# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:33:22 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 2-phenoxyacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)COc1ccccc1
#
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
 PO6  PO6  '2-phenoxyacetamide       '  ligand  20  11  .  2021-08-19  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PO6
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
 PO6  CF  C  CR16  0  -0.378  -1.3033   1.1560  -0.0045
 PO6  CD  C  CR16  0  -0.240  -2.6744   1.3951   0.0026
 PO6  CC  C  CR16  0  -0.281  -3.5817   0.3486  -0.0028
 PO6  CE  C  CR16  0  -0.241  -3.1047  -0.9587  -0.0152
 PO6  CG  C  CR16  0  -0.344  -1.7449  -1.2139  -0.0218
 PO6  CK  C  CR6   0   0.383  -0.8347  -0.1549  -0.0167
 PO6  OI  O  O2    0  -0.465   0.4712  -0.4992  -0.0235
 PO6  CH  C  CH2   0  -0.297   1.4318   0.5194  -0.0164
 PO6  CJ  C  C     0   0.476   2.8076  -0.1304  -0.0200
 PO6  OB  O  O     0  -0.472   2.9627  -1.3377  -0.0176
 PO6  NA  N  NH2   0  -0.801   3.8108   0.7571  -0.0240
 PO6  H1  H  HCR6  0   0.280  -0.6283   2.0007  -0.0003
 PO6  H2  H  HCR6  0   0.259  -3.0254   2.4191   0.0131
 PO6  H3  H  HCR6  0   0.253  -4.6458   0.5429   0.0026
 PO6  H4  H  HCR6  0   0.259  -3.7990  -1.7890  -0.0194
 PO6  H5  H  HCR6  0   0.262  -1.3763  -2.2324  -0.0316
 PO6  H6  H  HCH2  0   0.263   1.3407   1.1712  -0.8941
 PO6  H7  H  HCH2  0   0.263   1.3417   1.1584   0.8709
 PO6  H8  H  HNH2  0   0.412   3.6493   1.7501  -0.0269
 PO6  H9  H  HNH2  0   0.408   4.7682   0.4455  -0.0239

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
 PO6  OI  CK  single    1.350  0.020  1.350
 PO6  OI  CH  single    1.400  0.020  1.400
 PO6  OB  CJ  double    1.217  0.020  1.217
 PO6  CG  CK  aromatic  1.396  0.020  1.396
 PO6  CG  CE  aromatic  1.384  0.020  1.384
 PO6  NA  CJ  single    1.339  0.020  1.339
 PO6  CJ  CH  single    1.522  0.020  1.522
 PO6  CK  CF  aromatic  1.392  0.020  1.392
 PO6  CE  CC  aromatic  1.392  0.020  1.392
 PO6  CF  CD  aromatic  1.392  0.020  1.392
 PO6  CC  CD  aromatic  1.385  0.020  1.385
 PO6  CF  H1  single    0.930  0.020  1.080
 PO6  CD  H2  single    0.930  0.020  1.080
 PO6  CC  H3  single    0.930  0.020  1.080
 PO6  CE  H4  single    0.930  0.020  1.080
 PO6  CG  H5  single    0.930  0.020  1.080
 PO6  CH  H6  single    0.970  0.020  1.090
 PO6  CH  H7  single    0.970  0.020  1.090
 PO6  NA  H8  single    0.860  0.020  1.020
 PO6  NA  H9  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
 PO6  H1  CF  CK  121.70  3.000
 PO6  H1  CF  CD  118.74  3.000
 PO6  CK  CF  CD  119.56  3.000
 PO6  H2  CD  CC  120.16  3.000
 PO6  H2  CD  CF  118.81  3.000
 PO6  CC  CD  CF  121.03  3.000
 PO6  H3  CC  CE  120.39  3.000
 PO6  H3  CC  CD  120.58  3.000
 PO6  CE  CC  CD  119.03  3.000
 PO6  H4  CE  CG  119.27  3.000
 PO6  H4  CE  CC  120.05  3.000
 PO6  CG  CE  CC  120.67  3.000
 PO6  H5  CG  CK  119.43  3.000
 PO6  H5  CG  CE  120.53  3.000
 PO6  CK  CG  CE  120.05  3.000
 PO6  OI  CK  CG  115.90  3.000
 PO6  CG  CK  CF  119.65  3.000
 PO6  OI  CK  CF  124.45  3.000
 PO6  CH  OI  CK  118.54  3.000
 PO6  H7  CH  H6  107.12  3.000
 PO6  H7  CH  CJ  108.96  3.000
 PO6  H6  CH  CJ  109.08  3.000
 PO6  H7  CH  OI  111.80  3.000
 PO6  H6  CH  OI  111.79  3.000
 PO6  CJ  CH  OI  108.04  3.000
 PO6  NA  CJ  OB  124.18  3.000
 PO6  NA  CJ  CH  113.22  3.000
 PO6  OB  CJ  CH  122.60  3.000
 PO6  H9  NA  H8  117.27  3.000
 PO6  H9  NA  CJ  120.47  3.000
 PO6  H8  NA  CJ  122.26  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
 PO6  CONST_01  CE  CG  CK  CF    0.00   0.0  0
 PO6  CONST_02  CE  CC  CD  CF    0.00   0.0  0
 PO6  CONST_03  CG  CK  CF  CD    0.00   0.0  0
 PO6  CONST_04  CG  CE  CC  CD    0.00   0.0  0
 PO6  CONST_05  CK  CG  CE  CC    0.00   0.0  0
 PO6  CONST_06  CK  CF  CD  CC    0.00   0.0  0
 PO6  CONST_07  OI  CK  CF  CD  180.00   0.0  0
 PO6  CONST_08  OI  CK  CG  CE  180.00   0.0  0
 PO6  CONST_09  H5  CG  CK  CF  180.00   0.0  0
 PO6  CONST_10  H3  CC  CD  CF  180.00   0.0  0
 PO6  CONST_11  H4  CE  CC  CD  180.00   0.0  0
 PO6  CONST_12  H1  CF  CD  CC  180.00   0.0  0
 PO6  CONST_13  H2  CD  CC  CE  180.00   0.0  0
 PO6  CONST_14  H8  NA  CJ  CH    0.00   0.0  0
 PO6  CONST_15  H9  NA  CJ  CH  180.00   0.0  0
 PO6  Var_01    CJ  CH  OI  CK  179.75  30.0  3
 PO6  Var_02    OB  CJ  CH  OI   -0.57  30.0  2

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
 PO6  plan-1  CF  0.020
 PO6  plan-1  CD  0.020
 PO6  plan-1  CC  0.020
 PO6  plan-1  CE  0.020
 PO6  plan-1  CG  0.020
 PO6  plan-1  CK  0.020
 PO6  plan-1  OI  0.020
 PO6  plan-1  H1  0.020
 PO6  plan-1  H2  0.020
 PO6  plan-1  H3  0.020
 PO6  plan-1  H4  0.020
 PO6  plan-1  H5  0.020
 PO6  plan-2  CH  0.020
 PO6  plan-2  CJ  0.020
 PO6  plan-2  OB  0.020
 PO6  plan-2  NA  0.020
 PO6  plan-2  H8  0.020
 PO6  plan-2  H9  0.020

