# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 01:28:53 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-hydroxy-2-{[(4-methoxyphenyl)sulfonyl](2-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}ethyl)amino}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[S](=O)(=O)N(CCO[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)CC(=O)NO
#
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
 D3X  D3X  N-hydroxy-2-{[(4-methoxyphenyl)sulfonyl](2-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}ethyl)amino}acetamide  ligand  57  31  .  2022-07-24  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_D3X
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
 D3X  C1    C  CH1   0   0.296   3.2248   0.5653  -0.1285
 D3X  N1    N  NH1   0  -0.369  -2.8104  -2.4115  -1.4704
 D3X  O1    O  O     0  -0.452  -2.6693  -0.3573  -2.4053
 D3X  S1    S  S     0   1.402  -1.2977   0.6078   0.9293
 D3X  C2    C  CH1   0  -0.025   3.4422  -0.7739   0.5710
 D3X  N2    N  N     0  -0.562  -0.6246   0.2213  -0.5201
 D3X  O2    O  OS    0  -0.653  -0.8869  -0.4090   1.8882
 D3X  C3    C  C     0   0.539  -2.2038  -1.2413  -1.7136
 D3X  O3    O  OS    0  -0.646  -0.9726   2.0033   1.1772
 D3X  C4    C  CH2   0  -0.156   6.5684   1.4110  -1.3375
 D3X  O4    O  OH1   0  -0.669   2.4348  -1.0230   1.5193
 D3X  C5    C  CH1   0  -0.018   5.5301   0.9954  -0.3179
 D3X  O5    O  OH1   0  -0.673   5.1177  -1.9956   1.8463
 D3X  C6    C  CH1   0   0.035   5.8955  -0.3247   0.3648
 D3X  O6    O  OH1   0  -0.672   7.1029  -0.1420   1.0609
 D3X  C7    C  CH1   0  -0.014   4.7722  -0.7408   1.3082
 D3X  O7    O  O2    0  -0.455  -7.0573   0.1279  -0.0713
 D3X  O8    O  O2    0  -0.493   4.2947   0.8519  -0.9886
 D3X  C9    C  CH2   0  -0.339  -0.0984   1.2504  -1.4115
 D3X  O9    O  OH1   0  -0.670   6.2119   2.6677  -1.8613
 D3X  C10   C  CH2   0  -0.474  -0.8451  -1.1136  -1.0290
 D3X  O10   O  O2    0  -0.495   2.0750   0.4708  -0.8811
 D3X  C11   C  CR16  0  -0.328  -5.0854   1.3510  -0.1514
 D3X  O11   O  OH1   0  -0.534  -4.0182  -2.6938  -2.0234
 D3X  C12   C  CR6   0  -0.235  -3.0394   0.4570   0.7178
 D3X  C13   C  CR16  0  -0.227  -3.6923  -0.7047   1.0942
 D3X  C14   C  CR16  0  -0.199  -3.7391   1.4883   0.0926
 D3X  C15   C  CR16  0  -0.407  -5.0488  -0.8547   0.8383
 D3X  C16   C  CR6   0   0.404  -5.7541   0.1746   0.2131
 D3X  C17   C  CH3   0  -0.442  -7.7887  -1.0430   0.2496
 D3X  H1    H  HCH1  0   0.189   3.1312   1.3616   0.6341
 D3X  HN1   H  HNH1  0   0.421  -2.4223  -3.1300  -0.8765
 D3X  H2    H  HCH1  0   0.220   3.4789  -1.5606  -0.1990
 D3X  H4    H  HCH2  0   0.213   7.5452   1.4401  -0.8443
 D3X  H4A   H  HCH2  0   0.197   6.6252   0.6421  -2.1207
 D3X  HO4   H  HOH1  0   0.442   1.5785  -1.0179   1.0786
 D3X  H5    H  HCH1  0   0.223   5.4506   1.7778   0.4554
 D3X  HO5   H  HOH1  0   0.458   4.5331  -2.1852   2.5865
 D3X  H6    H  HCH1  0   0.212   6.0010  -1.0985  -0.4132
 D3X  HO6   H  HOH1  0   0.454   7.2899  -0.9510   1.5490
 D3X  H7    H  HCH1  0   0.218   4.7032   0.0175   2.1048
 D3X  H8    H  HCH2  0   0.230   1.7249   2.2865  -1.8392
 D3X  H8A   H  HCH2  0   0.223   1.3224   2.2385  -0.1203
 D3X  H9    H  HCH2  0   0.275  -0.1218   0.8356  -2.4177
 D3X  H9A   H  HCH2  0   0.272  -0.7330   2.1369  -1.4371
 D3X  HO9   H  HOH1  0   0.457   6.8957   2.9332  -2.4823
 D3X  H10   H  HCH2  0   0.321  -0.0680  -1.3267  -1.7645
 D3X  H10A  H  HCH2  0   0.292  -0.7146  -1.8534  -0.2372
 D3X  HO11  H  HOH1  0   0.468  -4.6805  -2.3431  -1.4093
 D3X  H13   H  HCR6  0   0.294  -3.1624  -1.5054   1.5915
 D3X  H14   H  HCR6  0   0.283  -3.2385   2.4003  -0.2046
 D3X  H15   H  HCR6  0   0.306  -5.5374  -1.7636   1.1621
 D3X  H17   H  HCH3  0   0.234  -7.4019  -1.9189  -0.2773
 D3X  H17A  H  HCH3  0   0.239  -7.7847  -1.2417   1.3233
 D3X  H17B  H  HCH3  0   0.268  -8.8106  -0.8635  -0.0726
 D3X  C8    C  CH2   0  -0.154   1.3173   1.6527  -1.0445
 D3X  H11   H  HCR6  0   0.281  -5.6357   2.1506  -0.6300

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
 D3X  C1   C2    single    1.526  0.020  1.526
 D3X  C1   O8    single    1.402  0.020  1.402
 D3X  C1   O10   single    1.377  0.020  1.377
 D3X  N1   C3    single    1.340  0.020  1.340
 D3X  N1   O11   single    1.358  0.020  1.358
 D3X  O1   C3    double    1.215  0.020  1.215
 D3X  S1   N2    single    1.644  0.020  1.644
 D3X  S1   O2    double    1.457  0.020  1.457
 D3X  S1   O3    double    1.454  0.020  1.454
 D3X  S1   C12   single    1.761  0.020  1.761
 D3X  C2   O4    single    1.406  0.020  1.406
 D3X  C2   C7    single    1.521  0.020  1.521
 D3X  N2   C9    single    1.460  0.020  1.460
 D3X  N2   C10   single    1.446  0.020  1.446
 D3X  C3   C10   single    1.527  0.020  1.527
 D3X  C4   C5    single    1.513  0.020  1.513
 D3X  C4   O9    single    1.407  0.020  1.407
 D3X  C5   C6    single    1.531  0.020  1.531
 D3X  C5   O8    single    1.413  0.020  1.413
 D3X  O5   C7    single    1.408  0.020  1.408
 D3X  C6   O6    single    1.406  0.020  1.406
 D3X  C6   C7    single    1.525  0.020  1.525
 D3X  O7   C16   single    1.335  0.020  1.335
 D3X  O7   C17   single    1.417  0.020  1.417
 D3X  C8   C9    single    1.517  0.020  1.517
 D3X  C8   O10   single    1.413  0.020  1.413
 D3X  C11  C14   aromatic  1.375  0.020  1.375
 D3X  C11  C16   aromatic  1.401  0.020  1.401
 D3X  C12  C13   aromatic  1.385  0.020  1.385
 D3X  C12  C14   aromatic  1.394  0.020  1.394
 D3X  C13  C15   aromatic  1.389  0.020  1.389
 D3X  C15  C16   aromatic  1.396  0.020  1.396
 D3X  C1   H1    single    0.970  0.020  1.090
 D3X  N1   HN1   single    0.860  0.020  1.020
 D3X  C2   H2    single    0.970  0.020  1.090
 D3X  C4   H4    single    0.970  0.020  1.090
 D3X  C4   H4A   single    0.970  0.020  1.090
 D3X  O4   HO4   single    0.850  0.020  0.980
 D3X  C5   H5    single    0.970  0.020  1.090
 D3X  O5   HO5   single    0.850  0.020  0.980
 D3X  C6   H6    single    0.970  0.020  1.090
 D3X  O6   HO6   single    0.850  0.020  0.980
 D3X  C7   H7    single    0.970  0.020  1.090
 D3X  C8   H8    single    0.970  0.020  1.090
 D3X  C8   H8A   single    0.970  0.020  1.090
 D3X  C9   H9    single    0.970  0.020  1.090
 D3X  C9   H9A   single    0.970  0.020  1.090
 D3X  O9   HO9   single    0.850  0.020  0.980
 D3X  C10  H10   single    0.970  0.020  1.090
 D3X  C10  H10A  single    0.970  0.020  1.090
 D3X  C11  H11   single    0.930  0.020  1.080
 D3X  O11  HO11  single    0.850  0.020  0.980
 D3X  C13  H13   single    0.930  0.020  1.080
 D3X  C14  H14   single    0.930  0.020  1.080
 D3X  C15  H15   single    0.930  0.020  1.080
 D3X  C17  H17   single    0.970  0.020  1.090
 D3X  C17  H17A  single    0.970  0.020  1.090
 D3X  C17  H17B  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
 D3X  H1    C1   O10   110.81  3.000
 D3X  H1    C1   O8    109.89  3.000
 D3X  O10   C1   O8    108.40  3.000
 D3X  H1    C1   C2    109.13  3.000
 D3X  O10   C1   C2    108.00  3.000
 D3X  O8    C1   C2    110.59  3.000
 D3X  HN1   N1   O11   115.69  3.000
 D3X  HN1   N1   C3    123.64  3.000
 D3X  O11   N1   C3    120.67  3.000
 D3X  C12   S1   O3    108.89  3.000
 D3X  C12   S1   O2    107.35  3.000
 D3X  O3    S1   O2    119.64  3.000
 D3X  C12   S1   N2    106.19  3.000
 D3X  O3    S1   N2    106.52  3.000
 D3X  O2    S1   N2    107.50  3.000
 D3X  H2    C2   C7    108.98  3.000
 D3X  H2    C2   O4    111.65  3.000
 D3X  C7    C2   O4    107.67  3.000
 D3X  H2    C2   C1    108.12  3.000
 D3X  C7    C2   C1    109.12  3.000
 D3X  O4    C2   C1    111.25  3.000
 D3X  C10   N2   C9    119.41  3.000
 D3X  C10   N2   S1    117.71  3.000
 D3X  C9    N2   S1    121.34  3.000
 D3X  C10   C3   O1    122.36  3.000
 D3X  C10   C3   N1    113.23  3.000
 D3X  O1    C3   N1    124.41  3.000
 D3X  H4A   C4   H4    107.07  3.000
 D3X  H4A   C4   O9    111.88  3.000
 D3X  H4    C4   O9    111.71  3.000
 D3X  H4A   C4   C5    108.87  3.000
 D3X  H4    C4   C5    108.42  3.000
 D3X  O9    C4   C5    108.79  3.000
 D3X  HO4   O4   C2    109.12  3.000
 D3X  H5    C5   O8    109.99  3.000
 D3X  H5    C5   C6    108.44  3.000
 D3X  O8    C5   C6    109.44  3.000
 D3X  H5    C5   C4    109.09  3.000
 D3X  O8    C5   C4    107.93  3.000
 D3X  C6    C5   C4    111.94  3.000
 D3X  HO5   O5   C7    108.69  3.000
 D3X  H6    C6   C7    108.40  3.000
 D3X  H6    C6   O6    111.01  3.000
 D3X  C7    C6   O6    111.22  3.000
 D3X  H6    C6   C5    108.27  3.000
 D3X  C7    C6   C5    109.60  3.000
 D3X  O6    C6   C5    108.29  3.000
 D3X  HO6   O6   C6    107.97  3.000
 D3X  H7    C7   C6    107.79  3.000
 D3X  H7    C7   O5    110.63  3.000
 D3X  C6    C7   O5    107.38  3.000
 D3X  H7    C7   C2    108.09  3.000
 D3X  C6    C7   C2    110.50  3.000
 D3X  O5    C7   C2    112.36  3.000
 D3X  C17   O7   C16   118.98  3.000
 D3X  C5    O8   C1    113.37  3.000
 D3X  H9A   C9   H9    105.99  3.000
 D3X  H9A   C9   C8    109.47  3.000
 D3X  H9    C9   C8    110.17  3.000
 D3X  H9A   C9   N2    112.19  3.000
 D3X  H9    C9   N2    106.74  3.000
 D3X  C8    C9   N2    112.07  3.000
 D3X  HO9   O9   C4    107.87  3.000
 D3X  H10A  C10  H10   105.76  3.000
 D3X  H10A  C10  C3    112.02  3.000
 D3X  H10   C10  C3    108.38  3.000
 D3X  H10A  C10  N2    110.63  3.000
 D3X  H10   C10  N2    108.00  3.000
 D3X  C3    C10  N2    111.77  3.000
 D3X  C8    O10  C1    116.95  3.000
 D3X  H11   C11  C16   119.51  3.000
 D3X  H11   C11  C14   120.17  3.000
 D3X  C16   C11  C14   120.32  3.000
 D3X  HO11  O11  N1    105.94  3.000
 D3X  C14   C12  C13   120.38  3.000
 D3X  C14   C12  S1    119.13  3.000
 D3X  C13   C12  S1    120.37  3.000
 D3X  H13   C13  C15   118.91  3.000
 D3X  H13   C13  C12   121.01  3.000
 D3X  C15   C13  C12   120.08  3.000
 D3X  H14   C14  C12   120.96  3.000
 D3X  H14   C14  C11   119.23  3.000
 D3X  C12   C14  C11   119.81  3.000
 D3X  H15   C15  C16   121.71  3.000
 D3X  H15   C15  C13   118.49  3.000
 D3X  C16   C15  C13   119.77  3.000
 D3X  C15   C16  C11   119.64  3.000
 D3X  C15   C16  O7    124.27  3.000
 D3X  C11   C16  O7    116.10  3.000
 D3X  H17B  C17  H17A  108.98  3.000
 D3X  H17B  C17  H17   108.81  3.000
 D3X  H17A  C17  H17   109.08  3.000
 D3X  H17B  C17  O7    106.36  3.000
 D3X  H17A  C17  O7    111.78  3.000
 D3X  H17   C17  O7    111.73  3.000
 D3X  H8A   C8   H8    107.54  3.000
 D3X  H8A   C8   O10   110.34  3.000
 D3X  H8    C8   O10   111.61  3.000
 D3X  H8A   C8   C9    110.53  3.000
 D3X  H8    C8   C9    108.98  3.000
 D3X  O10   C8   C9    107.85  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
 D3X  CONST_01  C13  C12  C14  C11     0.00   0.0  0
 D3X  CONST_02  C13  C15  C16  C11     0.00   0.0  0
 D3X  CONST_03  C16  C15  C13  C12     0.00   0.0  0
 D3X  CONST_04  C16  C11  C14  C12     0.00   0.0  0
 D3X  CONST_05  C15  C16  C11  C14     0.00   0.0  0
 D3X  CONST_06  C15  C13  C12  C14     0.00   0.0  0
 D3X  CONST_07  C15  C13  C12  S1    180.00   0.0  0
 D3X  CONST_08  C11  C14  C12  S1    180.00   0.0  0
 D3X  CONST_09  C14  C11  C16  O7    180.00   0.0  0
 D3X  CONST_10  C13  C15  C16  O7    180.00   0.0  0
 D3X  CONST_11  H15  C15  C16  C11   180.00   0.0  0
 D3X  CONST_12  H11  C11  C14  C12   180.00   0.0  0
 D3X  CONST_13  H14  C14  C12  C13   180.00   0.0  0
 D3X  CONST_14  H13  C13  C12  C14   180.00   0.0  0
 D3X  CONST_15  O11  N1   C3   O1      0.00   0.0  0
 D3X  CONST_16  O11  N1   C3   C10   180.00   0.0  0
 D3X  CONST_17  HN1  N1   C3   O1    180.00   0.0  0
 D3X  Var_01    C13  C12  S1   N2     96.55  30.0  2
 D3X  Var_02    C9   C8   O10  C1   -158.71  30.0  1
 D3X  Var_03    C12  S1   N2   C9    104.01  30.0  1
 D3X  Var_04    H17  C17  O7   C16   -60.98  30.0  3
 D3X  Var_05    N2   C10  C3   N1   -141.20  30.0  3
 D3X  Var_06    C8   C9   N2   S1     83.54  30.0  3
 D3X  Var_07    C3   C10  N2   S1     81.48  30.0  3
 D3X  Var_08    O10  C8   C9   N2     48.71  30.0  1

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
 D3X  chir_01  C1  C2  O8  O10  negativ
 D3X  chir_02  C2  O4  C1  C7   negativ
 D3X  chir_03  C5  O8  C6  C4   negativ
 D3X  chir_04  C6  O6  C5  C7   positiv
 D3X  chir_05  C7  O5  C6  C2   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
 D3X  plan-1  S1   0.020
 D3X  plan-1  O7   0.020
 D3X  plan-1  C11  0.020
 D3X  plan-1  C12  0.020
 D3X  plan-1  C13  0.020
 D3X  plan-1  C14  0.020
 D3X  plan-1  C15  0.020
 D3X  plan-1  C16  0.020
 D3X  plan-1  H13  0.020
 D3X  plan-1  H14  0.020
 D3X  plan-1  H15  0.020
 D3X  plan-1  H11  0.020
 D3X  plan-2  N1   0.020
 D3X  plan-2  O1   0.020
 D3X  plan-2  C3   0.020
 D3X  plan-2  C10  0.020
 D3X  plan-2  O11  0.020
 D3X  plan-2  HN1  0.020

