# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 07:09:09 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 4-hydroxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(O)cc1
#
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
 HBD  HBD  '4-hydroxybenzamide       '  ligand  17  10  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HBD
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
 HBD  C1    C  CR6   0  -0.065   0.0323  -0.0571   0.6755
 HBD  C2    C  CR16  0  -0.253  -1.1352   0.1091  -0.0656
 HBD  C3    C  CR16  0  -0.374  -1.0992   0.2099  -1.4444
 HBD  C4    C  CR6   0   0.361   0.1189   0.1207  -2.1172
 HBD  C5    C  CR16  0  -0.325   1.2930  -0.0701  -1.3895
 HBD  C6    C  CR16  0  -0.267   1.2440  -0.1536  -0.0101
 HBD  C1'   C  C     0   0.480  -0.0738  -0.1590   2.1581
 HBD  O1'   O  O     0  -0.487  -1.1132  -0.5178   2.6976
 HBD  N1'   N  NH2   0  -0.813   1.0310   0.1566   2.8560
 HBD  O4    O  OH1   0  -0.622   0.2166   0.2064  -3.4532
 HBD  H2    H  HCR6  0   0.265  -2.0892   0.1751   0.4407
 HBD  H3    H  HCR6  0   0.277  -2.0195   0.3566  -1.9980
 HBD  H5    H  HCR6  0   0.271   2.2392  -0.1586  -1.9079
 HBD  H6    H  HCR6  0   0.262   2.1715  -0.3239   0.5229
 HBD  HN'1  H  HNH2  0   0.402   1.0003   0.1406   3.8624
 HBD  HN'2  H  HNH2  0   0.410   1.8100   0.6330   2.4367
 HBD  HO4   H  HOH1  0   0.478  -0.6502   0.3566  -3.8477

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
 HBD  C1   C2    aromatic  1.393  0.020  1.393
 HBD  C1   C6    aromatic  1.396  0.020  1.396
 HBD  C1   C1'   single    1.490  0.020  1.490
 HBD  C2   C3    aromatic  1.383  0.020  1.383
 HBD  C2   H2    single    0.930  0.020  1.080
 HBD  C3   C4    aromatic  1.394  0.020  1.394
 HBD  C3   H3    single    0.930  0.020  1.080
 HBD  C4   C5    aromatic  1.394  0.020  1.394
 HBD  C4   O4    single    1.342  0.020  1.342
 HBD  C5   C6    aromatic  1.383  0.020  1.383
 HBD  C5   H5    single    0.930  0.020  1.080
 HBD  C6   H6    single    0.930  0.020  1.080
 HBD  C1'  O1'   double    1.225  0.020  1.225
 HBD  C1'  N1'   single    1.344  0.020  1.344
 HBD  N1'  HN'1  single    0.860  0.020  1.020
 HBD  N1'  HN'2  single    0.860  0.020  1.020
 HBD  O4   HO4   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
 HBD  C1'   C1   C6    123.09  3.000
 HBD  C1'   C1   C2    118.55  3.000
 HBD  C6    C1   C2    118.34  3.000
 HBD  H2    C2   C3    119.02  3.000
 HBD  H2    C2   C1    119.82  3.000
 HBD  C3    C2   C1    121.15  3.000
 HBD  H3    C3   C4    120.26  3.000
 HBD  H3    C3   C2    119.80  3.000
 HBD  C4    C3   C2    119.94  3.000
 HBD  O4    C4   C5    117.83  3.000
 HBD  O4    C4   C3    122.66  3.000
 HBD  C5    C4   C3    119.50  3.000
 HBD  H5    C5   C6    120.25  3.000
 HBD  H5    C5   C4    119.82  3.000
 HBD  C6    C5   C4    119.94  3.000
 HBD  H6    C6   C5    118.04  3.000
 HBD  H6    C6   C1    120.84  3.000
 HBD  C5    C6   C1    121.11  3.000
 HBD  N1'   C1'  O1'   122.51  3.000
 HBD  N1'   C1'  C1    116.23  3.000
 HBD  O1'   C1'  C1    121.25  3.000
 HBD  HN'2  N1'  HN'1  116.63  3.000
 HBD  HN'2  N1'  C1'   122.13  3.000
 HBD  HN'1  N1'  C1'   119.34  3.000
 HBD  HO4   O4   C4    110.60  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
 HBD  CONST_01  C4    C3   C2   C1    0.00   0.0  0
 HBD  CONST_02  C4    C5   C6   C1    0.00   0.0  0
 HBD  CONST_03  C5    C6   C1   C2    0.00   0.0  0
 HBD  CONST_04  C5    C4   C3   C2    0.00   0.0  0
 HBD  CONST_05  C6    C1   C2   C3    0.00   0.0  0
 HBD  CONST_06  C6    C5   C4   C3    0.00   0.0  0
 HBD  CONST_07  O4    C4   C3   C2  180.00   0.0  0
 HBD  CONST_08  C1'   C1   C2   C3  180.00   0.0  0
 HBD  CONST_09  C1'   C1   C6   C5  180.00   0.0  0
 HBD  CONST_10  O4    C4   C5   C6  180.00   0.0  0
 HBD  CONST_11  H3    C3   C2   C1  180.00   0.0  0
 HBD  CONST_12  H5    C5   C6   C1  180.00   0.0  0
 HBD  CONST_13  H6    C6   C1   C2  180.00   0.0  0
 HBD  CONST_14  H2    C2   C3   C4  180.00   0.0  0
 HBD  CONST_15  HN'1  N1'  C1'  C1  180.00   0.0  0
 HBD  CONST_16  HN'2  N1'  C1'  C1    0.00   0.0  0
 HBD  Var_01    O1'   C1'  C1   C2   23.24  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
 HBD  plan-1  C1    0.020
 HBD  plan-1  C2    0.020
 HBD  plan-1  C3    0.020
 HBD  plan-1  C4    0.020
 HBD  plan-1  C5    0.020
 HBD  plan-1  C6    0.020
 HBD  plan-1  C1'   0.020
 HBD  plan-1  O4    0.020
 HBD  plan-1  H2    0.020
 HBD  plan-1  H3    0.020
 HBD  plan-1  H5    0.020
 HBD  plan-1  H6    0.020
 HBD  plan-2  C1    0.020
 HBD  plan-2  C1'   0.020
 HBD  plan-2  O1'   0.020
 HBD  plan-2  N1'   0.020
 HBD  plan-2  HN'1  0.020
 HBD  plan-2  HN'2  0.020

