# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 00:57:16 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: (2S)-2-{[(2R)-2-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-2,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoyl]amino}propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@@H](C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O)[C@@H]1NC(C)=O)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
 UM0  UM0  '(2S)-2-{[(2R)-2-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-2,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoyl]amino}propanoic acid (non-preferred name)'  ligand  49  25  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UM0
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
 UM0  O1    O  OH1   0  -0.667  13.2622  -1.0331  15.1630
 UM0  C1    C  CH1   0   0.268  14.3394  -1.5841  15.8497
 UM0  C2    C  CH1   0  -0.153  14.6861  -0.6414  17.0088
 UM0  N2    N  NH1   0  -0.633  13.5408  -0.3995  17.8475
 UM0  CBC   C  C     0   0.524  13.3312  -1.0251  19.0273
 UM0  CBE   C  CH3   0  -0.786  12.0184  -0.6916  19.6898
 UM0  OBD   O  O     0  -0.489  14.1303  -1.8090  19.5164
 UM0  O5    O  O2    0  -0.501  15.4563  -1.7891  15.0326
 UM0  C5    C  CH1   0  -0.005  16.0056  -0.6193  14.4488
 UM0  C6    C  CH2   0  -0.184  17.1146  -1.0457  13.5119
 UM0  O6    O  OH1   0  -0.672  18.1527  -1.6551  14.2402
 UM0  C4    C  CH1   0   0.033  16.4591   0.3391  15.5494
 UM0  O4    O  OH1   0  -0.671  16.9564   1.4996  14.9344
 UM0  C3    C  CH1   0   0.010  15.2809   0.6580  16.4664
 UM0  O3    O  O2    0  -0.514  15.7763   1.4920  17.4929
 UM0  CBN   C  CH1   0  -0.066  14.8895   2.4364  18.0523
 UM0  CBQ   C  CH3   0  -0.669  15.5333   3.8161  18.0058
 UM0  CBO   C  C     0   0.537  14.5450   2.0908  19.4947
 UM0  OBP   O  O     0  -0.499  13.6053   2.6304  20.0641
 UM0  N     N  NH1   0  -0.631  15.3641   1.2305  20.1082
 UM0  CBA   C  CH1   0  -0.170  15.1801   0.8768  21.4902
 UM0  CBB   C  CH3   0  -0.701  16.2260  -0.1538  21.9029
 UM0  C     C  C     0   0.541  15.2731   2.0839  22.4087
 UM0  O     O  O     0  -0.445  14.6582   2.1746  23.4416
 UM0  OXT   O  OH1   0  -0.583  16.1516   2.9805  21.9911
 UM0  HO1   H  HOH1  0   0.467  12.8786  -1.6999  14.5833
 UM0  H1    H  HCH1  0   0.242  14.0935  -2.5745  16.2487
 UM0  H2    H  HCH1  0   0.280  15.4401  -1.1414  17.6204
 UM0  HN2   H  HNH1  0   0.400  12.7750   0.1211  17.4485
 UM0  HBE   H  HCH3  0   0.262  12.0972  -0.8307  20.7655
 UM0  HBEA  H  HCH3  0   0.254  11.6916   0.3272  19.4877
 UM0  HBEB  H  HCH3  0   0.276  11.2454  -1.3694  19.3220
 UM0  H5    H  HCH1  0   0.232  15.2563  -0.1072  13.8288
 UM0  H6    H  HCH2  0   0.214  16.6858  -1.7270  12.7647
 UM0  H6A   H  HCH2  0   0.211  17.4575  -0.1585  12.9683
 UM0  HO6   H  HOH1  0   0.458  18.8720  -1.8438  13.6316
 UM0  H4    H  HCH1  0   0.219  17.2355  -0.1541  16.1524
 UM0  HO4   H  HOH1  0   0.452  17.2649   2.0940  15.6262
 UM0  H3    H  HCH1  0   0.238  14.5251   1.2029  15.8825
 UM0  HBN   H  HCH1  0   0.253  13.9492   2.4652  17.4916
 UM0  HBQ   H  HCH3  0   0.243  14.8657   4.5660  18.4268
 UM0  HBQA  H  HCH3  0   0.237  16.4662   3.8320  18.5705
 UM0  HBQB  H  HCH3  0   0.247  15.7458   4.0935  16.9733
 UM0  HN    H  HNH1  0   0.407  16.1169   0.8106  19.5865
 UM0  HBA   H  HCH1  0   0.282  14.1859   0.4501  21.6434
 UM0  HBB   H  HCH3  0   0.258  16.0781  -0.4587  22.9371
 UM0  HBBA  H  HCH3  0   0.263  16.1312  -1.0383  21.2744
 UM0  HBBB  H  HCH3  0   0.246  17.2371   0.2410  21.7992
 UM0  HOXT  H  HOH1  0   0.483  16.2089   3.7093  22.6269

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
 UM0  O1   C1    single  1.391  0.020  1.391
 UM0  C1   C2    single  1.534  0.020  1.534
 UM0  C1   O5    single  1.399  0.020  1.399
 UM0  C2   N2    single  1.440  0.020  1.440
 UM0  C2   C3    single  1.528  0.020  1.528
 UM0  N2   CBC   single  1.352  0.020  1.352
 UM0  CBC  CBE   single  1.508  0.020  1.508
 UM0  CBC  OBD   double  1.222  0.020  1.222
 UM0  O5   C5    single  1.418  0.020  1.418
 UM0  C5   C6    single  1.513  0.020  1.513
 UM0  C5   C4    single  1.528  0.020  1.528
 UM0  C6   O6    single  1.407  0.020  1.407
 UM0  C4   O4    single  1.404  0.020  1.404
 UM0  C4   C3    single  1.527  0.020  1.527
 UM0  C3   O3    single  1.412  0.020  1.412
 UM0  O3   CBN   single  1.411  0.020  1.411
 UM0  CBN  CBQ   single  1.523  0.020  1.523
 UM0  CBN  CBO   single  1.523  0.020  1.523
 UM0  CBO  OBP   double  1.224  0.020  1.224
 UM0  CBO  N     single  1.337  0.020  1.337
 UM0  N    CBA   single  1.438  0.020  1.438
 UM0  CBA  CBB   single  1.525  0.020  1.525
 UM0  CBA  C     single  1.520  0.020  1.520
 UM0  C    O     double  1.206  0.020  1.206
 UM0  C    OXT   single  1.323  0.020  1.323
 UM0  O1   HO1   single  0.850  0.020  0.980
 UM0  C1   H1    single  0.970  0.020  1.090
 UM0  C2   H2    single  0.970  0.020  1.090
 UM0  N2   HN2   single  0.860  0.020  1.020
 UM0  CBE  HBE   single  0.970  0.020  1.090
 UM0  CBE  HBEA  single  0.970  0.020  1.090
 UM0  CBE  HBEB  single  0.970  0.020  1.090
 UM0  C5   H5    single  0.970  0.020  1.090
 UM0  C6   H6    single  0.970  0.020  1.090
 UM0  C6   H6A   single  0.970  0.020  1.090
 UM0  O6   HO6   single  0.850  0.020  0.980
 UM0  C4   H4    single  0.970  0.020  1.090
 UM0  O4   HO4   single  0.850  0.020  0.980
 UM0  C3   H3    single  0.970  0.020  1.090
 UM0  CBN  HBN   single  0.970  0.020  1.090
 UM0  CBQ  HBQ   single  0.970  0.020  1.090
 UM0  CBQ  HBQA  single  0.970  0.020  1.090
 UM0  CBQ  HBQB  single  0.970  0.020  1.090
 UM0  N    HN    single  0.860  0.020  1.020
 UM0  CBA  HBA   single  0.970  0.020  1.090
 UM0  CBB  HBB   single  0.970  0.020  1.090
 UM0  CBB  HBBA  single  0.970  0.020  1.090
 UM0  CBB  HBBB  single  0.970  0.020  1.090
 UM0  OXT  HOXT  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
 UM0  HO1   O1   C1    109.35  3.000
 UM0  H1    C1   O5    105.03  3.000
 UM0  H1    C1   C2    109.34  3.000
 UM0  O5    C1   C2    110.55  3.000
 UM0  H1    C1   O1    111.34  3.000
 UM0  O5    C1   O1    112.82  3.000
 UM0  C2    C1   O1    107.74  3.000
 UM0  H2    C2   C3    108.62  3.000
 UM0  H2    C2   N2    107.45  3.000
 UM0  C3    C2   N2    111.92  3.000
 UM0  H2    C2   C1    107.34  3.000
 UM0  C3    C2   C1    110.02  3.000
 UM0  N2    C2   C1    111.32  3.000
 UM0  HN2   N2   CBC   117.81  3.000
 UM0  HN2   N2   C2    117.41  3.000
 UM0  CBC   N2   C2    123.63  3.000
 UM0  OBD   CBC  CBE   122.39  3.000
 UM0  OBD   CBC  N2    123.02  3.000
 UM0  CBE   CBC  N2    114.59  3.000
 UM0  HBEB  CBE  HBEA  107.81  3.000
 UM0  HBEB  CBE  HBE   107.77  3.000
 UM0  HBEA  CBE  HBE   108.96  3.000
 UM0  HBEB  CBE  CBC   109.34  3.000
 UM0  HBEA  CBE  CBC   112.75  3.000
 UM0  HBE   CBE  CBC   110.07  3.000
 UM0  C5    O5   C1    115.39  3.000
 UM0  H5    C5   C4    108.44  3.000
 UM0  H5    C5   C6    106.36  3.000
 UM0  C4    C5   C6    113.90  3.000
 UM0  H5    C5   O5    110.64  3.000
 UM0  C4    C5   O5    109.62  3.000
 UM0  C6    C5   O5    107.84  3.000
 UM0  H6A   C6   H6    106.68  3.000
 UM0  H6A   C6   O6    112.13  3.000
 UM0  H6    C6   O6    111.81  3.000
 UM0  H6A   C6   C5    107.96  3.000
 UM0  H6    C6   C5    108.05  3.000
 UM0  O6    C6   C5    110.02  3.000
 UM0  HO6   O6   C6    108.03  3.000
 UM0  H4    C4   C3    108.00  3.000
 UM0  H4    C4   O4    111.14  3.000
 UM0  C3    C4   O4    111.33  3.000
 UM0  H4    C4   C5    108.85  3.000
 UM0  C3    C4   C5    109.55  3.000
 UM0  O4    C4   C5    107.94  3.000
 UM0  HO4   O4   C4    108.00  3.000
 UM0  H3    C3   O3    109.54  3.000
 UM0  H3    C3   C4    108.36  3.000
 UM0  O3    C3   C4    106.81  3.000
 UM0  H3    C3   C2    110.01  3.000
 UM0  O3    C3   C2    112.37  3.000
 UM0  C4    C3   C2    109.63  3.000
 UM0  CBN   O3   C3    117.58  3.000
 UM0  HBN   CBN  CBO   107.26  3.000
 UM0  HBN   CBN  CBQ   108.87  3.000
 UM0  CBO   CBN  CBQ   109.28  3.000
 UM0  HBN   CBN  O3    110.74  3.000
 UM0  CBO   CBN  O3    111.45  3.000
 UM0  CBQ   CBN  O3    109.18  3.000
 UM0  HBQB  CBQ  HBQA  108.66  3.000
 UM0  HBQB  CBQ  HBQ   108.10  3.000
 UM0  HBQA  CBQ  HBQ   108.31  3.000
 UM0  HBQB  CBQ  CBN   109.99  3.000
 UM0  HBQA  CBQ  CBN   111.03  3.000
 UM0  HBQ   CBQ  CBN   110.67  3.000
 UM0  N     CBO  OBP   122.72  3.000
 UM0  N     CBO  CBN   116.24  3.000
 UM0  OBP   CBO  CBN   120.95  3.000
 UM0  HN    N    CBA   119.38  3.000
 UM0  HN    N    CBO   119.23  3.000
 UM0  CBA   N    CBO   121.38  3.000
 UM0  HBA   CBA  C     106.33  3.000
 UM0  HBA   CBA  CBB   108.79  3.000
 UM0  C     CBA  CBB   109.34  3.000
 UM0  HBA   CBA  N     110.31  3.000
 UM0  C     CBA  N     112.19  3.000
 UM0  CBB   CBA  N     109.78  3.000
 UM0  HBBB  CBB  HBBA  108.66  3.000
 UM0  HBBB  CBB  HBB   108.53  3.000
 UM0  HBBA  CBB  HBB   107.99  3.000
 UM0  HBBB  CBB  CBA   111.44  3.000
 UM0  HBBA  CBB  CBA   109.45  3.000
 UM0  HBB   CBB  CBA   110.69  3.000
 UM0  OXT   C    O     123.94  3.000
 UM0  OXT   C    CBA   112.84  3.000
 UM0  O     C    CBA   123.12  3.000
 UM0  HOXT  OXT  C     109.99  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
 UM0  CONST_01  CBE   CBC  N2   C2    180.00   0.0  0
 UM0  CONST_02  OBD   CBC  N2   C2      0.00   0.0  0
 UM0  CONST_03  CBA   N    CBO  CBN   180.00   0.0  0
 UM0  CONST_04  CBA   N    CBO  OBP     0.00   0.0  0
 UM0  CONST_05  HN2   N2   CBC  CBE     0.00   0.0  0
 UM0  CONST_06  HN    N    CBO  CBN     0.00   0.0  0
 UM0  CONST_07  HOXT  OXT  C    CBA   180.00   0.0  0
 UM0  Var_01    HBE   CBE  CBC  N2   -154.12  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
 UM0  chir_01  C1   O1  C2   O5   positiv
 UM0  chir_02  C2   N2  C3   C1   positiv
 UM0  chir_03  C5   O5  C4   C6   negativ
 UM0  chir_04  C4   O4  C5   C3   positiv
 UM0  chir_05  C3   O3  C2   C4   positiv
 UM0  chir_06  CBN  O3  CBQ  CBO  positiv
 UM0  chir_07  CBA  N   CBB  C    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
 UM0  plan-1  C2    0.020
 UM0  plan-1  N2    0.020
 UM0  plan-1  CBC   0.020
 UM0  plan-1  CBE   0.020
 UM0  plan-1  OBD   0.020
 UM0  plan-1  HN2   0.020
 UM0  plan-2  CBN   0.020
 UM0  plan-2  CBO   0.020
 UM0  plan-2  OBP   0.020
 UM0  plan-2  N     0.020
 UM0  plan-2  CBA   0.020
 UM0  plan-2  HN    0.020
 UM0  plan-3  CBA   0.020
 UM0  plan-3  C     0.020
 UM0  plan-3  O     0.020
 UM0  plan-3  OXT   0.020
 UM0  plan-3  HOXT  0.020

