# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 02:31:25 2020
#   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  48  25  .  2021-08-24  2021-08-24  
;
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  -0.669   2.5904  -1.5614  -1.7174
 UM0  C1    C  CH1    0   0.265   2.8008  -1.4771  -0.3440
 UM0  C2    C  CH1    0  -0.143   1.5881  -0.7857   0.2791
 UM0  N2    N  NH1    0  -0.631   0.3655  -1.4674  -0.0526
 UM0  CBC   C  C      0   0.524  -0.3970  -2.1390   0.8350
 UM0  CBE   C  CH3    0  -0.793  -1.5925  -2.8325   0.2322
 UM0  OBD   O  O      0  -0.499  -0.1305  -2.2162   2.0251
 UM0  O5    O  O2     0  -0.500   3.9705  -0.7828  -0.0150
 UM0  C5    C  CH1    0  -0.014   4.0188   0.5699  -0.4371
 UM0  C6    C  CH2    0  -0.163   5.3566   1.1254   0.0014
 UM0  O6    O  OH1    0  -0.670   6.3835   0.4500  -0.6841
 UM0  C4    C  CH1    0   0.006   2.8564   1.3731   0.1632
 UM0  O4    O  OH1    0  -0.664   2.8129   2.6661  -0.3918
 UM0  C3    C  CH1    0   0.039   1.5312   0.6850  -0.1374
 UM0  O3    O  O2     0  -0.497   0.5071   1.3453   0.5589
 UM0  CBN   C  CH1    0  -0.071  -0.6683   1.6501  -0.1557
 UM0  CBQ   C  CH3    0  -0.667  -0.8696   3.1579  -0.1947
 UM0  CBO   C  C      0   0.545  -1.8536   0.9911   0.5466
 UM0  OBP   O  O      0  -0.511  -1.9605   1.0189   1.7656
 UM0  N     N  NH1    0  -0.636  -2.7598   0.4562  -0.2734
 UM0  CBA   C  CH1    0  -0.208  -4.0013  -0.1498   0.1506
 UM0  CBB   C  CH3    0  -0.649  -5.0298   0.8981   0.5726
 UM0  C     C  C      0   0.425  -4.5545  -1.0317  -0.9948
 UM0  O     O  O      0  -0.599  -3.9318  -1.0217  -2.0762
 UM0  OXT   O  OC    -1  -0.602  -5.5875  -1.6696  -0.7296
 UM0  HO1   H  HOH1   0   0.466   3.1994  -2.2057  -2.0938
 UM0  H1    H  HCH1   0   0.241   2.9264  -2.4711   0.0997
 UM0  H2    H  HCH1   0   0.275   1.7062  -0.8345   1.3631
 UM0  HN2   H  HNH1   0   0.397   0.1014  -1.5027  -1.0247
 UM0  HBE   H  HCH3   0   0.273  -1.3351  -3.8730   0.0253
 UM0  HBEA  H  HCH3   0   0.258  -2.4178  -2.8317   0.9407
 UM0  HBEB  H  HCH3   0   0.249  -1.9275  -2.3750  -0.6966
 UM0  H5    H  HCH1   0   0.223   3.9515   0.6376  -1.5319
 UM0  H6    H  HCH2   0   0.203   5.3723   2.2003  -0.2123
 UM0  H6A   H  HCH2   0   0.197   5.4481   1.0129   1.0911
 UM0  HO6   H  HOH1   0   0.456   7.2210   0.8485  -0.4317
 UM0  H4    H  HCH1   0   0.226   2.9828   1.4122   1.2552
 UM0  HO4   H  HOH1   0   0.460   3.2528   3.2789   0.2024
 UM0  H3    H  HCH1   0   0.229   1.3597   0.7469  -1.2220
 UM0  HBN   H  HCH1   0   0.233  -0.5946   1.2789  -1.1853
 UM0  HBQ   H  HCH3   0   0.243  -0.0280   3.6347  -0.6964
 UM0  HBQA  H  HCH3   0   0.228  -1.7813   3.4126  -0.7360
 UM0  HBQB  H  HCH3   0   0.232  -0.9480   3.5649   0.8139
 UM0  HN    H  HNH1   0   0.384  -2.5689   0.3678  -1.2618
 UM0  HBA   H  HCH1   0   0.238  -3.8042  -0.8040   1.0067
 UM0  HBB   H  HCH3   0   0.217  -5.2708   1.5631  -0.2586
 UM0  HBBA  H  HCH3   0   0.227  -5.9480   0.4161   0.9034
 UM0  HBBB  H  HCH3   0   0.228  -4.6520   1.5052   1.3946

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  1.392  0.020  1.392
 UM0  C1   C2    single  1.529  0.020  1.529
 UM0  C1   O5    single  1.399  0.020  1.399
 UM0  C2   N2    single  1.439  0.020  1.439
 UM0  C2   C3    single  1.530  0.020  1.530
 UM0  N2   CBC   single  1.349  0.020  1.349
 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  1.514  0.020  1.514
 UM0  C5   C4    single  1.535  0.020  1.535
 UM0  C6   O6    single  1.407  0.020  1.407
 UM0  C4   O4    single  1.408  0.020  1.408
 UM0  C4   C3    single  1.523  0.020  1.523
 UM0  C3   O3    single  1.403  0.020  1.403
 UM0  O3   CBN   single  1.409  0.020  1.409
 UM0  CBN  CBQ   single  1.522  0.020  1.522
 UM0  CBN  CBO   single  1.527  0.020  1.527
 UM0  CBO  OBP   double  1.224  0.020  1.224
 UM0  CBO  N     single  1.334  0.020  1.334
 UM0  N    CBA   single  1.445  0.020  1.445
 UM0  CBA  CBB   single  1.528  0.020  1.528
 UM0  CBA  C     single  1.548  0.020  1.548
 UM0  C    O     deloc   1.248  0.020  1.248
 UM0  C    OXT   deloc   1.243  0.020  1.243
 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

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    109.30  3.000
 UM0  H1    C1   O5    105.02  3.000
 UM0  H1    C1   C2    109.64  3.000
 UM0  O5    C1   C2    110.05  3.000
 UM0  H1    C1   O1    111.22  3.000
 UM0  O5    C1   O1    112.85  3.000
 UM0  C2    C1   O1    108.03  3.000
 UM0  H2    C2   C3    108.50  3.000
 UM0  H2    C2   N2    107.45  3.000
 UM0  C3    C2   N2    111.17  3.000
 UM0  H2    C2   C1    107.38  3.000
 UM0  C3    C2   C1    110.70  3.000
 UM0  N2    C2   C1    111.46  3.000
 UM0  HN2   N2   CBC   117.96  3.000
 UM0  HN2   N2   C2    117.49  3.000
 UM0  CBC   N2   C2    124.37  3.000
 UM0  OBD   CBC  CBE   122.22  3.000
 UM0  OBD   CBC  N2    123.29  3.000
 UM0  CBE   CBC  N2    114.46  3.000
 UM0  HBEB  CBE  HBEA  108.79  3.000
 UM0  HBEB  CBE  HBE   108.15  3.000
 UM0  HBEA  CBE  HBE   107.64  3.000
 UM0  HBEB  CBE  CBC   113.07  3.000
 UM0  HBEA  CBE  CBC   109.93  3.000
 UM0  HBE   CBE  CBC   109.10  3.000
 UM0  C5    O5   C1    115.58  3.000
 UM0  H5    C5   C4    108.12  3.000
 UM0  H5    C5   C6    108.67  3.000
 UM0  C4    C5   C6    111.35  3.000
 UM0  H5    C5   O5    110.69  3.000
 UM0  C4    C5   O5    110.91  3.000
 UM0  C6    C5   O5    107.10  3.000
 UM0  H6A   C6   H6    107.01  3.000
 UM0  H6A   C6   O6    111.90  3.000
 UM0  H6    C6   O6    111.42  3.000
 UM0  H6A   C6   C5    108.85  3.000
 UM0  H6    C6   C5    108.43  3.000
 UM0  O6    C6   C5    109.13  3.000
 UM0  HO6   O6   C6    107.99  3.000
 UM0  H4    C4   C3    108.18  3.000
 UM0  H4    C4   O4    111.24  3.000
 UM0  C3    C4   O4    108.08  3.000
 UM0  H4    C4   C5    108.65  3.000
 UM0  C3    C4   C5    110.20  3.000
 UM0  O4    C4   C5    110.47  3.000
 UM0  HO4   O4   C4    109.15  3.000
 UM0  H3    C3   O3    110.43  3.000
 UM0  H3    C3   C4    107.75  3.000
 UM0  O3    C3   C4    108.93  3.000
 UM0  H3    C3   C2    109.17  3.000
 UM0  O3    C3   C2    110.15  3.000
 UM0  C4    C3   C2    110.38  3.000
 UM0  CBN   O3   C3    117.32  3.000
 UM0  HBN   CBN  CBO   109.74  3.000
 UM0  HBN   CBN  CBQ   108.67  3.000
 UM0  CBO   CBN  CBQ   109.68  3.000
 UM0  HBN   CBN  O3    110.29  3.000
 UM0  CBO   CBN  O3    108.72  3.000
 UM0  CBQ   CBN  O3    109.74  3.000
 UM0  HBQB  CBQ  HBQA  108.17  3.000
 UM0  HBQB  CBQ  HBQ   108.55  3.000
 UM0  HBQA  CBQ  HBQ   108.36  3.000
 UM0  HBQB  CBQ  CBN   110.83  3.000
 UM0  HBQA  CBQ  CBN   110.78  3.000
 UM0  HBQ   CBQ  CBN   110.07  3.000
 UM0  N     CBO  OBP   124.19  3.000
 UM0  N     CBO  CBN   114.68  3.000
 UM0  OBP   CBO  CBN   121.06  3.000
 UM0  HN    N    CBA   114.37  3.000
 UM0  HN    N    CBO   120.52  3.000
 UM0  CBA   N    CBO   124.85  3.000
 UM0  HBA   CBA  C     107.60  3.000
 UM0  HBA   CBA  CBB   108.35  3.000
 UM0  C     CBA  CBB   110.77  3.000
 UM0  HBA   CBA  N     108.97  3.000
 UM0  C     CBA  N     109.20  3.000
 UM0  CBB   CBA  N     111.82  3.000
 UM0  HBBB  CBB  HBBA  108.05  3.000
 UM0  HBBB  CBB  HBB   108.16  3.000
 UM0  HBBA  CBB  HBB   108.35  3.000
 UM0  HBBB  CBB  CBA   110.93  3.000
 UM0  HBBA  CBB  CBA   110.38  3.000
 UM0  HBB   CBB  CBA   110.87  3.000
 UM0  OXT   C    O     127.14  3.000
 UM0  OXT   C    CBA   115.57  3.000
 UM0  O     C    CBA   117.28  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  Var_01    HBE  CBE  CBC  N2    95.40  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

