# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:00:33 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 6-deoxy-6-[(2R,3R,4R)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl]-L-idonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)CN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O
#
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
 W72  W72  '6-deoxy-6-[(2R,3R,4R)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl]-L-idonic acid'  ligand  41  21  .  2022-07-22  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_W72
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
 W72  C1    C  CH1    0   0.029  -4.5264  -0.2360  -0.0505
 W72  O1    O  OH1    0  -0.674  -5.7179  -0.0047  -0.7593
 W72  C2    C  CH1    0   0.012  -4.0014  -1.6845  -0.1008
 W72  O2    O  OH1    0  -0.677  -4.0768  -2.2318   1.1976
 W72  C3    C  CH2    0  -0.308  -2.5718  -1.5408  -0.6252
 W72  N4    N  NT     0  -0.481  -2.2189  -0.1607  -0.3434
 W72  C5    C  CH1    0  -0.081  -3.4073   0.6124  -0.6574
 W72  C6    C  CH2    0  -0.185  -3.3701   2.0379  -0.1435
 W72  O6    O  OH1    0  -0.661  -3.0985   2.0404   1.2366
 W72  C7    C  CH2    0  -0.310  -0.9704   0.2742  -0.9240
 W72  C8    C  CH1    0   0.007   0.1912  -0.2106  -0.0505
 W72  O8    O  OH1    0  -0.685  -0.1299   0.0310   1.2996
 W72  C9    C  CH1    0   0.011   1.4880   0.5206  -0.4174
 W72  O9    O  OH1    0  -0.669   1.4331   1.8569   0.0211
 W72  C10   C  CH1    0   0.013   2.7421  -0.2198   0.0605
 W72  O10   O  OH1    0  -0.673   2.8465  -0.2649   1.4640
 W72  C11   C  CH1    0  -0.136   4.0373   0.3282  -0.5448
 W72  O11   O  OH1    0  -0.689   4.4087   1.5407   0.0617
 W72  C12   C  C      0   0.404   5.1960  -0.6857  -0.3780
 W72  O12   O  OC    -1  -0.591   5.0369  -1.8292  -0.8294
 W72  O13   O  O      0  -0.609   6.2094  -0.2258   0.1967
 W72  H1    H  HCH1   0   0.222  -4.6411   0.0305   1.0074
 W72  HO1   H  HOH1   0   0.454  -6.4464  -0.3827  -0.2581
 W72  H2    H  HCH1   0   0.218  -4.5982  -2.2721  -0.8083
 W72  HO2   H  HOH1   0   0.450  -3.7953  -3.1505   1.1534
 W72  H31   H  HCH2   0   0.247  -1.8806  -2.2443  -0.1549
 W72  H32   H  HCH2   0   0.207  -2.5517  -1.7376  -1.7089
 W72  H5    H  HCH1   0   0.217  -3.5746   0.6676  -1.7486
 W72  H61   H  HCH2   0   0.212  -4.3399   2.4967  -0.3765
 W72  H62   H  HCH2   0   0.211  -2.6195   2.6121  -0.7020
 W72  HO6   H  HOH1   0   0.457  -3.0940   2.9533   1.5373
 W72  H71   H  HCH2   0   0.220  -0.8383  -0.0748  -1.9588
 W72  H72   H  HCH2   0   0.242  -0.9497   1.3655  -0.9477
 W72  H8    H  HCH1   0   0.205   0.3435  -1.2860  -0.2279
 W72  HO8   H  HOH1   0   0.440  -1.1025   0.0912   1.3064
 W72  H9    H  HCH1   0   0.221   1.5429   0.5371  -1.5145
 W72  HO9   H  HOH1   0   0.436   1.0223   1.8375   0.8945
 W72  H10   H  HCH1   0   0.223   2.6397  -1.2521  -0.2900
 W72  HO10  H  HOH1   0   0.432   3.2095   0.5860   1.7379
 W72  H11   H  HCH1   0   0.205   3.8798   0.4654  -1.6260
 W72  HO11  H  HOH1   0   0.429   5.3144   1.3339   0.3692

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
 W72  C1   O1    single  1.406  0.020  1.406
 W72  C1   C2    single  1.541  0.020  1.541
 W72  C1   C5    single  1.530  0.020  1.530
 W72  C1   H1    single  0.970  0.020  1.090
 W72  O1   HO1   single  0.850  0.020  0.980
 W72  C2   O2    single  1.411  0.020  1.411
 W72  C2   C3    single  1.529  0.020  1.529
 W72  C2   H2    single  0.970  0.020  1.090
 W72  O2   HO2   single  0.850  0.020  0.980
 W72  C3   N4    single  1.452  0.020  1.452
 W72  C3   H31   single  0.970  0.020  1.090
 W72  C3   H32   single  0.970  0.020  1.090
 W72  N4   C5    single  1.452  0.020  1.452
 W72  N4   C7    single  1.444  0.020  1.444
 W72  C5   C6    single  1.516  0.020  1.516
 W72  C5   H5    single  0.970  0.020  1.090
 W72  C6   O6    single  1.407  0.020  1.407
 W72  C6   H61   single  0.970  0.020  1.090
 W72  C6   H62   single  0.970  0.020  1.090
 W72  O6   HO6   single  0.850  0.020  0.980
 W72  C7   C8    single  1.532  0.020  1.532
 W72  C7   H71   single  0.970  0.020  1.090
 W72  C7   H72   single  0.970  0.020  1.090
 W72  C8   O8    single  1.409  0.020  1.409
 W72  C8   C9    single  1.533  0.020  1.533
 W72  C8   H8    single  0.970  0.020  1.090
 W72  O8   HO8   single  0.850  0.020  0.980
 W72  C9   O9    single  1.407  0.020  1.407
 W72  C9   C10   single  1.533  0.020  1.533
 W72  C9   H9    single  0.970  0.020  1.090
 W72  O9   HO9   single  0.850  0.020  0.980
 W72  C10  O10   single  1.408  0.020  1.408
 W72  C10  C11   single  1.531  0.020  1.531
 W72  C10  H10   single  0.970  0.020  1.090
 W72  O10  HO10  single  0.850  0.020  0.980
 W72  C11  O11   single  1.406  0.020  1.406
 W72  C11  C12   single  1.549  0.020  1.549
 W72  C11  H11   single  0.970  0.020  1.090
 W72  O11  HO11  single  0.850  0.020  0.980
 W72  C12  O12   deloc   1.240  0.020  1.240
 W72  C12  O13   deloc   1.253  0.020  1.253

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
 W72  H1    C1   C5   108.93  3.000
 W72  H1    C1   C2   107.18  3.000
 W72  C5    C1   C2   105.01  3.000
 W72  H1    C1   O1   110.96  3.000
 W72  C5    C1   O1   109.20  3.000
 W72  C2    C1   O1   115.27  3.000
 W72  HO1   O1   C1   108.35  3.000
 W72  H2    C2   C3   109.75  3.000
 W72  H2    C2   O2   110.90  3.000
 W72  C3    C2   O2   113.69  3.000
 W72  H2    C2   C1   109.84  3.000
 W72  C3    C2   C1   103.96  3.000
 W72  O2    C2   C1   108.44  3.000
 W72  HO2   O2   C2   108.21  3.000
 W72  H32   C3   H31  107.27  3.000
 W72  H32   C3   N4   110.86  3.000
 W72  H31   C3   N4   112.00  3.000
 W72  H32   C3   C2   109.73  3.000
 W72  H31   C3   C2   112.54  3.000
 W72  N4    C3   C2   104.47  3.000
 W72  C7    N4   C5   117.41  3.000
 W72  C7    N4   C3   114.74  3.000
 W72  C5    N4   C3   105.38  3.000
 W72  H5    C5   C6   106.95  3.000
 W72  H5    C5   N4   111.34  3.000
 W72  C6    C5   N4   114.03  3.000
 W72  H5    C5   C1   107.98  3.000
 W72  C6    C5   C1   113.89  3.000
 W72  N4    C5   C1   102.57  3.000
 W72  H62   C6   H61  106.11  3.000
 W72  H62   C6   O6   111.48  3.000
 W72  H61   C6   O6   112.21  3.000
 W72  H62   C6   C5   109.65  3.000
 W72  H61   C6   C5   107.42  3.000
 W72  O6    C6   C5   109.82  3.000
 W72  HO6   O6   C6   108.03  3.000
 W72  H72   C7   H71  107.12  3.000
 W72  H72   C7   C8   108.32  3.000
 W72  H71   C7   C8   110.17  3.000
 W72  H72   C7   N4   109.04  3.000
 W72  H71   C7   N4   112.74  3.000
 W72  C8    C7   N4   109.33  3.000
 W72  H8    C8   C9   108.08  3.000
 W72  H8    C8   O8   110.71  3.000
 W72  C9    C8   O8   109.90  3.000
 W72  H8    C8   C7   108.80  3.000
 W72  C9    C8   C7   110.73  3.000
 W72  O8    C8   C7   108.62  3.000
 W72  HO8   O8   C8   104.17  3.000
 W72  H9    C9   C10  106.13  3.000
 W72  H9    C9   O9   107.39  3.000
 W72  C10   C9   O9   113.17  3.000
 W72  H9    C9   C8   106.76  3.000
 W72  C10   C9   C8   112.77  3.000
 W72  O9    C9   C8   110.19  3.000
 W72  HO9   O9   C9   106.23  3.000
 W72  H10   C10  C11  106.86  3.000
 W72  H10   C10  O10  107.21  3.000
 W72  C11   C10  O10  110.05  3.000
 W72  H10   C10  C9   106.21  3.000
 W72  C11   C10  C9   113.32  3.000
 W72  O10   C10  C9   112.76  3.000
 W72  HO10  O10  C10  106.42  3.000
 W72  H11   C11  C12  107.12  3.000
 W72  H11   C11  O11  110.73  3.000
 W72  C12   C11  O11  108.70  3.000
 W72  H11   C11  C10  108.16  3.000
 W72  C12   C11  C10  110.85  3.000
 W72  O11   C11  C10  111.20  3.000
 W72  HO11  O11  C11  101.41  3.000
 W72  O13   C12  O12  127.57  3.000
 W72  O13   C12  C11  114.48  3.000
 W72  O12   C12  C11  117.95  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
 W72  Var_01  C5  N4  C3  C2  -40.77  30.0  1
 W72  Var_02  C8  C7  N4  C3  -80.30  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
 W72  chir_01  C1   O1   C2   C5   negativ
 W72  chir_02  C2   O2   C3   C1   positiv
 W72  chir_03  C5   N4   C1   C6   negativ
 W72  chir_04  C8   O8   C9   C7   positiv
 W72  chir_05  C9   O9   C8   C10  positiv
 W72  chir_06  C10  O10  C9   C11  negativ
 W72  chir_07  C11  O11  C10  C12  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
 W72  plan-1  C11  0.020
 W72  plan-1  C12  0.020
 W72  plan-1  O12  0.020
 W72  plan-1  O13  0.020

