# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 09:55:08 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: (2,5-dimethylphenyl) pyridine-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C)c(OC(=O)c2ccncc2)c1
#
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
 QL5  QL5  '(2,5-dimethylphenyl) pyridine-4-carboxylate'  ligand  30  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QL5
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
 QL5  N1   N  N     0  -0.391  5.6659  14.1739  -44.6552
 QL5  C4   C  CR16  0  -0.296  5.2820  11.0104  -52.4620
 QL5  C5   C  CR6   0   0.026  5.5238  11.6633  -51.2564
 QL5  C6   C  CH3   0  -0.730  6.8242  12.3554  -50.9761
 QL5  C7   C  CR6   0   0.344  4.4887  11.6459  -50.3296
 QL5  C8   C  C     0   0.594  5.1836  11.6992  -48.0975
 QL5  C10  C  CR16  0  -0.326  5.7823  12.0386  -45.7198
 QL5  C13  C  CR16  0  -0.337  5.0593  13.9499  -46.9571
 QL5  C2   C  CR6   0   0.079  3.0559  10.3615  -51.7713
 QL5  C3   C  CR16  0  -0.283  4.0774  10.3715  -52.7171
 QL5  O1   O  O2    0  -0.501  4.6513  12.3414  -49.1392
 QL5  O2   O  O     0  -0.403  5.4982  10.5410  -48.1155
 QL5  C9   C  CR6   0   0.010  5.3365  12.5888  -46.9152
 QL5  C11  C  CR16  0  -0.053  5.9266  12.8720  -44.6219
 QL5  C12  C  CR16  0  -0.052  5.2435  14.6932  -45.8004
 QL5  C14  C  CR16  0  -0.347  3.2806  11.0160  -50.5636
 QL5  H1   H  HCR6  0   0.256  6.0561  11.0052  -53.2196
 QL5  H2   H  HCH3  0   0.251  6.6785  13.3945  -50.6787
 QL5  H3   H  HCH3  0   0.249  7.3788  11.8638  -50.1741
 QL5  H4   H  HCH3  0   0.255  7.4590  12.3483  -51.8601
 QL5  H5   H  HCR6  0   0.283  6.0119  10.9858  -45.6345
 QL5  H6   H  HCR6  0   0.284  4.7125  14.4399  -47.8551
 QL5  H7   H  HCH3  0   0.251  1.8329   8.5976  -51.7298
 QL5  H8   H  HCH3  0   0.246  0.9390  10.0878  -51.4709
 QL5  H9   H  HCH3  0   0.246  1.5028   9.6616  -53.0873
 QL5  H10  H  HCR6  0   0.251  3.9308   9.8785  -53.6707
 QL5  H11  H  HCR6  0   0.276  6.2696  12.4675  -43.6770
 QL5  H12  H  HCR6  0   0.276  5.0382  15.7573  -45.8058
 QL5  H13  H  HCR6  0   0.264  2.5086  11.0428  -49.8034
 QL5  C1   C  CH3   0  -0.722  1.7629   9.6452  -52.0294

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
 QL5  C3   C4   aromatic  1.387  0.020  1.387
 QL5  C3   C2   aromatic  1.392  0.020  1.392
 QL5  C4   C5   aromatic  1.392  0.020  1.392
 QL5  C1   C2   single    1.500  0.020  1.500
 QL5  C2   C14  aromatic  1.392  0.020  1.392
 QL5  C5   C6   single    1.500  0.020  1.500
 QL5  C5   C7   aromatic  1.390  0.020  1.390
 QL5  C14  C7   aromatic  1.382  0.020  1.382
 QL5  C7   O1   single    1.388  0.020  1.388
 QL5  O1   C8   single    1.335  0.020  1.335
 QL5  O2   C8   double    1.200  0.020  1.200
 QL5  C8   C9   single    1.487  0.020  1.487
 QL5  C9   C13  aromatic  1.390  0.020  1.390
 QL5  C9   C10  aromatic  1.389  0.020  1.389
 QL5  C13  C12  aromatic  1.387  0.020  1.387
 QL5  C10  C11  aromatic  1.386  0.020  1.386
 QL5  C12  N1   aromatic  1.326  0.020  1.326
 QL5  C11  N1   aromatic  1.328  0.020  1.328
 QL5  C4   H1   single    0.930  0.020  1.080
 QL5  C6   H2   single    0.970  0.020  1.090
 QL5  C6   H3   single    0.970  0.020  1.090
 QL5  C6   H4   single    0.970  0.020  1.090
 QL5  C10  H5   single    0.930  0.020  1.080
 QL5  C13  H6   single    0.930  0.020  1.080
 QL5  C1   H7   single    0.970  0.020  1.090
 QL5  C1   H8   single    0.970  0.020  1.090
 QL5  C1   H9   single    0.970  0.020  1.090
 QL5  C3   H10  single    0.930  0.020  1.080
 QL5  C11  H11  single    0.930  0.020  1.080
 QL5  C12  H12  single    0.930  0.020  1.080
 QL5  C14  H13  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
 QL5  C12  N1   C11  117.90  3.000
 QL5  H1   C4   C3   119.33  3.000
 QL5  H1   C4   C5   118.94  3.000
 QL5  C3   C4   C5   121.74  3.000
 QL5  C7   C5   C6   121.81  3.000
 QL5  C7   C5   C4   116.25  3.000
 QL5  C6   C5   C4   121.93  3.000
 QL5  H4   C6   H3   107.30  3.000
 QL5  H4   C6   H2   107.80  3.000
 QL5  H3   C6   H2   107.25  3.000
 QL5  H4   C6   C5   110.55  3.000
 QL5  H3   C6   C5   111.71  3.000
 QL5  H2   C6   C5   112.01  3.000
 QL5  C14  C7   O1   118.41  3.000
 QL5  O1   C7   C5   118.58  3.000
 QL5  C14  C7   C5   122.94  3.000
 QL5  C9   C8   O2   124.20  3.000
 QL5  C9   C8   O1   111.94  3.000
 QL5  O2   C8   O1   123.86  3.000
 QL5  H5   C10  C11  120.07  3.000
 QL5  H5   C10  C9   121.45  3.000
 QL5  C11  C10  C9   118.48  3.000
 QL5  H6   C13  C12  119.52  3.000
 QL5  H6   C13  C9   122.24  3.000
 QL5  C12  C13  C9   118.25  3.000
 QL5  C14  C2   C3   117.88  3.000
 QL5  C14  C2   C1   120.85  3.000
 QL5  C3   C2   C1   121.26  3.000
 QL5  H10  C3   C2   119.69  3.000
 QL5  H10  C3   C4   119.27  3.000
 QL5  C2   C3   C4   121.04  3.000
 QL5  C8   O1   C7   118.35  3.000
 QL5  C13  C9   C10  118.54  3.000
 QL5  C10  C9   C8   118.68  3.000
 QL5  C13  C9   C8   122.78  3.000
 QL5  H11  C11  C10  119.95  3.000
 QL5  H11  C11  N1   116.74  3.000
 QL5  C10  C11  N1   123.30  3.000
 QL5  H12  C12  C13  119.79  3.000
 QL5  H12  C12  N1   116.68  3.000
 QL5  C13  C12  N1   123.53  3.000
 QL5  H13  C14  C2   120.35  3.000
 QL5  H13  C14  C7   119.50  3.000
 QL5  C2   C14  C7   120.15  3.000
 QL5  H9   C1   H8   108.13  3.000
 QL5  H9   C1   H7   107.23  3.000
 QL5  H8   C1   H7   107.31  3.000
 QL5  H9   C1   C2   111.44  3.000
 QL5  H8   C1   C2   111.69  3.000
 QL5  H7   C1   C2   110.83  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
 QL5  CONST_01  C9   C13  C12  N1     0.00   0.0  0
 QL5  CONST_02  C9   C10  C11  N1     0.00   0.0  0
 QL5  CONST_03  C14  C2   C3   C4     0.00   0.0  0
 QL5  CONST_04  C14  C7   C5   C4     0.00   0.0  0
 QL5  CONST_05  C2   C3   C4   C5     0.00   0.0  0
 QL5  CONST_06  C2   C14  C7   C5     0.00   0.0  0
 QL5  CONST_07  C3   C4   C5   C7     0.00   0.0  0
 QL5  CONST_08  C3   C2   C14  C7     0.00   0.0  0
 QL5  CONST_09  C12  C13  C9   C10    0.00   0.0  0
 QL5  CONST_10  C12  N1   C11  C10    0.00   0.0  0
 QL5  CONST_11  C11  C10  C9   C13    0.00   0.0  0
 QL5  CONST_12  C11  N1   C12  C13    0.00   0.0  0
 QL5  CONST_13  C1   C2   C3   C4   180.00   0.0  0
 QL5  CONST_14  O1   C7   C5   C4   180.00   0.0  0
 QL5  CONST_15  C3   C4   C5   C6   180.00   0.0  0
 QL5  CONST_16  C14  C7   C5   C6   180.00   0.0  0
 QL5  CONST_17  C1   C2   C14  C7   180.00   0.0  0
 QL5  CONST_18  C12  C13  C9   C8   180.00   0.0  0
 QL5  CONST_19  C11  C10  C9   C8   180.00   0.0  0
 QL5  CONST_20  O1   C7   C14  C2   180.00   0.0  0
 QL5  CONST_21  H6   C13  C12  N1   180.00   0.0  0
 QL5  CONST_22  H5   C10  C11  N1   180.00   0.0  0
 QL5  CONST_23  H10  C3   C4   C5   180.00   0.0  0
 QL5  CONST_24  H13  C14  C7   C5   180.00   0.0  0
 QL5  CONST_25  H1   C4   C5   C7   180.00   0.0  0
 QL5  CONST_26  H12  C12  C13  C9   180.00   0.0  0
 QL5  CONST_27  H11  C11  C10  C9   180.00   0.0  0
 QL5  Var_01    C9   C8   O1   C7   177.97  30.0  3
 QL5  Var_02    C14  C7   O1   C8    92.63  30.0  2
 QL5  Var_03    O1   C8   C9   C10  175.13  30.0  2
 QL5  Var_04    H2   C6   C5   C4   125.91  30.0  2
 QL5  Var_05    H7   C1   C2   C3    87.26  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
 QL5  plan-1  C4   0.020
 QL5  plan-1  C5   0.020
 QL5  plan-1  C6   0.020
 QL5  plan-1  C7   0.020
 QL5  plan-1  C2   0.020
 QL5  plan-1  C3   0.020
 QL5  plan-1  O1   0.020
 QL5  plan-1  C14  0.020
 QL5  plan-1  H1   0.020
 QL5  plan-1  H10  0.020
 QL5  plan-1  H13  0.020
 QL5  plan-1  C1   0.020
 QL5  plan-2  N1   0.020
 QL5  plan-2  C8   0.020
 QL5  plan-2  C10  0.020
 QL5  plan-2  C13  0.020
 QL5  plan-2  C9   0.020
 QL5  plan-2  C11  0.020
 QL5  plan-2  C12  0.020
 QL5  plan-2  H5   0.020
 QL5  plan-2  H6   0.020
 QL5  plan-2  H11  0.020
 QL5  plan-2  H12  0.020
 QL5  plan-3  C8   0.020
 QL5  plan-3  O1   0.020
 QL5  plan-3  O2   0.020
 QL5  plan-3  C9   0.020

