# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:02:14 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-{[(2E)-but-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C=C\C(=O)N[C@H]1[C@H](O)O[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
 9CD  9CD  2-{[(2E)-but-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose  D-saccharide  34  17  .  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_9CD
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
 9CD  O01  O  OH1   0  -0.662   0.1391   2.3244   0.4611
 9CD  C02  C  CH1   0   0.042   0.7401   1.2172  -0.1555
 9CD  C03  C  CH1   0  -0.003   2.1949   1.0476   0.2706
 9CD  O04  O  OH1   0  -0.674   2.9002   2.1692  -0.2148
 9CD  C05  C  CH1   0  -0.022   2.7482  -0.2646  -0.2930
 9CD  C06  C  CH2   0  -0.159   4.1646  -0.5335   0.1648
 9CD  O07  O  OH1   0  -0.669   4.6379  -1.6963  -0.4711
 9CD  O08  O  O2    0  -0.496   1.9351  -1.3317   0.1480
 9CD  C09  C  CH1   0   0.308   0.6178  -1.2739  -0.3407
 9CD  C10  C  CH1   0  -0.157  -0.0792  -0.0207   0.1958
 9CD  N11  N  NH1   0  -0.657  -1.4131   0.0859  -0.3292
 9CD  C12  C  C     0   0.556  -2.5367   0.0204   0.4125
 9CD  C13  C  C1    0  -0.396  -3.7814   0.1588  -0.3801
 9CD  C14  C  C1    0  -0.161  -4.9830   0.1723   0.1934
 9CD  C15  C  CH3   0  -0.712  -6.2704   0.3119  -0.5379
 9CD  O16  O  O     0  -0.501  -2.5330  -0.1333   1.6276
 9CD  H1   H  HOH1  0   0.451   0.6575   3.1039   0.2346
 9CD  H2   H  HCH1  0   0.207   0.7339   1.3331  -1.2536
 9CD  H3   H  HCH1  0   0.228   2.2332   1.0009   1.3684
 9CD  H4   H  HOH1  0   0.464   3.6001   2.3939   0.4041
 9CD  H5   H  HCH1  0   0.221   2.7368  -0.2056  -1.3944
 9CD  H6   H  HCH2  0   0.205   4.7784   0.3391  -0.0859
 9CD  H7   H  HCH2  0   0.199   4.1756  -0.6334   1.2592
 9CD  H8   H  HOH1  0   0.457   5.5602  -1.8138  -0.2268
 9CD  H9   H  HCH1  0   0.186   0.6439  -1.2312  -1.4441
 9CD  H11  H  HCH1  0   0.273  -0.1475  -0.1069   1.2832
 9CD  H12  H  HNH1  0   0.399  -1.5086   0.2347  -1.3221
 9CD  H13  H  H     0   0.259  -3.6914   0.2530  -1.4580
 9CD  H14  H  H     0   0.256  -5.0467   0.0783   1.2732
 9CD  H15  H  HCH3  0   0.250  -6.9157  -0.5475  -0.3442
 9CD  H16  H  HCH3  0   0.250  -6.8170   1.1896  -0.1866
 9CD  H17  H  HCH3  0   0.243  -6.1275   0.4006  -1.6139
 9CD  O1   O  OH1   0  -0.650  -0.0640  -2.3821   0.1066
 9CD  H10  H  HOH1  0   0.466   0.1545  -3.1374  -0.4494

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
 9CD  O01  C02  single  1.403  0.020  1.403
 9CD  C14  C15  single  1.487  0.020  1.487
 9CD  C14  C13  double  1.332  0.020  1.332
 9CD  O16  C12  double  1.225  0.020  1.225
 9CD  O04  C03  single  1.411  0.020  1.411
 9CD  C03  C02  single  1.525  0.020  1.525
 9CD  C03  C05  single  1.532  0.020  1.532
 9CD  C02  C10  single  1.525  0.020  1.525
 9CD  C12  C13  single  1.482  0.020  1.482
 9CD  C12  N11  single  1.348  0.020  1.348
 9CD  C10  N11  single  1.437  0.020  1.437
 9CD  C10  C09  single  1.531  0.020  1.531
 9CD  O07  C06  single  1.407  0.020  1.407
 9CD  O08  C05  single  1.412  0.020  1.412
 9CD  O08  C09  single  1.406  0.020  1.406
 9CD  C05  C06  single  1.513  0.020  1.513
 9CD  O01  H1   single  0.850  0.020  0.980
 9CD  C02  H2   single  0.970  0.020  1.090
 9CD  C03  H3   single  0.970  0.020  1.090
 9CD  O04  H4   single  0.850  0.020  0.980
 9CD  C05  H5   single  0.970  0.020  1.090
 9CD  C06  H6   single  0.970  0.020  1.090
 9CD  C06  H7   single  0.970  0.020  1.090
 9CD  O07  H8   single  0.850  0.020  0.980
 9CD  C09  H9   single  0.970  0.020  1.090
 9CD  C10  H11  single  0.970  0.020  1.090
 9CD  N11  H12  single  0.860  0.020  1.020
 9CD  C13  H13  single  0.930  0.020  1.080
 9CD  C14  H14  single  0.930  0.020  1.080
 9CD  C15  H15  single  0.970  0.020  1.090
 9CD  C15  H16  single  0.970  0.020  1.090
 9CD  C15  H17  single  0.970  0.020  1.090
 9CD  C09  O1   single  1.376  0.020  1.376
 9CD  O1   H10  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
 9CD  H1   O01  C02  107.75  3.000
 9CD  H2   C02  C10  108.13  3.000
 9CD  H2   C02  C03  107.15  3.000
 9CD  C10  C02  C03  110.95  3.000
 9CD  H2   C02  O01  110.61  3.000
 9CD  C10  C02  O01  108.01  3.000
 9CD  C03  C02  O01  111.94  3.000
 9CD  H3   C03  C05  108.57  3.000
 9CD  H3   C03  O04  111.09  3.000
 9CD  C05  C03  O04  111.95  3.000
 9CD  H3   C03  C02  108.48  3.000
 9CD  C05  C03  C02  109.70  3.000
 9CD  O04  C03  C02  106.99  3.000
 9CD  H4   O04  C03  109.18  3.000
 9CD  H5   C05  O08  110.26  3.000
 9CD  H5   C05  C06  108.74  3.000
 9CD  O08  C05  C06  108.07  3.000
 9CD  H5   C05  C03  108.54  3.000
 9CD  C06  C05  C03  112.28  3.000
 9CD  O08  C05  C03  108.93  3.000
 9CD  H7   C06  H6   107.13  3.000
 9CD  H7   C06  O07  111.81  3.000
 9CD  H6   C06  O07  111.48  3.000
 9CD  H7   C06  C05  109.08  3.000
 9CD  H6   C06  C05  108.28  3.000
 9CD  O07  C06  C05  108.97  3.000
 9CD  H8   O07  C06  107.99  3.000
 9CD  C09  O08  C05  113.56  3.000
 9CD  O1   C09  H9   111.57  3.000
 9CD  O1   C09  C10  108.65  3.000
 9CD  H9   C09  C10  109.22  3.000
 9CD  O1   C09  O08  108.55  3.000
 9CD  H9   C09  O08  109.07  3.000
 9CD  C10  C09  O08  109.77  3.000
 9CD  H11  C10  N11  108.13  3.000
 9CD  H11  C10  C09  108.21  3.000
 9CD  N11  C10  C09  110.80  3.000
 9CD  H11  C10  C02  109.07  3.000
 9CD  C09  C10  C02  109.82  3.000
 9CD  N11  C10  C02  110.74  3.000
 9CD  H12  N11  C12  118.04  3.000
 9CD  H12  N11  C10  117.28  3.000
 9CD  C12  N11  C10  124.68  3.000
 9CD  O16  C12  C13  123.01  3.000
 9CD  C13  C12  N11  113.66  3.000
 9CD  O16  C12  N11  123.33  3.000
 9CD  H13  C13  C14  120.10  3.000
 9CD  H13  C13  C12  118.00  3.000
 9CD  C14  C13  C12  121.91  3.000
 9CD  H14  C14  C15  116.51  3.000
 9CD  H14  C14  C13  118.71  3.000
 9CD  C15  C14  C13  124.78  3.000
 9CD  H17  C15  H16  108.55  3.000
 9CD  H17  C15  H15  108.48  3.000
 9CD  H16  C15  H15  106.25  3.000
 9CD  H17  C15  C14  112.32  3.000
 9CD  H16  C15  C14  110.52  3.000
 9CD  H15  C15  C14  110.51  3.000
 9CD  H10  O1   C09  109.36  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
 9CD  CONST_01  O16  C12  N11  C10     0.00   0.0  0
 9CD  CONST_02  C13  C12  N11  C10   180.00   0.0  0
 9CD  CONST_03  H12  N11  C12  C13     0.00   0.0  0
 9CD  Var_01    C15  C14  C13  C12   179.79   0.0  2
 9CD  Var_02    C14  C13  C12  N11  -177.24  30.0  2
 9CD  Var_03    H15  C15  C14  C13   121.48  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
 9CD  chir_01  C02  O01  C03  C10  negativ
 9CD  chir_02  C03  O04  C02  C05  negativ
 9CD  chir_03  C05  O08  C03  C06  negativ
 9CD  chir_04  C09  O08  O1   C10  negativ
 9CD  chir_05  C10  N11  C02  C09  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
 9CD  plan-1  C10  0.020
 9CD  plan-1  N11  0.020
 9CD  plan-1  C12  0.020
 9CD  plan-1  C13  0.020
 9CD  plan-1  O16  0.020
 9CD  plan-1  H12  0.020
 9CD  plan-2  C12  0.020
 9CD  plan-2  C13  0.020
 9CD  plan-2  C14  0.020
 9CD  plan-2  C15  0.020
 9CD  plan-2  H13  0.020
 9CD  plan-2  H14  0.020

