# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 06:41:05 2020
#   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  49  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.651  -3.2711   3.2085  -0.3437
 L42  CBE   C  CH1    0   0.306  -2.4561   2.2245  -0.8544
 L42  CBF   C  CH1    0  -0.146  -1.3574   1.9130   0.1621
 L42  NBN   N  NH1    0  -0.630  -0.4941   3.0435   0.3720
 L42  CBK   C  C      0   0.530  -0.1081   3.4800   1.5893
 L42  CBL   C  CH3    0  -0.790   1.0187   4.4811   1.5644
 L42  OBS   O  O      0  -0.500  -0.6086   3.0893   2.6323
 L42  OBQ   O  O2     0  -0.496  -3.2304   1.0732  -1.0848
 L42  CBI   C  CH1    0  -0.014  -2.4995   0.0035  -1.6489
 L42  CBJ   C  CH2    0  -0.157  -3.4715  -1.0884  -2.0383
 L42  OBR   O  OH1    0  -0.672  -4.3206  -0.5899  -3.0463
 L42  CBH   C  CH1    0  -0.010  -1.4275  -0.4691  -0.6704
 L42  OBP   O  OC2    0  -0.629  -2.0513  -0.9293   0.5186
 L42  SBW   S  S      0   1.568  -1.7719  -2.4642   1.0484
 L42  OBV   O  OS     0  -0.738  -1.9846  -3.3266  -0.1180
 L42  OBU   O  OS    -1  -0.719  -0.4036  -2.4884   1.5588
 L42  OBT   O  OS     0  -0.742  -2.8046  -2.5649   2.0791
 L42  CBG   C  CH1    0   0.041  -0.5355   0.7213  -0.3348
 L42  OBO   O  O2     0  -0.483   0.4135   0.3987   0.6481
 L42  CBX   C  CH1    0   0.306   1.7052   0.2649   0.2062
 L42  OCH   O  O2     0  -0.470   1.7610  -0.8612  -0.6446
 L42  CCD   C  C      0   0.182   2.9932  -1.2948  -0.9933
 L42  CCE   C  C      0   0.371   2.9932  -2.2373  -2.1931
 L42  OCG   O  OC    -1  -0.584   1.8881  -2.4679  -2.7078
 L42  OCF   O  O      0  -0.594   4.1049  -2.6809  -2.5367
 L42  CCC   C  C1     0  -0.415   4.0929  -0.9280  -0.3330
 L42  CCA   C  CH1    0   0.006   4.0569  -0.0297   0.8668
 L42  OCB   O  OH1    0  -0.673   4.8608  -0.5109   1.9285
 L42  CBY   C  CH1    0  -0.032   2.6322   0.0835   1.3957
 L42  OBZ   O  OH1    0  -0.657   2.4675   1.1788   2.2565
 L42  HBM   H  HOH1   0   0.465  -3.7826   3.6010  -1.0591
 L42  HBE   H  HCH1   0   0.184  -1.9900   2.5367  -1.8075
 L42  HBF   H  HCH1   0   0.274  -1.8265   1.6614   1.1153
 L42  HBN   H  HNH1   0   0.396  -0.0058   3.4080  -0.4318
 L42  HBG   H  HCH1   0   0.234  -0.0392   1.0237  -1.2694
 L42  HBL1  H  HCH3   0   0.249   1.0630   5.0507   0.6372
 L42  HBL2  H  HCH3   0   0.257   0.9322   5.1703   2.4013
 L42  HBL3  H  HCH3   0   0.270   1.9590   3.9366   1.6704
 L42  HBI   H  HCH1   0   0.226  -1.9798   0.3413  -2.5614
 L42  HBJ1  H  HCH2   0   0.205  -2.8907  -1.9507  -2.3852
 L42  HBJ2  H  HCH2   0   0.202  -4.0348  -1.4126  -1.1558
 L42  HBH   H  HCH1   0   0.274  -0.8185  -1.2463  -1.1443
 L42  HBR   H  HOH1   0   0.456  -4.9565  -1.2775  -3.2622
 L42  HBX   H  HCH1   0   0.200   2.0173   1.1510  -0.3771
 L42  HBY   H  HCH1   0   0.222   2.3624  -0.8646   1.8870
 L42  HCC   H  H      0   0.250   5.0514  -1.2859  -0.6838
 L42  HCA   H  HCH1   0   0.221   4.3887   0.9796   0.5811
 L42  HCB   H  HOH1   0   0.456   5.7829  -0.3532   1.7043
 L42  HBZ   H  HOH1   0   0.451   3.1129   1.0940   2.9662

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  1.376  0.020  1.376
 L42  CBE  CBF   single  1.529  0.020  1.529
 L42  CBE  OBQ   single  1.407  0.020  1.407
 L42  CBF  NBN   single  1.438  0.020  1.438
 L42  CBF  CBG   single  1.531  0.020  1.531
 L42  NBN  CBK   single  1.350  0.020  1.350
 L42  CBK  CBL   single  1.508  0.020  1.508
 L42  CBK  OBS   double  1.221  0.020  1.221
 L42  OBQ  CBI   single  1.413  0.020  1.413
 L42  CBI  CBJ   single  1.513  0.020  1.513
 L42  CBI  CBH   single  1.526  0.020  1.526
 L42  CBJ  OBR   single  1.409  0.020  1.409
 L42  CBH  OBP   single  1.419  0.020  1.419
 L42  CBH  CBG   single  1.525  0.020  1.525
 L42  OBP  SBW   single  1.648  0.020  1.648
 L42  SBW  OBV   deloc   1.466  0.020  1.466
 L42  SBW  OBU   deloc   1.461  0.020  1.461
 L42  SBW  OBT   deloc   1.463  0.020  1.463
 L42  CBG  OBO   single  1.404  0.020  1.404
 L42  OBO  CBX   single  1.372  0.020  1.372
 L42  CBX  OCH   single  1.412  0.020  1.412
 L42  CBX  CBY   single  1.519  0.020  1.519
 L42  OCH  CCD   single  1.352  0.020  1.352
 L42  CCD  CCE   single  1.526  0.020  1.526
 L42  CCD  CCC   double  1.334  0.020  1.334
 L42  CCE  OCG   deloc   1.241  0.020  1.241
 L42  CCE  OCF   deloc   1.245  0.020  1.245
 L42  CCC  CCA   single  1.499  0.020  1.499
 L42  CCA  OCB   single  1.416  0.020  1.416
 L42  CCA  CBY   single  1.524  0.020  1.524
 L42  CBY  OBZ   single  1.403  0.020  1.403
 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  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  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   109.29  3.000
 L42  HBE   CBE  OBQ   108.78  3.000
 L42  HBE   CBE  CBF   109.13  3.000
 L42  OBQ   CBE  CBF   109.74  3.000
 L42  HBE   CBE  OBM   111.57  3.000
 L42  OBQ   CBE  OBM   108.67  3.000
 L42  CBF   CBE  OBM   108.94  3.000
 L42  HBF   CBF  CBG   109.56  3.000
 L42  HBF   CBF  NBN   108.16  3.000
 L42  CBG   CBF  NBN   109.70  3.000
 L42  HBF   CBF  CBE   108.59  3.000
 L42  CBG   CBF  CBE   109.19  3.000
 L42  NBN   CBF  CBE   111.61  3.000
 L42  HBN   NBN  CBK   117.61  3.000
 L42  HBN   NBN  CBF   117.29  3.000
 L42  CBK   NBN  CBF   123.90  3.000
 L42  OBS   CBK  CBL   122.21  3.000
 L42  OBS   CBK  NBN   123.35  3.000
 L42  CBL   CBK  NBN   114.44  3.000
 L42  HBL3  CBL  HBL2  108.05  3.000
 L42  HBL3  CBL  HBL1  107.97  3.000
 L42  HBL2  CBL  HBL1  109.08  3.000
 L42  HBL3  CBL  CBK   108.12  3.000
 L42  HBL2  CBL  CBK   110.40  3.000
 L42  HBL1  CBL  CBK   113.06  3.000
 L42  CBI   OBQ  CBE   113.60  3.000
 L42  HBI   CBI  CBH   107.11  3.000
 L42  HBI   CBI  CBJ   108.11  3.000
 L42  CBH   CBI  CBJ   113.13  3.000
 L42  HBI   CBI  OBQ   110.00  3.000
 L42  CBH   CBI  OBQ   109.98  3.000
 L42  CBJ   CBI  OBQ   108.47  3.000
 L42  HBJ2  CBJ  HBJ1  107.12  3.000
 L42  HBJ2  CBJ  OBR   111.77  3.000
 L42  HBJ1  CBJ  OBR   111.80  3.000
 L42  HBJ2  CBJ  CBI   109.66  3.000
 L42  HBJ1  CBJ  CBI   107.99  3.000
 L42  OBR   CBJ  CBI   108.42  3.000
 L42  HBR   OBR  CBJ   107.84  3.000
 L42  HBH   CBH  CBG   108.90  3.000
 L42  HBH   CBH  OBP   112.13  3.000
 L42  CBG   CBH  OBP   109.01  3.000
 L42  HBH   CBH  CBI   109.44  3.000
 L42  CBG   CBH  CBI   108.07  3.000
 L42  OBP   CBH  CBI   109.19  3.000
 L42  SBW   OBP  CBH   119.79  3.000
 L42  OBT   SBW  OBU   114.46  3.000
 L42  OBT   SBW  OBV   114.69  3.000
 L42  OBU   SBW  OBV   113.84  3.000
 L42  OBT   SBW  OBP    99.85  3.000
 L42  OBU   SBW  OBP   106.66  3.000
 L42  OBV   SBW  OBP   105.52  3.000
 L42  HBG   CBG  OBO   110.66  3.000
 L42  HBG   CBG  CBH   106.94  3.000
 L42  OBO   CBG  CBH   111.73  3.000
 L42  HBG   CBG  CBF   107.69  3.000
 L42  OBO   CBG  CBF   108.34  3.000
 L42  CBH   CBG  CBF   111.41  3.000
 L42  CBX   OBO  CBG   115.69  3.000
 L42  HBX   CBX  CBY   109.67  3.000
 L42  HBX   CBX  OCH   108.06  3.000
 L42  CBY   CBX  OCH   110.63  3.000
 L42  HBX   CBX  OBO   110.95  3.000
 L42  CBY   CBX  OBO   109.52  3.000
 L42  OCH   CBX  OBO   108.00  3.000
 L42  CCD   OCH  CBX   116.56  3.000
 L42  CCC   CCD  CCE   123.99  3.000
 L42  CCC   CCD  OCH   122.37  3.000
 L42  CCE   CCD  OCH   113.64  3.000
 L42  OCF   CCE  OCG   127.92  3.000
 L42  OCF   CCE  CCD   115.91  3.000
 L42  OCG   CCE  CCD   116.17  3.000
 L42  HCC   CCC  CCA   118.62  3.000
 L42  HCC   CCC  CCD   118.62  3.000
 L42  CCA   CCC  CCD   122.75  3.000
 L42  HCA   CCA  CBY   107.69  3.000
 L42  HCA   CCA  OCB   109.58  3.000
 L42  CBY   CCA  OCB   107.21  3.000
 L42  HCA   CCA  CCC   109.55  3.000
 L42  CBY   CCA  CCC   110.17  3.000
 L42  OCB   CCA  CCC   112.51  3.000
 L42  HCB   OCB  CCA   108.29  3.000
 L42  HBY   CBY  OBZ   111.69  3.000
 L42  HBY   CBY  CCA   108.66  3.000
 L42  OBZ   CBY  CCA   112.38  3.000
 L42  HBY   CBY  CBX   107.62  3.000
 L42  OBZ   CBY  CBX   108.40  3.000
 L42  CCA   CBY  CBX   107.92  3.000
 L42  HBZ   OBZ  CBY   107.75  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  HBN   NBN  CBK  CBL    0.00   0.0  0
 L42  Var_01    CCC   CCD  OCH  CBX   16.57  30.0  1
 L42  Var_02    CCA   CCC  CCD  OCH    1.33  30.0  1
 L42  Var_03    OCG   CCE  CCD  OCH    1.23  30.0  2
 L42  Var_04    OBV   SBW  OBP  CBH  -49.33  30.0  3
 L42  Var_05    HBL1  CBL  CBK  NBN   26.57  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

