# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:31:05 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-[(1S)-1-benzyl-3,3,3-trifluoro-2,2-dihydroxypropyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccccc1)C(O)(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
 APL  APL  N-[(1S)-1-benzyl-3,3,3-trifluoro-2,2-dihydroxypropyl]acetamide  ligand  33  19  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_APL
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
 APL  CN2   C  CH3   0  -0.788   3.2746   0.3494   0.2460
 APL  CN1   C  C     0   0.519   1.9622  -0.3171  -0.0768
 APL  ON1   O  O     0  -0.476   1.8437  -1.5201  -0.2245
 APL  N3    N  NH1   0  -0.641   0.9153   0.5410  -0.1716
 APL  C3    C  CH1   0  -0.194  -0.4620   0.1198  -0.2360
 APL  C2    C  CT    0   0.349  -1.0918   0.4477  -1.6149
 APL  C1    C  CT    0   0.997  -0.4401  -0.3542  -2.7747
 APL  C4    C  CH2   0  -0.541  -1.2501   0.7781   0.9085
 APL  OY    O  OH1   0  -0.653  -2.4476   0.1685  -1.6371
 APL  OX    O  OH1   0  -0.655  -1.0191   1.7964  -1.9186
 APL  F11   F  F     0  -0.306  -1.0670  -0.1010  -3.9256
 APL  F12   F  F     0  -0.306   0.8489  -0.0544  -2.9617
 APL  F13   F  F     0  -0.310  -0.5208  -1.6729  -2.5617
 APL  CP1   C  CR6   0   0.156  -0.6880   0.3674   2.2408
 APL  CP2   C  CR16  0  -0.324   0.1930   1.1899   2.9374
 APL  CP3   C  CR16  0  -0.238   0.7441   0.7819   4.1457
 APL  CP4   C  CR16  0  -0.271   0.4188  -0.4587   4.6760
 APL  CP5   C  CR16  0  -0.239  -0.4639  -1.2858   3.9924
 APL  CP6   C  CR16  0  -0.300  -1.0108  -0.8736   2.7856
 APL  HC21  H  HCH3  0   0.266   4.0970  -0.3492   0.1177
 APL  HC22  H  HCH3  0   0.264   3.4496   1.2224  -0.3827
 APL  HC23  H  HCH3  0   0.268   3.2690   0.6912   1.2829
 APL  HN3   H  HNH1  0   0.402   1.0893   1.5022   0.0826
 APL  H3    H  HCH1  0   0.291  -0.4804  -0.9637  -0.0940
 APL  H41   H  HCH2  0   0.266  -1.2127   1.8649   0.8001
 APL  H42   H  HCH2  0   0.273  -2.3004   0.4934   0.8469
 APL  HY    H  HOH1  0   0.471  -2.6315  -0.6856  -1.2288
 APL  HX    H  HOH1  0   0.464  -0.1092   2.1102  -1.8573
 APL  HP2   H  HCR6  0   0.248   0.4473   2.1657   2.5390
 APL  HP3   H  HCR6  0   0.255   1.4273   1.4357   4.6722
 APL  HP4   H  HCR6  0   0.254   0.8466  -0.7774   5.6176
 APL  HP5   H  HCR6  0   0.254  -0.7287  -2.2530   4.4003
 APL  HP6   H  HCR6  0   0.247  -1.7015  -1.5259   2.2627

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
 APL  CN2  CN1   single    1.507  0.020  1.507
 APL  CN2  HC21  single    0.970  0.020  1.090
 APL  CN2  HC22  single    0.970  0.020  1.090
 APL  CN2  HC23  single    0.970  0.020  1.090
 APL  CN1  ON1   double    1.218  0.020  1.218
 APL  CN1  N3    single    1.357  0.020  1.357
 APL  N3   C3    single    1.442  0.020  1.442
 APL  N3   HN3   single    0.860  0.020  1.020
 APL  C3   C2    single    1.551  0.020  1.551
 APL  C3   C4    single    1.538  0.020  1.538
 APL  C3   H3    single    0.970  0.020  1.090
 APL  C2   C1    single    1.553  0.020  1.553
 APL  C2   OY    single    1.385  0.020  1.385
 APL  C2   OX    single    1.384  0.020  1.384
 APL  C1   F11   single    1.335  0.020  1.335
 APL  C1   F12   single    1.337  0.020  1.337
 APL  C1   F13   single    1.338  0.020  1.338
 APL  C4   CP1   single    1.503  0.020  1.503
 APL  C4   H41   single    0.970  0.020  1.090
 APL  C4   H42   single    0.970  0.020  1.090
 APL  OY   HY    single    0.850  0.020  0.980
 APL  OX   HX    single    0.850  0.020  0.980
 APL  CP1  CP2   aromatic  1.392  0.020  1.392
 APL  CP1  CP6   aromatic  1.393  0.020  1.393
 APL  CP2  CP3   aromatic  1.389  0.020  1.389
 APL  CP2  HP2   single    0.930  0.020  1.080
 APL  CP3  CP4   aromatic  1.388  0.020  1.388
 APL  CP3  HP3   single    0.930  0.020  1.080
 APL  CP4  CP5   aromatic  1.389  0.020  1.389
 APL  CP4  HP4   single    0.930  0.020  1.080
 APL  CP5  CP6   aromatic  1.388  0.020  1.388
 APL  CP5  HP5   single    0.930  0.020  1.080
 APL  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
 APL  HC23  CN2  HC22  107.33  3.000
 APL  HC23  CN2  HC21  108.50  3.000
 APL  HC22  CN2  HC21  108.98  3.000
 APL  HC23  CN2  CN1   109.72  3.000
 APL  HC22  CN2  CN1   111.75  3.000
 APL  HC21  CN2  CN1   110.45  3.000
 APL  N3    CN1  ON1   122.76  3.000
 APL  N3    CN1  CN2   114.03  3.000
 APL  ON1   CN1  CN2   123.21  3.000
 APL  HN3   N3   C3    117.01  3.000
 APL  HN3   N3   CN1   116.85  3.000
 APL  C3    N3   CN1   123.74  3.000
 APL  H3    C3   C4    108.61  3.000
 APL  H3    C3   C2    108.56  3.000
 APL  C4    C3   C2    111.29  3.000
 APL  H3    C3   N3    107.45  3.000
 APL  C4    C3   N3    109.35  3.000
 APL  C2    C3   N3    111.46  3.000
 APL  OX    C2   OY    104.14  3.000
 APL  OX    C2   C1    108.49  3.000
 APL  OY    C2   C1    107.14  3.000
 APL  OX    C2   C3    112.31  3.000
 APL  OY    C2   C3    111.67  3.000
 APL  C1    C2   C3    112.60  3.000
 APL  F13   C1   F12   107.54  3.000
 APL  F13   C1   F11   107.21  3.000
 APL  F12   C1   F11   106.84  3.000
 APL  F13   C1   C2    111.38  3.000
 APL  F12   C1   C2    113.16  3.000
 APL  F11   C1   C2    110.42  3.000
 APL  H42   C4   H41   106.68  3.000
 APL  H42   C4   CP1   109.81  3.000
 APL  H41   C4   CP1   110.29  3.000
 APL  H42   C4   C3    109.88  3.000
 APL  H41   C4   C3    109.54  3.000
 APL  CP1   C4   C3    110.55  3.000
 APL  HY    OY   C2    111.01  3.000
 APL  HX    OX   C2    110.64  3.000
 APL  CP6   CP1  CP2   118.51  3.000
 APL  CP6   CP1  C4    120.22  3.000
 APL  CP2   CP1  C4    121.24  3.000
 APL  HP2   CP2  CP3   119.39  3.000
 APL  HP2   CP2  CP1   119.76  3.000
 APL  CP3   CP2  CP1   120.84  3.000
 APL  HP3   CP3  CP4   120.13  3.000
 APL  HP3   CP3  CP2   119.74  3.000
 APL  CP4   CP3  CP2   120.12  3.000
 APL  HP4   CP4  CP5   120.26  3.000
 APL  HP4   CP4  CP3   120.20  3.000
 APL  CP5   CP4  CP3   119.54  3.000
 APL  HP5   CP5  CP6   119.78  3.000
 APL  HP5   CP5  CP4   120.12  3.000
 APL  CP6   CP5  CP4   120.09  3.000
 APL  HP6   CP6  CP5   119.46  3.000
 APL  HP6   CP6  CP1   119.65  3.000
 APL  CP5   CP6  CP1   120.89  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
 APL  CONST_01  CP4   CP3  CP2  CP1    0.00   0.0  0
 APL  CONST_02  CP4   CP5  CP6  CP1    0.00   0.0  0
 APL  CONST_03  CP5   CP6  CP1  CP2    0.00   0.0  0
 APL  CONST_04  CP5   CP4  CP3  CP2    0.00   0.0  0
 APL  CONST_05  CP6   CP1  CP2  CP3    0.00   0.0  0
 APL  CONST_06  CP6   CP5  CP4  CP3    0.00   0.0  0
 APL  CONST_07  CP3   CP2  CP1  C4   180.00   0.0  0
 APL  CONST_08  CP5   CP6  CP1  C4   180.00   0.0  0
 APL  CONST_09  HP3   CP3  CP2  CP1  180.00   0.0  0
 APL  CONST_10  HP5   CP5  CP6  CP1  180.00   0.0  0
 APL  CONST_11  HP6   CP6  CP1  CP2  180.00   0.0  0
 APL  CONST_12  HP4   CP4  CP3  CP2  180.00   0.0  0
 APL  CONST_13  HP2   CP2  CP3  CP4  180.00   0.0  0
 APL  CONST_14  C3    N3   CN1  CN2  180.00   0.0  0
 APL  CONST_15  C3    N3   CN1  ON1    0.00   0.0  0
 APL  CONST_16  HN3   N3   CN1  CN2    0.00   0.0  0
 APL  Var_01    CP2   CP1  C4   C3    98.54  30.0  2
 APL  Var_02    F11   C1   C2   C3   176.21  30.0  3
 APL  Var_03    HC21  CN2  CN1  ON1   11.89  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
 APL  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
 APL  plan-1  C4   0.020
 APL  plan-1  CP1  0.020
 APL  plan-1  CP2  0.020
 APL  plan-1  CP3  0.020
 APL  plan-1  CP4  0.020
 APL  plan-1  CP5  0.020
 APL  plan-1  CP6  0.020
 APL  plan-1  HP2  0.020
 APL  plan-1  HP3  0.020
 APL  plan-1  HP4  0.020
 APL  plan-1  HP5  0.020
 APL  plan-1  HP6  0.020
 APL  plan-2  CN2  0.020
 APL  plan-2  CN1  0.020
 APL  plan-2  ON1  0.020
 APL  plan-2  N3   0.020
 APL  plan-2  C3   0.020
 APL  plan-2  HN3  0.020

