# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 15:44:25 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-(acetylamino)-3,5-dideoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(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
 SLB  SLB  '5-(acetylamino)-3,5-dideoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid'  D-saccharide  40  21  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SLB
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
 SLB  C1    C  C     0   0.488  -2.5420   0.5188  -2.2147
 SLB  C2    C  CT    0   0.417  -1.8976  -0.2760  -1.0658
 SLB  C3    C  CH2   0  -0.524  -2.5683   0.1264   0.2464
 SLB  C4    C  CH1   0   0.070  -1.7952  -0.4267   1.4403
 SLB  C5    C  CH1   0  -0.123  -0.3396   0.0199   1.3512
 SLB  C6    C  CH1   0   0.030   0.2553  -0.3504  -0.0155
 SLB  C7    C  CH1   0  -0.025   1.6160   0.3064  -0.2521
 SLB  C8    C  CH1   0  -0.022   2.3269  -0.2772  -1.4884
 SLB  C9    C  CH2   0  -0.161   3.6608   0.4136  -1.7237
 SLB  C11   C  CH3   0  -0.782   1.7717  -0.7590   4.4015
 SLB  N5    N  NH1   0  -0.635   0.4482  -0.5810   2.3969
 SLB  O1A   O  O     0  -0.417  -2.0992   1.5463  -2.6515
 SLB  O1B   O  OH1   0  -0.582  -3.6661  -0.0470  -2.6161
 SLB  O2    O  OH1   0  -0.656  -2.0552  -1.6466  -1.2173
 SLB  O4    O  OH1   0  -0.662  -2.3137   0.0530   2.6553
 SLB  O6    O  O2    0  -0.517  -0.5606   0.1097  -1.0797
 SLB  O7    O  OH1   0  -0.661   1.4901   1.7054  -0.3289
 SLB  O8    O  OH1   0  -0.660   2.4760  -1.6734  -1.3619
 SLB  O9    O  OH1   0  -0.671   4.2595  -0.1423  -2.8714
 SLB  O10   O  O     0  -0.497   0.9824   1.3135   3.5144
 SLB  H31   H  HCH2  0   0.274  -3.6028  -0.2235   0.2630
 SLB  H32   H  HCH2  0   0.264  -2.5887   1.2178   0.3153
 SLB  H4    H  HCH1  0   0.219  -1.8273  -1.5248   1.4150
 SLB  H5    H  HCH1  0   0.268  -0.2996   1.1037   1.4818
 SLB  H6    H  HCH1  0   0.238   0.3703  -1.4402  -0.0641
 SLB  H7    H  HCH1  0   0.244   2.2461   0.1028   0.6214
 SLB  H8    H  HCH1  0   0.234   1.6959  -0.1259  -2.3711
 SLB  H91   H  HCH2  0   0.209   3.4930   1.4890  -1.8375
 SLB  H92   H  HCH2  0   0.187   4.2949   0.2829  -0.8322
 SLB  H111  H  HCH3  0   0.265   1.4711  -0.4890   5.4127
 SLB  H112  H  HCH3  0   0.248   1.6135  -1.8274   4.2659
 SLB  H113  H  HCH3  0   0.269   2.8404  -0.5587   4.3159
 SLB  HN5   H  HNH1  0   0.398   0.5011  -1.5878   2.4117
 SLB  HOB1  H  HOH1  0   0.490  -4.0832   0.4927  -3.3051
 SLB  HO2   H  HOH1  0   0.461  -1.6405  -1.9432  -2.0372
 SLB  HO4   H  HOH1  0   0.456  -3.1597  -0.3763   2.8162
 SLB  HO7   H  HOH1  0   0.444   0.8371   1.9091  -1.0092
 SLB  HO8   H  HOH1  0   0.444   3.1017  -1.8539  -0.6513
 SLB  HO9   H  HOH1  0   0.455   5.0595   0.3564  -3.0579
 SLB  C10   C  C     0   0.523   1.0260   0.0970   3.4079

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
 SLB  C1   C2    single  1.538  0.020  1.538
 SLB  C1   O1A   double  1.201  0.020  1.201
 SLB  C1   O1B   single  1.321  0.020  1.321
 SLB  C2   C3    single  1.528  0.020  1.528
 SLB  C2   O2    single  1.388  0.020  1.388
 SLB  C2   O6    single  1.392  0.020  1.392
 SLB  C3   C4    single  1.526  0.020  1.526
 SLB  C3   H31   single  0.970  0.020  1.090
 SLB  C3   H32   single  0.970  0.020  1.090
 SLB  C4   C5    single  1.525  0.020  1.525
 SLB  C4   O4    single  1.405  0.020  1.405
 SLB  C4   H4    single  0.970  0.020  1.090
 SLB  C5   C6    single  1.536  0.020  1.536
 SLB  C5   N5    single  1.441  0.020  1.441
 SLB  C5   H5    single  0.970  0.020  1.090
 SLB  C6   C7    single  1.529  0.020  1.529
 SLB  C6   O6    single  1.418  0.020  1.418
 SLB  C6   H6    single  0.970  0.020  1.090
 SLB  C7   C8    single  1.541  0.020  1.541
 SLB  C7   O7    single  1.407  0.020  1.407
 SLB  C7   H7    single  0.970  0.020  1.090
 SLB  C8   C9    single  1.521  0.020  1.521
 SLB  C8   O8    single  1.410  0.020  1.410
 SLB  C8   H8    single  0.970  0.020  1.090
 SLB  C9   O9    single  1.409  0.020  1.409
 SLB  C9   H91   single  0.970  0.020  1.090
 SLB  C9   H92   single  0.970  0.020  1.090
 SLB  C10  C11   single  1.509  0.020  1.509
 SLB  C10  N5    single  1.348  0.020  1.348
 SLB  C10  O10   double  1.222  0.020  1.222
 SLB  C11  H111  single  0.970  0.020  1.090
 SLB  C11  H112  single  0.970  0.020  1.090
 SLB  C11  H113  single  0.970  0.020  1.090
 SLB  N5   HN5   single  0.860  0.020  1.020
 SLB  O1B  HOB1  single  0.850  0.020  0.980
 SLB  O2   HO2   single  0.850  0.020  0.980
 SLB  O4   HO4   single  0.850  0.020  0.980
 SLB  O7   HO7   single  0.850  0.020  0.980
 SLB  O8   HO8   single  0.850  0.020  0.980
 SLB  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
 SLB  O1B   C1   O1A   124.72  3.000
 SLB  O1B   C1   C2    111.23  3.000
 SLB  O1A   C1   C2    124.00  3.000
 SLB  O6    C2   O2    112.44  3.000
 SLB  O6    C2   C3    110.94  3.000
 SLB  O2    C2   C3    107.70  3.000
 SLB  O6    C2   C1    104.58  3.000
 SLB  O2    C2   C1    112.40  3.000
 SLB  C3    C2   C1    108.76  3.000
 SLB  H32   C3   H31   107.52  3.000
 SLB  H32   C3   C4    108.77  3.000
 SLB  H31   C3   C4    110.61  3.000
 SLB  H32   C3   C2    108.97  3.000
 SLB  H31   C3   C2    110.15  3.000
 SLB  C4    C3   C2    110.74  3.000
 SLB  H4    C4   O4    110.50  3.000
 SLB  H4    C4   C5    108.61  3.000
 SLB  O4    C4   C5    107.62  3.000
 SLB  H4    C4   C3    109.23  3.000
 SLB  O4    C4   C3    111.45  3.000
 SLB  C5    C4   C3    109.37  3.000
 SLB  H5    C5   N5    107.88  3.000
 SLB  H5    C5   C6    109.35  3.000
 SLB  N5    C5   C6    109.48  3.000
 SLB  H5    C5   C4    108.57  3.000
 SLB  N5    C5   C4    110.94  3.000
 SLB  C6    C5   C4    110.55  3.000
 SLB  H6    C6   O6    110.46  3.000
 SLB  H6    C6   C7    109.06  3.000
 SLB  O6    C6   C7    104.86  3.000
 SLB  H6    C6   C5    108.63  3.000
 SLB  O6    C6   C5    111.52  3.000
 SLB  C7    C6   C5    112.26  3.000
 SLB  H7    C7   O7    106.24  3.000
 SLB  H7    C7   C8    107.69  3.000
 SLB  O7    C7   C8    111.97  3.000
 SLB  H7    C7   C6    107.96  3.000
 SLB  O7    C7   C6    110.85  3.000
 SLB  C8    C7   C6    111.84  3.000
 SLB  H8    C8   O8    105.66  3.000
 SLB  H8    C8   C9    108.53  3.000
 SLB  O8    C8   C9    111.78  3.000
 SLB  H8    C8   C7    109.17  3.000
 SLB  O8    C8   C7    110.60  3.000
 SLB  C9    C8   C7    110.91  3.000
 SLB  H92   C9   H91   106.80  3.000
 SLB  H92   C9   O9    111.58  3.000
 SLB  H91   C9   O9    111.60  3.000
 SLB  H92   C9   C8    109.01  3.000
 SLB  H91   C9   C8    109.15  3.000
 SLB  O9    C9   C8    108.64  3.000
 SLB  H113  C11  H112  108.24  3.000
 SLB  H113  C11  H111  107.32  3.000
 SLB  H112  C11  H111  108.60  3.000
 SLB  H113  C11  C10   109.17  3.000
 SLB  H112  C11  C10   113.77  3.000
 SLB  H111  C11  C10   109.54  3.000
 SLB  HN5   N5   C10   117.96  3.000
 SLB  HN5   N5   C5    117.12  3.000
 SLB  C10   N5   C5    124.70  3.000
 SLB  HOB1  O1B  C1    110.10  3.000
 SLB  HO2   O2   C2    110.32  3.000
 SLB  HO4   O4   C4    108.46  3.000
 SLB  C6    O6   C2    117.10  3.000
 SLB  HO7   O7   C7    108.00  3.000
 SLB  HO8   O8   C8    108.68  3.000
 SLB  HO9   O9   C9    107.89  3.000
 SLB  O10   C10  N5    123.44  3.000
 SLB  O10   C10  C11   121.68  3.000
 SLB  N5    C10  C11   114.87  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
 SLB  CONST_01  C11   C10  N5   C5    180.00   0.0  0
 SLB  CONST_02  O10   C10  N5   C5      0.00   0.0  0
 SLB  CONST_03  HOB1  O1B  C1   C2    180.00   0.0  0
 SLB  CONST_04  HN5   N5   C10  C11     0.00   0.0  0
 SLB  Var_01    H111  C11  C10  N5   -131.13  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
 SLB  chir_01  C2  C3  O2  O6  positiv
 SLB  chir_02  C4  O4  C5  C3  positiv
 SLB  chir_03  C5  N5  C6  C4  negativ
 SLB  chir_04  C6  O6  C7  C5  negativ
 SLB  chir_05  C7  O7  C6  C8  negativ
 SLB  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
 SLB  plan-1  C5    0.020
 SLB  plan-1  C11   0.020
 SLB  plan-1  N5    0.020
 SLB  plan-1  O10   0.020
 SLB  plan-1  HN5   0.020
 SLB  plan-1  C10   0.020
 SLB  plan-2  C1    0.020
 SLB  plan-2  C2    0.020
 SLB  plan-2  O1A   0.020
 SLB  plan-2  O1B   0.020
 SLB  plan-2  HOB1  0.020

