# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:13:45 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2-[(1S,2R)-1-amino-2-(sulfooxy)propyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[S](O)(=O)=O)[C@H](N)c1oc(O)c(n1)C(O)=S
#
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
 HM8  HM8  '2-[(1S,2R)-1-amino-2-(sulfooxy)propyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acid'  L-peptide  27  18  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HM8
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
 HM8  N     N  NH2    0  -0.781  -1.3596   2.6483  -1.4948
 HM8  CAA   C  CH1    0  -0.212  -0.9869   2.0958  -0.2121
 HM8  CAV   C  CH1    0   0.026  -2.1319   1.2709   0.3950
 HM8  CAW   C  CH3    0  -0.666  -3.4176   2.0593   0.5350
 HM8  OBW   O  OC2    0  -0.625  -2.3549   0.1421  -0.4519
 HM8  SBV   S  S      0   1.573  -2.1804  -1.3586   0.1948
 HM8  OBZ   O  OS     0  -0.733  -2.4396  -2.1888  -0.9778
 HM8  OBY   O  OS     0  -0.728  -0.8069  -1.4211   0.7043
 HM8  OBX   O  OS    -1  -0.740  -3.1955  -1.4465   1.2482
 HM8  CAZ   C  CR5    0   0.503   0.2678   1.2777  -0.2165
 HM8  NBA   N  N      0  -0.408   1.2098   1.2487   0.6405
 HM8  OBB   O  O      0  -0.417   0.4611   0.4005  -1.2483
 HM8  CBC   C  CR5    0   0.548   1.5894  -0.2371  -0.9706
 HM8  OBD   O  OH1    0  -0.554   2.0252  -1.1599  -1.7759
 HM8  CAB   C  CR5    0   0.038   2.0969   0.2745   0.1994
 HM8  C     C  C      0   0.110   3.2979  -0.0711   0.8885
 HM8  SBG   S  S1     0  -0.328   4.3717  -1.2266   0.3999
 HM8  OXT   O  OH1    0  -0.541   3.4735   0.6424   1.9852
 HM8  HN1   H  HNH2   0   0.361  -0.6086   3.2114  -1.8716
 HM8  HN2   H  HNH2   0   0.352  -1.5486   1.9166  -2.1679
 HM8  HAA   H  HCH1   0   0.281  -0.7962   2.9199   0.4807
 HM8  HAV   H  HCH1   0   0.248  -1.8028   0.9520   1.3892
 HM8  HAW1  H  HCH3   0   0.239  -4.1757   1.4507   1.0274
 HM8  HAW2  H  HCH3   0   0.228  -3.2502   2.9466   1.1466
 HM8  HAW3  H  HCH3   0   0.234  -3.7991   2.3829  -0.4319
 HM8  HBD   H  HOH1   0   0.508   1.4421  -1.2836  -2.5391
 HM8  HXT   H  HOH1   0   0.483   4.2989   0.3677   2.4120

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
 HM8  N    CAA   single    1.445  0.020  1.445
 HM8  CAA  CAV   single    1.536  0.020  1.536
 HM8  CAA  CAZ   single    1.498  0.020  1.498
 HM8  CAV  CAW   single    1.515  0.020  1.515
 HM8  CAV  OBW   single    1.429  0.020  1.429
 HM8  OBW  SBV   single    1.643  0.020  1.643
 HM8  SBV  OBZ   deloc     1.460  0.020  1.460
 HM8  SBV  OBY   deloc     1.466  0.020  1.466
 HM8  SBV  OBX   deloc     1.466  0.020  1.466
 HM8  CAZ  NBA   aromatic  1.274  0.020  1.274
 HM8  CAZ  OBB   aromatic  1.368  0.020  1.368
 HM8  NBA  CAB   aromatic  1.390  0.020  1.390
 HM8  OBB  CBC   aromatic  1.325  0.020  1.325
 HM8  CBC  OBD   single    1.300  0.020  1.300
 HM8  CBC  CAB   aromatic  1.374  0.020  1.374
 HM8  CAB  C     single    1.427  0.020  1.427
 HM8  C    SBG   double    1.651  0.020  1.651
 HM8  C    OXT   single    1.320  0.020  1.320
 HM8  N    HN1   single    0.890  0.020  1.040
 HM8  N    HN2   single    0.890  0.020  1.040
 HM8  CAA  HAA   single    0.970  0.020  1.090
 HM8  CAV  HAV   single    0.970  0.020  1.090
 HM8  CAW  HAW1  single    0.970  0.020  1.090
 HM8  CAW  HAW2  single    0.970  0.020  1.090
 HM8  CAW  HAW3  single    0.970  0.020  1.090
 HM8  OBD  HBD   single    0.850  0.020  0.980
 HM8  OXT  HXT   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
 HM8  HN2   N    HN1   107.06  3.000
 HM8  HN2   N    CAA   111.22  3.000
 HM8  HN1   N    CAA   110.61  3.000
 HM8  HAA   CAA  CAZ   105.51  3.000
 HM8  HAA   CAA  CAV   106.52  3.000
 HM8  CAZ   CAA  CAV   109.40  3.000
 HM8  HAA   CAA  N     108.61  3.000
 HM8  CAZ   CAA  N     114.97  3.000
 HM8  CAV   CAA  N     111.33  3.000
 HM8  HAV   CAV  OBW   110.79  3.000
 HM8  HAV   CAV  CAW   108.83  3.000
 HM8  OBW   CAV  CAW   109.49  3.000
 HM8  HAV   CAV  CAA   106.94  3.000
 HM8  OBW   CAV  CAA   107.84  3.000
 HM8  CAW   CAV  CAA   112.94  3.000
 HM8  HAW3  CAW  HAW2  108.06  3.000
 HM8  HAW3  CAW  HAW1  108.87  3.000
 HM8  HAW2  CAW  HAW1  107.93  3.000
 HM8  HAW3  CAW  CAV   111.72  3.000
 HM8  HAW2  CAW  CAV   110.19  3.000
 HM8  HAW1  CAW  CAV   109.98  3.000
 HM8  SBV   OBW  CAV   118.14  3.000
 HM8  OBX   SBV  OBY   113.36  3.000
 HM8  OBX   SBV  OBZ   114.85  3.000
 HM8  OBY   SBV  OBZ   114.90  3.000
 HM8  OBX   SBV  OBW   105.31  3.000
 HM8  OBY   SBV  OBW   105.97  3.000
 HM8  OBZ   SBV  OBW   100.63  3.000
 HM8  OBB   CAZ  NBA   112.85  3.000
 HM8  OBB   CAZ  CAA   118.08  3.000
 HM8  NBA   CAZ  CAA   129.05  3.000
 HM8  CAB   NBA  CAZ   105.94  3.000
 HM8  CBC   OBB  CAZ   105.71  3.000
 HM8  CAB   CBC  OBD   131.91  3.000
 HM8  CAB   CBC  OBB   108.28  3.000
 HM8  OBD   CBC  OBB   119.81  3.000
 HM8  HBD   OBD  CBC   112.15  3.000
 HM8  C     CAB  CBC   129.18  3.000
 HM8  C     CAB  NBA   123.63  3.000
 HM8  CBC   CAB  NBA   107.19  3.000
 HM8  OXT   C    SBG   122.51  3.000
 HM8  OXT   C    CAB   112.47  3.000
 HM8  SBG   C    CAB   125.02  3.000
 HM8  HXT   OXT  C     109.02  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
 HM8  CONST_01  CBC  CAB  NBA  CAZ     0.00   0.0  0
 HM8  CONST_02  CAB  CBC  OBB  CAZ     0.00   0.0  0
 HM8  CONST_03  CBC  OBB  CAZ  NBA     0.00   0.0  0
 HM8  CONST_04  OBB  CBC  CAB  NBA     0.00   0.0  0
 HM8  CONST_05  CAB  NBA  CAZ  OBB     0.00   0.0  0
 HM8  CONST_06  CAB  NBA  CAZ  CAA   180.00   0.0  0
 HM8  CONST_07  CBC  OBB  CAZ  CAA   180.00   0.0  0
 HM8  CONST_08  C    CAB  NBA  CAZ   180.00   0.0  0
 HM8  CONST_09  OBD  CBC  OBB  CAZ   180.00   0.0  0
 HM8  CONST_10  OBD  CBC  CAB  NBA   180.00   0.0  0
 HM8  CONST_11  C    CAB  CBC  OBB   180.00   0.0  0
 HM8  Var_01    SBG  C    CAB  NBA   179.69  30.0  2
 HM8  Var_02    OBZ  SBV  OBW  CAV  -178.03  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
 HM8  chir_01  CAA  N    CAV  CAZ  negativ
 HM8  chir_02  CAV  OBW  CAA  CAW  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
 HM8  plan-1  CAA  0.020
 HM8  plan-1  CAZ  0.020
 HM8  plan-1  NBA  0.020
 HM8  plan-1  OBB  0.020
 HM8  plan-1  CBC  0.020
 HM8  plan-1  OBD  0.020
 HM8  plan-1  CAB  0.020
 HM8  plan-1  C    0.020
 HM8  plan-2  CAB  0.020
 HM8  plan-2  C    0.020
 HM8  plan-2  SBG  0.020
 HM8  plan-2  OXT  0.020

