# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:29:10 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](OCc2ccccc2)[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
 YKR  YKR  2-amino-4-O-benzyl-2-deoxy-alpha-D-glucopyranose  D-saccharide  38  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YKR
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
 YKR  C1    C  CH1   0   0.248  -3.5612  -0.1313  -0.1856
 YKR  O1    O  OH1   0  -0.664  -3.5678  -0.1120  -1.5760
 YKR  C2    C  CH1   0  -0.137  -3.0178   1.1969   0.3340
 YKR  N2    N  NH2   0  -0.811  -3.7709   2.3136  -0.2093
 YKR  C3    C  CH1   0   0.034  -1.5387   1.3275  -0.0265
 YKR  O3    O  OH1   0  -0.672  -0.9748   2.4892   0.5457
 YKR  C4    C  CH1   0   0.028  -0.7701   0.1194   0.4923
 YKR  O4    O  O2    0  -0.503   0.5582   0.1382   0.0205
 YKR  C5    C  CH1   0   0.002  -1.4273  -1.1799   0.0127
 YKR  O5    O  O2    0  -0.502  -2.8061  -1.1929   0.3363
 YKR  C6    C  CH2   0  -0.169  -0.7999  -2.3906   0.6725
 YKR  O6    O  OH1   0  -0.670  -1.3566  -3.5561   0.1126
 YKR  CAL   C  CR16  0  -0.241   4.9378   1.2155  -0.5525
 YKR  CAM   C  CR16  0  -0.310   3.6870   1.4051   0.0241
 YKR  CAN   C  CR16  0  -0.265   5.3964  -0.0689  -0.8069
 YKR  CAO   C  CR6   0   0.076   2.8879   0.3183   0.3598
 YKR  CAP   C  CR16  0  -0.242   4.6016  -1.1623  -0.4797
 YKR  CAU   C  CH2   0  -0.217   1.5323   0.5166   0.9726
 YKR  CBC   C  CR16  0  -0.290   3.3563  -0.9682   0.0979
 YKR  H1    H  HCH1  0   0.232  -4.5720  -0.2968   0.2085
 YKR  H2    H  HCH1  0   0.222  -3.0877   1.1338   1.4320
 YKR  HN2   H  HNH2  0   0.348  -4.7562   2.1879  -0.0090
 YKR  HN2A  H  HNH2  0   0.346  -3.5098   3.1565   0.2870
 YKR  H3    H  HCH1  0   0.217  -1.4418   1.3574  -1.1194
 YKR  HO3   H  HOH1  0   0.456  -1.0878   3.2202  -0.0680
 YKR  H4    H  HCH1  0   0.219  -0.7955   0.1362   1.5935
 YKR  H5    H  HCH1  0   0.221  -1.2845  -1.2611  -1.0742
 YKR  H6    H  HCH2  0   0.214   0.2832  -2.3469   0.5133
 YKR  H6A   H  HCH2  0   0.194  -0.9680  -2.3370   1.7575
 YKR  HO6   H  HOH1  0   0.456  -0.8745  -4.3114   0.4601
 YKR  HAM   H  HCR6  0   0.253   3.3319   2.4105   0.2168
 YKR  HAN   H  HCR6  0   0.257   6.3690  -0.2213  -1.2570
 YKR  HAP   H  HCR6  0   0.257   4.9558  -2.1666  -0.6731
 YKR  HAU   H  HCH2  0   0.228   1.4050   1.5593   1.2793
 YKR  HAUA  H  HCH2  0   0.217   1.4421  -0.1031   1.8747
 YKR  HBC   H  HCR6  0   0.254   2.7470  -1.8264   0.3578
 YKR  H7    H  HOH1  0   0.460  -4.0497  -0.8825  -1.8953
 YKR  HAL   H  HCR6  0   0.256   5.5503   2.0719  -0.8036

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
 YKR  C1   O1    single    1.391  0.020  1.391
 YKR  C1   C2    single    1.526  0.020  1.526
 YKR  C1   O5    single    1.403  0.020  1.403
 YKR  C2   N2    single    1.452  0.020  1.452
 YKR  C2   C3    single    1.528  0.020  1.528
 YKR  C3   O3    single    1.412  0.020  1.412
 YKR  C3   C4    single    1.523  0.020  1.523
 YKR  C4   O4    single    1.410  0.020  1.410
 YKR  C4   C5    single    1.533  0.020  1.533
 YKR  O4   CAU   single    1.414  0.020  1.414
 YKR  C5   O5    single    1.416  0.020  1.416
 YKR  C5   C6    single    1.515  0.020  1.515
 YKR  C6   O6    single    1.408  0.020  1.408
 YKR  CAL  CAM   aromatic  1.390  0.020  1.390
 YKR  CAL  CAN   aromatic  1.387  0.020  1.387
 YKR  CAM  CAO   aromatic  1.390  0.020  1.390
 YKR  CAN  CAP   aromatic  1.391  0.020  1.391
 YKR  CAO  CAU   single    1.501  0.020  1.501
 YKR  CAO  CBC   aromatic  1.394  0.020  1.394
 YKR  CAP  CBC   aromatic  1.386  0.020  1.386
 YKR  C1   H1    single    0.970  0.020  1.090
 YKR  C2   H2    single    0.970  0.020  1.090
 YKR  N2   HN2   single    0.890  0.020  1.040
 YKR  N2   HN2A  single    0.890  0.020  1.040
 YKR  C3   H3    single    0.970  0.020  1.090
 YKR  O3   HO3   single    0.850  0.020  0.980
 YKR  C4   H4    single    0.970  0.020  1.090
 YKR  C5   H5    single    0.970  0.020  1.090
 YKR  C6   H6    single    0.970  0.020  1.090
 YKR  C6   H6A   single    0.970  0.020  1.090
 YKR  O6   HO6   single    0.850  0.020  0.980
 YKR  CAL  HAL   single    0.930  0.020  1.080
 YKR  CAM  HAM   single    0.930  0.020  1.080
 YKR  CAN  HAN   single    0.930  0.020  1.080
 YKR  CAP  HAP   single    0.930  0.020  1.080
 YKR  CAU  HAU   single    0.970  0.020  1.090
 YKR  CAU  HAUA  single    0.970  0.020  1.090
 YKR  CBC  HBC   single    0.930  0.020  1.080
 YKR  O1   H7    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
 YKR  H1    C1   O5   104.35  3.000
 YKR  H1    C1   C2   109.68  3.000
 YKR  O5    C1   C2   109.88  3.000
 YKR  H1    C1   O1   110.91  3.000
 YKR  O5    C1   O1   112.64  3.000
 YKR  C2    C1   O1   109.27  3.000
 YKR  H7    O1   C1   108.82  3.000
 YKR  H2    C2   C3   107.54  3.000
 YKR  H2    C2   N2   112.57  3.000
 YKR  C3    C2   N2   110.36  3.000
 YKR  H2    C2   C1   105.48  3.000
 YKR  C3    C2   C1   109.80  3.000
 YKR  N2    C2   C1   110.93  3.000
 YKR  HN2A  N2   HN2  104.90  3.000
 YKR  HN2A  N2   C2   108.85  3.000
 YKR  HN2   N2   C2   109.56  3.000
 YKR  H3    C3   C4   108.44  3.000
 YKR  H3    C3   O3   110.22  3.000
 YKR  C4    C3   O3   108.24  3.000
 YKR  H3    C3   C2   108.83  3.000
 YKR  C4    C3   C2   109.90  3.000
 YKR  O3    C3   C2   111.17  3.000
 YKR  HO3   O3   C3   108.66  3.000
 YKR  H4    C4   C5   108.41  3.000
 YKR  H4    C4   O4   110.86  3.000
 YKR  C5    C4   O4   108.09  3.000
 YKR  H4    C4   C3   108.47  3.000
 YKR  C5    C4   C3   110.45  3.000
 YKR  O4    C4   C3   110.54  3.000
 YKR  CAU   O4   C4   115.30  3.000
 YKR  H5    C5   C6   108.53  3.000
 YKR  H5    C5   O5   110.59  3.000
 YKR  C6    C5   O5   107.24  3.000
 YKR  H5    C5   C4   108.44  3.000
 YKR  C6    C5   C4   111.32  3.000
 YKR  O5    C5   C4   110.70  3.000
 YKR  C5    O5   C1   115.59  3.000
 YKR  H6A   C6   H6   107.01  3.000
 YKR  H6A   C6   O6   111.87  3.000
 YKR  H6    C6   O6   111.48  3.000
 YKR  H6A   C6   C5   109.13  3.000
 YKR  H6    C6   C5   108.32  3.000
 YKR  O6    C6   C5   108.94  3.000
 YKR  HO6   O6   C6   107.96  3.000
 YKR  HAL   CAL  CAN  120.19  3.000
 YKR  HAL   CAL  CAM  119.83  3.000
 YKR  CAN   CAL  CAM  119.98  3.000
 YKR  HAM   CAM  CAO  119.61  3.000
 YKR  HAM   CAM  CAL  119.68  3.000
 YKR  CAO   CAM  CAL  120.71  3.000
 YKR  HAN   CAN  CAP  120.04  3.000
 YKR  HAN   CAN  CAL  120.24  3.000
 YKR  CAP   CAN  CAL  119.72  3.000
 YKR  CBC   CAO  CAU  120.14  3.000
 YKR  CBC   CAO  CAM  118.88  3.000
 YKR  CAU   CAO  CAM  120.97  3.000
 YKR  HAP   CAP  CBC  119.89  3.000
 YKR  HAP   CAP  CAN  120.03  3.000
 YKR  CBC   CAP  CAN  120.08  3.000
 YKR  HAUA  CAU  HAU  107.33  3.000
 YKR  HAUA  CAU  CAO  109.58  3.000
 YKR  HAU   CAU  CAO  110.21  3.000
 YKR  HAUA  CAU  O4   110.22  3.000
 YKR  HAU   CAU  O4   111.32  3.000
 YKR  CAO   CAU  O4   108.18  3.000
 YKR  HBC   CBC  CAP  119.59  3.000
 YKR  HBC   CBC  CAO  119.78  3.000
 YKR  CAP   CBC  CAO  120.62  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
 YKR  CONST_01  CBC  CAO  CAM  CAL    0.00   0.0  0
 YKR  CONST_02  CBC  CAP  CAN  CAL    0.00   0.0  0
 YKR  CONST_03  CAP  CAN  CAL  CAM    0.00   0.0  0
 YKR  CONST_04  CAP  CBC  CAO  CAM    0.00   0.0  0
 YKR  CONST_05  CAO  CAM  CAL  CAN    0.00   0.0  0
 YKR  CONST_06  CAO  CBC  CAP  CAN    0.00   0.0  0
 YKR  CONST_07  CAU  CAO  CAM  CAL  180.00   0.0  0
 YKR  CONST_08  CAU  CAO  CBC  CAP  180.00   0.0  0
 YKR  CONST_09  HAP  CAP  CAN  CAL  180.00   0.0  0
 YKR  CONST_10  HAN  CAN  CAL  CAM  180.00   0.0  0
 YKR  CONST_11  HBC  CBC  CAO  CAM  180.00   0.0  0
 YKR  CONST_12  HAM  CAM  CAL  CAN  180.00   0.0  0
 YKR  CONST_13  HAL  CAL  CAM  CAO  180.00   0.0  0
 YKR  Var_01    CAO  CAU  O4   C4   173.04  30.0  3
 YKR  Var_02    CAM  CAO  CAU  O4   110.26  30.0  2

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
 YKR  chir_01  C1  O1  C2  O5  positiv
 YKR  chir_02  C2  N2  C1  C3  negativ
 YKR  chir_03  C3  O3  C2  C4  positiv
 YKR  chir_04  C4  O4  C5  C3  positiv
 YKR  chir_05  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
 YKR  plan-1  CAL  0.020
 YKR  plan-1  CAM  0.020
 YKR  plan-1  CAN  0.020
 YKR  plan-1  CAO  0.020
 YKR  plan-1  CAP  0.020
 YKR  plan-1  CAU  0.020
 YKR  plan-1  CBC  0.020
 YKR  plan-1  HAM  0.020
 YKR  plan-1  HAN  0.020
 YKR  plan-1  HAP  0.020
 YKR  plan-1  HBC  0.020
 YKR  plan-1  HAL  0.020

