C14  C13  120.80  3.000
 F55  H13  C13  C12  120.61  3.000
 F55  H13  C13  C14  120.29  3.000
 F55  C12  C13  C14  119.10  3.000
 F55  C11  C12  CL1  119.40  3.000
 F55  C11  C12  C13  121.19  3.000
 F55  CL1  C12  C13  119.41  3.000
 F55  H11  C11  C10  120.13  3.000
 F55  H11  C11  C12  120.75  3.000
 F55  C10  C11  C12  119.12  3.000
 F55  H10  C10  C9   121.56  3.000
 F55  H10  C10  C11  117.69  3.000
 F55  C9   C10  C11  120.73  3.000
 F55  C8   C9   C10  123.12  3.000
 F55  C8   C9   C14  117.79  3.000
 F55  C10  C9   C14  119.06  3.000
 F55  N2   C8   O8   124.01  3.000
 F55  N2   C8   C9   114.57  3.000
 F55  O8   C8   C9   121.41  3.000
 F55  HN2  N2   C7   117.04  3.000
 F55  HN2  N2   C8   116.86  3.000
 F55  C7   N2   C8   126.09  3.000
 F55  N1   C7   O7   124.17  3.000
 F55  N1   C7   N2   112.09  3.000
 F55  O7   C7   N2   123.70  3.000
 F55  HN1  N1   C1   117.18  3.000
 F55  HN1  N1   C7   119.43  3.000
 F55  C1   N1   C7   122.33  3.000
 F55  H1   C1   C2   108.87  3.000
 F55  H1   C1   O5   110.43  3.000
 F55  C2   C1   O5   110.04  3.000
 F55  H1   C1   N1   108.29  3.000
 F55  C2   C1   N1   110.38  3.000
 F55  O5   C1   N1   108.82  3.000
 F55  C5   O5   C1   113.40  3.000
 F55  H5   C5   C4   108.58  3.000
 F55  H5   C5   C6   108.93  3.000
 F55  C4   C5   C6   111.84  3.000
 F55  H5   C5   O5   109.96  3.000
 F55  C4   C5   O5   109.68  3.000
 F55  C6   C5   O5   107.84  3.000
 F55  H6A  C6   H6   107.07  3.000
 F55  H6A  C6   O6   111.91  3.000
 F55  H6   C6   O6   111.75  3.000
 F55  H6A  C6   C5   108.88  3.000
 F55  H6   C6   C5   108.33  3.000
 F55  O6   C6   C5   108.80  3.000
 F55  HO6  O6   C6   107.96  3.000
 F55  H4   C4   C3   108.32  3.000
 F55  H4   C4   O4   111.05  3.000
 F55  C3   C4   O4   111.27  3.000
 F55  H4   C4   C5   108.20  3.000
 F55  C3   C4   C5   109.73  3.000
 F55  O4   C4   C5   108.21  3.000
 F55  HO4  O4   C4   108.08  3.000
 F55  H3   C3   C2   108.02  3.000
 F55  H3   C3   O3   110.71  3.000
 F55  C2   C3   O3   112.04  3.000
 F55  H3   C3   C4   107.86  3.000
 F55  C2   C3   C4   110.68  3.000
 F55  O3   C3   C4   107.46  3.000
 F55  HO3  O3   C3   108.63  3.000
 F55  H2   C2   O2   111.48  3.000
 F55  H2   C2   C3   108.71  3.000
 F55  O2   C2   C3   107.71  3.000
 F55  H2   C2   C1   108.55  3.000
 F55  O2   C2   C1   111.46  3.000
 F55  C3   C2   C1   108.87  3.000
 F55  HO2  O2   C2   108.96  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
 F55  CONST_01  C11  C12  C13  C14    0.00   0.0  0
 F55  CONST_02  C11  C10  C9   C14    0.00   0.0  0
 F55  CONST_03  C10  C9   C14  C13    0.00   0.0  0
 F55  CONST_04  C10  C11  C12  C13    0.00   0.0  0
 F55  CONST_05  C9   C14  C13  C12    0.00   0.0  0
 F55  CONST_06  C9   C10  C11  C12    0.00   0.0  0
 F55  CONST_07  CL1  C12  C13  C14  180.00   0.0  0
 F55  CONST_08  C8   C9   C14  C13  180.00   0.0  0
 F55  CONST_09  C10  C11  C12  CL1  180.00   0.0  0
 F55  CONST_10  C8   C9   C10  C11  180.00   0.0  0
 F55  CONST_11  H10  C10  C9   C14  180.00   0.0  0
 F55  CONST_12  H11  C11  C12  C13  180.00   0.0  0
 F55  CONST_13  H14  C14  C13  C12  180.00   0.0  0
 F55  CONST_14  H13  C13  C12  C11  180.00   0.0  0
 F55  CONST_15  C7   N2   C8   C9   180.00   0.0  0
 F55  CONST_16  C1   N1   C7   O7     0.00   0.0  0
 F55  CONST_17  C1   N1   C7   N2   180.00   0.0  0
 F55  CONST_18  HN2  N2   C8   C9     0.00   0.0  0
 F55  CONST_19  O7   C7   N2   C8     0.00   0.0  0
 F55  CONST_20  C7   N2   C8   O8     0.00   0.0  0
 F55  CONST_21  N1   C7   N2   C8   180.00   0.0  0
 F55  CONST_22  HN1  N1   C7   O7   180.00   0.0  0
 F55  Var_01    O8   C8   C9   C14   23.66  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
 F55  chir_01  C1  N1  O5  C2  positiv
 F55  chir_02  C5  O5  C6  C4  positiv
 F55  chir_03  C4  O4  C5  C3  positiv
 F55  chir_04  C3  O3  C2  C4  positiv
 F55  chir_05  C2  O2  C3  C1  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
 F55  plan-1  C14  0.020
 F55  plan-1  C13  0.020
 F55  plan-1  C12  0.020
 F55  plan-1  CL1  0.020
 F55  plan-1  C11  0.020
 F55  plan-1  C10  0.020
 F55  plan-1  C9   0.020
 F55  plan-1  C8   0.020
 F55  plan-1  H14  0.020
 F55  plan-1  H13  0.020
 F55  plan-1  H11  0.020
 F55  plan-1  H10  0.020
 F55  plan-2  C9   0.020
 F55  plan-2  C8   0.020
 F55  plan-2  O8   0.020
 F55  plan-2  N2   0.020
 F55  plan-2  C7   0.020
 F55  plan-2  O7   0.020
 F55  plan-2  N1   0.020
 F55  plan-2  C1   0.020
 F55  plan-2  HN2  0.020
 F55  plan-2  HN1  0.020

