# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 20:07:09 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-deoxy-2-{[3-(4-hydroxyphenyl)propanoyl]amino}-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](NC(=O)CCc2ccc(O)cc2)[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
 4V5  4V5  2-deoxy-2-{[3-(4-hydroxyphenyl)propanoyl]amino}-alpha-D-glucopyranose  D-saccharide  44  23  .  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_4V5
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
 4V5  C21  C  CR16  0  -0.323   6.1628   1.3310   0.3957
 4V5  C01  C  CH1   0   0.045  -2.6194   1.1131   0.1032
 4V5  C02  C  CH1   0  -0.155  -1.9314  -0.1935  -0.2787
 4V5  C03  C  CH1   0   0.267  -2.6361  -1.3834   0.3764
 4V5  O04  O  O2    0  -0.500  -4.0000  -1.3794   0.0637
 4V5  C05  C  CH1   0  -0.014  -4.7157  -0.2181   0.4545
 4V5  C06  C  CH1   0  -0.009  -4.1082   1.0180  -0.2159
 4V5  N07  N  NH1   0  -0.639  -0.5309  -0.1759   0.0523
 4V5  O08  O  OH1   0  -0.674  -4.7137   2.2061   0.2468
 4V5  C10  C  CH2   0  -0.164  -6.1607  -0.4242   0.0557
 4V5  O11  O  OH1   0  -0.668  -2.3971  -1.3236   1.7464
 4V5  O12  O  OH1   0  -0.670  -6.6891  -1.5035   0.7886
 4V5  C13  C  C     0   0.568   0.4659  -0.2715  -0.8483
 4V5  C14  C  CH2   0  -0.583   1.8549  -0.2409  -0.2434
 4V5  O15  O  O     0  -0.499   0.2766  -0.3981  -2.0493
 4V5  C16  C  CH2   0  -0.500   2.9429   0.1290  -1.2476
 4V5  C17  C  CR6   0   0.105   4.3057   0.1341  -0.6108
 4V5  C18  C  CR16  0  -0.292   4.9888  -1.0543  -0.3663
 4V5  C19  C  CR16  0  -0.369   6.2329  -1.0650   0.2464
 4V5  C20  C  CR6   0   0.335   6.8292   0.1324   0.6335
 4V5  C22  C  CR16  0  -0.303   4.9183   1.3206  -0.2164
 4V5  O23  O  OH1   0  -0.636   8.0392   0.1849   1.2306
 4V5  H1   H  HCR6  0   0.259   6.6201   2.2687   0.6864
 4V5  H2   H  HCH1  0   0.212  -2.5150   1.2730   1.1883
 4V5  H3   H  HCH1  0   0.276  -2.0108  -0.3214  -1.3604
 4V5  H4   H  HCH1  0   0.242  -2.2498  -2.3137  -0.0537
 4V5  H5   H  HCH1  0   0.223  -4.6682  -0.0821   1.5441
 4V5  H6   H  HCH1  0   0.225  -4.2174   0.9186  -1.3057
 4V5  H7   H  HNH1  0   0.396  -0.2853  -0.0664   1.0238
 4V5  H8   H  HOH1  0   0.463  -5.4253   2.4517  -0.3502
 4V5  H10  H  HCH2  0   0.203  -6.7092   0.5031   0.2578
 4V5  H11  H  HCH2  0   0.197  -6.2139  -0.6009  -1.0278
 4V5  H12  H  HOH1  0   0.466  -2.6324  -2.1669   2.1480
 4V5  H13  H  HOH1  0   0.456  -7.6202  -1.5870   0.5652
 4V5  H14  H  HCH2  0   0.264   1.8750   0.4476   0.6058
 4V5  H15  H  HCH2  0   0.278   2.0578  -1.2338   0.1720
 4V5  H16  H  HCH2  0   0.247   2.9255  -0.5765  -2.0806
 4V5  H17  H  HCH2  0   0.246   2.7318   1.1147  -1.6678
 4V5  H18  H  HCR6  0   0.250   4.5474  -1.9993  -0.6625
 4V5  H19  H  HCR6  0   0.267   6.7393  -2.0083   0.4178
 4V5  H20  H  HCR6  0   0.247   4.4169   2.2650  -0.3945
 4V5  H21  H  HOH1  0   0.472   8.3911  -0.7038   1.3521
 4V5  O09  O  OH1   0  -0.664  -2.0005   2.1512  -0.6110
 4V5  H9   H  HOH1  0   0.450  -2.4408   2.9741  -0.3735

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
 4V5  O12  C10  single    1.408  0.020  1.408
 4V5  C10  C05  single    1.513  0.020  1.513
 4V5  O23  C20  single    1.350  0.020  1.350
 4V5  O04  C05  single    1.419  0.020  1.419
 4V5  O04  C03  single    1.399  0.020  1.399
 4V5  C05  C06  single    1.532  0.020  1.532
 4V5  C06  O08  single    1.411  0.020  1.411
 4V5  C06  C01  single    1.526  0.020  1.526
 4V5  C20  C19  aromatic  1.393  0.020  1.393
 4V5  C20  C21  aromatic  1.392  0.020  1.392
 4V5  C19  C18  aromatic  1.387  0.020  1.387
 4V5  C03  C02  single    1.530  0.020  1.530
 4V5  C03  O11  single    1.392  0.020  1.392
 4V5  O15  C13  double    1.222  0.020  1.222
 4V5  C02  C01  single    1.525  0.020  1.525
 4V5  C02  N07  single    1.439  0.020  1.439
 4V5  O09  C01  single    1.404  0.020  1.404
 4V5  C21  C22  aromatic  1.387  0.020  1.387
 4V5  C18  C17  aromatic  1.392  0.020  1.392
 4V5  C13  N07  single    1.347  0.020  1.347
 4V5  C13  C14  single    1.515  0.020  1.515
 4V5  C22  C17  aromatic  1.392  0.020  1.392
 4V5  C17  C16  single    1.504  0.020  1.504
 4V5  C16  C14  single    1.526  0.020  1.526
 4V5  C21  H1   single    0.930  0.020  1.080
 4V5  C01  H2   single    0.970  0.020  1.090
 4V5  C02  H3   single    0.970  0.020  1.090
 4V5  C03  H4   single    0.970  0.020  1.090
 4V5  C05  H5   single    0.970  0.020  1.090
 4V5  C06  H6   single    0.970  0.020  1.090
 4V5  N07  H7   single    0.860  0.020  1.020
 4V5  O08  H8   single    0.850  0.020  0.980
 4V5  O09  H9   single    0.850  0.020  0.980
 4V5  C10  H10  single    0.970  0.020  1.090
 4V5  C10  H11  single    0.970  0.020  1.090
 4V5  O11  H12  single    0.850  0.020  0.980
 4V5  O12  H13  single    0.850  0.020  0.980
 4V5  C14  H14  single    0.970  0.020  1.090
 4V5  C14  H15  single    0.970  0.020  1.090
 4V5  C16  H16  single    0.970  0.020  1.090
 4V5  C16  H17  single    0.970  0.020  1.090
 4V5  C18  H18  single    0.930  0.020  1.080
 4V5  C19  H19  single    0.930  0.020  1.080
 4V5  C22  H20  single    0.930  0.020  1.080
 4V5  O23  H21  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
 4V5  H1   C21  C22  120.25  3.000
 4V5  H1   C21  C20  119.84  3.000
 4V5  C22  C21  C20  119.91  3.000
 4V5  H2   C01  O09  110.60  3.000
 4V5  H2   C01  C06  107.91  3.000
 4V5  O09  C01  C06  111.71  3.000
 4V5  H2   C01  C02  109.16  3.000
 4V5  O09  C01  C02  107.89  3.000
 4V5  C06  C01  C02  109.54  3.000
 4V5  H3   C02  N07  107.46  3.000
 4V5  H3   C02  C03  107.43  3.000
 4V5  N07  C02  C03  111.05  3.000
 4V5  H3   C02  C01  108.40  3.000
 4V5  N07  C02  C01  111.77  3.000
 4V5  C03  C02  C01  110.56  3.000
 4V5  H4   C03  O11  111.25  3.000
 4V5  H4   C03  O04  104.97  3.000
 4V5  O11  C03  O04  112.78  3.000
 4V5  H4   C03  C02  109.26  3.000
 4V5  O11  C03  C02  107.99  3.000
 4V5  O04  C03  C02  110.55  3.000
 4V5  C05  O04  C03  115.62  3.000
 4V5  H5   C05  C10  108.63  3.000
 4V5  H5   C05  C06  108.47  3.000
 4V5  C10  C05  C06  111.92  3.000
 4V5  H5   C05  O04  110.64  3.000
 4V5  C06  C05  O04  109.86  3.000
 4V5  C10  C05  O04  107.32  3.000
 4V5  H6   C06  O08  111.00  3.000
 4V5  H6   C06  C05  108.75  3.000
 4V5  O08  C06  C05  111.45  3.000
 4V5  H6   C06  C01  108.05  3.000
 4V5  O08  C06  C01  107.31  3.000
 4V5  C05  C06  C01  110.23  3.000
 4V5  H7   N07  C13  118.15  3.000
 4V5  H7   N07  C02  117.40  3.000
 4V5  C13  N07  C02  124.44  3.000
 4V5  H8   O08  C06  109.22  3.000
 4V5  H11  C10  H10  107.07  3.000
 4V5  H11  C10  O12  111.83  3.000
 4V5  H10  C10  O12  111.40  3.000
 4V5  H11  C10  C05  109.14  3.000
 4V5  H10  C10  C05  108.30  3.000
 4V5  O12  C10  C05  109.00  3.000
 4V5  H12  O11  C03  109.31  3.000
 4V5  H13  O12  C10  108.01  3.000
 4V5  O15  C13  C14  122.43  3.000
 4V5  C14  C13  N07  114.21  3.000
 4V5  O15  C13  N07  123.35  3.000
 4V5  H15  C14  H14  105.83  3.000
 4V5  H15  C14  C16  109.71  3.000
 4V5  H14  C14  C16  110.20  3.000
 4V5  H15  C14  C13  107.63  3.000
 4V5  H14  C14  C13  109.85  3.000
 4V5  C16  C14  C13  113.31  3.000
 4V5  H17  C16  H16  106.65  3.000
 4V5  H17  C16  C17  109.57  3.000
 4V5  H16  C16  C17  109.86  3.000
 4V5  H17  C16  C14  109.52  3.000
 4V5  H16  C16  C14  109.52  3.000
 4V5  C17  C16  C14  111.60  3.000
 4V5  C22  C17  C18  117.50  3.000
 4V5  C22  C17  C16  121.43  3.000
 4V5  C18  C17  C16  121.06  3.000
 4V5  H18  C18  C19  118.63  3.000
 4V5  H18  C18  C17  119.75  3.000
 4V5  C19  C18  C17  121.62  3.000
 4V5  H19  C19  C20  120.28  3.000
 4V5  H19  C19  C18  119.70  3.000
 4V5  C20  C19  C18  120.02  3.000
 4V5  O23  C20  C19  122.69  3.000
 4V5  C19  C20  C21  119.21  3.000
 4V5  O23  C20  C21  118.11  3.000
 4V5  H20  C22  C17  119.49  3.000
 4V5  H20  C22  C21  118.76  3.000
 4V5  C17  C22  C21  121.75  3.000
 4V5  H21  O23  C20  110.32  3.000
 4V5  H9   O09  C01  107.75  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
 4V5  CONST_01  C18  C19  C20  C21     0.00   0.0  0
 4V5  CONST_02  C18  C17  C22  C21     0.00   0.0  0
 4V5  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 4V5  CONST_04  C20  C21  C22  C17     0.00   0.0  0
 4V5  CONST_05  C22  C21  C20  C19     0.00   0.0  0
 4V5  CONST_06  C22  C17  C18  C19     0.00   0.0  0
 4V5  CONST_07  C16  C17  C22  C21   180.00   0.0  0
 4V5  CONST_08  C19  C18  C17  C16   180.00   0.0  0
 4V5  CONST_09  O23  C20  C19  C18   180.00   0.0  0
 4V5  CONST_10  O23  C20  C21  C22   180.00   0.0  0
 4V5  CONST_11  H19  C19  C20  C21   180.00   0.0  0
 4V5  CONST_12  H1   C21  C22  C17   180.00   0.0  0
 4V5  CONST_13  H20  C22  C17  C18   180.00   0.0  0
 4V5  CONST_14  H18  C18  C19  C20   180.00   0.0  0
 4V5  CONST_15  O15  C13  N07  C02     0.00   0.0  0
 4V5  CONST_16  C14  C13  N07  C02   180.00   0.0  0
 4V5  CONST_17  H7   N07  C13  C14     0.00   0.0  0
 4V5  Var_01    C18  C17  C16  C14    78.22  30.0  2
 4V5  Var_02    C17  C16  C14  C13  -179.41  30.0  1
 4V5  Var_03    C16  C14  C13  N07  -160.23  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
 4V5  chir_01  C01  C06  C02  O09  negativ
 4V5  chir_02  C02  N07  C01  C03  positiv
 4V5  chir_03  C03  O04  O11  C02  positiv
 4V5  chir_04  C05  O04  C06  C10  negativ
 4V5  chir_05  C06  O08  C05  C01  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
 4V5  plan-1  C21  0.020
 4V5  plan-1  C16  0.020
 4V5  plan-1  C17  0.020
 4V5  plan-1  C18  0.020
 4V5  plan-1  C19  0.020
 4V5  plan-1  C20  0.020
 4V5  plan-1  C22  0.020
 4V5  plan-1  O23  0.020
 4V5  plan-1  H1   0.020
 4V5  plan-1  H18  0.020
 4V5  plan-1  H19  0.020
 4V5  plan-1  H20  0.020
 4V5  plan-2  C02  0.020
 4V5  plan-2  N07  0.020
 4V5  plan-2  C13  0.020
 4V5  plan-2  C14  0.020
 4V5  plan-2  O15  0.020
 4V5  plan-2  H7   0.020

