# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:35:43 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 3-[(1-methyl-6-oxidanylidene-pyridin-3-yl)carbonylamino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=CC1=O)C(=O)Nc2cccc(c2)C(O)=O
#
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
 5QR  5QR  '3-[(1-methyl-6-oxidanylidene-pyridin-3-yl)carbonylamino]benzoic acid'  ligand  31  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5QR
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
 5QR  C10  C  CR16   0  -0.234   3.5629  -2.2632   0.5723
 5QR  C13  C  C      0   0.403   4.7528   1.1938  -0.5014
 5QR  C17  C  CR16   0  -0.142  -2.5900  -1.2122  -0.6486
 5QR  C19  C  CR6    0   0.569  -4.8405  -0.3388  -0.2813
 5QR  N02  N  NR6    0  -0.506  -4.2230   0.7900   0.2648
 5QR  C01  C  CH3    0  -0.520  -5.0946   1.8518   0.7509
 5QR  C18  C  CR16   0  -0.447  -3.9344  -1.3514  -0.7496
 5QR  C04  C  CR6    0  -0.214  -2.0224  -0.0457  -0.0739
 5QR  C03  C  CR16   0   0.085  -2.8891   0.9207   0.3526
 5QR  C05  C  C      0   0.536  -0.5708   0.2214   0.0792
 5QR  O06  O  O      0  -0.469  -0.1529   1.3453   0.3079
 5QR  N07  N  NH1    0  -0.772   0.2307  -0.8667  -0.0415
 5QR  C08  C  CR6    0   0.395   1.6293  -0.9194   0.0673
 5QR  C16  C  CR16   0  -0.349   2.4672   0.1462  -0.2533
 5QR  C12  C  CR6    0  -0.093   3.8491   0.0145  -0.1505
 5QR  O15  O  OC    -1  -0.593   5.9783   1.0090  -0.3781
 5QR  O14  O  O      0  -0.591   4.1894   2.2384  -0.8802
 5QR  C11  C  CR16   0  -0.311   4.3946  -1.1960   0.2656
 5QR  C09  C  CR16   0  -0.353   2.1876  -2.1298   0.4791
 5QR  H1   H  HCR6   0   0.253   3.9832  -3.2074   0.8939
 5QR  H2   H  HCR6   0   0.275  -1.9630  -2.0039  -1.0402
 5QR  H3   H  HCH3   0   0.266  -5.7019   2.2452  -0.0611
 5QR  H4   H  HCH3   0   0.266  -5.7504   1.4759   1.5326
 5QR  H5   H  HCH3   0   0.262  -4.4843   2.6527   1.1559
 5QR  H6   H  HCR6   0   0.281  -4.3701  -2.2340  -1.1962
 5QR  H7   H  HCR6   0   0.314  -2.5301   1.8407   0.7914
 5QR  H8   H  HNH1   0   0.419  -0.2176  -1.7692  -0.0544
 5QR  H9   H  HCR6   0   0.259   2.0636   1.0850  -0.5960
 5QR  H11  H  HCR6   0   0.243   5.4677  -1.3025   0.3452
 5QR  H12  H  HCR6   0   0.266   1.5439  -2.9657   0.7284
 5QR  O20  O  O      0  -0.497  -6.0619  -0.4008  -0.3336

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
 5QR  O14  C13  deloc     1.246  0.020  1.246
 5QR  C13  O15  deloc     1.245  0.020  1.245
 5QR  C13  C12  single    1.527  0.020  1.527
 5QR  C12  C11  aromatic  1.391  0.020  1.391
 5QR  C12  C16  aromatic  1.392  0.020  1.392
 5QR  C11  C10  aromatic  1.387  0.020  1.387
 5QR  C10  C09  aromatic  1.385  0.020  1.385
 5QR  C16  C08  aromatic  1.393  0.020  1.393
 5QR  C08  C09  aromatic  1.395  0.020  1.395
 5QR  C08  N07  single    1.404  0.020  1.404
 5QR  N07  C05  single    1.357  0.020  1.357
 5QR  C01  N02  single    1.457  0.020  1.457
 5QR  C03  N02  single    1.343  0.020  1.343
 5QR  C03  C04  double    1.366  0.020  1.366
 5QR  C05  O06  double    1.221  0.020  1.221
 5QR  C05  C04  single    1.484  0.020  1.484
 5QR  N02  C19  single    1.398  0.020  1.398
 5QR  C04  C17  single    1.419  0.020  1.419
 5QR  C19  O20  double    1.224  0.020  1.224
 5QR  C19  C18  single    1.437  0.020  1.437
 5QR  C17  C18  double    1.355  0.020  1.355
 5QR  C10  H1   single    0.930  0.020  1.080
 5QR  C17  H2   single    0.930  0.020  1.080
 5QR  C01  H3   single    0.970  0.020  1.090
 5QR  C01  H4   single    0.970  0.020  1.090
 5QR  C01  H5   single    0.970  0.020  1.090
 5QR  C18  H6   single    0.930  0.020  1.080
 5QR  C03  H7   single    0.930  0.020  1.080
 5QR  N07  H8   single    0.860  0.020  1.020
 5QR  C16  H9   single    0.930  0.020  1.080
 5QR  C11  H11  single    0.930  0.020  1.080
 5QR  C09  H12  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
 5QR  H1   C10  C09  119.32  3.000
 5QR  H1   C10  C11  120.26  3.000
 5QR  C09  C10  C11  120.43  3.000
 5QR  O14  C13  O15  126.83  3.000
 5QR  O15  C13  C12  116.43  3.000
 5QR  O14  C13  C12  116.74  3.000
 5QR  H2   C17  C04  121.05  3.000
 5QR  H2   C17  C18  118.18  3.000
 5QR  C04  C17  C18  120.76  3.000
 5QR  C18  C19  N02  114.69  3.000
 5QR  C18  C19  O20  125.41  3.000
 5QR  N02  C19  O20  119.89  3.000
 5QR  C03  N02  C01  120.08  3.000
 5QR  C03  N02  C19  122.88  3.000
 5QR  C01  N02  C19  117.04  3.000
 5QR  H5   C01  H4   109.03  3.000
 5QR  H5   C01  H3   109.01  3.000
 5QR  H4   C01  H3   108.96  3.000
 5QR  H5   C01  N02  109.02  3.000
 5QR  H4   C01  N02  110.40  3.000
 5QR  H3   C01  N02  110.40  3.000
 5QR  H6   C18  C19  117.12  3.000
 5QR  H6   C18  C17  120.96  3.000
 5QR  C19  C18  C17  121.92  3.000
 5QR  C05  C04  C03  117.45  3.000
 5QR  C05  C04  C17  125.53  3.000
 5QR  C03  C04  C17  117.01  3.000
 5QR  H7   C03  C04  121.20  3.000
 5QR  H7   C03  N02  116.06  3.000
 5QR  C04  C03  N02  122.73  3.000
 5QR  N07  C05  O06  123.56  3.000
 5QR  O06  C05  C04  121.33  3.000
 5QR  N07  C05  C04  115.11  3.000
 5QR  H8   N07  C08  114.24  3.000
 5QR  H8   N07  C05  117.16  3.000
 5QR  C08  N07  C05  127.71  3.000
 5QR  C09  C08  C16  119.40  3.000
 5QR  C09  C08  N07  117.01  3.000
 5QR  C16  C08  N07  123.56  3.000
 5QR  H9   C16  C12  118.53  3.000
 5QR  H9   C16  C08  120.95  3.000
 5QR  C12  C16  C08  120.52  3.000
 5QR  C11  C12  C16  119.58  3.000
 5QR  C16  C12  C13  119.84  3.000
 5QR  C11  C12  C13  120.58  3.000
 5QR  H11  C11  C12  119.78  3.000
 5QR  H11  C11  C10  120.20  3.000
 5QR  C12  C11  C10  120.02  3.000
 5QR  H12  C09  C08  119.95  3.000
 5QR  H12  C09  C10  120.00  3.000
 5QR  C08  C09  C10  120.05  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
 5QR  CONST_01  C16  C12  C11  C10    0.00   0.0  0
 5QR  CONST_02  C16  C08  C09  C10    0.00   0.0  0
 5QR  CONST_03  C11  C12  C16  C08    0.00   0.0  0
 5QR  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 5QR  CONST_05  C09  C10  C11  C12    0.00   0.0  0
 5QR  CONST_06  C09  C08  C16  C12    0.00   0.0  0
 5QR  CONST_07  C03  N02  C19  C18    0.00   0.0  0
 5QR  CONST_08  C13  C12  C11  C10  180.00   0.0  0
 5QR  CONST_09  N07  C08  C09  C10  180.00   0.0  0
 5QR  CONST_10  C08  C16  C12  C13  180.00   0.0  0
 5QR  CONST_11  C12  C16  C08  N07  180.00   0.0  0
 5QR  CONST_12  C03  N02  C19  O20  180.00   0.0  0
 5QR  CONST_13  C18  C19  N02  C01  180.00   0.0  0
 5QR  CONST_14  H1   C10  C09  C08  180.00   0.0  0
 5QR  CONST_15  H11  C11  C12  C16  180.00   0.0  0
 5QR  CONST_16  H12  C09  C08  C16  180.00   0.0  0
 5QR  CONST_17  H9   C16  C12  C11  180.00   0.0  0
 5QR  CONST_18  C08  N07  C05  C04  180.00   0.0  0
 5QR  CONST_21  C01  N02  C19  O20    0.00   0.0  0
 5QR  CONST_23  C08  N07  C05  O06    0.00   0.0  0
 5QR  Var_01    N07  C05  C04  C17  -16.76  30.0  2
 5QR  Var_02    O14  C13  C12  C16   -0.46  30.0  2
 5QR  Var_03    H3   C01  N02  C19  -61.00  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
 5QR  plan-1  C17  0.020
 5QR  plan-1  C19  0.020
 5QR  plan-1  N02  0.020
 5QR  plan-1  C01  0.020
 5QR  plan-1  C18  0.020
 5QR  plan-1  C04  0.020
 5QR  plan-1  C03  0.020
 5QR  plan-1  C05  0.020
 5QR  plan-1  H2   0.020
 5QR  plan-1  H6   0.020
 5QR  plan-1  H7   0.020
 5QR  plan-1  O20  0.020
 5QR  plan-2  C10  0.020
 5QR  plan-2  C13  0.020
 5QR  plan-2  N07  0.020
 5QR  plan-2  C08  0.020
 5QR  plan-2  C16  0.020
 5QR  plan-2  C12  0.020
 5QR  plan-2  C11  0.020
 5QR  plan-2  C09  0.020
 5QR  plan-2  H1   0.020
 5QR  plan-2  H9   0.020
 5QR  plan-2  H11  0.020
 5QR  plan-2  H12  0.020
 5QR  plan-3  C04  0.020
 5QR  plan-3  C05  0.020
 5QR  plan-3  O06  0.020
 5QR  plan-3  N07  0.020
 5QR  plan-3  C08  0.020
 5QR  plan-3  H8   0.020
 5QR  plan-4  C13  0.020
 5QR  plan-4  C12  0.020
 5QR  plan-4  O15  0.020
 5QR  plan-4  O14  0.020

