# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:47:07 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2S)-2-[(2-acetyl-5-methylphenyl)amino]-2-(2,6-dichlorophenyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)c1ccc(C)cc1N[C@H](C(N)=O)c2c(Cl)cccc2Cl
#
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
 AAP  AAP  (2S)-2-[(2-acetyl-5-methylphenyl)amino]-2-(2,6-dichlorophenyl)ethanamide  ligand  39  23  .  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_AAP
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
 AAP  C     C   C     0   0.520  -0.8267  -2.1742  -0.9162
 AAP  CA    C   CH1   0  -0.312  -0.5041  -0.6995  -0.6316
 AAP  O     O   O     0  -0.463  -1.4164  -2.4704  -1.9429
 AAP  N     N   NH2   0  -0.775  -0.5144  -3.0295   0.0579
 AAP  C1    C   CR6   0   0.354   0.0401  -0.0113  -1.8615
 AAP  C2    C   CR6   0  -0.107   1.1726  -0.4836  -2.5263
 AAP  C3    C   CR16  0  -0.168   1.7049   0.1425  -3.6400
 AAP  C4    C   CR16  0  -0.263   1.1013   1.2934  -4.1177
 AAP  C5    C   CR16  0  -0.162  -0.0123   1.8118  -3.4805
 AAP  C6    C   CR6   0  -0.156  -0.5219   1.1624  -2.3662
 AAP  CL2   CL  CL    0  -0.095   1.9793  -1.9007  -1.9402
 AAP  CL6   CL  CL    0  -0.105  -1.9008   1.8779  -1.5957
 AAP  N'    N   NH1   0  -0.719   0.3475  -0.4525   0.5024
 AAP  C1'   C   CR6   0   0.404  -0.1030  -0.0681   1.7325
 AAP  C2'   C   CR6   0  -0.137   0.7643   0.5757   2.6576
 AAP  C3'   C   CR16  0  -0.255   0.2470   0.9296   3.9115
 AAP  C4'   C   CR16  0  -0.282  -1.0561   0.6772   4.2718
 AAP  C5'   C   CR6   0   0.131  -1.9107   0.0358   3.3686
 AAP  C6'   C   CR16  0  -0.366  -1.4259  -0.3306   2.1262
 AAP  C'    C   C     0   0.402   2.1628   0.8910   2.3317
 AAP  O'    O   O     0  -0.409   2.6686   0.5779   1.2598
 AAP  CM'   C   CH3   0  -0.783   2.9968   1.6260   3.3498
 AAP  CM5   C   CH3   0  -0.711  -3.3343  -0.2462   3.7403
 AAP  HA    H   HCH1  0   0.295  -1.4872  -0.2661  -0.4311
 AAP  HN1   H   HNH2  0   0.383  -0.6968  -4.0135  -0.0555
 AAP  HN2   H   HNH2  0   0.402   0.0809  -2.7507   0.8199
 AAP  H3    H   HCR6  0   0.267   2.5811  -0.2631  -4.1258
 AAP  H4    H   HCR6  0   0.259   1.5050   1.7937  -4.9871
 AAP  H5    H   HCR6  0   0.265  -0.4813   2.7157  -3.8429
 AAP  HN'   H   HNH1  0   0.416   1.3190  -0.2225   0.3311
 AAP  H3'   H   HCR6  0   0.233   0.8887   1.4226   4.6289
 AAP  H4'   H   HCR6  0   0.224  -1.4137   0.9652   5.2518
 AAP  H6'   H   HCR6  0   0.232  -2.0901  -0.8656   1.4595
 AAP  HM'1  H   HCH3  0   0.269   3.9918   1.8036   2.9488
 AAP  HM'2  H   HCH3  0   0.249   2.5488   2.5848   3.6125
 AAP  HM'3  H   HCH3  0   0.248   3.0908   1.0513   4.2722
 AAP  HM51  H   HCH3  0   0.246  -3.9431   0.6538   3.6338
 AAP  HM52  H   HCH3  0   0.233  -3.7721  -1.0155   3.1061
 AAP  HM53  H   HCH3  0   0.239  -3.4171  -0.5680   4.7781

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
 AAP  C    CA    single    1.536  0.020  1.536
 AAP  C    O     double    1.220  0.020  1.220
 AAP  C    N     single    1.333  0.020  1.333
 AAP  CA   C1    single    1.511  0.020  1.511
 AAP  CA   N'    single    1.440  0.020  1.440
 AAP  CA   HA    single    0.970  0.020  1.090
 AAP  N    HN1   single    0.860  0.020  1.020
 AAP  N    HN2   single    0.860  0.020  1.020
 AAP  C1   C2    aromatic  1.396  0.020  1.396
 AAP  C1   C6    aromatic  1.396  0.020  1.396
 AAP  C2   C3    aromatic  1.384  0.020  1.384
 AAP  C2   CL2   single    1.733  0.020  1.733
 AAP  C3   C4    aromatic  1.385  0.020  1.385
 AAP  C3   H3    single    0.930  0.020  1.080
 AAP  C4   C5    aromatic  1.384  0.020  1.384
 AAP  C4   H4    single    0.930  0.020  1.080
 AAP  C5   C6    aromatic  1.387  0.020  1.387
 AAP  C5   H5    single    0.930  0.020  1.080
 AAP  C6   CL6   single    1.734  0.020  1.734
 AAP  N'   C1'   single    1.365  0.020  1.365
 AAP  N'   HN'   single    0.890  0.020  1.040
 AAP  C1'  C2'   aromatic  1.422  0.020  1.422
 AAP  C1'  C6'   aromatic  1.405  0.020  1.405
 AAP  C2'  C3'   aromatic  1.402  0.020  1.402
 AAP  C2'  C'    single    1.470  0.020  1.470
 AAP  C3'  C4'   aromatic  1.375  0.020  1.375
 AAP  C3'  H3'   single    0.930  0.020  1.080
 AAP  C4'  C5'   aromatic  1.399  0.020  1.399
 AAP  C4'  H4'   single    0.930  0.020  1.080
 AAP  C5'  C6'   aromatic  1.383  0.020  1.383
 AAP  C5'  CM5   single    1.498  0.020  1.498
 AAP  C6'  H6'   single    0.930  0.020  1.080
 AAP  C'   O'    double    1.226  0.020  1.226
 AAP  C'   CM'   single    1.507  0.020  1.507
 AAP  CM'  HM'1  single    0.970  0.020  1.090
 AAP  CM'  HM'2  single    0.970  0.020  1.090
 AAP  CM'  HM'3  single    0.970  0.020  1.090
 AAP  CM5  HM51  single    0.970  0.020  1.090
 AAP  CM5  HM52  single    0.970  0.020  1.090
 AAP  CM5  HM53  single    0.970  0.020  1.090

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
 AAP  N     C    O     124.90  3.000
 AAP  N     C    CA    115.54  3.000
 AAP  O     C    CA    119.36  3.000
 AAP  HA    CA   N'    108.64  3.000
 AAP  HA    CA   C1    107.02  3.000
 AAP  N'    CA   C1    110.49  3.000
 AAP  HA    CA   C     103.05  3.000
 AAP  N'    CA   C     115.78  3.000
 AAP  C1    CA   C     111.23  3.000
 AAP  HN2   N    HN1   117.58  3.000
 AAP  HN2   N    C     120.93  3.000
 AAP  HN1   N    C     120.13  3.000
 AAP  C6    C1   C2    116.04  3.000
 AAP  C6    C1   CA    122.17  3.000
 AAP  C2    C1   CA    121.73  3.000
 AAP  CL2   C2   C3    117.59  3.000
 AAP  CL2   C2   C1    119.56  3.000
 AAP  C3    C2   C1    122.84  3.000
 AAP  H3    C3   C4    120.68  3.000
 AAP  H3    C3   C2    120.24  3.000
 AAP  C4    C3   C2    119.08  3.000
 AAP  H4    C4   C5    119.83  3.000
 AAP  H4    C4   C3    119.95  3.000
 AAP  C5    C4   C3    120.22  3.000
 AAP  H5    C5   C6    120.10  3.000
 AAP  H5    C5   C4    120.54  3.000
 AAP  C6    C5   C4    119.37  3.000
 AAP  CL6   C6   C5    117.13  3.000
 AAP  CL6   C6   C1    120.43  3.000
 AAP  C5    C6   C1    122.44  3.000
 AAP  HN'   N'   C1'   113.89  3.000
 AAP  HN'   N'   CA    118.24  3.000
 AAP  C1'   N'   CA    124.25  3.000
 AAP  C6'   C1'  C2'   118.46  3.000
 AAP  C6'   C1'  N'    120.71  3.000
 AAP  C2'   C1'  N'    120.82  3.000
 AAP  C'    C2'  C3'   119.68  3.000
 AAP  C'    C2'  C1'   122.21  3.000
 AAP  C3'   C2'  C1'   118.11  3.000
 AAP  H3'   C3'  C4'   118.17  3.000
 AAP  H3'   C3'  C2'   119.31  3.000
 AAP  C4'   C3'  C2'   122.52  3.000
 AAP  H4'   C4'  C5'   120.31  3.000
 AAP  H4'   C4'  C3'   120.10  3.000
 AAP  C5'   C4'  C3'   119.59  3.000
 AAP  CM5   C5'  C6'   120.40  3.000
 AAP  CM5   C5'  C4'   120.44  3.000
 AAP  C6'   C5'  C4'   119.16  3.000
 AAP  H6'   C6'  C5'   117.97  3.000
 AAP  H6'   C6'  C1'   119.83  3.000
 AAP  C5'   C6'  C1'   122.16  3.000
 AAP  CM'   C'   O'    119.13  3.000
 AAP  CM'   C'   C2'   118.76  3.000
 AAP  O'    C'   C2'   122.11  3.000
 AAP  HM'3  CM'  HM'2  107.15  3.000
 AAP  HM'3  CM'  HM'1  108.61  3.000
 AAP  HM'2  CM'  HM'1  108.73  3.000
 AAP  HM'3  CM'  C'    111.22  3.000
 AAP  HM'2  CM'  C'    111.35  3.000
 AAP  HM'1  CM'  C'    109.69  3.000
 AAP  HM53  CM5  HM52  108.39  3.000
 AAP  HM53  CM5  HM51  107.09  3.000
 AAP  HM52  CM5  HM51  107.54  3.000
 AAP  HM53  CM5  C5'   111.35  3.000
 AAP  HM52  CM5  C5'   111.75  3.000
 AAP  HM51  CM5  C5'   110.52  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
 AAP  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 AAP  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 AAP  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 AAP  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 AAP  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 AAP  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 AAP  CONST_07  C4'   C3'  C2'  C1'     0.00   0.0  0
 AAP  CONST_08  C4'   C5'  C6'  C1'     0.00   0.0  0
 AAP  CONST_09  C5'   C6'  C1'  C2'     0.00   0.0  0
 AAP  CONST_10  C5'   C4'  C3'  C2'     0.00   0.0  0
 AAP  CONST_11  C6'   C1'  C2'  C3'     0.00   0.0  0
 AAP  CONST_12  C6'   C5'  C4'  C3'     0.00   0.0  0
 AAP  CONST_13  C3    C2   C1   CA    180.00   0.0  0
 AAP  CONST_14  C5    C6   C1   CA    180.00   0.0  0
 AAP  CONST_15  CL6   C6   C1   C2    180.00   0.0  0
 AAP  CONST_16  CL2   C2   C3   C4    180.00   0.0  0
 AAP  CONST_17  CL6   C6   C5   C4    180.00   0.0  0
 AAP  CONST_18  CL2   C2   C1   C6    180.00   0.0  0
 AAP  CONST_19  C3'   C2'  C1'  N'    180.00   0.0  0
 AAP  CONST_20  C5'   C6'  C1'  N'    180.00   0.0  0
 AAP  CONST_21  CM5   C5'  C6'  C1'   180.00   0.0  0
 AAP  CONST_22  CM5   C5'  C4'  C3'   180.00   0.0  0
 AAP  CONST_23  C'    C2'  C3'  C4'   180.00   0.0  0
 AAP  CONST_24  C'    C2'  C1'  C6'   180.00   0.0  0
 AAP  CONST_25  H3    C3   C2   C1    180.00   0.0  0
 AAP  CONST_26  H5    C5   C6   C1    180.00   0.0  0
 AAP  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 AAP  CONST_28  H3'   C3'  C2'  C1'   180.00   0.0  0
 AAP  CONST_29  H6'   C6'  C1'  C2'   180.00   0.0  0
 AAP  CONST_30  H4'   C4'  C3'  C2'   180.00   0.0  0
 AAP  CONST_33  HN'   N'   C1'  C2'     0.00   0.0  0
 AAP  CONST_34  HN1   N    C    CA    180.00   0.0  0
 AAP  CONST_35  HN2   N    C    CA      0.00   0.0  0
 AAP  Var_01    O'    C'   C2'  C1'    -2.35  30.0  2
 AAP  Var_02    HM51  CM5  C5'  C4'    79.15  30.0  2
 AAP  Var_03    HM'1  CM'  C'   C2'  -178.55  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
 AAP  chir_01  CA  C  C1  N'  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
 AAP  plan-1  CA   0.020
 AAP  plan-1  C1   0.020
 AAP  plan-1  C2   0.020
 AAP  plan-1  C3   0.020
 AAP  plan-1  C4   0.020
 AAP  plan-1  C5   0.020
 AAP  plan-1  C6   0.020
 AAP  plan-1  CL2  0.020
 AAP  plan-1  CL6  0.020
 AAP  plan-1  H3   0.020
 AAP  plan-1  H4   0.020
 AAP  plan-1  H5   0.020
 AAP  plan-2  N'   0.020
 AAP  plan-2  C1'  0.020
 AAP  plan-2  C2'  0.020
 AAP  plan-2  C3'  0.020
 AAP  plan-2  C4'  0.020
 AAP  plan-2  C5'  0.020
 AAP  plan-2  C6'  0.020
 AAP  plan-2  C'   0.020
 AAP  plan-2  CM5  0.020
 AAP  plan-2  H3'  0.020
 AAP  plan-2  H4'  0.020
 AAP  plan-2  H6'  0.020
 AAP  plan-3  C    0.020
 AAP  plan-3  CA   0.020
 AAP  plan-3  O    0.020
 AAP  plan-3  N    0.020
 AAP  plan-3  HN1  0.020
 AAP  plan-3  HN2  0.020
 AAP  plan-4  CA   0.020
 AAP  plan-4  N'   0.020
 AAP  plan-4  C1'  0.020
 AAP  plan-4  HN'  0.020
 AAP  plan-5  C2'  0.020
 AAP  plan-5  C'   0.020
 AAP  plan-5  O'   0.020
 AAP  plan-5  CM'  0.020

