# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 08:27:56 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-3,4,5-trideoxy-4-[(diaminomethylidene)amino]-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](C=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)N=C(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
 ZMR  ZMR  '5-(acetylamino)-2,6-anhydro-3,4,5-trideoxy-4-[(diaminomethylidene)amino]-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  42  23  .  2023-02-15  2023-02-15
;
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   0.370  -3.5666  -0.1881   1.0575
 ZMR  O1A   O  OC    -1  -0.595  -3.5393  -0.5279   2.2517
 ZMR  O1B   O  O      0  -0.593  -4.5696  -0.0103   0.3410
 ZMR  C2    C  C      0   0.160  -2.2148   0.0359   0.3896
 ZMR  C3    C  C1     0  -0.347  -2.0691   0.3741  -0.8909
 ZMR  C4    C  CH1    0  -0.094  -0.7389   0.5210  -1.5739
 ZMR  C5    C  CH1    0  -0.106   0.3510  -0.0771  -0.6710
 ZMR  N5    N  NH1    0  -0.633   1.6597   0.3480  -1.0974
 ZMR  C10   C  C      0   0.524   2.5360  -0.4247  -1.7713
 ZMR  O10   O  O      0  -0.498   2.3848  -1.6243  -1.9453
 ZMR  C11   C  CH3    0  -0.785   3.7201   0.3230  -2.3314
 ZMR  C6    C  CH1    0   0.034   0.0960   0.3298   0.7834
 ZMR  O6    O  O2     0  -0.488  -1.1618  -0.1509   1.2234
 ZMR  C7    C  CH1    0  -0.034   1.1315  -0.2286   1.7552
 ZMR  O7    O  OH1    0  -0.661   1.1984  -1.6334   1.6829
 ZMR  C8    C  CH1    0  -0.013   0.8923   0.2472   3.2009
 ZMR  O8    O  OH1    0  -0.662   0.7467   1.6484   3.2620
 ZMR  C9    C  CH2    0  -0.161   2.0039  -0.2395   4.1176
 ZMR  O9    O  OH1    0  -0.671   1.6979   0.1368   5.4402
 ZMR  NE    N  N      0  -0.485  -0.7856  -0.1564  -2.8423
 ZMR  CZ    C  C      0   0.563  -0.1735   0.3013  -3.8713
 ZMR  NH1   N  NH2    0  -0.830  -0.1990  -0.4405  -5.0314
 ZMR  NH2   N  NH2    0  -0.830   0.6058   1.4264  -3.9549
 ZMR  H3    H  H      0   0.236  -2.9590   0.5259  -1.4854
 ZMR  H4    H  HCH1   0   0.204  -0.5330   1.6035  -1.6644
 ZMR  H5    H  HCH1   0   0.258   0.3089  -1.1632  -0.7565
 ZMR  HN5   H  HNH1   0   0.392   1.8487   1.3382  -1.0623
 ZMR  H111  H  HCH3   0   0.257   4.5932  -0.3242  -2.3749
 ZMR  H112  H  HCH3   0   0.267   3.4776   0.6368  -3.3485
 ZMR  H113  H  HCH3   0   0.248   3.9698   1.2174  -1.7621
 ZMR  H6    H  HCH1   0   0.230   0.1019   1.4274   0.8453
 ZMR  H7    H  HCH1   0   0.242   2.1126   0.1368   1.4325
 ZMR  HO7   H  HOH1   0   0.444   0.3235  -1.9883   1.8787
 ZMR  H8    H  HCH1   0   0.234  -0.0583  -0.1646   3.5564
 ZMR  HO8   H  HOH1   0   0.444   1.5872   2.0558   3.0244
 ZMR  H91   H  HCH2   0   0.207   2.1023  -1.3253   4.0191
 ZMR  H92   H  HCH2   0   0.188   2.9580   0.1975   3.7824
 ZMR  HO9   H  HOH1   0   0.454   2.3868  -0.2105   6.0132
 ZMR  HN11  H  HNH2   0   0.378  -0.1282   0.0665  -5.8993
 ZMR  HN12  H  HNH2   0   0.374  -0.9308  -1.1319  -5.0487
 ZMR  HN21  H  HNH2   0   0.388   0.7169   1.8485  -4.8627
 ZMR  HN22  H  HNH2   0   0.391   0.5181   2.1055  -3.2194

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   deloc   1.242  0.020  1.242
 ZMR  C1   O1B   deloc   1.245  0.020  1.245
 ZMR  C1   C2    single  1.524  0.020  1.524
 ZMR  C2   C3    double  1.332  0.020  1.332
 ZMR  C2   O6    single  1.356  0.020  1.356
 ZMR  C3   C4    single  1.502  0.020  1.502
 ZMR  C3   H3    single  0.930  0.020  1.080
 ZMR  C4   C5    single  1.537  0.020  1.537
 ZMR  C4   NE    single  1.439  0.020  1.439
 ZMR  C4   H4    single  0.970  0.020  1.090
 ZMR  C5   N5    single  1.441  0.020  1.441
 ZMR  C5   C6    single  1.532  0.020  1.532
 ZMR  C5   H5    single  0.970  0.020  1.090
 ZMR  N5   C10   single  1.349  0.020  1.349
 ZMR  N5   HN5   single  0.860  0.020  1.020
 ZMR  C10  O10   double  1.222  0.020  1.222
 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  1.417  0.020  1.417
 ZMR  C6   C7    single  1.526  0.020  1.526
 ZMR  C6   H6    single  0.970  0.020  1.090
 ZMR  C7   O7    single  1.408  0.020  1.408
 ZMR  C7   C8    single  1.541  0.020  1.541
 ZMR  C7   H7    single  0.970  0.020  1.090
 ZMR  O7   HO7   single  0.850  0.020  0.980
 ZMR  C8   O8    single  1.410  0.020  1.410
 ZMR  C8   C9    single  1.521  0.020  1.521
 ZMR  C8   H8    single  0.970  0.020  1.090
 ZMR  O8   HO8   single  0.850  0.020  0.980
 ZMR  C9   O9    single  1.409  0.020  1.409
 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    double  1.282  0.020  1.282
 ZMR  CZ   NH1   single  1.377  0.020  1.377
 ZMR  CZ   NH2   single  1.371  0.020  1.371
 ZMR  NH1  HN11  single  0.890  0.020  1.040
 ZMR  NH1  HN12  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

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   116.18  3.000
 ZMR  C2    C1   O1A   116.23  3.000
 ZMR  O1B   C1   O1A   127.59  3.000
 ZMR  O6    C2   C3    122.75  3.000
 ZMR  O6    C2   C1    113.52  3.000
 ZMR  C3    C2   C1    123.74  3.000
 ZMR  H3    C3   C4    117.72  3.000
 ZMR  H3    C3   C2    118.30  3.000
 ZMR  C4    C3   C2    123.96  3.000
 ZMR  H4    C4   NE    113.25  3.000
 ZMR  H4    C4   C5    107.28  3.000
 ZMR  NE    C4   C5    110.97  3.000
 ZMR  H4    C4   C3    107.33  3.000
 ZMR  NE    C4   C3    109.02  3.000
 ZMR  C5    C4   C3    108.83  3.000
 ZMR  H5    C5   C6    109.43  3.000
 ZMR  H5    C5   N5    107.81  3.000
 ZMR  C6    C5   N5    110.73  3.000
 ZMR  H5    C5   C4    108.31  3.000
 ZMR  C6    C5   C4    109.66  3.000
 ZMR  N5    C5   C4    110.83  3.000
 ZMR  HN5   N5   C10   117.26  3.000
 ZMR  HN5   N5   C5    116.72  3.000
 ZMR  C10   N5   C5    124.68  3.000
 ZMR  C11   C10  O10   122.08  3.000
 ZMR  C11   C10  N5    114.30  3.000
 ZMR  O10   C10  N5    123.60  3.000
 ZMR  H113  C11  H112  107.56  3.000
 ZMR  H113  C11  H111  109.00  3.000
 ZMR  H112  C11  H111  108.19  3.000
 ZMR  H113  C11  C10   113.14  3.000
 ZMR  H112  C11  C10   108.30  3.000
 ZMR  H111  C11  C10   110.49  3.000
 ZMR  H6    C6   C7    109.02  3.000
 ZMR  H6    C6   O6    109.03  3.000
 ZMR  C7    C6   O6    106.29  3.000
 ZMR  H6    C6   C5    108.53  3.000
 ZMR  C7    C6   C5    113.23  3.000
 ZMR  O6    C6   C5    110.65  3.000
 ZMR  C6    O6   C2    116.85  3.000
 ZMR  H7    C7   C8    108.20  3.000
 ZMR  H7    C7   O7    105.97  3.000
 ZMR  C8    C7   O7    111.32  3.000
 ZMR  H7    C7   C6    107.34  3.000
 ZMR  C8    C7   C6    112.28  3.000
 ZMR  O7    C7   C6    111.38  3.000
 ZMR  HO7   O7   C7    108.28  3.000
 ZMR  H8    C8   C9    108.57  3.000
 ZMR  H8    C8   O8    105.67  3.000
 ZMR  C9    C8   O8    111.55  3.000
 ZMR  H8    C8   C7    108.86  3.000
 ZMR  C9    C8   C7    110.69  3.000
 ZMR  O8    C8   C7    111.32  3.000
 ZMR  HO8   O8   C8    108.62  3.000
 ZMR  H92   C9   H91   106.75  3.000
 ZMR  H92   C9   O9    111.58  3.000
 ZMR  H91   C9   O9    111.65  3.000
 ZMR  H92   C9   C8    108.83  3.000
 ZMR  H91   C9   C8    109.20  3.000
 ZMR  O9    C9   C8    108.76  3.000
 ZMR  HO9   O9   C9    107.91  3.000
 ZMR  CZ    NE   C4    121.61  3.000
 ZMR  NH2   CZ   NH1   113.65  3.000
 ZMR  NH2   CZ   NE    127.83  3.000
 ZMR  NH1   CZ   NE    118.36  3.000
 ZMR  HN12  NH1  HN11  112.44  3.000
 ZMR  HN12  NH1  CZ    113.44  3.000
 ZMR  HN11  NH1  CZ    116.95  3.000
 ZMR  HN22  NH2  HN21  112.71  3.000
 ZMR  HN22  NH2  CZ    117.41  3.000
 ZMR  HN21  NH2  CZ    117.48  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   180.00   0.0  0
 ZMR  CONST_04  NH2   CZ   NE   C4     0.00   0.0  0
 ZMR  CONST_05  HN5   N5   C10  O10  180.00   0.0  0
 ZMR  Var_01    O6    C2   C3   C4     3.11  30.0  1
 ZMR  Var_02    C3    C2   C1   O1A  178.48  30.0  2
 ZMR  Var_03    H111  C11  C10  N5   149.86  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  C7  C5  negativ
 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  HN11  0.020
 ZMR  plan-2  HN12  0.020
 ZMR  plan-2  HN21  0.020
 ZMR  plan-2  HN22  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

