# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:36:39 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (phenylmethyl) (2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(=O)OCc2ccccc2
#
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
 M55  M55  '(phenylmethyl) (2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxane-2-carboxylate'  D-saccharide  36  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M55
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
 M55  C3   C  CH1   0   0.015  -2.6039  -1.2332   0.3253
 M55  C4   C  CH1   0   0.005  -1.2647  -0.7140  -0.1811
 M55  C1   C  CH1   0   0.220  -3.5357   1.0835   0.1021
 M55  C01  C  CH2   0  -0.251   2.3881   1.3543  -0.7697
 M55  C02  C  CR16  0  -0.281   4.0317   0.6024   0.9692
 M55  C03  C  CR16  0  -0.242   5.0153  -0.2658   1.4201
 M55  C04  C  CR16  0  -0.259   5.4484  -1.3081   0.6092
 M55  C05  C  CR16  0  -0.241   4.8950  -1.4780  -0.6527
 M55  C06  C  CR16  0  -0.293   3.9085  -0.6092  -1.1003
 M55  C07  C  CR6   0   0.072   3.4712   0.4374  -0.2949
 M55  C2   C  CH1   0  -0.018  -3.7484  -0.3921  -0.2281
 M55  C5   C  CH1   0  -0.079  -1.1781   0.8094   0.0889
 M55  C6   C  C     0   0.569   0.0233   1.4539  -0.5815
 M55  O01  O  O2    0  -0.470   1.1525   0.8664  -0.2077
 M55  O1   O  OH1   0  -0.659  -3.6253   1.2604   1.4733
 M55  O2   O  OH1   0  -0.669  -4.9464  -0.8942   0.3086
 M55  O3   O  OH1   0  -0.669  -2.7227  -2.5753  -0.0738
 M55  O4   O  OH1   0  -0.662  -0.2697  -1.4364   0.4892
 M55  O5   O  O2    0  -0.498  -2.2934   1.4917  -0.4197
 M55  O6B  O  O     0  -0.427  -0.0335   2.3768  -1.3469
 M55  H3   H  HCH1  0   0.218  -2.6046  -1.1505   1.4234
 M55  H4   H  HCH1  0   0.230  -1.2203  -0.8731  -1.2696
 M55  H1   H  HCH1  0   0.242  -4.2684   1.6998  -0.4311
 M55  H01  H  HCH2  0   0.261   2.5542   2.3787  -0.4326
 M55  H02  H  HCH2  0   0.261   2.3223   1.3553  -1.8586
 M55  H09  H  HCR6  0   0.260   5.4458  -0.1281   2.4034
 M55  H10  H  HCR6  0   0.260   6.2187  -1.9828   0.9596
 M55  H11  H  HCR6  0   0.260   5.2339  -2.2841  -1.2902
 M55  H12  H  HCR6  0   0.258   3.4810  -0.7434  -2.0869
 M55  H2   H  HCH1  0   0.235  -3.7401  -0.4792  -1.3230
 M55  H5   H  HCH1  0   0.269  -1.0694   0.9536   1.1740
 M55  HO1  H  HOH1  0   0.465  -3.7098   2.2004   1.6667
 M55  HO2  H  HOH1  0   0.461  -5.6687  -0.6818  -0.2897
 M55  HO3  H  HOH1  0   0.450  -3.5861  -2.8902   0.2145
 M55  HO4  H  HOH1  0   0.451   0.5901  -1.1930   0.1324
 M55  H08  H  HCR6  0   0.257   3.6989   1.4152   1.6038

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
 M55  O2   C2   single    1.405  0.020  1.405
 M55  C1   C2   single    1.527  0.020  1.527
 M55  C1   O1   single    1.385  0.020  1.385
 M55  C1   O5   single    1.408  0.020  1.408
 M55  C2   C3   single    1.524  0.020  1.524
 M55  O5   C5   single    1.403  0.020  1.403
 M55  C3   O3   single    1.405  0.020  1.405
 M55  C3   C4   single    1.523  0.020  1.523
 M55  C5   C4   single    1.550  0.020  1.550
 M55  C5   C6   single    1.519  0.020  1.519
 M55  C4   O4   single    1.400  0.020  1.400
 M55  O6B  C6   double    1.200  0.020  1.200
 M55  C6   O01  single    1.327  0.020  1.327
 M55  O01  C01  single    1.442  0.020  1.442
 M55  C01  C07  single    1.496  0.020  1.496
 M55  C07  C06  aromatic  1.391  0.020  1.391
 M55  C07  C02  aromatic  1.393  0.020  1.393
 M55  C06  C05  aromatic  1.389  0.020  1.389
 M55  C02  C03  aromatic  1.387  0.020  1.387
 M55  C05  C04  aromatic  1.388  0.020  1.388
 M55  C03  C04  aromatic  1.390  0.020  1.390
 M55  C3   H3   single    0.970  0.020  1.090
 M55  C4   H4   single    0.970  0.020  1.090
 M55  C1   H1   single    0.970  0.020  1.090
 M55  C01  H01  single    0.970  0.020  1.090
 M55  C01  H02  single    0.970  0.020  1.090
 M55  C02  H08  single    0.930  0.020  1.080
 M55  C03  H09  single    0.930  0.020  1.080
 M55  C04  H10  single    0.930  0.020  1.080
 M55  C05  H11  single    0.930  0.020  1.080
 M55  C06  H12  single    0.930  0.020  1.080
 M55  C2   H2   single    0.970  0.020  1.090
 M55  C5   H5   single    0.970  0.020  1.090
 M55  O1   HO1  single    0.850  0.020  0.980
 M55  O2   HO2  single    0.850  0.020  0.980
 M55  O3   HO3  single    0.850  0.020  0.980
 M55  O4   HO4  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
 M55  H3   C3   O3   110.79  3.000
 M55  H3   C3   C2   108.67  3.000
 M55  O3   C3   C2   111.13  3.000
 M55  H3   C3   C4   107.85  3.000
 M55  O3   C3   C4   107.79  3.000
 M55  C2   C3   C4   110.57  3.000
 M55  H4   C4   O4   111.72  3.000
 M55  H4   C4   C5   108.19  3.000
 M55  O4   C4   C5   112.58  3.000
 M55  H4   C4   C3   108.36  3.000
 M55  O4   C4   C3   106.84  3.000
 M55  C5   C4   C3   109.05  3.000
 M55  H1   C1   O5   104.27  3.000
 M55  H1   C1   O1   111.50  3.000
 M55  O5   C1   O1   112.76  3.000
 M55  H1   C1   C2   110.19  3.000
 M55  O5   C1   C2   108.84  3.000
 M55  O1   C1   C2   109.17  3.000
 M55  H02  C01  H01  108.46  3.000
 M55  H02  C01  O01  109.73  3.000
 M55  H01  C01  O01  109.12  3.000
 M55  H02  C01  C07  111.16  3.000
 M55  H01  C01  C07  111.53  3.000
 M55  O01  C01  C07  106.80  3.000
 M55  H08  C02  C07  119.79  3.000
 M55  H08  C02  C03  119.79  3.000
 M55  C07  C02  C03  120.42  3.000
 M55  H09  C03  C04  120.11  3.000
 M55  H09  C03  C02  119.85  3.000
 M55  C04  C03  C02  120.04  3.000
 M55  H10  C04  C05  120.10  3.000
 M55  H10  C04  C03  120.03  3.000
 M55  C05  C04  C03  119.87  3.000
 M55  H11  C05  C06  119.90  3.000
 M55  H11  C05  C04  120.13  3.000
 M55  C06  C05  C04  119.97  3.000
 M55  H12  C06  C07  119.75  3.000
 M55  H12  C06  C05  119.75  3.000
 M55  C07  C06  C05  120.49  3.000
 M55  C06  C07  C02  119.22  3.000
 M55  C02  C07  C01  120.45  3.000
 M55  C06  C07  C01  120.32  3.000
 M55  H2   C2   O2   111.03  3.000
 M55  H2   C2   C1   106.93  3.000
 M55  O2   C2   C1   112.42  3.000
 M55  H2   C2   C3   108.20  3.000
 M55  C1   C2   C3   110.49  3.000
 M55  O2   C2   C3   107.71  3.000
 M55  H5   C5   O5   111.87  3.000
 M55  H5   C5   C6   107.55  3.000
 M55  O5   C5   C6   105.21  3.000
 M55  H5   C5   C4   107.83  3.000
 M55  C6   C5   C4   112.60  3.000
 M55  O5   C5   C4   111.75  3.000
 M55  O6B  C6   O01  124.09  3.000
 M55  O01  C6   C5   111.15  3.000
 M55  O6B  C6   C5   124.76  3.000
 M55  C6   O01  C01  118.00  3.000
 M55  HO1  O1   C1   109.21  3.000
 M55  HO2  O2   C2   108.89  3.000
 M55  HO3  O3   C3   107.64  3.000
 M55  HO4  O4   C4   109.08  3.000
 M55  C5   O5   C1   115.22  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
 M55  CONST_01  C05  C06  C07  C02    0.00   0.0  0
 M55  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 M55  CONST_03  C06  C07  C02  C03    0.00   0.0  0
 M55  CONST_04  C06  C05  C04  C03    0.00   0.0  0
 M55  CONST_05  C07  C06  C05  C04    0.00   0.0  0
 M55  CONST_06  C07  C02  C03  C04    0.00   0.0  0
 M55  CONST_07  C05  C06  C07  C01  180.00   0.0  0
 M55  CONST_08  C03  C02  C07  C01  180.00   0.0  0
 M55  CONST_09  H12  C06  C07  C02  180.00   0.0  0
 M55  CONST_10  H10  C04  C03  C02  180.00   0.0  0
 M55  CONST_11  H11  C05  C04  C03  180.00   0.0  0
 M55  CONST_12  H08  C02  C03  C04  180.00   0.0  0
 M55  CONST_13  H09  C03  C04  C05  180.00   0.0  0
 M55  Var_01    O01  C01  C07  C02  -81.97  30.0  2
 M55  Var_02    C5   C6   O01  C01  179.32  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
 M55  chir_01  C3  C2  O3  C4  negativ
 M55  chir_02  C4  O4  C5  C3  positiv
 M55  chir_03  C1  O1  O5  C2  negativ
 M55  chir_04  C2  O2  C1  C3  negativ
 M55  chir_05  C5  O5  C4  C6  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
 M55  plan-1  C01  0.020
 M55  plan-1  C02  0.020
 M55  plan-1  C03  0.020
 M55  plan-1  C04  0.020
 M55  plan-1  C05  0.020
 M55  plan-1  C06  0.020
 M55  plan-1  C07  0.020
 M55  plan-1  H09  0.020
 M55  plan-1  H10  0.020
 M55  plan-1  H11  0.020
 M55  plan-1  H12  0.020
 M55  plan-1  H08  0.020
 M55  plan-2  C5   0.020
 M55  plan-2  C6   0.020
 M55  plan-2  O01  0.020
 M55  plan-2  O6B  0.020

