# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 03:23:03 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  33  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.790  -3.0510   1.5851   0.3868
 RH0  C1   C  CH1    0  -0.124  -2.9389   0.1442   0.2166
 RH0  C2   C  CH1    0   0.055  -1.5471  -0.3162  -0.2584
 RH0  O1   O  OH1    0  -0.661  -1.4584  -1.7229  -0.3560
 RH0  C3   C  CH2    0  -0.546  -4.0229  -0.3241  -0.7463
 RH0  C    C  C      0   0.408  -5.4412  -0.0124  -0.2459
 RH0  O    O  O      0  -0.622  -5.7125  -0.3714   0.9188
 RH0  OXT  O  OC    -1  -0.624  -6.2223   0.5449  -1.0444
 RH0  C5   C  CH2    0  -0.589  -0.4257   0.2327   0.6184
 RH0  S1   S  S2     0  -0.009   1.1531  -0.4842   0.0761
 RH0  C6   C  CH2    0  -0.620   2.3145   0.6876   0.8499
 RH0  C7   C  CR6    0   0.111   3.6995   0.3533   0.3851
 RH0  C8   C  CR16   0  -0.287   4.1997   0.9076  -0.7913
 RH0  C9   C  CR16   0  -0.242   5.4710   0.5826  -1.2426
 RH0  C10  C  CR16   0  -0.267   6.2570  -0.3109  -0.5253
 RH0  C11  C  CR16   0  -0.242   5.7636  -0.8747   0.6440
 RH0  C12  C  CR16   0  -0.290   4.4919  -0.5455   1.0943
 RH0  H    H  HNH2   0   0.348  -2.4200   1.9159   1.1050
 RH0  H1   H  HCH1   0   0.217  -3.1288  -0.3103   1.1963
 RH0  H3   H  HCH2   0   0.195  -3.8530   0.1324  -1.7277
 RH0  H4   H  HCH2   0   0.226  -3.9355  -1.4052  -0.8913
 RH0  H6   H  HCH2   0   0.264  -0.3557   1.3167   0.5164
 RH0  H7   H  HCH2   0   0.261  -0.6002   0.0035   1.6744
 RH0  H8   H  HCH2   0   0.278   2.0416   1.7033   0.5599
 RH0  H9   H  HCH2   0   0.278   2.2359   0.6131   1.9355
 RH0  H10  H  HCR6   0   0.252   3.5892   1.6038  -1.3542
 RH0  H11  H  HCR6   0   0.256   5.8483   1.0280  -2.1541
 RH0  H12  H  HCR6   0   0.256   7.2497  -0.5642  -0.8743
 RH0  H13  H  HCR6   0   0.256   6.3701  -1.5719   1.2075
 RH0  H14  H  HCR6   0   0.252   4.1143  -0.9882   2.0085
 RH0  H2   H  HNH2   0   0.335  -2.7853   2.0602  -0.4686
 RH0  H16  H  HCH1   0   0.221  -1.3904   0.0556  -1.2774
 RH0  H17  H  HOH1   0   0.444  -1.6426  -2.0981   0.5125

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    1.455  0.020  1.455
 RH0  N    H    single    0.860  0.020  0.860
 RH0  C1   C2   single    1.541  0.020  1.541
 RH0  C1   C3   single    1.524  0.020  1.524
 RH0  C1   H1   single    0.970  0.020  1.090
 RH0  C2   O1   single    1.413  0.020  1.413
 RH0  C2   C5   single    1.526  0.020  1.526
 RH0  C3   C    single    1.536  0.020  1.536
 RH0  C3   H3   single    0.970  0.020  1.090
 RH0  C3   H4   single    0.970  0.020  1.090
 RH0  C    O    deloc     1.231  0.020  1.231
 RH0  C    OXT  deloc     1.248  0.020  1.248
 RH0  C5   S1   single    1.817  0.020  1.817
 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  1.392  0.020  1.392
 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  1.389  0.020  1.389
 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    106.39  3.000
 RH0  H2   N    C1   110.19  3.000
 RH0  H    N    C1   111.03  3.000
 RH0  H1   C1   C3   108.31  3.000
 RH0  H1   C1   C2   107.93  3.000
 RH0  C3   C1   C2   110.85  3.000
 RH0  H1   C1   N    107.01  3.000
 RH0  C3   C1   N    108.87  3.000
 RH0  C2   C1   N    113.67  3.000
 RH0  H16  C2   C5   107.89  3.000
 RH0  H16  C2   O1   105.34  3.000
 RH0  C5   C2   O1   110.60  3.000
 RH0  H16  C2   C1   108.32  3.000
 RH0  C5   C2   C1   112.29  3.000
 RH0  O1   C2   C1   112.05  3.000
 RH0  H17  O1   C2   108.26  3.000
 RH0  H4   C3   H3   106.30  3.000
 RH0  H4   C3   C    108.51  3.000
 RH0  H3   C3   C    110.51  3.000
 RH0  H4   C3   C1   109.31  3.000
 RH0  H3   C3   C1   109.13  3.000
 RH0  C    C3   C1   112.87  3.000
 RH0  OXT  C    O    126.09  3.000
 RH0  OXT  C    C3   117.39  3.000
 RH0  O    C    C3   116.50  3.000
 RH0  H7   C5   H6   107.97  3.000
 RH0  H7   C5   S1   110.11  3.000
 RH0  H6   C5   S1   107.96  3.000
 RH0  H7   C5   C2   111.22  3.000
 RH0  H6   C5   C2   110.54  3.000
 RH0  S1   C5   C2   108.98  3.000
 RH0  C6   S1   C5    99.98  3.000
 RH0  H9   C6   H8   108.06  3.000
 RH0  H9   C6   C7   111.10  3.000
 RH0  H8   C6   C7   110.88  3.000
 RH0  H9   C6   S1   109.44  3.000
 RH0  H8   C6   S1   109.05  3.000
 RH0  C7   C6   S1   108.29  3.000
 RH0  C12  C7   C8   118.85  3.000
 RH0  C12  C7   C6   120.80  3.000
 RH0  C8   C7   C6   120.32  3.000
 RH0  H10  C8   C9   119.85  3.000
 RH0  H10  C8   C7   119.47  3.000
 RH0  C9   C8   C7   120.68  3.000
 RH0  H11  C9   C10  120.14  3.000
 RH0  H11  C9   C8   119.79  3.000
 RH0  C10  C9   C8   120.06  3.000
 RH0  H12  C10  C11  120.15  3.000
 RH0  H12  C10  C9   120.19  3.000
 RH0  C11  C10  C9   119.66  3.000
 RH0  H13  C11  C12  119.80  3.000
 RH0  H13  C11  C10  120.06  3.000
 RH0  C12  C11  C10  120.14  3.000
 RH0  H14  C12  C11  119.72  3.000
 RH0  H14  C12  C7   119.68  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  Var_01    C8   C7   C6   S1     87.74  30.0  2
 RH0  Var_02    C7   C6   S1   C5   -173.62  30.0  3
 RH0  Var_03    O    C    C3   C1    -50.91  30.0  3
 RH0  Var_04    H6   C5   S1   C6     42.25  30.0  1

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

