# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:33:04 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]\1[C@@H](O)[C@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
#
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
 OAN  OAN  'N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)'  ligand  44  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OAN
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
 OAN  CAH   C  CH3   0  -0.783   1.5373   4.7197  -0.2778
 OAN  CAG   C  C     0   0.529   1.9521   3.4734   0.4595
 OAN  OAN   O  O     0  -0.495   2.0156   3.4303   1.6786
 OAN  NAI   N  NH1   0  -0.623   2.2369   2.4159  -0.3277
 OAN  CAB   C  CH1   0  -0.195   2.5396   1.1144   0.1826
 OAN  CAC   C  CH1   0   0.046   3.7043   0.4720  -0.5639
 OAN  OAJ   O  OH1   0  -0.658   4.8270   1.2798  -0.3625
 OAN  CAD   C  CH1   0  -0.022   3.9166  -0.9404  -0.0325
 OAN  OAK   O  OH1   0  -0.666   4.9788  -1.5113  -0.7559
 OAN  CAE   C  CH1   0  -0.024   2.6408  -1.7575  -0.2283
 OAN  CAF   C  CH2   0  -0.158   2.7298  -3.1253   0.4074
 OAN  OAM   O  OH1   0  -0.664   1.5610  -3.8452   0.1100
 OAN  OAL   O  O2    0  -0.454   1.5096  -1.1008   0.3653
 OAN  CAA   C  C     0   0.499   1.3329   0.2002   0.1735
 OAN  NAY   N  N     0  -0.170   0.1843   0.7351   0.0924
 OAN  OAQ   O  O2    0  -0.405  -0.8102  -0.2192   0.1680
 OAN  CAP   C  C     0   0.748  -2.0417   0.2842  -0.0770
 OAN  OAR   O  O     0  -0.462  -2.2697   1.4185  -0.4042
 OAN  NAO   N  NH1   0  -0.776  -2.9349  -0.7179   0.1060
 OAN  CAS   C  CR6   0   0.372  -4.3235  -0.6750  -0.0455
 OAN  CAT   C  CR16  0  -0.317  -5.0281   0.4079  -0.5722
 OAN  CAU   C  CR16  0  -0.245  -6.4108   0.3361  -0.6855
 OAN  CAV   C  CR16  0  -0.273  -7.1110  -0.7933  -0.2892
 OAN  CAW   C  CR16  0  -0.245  -6.4055  -1.8714   0.2297
 OAN  CAX   C  CR16  0  -0.342  -5.0281  -1.8144   0.3516
 OAN  HAH1  H  HCH3  0   0.266   2.0381   5.5855   0.1515
 OAN  HAH2  H  HCH3  0   0.252   1.7492   4.6836  -1.3446
 OAN  HAH3  H  HCH3  0   0.271   0.4636   4.8658  -0.1500
 OAN  HAI   H  HNH1  0   0.405   2.0873   2.5019  -1.3207
 OAN  HAB   H  HCH1  0   0.307   2.8385   1.2253   1.2309
 OAN  HAC   H  HCH1  0   0.232   3.4485   0.4012  -1.6345
 OAN  HAJ   H  HOH1  0   0.456   5.5644   0.8889  -0.8438
 OAN  HAD   H  HCH1  0   0.245   4.1498  -0.8799   1.0398
 OAN  HAK   H  HOH1  0   0.468   5.4837  -2.0916  -0.1793
 OAN  HAE   H  HCH1  0   0.257   2.4502  -1.8641  -1.3036
 OAN  HAF1  H  HCH2  0   0.214   3.6228  -3.6212   0.0107
 OAN  HAF2  H  HCH2  0   0.208   2.8796  -3.0054   1.4893
 OAN  HAM   H  HOH1  0   0.460   1.6640  -4.7352   0.4585
 OAN  HAO   H  HNH1  0   0.419  -2.5605  -1.5990   0.4276
 OAN  HAT   H  HCR6  0   0.278  -4.5190   1.3002  -0.8973
 OAN  HAU   H  HCR6  0   0.259  -6.9417   1.1855  -1.0955
 OAN  HAV   H  HCR6  0   0.255  -8.1878  -0.8348  -0.3836
 OAN  HAW   H  HCR6  0   0.260  -6.9270  -2.7651   0.5467
 OAN  HAX   H  HCR6  0   0.271  -4.4920  -2.6622   0.7617

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
 OAN  CAH  CAG   single    1.506  0.020  1.506
 OAN  CAH  HAH1  single    0.970  0.020  1.090
 OAN  CAH  HAH2  single    0.970  0.020  1.090
 OAN  CAH  HAH3  single    0.970  0.020  1.090
 OAN  CAG  OAN   double    1.222  0.020  1.222
 OAN  CAG  NAI   single    1.349  0.020  1.349
 OAN  NAI  CAB   single    1.430  0.020  1.430
 OAN  NAI  HAI   single    0.860  0.020  1.020
 OAN  CAB  CAC   single    1.525  0.020  1.525
 OAN  CAB  CAA   single    1.514  0.020  1.514
 OAN  CAB  HAB   single    0.970  0.020  1.090
 OAN  CAC  OAJ   single    1.398  0.020  1.398
 OAN  CAC  CAD   single    1.524  0.020  1.524
 OAN  CAC  HAC   single    0.970  0.020  1.090
 OAN  OAJ  HAJ   single    0.850  0.020  0.980
 OAN  CAD  OAK   single    1.406  0.020  1.406
 OAN  CAD  CAE   single    1.528  0.020  1.528
 OAN  CAD  HAD   single    0.970  0.020  1.090
 OAN  OAK  HAK   single    0.850  0.020  0.980
 OAN  CAE  CAF   single    1.511  0.020  1.511
 OAN  CAE  OAL   single    1.436  0.020  1.436
 OAN  CAE  HAE   single    0.970  0.020  1.090
 OAN  CAF  OAM   single    1.405  0.020  1.405
 OAN  CAF  HAF1  single    0.970  0.020  1.090
 OAN  CAF  HAF2  single    0.970  0.020  1.090
 OAN  OAM  HAM   single    0.850  0.020  0.980
 OAN  OAL  CAA   single    1.327  0.020  1.327
 OAN  CAA  NAY   double    1.270  0.020  1.270
 OAN  NAY  OAQ   single    1.380  0.020  1.380
 OAN  OAQ  CAP   single    1.353  0.020  1.353
 OAN  CAP  OAR   double    1.202  0.020  1.202
 OAN  CAP  NAO   single    1.355  0.020  1.355
 OAN  NAO  CAS   single    1.398  0.020  1.398
 OAN  NAO  HAO   single    0.860  0.020  1.020
 OAN  CAS  CAT   aromatic  1.395  0.020  1.395
 OAN  CAS  CAX   aromatic  1.397  0.020  1.397
 OAN  CAT  CAU   aromatic  1.389  0.020  1.389
 OAN  CAT  HAT   single    0.930  0.020  1.080
 OAN  CAU  CAV   aromatic  1.387  0.020  1.387
 OAN  CAU  HAU   single    0.930  0.020  1.080
 OAN  CAV  CAW   aromatic  1.389  0.020  1.389
 OAN  CAV  HAV   single    0.930  0.020  1.080
 OAN  CAW  CAX   aromatic  1.384  0.020  1.384
 OAN  CAW  HAW   single    0.930  0.020  1.080
 OAN  CAX  HAX   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
 OAN  HAH3  CAH  HAH2  108.12  3.000
 OAN  HAH3  CAH  HAH1  107.46  3.000
 OAN  HAH2  CAH  HAH1  108.87  3.000
 OAN  HAH3  CAH  CAG   108.93  3.000
 OAN  HAH2  CAH  CAG   113.50  3.000
 OAN  HAH1  CAH  CAG   109.77  3.000
 OAN  NAI   CAG  OAN   122.94  3.000
 OAN  NAI   CAG  CAH   114.91  3.000
 OAN  OAN   CAG  CAH   122.15  3.000
 OAN  HAI   NAI  CAB   117.42  3.000
 OAN  HAI   NAI  CAG   118.48  3.000
 OAN  CAB   NAI  CAG   123.36  3.000
 OAN  HAB   CAB  CAA   106.52  3.000
 OAN  HAB   CAB  CAC   107.61  3.000
 OAN  CAA   CAB  CAC   110.57  3.000
 OAN  HAB   CAB  NAI   107.88  3.000
 OAN  CAA   CAB  NAI   112.25  3.000
 OAN  CAC   CAB  NAI   111.73  3.000
 OAN  HAC   CAC  CAD   108.14  3.000
 OAN  HAC   CAC  OAJ   111.30  3.000
 OAN  CAD   CAC  OAJ   111.93  3.000
 OAN  HAC   CAC  CAB   108.97  3.000
 OAN  CAD   CAC  CAB   109.03  3.000
 OAN  OAJ   CAC  CAB   107.42  3.000
 OAN  HAJ   OAJ  CAC   107.96  3.000
 OAN  HAD   CAD  CAE   109.38  3.000
 OAN  HAD   CAD  OAK   111.34  3.000
 OAN  CAE   CAD  OAK   110.35  3.000
 OAN  HAD   CAD  CAC   108.59  3.000
 OAN  CAE   CAD  CAC   109.56  3.000
 OAN  OAK   CAD  CAC   107.58  3.000
 OAN  HAK   OAK  CAD   109.46  3.000
 OAN  HAE   CAE  OAL   108.21  3.000
 OAN  HAE   CAE  CAF   109.55  3.000
 OAN  OAL   CAE  CAF   106.64  3.000
 OAN  HAE   CAE  CAD   108.83  3.000
 OAN  OAL   CAE  CAD   111.11  3.000
 OAN  CAF   CAE  CAD   112.40  3.000
 OAN  HAF2  CAF  HAF1  107.14  3.000
 OAN  HAF2  CAF  OAM   112.20  3.000
 OAN  HAF1  CAF  OAM   111.69  3.000
 OAN  HAF2  CAF  CAE   108.87  3.000
 OAN  HAF1  CAF  CAE   107.78  3.000
 OAN  OAM   CAF  CAE   109.02  3.000
 OAN  HAM   OAM  CAF   107.98  3.000
 OAN  CAA   OAL  CAE   119.56  3.000
 OAN  NAY   CAA  OAL   122.87  3.000
 OAN  NAY   CAA  CAB   117.84  3.000
 OAN  OAL   CAA  CAB   119.02  3.000
 OAN  OAQ   NAY  CAA   110.92  3.000
 OAN  CAP   OAQ  NAY   112.87  3.000
 OAN  NAO   CAP  OAR   127.56  3.000
 OAN  NAO   CAP  OAQ   107.49  3.000
 OAN  OAR   CAP  OAQ   124.96  3.000
 OAN  HAO   NAO  CAS   115.45  3.000
 OAN  HAO   NAO  CAP   116.35  3.000
 OAN  CAS   NAO  CAP   128.15  3.000
 OAN  CAX   CAS  CAT   119.05  3.000
 OAN  CAX   CAS  NAO   116.44  3.000
 OAN  CAT   CAS  NAO   124.51  3.000
 OAN  HAT   CAT  CAU   119.24  3.000
 OAN  HAT   CAT  CAS   121.21  3.000
 OAN  CAU   CAT  CAS   119.55  3.000
 OAN  HAU   CAU  CAV   119.99  3.000
 OAN  HAU   CAU  CAT   118.59  3.000
 OAN  CAV   CAU  CAT   121.43  3.000
 OAN  HAV   CAV  CAW   120.56  3.000
 OAN  HAV   CAV  CAU   120.60  3.000
 OAN  CAW   CAV  CAU   118.85  3.000
 OAN  HAW   CAW  CAX   119.19  3.000
 OAN  HAW   CAW  CAV   120.38  3.000
 OAN  CAX   CAW  CAV   120.43  3.000
 OAN  HAX   CAX  CAW   119.58  3.000
 OAN  HAX   CAX  CAS   119.73  3.000
 OAN  CAW   CAX  CAS   120.69  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
 OAN  CONST_01  CAV   CAU  CAT  CAS    0.00   0.0  0
 OAN  CONST_02  CAV   CAW  CAX  CAS    0.00   0.0  0
 OAN  CONST_03  CAW   CAX  CAS  CAT    0.00   0.0  0
 OAN  CONST_04  CAW   CAV  CAU  CAT    0.00   0.0  0
 OAN  CONST_05  CAX   CAS  CAT  CAU    0.00   0.0  0
 OAN  CONST_06  CAX   CAW  CAV  CAU    0.00   0.0  0
 OAN  CONST_07  CAU   CAT  CAS  NAO  180.00   0.0  0
 OAN  CONST_08  CAW   CAX  CAS  NAO  180.00   0.0  0
 OAN  CONST_09  HAU   CAU  CAT  CAS  180.00   0.0  0
 OAN  CONST_10  HAW   CAW  CAX  CAS  180.00   0.0  0
 OAN  CONST_11  HAX   CAX  CAS  CAT  180.00   0.0  0
 OAN  CONST_12  HAV   CAV  CAU  CAT  180.00   0.0  0
 OAN  CONST_13  HAT   CAT  CAU  CAV  180.00   0.0  0
 OAN  CONST_14  CAT   CAS  NAO  CAP    0.00   0.0  0
 OAN  CONST_15  CAX   CAS  NAO  CAP  180.00   0.0  0
 OAN  CONST_16  HAO   NAO  CAS  CAT  180.00   0.0  0
 OAN  CONST_17  CAB   NAI  CAG  CAH  180.00   0.0  0
 OAN  CONST_18  CAB   NAI  CAG  OAN    0.00   0.0  0
 OAN  CONST_19  CAS   NAO  CAP  OAQ  180.00   0.0  0
 OAN  CONST_20  CAS   NAO  CAP  OAR    0.00   0.0  0
 OAN  CONST_21  HAI   NAI  CAG  CAH    0.00   0.0  0
 OAN  Var_01    NAY   CAA  OAL  CAE  146.75  30.0  1
 OAN  Var_02    OAR   CAP  OAQ  NAY    4.12  30.0  3
 OAN  Var_03    HAH1  CAH  CAG  OAN   44.38  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
 OAN  chir_01  CAB  NAI  CAC  CAA  positiv
 OAN  chir_02  CAC  OAJ  CAB  CAD  positiv
 OAN  chir_03  CAD  OAK  CAE  CAC  positiv
 OAN  chir_04  CAE  OAL  CAD  CAF  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
 OAN  plan-1  NAO  0.020
 OAN  plan-1  CAS  0.020
 OAN  plan-1  CAT  0.020
 OAN  plan-1  CAU  0.020
 OAN  plan-1  CAV  0.020
 OAN  plan-1  CAW  0.020
 OAN  plan-1  CAX  0.020
 OAN  plan-1  HAT  0.020
 OAN  plan-1  HAU  0.020
 OAN  plan-1  HAV  0.020
 OAN  plan-1  HAW  0.020
 OAN  plan-1  HAX  0.020
 OAN  plan-2  CAP  0.020
 OAN  plan-2  NAO  0.020
 OAN  plan-2  CAS  0.020
 OAN  plan-2  HAO  0.020
 OAN  plan-3  CAH  0.020
 OAN  plan-3  CAG  0.020
 OAN  plan-3  OAN  0.020
 OAN  plan-3  NAI  0.020
 OAN  plan-3  CAB  0.020
 OAN  plan-3  HAI  0.020
 OAN  plan-4  CAB  0.020
 OAN  plan-4  OAL  0.020
 OAN  plan-4  CAA  0.020
 OAN  plan-4  NAY  0.020
 OAN  plan-4  OAQ  0.020
 OAN  plan-5  OAQ  0.020
 OAN  plan-5  CAP  0.020
 OAN  plan-5  OAR  0.020
 OAN  plan-5  NAO  0.020

