# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:50:37 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2,3-dihydroxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc(O)c1O
#
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
 DB1  DB1  '2,3-dihydroxybenzamide   '  ligand  18  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DB1
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
 DB1  O1    O  OH1   0  -0.648   1.8472   0.2865  -0.3885
 DB1  O4    O  OH1   0  -0.633   0.9165   0.2166  -2.9069
 DB1  O7    O  O     0  -0.537   1.4006   0.2308   2.0704
 DB1  N1    N  NH2   0  -0.814  -0.6559   0.0143   2.9265
 DB1  C1    C  CR6   0   0.254   0.5263   0.1633  -0.5477
 DB1  C4    C  CR6   0   0.305   0.0562   0.1290  -1.8730
 DB1  C7    C  CR16  0  -0.343  -1.2963   0.0060  -2.1183
 DB1  C10   C  CR16  0  -0.259  -2.1984  -0.0844  -1.0589
 DB1  C13   C  CR16  0  -0.318  -1.7473  -0.0533   0.2420
 DB1  C16   C  CR6   0  -0.172  -0.3786   0.0703   0.5183
 DB1  C19   C  C     0   0.586   0.1767   0.1103   1.8931
 DB1  HO1   H  HOH1  0   0.483   2.0023   0.2980   0.5958
 DB1  HO4   H  HOH1  0   0.474   1.8223   0.2850  -2.5811
 DB1  HN11  H  HNH2  0   0.414  -0.2877   0.0398   3.8639
 DB1  HN12  H  HNH2  0   0.423  -1.6511  -0.0808   2.8332
 DB1  H7    H  HCR6  0   0.272  -1.6479  -0.0197  -3.1425
 DB1  H10   H  HCR6  0   0.262  -3.2560  -0.1786  -1.2629
 DB1  H13   H  HCR6  0   0.251  -2.4745  -0.1242   1.0389

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
 DB1  O1   C1    single    1.336  0.020  1.336
 DB1  O1   HO1   single    0.850  0.020  0.980
 DB1  O4   C4    single    1.348  0.020  1.348
 DB1  O4   HO4   single    0.850  0.020  0.980
 DB1  O7   C19   double    1.242  0.020  1.242
 DB1  N1   C19   single    1.331  0.020  1.331
 DB1  N1   HN11  single    0.860  0.020  1.020
 DB1  N1   HN12  single    0.860  0.020  1.020
 DB1  C1   C4    aromatic  1.407  0.020  1.407
 DB1  C1   C16   aromatic  1.401  0.020  1.401
 DB1  C4   C7    aromatic  1.380  0.020  1.380
 DB1  C7   C10   aromatic  1.394  0.020  1.394
 DB1  C7   H7    single    0.930  0.020  1.080
 DB1  C10  C13   aromatic  1.377  0.020  1.377
 DB1  C10  H10   single    0.930  0.020  1.080
 DB1  C13  C16   aromatic  1.402  0.020  1.402
 DB1  C13  H13   single    0.930  0.020  1.080
 DB1  C16  C19   single    1.483  0.020  1.483

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
 DB1  HO1   O1   C1    105.82  3.000
 DB1  HO4   O4   C4    110.17  3.000
 DB1  HN12  N1   HN11  116.82  3.000
 DB1  HN12  N1   C19   123.70  3.000
 DB1  HN11  N1   C19   119.48  3.000
 DB1  C16   C1   C4    119.96  3.000
 DB1  C16   C1   O1    123.63  3.000
 DB1  C4    C1   O1    116.41  3.000
 DB1  C7    C4   C1    119.81  3.000
 DB1  C7    C4   O4    119.67  3.000
 DB1  C1    C4   O4    120.52  3.000
 DB1  H7    C7   C10   120.46  3.000
 DB1  H7    C7   C4    119.23  3.000
 DB1  C10   C7   C4    120.32  3.000
 DB1  H10   C10  C13   120.04  3.000
 DB1  H10   C10  C7    119.67  3.000
 DB1  C13   C10  C7    120.28  3.000
 DB1  H13   C13  C16   121.15  3.000
 DB1  H13   C13  C10   118.32  3.000
 DB1  C16   C13  C10   120.53  3.000
 DB1  C19   C16  C13   123.41  3.000
 DB1  C19   C16  C1    117.49  3.000
 DB1  C13   C16  C1    119.11  3.000
 DB1  C16   C19  N1    118.92  3.000
 DB1  C16   C19  O7    120.24  3.000
 DB1  N1    C19  O7    120.84  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
 DB1  CONST_01  C10   C7   C4   C1     0.00   0.0  0
 DB1  CONST_02  C10   C13  C16  C1     0.00   0.0  0
 DB1  CONST_03  C13   C16  C1   C4     0.00   0.0  0
 DB1  CONST_04  C13   C10  C7   C4     0.00   0.0  0
 DB1  CONST_05  C16   C1   C4   C7     0.00   0.0  0
 DB1  CONST_06  C16   C13  C10  C7     0.00   0.0  0
 DB1  CONST_07  C7    C4   C1   O1   180.00   0.0  0
 DB1  CONST_08  C13   C16  C1   O1   180.00   0.0  0
 DB1  CONST_09  C16   C1   C4   O4   180.00   0.0  0
 DB1  CONST_10  C10   C7   C4   O4   180.00   0.0  0
 DB1  CONST_11  C19   C16  C1   C4   180.00   0.0  0
 DB1  CONST_12  C19   C16  C13  C10  180.00   0.0  0
 DB1  CONST_13  H7    C7   C4   C1   180.00   0.0  0
 DB1  CONST_14  H13   C13  C16  C1   180.00   0.0  0
 DB1  CONST_15  H10   C10  C7   C4   180.00   0.0  0
 DB1  CONST_16  HN11  N1   C19  C16  180.00   0.0  0
 DB1  CONST_17  HN12  N1   C19  C16    0.00   0.0  0
 DB1  Var_01    C1    C16  C19  O7     0.44  30.0  3

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
 DB1  plan-1  O1    0.020
 DB1  plan-1  O4    0.020
 DB1  plan-1  C1    0.020
 DB1  plan-1  C4    0.020
 DB1  plan-1  C7    0.020
 DB1  plan-1  C10   0.020
 DB1  plan-1  C13   0.020
 DB1  plan-1  C16   0.020
 DB1  plan-1  C19   0.020
 DB1  plan-1  H7    0.020
 DB1  plan-1  H10   0.020
 DB1  plan-1  H13   0.020
 DB1  plan-2  O7    0.020
 DB1  plan-2  N1    0.020
 DB1  plan-2  C16   0.020
 DB1  plan-2  C19   0.020
 DB1  plan-2  HN11  0.020
 DB1  plan-2  HN12  0.020

