# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 19:14:34 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-amino-5-S-benzyl-2,3-dideoxy-5-thio-D-erythro-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)[C@H](O)CSCc1ccccc1
#
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
 RH0  RH0  '3-amino-5-S-benzyl-2,3-dideoxy-5-thio-D-erythro-pentonic acid'  peptide  34  17  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RH0
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
 RH0  N    N  NH2   0  -0.792  -3.1239   1.5123   0.2989
 RH0  C1   C  CH1   0  -0.130  -2.9350   0.0725   0.2814
 RH0  C2   C  CH1   0   0.046  -1.5603  -0.3809  -0.2415
 RH0  O1   O  OH1   0  -0.657  -1.4474  -1.7856  -0.2855
 RH0  C3   C  CH2   0  -0.549  -4.0541  -0.5498  -0.5526
 RH0  C    C  C     0   0.545  -5.3954  -0.1560   0.0008
 RH0  O    O  O     0  -0.456  -5.7302  -0.3227   1.1486
 RH0  OXT  O  OH1   0  -0.590  -6.1974   0.3783  -0.9129
 RH0  C5   C  CH2   0  -0.588  -0.4252   0.2389   0.5660
 RH0  S1   S  S2    0  -0.007   1.1570  -0.4271  -0.0242
 RH0  C6   C  CH2   0  -0.618   2.3042   0.7188   0.8063
 RH0  C7   C  CR6   0   0.109   3.6984   0.3784   0.3739
 RH0  C8   C  CR16  0  -0.290   4.2830   1.0320  -0.7080
 RH0  C9   C  CR16  0  -0.241   5.5638   0.6993  -1.1279
 RH0  C10  C  CR16  0  -0.267   6.2728  -0.3003  -0.4742
 RH0  C11  C  CR16  0  -0.242   5.6943  -0.9634   0.6008
 RH0  C12  C  CR16  0  -0.287   4.4147  -0.6266   1.0200
 RH0  H    H  HNH2  0   0.359  -2.5312   1.9490   0.9921
 RH0  H1   H  HCH1  0   0.243  -3.0386  -0.2784   1.3143
 RH0  H3   H  HCH2  0   0.256  -3.9604  -0.2418  -1.5962
 RH0  H4   H  HCH2  0   0.285  -3.9873  -1.6397  -0.5311
 RH0  HXT  H  HOH1  0   0.477  -7.0522   0.5981  -0.5122
 RH0  H6   H  HCH2  0   0.268  -0.4139   1.3222   0.4369
 RH0  H7   H  HCH2  0   0.265  -0.5436   0.0288   1.6337
 RH0  H8   H  HCH2  0   0.280   2.0496   1.7440   0.5334
 RH0  H9   H  HCH2  0   0.280   2.1920   0.6163   1.8869
 RH0  H10  H  HCR6  0   0.253   3.7325   1.8113  -1.2218
 RH0  H11  H  HCR6  0   0.256   6.0085   1.2219  -1.9650
 RH0  H12  H  HCR6  0   0.257   7.2721  -0.5595  -0.7990
 RH0  H13  H  HCR6  0   0.256   6.2421  -1.7426   1.1149
 RH0  H14  H  HCR6  0   0.253   3.9687  -1.1474   1.8594
 RH0  H2   H  HNH2  0   0.346  -2.8760   1.9190  -0.5961
 RH0  H16  H  HCH1  0   0.234  -1.4613  -0.0481  -1.2809
 RH0  H17  H  HOH1  0   0.447  -1.5052  -2.1266   0.6142

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
 RH0  N    C1   single    1.452  0.020  1.452
 RH0  N    H    single    0.860  0.020  0.860
 RH0  C1   C2   single    1.539  0.020  1.539
 RH0  C1   C3   single    1.528  0.020  1.528
 RH0  C1   H1   single    0.970  0.020  1.090
 RH0  C2   O1   single    1.410  0.020  1.410
 RH0  C2   C5   single    1.525  0.020  1.525
 RH0  C3   C    single    1.503  0.020  1.503
 RH0  C3   H3   single    0.970  0.020  1.090
 RH0  C3   H4   single    0.970  0.020  1.090
 RH0  C    O    double    1.231  0.020  1.231
 RH0  C    OXT  single    1.328  0.020  1.328
 RH0  OXT  HXT  single    0.850  0.020  0.980
 RH0  C5   S1   single    1.815  0.020  1.815
 RH0  C5   H6   single    0.970  0.020  1.090
 RH0  C5   H7   single    0.970  0.020  1.090
 RH0  S1   C6   single    1.822  0.020  1.822
 RH0  C6   C7   single    1.499  0.020  1.499
 RH0  C6   H8   single    0.970  0.020  1.090
 RH0  C6   H9   single    0.970  0.020  1.090
 RH0  C7   C8   aromatic  1.393  0.020  1.393
 RH0  C7   C12  aromatic  1.393  0.020  1.393
 RH0  C8   C9   aromatic  1.388  0.020  1.388
 RH0  C8   H10  single    0.930  0.020  1.080
 RH0  C9   C10  aromatic  1.389  0.020  1.389
 RH0  C9   H11  single    0.930  0.020  1.080
 RH0  C10  C11  aromatic  1.389  0.020  1.389
 RH0  C10  H12  single    0.930  0.020  1.080
 RH0  C11  C12  aromatic  1.388  0.020  1.388
 RH0  C11  H13  single    0.930  0.020  1.080
 RH0  C12  H14  single    0.930  0.020  1.080
 RH0  N    H2   single    0.890  0.020  1.040
 RH0  C2   H16  single    0.970  0.020  1.090
 RH0  O1   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
 RH0  H2   N    H    106.78  3.000
 RH0  H2   N    C1   110.81  3.000
 RH0  H    N    C1   111.11  3.000
 RH0  H1   C1   C3   108.35  3.000
 RH0  H1   C1   C2   108.08  3.000
 RH0  C3   C1   C2   110.41  3.000
 RH0  H1   C1   N    107.09  3.000
 RH0  C3   C1   N    108.37  3.000
 RH0  C2   C1   N    114.35  3.000
 RH0  H16  C2   C5   108.16  3.000
 RH0  H16  C2   O1   105.41  3.000
 RH0  C5   C2   O1   111.21  3.000
 RH0  H16  C2   C1   108.27  3.000
 RH0  C5   C2   C1   111.42  3.000
 RH0  O1   C2   C1   112.07  3.000
 RH0  H17  O1   C2   108.57  3.000
 RH0  H4   C3   H3   107.16  3.000
 RH0  H4   C3   C    107.98  3.000
 RH0  H3   C3   C    110.76  3.000
 RH0  H4   C3   C1   110.54  3.000
 RH0  H3   C3   C1   110.11  3.000
 RH0  C    C3   C1   110.23  3.000
 RH0  OXT  C    O    122.83  3.000
 RH0  OXT  C    C3   113.01  3.000
 RH0  O    C    C3   124.14  3.000
 RH0  HXT  OXT  C    109.84  3.000
 RH0  H7   C5   H6   107.89  3.000
 RH0  H7   C5   S1   109.94  3.000
 RH0  H6   C5   S1   108.47  3.000
 RH0  H7   C5   C2   110.98  3.000
 RH0  H6   C5   C2   110.40  3.000
 RH0  S1   C5   C2   109.12  3.000
 RH0  C6   S1   C5    99.78  3.000
 RH0  H9   C6   H8   108.18  3.000
 RH0  H9   C6   C7   111.10  3.000
 RH0  H8   C6   C7   110.99  3.000
 RH0  H9   C6   S1   109.12  3.000
 RH0  H8   C6   S1   109.27  3.000
 RH0  C7   C6   S1   108.14  3.000
 RH0  C12  C7   C8   118.88  3.000
 RH0  C12  C7   C6   120.55  3.000
 RH0  C8   C7   C6   120.54  3.000
 RH0  H10  C8   C9   119.84  3.000
 RH0  H10  C8   C7   119.51  3.000
 RH0  C9   C8   C7   120.65  3.000
 RH0  H11  C9   C10  120.11  3.000
 RH0  H11  C9   C8   119.82  3.000
 RH0  C10  C9   C8   120.07  3.000
 RH0  H12  C10  C11  120.16  3.000
 RH0  H12  C10  C9   120.16  3.000
 RH0  C11  C10  C9   119.68  3.000
 RH0  H13  C11  C12  119.86  3.000
 RH0  H13  C11  C10  120.03  3.000
 RH0  C12  C11  C10  120.12  3.000
 RH0  H14  C12  C11  119.78  3.000
 RH0  H14  C12  C7   119.62  3.000
 RH0  C11  C12  C7   120.60  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
 RH0  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 RH0  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 RH0  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 RH0  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 RH0  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 RH0  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 RH0  CONST_07  C9   C8   C7   C6    180.00   0.0  0
 RH0  CONST_08  C11  C12  C7   C6    180.00   0.0  0
 RH0  CONST_09  H11  C9   C8   C7    180.00   0.0  0
 RH0  CONST_10  H13  C11  C12  C7    180.00   0.0  0
 RH0  CONST_11  H14  C12  C7   C8    180.00   0.0  0
 RH0  CONST_12  H12  C10  C9   C8    180.00   0.0  0
 RH0  CONST_13  H10  C8   C9   C10   180.00   0.0  0
 RH0  CONST_14  HXT  OXT  C    C3    180.00   0.0  0
 RH0  Var_01    C8   C7   C6   S1     93.31  30.0  2
 RH0  Var_02    C7   C6   S1   C5   -176.73  30.0  3
 RH0  Var_03    O    C    C3   C1    -54.26  30.0  3
 RH0  Var_04    H6   C5   S1   C6     47.55  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
 RH0  chir_01  C1  N   C2  C3  positiv
 RH0  chir_02  C2  O1  C1  C5  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
 RH0  plan-1  C6   0.020
 RH0  plan-1  C7   0.020
 RH0  plan-1  C8   0.020
 RH0  plan-1  C9   0.020
 RH0  plan-1  C10  0.020
 RH0  plan-1  C11  0.020
 RH0  plan-1  C12  0.020
 RH0  plan-1  H10  0.020
 RH0  plan-1  H11  0.020
 RH0  plan-1  H12  0.020
 RH0  plan-1  H13  0.020
 RH0  plan-1  H14  0.020
 RH0  plan-2  C3   0.020
 RH0  plan-2  C    0.020
 RH0  plan-2  O    0.020
 RH0  plan-2  OXT  0.020
 RH0  plan-2  HXT  0.020

