# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 06:14:00 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N-[(1S)-1-benzyl-3,3,3-trifluoro-2-oxopropyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccccc1)C(=O)C(F)(F)F
#
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
 APF  APF  N-[(1S)-1-benzyl-3,3,3-trifluoro-2-oxopropyl]acetamide  ligand  30  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_APF
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
 APF  CN2   C  CH3   0  -0.785   3.6943  -0.1475   0.7413
 APF  CN1   C  C     0   0.515   2.3790  -0.5833   0.1482
 APF  ON1   O  O     0  -0.482   2.1718  -1.7091  -0.2726
 APF  N3    N  NH1   0  -0.613   1.4309   0.3820   0.1333
 APF  C3    C  CH1   0  -0.218   0.1031   0.1675  -0.3606
 APF  C2    C  C     0   0.228  -0.0000   0.6159  -1.8101
 APF  C1    C  CT    0   0.969  -0.9072  -0.2116  -2.7367
 APF  C4    C  CH2   0  -0.552  -0.9210   0.9504   0.4860
 APF  O2    O  O     0  -0.323   0.5898   1.5552  -2.2588
 APF  F11   F  F     0  -0.287  -1.1490   0.4173  -3.8757
 APF  F12   F  F     0  -0.302  -0.2999  -1.3687  -3.0120
 APF  F13   F  F     0  -0.296  -2.0748  -0.4927  -2.1543
 APF  CP1   C  CR6   0   0.157  -0.9116   0.4776   1.9127
 APF  CP2   C  CR16  0  -0.316  -0.2194   1.1766   2.8964
 APF  CP3   C  CR16  0  -0.240  -0.1909   0.7158   4.2066
 APF  CP4   C  CR16  0  -0.269  -0.8555  -0.4539   4.5479
 APF  CP5   C  CR16  0  -0.240  -1.5519  -1.1576   3.5729
 APF  CP6   C  CR16  0  -0.299  -1.5789  -0.6929   2.2659
 APF  HC21  H  HCH3  0   0.269   3.5717   0.1039   1.7957
 APF  HC22  H  HCH3  0   0.265   4.4301  -0.9420   0.6553
 APF  HC23  H  HCH3  0   0.267   4.0738   0.7412   0.2363
 APF  HN3   H  HNH1  0   0.409   1.6754   1.3070   0.4506
 APF  H3    H  HCH1  0   0.306  -0.1238  -0.8984  -0.2865
 APF  H41   H  HCH2  0   0.281  -0.6884   2.0167   0.4299
 APF  H42   H  HCH2  0   0.286  -1.9176   0.8250   0.0612
 APF  HP2   H  HCR6  0   0.251   0.2949   2.0953   2.6403
 APF  HP3   H  HCR6  0   0.256   0.3515   1.2721   4.9602
 APF  HP4   H  HCR6  0   0.256  -0.8356  -0.8135   5.5685
 APF  HP5   H  HCR6  0   0.257  -2.0777  -2.0677   3.8311
 APF  HP6   H  HCR6  0   0.249  -2.1312  -1.2445   1.5134

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
 APF  CN2  CN1   single    1.507  0.020  1.507
 APF  CN2  HC21  single    0.970  0.020  1.090
 APF  CN2  HC22  single    0.970  0.020  1.090
 APF  CN2  HC23  single    0.970  0.020  1.090
 APF  CN1  ON1   double    1.220  0.020  1.220
 APF  CN1  N3    single    1.353  0.020  1.353
 APF  N3   C3    single    1.433  0.020  1.433
 APF  N3   HN3   single    0.860  0.020  1.020
 APF  C3   C2    single    1.521  0.020  1.521
 APF  C3   C4    single    1.542  0.020  1.542
 APF  C3   H3    single    0.970  0.020  1.090
 APF  C2   C1    single    1.538  0.020  1.538
 APF  C2   O2    double    1.196  0.020  1.196
 APF  C1   F11   single    1.323  0.020  1.323
 APF  C1   F12   single    1.335  0.020  1.335
 APF  C1   F13   single    1.335  0.020  1.335
 APF  C4   CP1   single    1.503  0.020  1.503
 APF  C4   H41   single    0.970  0.020  1.090
 APF  C4   H42   single    0.970  0.020  1.090
 APF  CP1  CP2   aromatic  1.391  0.020  1.391
 APF  CP1  CP6   aromatic  1.393  0.020  1.393
 APF  CP2  CP3   aromatic  1.389  0.020  1.389
 APF  CP2  HP2   single    0.930  0.020  1.080
 APF  CP3  CP4   aromatic  1.388  0.020  1.388
 APF  CP3  HP3   single    0.930  0.020  1.080
 APF  CP4  CP5   aromatic  1.390  0.020  1.390
 APF  CP4  HP4   single    0.930  0.020  1.080
 APF  CP5  CP6   aromatic  1.387  0.020  1.387
 APF  CP5  HP5   single    0.930  0.020  1.080
 APF  CP6  HP6   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
 APF  HC23  CN2  HC22  108.88  3.000
 APF  HC23  CN2  HC21  107.40  3.000
 APF  HC22  CN2  HC21  108.73  3.000
 APF  HC23  CN2  CN1   110.92  3.000
 APF  HC22  CN2  CN1   110.39  3.000
 APF  HC21  CN2  CN1   110.43  3.000
 APF  N3    CN1  ON1   122.39  3.000
 APF  N3    CN1  CN2   114.17  3.000
 APF  ON1   CN1  CN2   123.43  3.000
 APF  HN3   N3   C3    118.08  3.000
 APF  HN3   N3   CN1   118.76  3.000
 APF  C3    N3   CN1   123.11  3.000
 APF  H3    C3   C4    108.68  3.000
 APF  H3    C3   C2    109.77  3.000
 APF  C4    C3   C2    109.18  3.000
 APF  H3    C3   N3    108.37  3.000
 APF  C4    C3   N3    110.49  3.000
 APF  C2    C3   N3    110.32  3.000
 APF  O2    C2   C1    119.16  3.000
 APF  O2    C2   C3    123.74  3.000
 APF  C1    C2   C3    117.10  3.000
 APF  F13   C1   F12   107.78  3.000
 APF  F13   C1   F11   108.41  3.000
 APF  F12   C1   F11   108.51  3.000
 APF  F13   C1   C2    111.49  3.000
 APF  F12   C1   C2    108.79  3.000
 APF  F11   C1   C2    111.75  3.000
 APF  H42   C4   H41   106.66  3.000
 APF  H42   C4   CP1   109.83  3.000
 APF  H41   C4   CP1   110.75  3.000
 APF  H42   C4   C3    109.55  3.000
 APF  H41   C4   C3    109.02  3.000
 APF  CP1   C4   C3    110.93  3.000
 APF  CP6   CP1  CP2   118.76  3.000
 APF  CP6   CP1  C4    120.14  3.000
 APF  CP2   CP1  C4    121.08  3.000
 APF  HP2   CP2  CP3   119.63  3.000
 APF  HP2   CP2  CP1   119.67  3.000
 APF  CP3   CP2  CP1   120.70  3.000
 APF  HP3   CP3  CP4   120.13  3.000
 APF  HP3   CP3  CP2   119.77  3.000
 APF  CP4   CP3  CP2   120.11  3.000
 APF  HP4   CP4  CP5   120.18  3.000
 APF  HP4   CP4  CP3   120.20  3.000
 APF  CP5   CP4  CP3   119.62  3.000
 APF  HP5   CP5  CP6   119.80  3.000
 APF  HP5   CP5  CP4   120.12  3.000
 APF  CP6   CP5  CP4   120.08  3.000
 APF  HP6   CP6  CP5   119.56  3.000
 APF  HP6   CP6  CP1   119.71  3.000
 APF  CP5   CP6  CP1   120.73  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
 APF  CONST_01  CP4   CP3  CP2  CP1     0.00   0.0  0
 APF  CONST_02  CP4   CP5  CP6  CP1     0.00   0.0  0
 APF  CONST_03  CP5   CP6  CP1  CP2     0.00   0.0  0
 APF  CONST_04  CP5   CP4  CP3  CP2     0.00   0.0  0
 APF  CONST_05  CP6   CP1  CP2  CP3     0.00   0.0  0
 APF  CONST_06  CP6   CP5  CP4  CP3     0.00   0.0  0
 APF  CONST_07  CP3   CP2  CP1  C4    180.00   0.0  0
 APF  CONST_08  CP5   CP6  CP1  C4    180.00   0.0  0
 APF  CONST_09  HP3   CP3  CP2  CP1   180.00   0.0  0
 APF  CONST_10  HP5   CP5  CP6  CP1   180.00   0.0  0
 APF  CONST_11  HP6   CP6  CP1  CP2   180.00   0.0  0
 APF  CONST_12  HP4   CP4  CP3  CP2   180.00   0.0  0
 APF  CONST_13  HP2   CP2  CP3  CP4   180.00   0.0  0
 APF  CONST_14  C3    N3   CN1  CN2   180.00   0.0  0
 APF  CONST_15  C3    N3   CN1  ON1     0.00   0.0  0
 APF  CONST_16  HN3   N3   CN1  CN2     0.00   0.0  0
 APF  Var_01    CP2   CP1  C4   C3     99.24  30.0  2
 APF  Var_02    F11   C1   C2   C3    166.51  30.0  3
 APF  Var_03    HC21  CN2  CN1  ON1  -115.35  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 APF  chir_01  C3  N3  C2  C4  positiv

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
 APF  plan-1  C4   0.020
 APF  plan-1  CP1  0.020
 APF  plan-1  CP2  0.020
 APF  plan-1  CP3  0.020
 APF  plan-1  CP4  0.020
 APF  plan-1  CP5  0.020
 APF  plan-1  CP6  0.020
 APF  plan-1  HP2  0.020
 APF  plan-1  HP3  0.020
 APF  plan-1  HP4  0.020
 APF  plan-1  HP5  0.020
 APF  plan-1  HP6  0.020
 APF  plan-2  CN2  0.020
 APF  plan-2  CN1  0.020
 APF  plan-2  ON1  0.020
 APF  plan-2  N3   0.020
 APF  plan-2  C3   0.020
 APF  plan-2  HN3  0.020
 APF  plan-3  C3   0.020
 APF  plan-3  C2   0.020
 APF  plan-3  C1   0.020
 APF  plan-3  O2   0.020

