# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 26 17:16:30 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: methyl 5-(acetylamino)-3,5,9-trideoxy-9-[(naphthalen-2-ylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CNC(=O)c2ccc3ccccc3c2)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
 SUW  SUW  'methyl 5-(acetylamino)-3,5,9-trideoxy-9-[(naphthalen-2-ylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid'  ligand  61  34  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SUW
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
 SUW  CX1   C  C      0   0.383   1.3809   0.6621  -0.0417
 SUW  O1A   O  O      0  -0.588   2.4570   0.0553  -0.2472
 SUW  O1B   O  OC    -1  -0.563   0.2514   0.2966  -0.3937
 SUW  CX2   C  CT     0   0.422   1.4514   2.0596   0.6642
 SUW  OX2   O  O2     0  -0.509   1.3829   3.0649  -0.3000
 SUW  CO2   C  CH3    0  -0.420   2.3323   3.0258  -1.3485
 SUW  CX3   C  CH2    0  -0.516   0.2970   2.3170   1.6308
 SUW  CX4   C  CH1    0   0.050   0.4338   1.5273   2.9298
 SUW  OX4   O  OH1    0  -0.659  -0.5866   1.8424   3.8457
 SUW  CX5   C  CH1    0  -0.112   1.8325   1.7192   3.5301
 SUW  NX5   N  NH1    0  -0.629   2.0155   0.8934   4.6951
 SUW  C10   C  C      0   0.523   2.0411   1.3547   5.9580
 SUW  O10   O  O      0  -0.506   1.9505   2.5401   6.2466
 SUW  C11   C  CH3    0  -0.782   2.2026   0.2949   7.0203
 SUW  CX6   C  CH1    0  -0.006   2.8501   1.3697   2.4434
 SUW  OX6   O  O2     0  -0.508   2.6651   2.2354   1.3484
 SUW  CX7   C  CH1    0   0.005   4.3071   1.4315   2.8698
 SUW  OX7   O  OH1    0  -0.693   4.5776   2.6591   3.4998
 SUW  CX8   C  CH1    0   0.048   5.2314   1.2193   1.6539
 SUW  OX8   O  OH1    0  -0.719   4.9300   0.0320   0.9690
 SUW  CX9   C  CH2    0  -0.355   6.7019   1.1833   2.0564
 SUW  NX6   N  NH1    0  -0.636   7.0389   0.1439   3.0058
 SUW  C12   C  C      0   0.553   7.0756   0.3350   4.3302
 SUW  O12   O  O      0  -0.510   6.8252   1.4191   4.8567
 SUW  C25   C  C1     0  -0.342   7.9937  -0.6153   6.4058
 SUW  C26   C  C      0  -0.023   7.4610  -0.8440   5.1619
 SUW  C27   C  C1     0  -0.296   7.2755  -2.1764   4.7190
 SUW  C28   C  C1     0  -0.298   7.6385  -3.2292   5.5095
 SUW  C2B   C  CR6    0   0.112   8.2126  -3.0164   6.7839
 SUW  C21   C  CR16   0  -0.308   8.6075  -4.0865   7.6192
 SUW  C22   C  CR16   0  -0.252   9.1562  -3.8416   8.8486
 SUW  C23   C  CR16   0  -0.255   9.3352  -2.5163   9.3004
 SUW  C24   C  CR16   0  -0.308   8.9605  -1.4620   8.5138
 SUW  C2A   C  CR6    0   0.140   8.3906  -1.6842   7.2374
 SUW  HO21  H  HCH3   0   0.219   3.3608   2.9922  -0.9842
 SUW  HO22  H  HCH3   0   0.233   2.1990   3.9449  -1.9171
 SUW  HO23  H  HCH3   0   0.211   2.1791   2.1822  -2.0272
 SUW  HX31  H  HCH2   0   0.252  -0.6578   2.0874   1.1585
 SUW  HX32  H  HCH2   0   0.232   0.3005   3.3866   1.8721
 SUW  HX4   H  HCH1   0   0.225   0.3067   0.4587   2.7161
 SUW  HA    H  HOH1   0   0.441  -0.5122   2.7750   4.0751
 SUW  HX5   H  HCH1   0   0.259   1.9669   2.7601   3.8317
 SUW  HB    H  HNH1   0   0.395   2.0418  -0.1051   4.5583
 SUW  H111  H  HCH3   0   0.264   3.1123   0.4866   7.5894
 SUW  H112  H  HCH3   0   0.264   1.3664   0.3513   7.7166
 SUW  H113  H  HCH3   0   0.247   2.2541  -0.7179   6.6250
 SUW  HX6   H  HCH1   0   0.223   2.6610   0.3266   2.1533
 SUW  HX7   H  HCH1   0   0.210   4.4479   0.5927   3.5648
 SUW  HC    H  HOH1   0   0.455   5.3517   2.5171   4.0638
 SUW  HX8   H  HCH1   0   0.207   5.1308   2.0976   1.0007
 SUW  HD    H  HOH1   0   0.462   4.0585   0.1291   0.5266
 SUW  HX91  H  HCH2   0   0.269   7.3053   1.0227   1.1624
 SUW  HX92  H  HCH2   0   0.255   6.9982   2.1500   2.4618
 SUW  HE    H  HNH1   0   0.411   7.3191  -0.7460   2.6294
 SUW  H27   H  H      0   0.257   6.8149  -2.3828   3.7613
 SUW  H28   H  H      0   0.263   7.4804  -4.2435   5.1648
 SUW  H21   H  HCR6   0   0.260   8.4698  -5.1032   7.2720
 SUW  H22   H  HCR6   0   0.263   9.4561  -4.6667   9.4815
 SUW  H23   H  HCR6   0   0.263   9.7723  -2.3373  10.2739
 SUW  H24   H  HCR6   0   0.260   9.0977  -0.4444   8.8584
 SUW  H25   H  H      0   0.261   8.1286   0.3990   6.7607

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
 SUW  CX1  O1A   deloc     1.252  0.020  1.252
 SUW  CX1  O1B   deloc     1.238  0.020  1.238
 SUW  CX1  CX2   single    1.567  0.020  1.567
 SUW  CX2  OX2   single    1.395  0.020  1.395
 SUW  CX2  CX3   single    1.528  0.020  1.528
 SUW  CX2  OX6   single    1.404  0.020  1.404
 SUW  OX2  CO2   single    1.415  0.020  1.415
 SUW  CO2  HO21  single    0.970  0.020  1.090
 SUW  CO2  HO22  single    0.970  0.020  1.090
 SUW  CO2  HO23  single    0.970  0.020  1.090
 SUW  CX3  CX4   single    1.526  0.020  1.526
 SUW  CX3  HX31  single    0.970  0.020  1.090
 SUW  CX3  HX32  single    0.970  0.020  1.090
 SUW  CX4  OX4   single    1.407  0.020  1.407
 SUW  CX4  CX5   single    1.534  0.020  1.534
 SUW  CX4  HX4   single    0.970  0.020  1.090
 SUW  OX4  HA    single    0.850  0.020  0.980
 SUW  CX5  NX5   single    1.440  0.020  1.440
 SUW  CX5  CX6   single    1.529  0.020  1.529
 SUW  CX5  HX5   single    0.970  0.020  1.090
 SUW  NX5  C10   single    1.345  0.020  1.345
 SUW  NX5  HB    single    0.860  0.020  1.020
 SUW  C10  O10   double    1.223  0.020  1.223
 SUW  C10  C11   single    1.509  0.020  1.509
 SUW  C11  H111  single    0.970  0.020  1.090
 SUW  C11  H112  single    0.970  0.020  1.090
 SUW  C11  H113  single    0.970  0.020  1.090
 SUW  CX6  OX6   single    1.408  0.020  1.408
 SUW  CX6  CX7   single    1.519  0.020  1.519
 SUW  CX6  HX6   single    0.970  0.020  1.090
 SUW  CX7  OX7   single    1.406  0.020  1.406
 SUW  CX7  CX8   single    1.542  0.020  1.542
 SUW  CX7  HX7   single    0.970  0.020  1.090
 SUW  OX7  HC    single    0.850  0.020  0.980
 SUW  CX8  OX8   single    1.403  0.020  1.403
 SUW  CX8  CX9   single    1.525  0.020  1.525
 SUW  CX8  HX8   single    0.970  0.020  1.090
 SUW  OX8  HD    single    0.850  0.020  0.980
 SUW  CX9  NX6   single    1.447  0.020  1.447
 SUW  CX9  HX91  single    0.970  0.020  1.090
 SUW  CX9  HX92  single    0.970  0.020  1.090
 SUW  NX6  C12   single    1.339  0.020  1.339
 SUW  NX6  HE    single    0.860  0.020  1.020
 SUW  C12  O12   double    1.231  0.020  1.231
 SUW  C12  C26   single    1.493  0.020  1.493
 SUW  C25  C26   aromatic  1.372  0.020  1.372
 SUW  C25  C2A   aromatic  1.411  0.020  1.411
 SUW  C25  H25   single    0.930  0.020  1.080
 SUW  C26  C27   aromatic  1.416  0.020  1.416
 SUW  C27  C28   aromatic  1.366  0.020  1.366
 SUW  C27  H27   single    0.930  0.020  1.080
 SUW  C28  C2B   aromatic  1.414  0.020  1.414
 SUW  C28  H28   single    0.930  0.020  1.080
 SUW  C2B  C21   aromatic  1.414  0.020  1.414
 SUW  C2B  C2A   aromatic  1.419  0.020  1.419
 SUW  C21  C22   aromatic  1.368  0.020  1.368
 SUW  C21  H21   single    0.930  0.020  1.080
 SUW  C22  C23   aromatic  1.412  0.020  1.412
 SUW  C22  H22   single    0.930  0.020  1.080
 SUW  C23  C24   aromatic  1.368  0.020  1.368
 SUW  C23  H23   single    0.930  0.020  1.080
 SUW  C24  C2A   aromatic  1.415  0.020  1.415
 SUW  C24  H24   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
 SUW  CX2   CX1  O1B   115.61  3.000
 SUW  CX2   CX1  O1A   117.86  3.000
 SUW  O1B   CX1  O1A   126.46  3.000
 SUW  OX6   CX2  CX3   108.89  3.000
 SUW  OX6   CX2  OX2   106.80  3.000
 SUW  CX3   CX2  OX2   106.19  3.000
 SUW  OX6   CX2  CX1   111.71  3.000
 SUW  CX3   CX2  CX1   113.66  3.000
 SUW  OX2   CX2  CX1   109.22  3.000
 SUW  CO2   OX2  CX2   117.35  3.000
 SUW  HO23  CO2  HO22  108.06  3.000
 SUW  HO23  CO2  HO21  108.38  3.000
 SUW  HO22  CO2  HO21  108.39  3.000
 SUW  HO23  CO2  OX2   112.78  3.000
 SUW  HO22  CO2  OX2   106.35  3.000
 SUW  HO21  CO2  OX2   112.69  3.000
 SUW  HX32  CX3  HX31  107.69  3.000
 SUW  HX32  CX3  CX4   108.49  3.000
 SUW  HX31  CX3  CX4   109.78  3.000
 SUW  HX32  CX3  CX2   107.53  3.000
 SUW  HX31  CX3  CX2   110.64  3.000
 SUW  CX4   CX3  CX2   112.56  3.000
 SUW  HX4   CX4  CX5   107.68  3.000
 SUW  HX4   CX4  OX4   105.12  3.000
 SUW  CX5   CX4  OX4   112.25  3.000
 SUW  HX4   CX4  CX3   109.13  3.000
 SUW  CX5   CX4  CX3   110.49  3.000
 SUW  OX4   CX4  CX3   111.91  3.000
 SUW  HA    OX4  CX4   108.41  3.000
 SUW  HX5   CX5  CX6   109.40  3.000
 SUW  HX5   CX5  NX5   107.91  3.000
 SUW  CX6   CX5  NX5   111.06  3.000
 SUW  HX5   CX5  CX4   109.85  3.000
 SUW  CX6   CX5  CX4   107.46  3.000
 SUW  NX5   CX5  CX4   111.15  3.000
 SUW  HB    NX5  C10   117.82  3.000
 SUW  HB    NX5  CX5   117.49  3.000
 SUW  C10   NX5  CX5   124.44  3.000
 SUW  C11   C10  O10   121.49  3.000
 SUW  C11   C10  NX5   114.97  3.000
 SUW  O10   C10  NX5   123.54  3.000
 SUW  H113  C11  H112  108.46  3.000
 SUW  H113  C11  H111  108.29  3.000
 SUW  H112  C11  H111  107.32  3.000
 SUW  H113  C11  C10   113.76  3.000
 SUW  H112  C11  C10   109.35  3.000
 SUW  H111  C11  C10   109.47  3.000
 SUW  HX6   CX6  CX7   106.12  3.000
 SUW  HX6   CX6  OX6   110.83  3.000
 SUW  CX7   CX6  OX6   108.62  3.000
 SUW  HX6   CX6  CX5   106.85  3.000
 SUW  CX7   CX6  CX5   115.43  3.000
 SUW  OX6   CX6  CX5   108.94  3.000
 SUW  CX6   OX6  CX2   114.55  3.000
 SUW  HX7   CX7  CX8   108.48  3.000
 SUW  HX7   CX7  OX7   111.01  3.000
 SUW  CX8   CX7  OX7   110.99  3.000
 SUW  HX7   CX7  CX6   105.63  3.000
 SUW  CX8   CX7  CX6   110.35  3.000
 SUW  OX7   CX7  CX6   110.23  3.000
 SUW  HC    OX7  CX7   106.67  3.000
 SUW  HX8   CX8  CX9   105.31  3.000
 SUW  HX8   CX8  OX8   111.49  3.000
 SUW  CX9   CX8  OX8   108.42  3.000
 SUW  HX8   CX8  CX7   107.68  3.000
 SUW  CX9   CX8  CX7   111.90  3.000
 SUW  OX8   CX8  CX7   111.87  3.000
 SUW  HD    OX8  CX8   109.07  3.000
 SUW  HX92  CX9  HX91  106.58  3.000
 SUW  HX92  CX9  NX6   109.26  3.000
 SUW  HX91  CX9  NX6   107.64  3.000
 SUW  HX92  CX9  CX8   109.85  3.000
 SUW  HX91  CX9  CX8   108.70  3.000
 SUW  NX6   CX9  CX8   114.49  3.000
 SUW  HE    NX6  C12   119.26  3.000
 SUW  HE    NX6  CX9   117.04  3.000
 SUW  C12   NX6  CX9   123.56  3.000
 SUW  C26   C12  O12   120.63  3.000
 SUW  C26   C12  NX6   116.45  3.000
 SUW  O12   C12  NX6   122.91  3.000
 SUW  H25   C25  C2A   118.77  3.000
 SUW  H25   C25  C26   120.09  3.000
 SUW  C2A   C25  C26   121.14  3.000
 SUW  C27   C26  C25   119.41  3.000
 SUW  C27   C26  C12   122.33  3.000
 SUW  C25   C26  C12   118.26  3.000
 SUW  H27   C27  C28   118.56  3.000
 SUW  H27   C27  C26   120.78  3.000
 SUW  C28   C27  C26   120.62  3.000
 SUW  H28   C28  C2B   119.16  3.000
 SUW  H28   C28  C27   119.93  3.000
 SUW  C2B   C28  C27   120.91  3.000
 SUW  C2A   C2B  C21   119.14  3.000
 SUW  C2A   C2B  C28   118.72  3.000
 SUW  C21   C2B  C28   122.14  3.000
 SUW  H21   C21  C22   120.46  3.000
 SUW  H21   C21  C2B   119.05  3.000
 SUW  C22   C21  C2B   120.49  3.000
 SUW  H22   C22  C23   119.56  3.000
 SUW  H22   C22  C21   120.01  3.000
 SUW  C23   C22  C21   120.42  3.000
 SUW  H23   C23  C24   120.04  3.000
 SUW  H23   C23  C22   119.64  3.000
 SUW  C24   C23  C22   120.33  3.000
 SUW  H24   C24  C2A   119.04  3.000
 SUW  H24   C24  C23   120.43  3.000
 SUW  C2A   C24  C23   120.53  3.000
 SUW  C24   C2A  C2B   119.10  3.000
 SUW  C24   C2A  C25   121.72  3.000
 SUW  C2B   C2A  C25   119.18  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
 SUW  CONST_01  C28   C27  C26  C25    0.00   0.0  0
 SUW  CONST_02  C28   C2B  C2A  C25    0.00   0.0  0
 SUW  CONST_03  C21   C2B  C2A  C25  180.00   0.0  0
 SUW  CONST_04  C23   C24  C2A  C25  180.00   0.0  0
 SUW  CONST_05  C2B   C2A  C25  C26    0.00   0.0  0
 SUW  CONST_06  C24   C2A  C25  C26  180.00   0.0  0
 SUW  CONST_07  C2B   C28  C27  C26    0.00   0.0  0
 SUW  CONST_08  C2A   C25  C26  C27    0.00   0.0  0
 SUW  CONST_09  C21   C2B  C28  C27  180.00   0.0  0
 SUW  CONST_10  C2A   C2B  C28  C27    0.00   0.0  0
 SUW  CONST_11  C22   C21  C2B  C28  180.00   0.0  0
 SUW  CONST_12  C24   C2A  C2B  C28  180.00   0.0  0
 SUW  CONST_13  C23   C22  C21  C2B    0.00   0.0  0
 SUW  CONST_14  C23   C24  C2A  C2B    0.00   0.0  0
 SUW  CONST_15  C24   C2A  C2B  C21    0.00   0.0  0
 SUW  CONST_16  C24   C23  C22  C21    0.00   0.0  0
 SUW  CONST_17  C2A   C2B  C21  C22    0.00   0.0  0
 SUW  CONST_18  C2A   C24  C23  C22    0.00   0.0  0
 SUW  CONST_19  C2A   C25  C26  C12  180.00   0.0  0
 SUW  CONST_20  C28   C27  C26  C12  180.00   0.0  0
 SUW  CONST_21  H27   C27  C26  C25  180.00   0.0  0
 SUW  CONST_22  H24   C24  C2A  C25    0.00   0.0  0
 SUW  CONST_23  H28   C28  C27  C26  180.00   0.0  0
 SUW  CONST_24  H25   C25  C26  C27  180.00   0.0  0
 SUW  CONST_25  H21   C21  C2B  C28    0.00   0.0  0
 SUW  CONST_26  H22   C22  C21  C2B  180.00   0.0  0
 SUW  CONST_27  H23   C23  C22  C21  180.00   0.0  0
 SUW  CONST_28  O10   C10  NX5  CX5    0.00   0.0  0
 SUW  CONST_29  C11   C10  NX5  CX5  180.00   0.0  0
 SUW  CONST_30  C26   C12  NX6  CX9  180.00   0.0  0
 SUW  CONST_31  HE    NX6  C12  C26    0.00   0.0  0
 SUW  CONST_32  O12   C12  NX6  CX9    0.00   0.0  0
 SUW  CONST_33  HB    NX5  C10  O10  180.00   0.0  0
 SUW  Var_01    C25   C26  C12  NX6  155.98  30.0  2
 SUW  Var_02    HO21  CO2  OX2  CX2  -54.46  30.0  3
 SUW  Var_03    C12   NX6  CX9  CX8  -94.16  30.0  3
 SUW  Var_04    H111  C11  C10  NX5  119.89  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
 SUW  chir_01  CX2  OX2  CX3  OX6  positiv
 SUW  chir_02  CX4  OX4  CX5  CX3  positiv
 SUW  chir_03  CX5  NX5  CX6  CX4  negativ
 SUW  chir_04  CX6  OX6  CX7  CX5  negativ
 SUW  chir_05  CX7  OX7  CX6  CX8  negativ
 SUW  chir_06  CX8  OX8  CX7  CX9  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
 SUW  plan-1  C12  0.020
 SUW  plan-1  C25  0.020
 SUW  plan-1  C26  0.020
 SUW  plan-1  C27  0.020
 SUW  plan-1  C28  0.020
 SUW  plan-1  C2B  0.020
 SUW  plan-1  C21  0.020
 SUW  plan-1  C22  0.020
 SUW  plan-1  C23  0.020
 SUW  plan-1  C24  0.020
 SUW  plan-1  C2A  0.020
 SUW  plan-1  H27  0.020
 SUW  plan-1  H28  0.020
 SUW  plan-1  H21  0.020
 SUW  plan-1  H22  0.020
 SUW  plan-1  H23  0.020
 SUW  plan-1  H24  0.020
 SUW  plan-1  H25  0.020
 SUW  plan-2  CX9  0.020
 SUW  plan-2  NX6  0.020
 SUW  plan-2  C12  0.020
 SUW  plan-2  O12  0.020
 SUW  plan-2  C26  0.020
 SUW  plan-2  HE   0.020
 SUW  plan-3  CX5  0.020
 SUW  plan-3  NX5  0.020
 SUW  plan-3  C10  0.020
 SUW  plan-3  O10  0.020
 SUW  plan-3  C11  0.020
 SUW  plan-3  HB   0.020
 SUW  plan-4  CX1  0.020
 SUW  plan-4  O1A  0.020
 SUW  plan-4  O1B  0.020
 SUW  plan-4  CX2  0.020

