# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 23:37:23 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-[(3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)N[C@H]1CN[C@H](CO)[C@@H](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
 1BW  1BW  N-[(3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]butanamide  D-saccharide  36  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1BW
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
 1BW  C1   C  CH2   0  -0.287   0.5999  -1.3626  -0.3629
 1BW  C2   C  CH1   0  -0.108  -0.0416  -0.0992   0.2005
 1BW  N2   N  NH1   0  -0.652  -1.3817   0.0777  -0.3094
 1BW  C7   C  C     0   0.557  -2.4991   0.1024   0.4438
 1BW  C8   C  CH2   0  -0.574  -3.7786   0.3431  -0.3292
 1BW  O7   O  O     0  -0.499  -2.4904  -0.0346   1.6589
 1BW  C3   C  CH1   0   0.022   0.8206   1.1168  -0.1399
 1BW  O3   O  OH1   0  -0.671   0.3475   2.2897   0.4805
 1BW  C4   C  CH1   0   0.069   2.2636   0.9085   0.3071
 1BW  O4   O  OH1   0  -0.675   3.0802   1.9743  -0.1152
 1BW  C5   C  CH1   0  -0.136   2.8113  -0.3903  -0.2811
 1BW  C6   C  CH2   0  -0.142   4.2319  -0.6515   0.1884
 1BW  O6   O  OH1   0  -0.675   4.6831  -1.8455  -0.4158
 1BW  N5   N  NH1   0  -0.612   1.9477  -1.4740   0.1504
 1BW  C9   C  CH2   0  -0.420  -4.9720  -0.4200   0.2320
 1BW  C10  C  CH3   0  -0.664  -6.2435  -0.1385  -0.5555
 1BW  H1   H  HCH2  0   0.250   0.0232  -2.2331  -0.0454
 1BW  H2   H  HCH2  0   0.196   0.5576  -1.3303  -1.4649
 1BW  H3   H  HCH1  0   0.257  -0.1089  -0.1950   1.2855
 1BW  H4   H  HNH1  0   0.397  -1.4862   0.1638  -1.3090
 1BW  H5   H  HCH2  0   0.266  -3.9814   1.4193  -0.2932
 1BW  H6   H  HCH2  0   0.246  -3.6417   0.0983  -1.3856
 1BW  H7   H  HCH1  0   0.205   0.8289   1.2351  -1.2359
 1BW  H8   H  HOH1  0   0.456  -0.4504   2.5769   0.0264
 1BW  H9   H  HCH1  0   0.200   2.2752   0.8119   1.4048
 1BW  H10  H  HOH1  0   0.450   2.7047   2.7912   0.2296
 1BW  H11  H  HCH1  0   0.206   2.8238  -0.2835  -1.3818
 1BW  H12  H  HCH2  0   0.208   4.8686   0.1966  -0.0827
 1BW  H13  H  HCH2  0   0.192   4.2341  -0.7305   1.2838
 1BW  H14  H  HOH1  0   0.458   5.5390  -2.0696  -0.0403
 1BW  H15  H  HNH1  0   0.359   2.3484  -2.3589  -0.1299
 1BW  H17  H  HCH2  0   0.225  -4.7608  -1.4924   0.2126
 1BW  H18  H  HCH2  0   0.226  -5.1186  -0.1518   1.2795
 1BW  H19  H  HCH3  0   0.220  -6.4985   0.9225  -0.5303
 1BW  H20  H  HCH3  0   0.219  -6.1337  -0.4256  -1.6028
 1BW  H21  H  HCH3  0   0.231  -7.0901  -0.6918  -0.1484

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
 1BW  O4   C4   single  1.408  0.020  1.408
 1BW  O6   C6   single  1.412  0.020  1.412
 1BW  O3   C3   single  1.409  0.020  1.409
 1BW  C4   C3   single  1.525  0.020  1.525
 1BW  C4   C5   single  1.527  0.020  1.527
 1BW  C6   C5   single  1.519  0.020  1.519
 1BW  C3   C2   single  1.529  0.020  1.529
 1BW  C5   N5   single  1.451  0.020  1.451
 1BW  O7   C7   double  1.223  0.020  1.223
 1BW  C2   N2   single  1.445  0.020  1.445
 1BW  C2   C1   single  1.525  0.020  1.525
 1BW  N5   C1   single  1.447  0.020  1.447
 1BW  C7   N2   single  1.348  0.020  1.348
 1BW  C7   C8   single  1.514  0.020  1.514
 1BW  C8   C9   single  1.524  0.020  1.524
 1BW  C9   C10  single  1.522  0.020  1.522
 1BW  C1   H1   single  0.970  0.020  1.090
 1BW  C1   H2   single  0.970  0.020  1.090
 1BW  C2   H3   single  0.970  0.020  1.090
 1BW  N2   H4   single  0.860  0.020  1.020
 1BW  C8   H5   single  0.970  0.020  1.090
 1BW  C8   H6   single  0.970  0.020  1.090
 1BW  C3   H7   single  0.970  0.020  1.090
 1BW  O3   H8   single  0.850  0.020  0.980
 1BW  C4   H9   single  0.970  0.020  1.090
 1BW  O4   H10  single  0.850  0.020  0.980
 1BW  C5   H11  single  0.970  0.020  1.090
 1BW  C6   H12  single  0.970  0.020  1.090
 1BW  C6   H13  single  0.970  0.020  1.090
 1BW  O6   H14  single  0.850  0.020  0.980
 1BW  N5   H15  single  0.890  0.020  1.040
 1BW  C9   H17  single  0.970  0.020  1.090
 1BW  C9   H18  single  0.970  0.020  1.090
 1BW  C10  H19  single  0.970  0.020  1.090
 1BW  C10  H20  single  0.970  0.020  1.090
 1BW  C10  H21  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
 1BW  H2   C1   H1   107.08  3.000
 1BW  H2   C1   N5   113.10  3.000
 1BW  H1   C1   N5   109.13  3.000
 1BW  H2   C1   C2   109.19  3.000
 1BW  H1   C1   C2   109.34  3.000
 1BW  N5   C1   C2   108.95  3.000
 1BW  H3   C2   C3   109.02  3.000
 1BW  H3   C2   N2   107.73  3.000
 1BW  C3   C2   N2   110.31  3.000
 1BW  H3   C2   C1   108.70  3.000
 1BW  N2   C2   C1   111.18  3.000
 1BW  C3   C2   C1   109.85  3.000
 1BW  H4   N2   C7   117.79  3.000
 1BW  H4   N2   C2   117.15  3.000
 1BW  C7   N2   C2   125.03  3.000
 1BW  O7   C7   C8   122.08  3.000
 1BW  C8   C7   N2   114.73  3.000
 1BW  O7   C7   N2   123.18  3.000
 1BW  H6   C8   H5   105.95  3.000
 1BW  H6   C8   C9   110.00  3.000
 1BW  H5   C8   C9   109.57  3.000
 1BW  H6   C8   C7   110.60  3.000
 1BW  H5   C8   C7   107.20  3.000
 1BW  C9   C8   C7   113.22  3.000
 1BW  H7   C3   C4   107.40  3.000
 1BW  H7   C3   O3   110.55  3.000
 1BW  C4   C3   O3   107.60  3.000
 1BW  H7   C3   C2   108.12  3.000
 1BW  C4   C3   C2   111.08  3.000
 1BW  O3   C3   C2   112.01  3.000
 1BW  H8   O3   C3   108.62  3.000
 1BW  H9   C4   C5   107.78  3.000
 1BW  H9   C4   O4   111.05  3.000
 1BW  C5   C4   O4   108.68  3.000
 1BW  H9   C4   C3   108.29  3.000
 1BW  C5   C4   C3   110.03  3.000
 1BW  O4   C4   C3   110.95  3.000
 1BW  H10  O4   C4   107.98  3.000
 1BW  H11  C5   N5   112.01  3.000
 1BW  H11  C5   C6   108.28  3.000
 1BW  N5   C5   C6   109.65  3.000
 1BW  H11  C5   C4   107.77  3.000
 1BW  N5   C5   C4   107.89  3.000
 1BW  C6   C5   C4   111.26  3.000
 1BW  H13  C6   H12  107.56  3.000
 1BW  H13  C6   O6   111.42  3.000
 1BW  H12  C6   O6   111.30  3.000
 1BW  H13  C6   C5   108.81  3.000
 1BW  H12  C6   C5   109.53  3.000
 1BW  O6   C6   C5   108.18  3.000
 1BW  H14  O6   C6   108.33  3.000
 1BW  H15  N5   C5   109.59  3.000
 1BW  H15  N5   C1   109.77  3.000
 1BW  C5   N5   C1   113.05  3.000
 1BW  H18  C9   H17  106.51  3.000
 1BW  H18  C9   C10  109.82  3.000
 1BW  H17  C9   C10  109.50  3.000
 1BW  H18  C9   C8   109.61  3.000
 1BW  H17  C9   C8   109.48  3.000
 1BW  C10  C9   C8   111.79  3.000
 1BW  H21  C10  H20  107.63  3.000
 1BW  H21  C10  H19  107.66  3.000
 1BW  H20  C10  H19  107.54  3.000
 1BW  H21  C10  C9   111.21  3.000
 1BW  H20  C10  C9   111.34  3.000
 1BW  H19  C10  C9   111.29  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
 1BW  CONST_01  O7   C7   N2  C2    0.00   0.0  0
 1BW  CONST_02  C8   C7   N2  C2  180.00   0.0  0
 1BW  CONST_03  H4   N2   C7  C8    0.00   0.0  0
 1BW  Var_01    C5   N5   C1  C2  -63.70  30.0  1
 1BW  Var_02    C9   C8   C7  N2  144.68  30.0  3
 1BW  Var_03    C10  C9   C8  C7  179.14  30.0  3
 1BW  Var_04    H19  C10  C9  C8  -60.19  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
 1BW  chir_01  C2  C3  N2  C1  negativ
 1BW  chir_02  C3  O3  C2  C4  positiv
 1BW  chir_03  C4  O4  C3  C5  negativ
 1BW  chir_04  C5  N5  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
 1BW  plan-1  C2  0.020
 1BW  plan-1  N2  0.020
 1BW  plan-1  C7  0.020
 1BW  plan-1  C8  0.020
 1BW  plan-1  O7  0.020
 1BW  plan-1  H4  0.020

