# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:30:59 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2OC(=S)Nc2c1
#
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
 5VM  5VM  5-chloranyl-3~{H}-1,3-benzoxazole-2-thione  ligand  15  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5VM
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
 5VM  OAG  O   O     0  -0.415   1.7212  -1.0738  -0.0344
 5VM  CAK  C   CR56  0   0.316   0.3711  -0.8856  -0.0202
 5VM  CAD  C   CR16  0  -0.339  -0.6277  -1.8291  -0.0077
 5VM  CAC  C   CR16  0  -0.221  -1.9325  -1.3465   0.0067
 5VM  CAH  C   CR6   0  -0.048  -2.1826   0.0234   0.0076
 5VM  CLB  CL  CL    0  -0.112  -3.8257   0.5682   0.0259
 5VM  CAE  C   CR16  0  -0.254  -1.1704   0.9756  -0.0053
 5VM  CAJ  C   CR56  0   0.336   0.1165   0.4757  -0.0194
 5VM  NAF  N   NR15  0  -0.668   1.3599   1.0686  -0.0338
 5VM  CAI  C   CR5   0   0.382   2.3241   0.1317  -0.0425
 5VM  SAA  S   S1    0  -0.321   3.9537   0.3234  -0.0599
 5VM  H1   H   HCR6  0   0.298  -0.4224  -2.8903  -0.0085
 5VM  H2   H   HCR6  0   0.293  -2.7573  -2.0444   0.0167
 5VM  H3   H   HCR6  0   0.307  -1.3767   2.0363  -0.0037
 5VM  H4   H   HNR5  0   0.445   1.5534   2.0590  -0.0390

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
 5VM  CLB  CAH  single    1.731  0.020  1.731
 5VM  CAE  CAH  aromatic  1.390  0.020  1.390
 5VM  CAE  CAJ  aromatic  1.381  0.020  1.381
 5VM  NAF  CAJ  single    1.378  0.020  1.378
 5VM  NAF  CAI  single    1.344  0.020  1.344
 5VM  CAH  CAC  aromatic  1.393  0.020  1.393
 5VM  CAJ  CAK  aromatic  1.385  0.020  1.385
 5VM  CAI  SAA  double    1.641  0.020  1.641
 5VM  CAI  OAG  single    1.348  0.020  1.348
 5VM  CAC  CAD  aromatic  1.391  0.020  1.391
 5VM  CAK  OAG  single    1.363  0.020  1.363
 5VM  CAK  CAD  aromatic  1.374  0.020  1.374
 5VM  CAD  H1   single    0.930  0.020  1.080
 5VM  CAC  H2   single    0.930  0.020  1.080
 5VM  CAE  H3   single    0.930  0.020  1.080
 5VM  NAF  H4   single    0.860  0.020  1.020

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
 5VM  CAI  OAG  CAK  108.64  3.000
 5VM  CAJ  CAK  CAD  122.77  3.000
 5VM  CAD  CAK  OAG  128.70  3.000
 5VM  CAJ  CAK  OAG  108.53  3.000
 5VM  H1   CAD  CAC  121.25  3.000
 5VM  H1   CAD  CAK  122.41  3.000
 5VM  CAC  CAD  CAK  116.34  3.000
 5VM  H2   CAC  CAH  119.89  3.000
 5VM  H2   CAC  CAD  119.46  3.000
 5VM  CAH  CAC  CAD  120.64  3.000
 5VM  CAE  CAH  CLB  118.41  3.000
 5VM  CAE  CAH  CAC  122.90  3.000
 5VM  CLB  CAH  CAC  118.68  3.000
 5VM  H3   CAE  CAJ  122.23  3.000
 5VM  H3   CAE  CAH  122.25  3.000
 5VM  CAJ  CAE  CAH  115.53  3.000
 5VM  NAF  CAJ  CAE  133.28  3.000
 5VM  NAF  CAJ  CAK  104.90  3.000
 5VM  CAE  CAJ  CAK  121.82  3.000
 5VM  H4   NAF  CAI  123.12  3.000
 5VM  H4   NAF  CAJ  126.55  3.000
 5VM  CAI  NAF  CAJ  110.33  3.000
 5VM  SAA  CAI  NAF  129.11  3.000
 5VM  SAA  CAI  OAG  123.28  3.000
 5VM  NAF  CAI  OAG  107.60  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
 5VM  CONST_01  CAH  CAE  CAJ  CAK    0.00  0.0  0
 5VM  CONST_02  CAH  CAC  CAD  CAK    0.00  0.0  0
 5VM  CONST_03  CAE  CAH  CAC  CAD    0.00  0.0  0
 5VM  CONST_04  CAE  CAJ  CAK  CAD    0.00  0.0  0
 5VM  CONST_05  CAJ  CAE  CAH  CAC    0.00  0.0  0
 5VM  CONST_06  CAJ  CAK  CAD  CAC    0.00  0.0  0
 5VM  CONST_07  CLB  CAH  CAC  CAD  180.00  0.0  0
 5VM  CONST_08  CAJ  CAE  CAH  CLB  180.00  0.0  0
 5VM  CONST_09  H1   CAD  CAK  OAG    0.00  0.0  0
 5VM  CONST_10  H3   CAE  CAJ  CAK  180.00  0.0  0
 5VM  CONST_11  H2   CAC  CAD  CAK  180.00  0.0  0

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
 5VM  plan-1  OAG  0.020
 5VM  plan-1  CAK  0.020
 5VM  plan-1  CAD  0.020
 5VM  plan-1  CAC  0.020
 5VM  plan-1  CAH  0.020
 5VM  plan-1  CLB  0.020
 5VM  plan-1  CAE  0.020
 5VM  plan-1  CAJ  0.020
 5VM  plan-1  NAF  0.020
 5VM  plan-1  CAI  0.020
 5VM  plan-1  SAA  0.020
 5VM  plan-1  H1   0.020
 5VM  plan-1  H2   0.020
 5VM  plan-1  H3   0.020
 5VM  plan-1  H4   0.020

