# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:36:35 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 5-{(2S)-2-amino-3-[(trihydroxy-lambda~5~-arsanyl)oxy]propyl}-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO[As](O)(O)O)Cc1[nH]cnc1
#
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
 GK8  GK8  5-{(2S)-2-amino-3-[(trihydroxy-lambda~5~-arsanyl)oxy]propyl}-1H-imidazole  ligand  27  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GK8
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
 GK8  C     C   CH2   0  -0.136  -0.0169   0.0552  -0.6048
 GK8  N     N   NH2   0  -0.785   1.4819  -1.4583   0.5813
 GK8  AS    AS  AS    0   1.256  -2.7612   0.3609  -0.0828
 GK8  O1    O   O     0  -0.791  -3.1864  -1.0677  -1.0012
 GK8  O2    O   O     0  -0.766  -4.3270   1.1436  -0.6142
 GK8  O3    O   O     0  -0.785  -3.2249   0.0073   1.5666
 GK8  O4    O   OC2   0  -0.589  -1.0399  -0.1478   0.3493
 GK8  CA    C   CH1   0  -0.126   1.3405  -0.1114   0.0633
 GK8  CB    C   CH2   0  -0.541   2.4392   0.3161  -0.9317
 GK8  CG    C   CR5   0   0.299   3.8058   0.2471  -0.3475
 GK8  ND1   N   NR15  0  -0.607   4.6221  -0.8469  -0.4421
 GK8  CD2   C   CR15  0  -0.262   4.5200   1.1376   0.4088
 GK8  CE1   C   CR15  0   0.075   5.7597  -0.5818   0.2325
 GK8  NE2   N   N     0  -0.442   5.7319   0.6131   0.7632
 GK8  H     H   HCH2  0   0.201  -0.0985  -0.6599  -1.4360
 GK8  HA    H   HCH2  0   0.216  -0.0657   1.0592  -1.0431
 GK8  HN    H   HNH2  0   0.337   1.5114  -2.1222  -0.1848
 GK8  HNA   H   HNH2  0   0.349   2.3603  -1.5523   1.0756
 GK8  HAA   H   HCH1  0   0.238   1.3825   0.5767   0.9141
 GK8  HB    H   HCH2  0   0.250   2.3836  -0.3153  -1.8248
 GK8  HBA   H   HCH2  0   0.254   2.2502   1.3406  -1.2606
 GK8  HND1  H   HNR5  0   0.414   4.4217  -1.6959  -0.9474
 GK8  HD2   H   HCR5  0   0.248   4.2167   2.1298   0.7091
 GK8  HE1   H   HCR5  0   0.274   6.5702  -1.2911   0.2993
 GK8  H11   H   H     0   0.473  -2.5627  -1.7895  -0.8475
 GK8  H12   H   H     0   0.469  -4.2551   2.1050  -0.5413
 GK8  H13   H   H     0   0.474  -4.1549   0.2221   1.7166

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
 GK8  C    O4    single    1.414  0.020  1.414
 GK8  C    CA    single    1.522  0.020  1.522
 GK8  C    H     single    0.970  0.020  1.090
 GK8  C    HA    single    0.970  0.020  1.090
 GK8  N    CA    single    1.450  0.020  1.450
 GK8  N    HN    single    0.890  0.020  1.040
 GK8  N    HNA   single    0.890  0.020  1.040
 GK8  AS   O1    single    1.751  0.020  1.751
 GK8  AS   O2    single    1.829  0.020  1.829
 GK8  AS   O3    single    1.749  0.020  1.749
 GK8  AS   O4    single    1.846  0.020  1.846
 GK8  CA   CB    single    1.543  0.020  1.543
 GK8  CA   HAA   single    0.970  0.020  1.090
 GK8  CB   CG    single    1.488  0.020  1.488
 GK8  CB   HB    single    0.970  0.020  1.090
 GK8  CB   HBA   single    0.970  0.020  1.090
 GK8  CG   ND1   aromatic  1.368  0.020  1.368
 GK8  CG   CD2   aromatic  1.369  0.020  1.369
 GK8  ND1  CE1   aromatic  1.349  0.020  1.349
 GK8  ND1  HND1  single    0.860  0.020  1.020
 GK8  CD2  NE2   aromatic  1.367  0.020  1.367
 GK8  CD2  HD2   single    0.930  0.020  1.080
 GK8  CE1  NE2   aromatic  1.308  0.020  1.308
 GK8  CE1  HE1   single    0.930  0.020  1.080
 GK8  O1   H11   single    0.850  0.020  0.980
 GK8  O2   H12   single    0.850  0.020  0.980
 GK8  O3   H13   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
 GK8  HA    C    H    106.86  3.000
 GK8  HA    C    CA   108.38  3.000
 GK8  H     C    CA   109.08  3.000
 GK8  HA    C    O4   111.66  3.000
 GK8  H     C    O4   111.29  3.000
 GK8  CA    C    O4   109.48  3.000
 GK8  HNA   N    HN   106.43  3.000
 GK8  HNA   N    CA   110.21  3.000
 GK8  HN    N    CA   109.94  3.000
 GK8  O4    AS   O3    88.32  3.000
 GK8  O4    AS   O2   169.70  3.000
 GK8  O3    AS   O2    97.67  3.000
 GK8  O4    AS   O1    97.15  3.000
 GK8  O3    AS   O1   105.38  3.000
 GK8  O2    AS   O1    89.36  3.000
 GK8  H11   O1   AS   111.67  3.000
 GK8  H12   O2   AS   109.87  3.000
 GK8  H13   O3   AS   110.89  3.000
 GK8  AS    O4   C    118.51  3.000
 GK8  HAA   CA   CB   107.44  3.000
 GK8  HAA   CA   N    107.60  3.000
 GK8  CB    CA   N    114.73  3.000
 GK8  HAA   CA   C    107.85  3.000
 GK8  CB    CA   C    108.77  3.000
 GK8  N     CA   C    110.21  3.000
 GK8  HBA   CB   HB   106.64  3.000
 GK8  HBA   CB   CG   108.70  3.000
 GK8  HB    CB   CG   109.88  3.000
 GK8  HBA   CB   CA   109.32  3.000
 GK8  HB    CB   CA   109.27  3.000
 GK8  CG    CB   CA   112.84  3.000
 GK8  CD2   CG   ND1  104.30  3.000
 GK8  CD2   CG   CB   131.74  3.000
 GK8  ND1   CG   CB   123.91  3.000
 GK8  HND1  ND1  CE1  125.72  3.000
 GK8  HND1  ND1  CG   126.12  3.000
 GK8  CE1   ND1  CG   108.14  3.000
 GK8  HD2   CD2  NE2  121.96  3.000
 GK8  HD2   CD2  CG   127.19  3.000
 GK8  NE2   CD2  CG   110.85  3.000
 GK8  HE1   CE1  NE2  126.26  3.000
 GK8  HE1   CE1  ND1  122.35  3.000
 GK8  NE2   CE1  ND1  111.39  3.000
 GK8  CE1   NE2  CD2  105.32  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
 GK8  CONST_01  NE2   CE1  ND1  CG     0.00   0.0  0
 GK8  CONST_02  CE1   NE2  CD2  CG     0.00   0.0  0
 GK8  CONST_03  NE2   CD2  CG   ND1    0.00   0.0  0
 GK8  CONST_04  CD2   NE2  CE1  ND1    0.00   0.0  0
 GK8  CONST_05  CE1   ND1  CG   CD2    0.00   0.0  0
 GK8  CONST_06  CE1   ND1  CG   CB   180.00   0.0  0
 GK8  CONST_07  NE2   CD2  CG   CB   180.00   0.0  0
 GK8  CONST_08  HE1   CE1  ND1  CG   180.00   0.0  0
 GK8  CONST_09  HD2   CD2  CG   ND1  180.00   0.0  0
 GK8  CONST_10  HND1  ND1  CG   CD2  180.00   0.0  0
 GK8  Var_01    ND1   CG   CB   CA    92.35  30.0  2
 GK8  Var_02    O1    AS   O4   C     82.06  30.0  2
 GK8  Var_03    CA    C    O4   AS   166.40  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
 GK8  chir_01  CA  C  N  CB  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
 GK8  plan-1  CB    0.020
 GK8  plan-1  CG    0.020
 GK8  plan-1  ND1   0.020
 GK8  plan-1  CD2   0.020
 GK8  plan-1  CE1   0.020
 GK8  plan-1  NE2   0.020
 GK8  plan-1  HND1  0.020
 GK8  plan-1  HD2   0.020
 GK8  plan-1  HE1   0.020

