# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:05:20 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-1-O-(propylcarbamoyl)-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=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
 GYU  GYU  2-(acetylamino)-2-deoxy-1-O-(propylcarbamoyl)-alpha-D-glucopyranose  D-saccharide  43  21  .  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_GYU
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
 GYU  C1    C  C     0   0.765   1.5230   1.9944   3.4190
 GYU  O1A   O  O     0  -0.507   2.5701   2.0277   4.0273
 GYU  O1B   O  O2    0  -0.519   1.3749   1.3950   2.2134
 GYU  C12   C  CH2   0  -0.304   0.2396   3.2937   5.0419
 GYU  C13   C  CH2   0  -0.432   0.6509   4.7537   4.8947
 GYU  C14   C  CH3   0  -0.666  -0.1849   5.5174   3.8778
 GYU  C5    C  CH1   0  -0.194   2.2529   0.5010   0.2085
 GYU  N5    N  NH1   0  -0.628   2.1725   1.7994  -0.4043
 GYU  C10   C  C     0   0.527   2.8020   2.1180  -1.5537
 GYU  O10   O  O     0  -0.501   3.5646   1.3563  -2.1310
 GYU  C11   C  CH3   0  -0.779   2.5078   3.4985  -2.0822
 GYU  C6    C  CH1   0   0.011   1.0411  -0.3757  -0.1149
 GYU  O6    O  OH1   0  -0.653   0.8718  -0.5547  -1.4998
 GYU  C7    C  CH1   0   0.027   1.1709  -1.7124   0.6160
 GYU  O7    O  OH1   0  -0.670   0.0213  -2.5030   0.4563
 GYU  C15   C  CH1   0   0.284   2.4509   0.6209   1.7184
 GYU  O8    O  O2    0  -0.496   2.4924  -0.6241   2.3216
 GYU  NAC   N  NH1   0  -0.653   0.3622   2.5223   3.8223
 GYU  C8    C  CH1   0  -0.034   1.3660  -1.4692   2.1098
 GYU  C9    C  CH2   0  -0.171   1.6467  -2.7468   2.8822
 GYU  O9    O  OH1   0  -0.665   1.7724  -2.5235   4.2652
 GYU  HAC   H  HNH1  0   0.405  -0.4378   2.4532   3.2145
 GYU  H15   H  HCH1  0   0.276   3.4041   1.1058   1.9368
 GYU  H121  H  HCH2  0   0.253   0.8265   2.8155   5.8265
 GYU  H122  H  HCH2  0   0.249  -0.8050   3.2335   5.3501
 GYU  H131  H  HCH2  0   0.229   0.5567   5.2229   5.8774
 GYU  H132  H  HCH2  0   0.226   1.7096   4.8083   4.6289
 GYU  H141  H  HCH3  0   0.218  -1.2467   5.4776   4.1288
 GYU  H142  H  HCH3  0   0.232   0.1061   6.5673   3.8408
 GYU  H143  H  HCH3  0   0.221  -0.0662   5.1122   2.8719
 GYU  H5    H  HCH1  0   0.286   3.1513   0.0102  -0.1758
 GYU  HA    H  HNH1  0   0.401   1.4966   2.4491  -0.0345
 GYU  H6    H  HCH1  0   0.244   0.1261   0.1185   0.2294
 GYU  H111  H  HCH3  0   0.267   3.4442   4.0280  -2.2543
 GYU  H112  H  HCH3  0   0.269   2.0030   3.4129  -3.0450
 GYU  H113  H  HCH3  0   0.250   1.8854   4.0969  -1.4200
 GYU  HB    H  HOH1  0   0.447   1.6956  -0.8849  -1.8770
 GYU  H7    H  HCH1  0   0.210   2.0650  -2.2303   0.2278
 GYU  HC    H  HOH1  0   0.454  -0.1530  -2.5882  -0.4873
 GYU  H8    H  HCH1  0   0.236   0.4581  -1.0016   2.5154
 GYU  H9C1  H  HCH2  0   0.202   2.5398  -3.2317   2.4636
 GYU  H9C2  H  HCH2  0   0.237   0.8109  -3.4322   2.7448
 GYU  H9    H  HOH1  0   0.448   2.5252  -1.9413   4.4078

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
 GYU  C1   O1A   double  1.211  0.020  1.211
 GYU  C1   O1B   single  1.354  0.020  1.354
 GYU  C12  C13   single  1.524  0.020  1.524
 GYU  C13  C14   single  1.522  0.020  1.522
 GYU  C5   N5    single  1.438  0.020  1.438
 GYU  N5   C10   single  1.349  0.020  1.349
 GYU  C10  O10   double  1.223  0.020  1.223
 GYU  C10  C11   single  1.507  0.020  1.507
 GYU  C5   C6    single  1.530  0.020  1.530
 GYU  C6   O6    single  1.407  0.020  1.407
 GYU  C6   C7    single  1.529  0.020  1.529
 GYU  C7   O7    single  1.404  0.020  1.404
 GYU  O1B  C15   single  1.415  0.020  1.415
 GYU  C5   C15   single  1.528  0.020  1.528
 GYU  C15  O8    single  1.384  0.020  1.384
 GYU  C1   NAC   single  1.337  0.020  1.337
 GYU  C12  NAC   single  1.448  0.020  1.448
 GYU  C7   C8    single  1.526  0.020  1.526
 GYU  O8   C8    single  1.424  0.020  1.424
 GYU  C8   C9    single  1.519  0.020  1.519
 GYU  C9   O9    single  1.406  0.020  1.406
 GYU  NAC  HAC   single  0.860  0.020  1.020
 GYU  C15  H15   single  0.970  0.020  1.090
 GYU  C12  H121  single  0.970  0.020  1.090
 GYU  C12  H122  single  0.970  0.020  1.090
 GYU  C13  H131  single  0.970  0.020  1.090
 GYU  C13  H132  single  0.970  0.020  1.090
 GYU  C14  H141  single  0.970  0.020  1.090
 GYU  C14  H142  single  0.970  0.020  1.090
 GYU  C14  H143  single  0.970  0.020  1.090
 GYU  C5   H5    single  0.970  0.020  1.090
 GYU  N5   HA    single  0.860  0.020  1.020
 GYU  C6   H6    single  0.970  0.020  1.090
 GYU  C11  H111  single  0.970  0.020  1.090
 GYU  C11  H112  single  0.970  0.020  1.090
 GYU  C11  H113  single  0.970  0.020  1.090
 GYU  O6   HB    single  0.850  0.020  0.980
 GYU  C7   H7    single  0.970  0.020  1.090
 GYU  O7   HC    single  0.850  0.020  0.980
 GYU  C8   H8    single  0.970  0.020  1.090
 GYU  C9   H9C1  single  0.970  0.020  1.090
 GYU  C9   H9C2  single  0.970  0.020  1.090
 GYU  O9   H9    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
 GYU  NAC   C1   O1B   110.38  3.000
 GYU  NAC   C1   O1A   126.01  3.000
 GYU  O1B   C1   O1A   123.61  3.000
 GYU  C15   O1B  C1    118.06  3.000
 GYU  H122  C12  H121  106.74  3.000
 GYU  H122  C12  NAC   106.83  3.000
 GYU  H121  C12  NAC   109.08  3.000
 GYU  H122  C12  C13   109.80  3.000
 GYU  H121  C12  C13   110.15  3.000
 GYU  NAC   C12  C13   113.96  3.000
 GYU  H132  C13  H131  106.30  3.000
 GYU  H132  C13  C14   110.15  3.000
 GYU  H131  C13  C14   109.76  3.000
 GYU  H132  C13  C12   109.44  3.000
 GYU  H131  C13  C12   107.52  3.000
 GYU  C14   C13  C12   113.39  3.000
 GYU  H143  C14  H142  107.30  3.000
 GYU  H143  C14  H141  107.72  3.000
 GYU  H142  C14  H141  107.60  3.000
 GYU  H143  C14  C13   111.72  3.000
 GYU  H142  C14  C13   111.06  3.000
 GYU  H141  C14  C13   111.23  3.000
 GYU  H5    C5   C15   106.03  3.000
 GYU  H5    C5   C6    108.61  3.000
 GYU  C15   C5   C6    110.89  3.000
 GYU  H5    C5   N5    107.54  3.000
 GYU  C15   C5   N5    110.95  3.000
 GYU  C6    C5   N5    112.52  3.000
 GYU  HA    N5   C10   118.26  3.000
 GYU  HA    N5   C5    117.59  3.000
 GYU  C10   N5   C5    123.40  3.000
 GYU  C11   C10  O10   121.79  3.000
 GYU  C11   C10  N5    115.10  3.000
 GYU  O10   C10  N5    123.12  3.000
 GYU  H113  C11  H112  108.40  3.000
 GYU  H113  C11  H111  108.69  3.000
 GYU  H112  C11  H111  107.25  3.000
 GYU  H113  C11  C10   113.70  3.000
 GYU  H112  C11  C10   109.15  3.000
 GYU  H111  C11  C10   109.44  3.000
 GYU  H6    C6   C7    108.37  3.000
 GYU  H6    C6   O6    105.44  3.000
 GYU  C7    C6   O6    111.69  3.000
 GYU  H6    C6   C5    109.66  3.000
 GYU  C7    C6   C5    109.43  3.000
 GYU  O6    C6   C5    112.11  3.000
 GYU  HB    O6   C6    109.02  3.000
 GYU  H7    C7   C8    108.39  3.000
 GYU  H7    C7   O7    111.04  3.000
 GYU  C8    C7   O7    107.79  3.000
 GYU  H7    C7   C6    108.11  3.000
 GYU  C8    C7   C6    109.85  3.000
 GYU  O7    C7   C6    111.61  3.000
 GYU  HC    O7   C7    108.01  3.000
 GYU  H15   C15  O8    106.63  3.000
 GYU  H15   C15  C5    110.24  3.000
 GYU  O8    C15  C5    111.35  3.000
 GYU  H15   C15  O1B   110.55  3.000
 GYU  O8    C15  O1B   111.25  3.000
 GYU  C5    C15  O1B   106.87  3.000
 GYU  C8    O8   C15   116.44  3.000
 GYU  HAC   NAC  C12   118.52  3.000
 GYU  HAC   NAC  C1    118.71  3.000
 GYU  C12   NAC  C1    122.52  3.000
 GYU  H8    C8   C9    108.84  3.000
 GYU  H8    C8   O8    110.25  3.000
 GYU  C9    C8   O8    106.10  3.000
 GYU  H8    C8   C7    108.88  3.000
 GYU  C9    C8   C7    112.79  3.000
 GYU  O8    C8   C7    109.95  3.000
 GYU  H9C2  C9   H9C1  107.32  3.000
 GYU  H9C2  C9   O9    107.00  3.000
 GYU  H9C1  C9   O9    111.84  3.000
 GYU  H9C2  C9   C8    108.85  3.000
 GYU  H9C1  C9   C8    109.12  3.000
 GYU  O9    C9   C8    112.52  3.000
 GYU  H9    O9   C9    108.16  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
 GYU  CONST_01  O10   C10  N5   C5      0.00   0.0  0
 GYU  CONST_02  C11   C10  N5   C5    180.00   0.0  0
 GYU  CONST_03  HA    N5   C10  O10   180.00   0.0  0
 GYU  Var_01    NAC   C1   O1B  C15  -171.27  30.0  1
 GYU  Var_02    C13   C12  NAC  C1     82.28  30.0  1
 GYU  Var_03    C12   NAC  C1   O1A     3.99  30.0  2
 GYU  Var_04    NAC   C12  C13  C14    60.72  30.0  1
 GYU  Var_05    H141  C14  C13  C12    57.20  30.0  3
 GYU  Var_06    H111  C11  C10  N5    126.63  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
 GYU  chir_01  C5   N5  C6   C15  positiv
 GYU  chir_02  C6   O6  C5   C7   positiv
 GYU  chir_03  C7   O7  C6   C8   negativ
 GYU  chir_04  C15  O8  O1B  C5   positiv
 GYU  chir_05  C8   O8  C7   C9   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
 GYU  plan-1  C5   0.020
 GYU  plan-1  N5   0.020
 GYU  plan-1  C10  0.020
 GYU  plan-1  O10  0.020
 GYU  plan-1  C11  0.020
 GYU  plan-1  HA   0.020
 GYU  plan-2  C1   0.020
 GYU  plan-2  O1A  0.020
 GYU  plan-2  O1B  0.020
 GYU  plan-2  NAC  0.020

