# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:14:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccc(F)c(F)c2)[C@H](NC(=O)C(F)F)[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
 14T  14T  '3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-glucopyranoside'  D-saccharide  40  25  .  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_14T
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
 14T  F1    F  F     0  -0.330   2.7728  -4.3686  -0.2305
 14T  C7    C  CH1   0   0.475   2.1020  -3.4390   0.4831
 14T  F2    F  F     0  -0.337   2.8160  -3.1952   1.6141
 14T  C8    C  C     0   0.419   1.9569  -2.1749  -0.3685
 14T  O5    O  O     0  -0.465   1.7700  -2.2866  -1.5637
 14T  N1    N  NH1   0  -0.635   2.0005  -1.0272   0.3160
 14T  C5    C  CH1   0  -0.166   1.7737   0.2629  -0.2854
 14T  C6    C  CH1   0   0.035   2.7722   1.2878   0.2433
 14T  O3    O  OH1   0  -0.659   4.0544   0.8771  -0.1405
 14T  C2    C  CH1   0   0.007   2.4347   2.6829  -0.2820
 14T  O2    O  OH1   0  -0.670   3.3243   3.5795   0.3405
 14T  C3    C  CH1   0  -0.032   0.9721   3.0104   0.0324
 14T  C4    C  CH2   0  -0.159   0.5320   4.3478  -0.5168
 14T  O4    O  OH1   0  -0.664  -0.7951   4.5814  -0.1146
 14T  O1    O  O2    0  -0.490   0.1552   2.0121  -0.5544
 14T  C1    C  CH1   0   0.315   0.3543   0.7537   0.0088
 14T  O6    O  O2    0  -0.489  -0.5333  -0.1341  -0.5830
 14T  C10   C  CR6   0   0.375  -1.8151  -0.1832  -0.1400
 14T  C9    C  CR16  0  -0.494  -2.4936  -1.3699  -0.4091
 14T  C14   C  CR6   0   0.410  -3.8044  -1.5000  -0.0109
 14T  F3    F  F     0  -0.304  -4.4674  -2.6320  -0.2624
 14T  C11   C  CR16  0  -0.345  -2.4578   0.8559   0.5242
 14T  C12   C  CR16  0  -0.396  -3.7778   0.6954   0.9295
 14T  C13   C  CR6   0   0.382  -4.4500  -0.4751   0.6608
 14T  F4    F  F     0  -0.308  -5.7249  -0.6371   1.0362
 14T  H7    H  HCH1  0   0.232   1.1277  -3.8406   0.7675
 14T  H1    H  HNH1  0   0.415   2.1874  -1.0534   1.3071
 14T  H5    H  HCH1  0   0.290   1.8914   0.1675  -1.3680
 14T  H6    H  HCH1  0   0.218   2.6824   1.3202   1.3432
 14T  HA    H  HCH1  0   0.216   0.1944   0.7885   1.1011
 14T  H3    H  HOH1  0   0.455   4.6857   1.5195   0.2013
 14T  H2    H  HCH1  0   0.234   2.5658   2.6838  -1.3736
 14T  HB    H  HOH1  0   0.466   3.4981   4.3144  -0.2539
 14T  HC    H  HCH1  0   0.232   0.8350   3.0147   1.1260
 14T  H41C  H  HCH2  0   0.207   1.2120   5.1180  -0.1341
 14T  H42C  H  HCH2  0   0.204   0.6360   4.3403  -1.6107
 14T  H4    H  HOH1  0   0.458  -1.0644   5.4383  -0.4576
 14T  H9    H  HCR6  0   0.300  -1.9968  -2.1850  -0.9197
 14T  H11   H  HCR6  0   0.300  -1.9717   1.8035   0.7082
 14T  H12   H  HCR6  0   0.298  -4.2868   1.4986   1.4457

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
 14T  F1   C7    single    1.350  0.020  1.350
 14T  C7   F2    single    1.360  0.020  1.360
 14T  C7   C8    single    1.531  0.020  1.531
 14T  C8   O5    double    1.215  0.020  1.215
 14T  C8   N1    single    1.337  0.020  1.337
 14T  N1   C5    single    1.441  0.020  1.441
 14T  C5   C6    single    1.525  0.020  1.525
 14T  C5   C1    single    1.530  0.020  1.530
 14T  C6   O3    single    1.400  0.020  1.400
 14T  C6   C2    single    1.528  0.020  1.528
 14T  C2   O2    single    1.408  0.020  1.408
 14T  C2   C3    single    1.531  0.020  1.531
 14T  C3   C4    single    1.511  0.020  1.511
 14T  C3   O1    single    1.417  0.020  1.417
 14T  C4   O4    single    1.406  0.020  1.406
 14T  O1   C1    single    1.393  0.020  1.393
 14T  C1   O6    single    1.388  0.020  1.388
 14T  O6   C10   single    1.357  0.020  1.357
 14T  C10  C9    aromatic  1.393  0.020  1.393
 14T  C10  C11   aromatic  1.391  0.020  1.391
 14T  C9   C14   aromatic  1.376  0.020  1.376
 14T  C14  F3    single    1.336  0.020  1.336
 14T  C14  C13   aromatic  1.385  0.020  1.385
 14T  C11  C12   aromatic  1.390  0.020  1.390
 14T  C12  C13   aromatic  1.376  0.020  1.376
 14T  C13  F4    single    1.339  0.020  1.339
 14T  C7   H7    single    0.970  0.020  1.090
 14T  N1   H1    single    0.860  0.020  1.020
 14T  C5   H5    single    0.970  0.020  1.090
 14T  C6   H6    single    0.970  0.020  1.090
 14T  C1   HA    single    0.970  0.020  1.090
 14T  O3   H3    single    0.850  0.020  0.980
 14T  C2   H2    single    0.970  0.020  1.090
 14T  O2   HB    single    0.850  0.020  0.980
 14T  C3   HC    single    0.970  0.020  1.090
 14T  C4   H41C  single    0.970  0.020  1.090
 14T  C4   H42C  single    0.970  0.020  1.090
 14T  O4   H4    single    0.850  0.020  0.980
 14T  C9   H9    single    0.930  0.020  1.080
 14T  C11  H11   single    0.930  0.020  1.080
 14T  C12  H12   single    0.930  0.020  1.080

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
 14T  H7    C7   C8    111.35  3.000
 14T  H7    C7   F2    108.54  3.000
 14T  C8    C7   F2    111.37  3.000
 14T  H7    C7   F1    109.14  3.000
 14T  C8    C7   F1    108.76  3.000
 14T  F2    C7   F1    107.59  3.000
 14T  N1    C8   O5    125.99  3.000
 14T  N1    C8   C7    114.89  3.000
 14T  O5    C8   C7    119.07  3.000
 14T  H1    N1   C5    117.53  3.000
 14T  H1    N1   C8    119.12  3.000
 14T  C5    N1   C8    123.34  3.000
 14T  H5    C5   C1    108.55  3.000
 14T  H5    C5   C6    109.36  3.000
 14T  C1    C5   C6    108.97  3.000
 14T  H5    C5   N1    108.55  3.000
 14T  C1    C5   N1    110.66  3.000
 14T  C6    C5   N1    110.72  3.000
 14T  H6    C6   C2    107.32  3.000
 14T  H6    C6   O3    110.86  3.000
 14T  C2    C6   O3    112.07  3.000
 14T  H6    C6   C5    108.17  3.000
 14T  C2    C6   C5    110.47  3.000
 14T  O3    C6   C5    107.90  3.000
 14T  H3    O3   C6    107.90  3.000
 14T  H2    C2   C3    108.51  3.000
 14T  H2    C2   O2    111.29  3.000
 14T  C3    C2   O2    112.11  3.000
 14T  H2    C2   C6    108.41  3.000
 14T  C3    C2   C6    109.60  3.000
 14T  O2    C2   C6    106.84  3.000
 14T  HB    O2   C2    109.13  3.000
 14T  HC    C3   O1    109.99  3.000
 14T  HC    C3   C4    108.72  3.000
 14T  O1    C3   C4    107.76  3.000
 14T  HC    C3   C2    108.87  3.000
 14T  O1    C3   C2    108.35  3.000
 14T  C4    C3   C2    113.13  3.000
 14T  H42C  C4   H41C  107.07  3.000
 14T  H42C  C4   O4    112.03  3.000
 14T  H41C  C4   O4    111.64  3.000
 14T  H42C  C4   C3    109.16  3.000
 14T  H41C  C4   C3    108.31  3.000
 14T  O4    C4   C3    108.53  3.000
 14T  H4    O4   C4    108.07  3.000
 14T  C1    O1   C3    112.74  3.000
 14T  HA    C1   O6    110.44  3.000
 14T  HA    C1   O1    110.53  3.000
 14T  O6    C1   O1    108.31  3.000
 14T  HA    C1   C5    109.54  3.000
 14T  O6    C1   C5    107.82  3.000
 14T  O1    C1   C5    110.15  3.000
 14T  C10   O6   C1    119.21  3.000
 14T  C11   C10  C9    120.24  3.000
 14T  C11   C10  O6    124.43  3.000
 14T  C9    C10  O6    115.32  3.000
 14T  H9    C9   C14   120.16  3.000
 14T  H9    C9   C10   120.60  3.000
 14T  C14   C9   C10   119.25  3.000
 14T  C13   C14  F3    119.15  3.000
 14T  C13   C14  C9    120.95  3.000
 14T  F3    C14  C9    119.90  3.000
 14T  H11   C11  C12   118.60  3.000
 14T  H11   C11  C10   121.91  3.000
 14T  C12   C11  C10   119.46  3.000
 14T  H12   C12  C13   119.65  3.000
 14T  H12   C12  C11   120.01  3.000
 14T  C13   C12  C11   120.33  3.000
 14T  F4    C13  C12   120.88  3.000
 14T  F4    C13  C14   119.36  3.000
 14T  C12   C13  C14   119.76  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
 14T  CONST_01  C13  C14  C9   C10     0.00   0.0  0
 14T  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 14T  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 14T  CONST_04  C12  C13  C14  C9      0.00   0.0  0
 14T  CONST_05  C11  C10  C9   C14     0.00   0.0  0
 14T  CONST_06  C11  C12  C13  C14     0.00   0.0  0
 14T  CONST_07  C14  C9   C10  O6    180.00   0.0  0
 14T  CONST_08  C12  C11  C10  O6    180.00   0.0  0
 14T  CONST_09  F3   C14  C9   C10   180.00   0.0  0
 14T  CONST_10  F4   C13  C14  C9    180.00   0.0  0
 14T  CONST_11  C12  C13  C14  F3    180.00   0.0  0
 14T  CONST_12  F4   C13  C12  C11   180.00   0.0  0
 14T  CONST_13  H12  C12  C11  C10   180.00   0.0  0
 14T  CONST_14  H11  C11  C10  C9    180.00   0.0  0
 14T  CONST_15  H9   C9   C10  C11   180.00   0.0  0
 14T  CONST_16  C5   N1   C8   C7    180.00   0.0  0
 14T  CONST_17  C5   N1   C8   O5      0.00   0.0  0
 14T  CONST_18  H1   N1   C8   C7      0.00   0.0  0
 14T  Var_01    C9   C10  O6   C1   -157.70  30.0  2
 14T  Var_02    O5   C8   C7   F1     36.77  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
 14T  chir_01  C5  N1  C6  C1  positiv
 14T  chir_02  C6  O3  C5  C2  positiv
 14T  chir_03  C2  O2  C3  C6  positiv
 14T  chir_04  C3  O1  C2  C4  negativ
 14T  chir_05  C1  O1  O6  C5  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
 14T  plan-1  O6   0.020
 14T  plan-1  C10  0.020
 14T  plan-1  C9   0.020
 14T  plan-1  C14  0.020
 14T  plan-1  F3   0.020
 14T  plan-1  C11  0.020
 14T  plan-1  C12  0.020
 14T  plan-1  C13  0.020
 14T  plan-1  F4   0.020
 14T  plan-1  H9   0.020
 14T  plan-1  H11  0.020
 14T  plan-1  H12  0.020
 14T  plan-2  C7   0.020
 14T  plan-2  C8   0.020
 14T  plan-2  O5   0.020
 14T  plan-2  N1   0.020
 14T  plan-2  C5   0.020
 14T  plan-2  H1   0.020

