# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:38:16 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)[C@@H]1OC(=C[C@H](O)[C@H]1NC(=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
 GC9  GC9  '2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic acid'  L-saccharide  38  21  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GC9
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
 GC9  CAA  C  CH1   0   0.061   0.6974   2.2234   0.7200
 GC9  CAB  C  C1    0  -0.365  -0.7316   2.6495   0.5617
 GC9  CAC  C  C     0   0.245  -1.6717   1.8143   0.1259
 GC9  CAE  C  CH1   0   0.040  -0.2666  -0.0500   0.3812
 GC9  CAF  C  CH1   0  -0.142   0.9159   0.8724   0.0412
 GC9  CAG  C  C     0   0.503  -3.0719   2.2688  -0.0945
 GC9  CAJ  C  CH1   0  -0.032  -0.1663  -1.4708  -0.1963
 GC9  CAL  C  CH1   0  -0.013  -1.4972  -2.2318  -0.0914
 GC9  CAM  C  CH2   0  -0.167  -1.3795  -3.6027  -0.7372
 GC9  CAS  C  CH2   0  -0.271   4.2106  -0.9388   0.2780
 GC9  NAP  N  NH1   0  -0.637   2.1926   0.3403   0.4288
 GC9  OAD  O  O2    0  -0.481  -1.4566   0.5160  -0.1542
 GC9  OAH  O  OH1   0  -0.582  -3.8515   1.3001  -0.5385
 GC9  OAI  O  O     0  -0.431  -3.4399   3.3993   0.1085
 GC9  OAK  O  OH1   0  -0.657   0.8801  -2.1882   0.4167
 GC9  OAN  O  OH1   0  -0.669  -1.9487  -2.3048   1.2447
 GC9  OAO  O  OH1   0  -0.671  -2.6595  -4.1897  -0.7763
 GC9  OAR  O  O     0  -0.485   2.8632  -0.3483  -1.6225
 GC9  OAT  O  OH1   0  -0.659   5.1482  -1.3227  -0.6837
 GC9  OAU  O  OH1   0  -0.658   1.5811   3.1494   0.1375
 GC9  H1   H  HCH1  0   0.237   0.9112   2.1081   1.7935
 GC9  H2   H  H     0   0.282  -0.9974   3.6701   0.8023
 GC9  H3   H  HCH1  0   0.243  -0.3761  -0.1145   1.4750
 GC9  H4   H  HCH1  0   0.280   0.9274   1.0212  -1.0417
 GC9  H5   H  HCH1  0   0.246   0.0996  -1.3971  -1.2560
 GC9  H6   H  HCH1  0   0.244  -2.2576  -1.6724  -0.6415
 GC9  H7   H  HCH2  0   0.202  -0.9596  -3.4787  -1.7444
 GC9  H8   H  HCH2  0   0.200  -0.6697  -4.2218  -0.1723
 GC9  H9   H  HCH2  0   0.229   4.6244  -0.2384   1.0156
 GC9  H10  H  HCH2  0   0.237   3.8168  -1.7933   0.8458
 GC9  H11  H  HNH1  0   0.398   2.3918   0.2913   1.4169
 GC9  H12  H  HOH1  0   0.490  -4.7496   1.6384  -0.6749
 GC9  H13  H  HOH1  0   0.443   0.7646  -2.1670   1.3729
 GC9  H14  H  HOH1  0   0.445  -1.4985  -3.0287   1.6922
 GC9  H15  H  HOH1  0   0.456  -2.5687  -5.0766  -1.1354
 GC9  H16  H  HOH1  0   0.461   5.8501  -1.8008  -0.2335
 GC9  H17  H  HOH1  0   0.460   1.6219   3.9294   0.6995
 GC9  CAQ  C  C     0   0.518   3.0289  -0.2899  -0.4178

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
 GC9  OAO  CAM  single  1.409  0.020  1.409
 GC9  CAM  CAL  single  1.520  0.020  1.520
 GC9  CAL  OAN  single  1.412  0.020  1.412
 GC9  CAL  CAJ  single  1.537  0.020  1.537
 GC9  OAK  CAJ  single  1.409  0.020  1.409
 GC9  CAJ  CAE  single  1.537  0.020  1.537
 GC9  OAR  CAQ  double  1.217  0.020  1.217
 GC9  CAS  CAQ  single  1.517  0.020  1.517
 GC9  CAS  OAT  single  1.397  0.020  1.397
 GC9  CAQ  NAP  single  1.347  0.020  1.347
 GC9  CAE  OAD  single  1.422  0.020  1.422
 GC9  CAE  CAF  single  1.538  0.020  1.538
 GC9  OAD  CAC  single  1.345  0.020  1.345
 GC9  NAP  CAF  single  1.436  0.020  1.436
 GC9  CAF  CAA  single  1.528  0.020  1.528
 GC9  OAI  CAG  double  1.206  0.020  1.206
 GC9  CAC  CAG  single  1.489  0.020  1.489
 GC9  CAC  CAB  double  1.331  0.020  1.331
 GC9  CAG  OAH  single  1.320  0.020  1.320
 GC9  CAA  CAB  single  1.500  0.020  1.500
 GC9  CAA  OAU  single  1.406  0.020  1.406
 GC9  CAA  H1   single  0.970  0.020  1.090
 GC9  CAB  H2   single  0.930  0.020  1.080
 GC9  CAE  H3   single  0.970  0.020  1.090
 GC9  CAF  H4   single  0.970  0.020  1.090
 GC9  CAJ  H5   single  0.970  0.020  1.090
 GC9  CAL  H6   single  0.970  0.020  1.090
 GC9  CAM  H7   single  0.970  0.020  1.090
 GC9  CAM  H8   single  0.970  0.020  1.090
 GC9  CAS  H9   single  0.970  0.020  1.090
 GC9  CAS  H10  single  0.970  0.020  1.090
 GC9  NAP  H11  single  0.860  0.020  1.020
 GC9  OAH  H12  single  0.850  0.020  0.980
 GC9  OAK  H13  single  0.850  0.020  0.980
 GC9  OAN  H14  single  0.850  0.020  0.980
 GC9  OAO  H15  single  0.850  0.020  0.980
 GC9  OAT  H16  single  0.850  0.020  0.980
 GC9  OAU  H17  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
 GC9  H1   CAA  OAU  110.54  3.000
 GC9  H1   CAA  CAF  108.24  3.000
 GC9  OAU  CAA  CAF  107.96  3.000
 GC9  H1   CAA  CAB  108.54  3.000
 GC9  OAU  CAA  CAB  111.59  3.000
 GC9  CAF  CAA  CAB  109.92  3.000
 GC9  H2   CAB  CAC  119.43  3.000
 GC9  H2   CAB  CAA  118.60  3.000
 GC9  CAC  CAB  CAA  121.96  3.000
 GC9  OAD  CAC  CAG  114.47  3.000
 GC9  CAG  CAC  CAB  121.42  3.000
 GC9  OAD  CAC  CAB  124.11  3.000
 GC9  H3   CAE  OAD  108.30  3.000
 GC9  H3   CAE  CAJ  109.00  3.000
 GC9  OAD  CAE  CAJ  106.32  3.000
 GC9  H3   CAE  CAF  109.34  3.000
 GC9  OAD  CAE  CAF  108.75  3.000
 GC9  CAJ  CAE  CAF  114.91  3.000
 GC9  H4   CAF  NAP  107.96  3.000
 GC9  H4   CAF  CAE  107.98  3.000
 GC9  NAP  CAF  CAE  113.68  3.000
 GC9  H4   CAF  CAA  108.74  3.000
 GC9  NAP  CAF  CAA  109.56  3.000
 GC9  CAE  CAF  CAA  108.80  3.000
 GC9  OAI  CAG  OAH  124.34  3.000
 GC9  OAH  CAG  CAC  112.41  3.000
 GC9  OAI  CAG  CAC  123.25  3.000
 GC9  H5   CAJ  OAK  105.96  3.000
 GC9  H5   CAJ  CAL  108.04  3.000
 GC9  OAK  CAJ  CAL  111.19  3.000
 GC9  H5   CAJ  CAE  108.49  3.000
 GC9  OAK  CAJ  CAE  110.83  3.000
 GC9  CAL  CAJ  CAE  112.06  3.000
 GC9  H6   CAL  OAN  106.28  3.000
 GC9  H6   CAL  CAM  107.56  3.000
 GC9  OAN  CAL  CAM  112.34  3.000
 GC9  H6   CAL  CAJ  108.35  3.000
 GC9  OAN  CAL  CAJ  111.54  3.000
 GC9  CAM  CAL  CAJ  110.52  3.000
 GC9  H8   CAM  H7   106.76  3.000
 GC9  H8   CAM  OAO  111.50  3.000
 GC9  H7   CAM  OAO  111.65  3.000
 GC9  H8   CAM  CAL  109.88  3.000
 GC9  H7   CAM  CAL  108.51  3.000
 GC9  OAO  CAM  CAL  108.50  3.000
 GC9  H10  CAS  H9   106.50  3.000
 GC9  H10  CAS  OAT  112.49  3.000
 GC9  H9   CAS  OAT  112.63  3.000
 GC9  H10  CAS  CAQ  106.88  3.000
 GC9  H9   CAS  CAQ  109.20  3.000
 GC9  OAT  CAS  CAQ  108.94  3.000
 GC9  H11  NAP  CAQ  118.05  3.000
 GC9  H11  NAP  CAF  117.23  3.000
 GC9  CAQ  NAP  CAF  123.76  3.000
 GC9  CAE  OAD  CAC  116.06  3.000
 GC9  H12  OAH  CAG  109.78  3.000
 GC9  H13  OAK  CAJ  109.37  3.000
 GC9  H14  OAN  CAL  109.21  3.000
 GC9  H15  OAO  CAM  108.00  3.000
 GC9  H16  OAT  CAS  107.72  3.000
 GC9  H17  OAU  CAA  108.57  3.000
 GC9  OAR  CAQ  NAP  124.06  3.000
 GC9  NAP  CAQ  CAS  113.30  3.000
 GC9  OAR  CAQ  CAS  122.64  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
 GC9  CONST_01  OAR  CAQ  NAP  CAF     0.00   0.0  0
 GC9  CONST_02  CAS  CAQ  NAP  CAF   180.00   0.0  0
 GC9  CONST_03  H12  OAH  CAG  CAC   180.00   0.0  0
 GC9  CONST_04  H11  NAP  CAQ  CAS     0.00   0.0  0
 GC9  Var_01    OAD  CAC  CAB  CAA     3.05  30.0  1
 GC9  Var_02    OAI  CAG  CAC  CAB    -0.31  30.0  2
 GC9  Var_03    OAT  CAS  CAQ  NAP  -168.06  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
 GC9  chir_01  CAA  CAF  CAB  OAU  positiv
 GC9  chir_02  CAE  OAD  CAF  CAJ  positiv
 GC9  chir_03  CAF  NAP  CAA  CAE  positiv
 GC9  chir_04  CAJ  OAK  CAL  CAE  negativ
 GC9  chir_05  CAL  OAN  CAJ  CAM  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
 GC9  plan-1  CAF  0.020
 GC9  plan-1  CAS  0.020
 GC9  plan-1  NAP  0.020
 GC9  plan-1  OAR  0.020
 GC9  plan-1  H11  0.020
 GC9  plan-1  CAQ  0.020
 GC9  plan-2  CAC  0.020
 GC9  plan-2  CAG  0.020
 GC9  plan-2  OAH  0.020
 GC9  plan-2  OAI  0.020
 GC9  plan-2  H12  0.020

