# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:04:14 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: (4-chlorophenyl)methyl pyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(COC(=O)c2cccnc2)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
 QKW  QKW  '(4-chlorophenyl)methyl pyridine-3-carboxylate'  ligand  27  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 PERFECT
;

data_comp_QKW
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
 QKW  N1   N   N     0  -0.401  -10.2457   9.6750  -96.4691
 QKW  C4   C   CR6   0   0.073   -4.9764   7.6455  -94.0006
 QKW  C5   C   CH2   0  -0.261   -5.0212   8.7097  -95.0586
 QKW  C6   C   C     0   0.617   -6.8858   8.0056  -96.3269
 QKW  C7   C   CR6   0  -0.186   -8.2934   8.3090  -96.6826
 QKW  C8   C   CR16  0  -0.139   -8.9638   7.4671  -97.5647
 QKW  C10  C   CR16  0  -0.048  -10.8728   8.8647  -97.3142
 QKW  C13  C   CR16  0  -0.197   -4.1328   5.5364  -93.1758
 QKW  C1   C   CR6   0  -0.050   -4.8838   5.7016  -92.0238
 QKW  C2   C   CR16  0  -0.199   -5.6815   6.8218  -91.8405
 QKW  C3   C   CR16  0  -0.282   -5.7189   7.7896  -92.8313
 QKW  O1   O   O2    0  -0.461   -6.3565   8.9248  -95.5333
 QKW  O2   O   O     0  -0.430   -6.2931   7.0336  -96.7226
 QKW  C9   C   CR16  0  -0.316  -10.2775   7.7505  -97.8885
 QKW  C11  C   CR16  0  -0.050   -8.9854   9.4016  -96.1629
 QKW  C12  C   CR16  0  -0.293   -4.1920   6.5106  -94.1625
 QKW  H1   H   HCH2  0   0.265   -4.3514   8.4717  -95.8861
 QKW  H2   H   HCH2  0   0.275   -4.7234   9.6745  -94.6507
 QKW  H3   H   HCR6  0   0.281   -8.4646   6.6066  -97.9895
 QKW  H4   H   HCR6  0   0.277  -11.9020   9.1123  -97.5474
 QKW  H5   H   HCR6  0   0.281   -3.5161   4.6583  -93.3104
 QKW  H6   H   HCR6  0   0.281   -6.2613   6.9421  -90.9354
 QKW  H7   H   HCR6  0   0.268   -6.3357   8.6674  -92.6813
 QKW  H8   H   HCR6  0   0.282  -10.8346   7.1247  -98.5710
 QKW  H9   H   HCR6  0   0.276   -8.5061  10.0831  -95.4707
 QKW  H10  H   HCR6  0   0.265   -3.6141   6.3777  -95.0684
 QKW  CL1  CL  CL    0  -0.127   -4.8257   4.4879  -90.7872

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
 QKW  C9   C8   aromatic  1.382  0.020  1.382
 QKW  C9   C10  aromatic  1.388  0.020  1.388
 QKW  C8   C7   aromatic  1.391  0.020  1.391
 QKW  C10  N1   aromatic  1.328  0.020  1.328
 QKW  O2   C6   double    1.205  0.020  1.205
 QKW  C7   C6   single    1.483  0.020  1.483
 QKW  C7   C11  aromatic  1.394  0.020  1.394
 QKW  C6   O1   single    1.325  0.020  1.325
 QKW  N1   C11  aromatic  1.325  0.020  1.325
 QKW  O1   C5   single    1.433  0.020  1.433
 QKW  C5   C4   single    1.501  0.020  1.501
 QKW  C12  C4   aromatic  1.389  0.020  1.389
 QKW  C12  C13  aromatic  1.388  0.020  1.388
 QKW  C4   C3   aromatic  1.393  0.020  1.393
 QKW  C13  C1   aromatic  1.385  0.020  1.385
 QKW  C3   C2   aromatic  1.386  0.020  1.386
 QKW  C1   C2   aromatic  1.387  0.020  1.387
 QKW  C1   CL1  single    1.734  0.020  1.734
 QKW  C5   H1   single    0.970  0.020  1.090
 QKW  C5   H2   single    0.970  0.020  1.090
 QKW  C8   H3   single    0.930  0.020  1.080
 QKW  C10  H4   single    0.930  0.020  1.080
 QKW  C13  H5   single    0.930  0.020  1.080
 QKW  C2   H6   single    0.930  0.020  1.080
 QKW  C3   H7   single    0.930  0.020  1.080
 QKW  C9   H8   single    0.930  0.020  1.080
 QKW  C11  H9   single    0.930  0.020  1.080
 QKW  C12  H10  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
 QKW  C11  N1   C10  118.04  3.000
 QKW  C12  C4   C3   118.92  3.000
 QKW  C3   C4   C5   120.17  3.000
 QKW  C12  C4   C5   120.91  3.000
 QKW  H2   C5   H1   108.03  3.000
 QKW  H2   C5   O1   104.23  3.000
 QKW  H1   C5   O1   110.70  3.000
 QKW  H2   C5   C4   110.85  3.000
 QKW  H1   C5   C4   111.21  3.000
 QKW  O1   C5   C4   111.56  3.000
 QKW  O2   C6   O1   124.04  3.000
 QKW  O1   C6   C7   112.39  3.000
 QKW  O2   C6   C7   123.57  3.000
 QKW  C11  C7   C8   118.13  3.000
 QKW  C11  C7   C6   122.83  3.000
 QKW  C8   C7   C6   119.04  3.000
 QKW  H3   C8   C9   120.64  3.000
 QKW  H3   C8   C7   120.53  3.000
 QKW  C9   C8   C7   118.83  3.000
 QKW  H4   C10  C9   120.11  3.000
 QKW  H4   C10  N1   116.48  3.000
 QKW  C9   C10  N1   123.41  3.000
 QKW  H5   C13  C12  120.38  3.000
 QKW  H5   C13  C1   120.64  3.000
 QKW  C12  C13  C1   118.98  3.000
 QKW  C2   C1   CL1  119.36  3.000
 QKW  CL1  C1   C13  119.44  3.000
 QKW  C2   C1   C13  121.20  3.000
 QKW  H6   C2   C3   120.41  3.000
 QKW  H6   C2   C1   120.58  3.000
 QKW  C3   C2   C1   119.01  3.000
 QKW  H7   C3   C2   118.84  3.000
 QKW  H7   C3   C4   120.24  3.000
 QKW  C2   C3   C4   120.91  3.000
 QKW  C6   O1   C5   117.80  3.000
 QKW  H8   C9   C10  120.35  3.000
 QKW  H8   C9   C8   121.27  3.000
 QKW  C10  C9   C8   118.38  3.000
 QKW  H9   C11  C7   120.78  3.000
 QKW  H9   C11  N1   116.01  3.000
 QKW  C7   C11  N1   123.21  3.000
 QKW  H10  C12  C13  119.07  3.000
 QKW  H10  C12  C4   119.95  3.000
 QKW  C13  C12  C4   120.98  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
 QKW  CONST_01  C8   C9   C10  N1     0.00   0.0  0
 QKW  CONST_02  C8   C7   C11  N1     0.00   0.0  0
 QKW  CONST_03  C1   C13  C12  C4     0.00   0.0  0
 QKW  CONST_04  C1   C2   C3   C4     0.00   0.0  0
 QKW  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 QKW  CONST_06  C10  N1   C11  C7     0.00   0.0  0
 QKW  CONST_07  C3   C4   C12  C13    0.00   0.0  0
 QKW  CONST_08  C3   C2   C1   C13    0.00   0.0  0
 QKW  CONST_09  C12  C4   C3   C2     0.00   0.0  0
 QKW  CONST_10  C12  C13  C1   C2     0.00   0.0  0
 QKW  CONST_11  C11  C7   C8   C9     0.00   0.0  0
 QKW  CONST_12  C11  N1   C10  C9     0.00   0.0  0
 QKW  CONST_13  C6   C7   C11  N1   180.00   0.0  0
 QKW  CONST_14  C13  C12  C4   C5   180.00   0.0  0
 QKW  CONST_15  C2   C3   C4   C5   180.00   0.0  0
 QKW  CONST_16  C9   C8   C7   C6   180.00   0.0  0
 QKW  CONST_17  C12  C13  C1   CL1  180.00   0.0  0
 QKW  CONST_18  C3   C2   C1   CL1  180.00   0.0  0
 QKW  CONST_19  H8   C9   C10  N1   180.00   0.0  0
 QKW  CONST_20  H5   C13  C12  C4   180.00   0.0  0
 QKW  CONST_21  H6   C2   C3   C4   180.00   0.0  0
 QKW  CONST_22  H4   C10  C9   C8   180.00   0.0  0
 QKW  CONST_23  H9   C11  C7   C8   180.00   0.0  0
 QKW  CONST_24  H3   C8   C9   C10  180.00   0.0  0
 QKW  CONST_25  H10  C12  C13  C1   180.00   0.0  0
 QKW  CONST_26  H7   C3   C2   C1   180.00   0.0  0
 QKW  Var_01    O2   C6   C7   C8    -2.84  30.0  2
 QKW  Var_02    O1   C5   C4   C3   -58.61  30.0  2
 QKW  Var_03    C7   C6   O1   C5   176.71  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
 QKW  plan-1  N1   0.020
 QKW  plan-1  C6   0.020
 QKW  plan-1  C7   0.020
 QKW  plan-1  C8   0.020
 QKW  plan-1  C10  0.020
 QKW  plan-1  C9   0.020
 QKW  plan-1  C11  0.020
 QKW  plan-1  H3   0.020
 QKW  plan-1  H4   0.020
 QKW  plan-1  H8   0.020
 QKW  plan-1  H9   0.020
 QKW  plan-2  C4   0.020
 QKW  plan-2  C5   0.020
 QKW  plan-2  C13  0.020
 QKW  plan-2  C1   0.020
 QKW  plan-2  C2   0.020
 QKW  plan-2  C3   0.020
 QKW  plan-2  C12  0.020
 QKW  plan-2  H5   0.020
 QKW  plan-2  H6   0.020
 QKW  plan-2  H7   0.020
 QKW  plan-2  H10  0.020
 QKW  plan-2  CL1  0.020
 QKW  plan-3  C6   0.020
 QKW  plan-3  C7   0.020
 QKW  plan-3  O1   0.020
 QKW  plan-3  O2   0.020

