# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:30:40 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-3-O-(4-deoxy-alpha-L-threo-hex-4-enopyranuronosyl)-4-O-sulfo-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[S](O)(=O)=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
 L42  L42  2-(acetylamino)-2-deoxy-3-O-(4-deoxy-alpha-L-threo-hex-4-enopyranuronosyl)-4-O-sulfo-beta-D-galactopyranose  ligand  51  30  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L42
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
 L42  OBM   O  OH1   0  -0.645  33.1131  19.8905  30.3853
 L42  CBE   C  CH1   0   0.309  31.9029  20.5295  30.2892
 L42  CBF   C  CH1   0  -0.163  30.7969  19.4727  30.2297
 L42  NBN   N  NH1   0  -0.632  30.9068  18.6693  29.0454
 L42  CBK   C  C     0   0.541  30.9137  17.3204  29.0550
 L42  CBL   C  CH3   0  -0.783  30.9571  16.6697  27.6966
 L42  OBS   O  O     0  -0.501  30.9138  16.6605  30.0828
 L42  OBQ   O  O2    0  -0.498  31.7268  21.3374  31.4327
 L42  CBI   C  CH1   0  -0.012  30.5285  22.0772  31.4216
 L42  CBJ   C  CH2   0  -0.196  30.5783  23.0938  32.5527
 L42  OBR   O  OH1   0  -0.651  30.6976  22.5440  33.8378
 L42  CBH   C  CH1   0  -0.057  29.3349  21.1324  31.4448
 L42  OBP   O  OC2   0  -0.580  29.3583  20.3427  32.6509
 L42  SBW   S  S     0   1.652  28.2403  20.5043  33.7654
 L42  OBV   O  OS    0  -0.628  28.8165  19.9950  34.9765
 L42  OBU   O  OS    0  -0.728  27.1724  19.4205  33.3381
 L42  OBT   O  OS    0  -0.628  27.6609  21.8221  33.7052
 L42  CBG   C  CH1   0   0.035  29.4290  20.1551  30.2787
 L42  OBO   O  O2    0  -0.480  28.4568  19.1385  30.3557
 L42  CBX   C  CH1   0   0.279  27.2612  19.3331  29.7272
 L42  OCH   O  O2    0  -0.555  26.3519  19.8698  30.7063
 L42  CCD   C  C     0   0.258  25.0531  19.9472  30.3102
 L42  CCE   C  C     0   0.516  24.2172  20.8902  31.1007
 L42  OCG   O  OH1   0  -0.583  24.9086  21.4727  32.0608
 L42  OCF   O  O     0  -0.423  23.0476  21.0775  30.8812
 L42  CCC   C  C1    0  -0.345  24.5538  19.2389  29.3024
 L42  CCA   C  CH1   0   0.002  25.3722  18.2578  28.5167
 L42  OCB   O  OH1   0  -0.650  24.6643  17.0730  28.2608
 L42  CBY   C  CH1   0  -0.054  26.7178  18.0037  29.2037
 L42  OBZ   O  OH1   0  -0.640  27.6350  17.3617  28.3689
 L42  HBM   H  HOH1  0   0.469  33.8185  20.4998  30.1415
 L42  HBE   H  HCH1  0   0.197  31.8462  21.1709  29.3919
 L42  HBF   H  HCH1  0   0.288  30.9070  18.8134  31.0937
 L42  HBN   H  HNH1  0   0.399  30.8817  19.1411  28.1549
 L42  HBG   H  HCH1  0   0.267  29.2954  20.7459  29.3613
 L42  HBL1  H  HCH3  0   0.245  30.8969  17.3730  26.8684
 L42  HBL2  H  HCH3  0   0.267  31.8832  16.1026  27.5998
 L42  HBL3  H  HCH3  0   0.265  30.1316  15.9645  27.6119
 L42  HBI   H  HCH1  0   0.248  30.4396  22.6621  30.4915
 L42  HBJ1  H  HCH2  0   0.228  31.3971  23.7904  32.3328
 L42  HBJ2  H  HCH2  0   0.237  29.6552  23.6750  32.5304
 L42  HBH   H  HCH1  0   0.300  28.4149  21.7198  31.3758
 L42  HBR   H  HOH1  0   0.450  31.5178  22.0422  33.8804
 L42  HBU   H  H     0   0.502  26.7666  19.5992  32.4588
 L42  HBX   H  HCH1  0   0.250  27.3358  20.0736  28.9147
 L42  HBY   H  HCH1  0   0.269  26.5628  17.3402  30.0632
 L42  HCC   H  H     0   0.294  23.5175  19.3762  29.0246
 L42  HCG   H  HOH1  0   0.495  24.3418  22.0680  32.5750
 L42  HCA   H  HCH1  0   0.269  25.5659  18.6982  27.5301
 L42  HCB   H  HOH1  0   0.451  24.4334  16.6625  29.1019
 L42  HBZ   H  HOH1  0   0.450  27.7434  17.8706  27.5580

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
 L42  OBM  CBE   single  1.372  0.020  1.372
 L42  CBE  CBF   single  1.531  0.020  1.531
 L42  CBE  OBQ   single  1.411  0.020  1.411
 L42  CBF  NBN   single  1.435  0.020  1.435
 L42  CBF  CBG   single  1.530  0.020  1.530
 L42  NBN  CBK   single  1.349  0.020  1.349
 L42  CBK  CBL   single  1.507  0.020  1.507
 L42  CBK  OBS   double  1.221  0.020  1.221
 L42  OBQ  CBI   single  1.408  0.020  1.408
 L42  CBI  CBJ   single  1.522  0.020  1.522
 L42  CBI  CBH   single  1.522  0.020  1.522
 L42  CBJ  OBR   single  1.403  0.020  1.403
 L42  CBH  OBP   single  1.442  0.020  1.442
 L42  CBH  CBG   single  1.524  0.020  1.524
 L42  OBP  SBW   single  1.587  0.020  1.587
 L42  SBW  OBV   double  1.435  0.020  1.435
 L42  SBW  OBU   single  1.580  0.020  1.580
 L42  SBW  OBT   double  1.441  0.020  1.441
 L42  CBG  OBO   single  1.409  0.020  1.409
 L42  OBO  CBX   single  1.365  0.020  1.365
 L42  CBX  OCH   single  1.440  0.020  1.440
 L42  CBX  CBY   single  1.529  0.020  1.529
 L42  OCH  CCD   single  1.360  0.020  1.360
 L42  CCD  CCE   single  1.488  0.020  1.488
 L42  CCD  CCC   double  1.329  0.020  1.329
 L42  CCE  OCG   single  1.319  0.020  1.319
 L42  CCE  OCF   double  1.205  0.020  1.205
 L42  CCC  CCA   single  1.500  0.020  1.500
 L42  CCA  OCB   single  1.404  0.020  1.404
 L42  CCA  CBY   single  1.532  0.020  1.532
 L42  CBY  OBZ   single  1.397  0.020  1.397
 L42  OBM  HBM   single  0.850  0.020  0.980
 L42  CBE  HBE   single  0.970  0.020  1.090
 L42  CBF  HBF   single  0.970  0.020  1.090
 L42  NBN  HBN   single  0.860  0.020  1.020
 L42  CBG  HBG   single  0.970  0.020  1.090
 L42  CBL  HBL1  single  0.970  0.020  1.090
 L42  CBL  HBL2  single  0.970  0.020  1.090
 L42  CBL  HBL3  single  0.970  0.020  1.090
 L42  CBI  HBI   single  0.970  0.020  1.090
 L42  CBJ  HBJ1  single  0.970  0.020  1.090
 L42  CBJ  HBJ2  single  0.970  0.020  1.090
 L42  CBH  HBH   single  0.970  0.020  1.090
 L42  OBR  HBR   single  0.850  0.020  0.980
 L42  OBU  HBU   single  0.850  0.020  0.980
 L42  CBX  HBX   single  0.970  0.020  1.090
 L42  CBY  HBY   single  0.970  0.020  1.090
 L42  CCC  HCC   single  0.930  0.020  1.080
 L42  OCG  HCG   single  0.850  0.020  0.980
 L42  CCA  HCA   single  0.970  0.020  1.090
 L42  OCB  HCB   single  0.850  0.020  0.980
 L42  OBZ  HBZ   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
 L42  HBM   OBM  CBE   109.49  3.000
 L42  HBE   CBE  OBQ   108.63  3.000
 L42  HBE   CBE  CBF   109.40  3.000
 L42  OBQ   CBE  CBF   109.67  3.000
 L42  HBE   CBE  OBM   111.88  3.000
 L42  OBQ   CBE  OBM   108.66  3.000
 L42  CBF   CBE  OBM   108.57  3.000
 L42  HBF   CBF  CBG   109.52  3.000
 L42  HBF   CBF  NBN   107.89  3.000
 L42  CBG   CBF  NBN   110.16  3.000
 L42  HBF   CBF  CBE   108.24  3.000
 L42  CBG   CBF  CBE   109.69  3.000
 L42  NBN   CBF  CBE   111.29  3.000
 L42  HBN   NBN  CBK   118.32  3.000
 L42  HBN   NBN  CBF   117.71  3.000
 L42  CBK   NBN  CBF   123.65  3.000
 L42  OBS   CBK  CBL   121.68  3.000
 L42  OBS   CBK  NBN   123.12  3.000
 L42  CBL   CBK  NBN   115.18  3.000
 L42  HBL3  CBL  HBL2  107.47  3.000
 L42  HBL3  CBL  HBL1  108.51  3.000
 L42  HBL2  CBL  HBL1  108.39  3.000
 L42  HBL3  CBL  CBK   109.14  3.000
 L42  HBL2  CBL  CBK   109.22  3.000
 L42  HBL1  CBL  CBK   113.91  3.000
 L42  CBI   OBQ  CBE   113.61  3.000
 L42  HBI   CBI  CBH   106.20  3.000
 L42  HBI   CBI  CBJ   105.98  3.000
 L42  CBH   CBI  CBJ   115.40  3.000
 L42  HBI   CBI  OBQ   110.73  3.000
 L42  CBH   CBI  OBQ   109.94  3.000
 L42  CBJ   CBI  OBQ   108.50  3.000
 L42  HBJ2  CBJ  HBJ1  106.80  3.000
 L42  HBJ2  CBJ  OBR   107.42  3.000
 L42  HBJ1  CBJ  OBR   111.65  3.000
 L42  HBJ2  CBJ  CBI   108.24  3.000
 L42  HBJ1  CBJ  CBI   107.43  3.000
 L42  OBR   CBJ  CBI   114.96  3.000
 L42  HBR   OBR  CBJ   108.50  3.000
 L42  HBH   CBH  CBG   110.36  3.000
 L42  HBH   CBH  OBP   111.14  3.000
 L42  CBG   CBH  OBP   106.72  3.000
 L42  HBH   CBH  CBI   108.98  3.000
 L42  CBG   CBH  CBI   109.75  3.000
 L42  OBP   CBH  CBI   109.87  3.000
 L42  SBW   OBP  CBH   121.35  3.000
 L42  OBT   SBW  OBU   110.13  3.000
 L42  OBT   SBW  OBV   121.43  3.000
 L42  OBU   SBW  OBV   104.84  3.000
 L42  OBT   SBW  OBP   110.31  3.000
 L42  OBU   SBW  OBP   102.49  3.000
 L42  OBV   SBW  OBP   105.89  3.000
 L42  HBU   OBU  SBW   113.29  3.000
 L42  HBG   CBG  OBO   110.46  3.000
 L42  HBG   CBG  CBH   106.64  3.000
 L42  OBO   CBG  CBH   112.23  3.000
 L42  HBG   CBG  CBF   108.76  3.000
 L42  OBO   CBG  CBF   107.27  3.000
 L42  CBH   CBG  CBF   111.46  3.000
 L42  CBX   OBO  CBG   118.46  3.000
 L42  HBX   CBX  CBY   110.86  3.000
 L42  HBX   CBX  OCH   107.08  3.000
 L42  CBY   CBX  OCH   109.42  3.000
 L42  HBX   CBX  OBO   112.09  3.000
 L42  CBY   CBX  OBO   110.19  3.000
 L42  OCH   CBX  OBO   107.06  3.000
 L42  CCD   OCH  CBX   115.23  3.000
 L42  CCC   CCD  CCE   121.98  3.000
 L42  CCC   CCD  OCH   123.31  3.000
 L42  CCE   CCD  OCH   114.70  3.000
 L42  OCF   CCE  OCG   124.96  3.000
 L42  OCF   CCE  CCD   123.18  3.000
 L42  OCG   CCE  CCD   111.86  3.000
 L42  HCG   OCG  CCE   110.54  3.000
 L42  HCC   CCC  CCA   118.11  3.000
 L42  HCC   CCC  CCD   119.14  3.000
 L42  CCA   CCC  CCD   122.74  3.000
 L42  HCA   CCA  CBY   108.34  3.000
 L42  HCA   CCA  OCB   105.30  3.000
 L42  CBY   CCA  OCB   112.62  3.000
 L42  HCA   CCA  CCC   107.74  3.000
 L42  CBY   CCA  CCC   110.66  3.000
 L42  OCB   CCA  CCC   111.86  3.000
 L42  HCB   OCB  CCA   108.74  3.000
 L42  HBY   CBY  OBZ   106.45  3.000
 L42  HBY   CBY  CCA   109.12  3.000
 L42  OBZ   CBY  CCA   112.65  3.000
 L42  HBY   CBY  CBX   107.93  3.000
 L42  OBZ   CBY  CBX   111.78  3.000
 L42  CCA   CBY  CBX   108.75  3.000
 L42  HBZ   OBZ  CBY   109.52  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
 L42  CONST_01  CBL   CBK  NBN  CBF   180.00   0.0  0
 L42  CONST_02  OBS   CBK  NBN  CBF     0.00   0.0  0
 L42  CONST_03  HCG   OCG  CCE  CCD   180.00   0.0  0
 L42  CONST_04  HBN   NBN  CBK  CBL     0.00   0.0  0
 L42  Var_01    CCC   CCD  OCH  CBX    19.85  30.0  1
 L42  Var_02    CCA   CCC  CCD  OCH     1.30  30.0  1
 L42  Var_03    OCG   CCE  CCD  OCH    -0.56  30.0  2
 L42  Var_04    OBV   SBW  OBP  CBH  -158.59  30.0  3
 L42  Var_05    HBL1  CBL  CBK  NBN    -4.66  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
 L42  chir_01  CBE  OBM  CBF  OBQ  negativ
 L42  chir_02  CBF  NBN  CBG  CBE  positiv
 L42  chir_03  CBI  OBQ  CBH  CBJ  negativ
 L42  chir_04  CBH  OBP  CBG  CBI  positiv
 L42  chir_05  CBG  OBO  CBF  CBH  positiv
 L42  chir_06  CBX  OBO  OCH  CBY  positiv
 L42  chir_07  CCA  OCB  CBY  CCC  positiv
 L42  chir_08  CBY  OBZ  CBX  CCA  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
 L42  plan-1  CBF  0.020
 L42  plan-1  NBN  0.020
 L42  plan-1  CBK  0.020
 L42  plan-1  CBL  0.020
 L42  plan-1  OBS  0.020
 L42  plan-1  HBN  0.020
 L42  plan-2  CCD  0.020
 L42  plan-2  CCE  0.020
 L42  plan-2  OCG  0.020
 L42  plan-2  OCF  0.020
 L42  plan-2  HCG  0.020

