# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 16:34:09 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-(8-azanyl-2-methanoyl-quinolin-4-yl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc2c(CC(O)=O)cc(C=O)nc12
#
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
 QDD  QDD  '2-(8-azanyl-2-methanoyl-quinolin-4-yl)ethanoic acid'  ligand  27  17  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QDD
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
 QDD  OD1  O  O     0  -0.426  -2.7920   0.3505   1.5062
 QDD  CG   C  C     0   0.557  -3.2029   0.3303   0.3752
 QDD  OD2  O  OH1   0  -0.588  -4.4653   0.0863   0.0514
 QDD  CB   C  CH2   0  -0.726  -2.3628   0.6081  -0.8489
 QDD  C8   C  CR6   0   0.254  -0.8969   0.5788  -0.5495
 QDD  C9   C  CR16  0  -0.391  -0.1751   1.7392  -0.4754
 QDD  C10  C  CR6   0   0.125   1.2009   1.6900  -0.1880
 QDD  C    C  C1    0   0.125   1.9594   2.9595  -0.1014
 QDD  O    O  O     0  -0.367   3.1389   3.0274   0.1380
 QDD  N11  N  N     0  -0.433   1.8497   0.5688   0.0088
 QDD  C7   C  CR66  0   0.136   1.1765  -0.5849  -0.0668
 QDD  C6   C  CR66  0   0.098  -0.2195  -0.6516  -0.3423
 QDD  C5   C  CR16  0  -0.388  -0.8542  -1.9078  -0.3938
 QDD  C4   C  CR16  0  -0.233  -0.1135  -3.0430  -0.1723
 QDD  C3   C  CR16  0  -0.361   1.2588  -2.9991   0.1019
 QDD  C2   C  CR6   0   0.301   1.9306  -1.7902   0.1518
 QDD  N    N  NH2   0  -0.842   3.2656  -1.6954   0.3594
 QDD  H1   H  HOH1  0   0.484  -4.9933  -0.0578   0.8514
 QDD  H2   H  HCH2  0   0.308  -2.6249  -0.0934  -1.6442
 QDD  H3   H  HCH2  0   0.330  -2.6481   1.5970  -1.2195
 QDD  H4   H  HCR6  0   0.278  -0.6545   2.6977  -0.6362
 QDD  H5   H  H     0   0.200   1.3545   3.8662  -0.2757
 QDD  H6   H  HCR6  0   0.249  -1.9105  -1.9918  -0.6083
 QDD  H7   H  HCR6  0   0.264  -0.6003  -4.0093  -0.2097
 QDD  H8   H  HCR6  0   0.263   1.8006  -3.9210   0.2719
 QDD  H9   H  HNH2  0   0.392   3.7508  -2.4855   0.7485
 QDD  H10  H  HNH2  0   0.392   3.6377  -0.7905   0.5951

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
 QDD  OD1  CG   double    1.204  0.020  1.204
 QDD  C3   C4   aromatic  1.400  0.020  1.400
 QDD  C3   C2   aromatic  1.384  0.020  1.384
 QDD  N    C2   single    1.354  0.020  1.354
 QDD  OD2  CG   single    1.326  0.020  1.326
 QDD  C4   C5   aromatic  1.374  0.020  1.374
 QDD  C2   C7   aromatic  1.439  0.020  1.439
 QDD  CG   CB   single    1.510  0.020  1.510
 QDD  C5   C6   aromatic  1.408  0.020  1.408
 QDD  C7   C6   aromatic  1.424  0.020  1.424
 QDD  C7   N11  aromatic  1.338  0.020  1.338
 QDD  C6   C8   aromatic  1.420  0.020  1.420
 QDD  N11  C10  aromatic  1.310  0.020  1.310
 QDD  C10  C9   aromatic  1.407  0.020  1.407
 QDD  C10  C    single    1.481  0.020  1.481
 QDD  C8   C9   aromatic  1.369  0.020  1.369
 QDD  C8   CB   single    1.496  0.020  1.496
 QDD  C    O    double    1.205  0.020  1.205
 QDD  OD2  H1   single    0.850  0.020  0.980
 QDD  CB   H2   single    0.970  0.020  1.090
 QDD  CB   H3   single    0.970  0.020  1.090
 QDD  C9   H4   single    0.930  0.020  1.080
 QDD  C    H5   single    0.930  0.020  1.080
 QDD  C5   H6   single    0.930  0.020  1.080
 QDD  C4   H7   single    0.930  0.020  1.080
 QDD  C3   H8   single    0.930  0.020  1.080
 QDD  N    H9   single    0.890  0.020  1.040
 QDD  N    H10  single    0.890  0.020  1.040

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
 QDD  CB   CG   OD2  111.45  3.000
 QDD  CB   CG   OD1  124.65  3.000
 QDD  OD2  CG   OD1  123.89  3.000
 QDD  H1   OD2  CG   110.15  3.000
 QDD  H3   CB   H2   105.74  3.000
 QDD  H3   CB   C8   109.93  3.000
 QDD  H2   CB   C8   111.60  3.000
 QDD  H3   CB   CG   107.20  3.000
 QDD  H2   CB   CG   109.79  3.000
 QDD  C8   CB   CG   112.28  3.000
 QDD  C6   C8   C9   118.38  3.000
 QDD  C9   C8   CB   120.72  3.000
 QDD  C6   C8   CB   120.90  3.000
 QDD  H4   C9   C10  119.60  3.000
 QDD  H4   C9   C8   120.57  3.000
 QDD  C10  C9   C8   119.83  3.000
 QDD  N11  C10  C    118.10  3.000
 QDD  C    C10  C9   118.88  3.000
 QDD  N11  C10  C9   123.03  3.000
 QDD  H5   C    O    121.42  3.000
 QDD  H5   C    C10  114.46  3.000
 QDD  O    C    C10  124.12  3.000
 QDD  C7   N11  C10  118.70  3.000
 QDD  C2   C7   C6   120.26  3.000
 QDD  C6   C7   N11  122.99  3.000
 QDD  C2   C7   N11  116.75  3.000
 QDD  C5   C6   C7   119.38  3.000
 QDD  C7   C6   C8   117.08  3.000
 QDD  C5   C6   C8   123.55  3.000
 QDD  H6   C5   C4   119.65  3.000
 QDD  H6   C5   C6   121.12  3.000
 QDD  C4   C5   C6   119.23  3.000
 QDD  H7   C4   C3   118.39  3.000
 QDD  H7   C4   C5   119.32  3.000
 QDD  C3   C4   C5   122.29  3.000
 QDD  H8   C3   C2   119.68  3.000
 QDD  H8   C3   C4   119.63  3.000
 QDD  C2   C3   C4   120.68  3.000
 QDD  N    C2   C3   123.04  3.000
 QDD  N    C2   C7   118.77  3.000
 QDD  C3   C2   C7   118.16  3.000
 QDD  H10  N    H9   115.95  3.000
 QDD  H10  N    C2   117.60  3.000
 QDD  H9   N    C2   118.68  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
 QDD  CONST_01  C4   C5   C6   C8    180.00   0.0  0
 QDD  CONST_02  C2   C7   C6   C8    180.00   0.0  0
 QDD  CONST_03  N11  C7   C6   C8      0.00   0.0  0
 QDD  CONST_04  N11  C10  C9   C8      0.00   0.0  0
 QDD  CONST_05  C7   N11  C10  C9      0.00   0.0  0
 QDD  CONST_06  C5   C6   C8   C9    180.00   0.0  0
 QDD  CONST_07  C7   C6   C8   C9      0.00   0.0  0
 QDD  CONST_08  C2   C7   N11  C10   180.00   0.0  0
 QDD  CONST_09  C6   C7   N11  C10     0.00   0.0  0
 QDD  CONST_10  C6   C8   C9   C10     0.00   0.0  0
 QDD  CONST_11  C3   C2   C7   N11   180.00   0.0  0
 QDD  CONST_12  C5   C6   C7   N11   180.00   0.0  0
 QDD  CONST_13  C4   C3   C2   C7      0.00   0.0  0
 QDD  CONST_14  C4   C5   C6   C7      0.00   0.0  0
 QDD  CONST_15  C3   C4   C5   C6      0.00   0.0  0
 QDD  CONST_16  C3   C2   C7   C6      0.00   0.0  0
 QDD  CONST_17  C2   C3   C4   C5      0.00   0.0  0
 QDD  CONST_18  C2   C7   C6   C5      0.00   0.0  0
 QDD  CONST_19  C5   C6   C8   CB      0.00   0.0  0
 QDD  CONST_20  C7   C6   C8   CB    180.00   0.0  0
 QDD  CONST_21  C10  C9   C8   CB    180.00   0.0  0
 QDD  CONST_22  C    C10  C9   C8    180.00   0.0  0
 QDD  CONST_23  C7   N11  C10  C     180.00   0.0  0
 QDD  CONST_24  N    C2   C7   N11     0.00   0.0  0
 QDD  CONST_25  N    C2   C7   C6    180.00   0.0  0
 QDD  CONST_26  N    C2   C3   C4    180.00   0.0  0
 QDD  CONST_27  H6   C5   C6   C8      0.00   0.0  0
 QDD  CONST_28  H4   C9   C10  N11   180.00   0.0  0
 QDD  CONST_29  H8   C3   C2   C7    180.00   0.0  0
 QDD  CONST_30  H7   C4   C5   C6    180.00   0.0  0
 QDD  CONST_33  H1   OD2  CG   OD1     0.00   0.0  0
 QDD  Var_01    C6   C8   CB   CG     74.89  30.0  2
 QDD  Var_02    O    C    C10  C9   -179.95  30.0  2
 QDD  Var_03    C8   CB   CG   OD1    14.27  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
 QDD  plan-1  CB   0.020
 QDD  plan-1  C8   0.020
 QDD  plan-1  C9   0.020
 QDD  plan-1  C10  0.020
 QDD  plan-1  C    0.020
 QDD  plan-1  N11  0.020
 QDD  plan-1  C7   0.020
 QDD  plan-1  C6   0.020
 QDD  plan-1  C5   0.020
 QDD  plan-1  C4   0.020
 QDD  plan-1  C3   0.020
 QDD  plan-1  C2   0.020
 QDD  plan-1  N    0.020
 QDD  plan-1  H4   0.020
 QDD  plan-1  H6   0.020
 QDD  plan-1  H7   0.020
 QDD  plan-1  H8   0.020
 QDD  plan-2  C2   0.020
 QDD  plan-2  N    0.020
 QDD  plan-2  H9   0.020
 QDD  plan-2  H10  0.020
 QDD  plan-3  OD1  0.020
 QDD  plan-3  CG   0.020
 QDD  plan-3  OD2  0.020
 QDD  plan-3  CB   0.020
 QDD  plan-3  H1   0.020
 QDD  plan-4  C10  0.020
 QDD  plan-4  C    0.020
 QDD  plan-4  O    0.020
 QDD  plan-4  H5   0.020

