# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:27:02 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R,5R)-3-(acetylamino)-6-carboxy-5-fluoro-2-[(1R,2R)-1,2,3-trihydroxypropyl]-2,3,4,5-tetrahydropyranium (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1C[C@@H](F)C(=[O+][C@H]1[C@H](O)[C@H](O)CO)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
 9WM  9WM  '(2R,3R,5R)-3-(acetylamino)-6-carboxy-5-fluoro-2-[(1R,2R)-1,2,3-trihydroxypropyl]-2,3,4,5-tetrahydropyranium (non-preferred name)'  ligand  37  20  .  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_9WM
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
 9WM  O1B  O  OH1   0  -0.546  -2.6635  -2.4938   0.4613
 9WM  C1   C  C     0   0.554  -1.6263  -3.0714  -0.0672
 9WM  O1A  O  O     0  -0.350  -1.4523  -4.2184  -0.3527
 9WM  C2   C  C     0   0.400  -0.5189  -2.0624  -0.3465
 9WM  C3   C  CH1   0   0.116   0.8906  -2.5509  -0.5274
 9WM  F1   F  F     0  -0.339   1.1952  -3.0247   0.7390
 9WM  C4   C  CH2   0  -0.529   1.8224  -1.4530  -0.9598
 9WM  O6   O  OC2   1  -0.291  -0.8491  -0.8767  -0.3875
 9WM  C6   C  CH1   0   0.002   0.0850   0.2866  -0.5537
 9WM  C7   C  CH1   0  -0.044  -0.4865   1.3636   0.3644
 9WM  C8   C  CH1   0  -0.032  -1.8715   1.8645  -0.0917
 9WM  C9   C  CH2   0  -0.162  -2.2648   3.1000   0.7043
 9WM  O9   O  OH1   0  -0.666  -3.5748   3.4597   0.3457
 9WM  O7   O  OH1   0  -0.641  -0.4732   0.9443   1.6993
 9WM  C5   C  CH1   0  -0.140   1.5143  -0.1462  -0.2402
 9WM  N5   N  NH1   0  -0.645   2.4039   0.8958  -0.6658
 9WM  C10  C  C     0   0.534   3.0627   1.7162   0.1904
 9WM  O10  O  O     0  -0.478   2.9066   1.6658   1.3979
 9WM  C11  C  CH3   0  -0.778   4.0032   2.6923  -0.4635
 9WM  O8   O  OH1   0  -0.650  -1.8955   2.0910  -1.4770
 9WM  H1   H  HOH1  0   0.523  -3.3807  -3.1280   0.6329
 9WM  H3   H  HCH1  0   0.333   0.8922  -3.3840  -1.2335
 9WM  H4   H  HCH2  0   0.331   2.8488  -1.7672  -0.7685
 9WM  H5   H  HCH2  0   0.300   1.7182  -1.3290  -2.0410
 9WM  H6   H  HCH1  0   0.347  -0.0296   0.5537  -1.6058
 9WM  H7   H  HCH1  0   0.284   0.2181   2.1994   0.2829
 9WM  H8   H  HCH1  0   0.249  -2.6143   1.0795   0.0976
 9WM  H9   H  HCH2  0   0.215  -2.1794   2.8829   1.7747
 9WM  H10  H  HCH2  0   0.203  -1.5446   3.9037   0.4856
 9WM  H11  H  HOH1  0   0.460  -3.8351   4.2135   0.8825
 9WM  H12  H  HOH1  0   0.458  -1.2860   0.4687   1.9055
 9WM  H13  H  HCH1  0   0.315   1.6347  -0.2734   0.8373
 9WM  H14  H  HNH1  0   0.414   2.5893   0.9778  -1.6538
 9WM  H15  H  HCH3  0   0.254   3.9866   2.6539  -1.5506
 9WM  H16  H  HCH3  0   0.273   3.7515   3.7036  -0.1468
 9WM  H17  H  HCH3  0   0.275   5.0196   2.4889  -0.1266
 9WM  H18  H  HOH1  0   0.455  -1.4220   2.9073  -1.6748

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
 9WM  C11  C10  single  1.505  0.020  1.505
 9WM  O8   C8   single  1.404  0.020  1.404
 9WM  O9   C9   single  1.405  0.020  1.405
 9WM  N5   C10  single  1.357  0.020  1.357
 9WM  N5   C5   single  1.435  0.020  1.435
 9WM  C10  O10  double  1.219  0.020  1.219
 9WM  C8   C9   single  1.521  0.020  1.521
 9WM  C8   C7   single  1.542  0.020  1.542
 9WM  C7   C6   single  1.526  0.020  1.526
 9WM  C7   O7   single  1.399  0.020  1.399
 9WM  C6   C5   single  1.526  0.020  1.526
 9WM  C6   O6   single  1.501  0.020  1.501
 9WM  C4   C5   single  1.523  0.020  1.523
 9WM  C4   C3   single  1.504  0.020  1.504
 9WM  O6   C2   double  1.231  0.020  1.231
 9WM  C3   C2   single  1.503  0.020  1.503
 9WM  C3   F1   single  1.386  0.020  1.386
 9WM  C2   C1   single  1.524  0.020  1.524
 9WM  C1   O1A  double  1.195  0.020  1.195
 9WM  C1   O1B  single  1.300  0.020  1.300
 9WM  O1B  H1   single  0.850  0.020  0.980
 9WM  C3   H3   single  0.970  0.020  1.090
 9WM  C4   H4   single  0.970  0.020  1.090
 9WM  C4   H5   single  0.970  0.020  1.090
 9WM  C6   H6   single  0.970  0.020  1.090
 9WM  C7   H7   single  0.970  0.020  1.090
 9WM  C8   H8   single  0.970  0.020  1.090
 9WM  C9   H9   single  0.970  0.020  1.090
 9WM  C9   H10  single  0.970  0.020  1.090
 9WM  O9   H11  single  0.850  0.020  0.980
 9WM  O7   H12  single  0.850  0.020  0.980
 9WM  C5   H13  single  0.970  0.020  1.090
 9WM  N5   H14  single  0.860  0.020  1.020
 9WM  C11  H15  single  0.970  0.020  1.090
 9WM  C11  H16  single  0.970  0.020  1.090
 9WM  C11  H17  single  0.970  0.020  1.090
 9WM  O8   H18  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
 9WM  H1   O1B  C1   111.74  3.000
 9WM  C2   C1   O1A  119.08  3.000
 9WM  O1A  C1   O1B  129.81  3.000
 9WM  C2   C1   O1B  111.11  3.000
 9WM  O6   C2   C3   124.09  3.000
 9WM  C3   C2   C1   119.23  3.000
 9WM  O6   C2   C1   116.67  3.000
 9WM  H3   C3   C4   111.73  3.000
 9WM  H3   C3   F1   109.25  3.000
 9WM  C4   C3   F1   112.10  3.000
 9WM  H3   C3   C2   109.10  3.000
 9WM  F1   C3   C2   101.96  3.000
 9WM  C4   C3   C2   112.24  3.000
 9WM  H5   C4   H4   107.21  3.000
 9WM  H5   C4   C5   110.53  3.000
 9WM  H4   C4   C5   110.78  3.000
 9WM  H5   C4   C3   107.95  3.000
 9WM  H4   C4   C3   108.82  3.000
 9WM  C5   C4   C3   111.42  3.000
 9WM  C6   O6   C2   125.66  3.000
 9WM  H6   C6   C5   111.45  3.000
 9WM  H6   C6   C7   111.58  3.000
 9WM  C5   C6   C7   115.30  3.000
 9WM  H6   C6   O6   103.35  3.000
 9WM  C5   C6   O6   109.89  3.000
 9WM  C7   C6   O6   104.32  3.000
 9WM  H7   C7   O7   107.05  3.000
 9WM  H7   C7   C8   107.92  3.000
 9WM  O7   C7   C8   112.83  3.000
 9WM  H7   C7   C6   104.64  3.000
 9WM  O7   C7   C6   111.03  3.000
 9WM  C8   C7   C6   112.81  3.000
 9WM  H8   C8   O8   105.91  3.000
 9WM  H8   C8   C9   108.40  3.000
 9WM  O8   C8   C9   112.39  3.000
 9WM  H8   C8   C7   108.94  3.000
 9WM  C9   C8   C7   109.96  3.000
 9WM  O8   C8   C7   111.08  3.000
 9WM  H10  C9   H9   106.72  3.000
 9WM  H10  C9   O9   111.85  3.000
 9WM  H9   C9   O9   111.89  3.000
 9WM  H10  C9   C8   108.65  3.000
 9WM  H9   C9   C8   109.28  3.000
 9WM  O9   C9   C8   108.39  3.000
 9WM  H11  O9   C9   108.11  3.000
 9WM  H12  O7   C7   110.11  3.000
 9WM  H13  C5   N5   108.00  3.000
 9WM  H13  C5   C6   109.82  3.000
 9WM  N5   C5   C6   108.29  3.000
 9WM  H13  C5   C4   110.12  3.000
 9WM  C6   C5   C4   109.62  3.000
 9WM  N5   C5   C4   110.95  3.000
 9WM  H14  N5   C10  118.68  3.000
 9WM  H14  N5   C5   117.62  3.000
 9WM  C10  N5   C5   123.58  3.000
 9WM  C11  C10  O10  122.51  3.000
 9WM  O10  C10  N5   122.56  3.000
 9WM  C11  C10  N5   114.93  3.000
 9WM  H17  C11  H16  107.39  3.000
 9WM  H17  C11  H15  108.45  3.000
 9WM  H16  C11  H15  108.66  3.000
 9WM  H17  C11  C10  109.11  3.000
 9WM  H16  C11  C10  109.35  3.000
 9WM  H15  C11  C10  113.69  3.000
 9WM  H18  O8   C8   109.30  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
 9WM  CONST_01  C11  C10  N5   C5   180.00   0.0  0
 9WM  CONST_02  O10  C10  N5   C5     0.00   0.0  0
 9WM  CONST_03  H1   O1B  C1   C2   180.00   0.0  0
 9WM  CONST_04  H14  N5   C10  O10  180.00   0.0  0
 9WM  Var_01    O6   C2   C1   O1B  -18.61  30.0  2
 9WM  Var_02    H15  C11  C10  N5     3.58  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
 9WM  chir_01  C3  C4  C2  F1  positiv
 9WM  chir_02  C6  O6  C5  C7  positiv
 9WM  chir_03  C7  O7  C6  C8  negativ
 9WM  chir_04  C8  O8  C7  C9  negativ
 9WM  chir_05  C5  N5  C4  C6  positiv

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
 9WM  plan-1  C5   0.020
 9WM  plan-1  N5   0.020
 9WM  plan-1  C10  0.020
 9WM  plan-1  O10  0.020
 9WM  plan-1  C11  0.020
 9WM  plan-1  H14  0.020
 9WM  plan-2  O1B  0.020
 9WM  plan-2  C1   0.020
 9WM  plan-2  O1A  0.020
 9WM  plan-2  C2   0.020
 9WM  plan-2  H1   0.020

