# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  1 12:14:53 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-3-O-(4-deoxy-alpha-L-threo-hex-4-enopyranuronosyl)-beta-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O[C@@H]2OC(=C[C@H](O)[C@H]2O)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
 UCD  UCD  2-(acetylamino)-2-deoxy-3-O-(4-deoxy-alpha-L-threo-hex-4-enopyranuronosyl)-beta-D-galactopyranose  saccharide  46  26  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UCD
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
 UCD  CAA   C  CH3    0  -0.792   2.1481   3.9994   0.9422
 UCD  CAP   C  C      0   0.531   2.3647   2.8156   0.0345
 UCD  OAB   O  O      0  -0.503   2.5735   2.9418  -1.1626
 UCD  N2    N  NH1    0  -0.625   2.2937   1.6187   0.6517
 UCD  C2    C  CH1    0  -0.153   2.2529   0.3583  -0.0387
 UCD  C1    C  CH1    0   0.307   3.2627  -0.6266   0.5546
 UCD  O1    O  OH1    0  -0.651   4.5323  -0.1361   0.3510
 UCD  O5    O  O2     0  -0.495   3.1548  -1.8719  -0.0873
 UCD  C5    C  CH1    0  -0.010   1.8923  -2.4836   0.0771
 UCD  C6    C  CH2    0  -0.166   1.9580  -3.8786  -0.5048
 UCD  O6    O  OH1    0  -0.669   2.8437  -4.6536   0.2666
 UCD  C4    C  CH1    0  -0.012   0.7993  -1.6345  -0.5762
 UCD  O4    O  OH1    0  -0.673   0.9933  -1.4976  -1.9633
 UCD  C3    C  CH1    0   0.032   0.8495  -0.2442   0.0527
 UCD  O3    O  O2     0  -0.488  -0.0471   0.6580  -0.5537
 UCD  CAX   C  CH1    0   0.292  -1.2439   0.8396   0.0918
 UCD  OAM   O  O2     0  -0.479  -2.0228  -0.3213  -0.1217
 UCD  CAR   C  C      0   0.180  -3.3266  -0.2547   0.2388
 UCD  CAQ   C  C      0   0.375  -3.9962  -1.6204   0.3507
 UCD  OAE   O  OC    -1  -0.587  -3.2692  -2.6041   0.1376
 UCD  OAC   O  O      0  -0.590  -5.2055  -1.6112   0.6437
 UCD  CAJ   C  C1     0  -0.408  -3.9450   0.9055   0.4602
 UCD  CAS   C  CH1    0   0.002  -3.2630   2.2318   0.2993
 UCD  OAF   O  OH1    0  -0.672  -4.0497   3.1609  -0.4226
 UCD  CAU   C  CH1    0  -0.024  -1.9558   2.0615  -0.4665
 UCD  OAH   O  OH1    0  -0.655  -1.1071   3.1695  -0.3316
 UCD  HAA1  H  HCH3   0   0.257   2.6905   4.8657   0.5704
 UCD  HAA2  H  HCH3   0   0.271   1.0840   4.2407   0.9446
 UCD  HAA3  H  HCH3   0   0.249   2.4485   3.8077   1.9714
 UCD  HN2   H  HNH1   0   0.396   2.0727   1.6118   1.6358
 UCD  H2    H  HCH1   0   0.275   2.5115   0.5351  -1.0848
 UCD  H1    H  HCH1   0   0.183   3.0464  -0.7584   1.6315
 UCD  HO1   H  HOH1   0   0.465   5.1406  -0.5592   0.9660
 UCD  H5    H  HCH1   0   0.220   1.6475  -2.5714   1.1494
 UCD  H61   H  HCH2   0   0.204   0.9418  -4.2949  -0.4972
 UCD  H62   H  HCH2   0   0.202   2.2770  -3.8232  -1.5529
 UCD  HO6   H  HOH1   0   0.457   2.9053  -5.5239  -0.1367
 UCD  H4    H  HCH1   0   0.251  -0.1743  -2.0845  -0.3472
 UCD  HO4   H  HOH1   0   0.458   0.5601  -2.2280  -2.4125
 UCD  H3    H  HCH1   0   0.234   0.6017  -0.3624   1.1190
 UCD  HAX   H  HCH1   0   0.206  -1.0963   0.9617   1.1798
 UCD  HAJ   H  H      0   0.253  -4.9803   0.8886   0.7731
 UCD  HAS   H  HCH1   0   0.225  -3.0218   2.6440   1.2905
 UCD  HAF   H  HOH1   0   0.457  -4.7431   3.4869   0.1591
 UCD  HAU   H  HCH1   0   0.220  -2.1971   1.8637  -1.5235
 UCD  HAH   H  HOH1   0   0.451  -1.6074   3.9550  -0.5768

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
 UCD  CAA  CAP   single  1.507  0.020  1.507
 UCD  CAA  HAA1  single  0.970  0.020  1.090
 UCD  CAA  HAA2  single  0.970  0.020  1.090
 UCD  CAA  HAA3  single  0.970  0.020  1.090
 UCD  CAP  OAB   double  1.222  0.020  1.222
 UCD  CAP  N2    single  1.348  0.020  1.348
 UCD  N2   C2    single  1.438  0.020  1.438
 UCD  N2   HN2   single  0.860  0.020  1.020
 UCD  C2   C1    single  1.530  0.020  1.530
 UCD  C2   C3    single  1.530  0.020  1.530
 UCD  C2   H2    single  0.970  0.020  1.090
 UCD  C1   O1    single  1.376  0.020  1.376
 UCD  C1   O5    single  1.405  0.020  1.405
 UCD  C1   H1    single  0.970  0.020  1.090
 UCD  O1   HO1   single  0.850  0.020  0.980
 UCD  O5   C5    single  1.412  0.020  1.412
 UCD  C5   C6    single  1.513  0.020  1.513
 UCD  C5   C4    single  1.530  0.020  1.530
 UCD  C5   H5    single  0.970  0.020  1.090
 UCD  C6   O6    single  1.407  0.020  1.407
 UCD  C6   H61   single  0.970  0.020  1.090
 UCD  C6   H62   single  0.970  0.020  1.090
 UCD  O6   HO6   single  0.850  0.020  0.980
 UCD  C4   O4    single  1.407  0.020  1.407
 UCD  C4   C3    single  1.527  0.020  1.527
 UCD  C4   H4    single  0.970  0.020  1.090
 UCD  O4   HO4   single  0.850  0.020  0.980
 UCD  C3   O3    single  1.409  0.020  1.409
 UCD  C3   H3    single  0.970  0.020  1.090
 UCD  O3   CAX   single  1.372  0.020  1.372
 UCD  CAX  OAM   single  1.414  0.020  1.414
 UCD  CAX  CAU   single  1.520  0.020  1.520
 UCD  CAX  HAX   single  0.970  0.020  1.090
 UCD  OAM  CAR   single  1.354  0.020  1.354
 UCD  CAR  CAQ   single  1.525  0.020  1.525
 UCD  CAR  CAJ   double  1.333  0.020  1.333
 UCD  CAQ  OAE   deloc   1.242  0.020  1.242
 UCD  CAQ  OAC   deloc   1.244  0.020  1.244
 UCD  CAJ  CAS   single  1.500  0.020  1.500
 UCD  CAJ  HAJ   single  0.930  0.020  1.080
 UCD  CAS  OAF   single  1.415  0.020  1.415
 UCD  CAS  CAU   single  1.525  0.020  1.525
 UCD  CAS  HAS   single  0.970  0.020  1.090
 UCD  OAF  HAF   single  0.850  0.020  0.980
 UCD  CAU  OAH   single  1.402  0.020  1.402
 UCD  CAU  HAU   single  0.970  0.020  1.090
 UCD  OAH  HAH   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
 UCD  HAA3  CAA  HAA2  107.81  3.000
 UCD  HAA3  CAA  HAA1  109.01  3.000
 UCD  HAA2  CAA  HAA1  108.12  3.000
 UCD  HAA3  CAA  CAP   113.02  3.000
 UCD  HAA2  CAA  CAP   108.37  3.000
 UCD  HAA1  CAA  CAP   110.37  3.000
 UCD  N2    CAP  OAB   123.31  3.000
 UCD  N2    CAP  CAA   114.45  3.000
 UCD  OAB   CAP  CAA   122.23  3.000
 UCD  HN2   N2   C2    117.15  3.000
 UCD  HN2   N2   CAP   117.66  3.000
 UCD  C2    N2   CAP   124.04  3.000
 UCD  H2    C2   C3    109.77  3.000
 UCD  H2    C2   C1    108.62  3.000
 UCD  C3    C2   C1    109.19  3.000
 UCD  H2    C2   N2    108.14  3.000
 UCD  C3    C2   N2    110.03  3.000
 UCD  C1    C2   N2    111.06  3.000
 UCD  H1    C1   O5    108.91  3.000
 UCD  H1    C1   O1    111.52  3.000
 UCD  O5    C1   O1    108.61  3.000
 UCD  H1    C1   C2    108.97  3.000
 UCD  O5    C1   C2    110.03  3.000
 UCD  O1    C1   C2    108.79  3.000
 UCD  HO1   O1   C1    109.37  3.000
 UCD  C5    O5   C1    113.54  3.000
 UCD  H5    C5   C4    107.49  3.000
 UCD  H5    C5   C6    108.06  3.000
 UCD  C4    C5   C6    112.24  3.000
 UCD  H5    C5   O5    110.23  3.000
 UCD  C4    C5   O5    110.38  3.000
 UCD  C6    C5   O5    108.40  3.000
 UCD  H62   C6   H61   107.15  3.000
 UCD  H62   C6   O6    111.63  3.000
 UCD  H61   C6   O6    111.71  3.000
 UCD  H62   C6   C5    109.48  3.000
 UCD  H61   C6   C5    107.86  3.000
 UCD  O6    C6   C5    108.92  3.000
 UCD  HO6   O6   C6    107.99  3.000
 UCD  H4    C4   C3    108.47  3.000
 UCD  H4    C4   O4    111.59  3.000
 UCD  C3    C4   O4    108.24  3.000
 UCD  H4    C4   C5    108.49  3.000
 UCD  C3    C4   C5    107.81  3.000
 UCD  O4    C4   C5    112.10  3.000
 UCD  HO4   O4   C4    108.96  3.000
 UCD  H3    C3   O3    110.02  3.000
 UCD  H3    C3   C4    107.08  3.000
 UCD  O3    C3   C4    112.63  3.000
 UCD  H3    C3   C2    107.86  3.000
 UCD  O3    C3   C2    107.81  3.000
 UCD  C4    C3   C2    111.35  3.000
 UCD  CAX   O3   C3    115.94  3.000
 UCD  HAX   CAX  CAU   109.59  3.000
 UCD  HAX   CAX  OAM   108.24  3.000
 UCD  CAU   CAX  OAM   110.27  3.000
 UCD  HAX   CAX  O3    111.19  3.000
 UCD  CAU   CAX  O3    110.00  3.000
 UCD  OAM   CAX  O3    107.51  3.000
 UCD  CAR   OAM  CAX   116.73  3.000
 UCD  CAJ   CAR  CAQ   124.29  3.000
 UCD  CAJ   CAR  OAM   122.24  3.000
 UCD  CAQ   CAR  OAM   113.46  3.000
 UCD  OAC   CAQ  OAE   127.98  3.000
 UCD  OAC   CAQ  CAR   115.93  3.000
 UCD  OAE   CAQ  CAR   116.09  3.000
 UCD  HAJ   CAJ  CAS   118.69  3.000
 UCD  HAJ   CAJ  CAR   118.58  3.000
 UCD  CAS   CAJ  CAR   122.73  3.000
 UCD  HAS   CAS  CAU   107.85  3.000
 UCD  HAS   CAS  OAF   109.60  3.000
 UCD  CAU   CAS  OAF   107.08  3.000
 UCD  HAS   CAS  CAJ   109.53  3.000
 UCD  CAU   CAS  CAJ   110.18  3.000
 UCD  OAF   CAS  CAJ   112.48  3.000
 UCD  HAF   OAF  CAS   108.34  3.000
 UCD  HAU   CAU  OAH   111.51  3.000
 UCD  HAU   CAU  CAS   108.30  3.000
 UCD  OAH   CAU  CAS   112.48  3.000
 UCD  HAU   CAU  CAX   108.08  3.000
 UCD  OAH   CAU  CAX   108.44  3.000
 UCD  CAS   CAU  CAX   107.86  3.000
 UCD  HAH   OAH  CAU   107.79  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
 UCD  CONST_01  C2    N2   CAP  CAA  180.00   0.0  0
 UCD  CONST_02  C2    N2   CAP  OAB    0.00   0.0  0
 UCD  CONST_03  HN2   N2   CAP  CAA    0.00   0.0  0
 UCD  Var_01    CAJ   CAR  OAM  CAX   16.63  30.0  1
 UCD  Var_02    CAS   CAJ  CAR  OAM    1.45  30.0  1
 UCD  Var_03    OAE   CAQ  CAR  OAM    1.85  30.0  2
 UCD  Var_04    HAA1  CAA  CAP  OAB  -29.80  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
 UCD  chir_01  C2   N2   C1   C3   negativ
 UCD  chir_02  C1   O1   O5   C2   positiv
 UCD  chir_03  C5   O5   C4   C6   negativ
 UCD  chir_04  C4   O4   C5   C3   negativ
 UCD  chir_05  C3   O3   C2   C4   positiv
 UCD  chir_06  CAX  O3   OAM  CAU  positiv
 UCD  chir_07  CAS  OAF  CAU  CAJ  positiv
 UCD  chir_08  CAU  OAH  CAX  CAS  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
 UCD  plan-1  CAA  0.020
 UCD  plan-1  CAP  0.020
 UCD  plan-1  OAB  0.020
 UCD  plan-1  N2   0.020
 UCD  plan-1  C2   0.020
 UCD  plan-1  HN2  0.020
 UCD  plan-2  CAR  0.020
 UCD  plan-2  CAQ  0.020
 UCD  plan-2  OAE  0.020
 UCD  plan-2  OAC  0.020

