# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:03:25 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-D-glycero-D-galacto-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](NC(N)=N)C=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
 ZMR  ZMR  '5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  43  23  .  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 (reasonable std)
;

data_comp_ZMR
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
 ZMR  C1    C  C     0   0.497  29.8337  39.9983  -31.0609
 ZMR  O1A   O  O     0  -0.433  29.9115  40.4324  -32.1818
 ZMR  O1B   O  OH1   0  -0.589  29.2969  40.6541  -30.0441
 ZMR  C2    C  C     0   0.237  30.3418  38.6542  -30.6778
 ZMR  C3    C  C1    0  -0.321  30.2710  38.1497  -29.4448
 ZMR  C4    C  CH1   0  -0.055  30.8400  36.8062  -29.1080
 ZMR  C5    C  CH1   0  -0.128  31.7997  36.3676  -30.2231
 ZMR  N5    N  NH1   0  -0.618  32.1624  34.9869  -30.0657
 ZMR  C10   C  C     0   0.509  33.3560  34.5735  -29.5835
 ZMR  O10   O  O     0  -0.490  34.3142  35.3148  -29.4328
 ZMR  C11   C  CH3   0  -0.789  33.3939  33.1049  -29.2417
 ZMR  C6    C  CH1   0   0.035  31.1313  36.6268  -31.5773
 ZMR  O6    O  O2    0  -0.483  30.8854  38.0208  -31.7325
 ZMR  C7    C  CH1   0   0.009  31.9718  36.1730  -32.7608
 ZMR  O7    O  OH1   0  -0.674  33.1990  36.8591  -32.7233
 ZMR  C8    C  CH1   0  -0.006  31.2465  36.3842  -34.0989
 ZMR  O8    O  OH1   0  -0.678  30.1419  35.5018  -34.0883
 ZMR  C9    C  CH2   0  -0.194  32.1600  36.1451  -35.2899
 ZMR  O9    O  OH1   0  -0.675  32.8086  34.9010  -35.1548
 ZMR  NE    N  NH1   0  -0.658  31.4653  36.8243  -27.8121
 ZMR  CZ    C  C     0   0.575  31.4278  35.7350  -26.9764
 ZMR  NH1   N  N     0  -0.710  30.6571  34.7408  -27.2210
 ZMR  NH2   N  NH2   0  -0.843  32.2962  35.8428  -25.9128
 ZMR  H3    H  H     0   0.278  29.7950  38.7105  -28.6533
 ZMR  H4    H  HCH1  0   0.281  30.0221  36.0813  -29.0440
 ZMR  H5    H  HCH1  0   0.277  32.7129  36.9619  -30.1668
 ZMR  HN5   H  HNH1  0   0.396  31.4008  34.3275  -30.0124
 ZMR  H111  H  HCH3  0   0.259  34.4038  32.7939  -28.9887
 ZMR  H112  H  HCH3  0   0.264  32.7404  32.9146  -28.3883
 ZMR  H113  H  HCH3  0   0.261  33.0309  32.4942  -30.0686
 ZMR  H6    H  HCH1  0   0.254  30.1706  36.0955  -31.6107
 ZMR  H7    H  HCH1  0   0.236  32.1168  35.0942  -32.6332
 ZMR  HO7   H  HOH1  0   0.456  33.8714  36.2903  -33.1086
 ZMR  H8    H  HCH1  0   0.226  30.9138  37.4275  -34.1748
 ZMR  HO8   H  HOH1  0   0.456  29.4948  35.8167  -34.7256
 ZMR  H91   H  HCH2  0   0.213  31.5515  36.1884  -36.2041
 ZMR  H92   H  HCH2  0   0.203  32.8746  36.9740  -35.3573
 ZMR  HO9   H  HOH1  0   0.458  33.4130  34.7942  -35.8944
 ZMR  HNH1  H  H     0   0.319  30.7011  34.0603  -26.4722
 ZMR  HN21  H  HNH2  0   0.386  32.0936  35.2358  -25.1346
 ZMR  HN22  H  HNH2  0   0.384  32.5176  36.7773  -25.6044
 ZMR  HO1B  H  HOH1  0   0.491  28.9764  41.5190  -30.3405
 ZMR  HNE   H  HNH1  0   0.383  32.2617  37.4367  -27.7249

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
 ZMR  C1   O1A   double  1.205  0.020  1.205
 ZMR  C1   O1B   single  1.324  0.020  1.324
 ZMR  C1   C2    single  1.487  0.020  1.487
 ZMR  C2   C3    double  1.334  0.020  1.334
 ZMR  C2   O6    single  1.345  0.020  1.345
 ZMR  C3   C4    single  1.497  0.020  1.497
 ZMR  C3   H3    single  0.930  0.020  1.080
 ZMR  C4   C5    single  1.535  0.020  1.535
 ZMR  C4   NE    single  1.439  0.020  1.439
 ZMR  C4   H4    single  0.970  0.020  1.090
 ZMR  C5   N5    single  1.436  0.020  1.436
 ZMR  C5   C6    single  1.532  0.020  1.532
 ZMR  C5   H5    single  0.970  0.020  1.090
 ZMR  N5   C10   single  1.352  0.020  1.352
 ZMR  N5   HN5   single  0.890  0.020  1.040
 ZMR  C10  O10   double  1.221  0.020  1.221
 ZMR  C10  C11   single  1.508  0.020  1.508
 ZMR  C11  H111  single  0.970  0.020  1.090
 ZMR  C11  H112  single  0.970  0.020  1.090
 ZMR  C11  H113  single  0.970  0.020  1.090
 ZMR  C6   O6    single  1.424  0.020  1.424
 ZMR  C6   C7    single  1.521  0.020  1.521
 ZMR  C6   H6    single  0.970  0.020  1.090
 ZMR  C7   O7    single  1.407  0.020  1.407
 ZMR  C7   C8    single  1.537  0.020  1.537
 ZMR  C7   H7    single  0.970  0.020  1.090
 ZMR  O7   HO7   single  0.850  0.020  0.980
 ZMR  C8   O8    single  1.414  0.020  1.414
 ZMR  C8   C9    single  1.520  0.020  1.520
 ZMR  C8   H8    single  0.970  0.020  1.090
 ZMR  O8   HO8   single  0.850  0.020  0.980
 ZMR  C9   O9    single  1.410  0.020  1.410
 ZMR  C9   H91   single  0.970  0.020  1.090
 ZMR  C9   H92   single  0.970  0.020  1.090
 ZMR  O9   HO9   single  0.850  0.020  0.980
 ZMR  NE   CZ    single  1.373  0.020  1.373
 ZMR  CZ   NH1   double  1.282  0.020  1.282
 ZMR  CZ   NH2   single  1.377  0.020  1.377
 ZMR  NH1  HNH1  single  0.890  0.020  1.040
 ZMR  NH2  HN21  single  0.890  0.020  1.040
 ZMR  NH2  HN22  single  0.890  0.020  1.040
 ZMR  O1B  HO1B  single  0.850  0.020  0.980
 ZMR  NE   HNE   single  0.890  0.020  1.040

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
 ZMR  C2    C1   O1B   112.86  3.000
 ZMR  C2    C1   O1A   122.91  3.000
 ZMR  O1B   C1   O1A   124.22  3.000
 ZMR  HO1B  O1B  C1    109.97  3.000
 ZMR  O6    C2   C3    124.62  3.000
 ZMR  O6    C2   C1    111.21  3.000
 ZMR  C3    C2   C1    124.18  3.000
 ZMR  H3    C3   C4    117.92  3.000
 ZMR  H3    C3   C2    120.27  3.000
 ZMR  C4    C3   C2    121.80  3.000
 ZMR  H4    C4   NE    106.28  3.000
 ZMR  H4    C4   C5    108.68  3.000
 ZMR  NE    C4   C5    112.71  3.000
 ZMR  H4    C4   C3    108.86  3.000
 ZMR  NE    C4   C3    110.88  3.000
 ZMR  C5    C4   C3    109.30  3.000
 ZMR  H5    C5   C6    108.58  3.000
 ZMR  H5    C5   N5    107.86  3.000
 ZMR  C6    C5   N5    111.69  3.000
 ZMR  H5    C5   C4    109.28  3.000
 ZMR  C6    C5   C4    108.72  3.000
 ZMR  N5    C5   C4    110.67  3.000
 ZMR  HN5   N5   C10   116.60  3.000
 ZMR  HN5   N5   C5    116.33  3.000
 ZMR  C10   N5   C5    123.78  3.000
 ZMR  C11   C10  O10   122.92  3.000
 ZMR  C11   C10  N5    113.62  3.000
 ZMR  O10   C10  N5    123.45  3.000
 ZMR  H113  C11  H112  107.22  3.000
 ZMR  H113  C11  H111  109.01  3.000
 ZMR  H112  C11  H111  108.94  3.000
 ZMR  H113  C11  C10   111.42  3.000
 ZMR  H112  C11  C10   109.38  3.000
 ZMR  H111  C11  C10   110.78  3.000
 ZMR  H6    C6   C7    108.39  3.000
 ZMR  H6    C6   O6    108.61  3.000
 ZMR  C7    C6   O6    107.62  3.000
 ZMR  H6    C6   C5    109.06  3.000
 ZMR  C7    C6   C5    113.34  3.000
 ZMR  O6    C6   C5    109.71  3.000
 ZMR  C6    O6   C2    116.44  3.000
 ZMR  H7    C7   C8    107.40  3.000
 ZMR  H7    C7   O7    111.20  3.000
 ZMR  C8    C7   O7    111.59  3.000
 ZMR  H7    C7   C6    106.04  3.000
 ZMR  C8    C7   C6    112.07  3.000
 ZMR  O7    C7   C6    108.42  3.000
 ZMR  HO7   O7   C7    108.12  3.000
 ZMR  H8    C8   C9    106.11  3.000
 ZMR  H8    C8   O8    110.91  3.000
 ZMR  C9    C8   O8    112.16  3.000
 ZMR  H8    C8   C7    109.51  3.000
 ZMR  C9    C8   C7    112.15  3.000
 ZMR  O8    C8   C7    106.05  3.000
 ZMR  HO8   O8   C8    108.45  3.000
 ZMR  H92   C9   H91   106.26  3.000
 ZMR  H92   C9   O9    111.92  3.000
 ZMR  H91   C9   O9    111.67  3.000
 ZMR  H92   C9   C8    108.72  3.000
 ZMR  H91   C9   C8    108.23  3.000
 ZMR  O9    C9   C8    109.89  3.000
 ZMR  HO9   O9   C9    108.28  3.000
 ZMR  HNE   NE   CZ    116.78  3.000
 ZMR  HNE   NE   C4    115.39  3.000
 ZMR  CZ    NE   C4    121.75  3.000
 ZMR  NH2   CZ   NH1   125.96  3.000
 ZMR  NH2   CZ   NE    112.99  3.000
 ZMR  NH1   CZ   NE    121.04  3.000
 ZMR  HNH1  NH1  CZ    110.74  3.000
 ZMR  HN22  NH2  HN21  111.48  3.000
 ZMR  HN22  NH2  CZ    116.54  3.000
 ZMR  HN21  NH2  CZ    115.00  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
 ZMR  CONST_01  O10   C10  N5   C5     0.00   0.0  0
 ZMR  CONST_02  C11   C10  N5   C5   180.00   0.0  0
 ZMR  CONST_03  NH1   CZ   NE   C4     0.00   0.0  0
 ZMR  CONST_04  NH2   CZ   NE   C4   180.00   0.0  0
 ZMR  CONST_05  HO1B  O1B  C1   C2   180.00   0.0  0
 ZMR  CONST_06  HN5   N5   C10  O10  180.00   0.0  0
 ZMR  CONST_07  HNH1  NH1  CZ   NE   180.00   0.0  0
 ZMR  Var_01    O6    C2   C3   C4     1.66  30.0  1
 ZMR  Var_02    C3    C2   C1   O1A  179.87  30.0  2
 ZMR  Var_03    H111  C11  C10  N5   172.31  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
 ZMR  chir_01  C4  C3  C5  NE  negativ
 ZMR  chir_02  C5  N5  C6  C4  negativ
 ZMR  chir_03  C6  O6  C5  C7  positiv
 ZMR  chir_04  C7  O7  C6  C8  negativ
 ZMR  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
 ZMR  plan-1  C5    0.020
 ZMR  plan-1  N5    0.020
 ZMR  plan-1  C10   0.020
 ZMR  plan-1  O10   0.020
 ZMR  plan-1  C11   0.020
 ZMR  plan-1  HN5   0.020
 ZMR  plan-2  C4    0.020
 ZMR  plan-2  NE    0.020
 ZMR  plan-2  CZ    0.020
 ZMR  plan-2  NH1   0.020
 ZMR  plan-2  NH2   0.020
 ZMR  plan-2  HNH1  0.020
 ZMR  plan-2  HN21  0.020
 ZMR  plan-2  HN22  0.020
 ZMR  plan-2  HNE   0.020
 ZMR  plan-3  C1    0.020
 ZMR  plan-3  O1A   0.020
 ZMR  plan-3  O1B   0.020
 ZMR  plan-3  C2    0.020
 ZMR  plan-3  HO1B  0.020

