# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 04:31:27 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-alpha-L-galactopyranosyl]-1,5-anhydro-2-deoxy-D-mannitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1CO[C@H](CO)[C@@H](O[C@@H]2O[C@@H](CO)[C@@H](O)[C@@H](O)[C@@H]2NC(C)=O)[C@@H]1O
#
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
 AS5  AS5  2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-alpha-L-galactopyranosyl]-1,5-anhydro-2-deoxy-D-mannitol  ligand  56  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AS5
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
 AS5  O7B   O  O     0  -0.495   4.3121   1.9582  -1.3533
 AS5  C7B   C  C     0   0.502   3.6428   2.2009  -0.3597
 AS5  C8B   C  CH3   0  -0.786   3.5578   3.5810   0.2460
 AS5  N2B   N  NH1   0  -0.620   2.8814   1.2814   0.2655
 AS5  C2B   C  CH1   0  -0.153   2.7181  -0.0820  -0.1646
 AS5  C3B   C  CH1   0   0.058   3.0860  -1.0727   0.9370
 AS5  O3B   O  OH1   0  -0.662   4.4212  -0.8448   1.2958
 AS5  C4B   C  CH1   0  -0.047   2.8369  -2.4964   0.4389
 AS5  C5B   C  CH1   0   0.006   1.3792  -2.6241  -0.0072
 AS5  C6B   C  CH2   0  -0.176   1.1049  -3.9885  -0.6028
 AS5  O6B   O  OH1   0  -0.661  -0.2749  -4.1428  -0.8277
 AS5  O5B   O  O2    0  -0.493   1.0613  -1.6495  -0.9898
 AS5  C1B   C  CH1   0   0.285   1.2742  -0.3260  -0.6279
 AS5  O4A   O  O2    0  -0.515   0.4447   0.0984   0.4149
 AS5  C4A   C  CH1   0   0.016  -0.8891   0.4585   0.1148
 AS5  C3A   C  CH1   0   0.001  -1.7985  -0.2535   1.1152
 AS5  O3A   O  OH1   0  -0.638  -1.7463  -1.6255   0.8412
 AS5  C2A   C  CH1   0  -0.140  -3.2286   0.2968   1.0804
 AS5  N2A   N  NH1   0  -0.629  -3.8960  -0.1113  -0.1375
 AS5  C7A   C  C     0   0.528  -5.2300  -0.0615  -0.2912
 AS5  O7A   O  O     0  -0.508  -5.9779   0.3916   0.5660
 AS5  C8A   C  CH3   0  -0.777  -5.7503  -0.5882  -1.6053
 AS5  C5A   C  CH1   0   0.010  -1.0374   1.9861   0.2494
 AS5  C6A   C  CH2   0  -0.167  -0.3131   2.7256  -0.8563
 AS5  O6A   O  OH1   0  -0.669  -0.3334   4.1040  -0.5717
 AS5  O5A   O  O2    0  -0.480  -2.3895   2.3729   0.1937
 AS5  C1A   C  CH2   0  -0.192  -3.1651   1.8112   1.2210
 AS5  O4B   O  OH1   0  -0.675   3.7444  -2.7660  -0.6051
 AS5  H8B1  H  HCH3  0   0.263   4.4034   4.1872  -0.0687
 AS5  H8B2  H  HCH3  0   0.264   2.6427   4.0715  -0.0939
 AS5  H8B3  H  HCH3  0   0.258   3.5260   3.5520   1.3348
 AS5  H2B   H  HNH1  0   0.396   2.3674   1.5705   1.0831
 AS5  HA    H  HCH1  0   0.279   3.3764  -0.2365  -1.0208
 AS5  H1B   H  HCH1  0   0.240   1.0798   0.2523  -1.5397
 AS5  H3B   H  HOH1  0   0.452   4.6323  -1.4047   2.0497
 AS5  H4B   H  HCH1  0   0.244   2.9868  -3.1895   1.2789
 AS5  H5B   H  HCH1  0   0.233   0.7377  -2.4975   0.8727
 AS5  HB    H  HOH1  0   0.458   3.9368  -3.7070  -0.6172
 AS5  H6B1  H  HCH2  0   0.197   1.6787  -4.1040  -1.5310
 AS5  H6B2  H  HCH2  0   0.199   1.4844  -4.7393   0.1049
 AS5  H6B   H  HOH1  0   0.452  -0.4021  -4.9828  -1.2774
 AS5  H4A   H  HCH1  0   0.237  -1.1520   0.1528  -0.9080
 AS5  H3A   H  HCH1  0   0.235  -1.4112  -0.0275   2.1202
 AS5  H5A   H  HCH1  0   0.216  -0.6002   2.2759   1.2204
 AS5  HC    H  HOH1  0   0.454  -2.1864  -2.1001   1.5538
 AS5  H2A   H  HCH1  0   0.267  -3.7726  -0.1047   1.9428
 AS5  HD    H  HNH1  0   0.400  -3.3600  -0.5915  -0.8416
 AS5  H1A1  H  HCH2  0   0.255  -4.1609   2.2479   1.1571
 AS5  H1A2  H  HCH2  0   0.216  -2.7555   2.0598   2.2107
 AS5  H8A1  H  HCH3  0   0.264  -6.5312  -1.3245  -1.4190
 AS5  H8A2  H  HCH3  0   0.267  -6.2019   0.2293  -2.1676
 AS5  H8A3  H  HCH3  0   0.249  -4.9819  -1.0461  -2.2251
 AS5  H6A1  H  HCH2  0   0.201   0.7136   2.3539  -0.9198
 AS5  H6A2  H  HCH2  0   0.208  -0.8009   2.4951  -1.8133
 AS5  H6A   H  HOH1  0   0.458   0.0654   4.5673  -1.3135
 AS5  H3B1  H  HCH1  0   0.218   2.4168  -0.9108   1.7948

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
 AS5  O7B  C7B   double  1.222  0.020  1.222
 AS5  C7B  C8B   single  1.510  0.020  1.510
 AS5  C7B  N2B   single  1.348  0.020  1.348
 AS5  N2B  C2B   single  1.439  0.020  1.439
 AS5  C2B  C3B   single  1.527  0.020  1.527
 AS5  C2B  C1B   single  1.536  0.020  1.536
 AS5  C3B  O3B   single  1.401  0.020  1.401
 AS5  C3B  C4B   single  1.529  0.020  1.529
 AS5  C4B  C5B   single  1.530  0.020  1.530
 AS5  C4B  O4B   single  1.409  0.020  1.409
 AS5  C5B  C6B   single  1.514  0.020  1.514
 AS5  C5B  O5B   single  1.420  0.020  1.420
 AS5  C6B  O6B   single  1.407  0.020  1.407
 AS5  O5B  C1B   single  1.388  0.020  1.388
 AS5  C1B  O4A   single  1.398  0.020  1.398
 AS5  O4A  C4A   single  1.414  0.020  1.414
 AS5  C4A  C3A   single  1.528  0.020  1.528
 AS5  C4A  C5A   single  1.541  0.020  1.541
 AS5  C3A  O3A   single  1.400  0.020  1.400
 AS5  C3A  C2A   single  1.533  0.020  1.533
 AS5  C2A  N2A   single  1.448  0.020  1.448
 AS5  C2A  C1A   single  1.522  0.020  1.522
 AS5  N2A  C7A   single  1.344  0.020  1.344
 AS5  C7A  O7A   double  1.225  0.020  1.225
 AS5  C7A  C8A   single  1.508  0.020  1.508
 AS5  C5A  C6A   single  1.515  0.020  1.515
 AS5  C5A  O5A   single  1.407  0.020  1.407
 AS5  C6A  O6A   single  1.408  0.020  1.408
 AS5  O5A  C1A   single  1.404  0.020  1.404
 AS5  C8B  H8B1  single  0.970  0.020  1.090
 AS5  C8B  H8B2  single  0.970  0.020  1.090
 AS5  C8B  H8B3  single  0.970  0.020  1.090
 AS5  N2B  H2B   single  0.860  0.020  1.020
 AS5  C2B  HA    single  0.970  0.020  1.090
 AS5  C1B  H1B   single  0.970  0.020  1.090
 AS5  O3B  H3B   single  0.850  0.020  0.980
 AS5  C4B  H4B   single  0.970  0.020  1.090
 AS5  C5B  H5B   single  0.970  0.020  1.090
 AS5  O4B  HB    single  0.850  0.020  0.980
 AS5  C6B  H6B1  single  0.970  0.020  1.090
 AS5  C6B  H6B2  single  0.970  0.020  1.090
 AS5  O6B  H6B   single  0.850  0.020  0.980
 AS5  C4A  H4A   single  0.970  0.020  1.090
 AS5  C3A  H3A   single  0.970  0.020  1.090
 AS5  C5A  H5A   single  0.970  0.020  1.090
 AS5  O3A  HC    single  0.850  0.020  0.980
 AS5  C2A  H2A   single  0.970  0.020  1.090
 AS5  N2A  HD    single  0.860  0.020  1.020
 AS5  C1A  H1A1  single  0.970  0.020  1.090
 AS5  C1A  H1A2  single  0.970  0.020  1.090
 AS5  C8A  H8A1  single  0.970  0.020  1.090
 AS5  C8A  H8A2  single  0.970  0.020  1.090
 AS5  C8A  H8A3  single  0.970  0.020  1.090
 AS5  C6A  H6A1  single  0.970  0.020  1.090
 AS5  C6A  H6A2  single  0.970  0.020  1.090
 AS5  O6A  H6A   single  0.850  0.020  0.980
 AS5  C3B  H3B1  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
 AS5  N2B   C7B  C8B   113.95  3.000
 AS5  N2B   C7B  O7B   123.43  3.000
 AS5  C8B   C7B  O7B   122.58  3.000
 AS5  H8B3  C8B  H8B2  107.36  3.000
 AS5  H8B3  C8B  H8B1  109.08  3.000
 AS5  H8B2  C8B  H8B1  108.13  3.000
 AS5  H8B3  C8B  C7B   112.22  3.000
 AS5  H8B2  C8B  C7B   109.44  3.000
 AS5  H8B1  C8B  C7B   110.48  3.000
 AS5  H2B   N2B  C2B   117.15  3.000
 AS5  H2B   N2B  C7B   117.95  3.000
 AS5  C2B   N2B  C7B   124.89  3.000
 AS5  HA    C2B  C1B   107.94  3.000
 AS5  HA    C2B  C3B   109.20  3.000
 AS5  C1B   C2B  C3B   109.95  3.000
 AS5  HA    C2B  N2B   107.48  3.000
 AS5  C1B   C2B  N2B   110.33  3.000
 AS5  C3B   C2B  N2B   111.83  3.000
 AS5  H3B1  C3B  C4B   106.98  3.000
 AS5  H3B1  C3B  O3B   110.86  3.000
 AS5  C4B   C3B  O3B   112.96  3.000
 AS5  H3B1  C3B  C2B   108.70  3.000
 AS5  C4B   C3B  C2B   109.27  3.000
 AS5  O3B   C3B  C2B   107.99  3.000
 AS5  H3B   O3B  C3B   108.36  3.000
 AS5  H4B   C4B  O4B   110.96  3.000
 AS5  H4B   C4B  C5B   107.47  3.000
 AS5  O4B   C4B  C5B   112.43  3.000
 AS5  H4B   C4B  C3B   108.42  3.000
 AS5  O4B   C4B  C3B   108.33  3.000
 AS5  C5B   C4B  C3B   109.15  3.000
 AS5  H5B   C5B  O5B   110.19  3.000
 AS5  H5B   C5B  C6B   108.29  3.000
 AS5  O5B   C5B  C6B   107.81  3.000
 AS5  H5B   C5B  C4B   108.29  3.000
 AS5  O5B   C5B  C4B   110.97  3.000
 AS5  C6B   C5B  C4B   111.26  3.000
 AS5  H6B2  C6B  H6B1  106.99  3.000
 AS5  H6B2  C6B  O6B   111.51  3.000
 AS5  H6B1  C6B  O6B   111.48  3.000
 AS5  H6B2  C6B  C5B   107.45  3.000
 AS5  H6B1  C6B  C5B   109.45  3.000
 AS5  O6B   C6B  C5B   109.85  3.000
 AS5  H6B   O6B  C6B   107.49  3.000
 AS5  C1B   O5B  C5B   116.07  3.000
 AS5  H1B   C1B  O4A   110.78  3.000
 AS5  H1B   C1B  O5B   104.99  3.000
 AS5  O4A   C1B  O5B   113.12  3.000
 AS5  H1B   C1B  C2B   109.48  3.000
 AS5  O4A   C1B  C2B   106.53  3.000
 AS5  O5B   C1B  C2B   111.98  3.000
 AS5  C4A   O4A  C1B   118.59  3.000
 AS5  H4A   C4A  C5A   109.51  3.000
 AS5  H4A   C4A  C3A   109.71  3.000
 AS5  C5A   C4A  C3A   110.34  3.000
 AS5  H4A   C4A  O4A   110.62  3.000
 AS5  C5A   C4A  O4A   108.96  3.000
 AS5  C3A   C4A  O4A   107.69  3.000
 AS5  H3A   C3A  C2A   105.98  3.000
 AS5  H3A   C3A  O3A   111.52  3.000
 AS5  C2A   C3A  O3A   112.47  3.000
 AS5  H3A   C3A  C4A   107.02  3.000
 AS5  C2A   C3A  C4A   111.91  3.000
 AS5  O3A   C3A  C4A   107.84  3.000
 AS5  HC    O3A  C3A   108.74  3.000
 AS5  H2A   C2A  C1A   108.21  3.000
 AS5  H2A   C2A  N2A   109.27  3.000
 AS5  C1A   C2A  N2A   112.18  3.000
 AS5  H2A   C2A  C3A   108.28  3.000
 AS5  C1A   C2A  C3A   108.43  3.000
 AS5  N2A   C2A  C3A   110.37  3.000
 AS5  HD    N2A  C7A   117.79  3.000
 AS5  HD    N2A  C2A   118.52  3.000
 AS5  C7A   N2A  C2A   122.92  3.000
 AS5  C8A   C7A  O7A   121.90  3.000
 AS5  C8A   C7A  N2A   115.42  3.000
 AS5  O7A   C7A  N2A   122.68  3.000
 AS5  H8A3  C8A  H8A2  108.31  3.000
 AS5  H8A3  C8A  H8A1  108.62  3.000
 AS5  H8A2  C8A  H8A1  107.34  3.000
 AS5  H8A3  C8A  C7A   113.55  3.000
 AS5  H8A2  C8A  C7A   109.30  3.000
 AS5  H8A1  C8A  C7A   109.53  3.000
 AS5  H5A   C5A  O5A   110.07  3.000
 AS5  H5A   C5A  C6A   108.95  3.000
 AS5  O5A   C5A  C6A   107.24  3.000
 AS5  H5A   C5A  C4A   107.40  3.000
 AS5  O5A   C5A  C4A   111.19  3.000
 AS5  C6A   C5A  C4A   111.98  3.000
 AS5  H6A2  C6A  H6A1  107.15  3.000
 AS5  H6A2  C6A  O6A   112.04  3.000
 AS5  H6A1  C6A  O6A   110.98  3.000
 AS5  H6A2  C6A  C5A   108.73  3.000
 AS5  H6A1  C6A  C5A   108.99  3.000
 AS5  O6A   C6A  C5A   108.88  3.000
 AS5  H6A   O6A  C6A   108.06  3.000
 AS5  C1A   O5A  C5A   113.06  3.000
 AS5  H1A2  C1A  H1A1  107.62  3.000
 AS5  H1A2  C1A  O5A   111.24  3.000
 AS5  H1A1  C1A  O5A   107.55  3.000
 AS5  H1A2  C1A  C2A   108.88  3.000
 AS5  H1A1  C1A  C2A   110.81  3.000
 AS5  O5A   C1A  C2A   110.70  3.000
 AS5  HB    O4B  C4B   109.01  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
 AS5  CONST_01  C2B   N2B  C7B  O7B    0.00   0.0  0
 AS5  CONST_02  C2B   N2B  C7B  C8B  180.00   0.0  0
 AS5  CONST_03  O7A   C7A  N2A  C2A    0.00   0.0  0
 AS5  CONST_04  C8A   C7A  N2A  C2A  180.00   0.0  0
 AS5  CONST_05  H2B   N2B  C7B  O7B  180.00   0.0  0
 AS5  CONST_06  HD    N2A  C7A  O7A  180.00   0.0  0
 AS5  Var_01    H1A1  C1A  O5A  C5A  174.13  30.0  1
 AS5  Var_02    H8B1  C8B  C7B  O7B  -20.57  30.0  3
 AS5  Var_03    H8A1  C8A  C7A  N2A  127.96  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
 AS5  chir_01  C2B  N2B  C3B  C1B  negativ
 AS5  chir_02  C3B  O3B  C2B  C4B  negativ
 AS5  chir_03  C4B  O4B  C5B  C3B  positiv
 AS5  chir_04  C5B  O5B  C4B  C6B  positiv
 AS5  chir_05  C1B  O5B  O4A  C2B  negativ
 AS5  chir_06  C4A  O4A  C3A  C5A  negativ
 AS5  chir_07  C3A  O3A  C4A  C2A  negativ
 AS5  chir_08  C2A  N2A  C3A  C1A  negativ
 AS5  chir_09  C5A  O5A  C4A  C6A  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
 AS5  plan-1  O7B  0.020
 AS5  plan-1  C7B  0.020
 AS5  plan-1  C8B  0.020
 AS5  plan-1  N2B  0.020
 AS5  plan-1  C2B  0.020
 AS5  plan-1  H2B  0.020
 AS5  plan-2  C2A  0.020
 AS5  plan-2  N2A  0.020
 AS5  plan-2  C7A  0.020
 AS5  plan-2  O7A  0.020
 AS5  plan-2  C8A  0.020
 AS5  plan-2  HD   0.020

