# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 02:05:49 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: N-(hydroxymethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCNC(=O)c1ccccc1
#
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
 1Q8  1Q8  N-(hydroxymethyl)benzamide  ligand  20  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1Q8
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
 1Q8  O6   O  O     0  -0.478   1.1135  -1.5737   0.6310
 1Q8  C2   C  C     0   0.535   0.7647  -0.4383   0.3485
 1Q8  N5   N  NH1   0  -0.663   1.6384   0.5806   0.1982
 1Q8  C9   C  CH2   0  -0.028   3.0497   0.4188   0.3493
 1Q8  O11  O  OH1   0  -0.664   3.5976  -0.0643  -0.8526
 1Q8  C1   C  CR6   0  -0.035  -0.6784  -0.0968   0.1580
 1Q8  C4   C  CR16  0  -0.267  -1.5502  -1.1155  -0.2219
 1Q8  C8   C  CR16  0  -0.242  -2.8998  -0.8534  -0.3983
 1Q8  C10  C  CR16  0  -0.250  -3.3964   0.4250  -0.1764
 1Q8  C7   C  CR16  0  -0.241  -2.5369   1.4402   0.2204
 1Q8  C3   C  CR16  0  -0.290  -1.1834   1.1824   0.3845
 1Q8  H1   H  HNH1  0   0.411   1.3110   1.4523  -0.1848
 1Q8  H2   H  HCH2  0   0.224   3.4591   1.3975   0.6137
 1Q8  H3   H  HCH2  0   0.216   3.2387  -0.2630   1.1823
 1Q8  H4   H  HOH1  0   0.457   4.5470  -0.1617  -0.7268
 1Q8  H5   H  HCR6  0   0.261  -1.1702  -2.1147  -0.3890
 1Q8  H6   H  HCR6  0   0.263  -3.5660  -1.6491  -0.7052
 1Q8  H7   H  HCR6  0   0.265  -4.4513   0.6276  -0.3078
 1Q8  H8   H  HCR6  0   0.265  -2.9192   2.4345   0.4100
 1Q8  H9   H  HCR6  0   0.262  -0.5376   1.9867   0.7147

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
 1Q8  C7   C10  aromatic  1.388  0.020  1.388
 1Q8  C7   C3   aromatic  1.388  0.020  1.388
 1Q8  C10  C8   aromatic  1.389  0.020  1.389
 1Q8  C3   C1   aromatic  1.394  0.020  1.394
 1Q8  C8   C4   aromatic  1.386  0.020  1.386
 1Q8  C1   C4   aromatic  1.394  0.020  1.394
 1Q8  C1   C2   single    1.495  0.020  1.495
 1Q8  O6   C2   double    1.221  0.020  1.221
 1Q8  C2   N5   single    1.351  0.020  1.351
 1Q8  N5   C9   single    1.429  0.020  1.429
 1Q8  C9   O11  single    1.407  0.020  1.407
 1Q8  N5   H1   single    0.860  0.020  1.020
 1Q8  C9   H2   single    0.970  0.020  1.090
 1Q8  C9   H3   single    0.970  0.020  1.090
 1Q8  O11  H4   single    0.850  0.020  0.980
 1Q8  C4   H5   single    0.930  0.020  1.080
 1Q8  C8   H6   single    0.930  0.020  1.080
 1Q8  C10  H7   single    0.930  0.020  1.080
 1Q8  C7   H8   single    0.930  0.020  1.080
 1Q8  C3   H9   single    0.930  0.020  1.080

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
 1Q8  C1   C2   N5   115.97  3.000
 1Q8  N5   C2   O6   122.85  3.000
 1Q8  C1   C2   O6   121.18  3.000
 1Q8  H1   N5   C9   117.36  3.000
 1Q8  H1   N5   C2   119.01  3.000
 1Q8  C9   N5   C2   122.82  3.000
 1Q8  H3   C9   H2   108.02  3.000
 1Q8  H3   C9   O11  111.70  3.000
 1Q8  H2   C9   O11  111.61  3.000
 1Q8  H3   C9   N5   108.79  3.000
 1Q8  H2   C9   N5   107.11  3.000
 1Q8  O11  C9   N5   109.47  3.000
 1Q8  H4   O11  C9   107.89  3.000
 1Q8  C3   C1   C4   119.24  3.000
 1Q8  C4   C1   C2   118.14  3.000
 1Q8  C3   C1   C2   122.59  3.000
 1Q8  H5   C4   C8   119.80  3.000
 1Q8  H5   C4   C1   119.83  3.000
 1Q8  C8   C4   C1   120.37  3.000
 1Q8  H6   C8   C10  120.12  3.000
 1Q8  H6   C8   C4   119.77  3.000
 1Q8  C10  C8   C4   120.11  3.000
 1Q8  H7   C10  C7   120.09  3.000
 1Q8  H7   C10  C8   120.09  3.000
 1Q8  C7   C10  C8   119.82  3.000
 1Q8  H8   C7   C3   119.65  3.000
 1Q8  H8   C7   C10  120.23  3.000
 1Q8  C3   C7   C10  120.12  3.000
 1Q8  H9   C3   C7   118.67  3.000
 1Q8  H9   C3   C1   121.00  3.000
 1Q8  C7   C3   C1   120.31  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
 1Q8  CONST_01  C10  C7   C3   C1     0.00   0.0  0
 1Q8  CONST_02  C10  C8   C4   C1     0.00   0.0  0
 1Q8  CONST_03  C7   C10  C8   C4     0.00   0.0  0
 1Q8  CONST_04  C7   C3   C1   C4     0.00   0.0  0
 1Q8  CONST_05  C3   C7   C10  C8     0.00   0.0  0
 1Q8  CONST_06  C3   C1   C4   C8     0.00   0.0  0
 1Q8  CONST_07  C7   C3   C1   C2   180.00   0.0  0
 1Q8  CONST_08  C8   C4   C1   C2   180.00   0.0  0
 1Q8  CONST_09  H8   C7   C3   C1   180.00   0.0  0
 1Q8  CONST_10  H6   C8   C4   C1   180.00   0.0  0
 1Q8  CONST_11  H7   C10  C8   C4   180.00   0.0  0
 1Q8  CONST_12  H9   C3   C1   C4   180.00   0.0  0
 1Q8  CONST_13  H5   C4   C8   C10  180.00   0.0  0
 1Q8  CONST_14  C1   C2   N5   C9   180.00   0.0  0
 1Q8  CONST_15  H1   N5   C2   C1     0.00   0.0  0
 1Q8  CONST_16  C9   N5   C2   O6     0.00   0.0  0
 1Q8  Var_01    C3   C1   C2   O6   152.70  30.0  3
 1Q8  Var_02    O11  C9   N5   C2    83.28  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
 1Q8  plan-1  C2   0.020
 1Q8  plan-1  C1   0.020
 1Q8  plan-1  C4   0.020
 1Q8  plan-1  C8   0.020
 1Q8  plan-1  C10  0.020
 1Q8  plan-1  C7   0.020
 1Q8  plan-1  C3   0.020
 1Q8  plan-1  H5   0.020
 1Q8  plan-1  H6   0.020
 1Q8  plan-1  H7   0.020
 1Q8  plan-1  H8   0.020
 1Q8  plan-1  H9   0.020
 1Q8  plan-2  O6   0.020
 1Q8  plan-2  C2   0.020
 1Q8  plan-2  N5   0.020
 1Q8  plan-2  C9   0.020
 1Q8  plan-2  C1   0.020
 1Q8  plan-2  H1   0.020

