# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 08:53:42 2021
#   Inital geometry file: a 86 line input string
#   Ligand name: N-[(2-chloro-6-fluorophenyl)methyl]-N,2-dimethylpyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1c(F)cccc1Cl)C(=O)c2ccnc(C)n2
#
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
 PJS  PJS  N-[(2-chloro-6-fluorophenyl)methyl]-N,2-dimethylpyrimidine-4-carboxamide  ligand  33  20  .  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_PJS
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
 PJS  C1    C   CH3   0  -0.731   4.6519  17.3206  -12.8209
 PJS  C2    C   CR6   0   0.350   3.5849  17.8494  -13.7231
 PJS  C11   C   CH2   0  -0.376  -2.1812  19.3062  -13.2934
 PJS  C12   C   CR6   0  -0.009  -2.8741  18.3025  -14.1755
 PJS  C13   C   CR6   0   0.538  -3.4723  17.1615  -13.6564
 PJS  C15   C   CR16  0  -0.405  -4.1265  16.2234  -14.4290
 PJS  C16   C   CR16  0  -0.259  -4.1893  16.4208  -15.7992
 PJS  C17   C   CR16  0  -0.222  -3.6102  17.5412  -16.3733
 PJS  C18   C   CR6   0  -0.077  -2.9675  18.4584  -15.5564
 PJS  C10   C   CH3   0  -0.539  -0.1947  20.7484  -13.6185
 PJS  C4    C   CR16  0  -0.018   2.9797  18.7464  -15.7164
 PJS  C5    C   CR16  0  -0.313   1.6636  18.8382  -15.3012
 PJS  C6    C   CR6   0   0.126   1.3993  18.3727  -14.0229
 PJS  C7    C   C     0   0.531  -0.0123  18.2887  -13.5067
 PJS  F14   F   F     0  -0.306  -3.4207  16.9571  -12.3341
 PJS  N20   N   N     0  -0.410   2.3443  17.8740  -13.2424
 PJS  N3    N   N     0  -0.406   3.9376  18.2626  -14.9371
 PJS  N9    N   NT    0  -0.451  -0.7523  19.4081  -13.5606
 PJS  O8    O   O     0  -0.459  -0.4413  17.2083  -13.1374
 PJS  CL19  CL  CL    0  -0.106  -2.2634  19.8551  -16.3032
 PJS  H1    H   HCH3  0   0.252   5.5993  17.2299  -13.3456
 PJS  H2    H   HCH3  0   0.262   4.7905  17.9880  -11.9689
 PJS  H3    H   HCH3  0   0.259   4.3701  16.3463  -12.4220
 PJS  H4    H   HCH2  0   0.289  -2.6088  20.2918  -13.4784
 PJS  H5    H   HCH2  0   0.288  -2.3574  19.0826  -12.2409
 PJS  H6    H   HCR6  0   0.285  -4.5723  15.3539  -13.9653
 PJS  H7    H   HCR6  0   0.280  -4.6945  15.6977  -16.4245
 PJS  H8    H   HCR6  0   0.285  -3.6594  17.7022  -17.4410
 PJS  H9    H   HCH3  0   0.268  -0.6194  21.3481  -12.8135
 PJS  H10   H   HCH3  0   0.267   0.8812  20.7358  -13.4736
 PJS  H11   H   HCH3  0   0.246  -0.4152  21.2357  -14.5679
 PJS  H12   H   HCR6  0   0.284   3.2718  19.0737  -16.7075
 PJS  H13   H   HCR6  0   0.278   0.8908  19.2372  -15.9437

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
 PJS  C17   C16  aromatic  1.386  0.020  1.386
 PJS  C17   C18  aromatic  1.386  0.020  1.386
 PJS  CL19  C18  single    1.733  0.020  1.733
 PJS  C16   C15  aromatic  1.386  0.020  1.386
 PJS  C4    C5   aromatic  1.383  0.020  1.383
 PJS  C4    N3   aromatic  1.326  0.020  1.326
 PJS  C18   C12  aromatic  1.393  0.020  1.393
 PJS  C5    C6   aromatic  1.386  0.020  1.386
 PJS  N3    C2   aromatic  1.330  0.020  1.330
 PJS  C15   C13  aromatic  1.380  0.020  1.380
 PJS  C12   C13  aromatic  1.389  0.020  1.389
 PJS  C12   C11  single    1.505  0.020  1.505
 PJS  C6    C7   single    1.505  0.020  1.505
 PJS  C6    N20  aromatic  1.323  0.020  1.323
 PJS  C10   N9   single    1.453  0.020  1.453
 PJS  C7    N9   single    1.343  0.020  1.343
 PJS  C7    O8   double    1.220  0.020  1.220
 PJS  N9    C11  single    1.457  0.020  1.457
 PJS  C13   F14  single    1.339  0.020  1.339
 PJS  C2    N20  aromatic  1.331  0.020  1.331
 PJS  C2    C1   single    1.494  0.020  1.494
 PJS  C1    H1   single    0.970  0.020  1.090
 PJS  C1    H2   single    0.970  0.020  1.090
 PJS  C1    H3   single    0.970  0.020  1.090
 PJS  C11   H4   single    0.970  0.020  1.090
 PJS  C11   H5   single    0.970  0.020  1.090
 PJS  C15   H6   single    0.930  0.020  1.080
 PJS  C16   H7   single    0.930  0.020  1.080
 PJS  C17   H8   single    0.930  0.020  1.080
 PJS  C10   H9   single    0.970  0.020  1.090
 PJS  C10   H10  single    0.970  0.020  1.090
 PJS  C10   H11  single    0.970  0.020  1.090
 PJS  C4    H12  single    0.930  0.020  1.080
 PJS  C5    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
 PJS  H3    C1   H2   107.09  3.000
 PJS  H3    C1   H1   109.12  3.000
 PJS  H2    C1   H1   108.50  3.000
 PJS  H3    C1   C2   110.66  3.000
 PJS  H2    C1   C2   110.22  3.000
 PJS  H1    C1   C2   111.14  3.000
 PJS  N3    C2   N20  124.84  3.000
 PJS  N20   C2   C1   117.01  3.000
 PJS  N3    C2   C1   118.15  3.000
 PJS  H5    C11  H4   106.61  3.000
 PJS  H5    C11  N9   110.48  3.000
 PJS  H4    C11  N9   106.87  3.000
 PJS  H5    C11  C12  110.76  3.000
 PJS  H4    C11  C12  108.83  3.000
 PJS  N9    C11  C12  112.99  3.000
 PJS  C18   C12  C13  115.70  3.000
 PJS  C13   C12  C11  121.80  3.000
 PJS  C18   C12  C11  122.50  3.000
 PJS  F14   C13  C15  117.86  3.000
 PJS  F14   C13  C12  118.55  3.000
 PJS  C15   C13  C12  123.59  3.000
 PJS  H6    C15  C16  121.32  3.000
 PJS  H6    C15  C13  120.12  3.000
 PJS  C16   C15  C13  118.57  3.000
 PJS  H7    C16  C17  119.76  3.000
 PJS  H7    C16  C15  119.85  3.000
 PJS  C17   C16  C15  120.39  3.000
 PJS  H8    C17  C18  120.31  3.000
 PJS  H8    C17  C16  120.71  3.000
 PJS  C18   C17  C16  118.99  3.000
 PJS  CL19  C18  C17  117.88  3.000
 PJS  CL19  C18  C12  119.35  3.000
 PJS  C17   C18  C12  122.77  3.000
 PJS  H11   C10  H10  108.78  3.000
 PJS  H11   C10  H9   108.58  3.000
 PJS  H10   C10  H9   107.10  3.000
 PJS  H11   C10  N9   111.68  3.000
 PJS  H10   C10  N9   111.36  3.000
 PJS  H9    C10  N9   109.18  3.000
 PJS  H12   C4   N3   116.93  3.000
 PJS  H12   C4   C5   120.72  3.000
 PJS  N3    C4   C5   122.35  3.000
 PJS  H13   C5   C6   122.39  3.000
 PJS  H13   C5   C4   121.75  3.000
 PJS  C6    C5   C4   115.85  3.000
 PJS  N20   C6   C7   116.51  3.000
 PJS  N20   C6   C5   122.31  3.000
 PJS  C7    C6   C5   120.92  3.000
 PJS  O8    C7   N9   123.83  3.000
 PJS  O8    C7   C6   118.88  3.000
 PJS  N9    C7   C6   117.15  3.000
 PJS  C6    N20  C2   117.37  3.000
 PJS  C4    N3   C2   117.27  3.000
 PJS  C7    N9   C10  123.99  3.000
 PJS  C7    N9   C11  118.33  3.000
 PJS  C10   N9   C11  116.63  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
 PJS  CONST_01  C5    C4   N3   C2     0.00   0.0  0
 PJS  CONST_02  C5    C6   N20  C2     0.00   0.0  0
 PJS  CONST_03  C16   C17  C18  C12    0.00   0.0  0
 PJS  CONST_04  C16   C15  C13  C12    0.00   0.0  0
 PJS  CONST_05  C17   C16  C15  C13    0.00   0.0  0
 PJS  CONST_06  C17   C18  C12  C13    0.00   0.0  0
 PJS  CONST_07  C18   C17  C16  C15    0.00   0.0  0
 PJS  CONST_08  C18   C12  C13  C15    0.00   0.0  0
 PJS  CONST_09  N20   C6   C5   C4     0.00   0.0  0
 PJS  CONST_10  N20   C2   N3   C4     0.00   0.0  0
 PJS  CONST_11  N3    C4   C5   C6     0.00   0.0  0
 PJS  CONST_12  N3    C2   N20  C6     0.00   0.0  0
 PJS  CONST_13  C4    N3   C2   C1   180.00   0.0  0
 PJS  CONST_14  C6    N20  C2   C1   180.00   0.0  0
 PJS  CONST_15  C7    C6   N20  C2   180.00   0.0  0
 PJS  CONST_16  C17   C18  C12  C11  180.00   0.0  0
 PJS  CONST_17  C15   C13  C12  C11  180.00   0.0  0
 PJS  CONST_18  CL19  C18  C12  C13  180.00   0.0  0
 PJS  CONST_19  CL19  C18  C17  C16  180.00   0.0  0
 PJS  CONST_20  F14   C13  C15  C16  180.00   0.0  0
 PJS  CONST_21  F14   C13  C12  C18  180.00   0.0  0
 PJS  CONST_22  C7    C6   C5   C4   180.00   0.0  0
 PJS  CONST_23  H12   C4   N3   C2   180.00   0.0  0
 PJS  CONST_24  H8    C17  C18  C12  180.00   0.0  0
 PJS  CONST_25  H6    C15  C13  C12  180.00   0.0  0
 PJS  CONST_26  H7    C16  C15  C13  180.00   0.0  0
 PJS  CONST_27  H13   C5   C6   N20  180.00   0.0  0
 PJS  CONST_28  C6    C7   N9   C11  180.00   0.0  0
 PJS  CONST_30  O8    C7   N9   C11    0.00   0.0  0
 PJS  Var_01    N9    C11  C12  C13  115.96  30.0  2
 PJS  Var_02    N9    C7   C6   C5   -54.21  30.0  2
 PJS  Var_03    H1    C1   C2   N20  173.08  30.0  2
 PJS  Var_04    C10   N9   C11  C12  136.15  30.0  2
 PJS  Var_05    H9    C10  N9   C11   42.11  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
 PJS  plan-1  C11   0.020
 PJS  plan-1  C12   0.020
 PJS  plan-1  C13   0.020
 PJS  plan-1  C15   0.020
 PJS  plan-1  C16   0.020
 PJS  plan-1  C17   0.020
 PJS  plan-1  C18   0.020
 PJS  plan-1  F14   0.020
 PJS  plan-1  CL19  0.020
 PJS  plan-1  H6    0.020
 PJS  plan-1  H7    0.020
 PJS  plan-1  H8    0.020
 PJS  plan-2  C1    0.020
 PJS  plan-2  C2    0.020
 PJS  plan-2  C4    0.020
 PJS  plan-2  C5    0.020
 PJS  plan-2  C6    0.020
 PJS  plan-2  C7    0.020
 PJS  plan-2  N20   0.020
 PJS  plan-2  N3    0.020
 PJS  plan-2  H12   0.020
 PJS  plan-2  H13   0.020
 PJS  plan-3  C11   0.020
 PJS  plan-3  C10   0.020
 PJS  plan-3  C6    0.020
 PJS  plan-3  C7    0.020
 PJS  plan-3  N9    0.020
 PJS  plan-3  O8    0.020

