# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:03:32 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: (2S)-amino{4-[(2-O-alpha-D-mannopyranosyl-alpha-D-mannopyranosyl)oxy]phenyl}ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C(O)=O)c1ccc(O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)cc1
#
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
 SHP  SHP  '(2S)-amino{4-[(2-O-alpha-D-mannopyranosyl-alpha-D-mannopyranosyl)oxy]phenyl}ethanoic acid'  L-peptide  62  34  .  2012-08-28  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SHP
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
 SHP  N     N  NH2    0  -0.798  21.5197  20.2213  17.2864
 SHP  CA    C  CH1    0  -0.257  21.6035  18.7779  17.3729
 SHP  C     C  C      0   0.410  22.3175  18.3495  18.6920
 SHP  O     O  O      0  -0.591  23.1551  19.1505  19.1474
 SHP  OXT   O  OC    -1  -0.595  22.0138  17.2294  19.1383
 SHP  C1B   C  CR6    0   0.108  22.3416  18.0919  16.2400
 SHP  C2B   C  CR16   0  -0.298  22.0210  16.7836  15.8815
 SHP  C3B   C  CR16   0  -0.314  22.7068  16.1211  14.8747
 SHP  C4B   C  CR6    0   0.333  23.7311  16.7714  14.2006
 SHP  O4B   O  O2     0  -0.525  24.3708  16.1377  13.1644
 SHP  C5B   C  CR16   0  -0.313  24.0643  18.0752  14.5359
 SHP  C6B   C  CR16   0  -0.324  23.3747  18.7225  15.5527
 SHP  C1    C  CH1    0   0.307  25.6412  15.6331  13.4333
 SHP  C2    C  CH1    0  -0.012  26.3547  15.3961  12.1039
 SHP  C3    C  CH1    0  -0.028  27.6745  14.6696  12.3385
 SHP  C4    C  CH1    0  -0.000  27.4358  13.3944  13.1540
 SHP  C5    C  CH1    0  -0.048  26.5990  13.6569  14.4113
 SHP  C6    C  CH2    0  -0.182  27.3595  14.2523  15.5961
 SHP  O1    O  O2     0  -0.513  26.6349  16.6053  11.4453
 SHP  O3    O  OH1    0  -0.659  28.5433  15.5579  12.9958
 SHP  O4    O  OH1    0  -0.672  26.7753  12.5011  12.2837
 SHP  O5    O  O2     0  -0.491  25.4450  14.4183  14.1072
 SHP  O6    O  OH1    0  -0.666  28.3286  13.3082  15.9926
 SHP  C1'   C  CH1    0   0.242  25.6654  17.1147  10.5683
 SHP  C2'   C  CH1    0  -0.011  26.1810  17.0031   9.1336
 SHP  C3'   C  CH1    0   0.008  27.3354  17.9722   8.9141
 SHP  C4'   C  CH1    0  -0.001  26.9276  19.3813   9.3238
 SHP  C5'   C  CH1    0  -0.020  26.4251  19.3614  10.7722
 SHP  C6'   C  CH2    0  -0.158  25.8965  20.7100  11.2105
 SHP  O2'   O  OH1    0  -0.668  25.0919  17.2898   8.2905
 SHP  O3'   O  OH1    0  -0.671  27.6985  17.9008   7.5565
 SHP  O4'   O  OH1    0  -0.670  28.0686  20.2002   9.1773
 SHP  O5'   O  O2     0  -0.490  25.3623  18.4273  10.9056
 SHP  O6'   O  OH1    0  -0.660  25.6304  20.6727  12.5929
 SHP  H     H  HNH2   0   0.334  21.3563  20.5190  16.3327
 SHP  H2    H  HNH2   0   0.336  22.4019  20.6190  17.5836
 SHP  HA    H  HCH1   0   0.222  20.5887  18.3676  17.3974
 SHP  H2B   H  HCR6   0   0.240  21.2162  16.2729  16.3964
 SHP  H3B   H  HCR6   0   0.253  22.4377  15.1085  14.6015
 SHP  H5B   H  HCR6   0   0.263  24.8409  18.5955  13.9891
 SHP  H6'   H  HCR6   0   0.238  23.6404  19.7449  15.7924
 SHP  H1    H  HCH1   0   0.210  26.2085  16.3470  14.0499
 SHP  HC2   H  HCH1   0   0.251  25.7198  14.7455  11.4884
 SHP  H3    H  HCH1   0   0.242  28.0826  14.3758  11.3610
 SHP  H4    H  HCH1   0   0.238  28.4091  12.9870  13.4598
 SHP  H5    H  HCH1   0   0.255  26.2096  12.6906  14.7533
 SHP  H61   H  HCH2   0   0.212  27.8157  15.2124  15.3409
 SHP  H62   H  HCH2   0   0.207  26.6295  14.4400  16.3942
 SHP  HO3   H  HOH1   0   0.457  29.3954  15.1248  13.1099
 SHP  HO4   H  HOH1   0   0.453  26.6674  11.6561  12.7314
 SHP  HO6   H  HOH1   0   0.457  28.8703  13.7032  16.6814
 SHP  H1'   H  HCH1   0   0.249  24.7271  16.5577  10.6496
 SHP  H2'   H  HCH1   0   0.231  26.5380  15.9740   8.9772
 SHP  H3'   H  HCH1   0   0.214  28.1718  17.6605   9.5583
 SHP  H4'   H  HCH1   0   0.223  26.1130  19.7215   8.6706
 SHP  H5'   H  HCH1   0   0.225  27.2647  19.0876  11.4271
 SHP  H6'1  H  HCH2   0   0.201  26.6475  21.4730  10.9743
 SHP  H6'2  H  HCH2   0   0.201  24.9981  20.9497  10.6253
 SHP  HO2'  H  HOH1   0   0.450  25.4235  17.3487   7.3881
 SHP  HO3'  H  HOH1   0   0.450  28.3246  18.6108   7.3760
 SHP  HO4'  H  HOH1   0   0.460  27.7933  21.0894   8.9374
 SHP  HO6'  H  HOH1   0   0.456  25.2523  21.5179  12.8520

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
 SHP  N    CA    single    1.451  0.016  1.451
 SHP  N    H     single    0.860  0.020  0.860
 SHP  N    H2    single    0.890  0.020  1.040
 SHP  CA   C     single    1.516  0.018  1.516
 SHP  CA   C1B   single    1.516  0.020  1.516
 SHP  CA   HA    single    0.970  0.020  1.090
 SHP  C    O     deloc     1.231  0.020  1.231
 SHP  C    OXT   deloc     1.243  0.020  1.243
 SHP  C1B  C2B   aromatic  1.394  0.020  1.394
 SHP  C1B  C6B   aromatic  1.392  0.020  1.392
 SHP  C2B  C3B   aromatic  1.387  0.020  1.387
 SHP  C2B  H2B   single    0.930  0.020  1.080
 SHP  C3B  C4B   aromatic  1.388  0.020  1.388
 SHP  C3B  H3B   single    0.930  0.020  1.080
 SHP  C4B  O4B   single    1.373  0.020  1.373
 SHP  C4B  C5B   aromatic  1.387  0.020  1.387
 SHP  O4B  C1    single    1.393  0.020  1.393
 SHP  C5B  C6B   aromatic  1.389  0.020  1.389
 SHP  C5B  H5B   single    0.930  0.020  1.080
 SHP  C6B  H6'   single    0.930  0.020  1.080
 SHP  C1   C2    single    1.527  0.020  1.527
 SHP  C1   O5    single    1.403  0.020  1.403
 SHP  C1   H1    single    0.970  0.020  1.090
 SHP  C2   C3    single    1.525  0.020  1.525
 SHP  C2   O1    single    1.405  0.020  1.405
 SHP  C2   HC2   single    0.970  0.020  1.090
 SHP  C3   C4    single    1.532  0.020  1.532
 SHP  C3   O3    single    1.406  0.020  1.406
 SHP  C3   H3    single    0.970  0.020  1.090
 SHP  C4   C5    single    1.533  0.020  1.533
 SHP  C4   O4    single    1.411  0.020  1.411
 SHP  C4   H4    single    0.970  0.020  1.090
 SHP  C5   C6    single    1.529  0.020  1.529
 SHP  C5   O5    single    1.416  0.020  1.416
 SHP  C5   H5    single    0.970  0.020  1.090
 SHP  C6   O6    single    1.410  0.020  1.410
 SHP  C6   H61   single    0.970  0.020  1.090
 SHP  C6   H62   single    0.970  0.020  1.090
 SHP  O1   C1'   single    1.403  0.020  1.403
 SHP  O3   HO3   single    0.850  0.020  0.980
 SHP  O4   HO4   single    0.850  0.020  0.980
 SHP  O6   HO6   single    0.850  0.020  0.980
 SHP  C1'  C2'   single    1.529  0.020  1.529
 SHP  C1'  O5'   single    1.389  0.020  1.389
 SHP  C1'  H1'   single    0.970  0.020  1.090
 SHP  C2'  C3'   single    1.523  0.020  1.523
 SHP  C2'  O2'   single    1.407  0.020  1.407
 SHP  C2'  H2'   single    0.970  0.020  1.090
 SHP  C3'  C4'   single    1.523  0.020  1.523
 SHP  C3'  O3'   single    1.407  0.020  1.407
 SHP  C3'  H3'   single    0.970  0.020  1.090
 SHP  C4'  C5'   single    1.533  0.020  1.533
 SHP  C4'  O4'   single    1.412  0.020  1.412
 SHP  C4'  H4'   single    0.970  0.020  1.090
 SHP  C5'  C6'   single    1.513  0.020  1.513
 SHP  C5'  O5'   single    1.421  0.020  1.421
 SHP  C5'  H5'   single    0.970  0.020  1.090
 SHP  C6'  O6'   single    1.408  0.020  1.408
 SHP  C6'  H6'1  single    0.970  0.020  1.090
 SHP  C6'  H6'2  single    0.970  0.020  1.090
 SHP  O2'  HO2'  single    0.850  0.020  0.980
 SHP  O3'  HO3'  single    0.850  0.020  0.980
 SHP  O4'  HO4'  single    0.850  0.020  0.980
 SHP  O6'  HO6'  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
 SHP  H2    N    H     107.56  3.000
 SHP  H2    N    CA    108.88  3.000
 SHP  H     N    CA    114.00  3.000
 SHP  HA    CA   C1B   107.36  3.000
 SHP  HA    CA   C     107.60  3.000
 SHP  C1B   CA   C     106.55  3.000
 SHP  HA    CA   N     108.73  3.000
 SHP  C1B   CA   N     115.75  3.000
 SHP  C     CA   N     113.30  2.900
 SHP  OXT   C    O     127.77  3.000
 SHP  OXT   C    CA    116.05  3.000
 SHP  O     C    CA    120.80  2.100
 SHP  C6B   C1B  C2B   117.97  3.000
 SHP  C6B   C1B  CA    121.69  3.000
 SHP  C2B   C1B  CA    120.32  3.000
 SHP  H2B   C2B  C3B   119.16  3.000
 SHP  H2B   C2B  C1B   119.41  3.000
 SHP  C3B   C2B  C1B   121.43  3.000
 SHP  H3B   C3B  C4B   119.93  3.000
 SHP  H3B   C3B  C2B   120.47  3.000
 SHP  C4B   C3B  C2B   119.59  3.000
 SHP  C5B   C4B  O4B   120.30  3.000
 SHP  C5B   C4B  C3B   120.02  3.000
 SHP  O4B   C4B  C3B   119.62  3.000
 SHP  C1    O4B  C4B   116.51  3.000
 SHP  H5B   C5B  C6B   120.12  3.000
 SHP  H5B   C5B  C4B   120.12  3.000
 SHP  C6B   C5B  C4B   119.73  3.000
 SHP  H6'   C6B  C5B   118.70  3.000
 SHP  H6'   C6B  C1B   120.03  3.000
 SHP  C5B   C6B  C1B   121.26  3.000
 SHP  H1    C1   O5    111.38  3.000
 SHP  H1    C1   C2    110.33  3.000
 SHP  O5    C1   C2    110.43  3.000
 SHP  H1    C1   O4B   110.07  3.000
 SHP  O5    C1   O4B   106.19  3.000
 SHP  C2    C1   O4B   108.31  3.000
 SHP  HC2   C2   O1    111.25  3.000
 SHP  HC2   C2   C3    107.73  3.000
 SHP  O1    C2   C3    108.03  3.000
 SHP  HC2   C2   C1    108.05  3.000
 SHP  O1    C2   C1    111.57  3.000
 SHP  C3    C2   C1    110.15  3.000
 SHP  H3    C3   O3    110.81  3.000
 SHP  H3    C3   C4    107.98  3.000
 SHP  O3    C3   C4    111.92  3.000
 SHP  H3    C3   C2    108.17  3.000
 SHP  O3    C3   C2    107.81  3.000
 SHP  C4    C3   C2    110.09  3.000
 SHP  H4    C4   O4    110.58  3.000
 SHP  H4    C4   C5    108.59  3.000
 SHP  O4    C4   C5    111.02  3.000
 SHP  H4    C4   C3    108.59  3.000
 SHP  O4    C4   C3    105.75  3.000
 SHP  C5    C4   C3    112.28  3.000
 SHP  H5    C5   O5    104.57  3.000
 SHP  H5    C5   C6    106.15  3.000
 SHP  O5    C5   C6    111.26  3.000
 SHP  H5    C5   C4    107.39  3.000
 SHP  O5    C5   C4    111.15  3.000
 SHP  C6    C5   C4    115.52  3.000
 SHP  H62   C6   H61   107.28  3.000
 SHP  H62   C6   O6    111.53  3.000
 SHP  H61   C6   O6    111.53  3.000
 SHP  H62   C6   C5    107.41  3.000
 SHP  H61   C6   C5    111.65  3.000
 SHP  O6    C6   C5    107.40  3.000
 SHP  C1'   O1   C2    117.88  3.000
 SHP  HO3   O3   C3    108.55  3.000
 SHP  HO4   O4   C4    108.75  3.000
 SHP  C5    O5   C1    117.06  3.000
 SHP  HO6   O6   C6    108.28  3.000
 SHP  H1'   C1'  O5'   106.01  3.000
 SHP  H1'   C1'  C2'   108.77  3.000
 SHP  O5'   C1'  C2'   111.75  3.000
 SHP  H1'   C1'  O1    111.18  3.000
 SHP  O5'   C1'  O1    110.01  3.000
 SHP  C2'   C1'  O1    109.09  3.000
 SHP  H2'   C2'  O2'   110.89  3.000
 SHP  H2'   C2'  C3'   109.18  3.000
 SHP  O2'   C2'  C3'   111.76  3.000
 SHP  H2'   C2'  C1'   108.13  3.000
 SHP  O2'   C2'  C1'   106.65  3.000
 SHP  C3'   C2'  C1'   110.15  3.000
 SHP  H3'   C3'  O3'   110.74  3.000
 SHP  H3'   C3'  C4'   107.94  3.000
 SHP  O3'   C3'  C4'   112.06  3.000
 SHP  H3'   C3'  C2'   108.15  3.000
 SHP  O3'   C3'  C2'   107.60  3.000
 SHP  C4'   C3'  C2'   110.30  3.000
 SHP  H4'   C4'  O4'   110.98  3.000
 SHP  H4'   C4'  C5'   108.83  3.000
 SHP  O4'   C4'  C5'   111.74  3.000
 SHP  H4'   C4'  C3'   108.98  3.000
 SHP  O4'   C4'  C3'   107.00  3.000
 SHP  C5'   C4'  C3'   109.26  3.000
 SHP  H5'   C5'  O5'   110.58  3.000
 SHP  H5'   C5'  C6'   108.44  3.000
 SHP  O5'   C5'  C6'   107.30  3.000
 SHP  H5'   C5'  C4'   108.39  3.000
 SHP  O5'   C5'  C4'   110.02  3.000
 SHP  C6'   C5'  C4'   112.12  3.000
 SHP  H6'2  C6'  H6'1  107.08  3.000
 SHP  H6'2  C6'  O6'   111.97  3.000
 SHP  H6'1  C6'  O6'   111.06  3.000
 SHP  H6'2  C6'  C5'   109.02  3.000
 SHP  H6'1  C6'  C5'   108.57  3.000
 SHP  O6'   C6'  C5'   109.06  3.000
 SHP  HO2'  O2'  C2'   107.91  3.000
 SHP  HO3'  O3'  C3'   108.11  3.000
 SHP  HO4'  O4'  C4'   109.33  3.000
 SHP  C5'   O5'  C1'   115.80  3.000
 SHP  HO6'  O6'  C6'   108.39  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
 SHP  CONST_01  C4B  C3B  C2B  C1B    0.00  0.0  0
 SHP  CONST_02  C4B  C5B  C6B  C1B    0.00  0.0  0
 SHP  CONST_03  C5B  C6B  C1B  C2B    0.00  0.0  0
 SHP  CONST_04  C5B  C4B  C3B  C2B    0.00  0.0  0
 SHP  CONST_05  C6B  C1B  C2B  C3B    0.00  0.0  0
 SHP  CONST_06  C6B  C5B  C4B  C3B    0.00  0.0  0
 SHP  CONST_07  C3B  C2B  C1B  CA   180.00  0.0  0
 SHP  CONST_08  C5B  C6B  C1B  CA   180.00  0.0  0
 SHP  CONST_09  O4B  C4B  C3B  C2B  180.00  0.0  0
 SHP  CONST_10  C6B  C5B  C4B  O4B  180.00  0.0  0
 SHP  CONST_11  H3B  C3B  C2B  C1B  180.00  0.0  0
 SHP  CONST_12  H5B  C5B  C6B  C1B  180.00  0.0  0
 SHP  CONST_13  H6'  C6B  C1B  C2B  180.00  0.0  0
 SHP  CONST_14  H2B  C2B  C3B  C4B  180.00  0.0  0

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
 SHP  chir_01  CA   N    C    C1B  positiv
 SHP  chir_02  C1   O4B  O5   C2   negativ
 SHP  chir_03  C2   O1   C3   C1   negativ
 SHP  chir_04  C3   O3   C2   C4   positiv
 SHP  chir_05  C4   O4   C5   C3   positiv
 SHP  chir_06  C5   O5   C4   C6   negativ
 SHP  chir_07  C1'  O1   O5'  C2'  negativ
 SHP  chir_08  C2'  O2'  C1'  C3'  positiv
 SHP  chir_09  C3'  O3'  C2'  C4'  positiv
 SHP  chir_10  C4'  O4'  C5'  C3'  positiv
 SHP  chir_11  C5'  O5'  C4'  C6'  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
 SHP  plan-1  CA   0.020
 SHP  plan-1  C1B  0.020
 SHP  plan-1  C2B  0.020
 SHP  plan-1  C3B  0.020
 SHP  plan-1  C4B  0.020
 SHP  plan-1  O4B  0.020
 SHP  plan-1  C5B  0.020
 SHP  plan-1  C6B  0.020
 SHP  plan-1  H2B  0.020
 SHP  plan-1  H3B  0.020
 SHP  plan-1  H5B  0.020
 SHP  plan-1  H6'  0.020
 SHP  plan-2  CA   0.020
 SHP  plan-2  C    0.020
 SHP  plan-2  O    0.020
 SHP  plan-2  OXT  0.020

