# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 03:40:33 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (1R)-4-(acetylamino)-1,5-anhydro-3-carbamimidamido-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@H](C[C@H](O[C@H]1[C@H](O)[C@H](O)CO)[S](O)(=O)=O)NC(N)=N
#
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
 GYG  GYG  (1R)-4-(acetylamino)-1,5-anhydro-3-carbamimidamido-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol  D-saccharide  45  24  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GYG
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
 GYG  C2    C  CH1    0  -0.182   7.2219  24.9925   9.6810
 GYG  C3    C  CH2    0  -0.447   7.6908  26.4131   9.4347
 GYG  C4    C  CH1    0  -0.099   8.6661  26.8151  10.5332
 GYG  C5    C  CH1    0  -0.085   9.7948  25.7755  10.6270
 GYG  C11   C  CH3    0  -0.779  12.6211  26.9945  12.8233
 GYG  C6    C  CH1    0   0.053   9.1987  24.3685  10.7941
 GYG  C7    C  CH1    0   0.013  10.2639  23.2794  10.8005
 GYG  C8    C  CH1    0  -0.000   9.6718  21.8868  11.0652
 GYG  C9    C  CH2    0  -0.198  10.6957  20.7789  10.8693
 GYG  N06   N  NH1    0  -0.620   9.1708  28.1509  10.2957
 GYG  N08   N  N      0  -0.706  10.6476  29.7447  11.0253
 GYG  N09   N  NH2    0  -0.823   8.9974  28.8894  12.4931
 GYG  N5    N  NH1    0  -0.629  10.6838  26.0942  11.7136
 GYG  O01   O  OS     0  -0.755   5.0432  25.4073   8.3266
 GYG  O10   O  O      0  -0.489  12.5209  26.5598  10.4743
 GYG  O7    O  OH1    0  -0.673  10.9447  23.3152   9.5674
 GYG  O8    O  OH1    0  -0.673   9.1673  21.9196  12.3846
 GYG  O9    O  OH1    0  -0.671  11.8602  21.0592  11.6124
 GYG  O6    O  O2     0  -0.494   8.2997  24.1001   9.7384
 GYG  O23   O  OS     0  -0.754   6.9327  24.3548   7.1393
 GYG  O24   O  OS    -1  -0.751   5.6596  23.0685   8.8146
 GYG  S02   S  S      0   1.414   6.1149  24.3954   8.3650
 GYG  H031  H  HCH1   0   0.237   6.6332  24.9564  10.6115
 GYG  H32   H  HCH2   0   0.239   8.1803  26.4764   8.4581
 GYG  H31   H  HCH2   0   0.258   6.8411  27.0954   9.4303
 GYG  H4    H  HCH1   0   0.247   8.1184  26.8078  11.4803
 GYG  H5    H  HCH1   0   0.262  10.3741  25.8060   9.7024
 GYG  H111  H  HCH3   0   0.259  13.6686  26.6997  12.8272
 GYG  H113  H  HCH3   0   0.263  12.5841  28.0853  12.8477
 GYG  H112  H  HCH3   0   0.248  12.1460  26.6218  13.7292
 GYG  H6    H  HCH1   0   0.229   8.6666  24.3360  11.7580
 GYG  H7    H  HCH1   0   0.230  10.9406  23.5103  11.6318
 GYG  H8    H  HCH1   0   0.217   8.8699  21.6924  10.3401
 GYG  H92   H  HCH2   0   0.212  10.2368  19.8287  11.1783
 GYG  H91   H  HCH2   0   0.201  10.9074  20.6816   9.7978
 GYG  H061  H  HNH1   0   0.370   9.7278  28.2252   9.4556
 GYG  H081  H  H      0   0.314  10.8193  30.3859  11.7911
 GYG  H1    H  HNH2   0   0.388   9.2064  29.6278  13.1460
 GYG  H091  H  HNH2   0   0.389   8.0098  28.6893  12.4579
 GYG  HN5   H  HNH1   0   0.395  10.2789  26.1485  12.6357
 GYG  HO7   H  HOH1   0   0.454  11.8449  23.0099   9.7112
 GYG  HO8   H  HOH1   0   0.452   8.6155  21.1437  12.5206
 GYG  HO9   H  HOH1   0   0.455  12.5060  20.3696  11.4348
 GYG  C07   C  C      0   0.518   9.6545  28.9766  11.2871
 GYG  C10   C  C      0   0.514  11.9533  26.5238  11.5559

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
 GYG  O23  S02   deloc   1.474  0.020  1.474
 GYG  O01  S02   deloc   1.474  0.020  1.474
 GYG  S02  O24   deloc   1.473  0.020  1.473
 GYG  S02  C2    single  1.820  0.020  1.820
 GYG  C3   C2    single  1.516  0.020  1.516
 GYG  C3   C4    single  1.523  0.020  1.523
 GYG  O7   C7    single  1.409  0.020  1.409
 GYG  O6   C2    single  1.400  0.020  1.400
 GYG  O6   C6    single  1.412  0.020  1.412
 GYG  N06  C4    single  1.448  0.020  1.448
 GYG  N06  C07   single  1.378  0.020  1.378
 GYG  C4   C5    single  1.537  0.020  1.537
 GYG  O10  C10   double  1.222  0.020  1.222
 GYG  C5   C6    single  1.537  0.020  1.537
 GYG  C5   N5    single  1.440  0.020  1.440
 GYG  C6   C7    single  1.523  0.020  1.523
 GYG  C7   C8    single  1.536  0.020  1.536
 GYG  N08  C07   double  1.283  0.020  1.283
 GYG  C9   C8    single  1.521  0.020  1.521
 GYG  C9   O9    single  1.410  0.020  1.410
 GYG  C8   O8    single  1.413  0.020  1.413
 GYG  C07  N09   single  1.376  0.020  1.376
 GYG  C10  N5    single  1.349  0.020  1.349
 GYG  C10  C11   single  1.508  0.020  1.508
 GYG  C2   H031  single  0.970  0.020  1.090
 GYG  C3   H32   single  0.970  0.020  1.090
 GYG  C3   H31   single  0.970  0.020  1.090
 GYG  C4   H4    single  0.970  0.020  1.090
 GYG  C5   H5    single  0.970  0.020  1.090
 GYG  C11  H111  single  0.970  0.020  1.090
 GYG  C11  H113  single  0.970  0.020  1.090
 GYG  C11  H112  single  0.970  0.020  1.090
 GYG  C6   H6    single  0.970  0.020  1.090
 GYG  C7   H7    single  0.970  0.020  1.090
 GYG  C8   H8    single  0.970  0.020  1.090
 GYG  C9   H92   single  0.970  0.020  1.090
 GYG  C9   H91   single  0.970  0.020  1.090
 GYG  N06  H061  single  0.890  0.020  1.040
 GYG  N08  H081  single  0.890  0.020  1.040
 GYG  N09  H1    single  0.890  0.020  1.040
 GYG  N09  H091  single  0.890  0.020  1.040
 GYG  N5   HN5   single  0.860  0.020  1.020
 GYG  O7   HO7   single  0.850  0.020  0.980
 GYG  O8   HO8   single  0.850  0.020  0.980
 GYG  O9   HO9   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
 GYG  H031  C2   S02   105.95  3.000
 GYG  H031  C2   O6    110.84  3.000
 GYG  S02   C2   O6    106.77  3.000
 GYG  H031  C2   C3    109.46  3.000
 GYG  O6    C2   C3    111.46  3.000
 GYG  S02   C2   C3    112.21  3.000
 GYG  H31   C3   H32   108.00  3.000
 GYG  H31   C3   C4    109.69  3.000
 GYG  H32   C3   C4    110.00  3.000
 GYG  H31   C3   C2    110.25  3.000
 GYG  H32   C3   C2    109.72  3.000
 GYG  C4    C3   C2    109.16  3.000
 GYG  H4    C4   N06   108.82  3.000
 GYG  H4    C4   C5    108.07  3.000
 GYG  N06   C4   C5    112.21  3.000
 GYG  H4    C4   C3    107.58  3.000
 GYG  C5    C4   C3    109.62  3.000
 GYG  N06   C4   C3    110.40  3.000
 GYG  H5    C5   N5    107.79  3.000
 GYG  H5    C5   C6    108.87  3.000
 GYG  N5    C5   C6    111.10  3.000
 GYG  H5    C5   C4    108.60  3.000
 GYG  N5    C5   C4    110.47  3.000
 GYG  C6    C5   C4    109.93  3.000
 GYG  H112  C11  H113  107.98  3.000
 GYG  H112  C11  H111  108.92  3.000
 GYG  H113  C11  H111  107.65  3.000
 GYG  H112  C11  C10   113.53  3.000
 GYG  H113  C11  C10   108.40  3.000
 GYG  H111  C11  C10   110.16  3.000
 GYG  H6    C6   O6    109.94  3.000
 GYG  H6    C6   C7    108.24  3.000
 GYG  O6    C6   C7    108.20  3.000
 GYG  H6    C6   C5    108.03  3.000
 GYG  C7    C6   C5    112.56  3.000
 GYG  O6    C6   C5    109.85  3.000
 GYG  H7    C7   O7    111.10  3.000
 GYG  H7    C7   C8    107.35  3.000
 GYG  O7    C7   C8    111.10  3.000
 GYG  H7    C7   C6    106.51  3.000
 GYG  C8    C7   C6    112.29  3.000
 GYG  O7    C7   C6    108.42  3.000
 GYG  H8    C8   O8    111.10  3.000
 GYG  H8    C8   C9    106.11  3.000
 GYG  O8    C8   C9    112.18  3.000
 GYG  H8    C8   C7    109.15  3.000
 GYG  O8    C8   C7    106.11  3.000
 GYG  C9    C8   C7    112.25  3.000
 GYG  H91   C9   H92   106.17  3.000
 GYG  H91   C9   O9    111.92  3.000
 GYG  H92   C9   O9    111.62  3.000
 GYG  H91   C9   C8    108.69  3.000
 GYG  H92   C9   C8    108.20  3.000
 GYG  O9    C9   C8    110.08  3.000
 GYG  H061  N06  C07   111.13  3.000
 GYG  H061  N06  C4    113.35  3.000
 GYG  C07   N06  C4    123.87  3.000
 GYG  H081  N08  C07   110.85  3.000
 GYG  H091  N09  H1    111.79  3.000
 GYG  H091  N09  C07   116.72  3.000
 GYG  H1    N09  C07   114.99  3.000
 GYG  HN5   N5   C10   117.87  3.000
 GYG  HN5   N5   C5    117.01  3.000
 GYG  C10   N5   C5    124.27  3.000
 GYG  HO7   O7   C7    108.27  3.000
 GYG  HO8   O8   C8    108.55  3.000
 GYG  HO9   O9   C9    108.36  3.000
 GYG  C6    O6   C2    113.54  3.000
 GYG  O24   S02  O23   113.60  3.000
 GYG  O24   S02  O01   113.67  3.000
 GYG  O23   S02  O01   113.61  3.000
 GYG  O24   S02  C2    105.24  3.000
 GYG  O01   S02  C2    103.64  3.000
 GYG  O23   S02  C2    105.83  3.000
 GYG  N09   C07  N08   125.91  3.000
 GYG  N09   C07  N06   115.15  3.000
 GYG  N08   C07  N06   118.94  3.000
 GYG  O10   C10  N5    123.35  3.000
 GYG  N5    C10  C11   114.69  3.000
 GYG  O10   C10  C11   121.94  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
 GYG  CONST_01  O10   C10  N5   C5     0.00   0.0  0
 GYG  CONST_02  C11   C10  N5   C5   180.00   0.0  0
 GYG  CONST_05  HN5   N5   C10  C11    0.00   0.0  0
 GYG  CONST_06  H081  N08  C07  N06  180.00   0.0  0
 GYG  CONST_07  H1    N09  C07  N06  180.00   0.0  0
 GYG  CONST_09  H061  N06  C07  N08    0.00   0.0  0
 GYG  Var_01    H111  C11  C10  N5   142.31  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
 GYG  chir_01  C2  S02  C3  O6  positiv
 GYG  chir_02  C4  N06  C5  C3  positiv
 GYG  chir_03  C5  N5   C6  C4  negativ
 GYG  chir_04  C6  O6   C5  C7  positiv
 GYG  chir_05  C7  O7   C6  C8  negativ
 GYG  chir_06  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
 GYG  plan-1  C5    0.020
 GYG  plan-1  C11   0.020
 GYG  plan-1  N5    0.020
 GYG  plan-1  O10   0.020
 GYG  plan-1  HN5   0.020
 GYG  plan-1  C10   0.020
 GYG  plan-2  C4    0.020
 GYG  plan-2  N06   0.020
 GYG  plan-2  N08   0.020
 GYG  plan-2  N09   0.020
 GYG  plan-2  H061  0.020
 GYG  plan-2  H081  0.020
 GYG  plan-2  H1    0.020
 GYG  plan-2  H091  0.020
 GYG  plan-2  C07   0.020

